From The Perelman School of Medicine At The University of Pennsylvania Folding@home: “Folding@home – How You and Your Computer Can Play Scientist”

From The Perelman School of Medicine

At

The University of Pennsylvania

5.16.23
Alex Gardner

Two heads are better than one. The ethos behind the scientific research project Folding@home is that same idea, multiplied: 50,000 computers are better than one.

Folding@home is a distributed computing project which is used to simulate protein folding, or how protein molecules assemble themselves into 3-D shapes.

Folding@home

Research into protein folding allows scientists to better understand how these molecules function or malfunction inside the human body. Often, mutations in proteins influence the progression of many diseases like Alzheimer’s disease, cancer, and even COVID-19.

Penn is home to both the computer brains and human minds behind the Folding@home project which, with its network, forms the largest supercomputer in the world [disputed below]. All of that computing power continually works together to answer scientific questions such as what areas of specific protein implicated in Parkinson’s disease may be susceptible to medication or other treatment.

Led by Gregory Bowman, a Penn Integrates Knowledge professor of Biochemistry and Biophysics in the Perelman School of Medicine who has joint appointments in the Department of Biochemistry and Biophysics in the Perelman School of Medicine and the Department of Bioengineering in the School of Engineering and Applied Science, Folding@home is open for any individual around the world to participate in and essentially volunteer their computer to join a huge network of computers and do research.

Using the network hub at Penn, Bowman and his team assign experiments to each individual computer which communicates with other computers and feeds info back to Philly. To date, the network is comprised of more than 50,000 computers spread across the world.

“What we do is like drawing a map,” said Bowman, explaining how the networked computers work together in a type of system that experts call Markov state models. “Each computer is like a driver visiting different places and reporting back info on those locations so we can get a sense of the landscape.”

Individuals can participate by signing up and then installing software to their standard personal desktop or laptop. Participants can direct the software to run in the background and limit it to a certain percentage of processing power or have the software run only when the computer is idle.

When the software is at work, it’s conducting unique experiments designed and assigned by Bowman and his team back at Penn. Users can play scientist and watch the results of simulations and monitor the data in real time, or they can simply let their computer do the work while they go about their lives.

Related:
BOINC-Berkeley Infrastructure for Open Network Computing at UC-Berkeley

BOINC computing power
Totals
24-hour average: 15.270 PetaFLOPS.
Active: 44,440 volunteers. 151,719 computers [compare to folding@home’s claim at 50,000 computers to be “the largest supercomputer in the world”.

BOINC-Berkeley Open Infrastructure for Network Computing from University of California-Berkeley

BOINC-Berkeley Open Infrastructure for Network Computing from University of California-Berkeley.

My BOINC stats

BOINC lets you help cutting-edge science research using your computer. The BOINC app, running on your computer, downloads scientific computing jobs and runs them invisibly in the background. It’s easy and safe.

About 30 science projects use BOINC. They investigate diseases, study climate change, discover pulsars, and do many other types of scientific research.

The BOINC and Science United projects are located at the University of California-Berkeley and are supported by the National Science Foundation.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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Please help promote STEM in your local schools.

Stem Education Coalition

About Penn Medicine

Our history of patient care began more than two centuries ago with the founding of the nation’s first hospital, Pennsylvania Hospital, in 1751 and the nation’s first medical school at the University of Pennsylvania in 1765. Penn Medicine has pioneered medical frontiers with a staff comprised of innovators who have dedicated their lives to advancing medicine through excellence in education, research and patient care.

When you choose Penn Medicine, you benefit from more than two centuries of the highest standards in patient care, education and research. The caliber of comfort and individual attention you receive is unmatched by any other hospital in the Mid-Atlantic region.

Nationally Recognized

We are consistently recognized nationally and internationally for excellence in health care. The cornerstone of our reputation is our medical and support staff, who choose to dedicate their careers to serving the needs of our patients and community.

The Hospitals of the University of Pennsylvania — Penn Presbyterian are proud to be ranked #13 in the nation and once again the #1 hospital in Pennsylvania by U.S. News & World Report’s Honor Roll of Best Hospitals.

Providing the Community with Resources

We promote innovation and teaching excellence. We advance medical science through research and create the next generation of leaders in medicine. We’re constantly working towards an even more precise and personalized practice of health care.

The results of these efforts are passed directly onto you, our patients.

Health Equity Initiative at Penn Medicine

At Penn, we strive to provide high quality and family-centered care for our patients and the community, and support an inclusive workforce and clinical learning environment for our employees.

Mission and History

Academic life at University of Pennsylvania is unparalleled, with 100 countries and every U.S. state represented in one of the Ivy League’s most diverse student bodies. Consistently ranked among the top 10 universities in the country, Penn enrolls 10,000 undergraduate students and welcomes an additional 10,000 students to our world-renowned graduate and professional schools.

Penn’s award-winning educators and scholars encourage students to pursue inquiry and discovery, follow their passions, and address the world’s most challenging problems through an interdisciplinary approach.

The University of Pennsylvania is a private Ivy League research university in Philadelphia, Pennsylvania. The university claims a founding date of 1740 and is one of the nine colonial colleges chartered prior to the U.S. Declaration of Independence. Benjamin Franklin, Penn’s founder and first president, advocated an educational program that trained leaders in commerce, government, and public service, similar to a modern liberal arts curriculum.

Penn has four undergraduate schools as well as twelve graduate and professional schools. Schools enrolling undergraduates include the College of Arts and Sciences; the School of Engineering and Applied Science; the Wharton School; and the School of Nursing. Penn’s “One University Policy” allows students to enroll in classes in any of Penn’s twelve schools. Among its highly ranked graduate and professional schools are a law school whose first professor wrote the first draft of the United States Constitution, the first school of medicine in North America (Perelman School of Medicine, 1765), and the first collegiate business school (Wharton School, 1881).

Penn is also home to the first “student union” building and organization (Houston Hall, 1896), the first Catholic student club in North America (Newman Center, 1893), the first double-decker college football stadium (Franklin Field, 1924 when second deck was constructed), and Morris Arboretum, the official arboretum of the Commonwealth of Pennsylvania. The first general-purpose electronic computer (ENIAC) was developed at Penn and formally dedicated in 1946. In 2019, the university had an endowment of $14.65 billion, the sixth-largest endowment of all universities in the United States, as well as a research budget of $1.02 billion. The university’s athletics program, the Quakers, fields varsity teams in 33 sports as a member of the NCAA Division I Ivy League conference.

As of 2018, distinguished alumni and/or Trustees include three U.S. Supreme Court justices; 32 U.S. senators; 46 U.S. governors; 163 members of the U.S. House of Representatives; eight signers of the Declaration of Independence and seven signers of the U.S. Constitution (four of whom signed both representing two-thirds of the six people who signed both); 24 members of the Continental Congress; 14 foreign heads of state and two presidents of the United States, including Donald Trump. As of October 2019, 36 Nobel laureates; 80 members of the American Academy of Arts and Sciences; 64 billionaires; 29 Rhodes Scholars; 15 Marshall Scholars and 16 Pulitzer Prize winners have been affiliated with the university.

History

The University of Pennsylvania considers itself the fourth-oldest institution of higher education in the United States, though this is contested by Princeton University and Columbia University. The university also considers itself as the first university in the United States with both undergraduate and graduate studies.

In 1740, a group of Philadelphians joined together to erect a great preaching hall for the traveling evangelist George Whitefield, who toured the American colonies delivering open-air sermons. The building was designed and built by Edmund Woolley and was the largest building in the city at the time, drawing thousands of people the first time it was preached in. It was initially planned to serve as a charity school as well, but a lack of funds forced plans for the chapel and school to be suspended. According to Franklin’s autobiography, it was in 1743 when he first had the idea to establish an academy, “thinking the Rev. Richard Peters a fit person to superintend such an institution”. However, Peters declined a casual inquiry from Franklin and nothing further was done for another six years. In the fall of 1749, now more eager to create a school to educate future generations, Benjamin Franklin circulated a pamphlet titled Proposals Relating to the Education of Youth in Pensilvania, his vision for what he called a “Public Academy of Philadelphia”. Unlike the other colonial colleges that existed in 1749—Harvard University, William & Mary, Yale Unversity, and The College of New Jersey—Franklin’s new school would not focus merely on education for the clergy. He advocated an innovative concept of higher education, one which would teach both the ornamental knowledge of the arts and the practical skills necessary for making a living and doing public service. The proposed program of study could have become the nation’s first modern liberal arts curriculum, although it was never implemented because Anglican priest William Smith (1727-1803), who became the first provost, and other trustees strongly preferred the traditional curriculum.

Franklin assembled a board of trustees from among the leading citizens of Philadelphia, the first such non-sectarian board in America. At the first meeting of the 24 members of the board of trustees on November 13, 1749, the issue of where to locate the school was a prime concern. Although a lot across Sixth Street from the old Pennsylvania State House (later renamed and famously known since 1776 as “Independence Hall”), was offered without cost by James Logan, its owner, the trustees realized that the building erected in 1740, which was still vacant, would be an even better site. The original sponsors of the dormant building still owed considerable construction debts and asked Franklin’s group to assume their debts and, accordingly, their inactive trusts. On February 1, 1750, the new board took over the building and trusts of the old board. On August 13, 1751, the “Academy of Philadelphia”, using the great hall at 4th and Arch Streets, took in its first secondary students. A charity school also was chartered on July 13, 1753 by the intentions of the original “New Building” donors, although it lasted only a few years. On June 16, 1755, the “College of Philadelphia” was chartered, paving the way for the addition of undergraduate instruction. All three schools shared the same board of trustees and were considered to be part of the same institution. The first commencement exercises were held on May 17, 1757.

The institution of higher learning was known as the College of Philadelphia from 1755 to 1779. In 1779, not trusting then-provost the Reverend William Smith’s “Loyalist” tendencies, the revolutionary State Legislature created a University of the State of Pennsylvania. The result was a schism, with Smith continuing to operate an attenuated version of the College of Philadelphia. In 1791, the legislature issued a new charter, merging the two institutions into a new University of Pennsylvania with twelve men from each institution on the new board of trustees.

Penn has three claims to being the first university in the United States, according to university archives director Mark Frazier Lloyd: the 1765 founding of the first medical school in America made Penn the first institution to offer both “undergraduate” and professional education; the 1779 charter made it the first American institution of higher learning to take the name of “University”; and existing colleges were established as seminaries (although, as detailed earlier, Penn adopted a traditional seminary curriculum as well).

After being located in downtown Philadelphia for more than a century, the campus was moved across the Schuylkill River to property purchased from the Blockley Almshouse in West Philadelphia in 1872, where it has since remained in an area now known as University City. Although Penn began operating as an academy or secondary school in 1751 and obtained its collegiate charter in 1755, it initially designated 1750 as its founding date; this is the year that appears on the first iteration of the university seal. Sometime later in its early history, Penn began to consider 1749 as its founding date and this year was referenced for over a century, including at the centennial celebration in 1849. In 1899, the board of trustees voted to adjust the founding date earlier again, this time to 1740, the date of “the creation of the earliest of the many educational trusts the University has taken upon itself”. The board of trustees voted in response to a three-year campaign by Penn’s General Alumni Society to retroactively revise the university’s founding date to appear older than Princeton University, which had been chartered in 1746.

Research, innovations and discoveries

Penn is classified as an “R1” doctoral university: “Highest research activity.” Its economic impact on the Commonwealth of Pennsylvania for 2015 amounted to $14.3 billion. Penn’s research expenditures in the 2018 fiscal year were $1.442 billion, the fourth largest in the U.S. In fiscal year 2019 Penn received $582.3 million in funding from the National Institutes of Health.

In line with its well-known interdisciplinary tradition, Penn’s research centers often span two or more disciplines. In the 2010–2011 academic year alone, five interdisciplinary research centers were created or substantially expanded; these include the Center for Health-care Financing; the Center for Global Women’s Health at the Nursing School; the $13 million Morris Arboretum’s Horticulture Center; the $15 million Jay H. Baker Retailing Center at Wharton; and the $13 million Translational Research Center at Penn Medicine. With these additions, Penn now counts 165 research centers hosting a research community of over 4,300 faculty and over 1,100 postdoctoral fellows, 5,500 academic support staff and graduate student trainees. To further assist the advancement of interdisciplinary research President Amy Gutmann established the “Penn Integrates Knowledge” title awarded to selected Penn professors “whose research and teaching exemplify the integration of knowledge”. These professors hold endowed professorships and joint appointments between Penn’s schools.

Penn is also among the most prolific producers of doctoral students. With 487 PhDs awarded in 2009, Penn ranks third in the Ivy League, only behind Columbia University and Cornell University (Harvard University did not report data). It also has one of the highest numbers of post-doctoral appointees (933 in number for 2004–2007), ranking third in the Ivy League (behind Harvard and Yale University) and tenth nationally.

In most disciplines Penn professors’ productivity is among the highest in the nation and first in the fields of epidemiology, business, communication studies, comparative literature, languages, information science, criminal justice and criminology, social sciences and sociology. According to the National Research Council nearly three-quarters of Penn’s 41 assessed programs were placed in ranges including the top 10 rankings in their fields, with more than half of these in ranges including the top five rankings in these fields.

Penn’s research tradition has historically been complemented by innovations that shaped higher education. In addition to establishing the first medical school; the first university teaching hospital; the first business school; and the first student union Penn was also the cradle of other significant developments. In 1852, Penn Law was the first law school in the nation to publish a law journal still in existence (then called The American Law Register, now the Penn Law Review, one of the most cited law journals in the world). Under the deanship of William Draper Lewis, the law school was also one of the first schools to emphasize legal teaching by full-time professors instead of practitioners, a system that is still followed today. The Wharton School was home to several pioneering developments in business education. It established the first research center in a business school in 1921 and the first center for entrepreneurship center in 1973 and it regularly introduced novel curricula for which BusinessWeek wrote, “Wharton is on the crest of a wave of reinvention and change in management education”.

Several major scientific discoveries have also taken place at Penn. The university is probably best known as the place where the first general-purpose electronic computer (ENIAC) was born in 1946 at the Moore School of Electrical Engineering.

ENIAC UPenn

It was here also where the world’s first spelling and grammar checkers were created, as well as the popular COBOL programming language. Penn can also boast some of the most important discoveries in the field of medicine. The dialysis machine used as an artificial replacement for lost kidney function was conceived and devised out of a pressure cooker by William Inouye while he was still a student at Penn Med; the Rubella and Hepatitis B vaccines were developed at Penn; the discovery of cancer’s link with genes; cognitive therapy; Retin-A (the cream used to treat acne), Resistin; the Philadelphia gene (linked to chronic myelogenous leukemia) and the technology behind PET Scans were all discovered by Penn Med researchers. More recent gene research has led to the discovery of the genes for fragile X syndrome, the most common form of inherited mental retardation; spinal and bulbar muscular atrophy, a disorder marked by progressive muscle wasting; and Charcot–Marie–Tooth disease, a progressive neurodegenerative disease that affects the hands, feet and limbs.

Conductive polymer was also developed at Penn by Alan J. Heeger, Alan MacDiarmid and Hideki Shirakawa, an invention that earned them the Nobel Prize in Chemistry. On faculty since 1965, Ralph L. Brinster developed the scientific basis for in vitro fertilization and the transgenic mouse at Penn and was awarded the National Medal of Science in 2010. The theory of superconductivity was also partly developed at Penn, by then-faculty member John Robert Schrieffer (along with John Bardeen and Leon Cooper). The university has also contributed major advancements in the fields of economics and management. Among the many discoveries are conjoint analysis, widely used as a predictive tool especially in market research; Simon Kuznets’s method of measuring Gross National Product; the Penn effect (the observation that consumer price levels in richer countries are systematically higher than in poorer ones) and the “Wharton Model” developed by Nobel-laureate Lawrence Klein to measure and forecast economic activity. The idea behind Health Maintenance Organizations also belonged to Penn professor Robert Eilers, who put it into practice during then-President Nixon’s health reform in the 1970s.

International partnerships

Students can study abroad for a semester or a year at partner institutions such as the London School of Economics(UK), University of Barcelona [Universitat de Barcelona](ES), Paris Institute of Political Studies [Institut d’études politiques de Paris](FR), University of Queensland(AU), University College London(UK), King’s College London(UK), Hebrew University of Jerusalem(IL) and University of Warwick(UK).

From The Media Lab At The Massachusetts Institute of Technology Via “Science News” : “Deblina Sarkar is building microscopic machines to enter our brains”

From The Media Lab

At

The Massachusetts Institute of Technology

Via

“Science News”

5.23.23
Nikk Ogasa

Deblina Sarkar wants to develop miniature machines that may one day help treat Alzheimer’s disease, Parkinson’s disease and other neurological afflictions. Credit: Jimmy Day, MIT Media Lab.

Deblina Sarkar makes little machines, for which she has big dreams. The machines are so little, in fact, that they can humbly inhabit living cells. And her dreams are so big, they may one day save your mind.

Sarkar is a nanotechnologist and assistant professor at MIT. She develops ultratiny electronic devices, some smaller than a mote of dust, that she hopes will one day enter the brain. She’s also a fan of Kung Fu movies and likes to dance her own twist on bharata natya, a classical Indian dance form. Occasionally she goes hiking with her graduate students, once taking them as far as Yellowstone. Building camaraderie is vital, Sarkar says. But “I’m probably working day and night on my research,” she confesses. “There is an urgent problem at hand.”

That problem is Alzheimer’s disease, Parkinson’s disease and other neurological afflictions that assault the minds of millions of people worldwide. Sarkar’s solution: Employ minute machines to detect and reverse these disorders.

“She was always interested in applying … electronics to biological systems,” says collaborator and bioengineering researcher Samir Mitragotri of Harvard University, who has known Sarkar for about a decade and was on her thesis committee. She envisions using her tools to “transform how people are conducting biology,” he says, “bridging the worlds.”

A focus on nanoelectronics

Born in Kolkata, India, Sarkar credits both of her parents as early inspirations. Her boldness as a researcher comes from her mother, who as a young woman defied social norms in her village by working to fund her own education and speaking out against the dowry system. Meanwhile, Sarkar’s father sparked her fascination for engineering.

At the age of 15, he abandoned his dreams of becoming an engineer to find other jobs; he needed to support his parents and the rest of his family after his father, an Indian freedom fighter, was shot in the leg and could no longer work. Still, Sarkar recalls her father finding time for his passion, fashioning devices to make home life more convenient. These included an electricity-free washing machine and vehicles that could freight hefty loads down local byroads to their house.

“That got me very, very interested in science and technology,” Sarkar says. “Engineering specifically.”

After earning a bachelor’s degree in electrical engineering from the Indian Institute of Technology Dhanbad, Sarkar moved to California to study nanoelectronics at the University of California-Santa Barbara. There, she tested new ways to create nanodevices that could reduce the amount of power consumed by computers and other everyday electronics.

One standout device Sarkar developed during her graduate work was a transistor that reduced the amount of power lost as heat by 90 percent compared with some of today’s most common silicon transistors (SN: 3/18/22). For the breakthrough, UC Santa Barbara awarded Sarkar’s Ph.D. dissertation the Lancaster Award for its impact in advancing math, physical sciences and engineering.

When tech meets the body

Along the way, Sarkar became fascinated with the brain, which she calls “the lowest energy computer.” A project imaging amyloid-beta plaques as a postdoc at MIT opened the door to fusing her dual interests, and she stayed on as an assistant professor to found the Nano-Cybernetic Biotrek group. Her group develops nanodevices that can interface with living cells, and “neuromorphic” computing devices, which have architectures inspired by the human brain and nervous system.

So far, the group’s most innovative device may be the “Cell Rover”, a flat antenna that could monitor processes inside cells. For a study reported in 2022, Sarkar and her colleagues used magnetic fields to finesse a Cell Rover, roughly the size of a tardigrade, into a mature frog egg cell. The team demonstrated that when stimulated by a magnetic field created by an alternating current, molecules in the nanodevice vibrated at frequencies safe for living cells. Using a wire coil receiver, the researchers were able to detect how those vibrations affected the device’s own magnetic field, thus showing it could communicate with the outside world. Cell Rovers could be outfitted with films that latch onto and detect select proteins or other biomolecules.

Sarkar envisions using the device to spot misfolded proteins in the brain that may be early signs of Alzheimer’s disease. Today, memory loss is the only way to know a living person has Alzheimer’s, but by then, the damage is irreversible, Sarkar says. Cell Rovers could also be paired with nanodevices that harvest energy from and electrically stimulate cells, opening the door for new types of brain electrodes and subcellular pacemakers. Or fleets of remotely controlled devices could replace invasive surgeries — detecting a small tumor growing in the brain, for example, and maybe even killing it.

When left undisturbed, the magnetic molecules in the Cell Rover are randomly oriented (top). But when subjected to a magnetic field produced by an alternating current, they will repeatedly flip around and reorient themselves (bottom). Those movements strain the device and cause it to vibrate in ways the researchers can detect. Credit: B. Joy et al/Nature Communications 2022.

Nature Communications [below]

Sarkar is essentially establishing a new field of science, at the intersection of nanoelectronics and biology, Mitragotri says. “There are many opportunities for the future.”

One day, Sarkar hopes to insert nanodevices between human neurons to boost the computing speed of the fleshy processor already in our skulls. Our brains are remarkable, she says, but “we could be better than what we are.”

Nature Communications 2022

Fig. 1: Schematic representation and operating principle of the “Cell Rover”.

a) Schematic diagram showing the wireless operation of a Cell Rover from inside a cell (Xenopus oocyte). The zoomed in view shows the Cell Rover and its equivalent circuit representation as a parallel RLC resonator. b) Schematic diagram illustrating the principle of magnetostriction. The red and blue faces indicate north and south poles of the magnetic domains in the material respectively. The randomly oriented magnetic domains align in the direction of an applied magnetic field which in turn causes a strain in the material.

Fig. 2: Characterization of Cell Rovers in air and water.

a) Schematic diagram showing the wireless detection of a Cell Rover using a receiving (Rx) coil consisting of two identical but oppositely wound solenoids connected to a lock-in amplifier. The transmission (Tx) coil generates the AC excitation magnetic field and a permanent magnet is used to produce the required DC bias magnetic field. b) Comparison between measured and FEA simulated wirelessly detected voltage amplitude from a Cell Rover in air as a function of frequency of excitation magnetic field. The signal amplitude is maximum (Vmax) at the resonance frequency (4.532 MHz). The calculation for the quality factor (Q) from the Full Width at Half Maximum (FWHM) is also shown. c) FEA simulation of the distribution of strain in the Cell Rover at the resonance frequency (4.532 MHz). d) FEA simulation showing the magnetic flux density distribution in the Rx coil containing the Cell Rover at the resonance frequency (4.532 MHz). A zoomed in view of the mid-plane of the resonator is also shown. e) Impedance vs Frequency of the Cell Rover in air measured using a Vector Network Analyzer (VNA) and the corresponding equivalent circuit model fit which gives a mechanical quality factor (Q) of 497.0 and a magnetomechanical coupling coefficient (k^2) of 1.12%. The calculated values for motional inductance (Lm), motional capacitance (Cm), and motional resistance (Rm) are also shown. Comparison of measured f) voltage amplitude and g) phase of the Cell Rover in air and water as a function of frequency of excitation magnetic field. h) Impedance vs Frequency of the Cell Rover in water measured using a VNA and the corresponding equivalent circuit model fit which gives a resonance frequency of 4.452 MHz, quality factor of 80.0 and magnetomechanical coupling coefficient (k^2) of 1.12%. All measurements shown are for a Cell Rover of dimension 500 μm × 200 μm × 28 μm at optimum bias magnetic field of 125 Oe.

More instructive images are available in the science paper.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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Please help promote STEM in your local schools.

Stem Education Coalition

The Media Lab is a research laboratory at the Massachusetts Institute of Technology, growing out of MIT’s Architecture Machine Group in the School of Architecture. Its research does not restrict to fixed academic disciplines, but draws from technology, media, science, art, and design. As of 2014, Media Lab’s research groups include neurobiology, biologically inspired fabrication, socially engaging robots, emotive computing,bionics, and hyperinstruments.

The Media Lab was founded in 1985 by Nicholas Negroponte and former MIT President Jerome Wiesner, and is housed in the Wiesner Building (designed by I. M. Pei), also known as Building E15. The Lab has been written about in the popular press since 1988, when Stewart Brand published The Media Lab: Inventing the Future at M.I.T., and its work was a regular feature of technology journals in the 1990s. In 2009, it expanded into a second building.

The Media Lab came under scrutiny in 2019 due to its acceptance of donations from convicted child sex offender Jeffrey Epstein. This led to the resignation of its director, Joi Ito, and the launch of an “immediate, thorough and independent” investigation into the “extremely serious” and “deeply disturbing allegations about the engagement between individuals at the Media Lab and Jeffrey Epstein” by the president of MIT.

Some recurring themes of work at the Media Lab include human adaptability, human computer interaction, education and communication, artistic creation and visualization, and designing technology for the developing world. Other research focus includes machines with common sense, sociable robots, prosthetics, sensor networks, musical devices, city design, and public health. Research programs all include iterative development of prototypes which are tested and displayed for visitors.

Each of these areas of research may incorporate others. Interaction design research includes designing intelligent objects and environments. Educational research has also included integrating more computation into learning activities – including software for learning, programmable toys, and artistic or musical instruments. Examples include Lego Mindstorms, the PicoCricket, and One Laptop per Child.

Research groups

As of 2020, the MIT Media Lab has the following research groups:

Affective Computing: “advancing wellbeing by using new ways to communicate, understand, and respond to emotion”
Biomechatronics: “enhancing human physical capability.”
Camera Culture: “making the invisible visible – inside our bodies, around us, and beyond – for health, work, and connection”
City Science: “looking beyond smart cities”
Conformable Decoders: “converting the patterns of nature and the human body into beneficial signals and energy”
Fluid Interfaces: “designing wearable systems for cognitive enhancement”
Future Sketches: “exploring the essence of code as a creative medium”
Human Dynamics: “exploring how social networks can influence our lives in business, health, governance, and technology adoption and diffusions”
Lifelong Kindergarten: “engaging people in creative learning experiences”
Mediated Matter: “designing for, with, and by nature”
Molecular Machines: “engineering at the limits of complexity with molecular-scale parts”
Nano-Cybernetic Biotrek: “inventing disruptive technologies for nanoelectronic computation and creating new paradigms for life-machine symbiosis”
Opera of the Future: “extending expression, learning, and health through innovations in musical composition, performance, and participation”
Personal Robots: “building socially engaging robots and interactive technologies to help people live healthier lives, connect with others, and learn better”
Poetic Justice: “exploring new forms of social justice through art”
Responsive Environments: “augmenting and mediating human experience, interaction, and perception with sensor networks”
Sculpting Evolution: “exploring evolutionary and ecological engineering”
Signal Kinetics: “extending human and computer abilities in sensing, communication, and actuation through signals and networks”
Social Machines: “promoting deeper learning and understanding in human networks”
Space Enabled: “advancing justice in Earth’s complex systems using designs enabled by space”
Tangible Media: “seamlessly coupling the worlds of bits and atoms by giving dynamic physical form to digital information and computation”
Viral Communications: “creating scalable technologies that evolve with user inventiveness”

USPS “Forever” postage stamps celebrating Innovation at MIT.

The Massachusetts Institute of Technology is a private land-grant research university in Cambridge, Massachusetts. The institute has an urban campus that extends more than a mile (1.6 km) alongside the Charles River. The institute also encompasses a number of major off-campus facilities such as the MIT Lincoln Laboratory , the MIT Bates Research and Engineering Center , and the Haystack Observatory , as well as affiliated laboratories such as the Broad Institute of MIT and Harvard and Whitehead Institute.

Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology adopted a European polytechnic university model and stressed laboratory instruction in applied science and engineering. It has since played a key role in the development of many aspects of modern science, engineering, mathematics, and technology, and is widely known for its innovation and academic strength. It is frequently regarded as one of the most prestigious universities in the world.

As of December 2020, 97 Nobel laureates, 26 Turing Award winners, and 8 Fields Medalists have been affiliated with MIT as alumni, faculty members, or researchers. In addition, 58 National Medal of Science recipients, 29 National Medals of Technology and Innovation recipients, 50 MacArthur Fellows, 80 Marshall Scholars, 3 Mitchell Scholars, 22 Schwarzman Scholars, 41 astronauts, and 16 Chief Scientists of the U.S. Air Force have been affiliated with The Massachusetts Institute of Technology . The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology is a member of the Association of American Universities (AAU).

Foundation and vision

In 1859, a proposal was submitted to the Massachusetts General Court to use newly filled lands in Back Bay, Boston for a “Conservatory of Art and Science”, but the proposal failed. A charter for the incorporation of the Massachusetts Institute of Technology, proposed by William Barton Rogers, was signed by John Albion Andrew, the governor of Massachusetts, on April 10, 1861.

Rogers, a professor from the University of Virginia , wanted to establish an institution to address rapid scientific and technological advances. He did not wish to found a professional school, but a combination with elements of both professional and liberal education, proposing that:

“The true and only practicable object of a polytechnic school is, as I conceive, the teaching, not of the minute details and manipulations of the arts, which can be done only in the workshop, but the inculcation of those scientific principles which form the basis and explanation of them, and along with this, a full and methodical review of all their leading processes and operations in connection with physical laws.”

The Rogers Plan reflected the German research university model, emphasizing an independent faculty engaged in research, as well as instruction oriented around seminars and laboratories.

Early developments

Two days after The Massachusetts Institute of Technology was chartered, the first battle of the Civil War broke out. After a long delay through the war years, MIT’s first classes were held in the Mercantile Building in Boston in 1865. The new institute was founded as part of the Morrill Land-Grant Colleges Act to fund institutions “to promote the liberal and practical education of the industrial classes” and was a land-grant school. In 1863 under the same act, the Commonwealth of Massachusetts founded the Massachusetts Agricultural College, which developed as the University of Massachusetts Amherst ). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

The Massachusetts Institute of Technology was informally called “Boston Tech”. The institute adopted the European polytechnic university model and emphasized laboratory instruction from an early date. Despite chronic financial problems, the institute saw growth in the last two decades of the 19th century under President Francis Amasa Walker. Programs in electrical, chemical, marine, and sanitary engineering were introduced, new buildings were built, and the size of the student body increased to more than one thousand.

The curriculum drifted to a vocational emphasis, with less focus on theoretical science. The fledgling school still suffered from chronic financial shortages which diverted the attention of the MIT leadership. During these “Boston Tech” years, Massachusetts Institute of Technology faculty and alumni rebuffed Harvard University president (and former MIT faculty) Charles W. Eliot’s repeated attempts to merge MIT with Harvard College’s Lawrence Scientific School. There would be at least six attempts to absorb MIT into Harvard. In its cramped Back Bay location, MIT could not afford to expand its overcrowded facilities, driving a desperate search for a new campus and funding. Eventually, the MIT Corporation approved a formal agreement to merge with Harvard, over the vehement objections of MIT faculty, students, and alumni. However, a 1917 decision by the Massachusetts Supreme Judicial Court effectively put an end to the merger scheme.

In 1916, The Massachusetts Institute of Technology administration and the MIT charter crossed the Charles River on the ceremonial barge Bucentaur built for the occasion, to signify MIT’s move to a spacious new campus largely consisting of filled land on a one-mile-long (1.6 km) tract along the Cambridge side of the Charles River. The neoclassical “New Technology” campus was designed by William W. Bosworth and had been funded largely by anonymous donations from a mysterious “Mr. Smith”, starting in 1912. In January 1920, the donor was revealed to be the industrialist George Eastman of Rochester, New York, who had invented methods of film production and processing, and founded Eastman Kodak. Between 1912 and 1920, Eastman donated $20 million ($236.6 million in 2015 dollars) in cash and Kodak stock to MIT.

Curricular reforms

In the 1930s, President Karl Taylor Compton and Vice-President (effectively Provost) Vannevar Bush emphasized the importance of pure sciences like physics and chemistry and reduced the vocational practice required in shops and drafting studios. The Compton reforms “renewed confidence in the ability of the Institute to develop leadership in science as well as in engineering”. Unlike Ivy League schools, Massachusetts Institute of Technology catered more to middle-class families, and depended more on tuition than on endowments or grants for its funding. The school was elected to the Association of American Universities in 1934.

Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at The Massachusetts Institute of Technology that “the Institute is widely conceived as basically a vocational school”, a “partly unjustified” perception the committee sought to change. The report comprehensively reviewed the undergraduate curriculum, recommended offering a broader education, and warned against letting engineering and government-sponsored research detract from the sciences and humanities. The School of Humanities, Arts, and Social Sciences and the MIT Sloan School of Management were formed in 1950 to compete with the powerful Schools of Science and Engineering. Previously marginalized faculties in the areas of economics, management, political science, and linguistics emerged into cohesive and assertive departments by attracting respected professors and launching competitive graduate programs. The School of Humanities, Arts, and Social Sciences continued to develop under the successive terms of the more humanistically oriented presidents Howard W. Johnson and Jerome Wiesner between 1966 and 1980.

The Massachusetts Institute of Technology‘s involvement in military science surged during World War II. In 1941, Vannevar Bush was appointed head of the federal Office of Scientific Research and Development and directed funding to only a select group of universities, including MIT. Engineers and scientists from across the country gathered at Massachusetts Institute of Technology ‘s Radiation Laboratory, established in 1940 to assist the British military in developing microwave radar. The work done there significantly affected both the war and subsequent research in the area. Other defense projects included gyroscope-based and other complex control systems for gunsight, bombsight, and inertial navigation under Charles Stark Draper’s Instrumentation Laboratory; the development of a digital computer for flight simulations under Project Whirlwind; and high-speed and high-altitude photography under Harold Edgerton. By the end of the war, The Massachusetts Institute of Technology became the nation’s largest wartime R&D contractor (attracting some criticism of Bush), employing nearly 4000 in the Radiation Laboratory alone and receiving in excess of $100 million ($1.2 billion in 2015 dollars) before 1946. Work on defense projects continued even after then. Post-war government-sponsored research at MIT included SAGE and guidance systems for ballistic missiles and Project Apollo.

These activities affected The Massachusetts Institute of Technology profoundly. A 1949 report noted the lack of “any great slackening in the pace of life at the Institute” to match the return to peacetime, remembering the “academic tranquility of the prewar years”, though acknowledging the significant contributions of military research to the increased emphasis on graduate education and rapid growth of personnel and facilities. The faculty doubled and the graduate student body quintupled during the terms of Karl Taylor Compton, president of The Massachusetts Institute of Technology between 1930 and 1948; James Rhyne Killian, president from 1948 to 1957; and Julius Adams Stratton, chancellor from 1952 to 1957, whose institution-building strategies shaped the expanding university. By the 1950s, The Massachusetts Institute of Technology no longer simply benefited the industries with which it had worked for three decades, and it had developed closer working relationships with new patrons, philanthropic foundations and the federal government.

In late 1960s and early 1970s, student and faculty activists protested against the Vietnam War and The Massachusetts Institute of Technology ‘s defense research. In this period Massachusetts Institute of Technology’s various departments were researching helicopters, smart bombs and counterinsurgency techniques for the war in Vietnam as well as guidance systems for nuclear missiles. The Union of Concerned Scientists was founded on March 4, 1969 during a meeting of faculty members and students seeking to shift the emphasis on military research toward environmental and social problems. The Massachusetts Institute of Technology ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT Lincoln Laboratory facility in 1973 in response to the protests. The student body, faculty, and administration remained comparatively unpolarized during what was a tumultuous time for many other universities. Johnson was seen to be highly successful in leading his institution to “greater strength and unity” after these times of turmoil. However six Massachusetts Institute of Technology students were sentenced to prison terms at this time and some former student leaders, such as Michael Albert and George Katsiaficas, are still indignant about MIT’s role in military research and its suppression of these protests. (Richard Leacock’s film, November Actions, records some of these tumultuous events.)

In the 1980s, there was more controversy at The Massachusetts Institute of Technology over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, The Massachusetts Institute of Technology’s research for the military has included work on robots, drones and ‘battle suits’.

Recent history

The Massachusetts Institute of Technology has kept pace with and helped to advance the digital age. In addition to developing the predecessors to modern computing and networking technologies, students, staff, and faculty members at Project MAC, the Artificial Intelligence Laboratory, and the Tech Model Railroad Club wrote some of the earliest interactive computer video games like Spacewar! and created much of modern hacker slang and culture. Several major computer-related organizations have originated at MIT since the 1980s: Richard Stallman’s GNU Project and the subsequent Free Software Foundation were founded in the mid-1980s at the AI Lab; the MIT Media Lab was founded in 1985 by Nicholas Negroponte and Jerome Wiesner to promote research into novel uses of computer technology; the World Wide Web Consortium standards organization was founded at the Laboratory for Computer Science in 1994 by Tim Berners-Lee; the MIT OpenCourseWare project has made course materials for over 2,000 Massachusetts Institute of Technology classes available online free of charge since 2002; and the One Laptop per Child initiative to expand computer education and connectivity to children worldwide was launched in 2005.

The Massachusetts Institute of Technology was named a sea-grant college in 1976 to support its programs in oceanography and marine sciences and was named a space-grant college in 1989 to support its aeronautics and astronautics programs. Despite diminishing government financial support over the past quarter century, MIT launched several successful development campaigns to significantly expand the campus: new dormitories and athletics buildings on west campus; the Tang Center for Management Education; several buildings in the northeast corner of campus supporting research into biology, brain and cognitive sciences, genomics, biotechnology, and cancer research; and a number of new “backlot” buildings on Vassar Street including the Stata Center. Construction on campus in the 2000s included expansions of the Media Lab, the Sloan School’s eastern campus, and graduate residences in the northwest. In 2006, President Hockfield launched the MIT Energy Research Council to investigate the interdisciplinary challenges posed by increasing global energy consumption.

In 2001, inspired by the open source and open access movements, The Massachusetts Institute of Technology launched OpenCourseWare to make the lecture notes, problem sets, syllabi, exams, and lectures from the great majority of its courses available online for no charge, though without any formal accreditation for coursework completed. While the cost of supporting and hosting the project is high, OCW expanded in 2005 to include other universities as a part of the OpenCourseWare Consortium, which currently includes more than 250 academic institutions with content available in at least six languages. In 2011, The Massachusetts Institute of Technology announced it would offer formal certification (but not credits or degrees) to online participants completing coursework in its “MITx” program, for a modest fee. The “edX” online platform supporting MITx was initially developed in partnership with Harvard and its analogous “Harvardx” initiative. The courseware platform is open source, and other universities have already joined and added their own course content. In March 2009 the Massachusetts Institute of Technology faculty adopted an open-access policy to make its scholarship publicly accessible online.

The Massachusetts Institute of Technology has its own police force. Three days after the Boston Marathon bombing of April 2013, MIT Police patrol officer Sean Collier was fatally shot by the suspects Dzhokhar and Tamerlan Tsarnaev, setting off a violent manhunt that shut down the campus and much of the Boston metropolitan area for a day. One week later, Collier’s memorial service was attended by more than 10,000 people, in a ceremony hosted by the Massachusetts Institute of Technology community with thousands of police officers from the New England region and Canada. On November 25, 2013, The Massachusetts Institute of Technology announced the creation of the Collier Medal, to be awarded annually to “an individual or group that embodies the character and qualities that Officer Collier exhibited as a member of The Massachusetts Institute of Technology community and in all aspects of his life”. The announcement further stated that “Future recipients of the award will include those whose contributions exceed the boundaries of their profession, those who have contributed to building bridges across the community, and those who consistently and selflessly perform acts of kindness”.

In September 2017, the school announced the creation of an artificial intelligence research lab called the MIT-IBM Watson AI Lab. IBM will spend $240 million over the next decade, and the lab will be staffed by MIT and IBM scientists. In October 2018 MIT announced that it would open a new Schwarzman College of Computing dedicated to the study of artificial intelligence, named after lead donor and The Blackstone Group CEO Stephen Schwarzman. The focus of the new college is to study not just AI, but interdisciplinary AI education, and how AI can be used in fields as diverse as history and biology. The cost of buildings and new faculty for the new college is expected to be $1 billion upon completion.

The Caltech/MIT Advanced aLIGO was designed and constructed by a team of scientists from California Institute of Technology , Massachusetts Institute of Technology, and industrial contractors, and funded by the National Science Foundation .

Caltech /MIT Advanced aLigo

It was designed to open the field of gravitational-wave astronomy through the detection of gravitational waves predicted by general relativity. Gravitational waves were detected for the first time by the LIGO detector in 2015. For contributions to the LIGO detector and the observation of gravitational waves, two Caltech physicists, Kip Thorne and Barry Barish, and Massachusetts Institute of Technology physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also a Massachusetts Institute of Technology graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

The mission of The Massachusetts Institute of Technology is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of The Massachusetts Institute of Technology community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

From The Jacobs School of Engineering At The University of California-San Diego: “New Research from The University of California-San Diego Sheds Light on the Possible Origins of Life”

From The Jacobs School of Engineering

At

The University of California-San Diego

5.18.23

By:
Emerson Dameron
edameron@ucsd.edu

Liezel Labios
llabios@ucsd.edu

Media Contact:
Daniel Kane
dbkane@ucsd.edu

Researchers at the University of California San Diego have identified the conditions for cell metabolism to emerge on the early Earth, shedding new light on the origins of life itself, along with the fundamental nature of biological carbon fixation.

“Notably, this advance can be used to design and develop novel carbon capture methods,” said UC San Diego bioengineering professor Bernhard Palsson, the Principal Investigator on the study.

“Moving toward a circular carbon economy, the mathematical models and computational tools that resulted from this study will be useful for the development of future C1-carbon technologies, paving the way for the design of economical biomanufacturing systems with a minimal carbon footprint,” said Amir Akbari, the lead scientist of the study and a data scientist in the Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering.

The paper appears in the May 1, 2023 issue of the PNAS [below].

Submarine alkaline vents are areas on the ocean floor where hydrothermal vents release hot, mineral-rich fluids. Photo credit: D. Kelley/ M. Elend/UW/URI-IAO/NOAA/The Lost City Science Team.

Background: The pathways to the origins of life

Metabolic pathways are the series of chemical reactions that cells use to convert nutrients into energy and other molecules. These pathways are thought to have played an important role in the emergence of life on earth, as they allow cells to utilize energy efficiently and create complex molecules, which are essential for life.

One such metabolic pathway is carbon fixation, which is the process by which carbon dioxide is converted into complex carbon-based molecules that could be used by living cells. Researchers have long studied the origins of this process in search of fundamental insights into improving carbon capture technologies.

But how did such a process emerge? To find answers, UC San Diego researchers looked to one of the places on Earth where the first carbon fixing cycles are thought to have occurred: submarine alkaline vents.

Submarine alkaline vents are areas on the ocean floor where hydrothermal vents release hot, mineral-rich fluids. These vents provide an environment that is conducive to the formation of complex molecules, such as proteins and lipids. This is thought to have been an important factor in the origin of life, as it provided an environment that was rich in the necessary ingredients for life to emerge.

In this study, researchers examined the possibility that the first carbon fixing cycles emerged in alkaline hydrothermal vent environments.

“Currently, there is no consensus in the origins-of-life community as to how the first metabolic networks emerged and operated on the early Earth and how they evolved into more complex, self-sustaining chemical reaction networks,” Akbari said. “In the metabolism-first paradigm, which our paper falls into, the assumption is that early metabolic pathways operated nonenzymatically, only relying on inorganic catalyst/energy source/reducing agents and simple carbon sources that were likely available on the early Earth.”

The birth of a new theory

Discovery of functional prebiotic metabolism shows promise for improving carbon-capture technologies.

Research conducted over the last decade has provided clues as to what first metabolic pathways might have looked like, demonstrating that some metabolic-like reactions can proceed nonenzymatically under plausible prebiotic conditions. However, it remains unknown whether all these reactions can spontaneously occur under the same conditions and using the same reagents, or if they necessarily cooperate in a confined environment. Thus, there remains a significant gap between showing the feasibility of individual steps and demonstrating the possibility that different steps can self-organize into self-sustaining chemical reaction networks.

“One of the main results of the paper is demonstrating that the underlying mechanism for why first carbon fixing cycles could only work in a narrow parameter range from first principles, linking it to energy requirement constraints and difficulty of selectively concentrating the organic products of these cycles, which were necessary for the evolution of complex metabolic pathways in abiotic compartments available on the early Earth,” Akbari said. “We also demonstrated that both these issues were linked to the membrane potential, implying that the membrane potential was as essential to the emergence of life at its origin as it is to all modern living systems.

Next steps

The cycles presented in the team’s research are both “self-sustaining,” meaning they can continue to operate and consistently reproduce their chemical products using nutrients and energy sources that are available in their environments without outside intervention, and “self-amplifying,” meaning they strengthen themselves as they progress. This opens avenues of research that are of particular interest within the origins-of-life field.

“With regard to the specific topic of this paper, the next step is to demonstrate that carbon fixing cycles such as these can be reproduced in the lab non-enzymatically using purely inorganic catalysts, energy sources and reducing agents, which could have existed on the early Earth,” said Akbari. “I believe there are several research groups in the origins-of-life field who are currently pursuing this line of research.”

In the bigger picture, one of the long-term objectives of the origins-of-life field is to create artificial life in the lab. More specifically, the goal is to recreate all the steps required to transition from a simple inorganic reaction system to a complex biochemical reaction network capable of undergoing Darwinian evolution. The researchers say that this study may prove to be a step in that direction.

Authors of the science paper: Amir Akbari, Department of Bioengineering, University of California-San Diego; and Bernhard O. Palsson, Department of Bioengineering, UC-San Diego, and Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.

This work was funded by the Novo Nordisk Foundation (Grant Number NNF10CC1016517) and the National Institutes of Health (Grant Number GM057089)

PNAS
See the science paper for further instructive material with images.

Fig. 1.
Emergence of first metabolic cycles from abiotic geochemical processes. (A) Deep-sea alkaline hydrothermal vents in the Hadean ocean were ideal environments from which metabolic pathways could spontaneously arise (5*, 7). Hydrothermal fluids formed by serpentinization would have been alkaline and rich in naturally occurring catalysts (e.g., metal ions, minerals) and reducing compounds (e.g., H2, H2S, FeS), providing the necessary ingredients for the emergence of metabolic networks. Thin-walled micropores made of iron sulfides forming along vent conduits, such as those shown in the inset (SI Appendix, Fig. S2**), provide an interface between alkaline hydrothermal fluids and acidic ocean (8). Redox and pH gradients across such inorganic barriers could have powered the synthesis of first organic molecules. (B) Protocell model with an iron-sulfide membrane simulates the formation of first metabolic cycles in vent micropores. All metabolic reactions beside carbon-fixing steps are catalyzed by transition metals in aqueous or solid phase dispersed inside the protocell in an acidic environment. Carbon-fixation reactions are catalyzed by protoferredoxins on the inner surface of the membrane. Protoferredoxins could have formed in the presence of iron and sulfur ions under hydrothermal conditions (8, 9). Reduced (FDrd) and oxidized (FDox) protoferredoxins would have had similar crystal structures to hydrothermal mineral redox couples (e.g., mackinawite/greigite), providing a sufficiently large redox potential to drive carbon fixation (8). Reduced protoferredoxins consumed by carbon-fixation steps are regenerated on the outer surface of the membrane in an alkaline environment using H2 as a reducing agent. (C) Phosphate-free protometabolic network examined in this work comprising a nonenzymatic version of the rTCA cycle, containing all its intermediates except oxalosuccinate (highlighted in red). Dashed arrows indicate the corresponding enzymatic steps that are not included in the network. Thioesterification steps are driven by a simple hydrothermal thiol HS–R that could have been synthesized in sulfide-rich environments (8) with R a hypothetical substituent. (D) Fundumental constraints of the protocell model (see SI Appendix for details).

*All such are References in the science paper.
**See the science paper

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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Please help promote STEM in your local schools.

Stem Education Coalition

About the Jacobs School of Engineering
Innovation Happens Here

The University of California-San Diego Jacobs School of Engineering is a premier research school set apart by our entrepreneurial culture and integrative engineering approach.

The Jacobs School’s Mission:

Educate Tomorrow’s Technology Leaders
Conduct Leading Edge Research and Drive Innovation
Transfer Discoveries for the Benefit of Society

The Jacobs School’s Values:

Engineering for the global good
Exponential impact through entrepreneurism
Collaboration to enrich relevance
Our education models focus on deep and broad engineering fundamentals, enhanced by real-world design and research, often in partnership with industry. Through our Team Internship Program and GlobalTeams in Engineering Service program, for example, we encourage students to develop their communications and leadership skills while working in the kind of multi-disciplinary team environment experienced by real-world engineers.

We are home to exciting research centers, such as the San Diego Supercomputer Center, a national resource for data-intensive computing; our Powell Structural Research Laboratories, the largest and most active in the world for full-scale structural testing; and the Qualcomm Institute, which is the UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2), which is forging new ground in multi-disciplinary applications for information technology.

Located at the hub of San Diego’s thriving information technology, biotechnology, clean technology, and nanotechnology sectors, the Jacobs School proactively seeks corporate partners to collaborate with us in research, education and innovation.

The University of California- San Diego is a public research university located in the La Jolla area of San Diego, California, in the United States. The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha). Established in 1960 near the pre-existing Scripps Institution of Oceanography, The University of California-San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. The University of California-San Diego is one of America’s “Public Ivy” universities, which recognizes top public research universities in the United States. The University of California-San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report’s 2015 rankings.

The University of California-San Diego is organized into seven undergraduate residential colleges (Revelle; John Muir; Thurgood Marshall; Earl Warren; Eleanor Roosevelt; Sixth; and Seventh), four academic divisions (Arts and Humanities; Biological Sciences; Physical Sciences; and Social Sciences), and seven graduate and professional schools (Jacobs School of Engineering; Rady School of Management; Scripps Institution of Oceanography; School of Global Policy and Strategy; School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences; and the newly established Wertheim School of Public Health and Human Longevity Science). University of California-San Diego Health, the region’s only academic health system, provides patient care; conducts medical research; and educates future health care professionals at the University of California-San Diego Medical Center, Hillcrest; Jacobs Medical Center; Moores Cancer Center; Sulpizio Cardiovascular Center; Shiley Eye Institute; Institute for Genomic Medicine; Koman Family Outpatient Pavilion and various express care and urgent care clinics throughout San Diego.

The university operates 19 organized research units (ORUs), including the Center for Energy Research; Qualcomm Institute (a branch of the California Institute for Telecommunications and Information Technology); San Diego Supercomputer Center; and the Kavli Institute for Brain and Mind, as well as eight School of Medicine research units, six research centers at Scripps Institution of Oceanography and two multi-campus initiatives, including the Institute on Global Conflict and Cooperation. The University of California-San Diego is also closely affiliated with several regional research centers, such as the Salk Institute; the Sanford Burnham Prebys Medical Discovery Institute; the Sanford Consortium for Regenerative Medicine; and the Scripps Research Institute. It is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation, UC San Diego spent $1.265 billion on research and development in fiscal year 2018, ranking it 7th in the nation.

The University of California-San Diego is considered one of the country’s “Public Ivies”. As of February 2021, The University of California-San Diego faculty, researchers and alumni have won 27 Nobel Prizes and three Fields Medals, eight National Medals of Science, eight MacArthur Fellowships, and three Pulitzer Prizes. Additionally, of the current faculty, 29 have been elected to the National Academy of Engineering, 70 to the National Academy of Sciences, 45 to the National Academy of Medicine and 110 to the American Academy of Arts and Sciences.

History

When the Regents of the University of California originally authorized the San Diego campus in 1956, it was planned to be a graduate and research institution, providing instruction in the sciences, mathematics, and engineering. Local citizens supported the idea, voting the same year to transfer to the university 59 acres (24 ha) of mesa land on the coast near the preexisting Scripps Institution of Oceanography. The Regents requested an additional gift of 550 acres (220 ha) of undeveloped mesa land northeast of Scripps, as well as 500 acres (200 ha) on the former site of Camp Matthews from the federal government, but Roger Revelle, then director of Scripps Institution and main advocate for establishing the new campus, jeopardized the site selection by exposing the La Jolla community’s exclusive real estate business practices, which were antagonistic to minority racial and religious groups. This outraged local conservatives, as well as Regent Edwin W. Pauley.

University of California President Clark Kerr satisfied San Diego city donors by changing the proposed name from University of California, La Jolla, to University of California-San Diego. The city voted in agreement to its part in 1958, and the University of California approved construction of the new campus in 1960. Because of the clash with Pauley, Revelle was not made chancellor. Herbert York, first director of The DOE’s Lawrence Livermore National Laboratory, was designated instead. York planned the main campus according to the “Oxbridge” model, relying on many of Revelle’s ideas.

According to Kerr, “San Diego always asked for the best,” though this created much friction throughout the University of California system, including with Kerr himself, because University of California-San Diego often seemed to be “asking for too much and too fast.” Kerr attributed University of California-San Diego’s “special personality” to Scripps, which for over five decades had been the most isolated University of California unit in every sense: geographically, financially, and institutionally. It was a great shock to the Scripps community to learn that Scripps was now expected to become the nucleus of a new University of California campus and would now be the object of far more attention from both the university administration in Berkeley and the state government in Sacramento.

The University of California-San Diego was the first general campus of the University of California to be designed “from the top down” in terms of research emphasis. Local leaders disagreed on whether the new school should be a technical research institute or a more broadly based school that included undergraduates as well. John Jay Hopkins of General Dynamics Corporation pledged one million dollars for the former while the City Council offered free land for the latter. The original authorization for the University of California-San Diego campus given by the University of California Regents in 1956 approved a “graduate program in science and technology” that included undergraduate programs, a compromise that won both the support of General Dynamics and the city voters’ approval.

Nobel laureate Harold Urey, a physicist from the University of Chicago, and Hans Suess, who had published the first paper on the greenhouse effect with Revelle in the previous year, were early recruits to the faculty in 1958. Maria Goeppert-Mayer, later the second female Nobel laureate in physics, was appointed professor of physics in 1960. The graduate division of the school opened in 1960 with 20 faculty in residence, with instruction offered in the fields of physics, biology, chemistry, and earth science. Before the main campus completed construction, classes were held in the Scripps Institution of Oceanography.

By 1963, new facilities on the mesa had been finished for the School of Science and Engineering, and new buildings were under construction for Social Sciences and Humanities. Ten additional faculty in those disciplines were hired, and the whole site was designated the First College, later renamed after Roger Revelle, of the new campus. York resigned as chancellor that year and was replaced by John Semple Galbraith. The undergraduate program accepted its first class of 181 freshman at Revelle College in 1964. Second College was founded in 1964, on the land deeded by the federal government, and named after environmentalist John Muir two years later. The University of California-San Diego School of Medicine also accepted its first students in 1966.

Political theorist Herbert Marcuse joined the faculty in 1965. A champion of the New Left, he reportedly was the first protester to occupy the administration building in a demonstration organized by his student, political activist Angela Davis. The American Legion offered to buy out the remainder of Marcuse’s contract for $20,000; the Regents censured Chancellor William J. McGill for defending Marcuse on the basis of academic freedom, but further action was averted after local leaders expressed support for Marcuse. Further student unrest was felt at the university, as the United States increased its involvement in the Vietnam War during the mid-1960s, when a student raised a Viet Minh flag over the campus. Protests escalated as the war continued and were only exacerbated after the National Guard fired on student protesters at Kent State University in 1970. Over 200 students occupied Urey Hall, with one student setting himself on fire in protest of the war.

Early research activity and faculty quality, notably in the sciences, was integral to shaping the focus and culture of the university. Even before The University of California-San Diego had its own campus, faculty recruits had already made significant research breakthroughs, such as the Keeling Curve, a graph that plots rapidly increasing carbon dioxide levels in the atmosphere and was the first significant evidence for global climate change; the Kohn–Sham equations, used to investigate particular atoms and molecules in quantum chemistry; and the Miller–Urey experiment, which gave birth to the field of prebiotic chemistry.

Engineering, particularly computer science, became an important part of the university’s academics as it matured. University researchers helped develop The University of California-San Diego Pascal, an early machine-independent programming language that later heavily influenced Java; the National Science Foundation Network, a precursor to the Internet; and the Network News Transfer Protocol during the late 1970s to 1980s. In economics, the methods for analyzing economic time series with time-varying volatility (ARCH), and with common trends (cointegration) were developed. The University of California-San Diego maintained its research intense character after its founding, racking up 25 Nobel Laureates affiliated within 50 years of history; a rate of five per decade.

Under Richard C. Atkinson’s leadership as chancellor from 1980 to 1995, the university strengthened its ties with the city of San Diego by encouraging technology transfer with developing companies, transforming San Diego into a world leader in technology-based industries. He oversaw a rapid expansion of the School of Engineering, later renamed after Qualcomm founder Irwin M. Jacobs, with the construction of the San Diego Supercomputer Center and establishment of the computer science, electrical engineering, and bioengineering departments. Private donations increased from $15 million to nearly $50 million annually, faculty expanded by nearly 50%, and enrollment doubled to about 18,000 students during his administration. By the end of his chancellorship, the quality of The University of California-San Diego graduate programs was ranked 10th in the nation by the National Research Council.

The university continued to undergo further expansion during the first decade of the new millennium with the establishment and construction of two new professional schools — the Skaggs School of Pharmacy and Rady School of Management—and the California Institute for Telecommunications and Information Technology, a research institute run jointly with University of California Irvine. The University of California-San Diego also reached two financial milestones during this time, becoming the first university in the western region to raise over $1 billion in its eight-year fundraising campaign in 2007 and also obtaining an additional $1 billion through research contracts and grants in a single fiscal year for the first time in 2010. Despite this, due to the California budget crisis, the university loaned $40 million against its own assets in 2009 to offset a significant reduction in state educational appropriations. The salary of Pradeep Khosla, who became chancellor in 2012, has been the subject of controversy amidst continued budget cuts and tuition increases.

On November 27, 2017, the university announced it would leave its longtime athletic home of the California Collegiate Athletic Association, an NCAA Division II league, to begin a transition to Division I in 2020. At that time, it will join the Big West Conference, already home to four other UC campuses (Davis, Irvine, Riverside, Santa Barbara). The transition period will run through the 2023–24 school year. The university prepares to transition to NCAA Division I competition on July 1, 2020.

Research

Applied Physics and Mathematics

The Nature Index lists The University of California-San Diego as 6th in the United States for research output by article count in 2019. In 2017, The University of California-San Diego spent $1.13 billion on research, the 7th highest expenditure among academic institutions in the U.S. The university operates several organized research units, including the Center for Astrophysics and Space Sciences (CASS), the Center for Drug Discovery Innovation, and the Institute for Neural Computation. The University of California-San Diego also maintains close ties to the nearby Scripps Research Institute and Salk Institute for Biological Studies. In 1977, The University of California-San Diego developed and released The University of California-San Diego Pascal programming language. The university was designated as one of the original national Alzheimer’s disease research centers in 1984 by the National Institute on Aging. In 2018, The University of California-San Diego received $10.5 million from the DOE National Nuclear Security Administration to establish the Center for Matters under Extreme Pressure (CMEC).

The university founded the San Diego Supercomputer Center in 1985, which provides high performance computing for research in various scientific disciplines. In 2000, The University of California-San Diego partnered with The University of California-Irvine to create the Qualcomm Institute , which integrates research in photonics, nanotechnology, and wireless telecommunication to develop solutions to problems in energy, health, and the environment.

The University of California-San Diego also operates the Scripps Institution of Oceanography, one of the largest centers of research in earth science in the world, which predates the university itself. Together, SDSC and SIO, along with funding partner universities California Institute of Technology, San Diego State University, and The University of California-Santa Barbara, manage the High Performance Wireless Research and Education Network.

From The MIT-IBM Watson AI Lab At The Massachusetts Institute of Technology: “AI system can generate novel proteins that meet structural design targets”

From The MIT-IBM Watson AI Lab

At

The Massachusetts Institute of Technology

4.20.23
Adam Zewe

A new machine-learning system can generate protein designs with certain structural features, and which do not exist in nature. These proteins could be utilized to make materials that have similar mechanical properties to existing materials, like polymers, but which would have a much smaller carbon footprint. Image: Jose-Luis Olivares/MIT with figures courtesy of the researchers.

Graphical abstract:

MIT researchers are using artificial intelligence to design new proteins that go beyond those found in nature.

They developed machine-learning algorithms that can generate proteins with specific structural features, which could be used to make materials that have certain mechanical properties, like stiffness or elasticity. Such biologically inspired materials could potentially replace materials made from petroleum or ceramics, but with a much smaller carbon footprint.

The researchers from MIT, the MIT-IBM Watson AI Lab, and Tufts University employed a generative model, which is the same type of machine-learning model architecture used in AI systems like DALL-E 2. But instead of using it to generate realistic images from natural language prompts, like DALL-E 2 does, they adapted the model architecture so it could predict amino acid sequences of proteins that achieve specific structural objectives.

In a paper published today in Chem [below], the researchers demonstrate how these models can generate realistic, yet novel, proteins. The models, which learn biochemical relationships that control how proteins form, can produce new proteins that could enable unique applications, says senior author Markus Buehler, the Jerry McAfee Professor in Engineering and professor of civil and environmental engineering and of mechanical engineering.

For instance, this tool could be used to develop protein-inspired food coatings, which could keep produce fresh longer while being safe for humans to eat. And the models can generate millions of proteins in a few days, quickly giving scientists a portfolio of new ideas to explore, he adds.

“When you think about designing proteins nature has not discovered yet, it is such a huge design space that you can’t just sort it out with a pencil and paper. You have to figure out the language of life, the way amino acids are encoded by DNA and then come together to form protein structures. Before we had deep learning, we really couldn’t do this,” says Buehler, who is also a member of the MIT-IBM Watson AI Lab.

Joining Buehler on the paper are lead author Bo Ni, a postdoc in Buehler’s Laboratory for Atomistic and Molecular Mechanics; and David Kaplan, the Stern Family Professor of Engineering and professor of bioengineering at Tufts.

Adapting new tools for the task

Proteins are formed by chains of amino acids, folded together in 3D patterns. The sequence of amino acids determines the mechanical properties of the protein. While scientists have identified thousands of proteins created through evolution, they estimate that an enormous number of amino acid sequences remain undiscovered.

To streamline protein discovery, researchers have recently developed deep learning models that can predict the 3D structure of a protein for a set of amino acid sequences. But the inverse problem — predicting a sequence of amino acid structures that meet design targets — has proven even more challenging.

A new advent in machine learning enabled Buehler and his colleagues to tackle this thorny challenge: attention-based diffusion models.

Attention-based models can learn very long-range relationships, which is key to developing proteins because one mutation in a long amino acid sequence can make or break the entire design, Buehler says. A diffusion model learns to generate new data through a process that involves adding noise to training data, then learning to recover the data by removing the noise. They are often more effective than other models at generating high-quality, realistic data that can be conditioned to meet a set of target objectives to meet a design demand.

The researchers used this architecture to build two machine-learning models that can predict a variety of new amino acid sequences which form proteins that meet structural design targets.

“In the biomedical industry, you might not want a protein that is completely unknown because then you don’t know its properties. But in some applications, you might want a brand-new protein that is similar to one found in nature, but does something different. We can generate a spectrum with these models, which we control by tuning certain knobs,” Buehler says.

Common folding patterns of amino acids, known as secondary structures, produce different mechanical properties. For instance, proteins with alpha helix structures yield stretchy materials while those with beta sheet structures yield rigid materials. Combining alpha helices and beta sheets can create materials that are stretchy and strong, like silks.

The researchers developed two models, one that operates on overall structural properties of the protein and one that operates at the amino acid level. Both models work by combining these amino acid structures to generate proteins. For the model that operates on the overall structural properties, a user inputs a desired percentage of different structures (40 percent alpha-helix and 60 percent beta sheet, for instance). Then the model generates sequences that meet those targets. For the second model, the scientist also specifies the order of amino acid structures, which gives much finer-grained control.

The models are connected to an algorithm that predicts protein folding, which the researchers use to determine the protein’s 3D structure. Then they calculate its resulting properties and check those against the design specifications.

Realistic yet novel designs

They tested their models by comparing the new proteins to known proteins that have similar structural properties. Many had some overlap with existing amino acid sequences, about 50 to 60 percent in most cases, but also some entirely new sequences. The level of similarity suggests that many of the generated proteins are synthesizable, Buehler adds.

To ensure the predicted proteins are reasonable, the researchers tried to trick the models by inputting physically impossible design targets. They were impressed to see that, instead of producing improbable proteins, the models generated the closest synthesizable solution.

“The learning algorithm can pick up the hidden relationships in nature. This gives us confidence to say that whatever comes out of our model is very likely to be realistic,” Ni says.

Next, the researchers plan to experimentally validate some of the new protein designs by making them in a lab. They also want to continue augmenting and refining the models so they can develop amino acid sequences that meet more criteria, such as biological functions.

“For the applications we are interested in, like sustainability, medicine, food, health, and materials design, we are going to need to go beyond what nature has done. Here is a new design tool that we can use to create potential solutions that might help us solve some of the really pressing societal issues we are facing,” Buehler says.

“In addition to their natural role in living cells, proteins are increasingly playing a key role in technological applications ranging from biologic drugs to functional materials. In this context, a key challenge is to design protein sequences with desired properties suitable for specific applications. Generative machine-learning approaches, including ones leveraging diffusion models, have recently emerged as powerful tools in this space,” says Tuomas Knowles, professor of physical chemistry and biophysics at Cambridge University, who was not involved with this research. “Buehler and colleagues demonstrate a crucial advance in this area by providing a design approach which allows the secondary structure of the designed protein to be tailored. This is an exciting advance with implications for many potential areas, including for designing building blocks for functional materials, the properties of which are governed by secondary structure elements.”

“This particular work is fascinating because it is examining the creation of new proteins that mostly do not exist, but then it examines what their characteristics would be from a mechanics-based direction,” adds Philip LeDuc, the William J. Brown Professor of Mechanical Engineering at Carnegie Mellon University, who was also not involved with this work. “I personally have been fascinated by the idea of creating molecules that do not exist that have functionality that we haven’t even imagined yet. This is a tremendous step in that direction.”

This research was supported, in part, by the MIT-IBM Watson AI Lab, the U.S. Department of Agriculture, the U.S. Department of Energy, the Army Research Office, the National Institutes of Health, and the Office of Naval Research.

Chem

See the full article here .

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MIT-IBM Watson AI Lab, 314 Main St. in the Kendall Square technology center of Cambridge, Massachusetts.

We are a community of scientists at MIT and IBM Research. We conduct AI research and work with global organizations to bridge algorithms to impact business and society.

A Sustainable Model for Industry-University Collaboration

The MIT-IBM Watson AI Lab is a community of scientists from MIT and IBM Research dedicated to pushing the frontiers of artificial intelligence and translating breakthroughs into real-world impact. Founded in 2017, the Lab works with industry to translate fundamental science into applications that solve immediate problems in the business world and beyond. The Lab currently manages a research portfolio of more than 80 projects, with an emphasis on data-driven, deep learning approaches to understanding language and the visual world and techniques for making large-scale AI systems more efficient and robust. The Lab is also developing AI systems for healthcare and a variety of decision-making applications. In all of its work, the Lab is committed to building trustworthy and socially responsible AI systems.

We’re located in one of the fastest-growing technology centers in the world: Kendall Square in Cambridge, Massachusetts. Across the street from MIT, down the road from Harvard, and situated in a dense cluster of the world’s leading technology companies, Kendall Square is a vibrant ecosystem for innovators. In 2021, our IBM Research team moved into our new offices on MIT’s campus at 314 Main St.

USPS “Forever” postage stamps celebrating Innovation at MIT.

The Massachusetts Institute of Technology is a private land-grant research university in Cambridge, Massachusetts. The institute has an urban campus that extends more than a mile (1.6 km) alongside the Charles River. The institute also encompasses a number of major off-campus facilities such as the MIT Lincoln Laboratory , the MIT Bates Research and Engineering Center , and the Haystack Observatory , as well as affiliated laboratories such as the Broad Institute of MIT and Harvard and Whitehead Institute.

MIT Lincoln Laboratory campus

Massachusettes Institute of Technology-Haystack Observatory Westford, Massachusetts, USA, Altitude 131 m (430 ft).

MIT AeroAstro campus

The Computer Science and Artificial Intelligence Laboratory (CSAIL)

The Kavli Institute For Astrophysics and Space Research

MIT’s Institute for Medical Engineering and Science is a research institute at the Massachusetts Institute of Technology

The MIT Laboratory for Nuclear Science

The MIT Media Lab

MIT PLasma Science and Fusion Center

The MIT School of Engineering

The MIT Sloan School of Management

Spectrum

MIT School of Architecture and Planning campus.

MIT Electrical Engineering & Computer Science campus.

MIT.nano

Lisa T. Su Building at MIT

Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology adopted a European polytechnic university model and stressed laboratory instruction in applied science and engineering. It has since played a key role in the development of many aspects of modern science, engineering, mathematics, and technology, and is widely known for its innovation and academic strength. It is frequently regarded as one of the most prestigious universities in the world.

As of December 2020, 97 Nobel laureates, 26 Turing Award winners, and 8 Fields Medalists have been affiliated with MIT as alumni, faculty members, or researchers. In addition, 58 National Medal of Science recipients, 29 National Medals of Technology and Innovation recipients, 50 MacArthur Fellows, 80 Marshall Scholars, 3 Mitchell Scholars, 22 Schwarzman Scholars, 41 astronauts, and 16 Chief Scientists of the U.S. Air Force have been affiliated with The Massachusetts Institute of Technology . The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology is a member of the Association of American Universities (AAU).

Foundation and vision

In 1859, a proposal was submitted to the Massachusetts General Court to use newly filled lands in Back Bay, Boston for a “Conservatory of Art and Science”, but the proposal failed. A charter for the incorporation of the Massachusetts Institute of Technology, proposed by William Barton Rogers, was signed by John Albion Andrew, the governor of Massachusetts, on April 10, 1861.

Rogers, a professor from the University of Virginia , wanted to establish an institution to address rapid scientific and technological advances. He did not wish to found a professional school, but a combination with elements of both professional and liberal education, proposing that:

“The true and only practicable object of a polytechnic school is, as I conceive, the teaching, not of the minute details and manipulations of the arts, which can be done only in the workshop, but the inculcation of those scientific principles which form the basis and explanation of them, and along with this, a full and methodical review of all their leading processes and operations in connection with physical laws.”

The Rogers Plan reflected the German research university model, emphasizing an independent faculty engaged in research, as well as instruction oriented around seminars and laboratories.

Early developments

Two days after The Massachusetts Institute of Technology was chartered, the first battle of the Civil War broke out. After a long delay through the war years, MIT’s first classes were held in the Mercantile Building in Boston in 1865. The new institute was founded as part of the Morrill Land-Grant Colleges Act to fund institutions “to promote the liberal and practical education of the industrial classes” and was a land-grant school. In 1863 under the same act, the Commonwealth of Massachusetts founded the Massachusetts Agricultural College, which developed as the University of Massachusetts Amherst ). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

The Massachusetts Institute of Technology was informally called “Boston Tech”. The institute adopted the European polytechnic university model and emphasized laboratory instruction from an early date. Despite chronic financial problems, the institute saw growth in the last two decades of the 19th century under President Francis Amasa Walker. Programs in electrical, chemical, marine, and sanitary engineering were introduced, new buildings were built, and the size of the student body increased to more than one thousand.

The curriculum drifted to a vocational emphasis, with less focus on theoretical science. The fledgling school still suffered from chronic financial shortages which diverted the attention of the MIT leadership. During these “Boston Tech” years, Massachusetts Institute of Technology faculty and alumni rebuffed Harvard University president (and former MIT faculty) Charles W. Eliot’s repeated attempts to merge MIT with Harvard College’s Lawrence Scientific School. There would be at least six attempts to absorb MIT into Harvard. In its cramped Back Bay location, MIT could not afford to expand its overcrowded facilities, driving a desperate search for a new campus and funding. Eventually, the MIT Corporation approved a formal agreement to merge with Harvard, over the vehement objections of MIT faculty, students, and alumni. However, a 1917 decision by the Massachusetts Supreme Judicial Court effectively put an end to the merger scheme.

In 1916, The Massachusetts Institute of Technology administration and the MIT charter crossed the Charles River on the ceremonial barge Bucentaur built for the occasion, to signify MIT’s move to a spacious new campus largely consisting of filled land on a one-mile-long (1.6 km) tract along the Cambridge side of the Charles River. The neoclassical “New Technology” campus was designed by William W. Bosworth and had been funded largely by anonymous donations from a mysterious “Mr. Smith”, starting in 1912. In January 1920, the donor was revealed to be the industrialist George Eastman of Rochester, New York, who had invented methods of film production and processing, and founded Eastman Kodak. Between 1912 and 1920, Eastman donated $20 million ($236.6 million in 2015 dollars) in cash and Kodak stock to MIT.

Curricular reforms

In the 1930s, President Karl Taylor Compton and Vice-President (effectively Provost) Vannevar Bush emphasized the importance of pure sciences like physics and chemistry and reduced the vocational practice required in shops and drafting studios. The Compton reforms “renewed confidence in the ability of the Institute to develop leadership in science as well as in engineering”. Unlike Ivy League schools, Massachusetts Institute of Technology catered more to middle-class families, and depended more on tuition than on endowments or grants for its funding. The school was elected to the Association of American Universities in 1934.

Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at The Massachusetts Institute of Technology that “the Institute is widely conceived as basically a vocational school”, a “partly unjustified” perception the committee sought to change. The report comprehensively reviewed the undergraduate curriculum, recommended offering a broader education, and warned against letting engineering and government-sponsored research detract from the sciences and humanities. The School of Humanities, Arts, and Social Sciences and the MIT Sloan School of Management were formed in 1950 to compete with the powerful Schools of Science and Engineering. Previously marginalized faculties in the areas of economics, management, political science, and linguistics emerged into cohesive and assertive departments by attracting respected professors and launching competitive graduate programs. The School of Humanities, Arts, and Social Sciences continued to develop under the successive terms of the more humanistically oriented presidents Howard W. Johnson and Jerome Wiesner between 1966 and 1980.

The Massachusetts Institute of Technology‘s involvement in military science surged during World War II. In 1941, Vannevar Bush was appointed head of the federal Office of Scientific Research and Development and directed funding to only a select group of universities, including MIT. Engineers and scientists from across the country gathered at Massachusetts Institute of Technology ‘s Radiation Laboratory, established in 1940 to assist the British military in developing microwave radar. The work done there significantly affected both the war and subsequent research in the area. Other defense projects included gyroscope-based and other complex control systems for gunsight, bombsight, and inertial navigation under Charles Stark Draper’s Instrumentation Laboratory; the development of a digital computer for flight simulations under Project Whirlwind; and high-speed and high-altitude photography under Harold Edgerton. By the end of the war, The Massachusetts Institute of Technology became the nation’s largest wartime R&D contractor (attracting some criticism of Bush), employing nearly 4000 in the Radiation Laboratory alone and receiving in excess of $100 million ($1.2 billion in 2015 dollars) before 1946. Work on defense projects continued even after then. Post-war government-sponsored research at MIT included SAGE and guidance systems for ballistic missiles and Project Apollo.

These activities affected The Massachusetts Institute of Technology profoundly. A 1949 report noted the lack of “any great slackening in the pace of life at the Institute” to match the return to peacetime, remembering the “academic tranquility of the prewar years”, though acknowledging the significant contributions of military research to the increased emphasis on graduate education and rapid growth of personnel and facilities. The faculty doubled and the graduate student body quintupled during the terms of Karl Taylor Compton, president of The Massachusetts Institute of Technology between 1930 and 1948; James Rhyne Killian, president from 1948 to 1957; and Julius Adams Stratton, chancellor from 1952 to 1957, whose institution-building strategies shaped the expanding university. By the 1950s, The Massachusetts Institute of Technology no longer simply benefited the industries with which it had worked for three decades, and it had developed closer working relationships with new patrons, philanthropic foundations and the federal government.

In late 1960s and early 1970s, student and faculty activists protested against the Vietnam War and The Massachusetts Institute of Technology ‘s defense research. In this period Massachusetts Institute of Technology’s various departments were researching helicopters, smart bombs and counterinsurgency techniques for the war in Vietnam as well as guidance systems for nuclear missiles. The Union of Concerned Scientists was founded on March 4, 1969 during a meeting of faculty members and students seeking to shift the emphasis on military research toward environmental and social problems. The Massachusetts Institute of Technology ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT Lincoln Laboratory facility in 1973 in response to the protests. The student body, faculty, and administration remained comparatively unpolarized during what was a tumultuous time for many other universities. Johnson was seen to be highly successful in leading his institution to “greater strength and unity” after these times of turmoil. However six Massachusetts Institute of Technology students were sentenced to prison terms at this time and some former student leaders, such as Michael Albert and George Katsiaficas, are still indignant about MIT’s role in military research and its suppression of these protests. (Richard Leacock’s film, November Actions, records some of these tumultuous events.)

In the 1980s, there was more controversy at The Massachusetts Institute of Technology over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, The Massachusetts Institute of Technology’s research for the military has included work on robots, drones and ‘battle suits’.

Recent history

The Massachusetts Institute of Technology has kept pace with and helped to advance the digital age. In addition to developing the predecessors to modern computing and networking technologies, students, staff, and faculty members at Project MAC, the Artificial Intelligence Laboratory, and the Tech Model Railroad Club wrote some of the earliest interactive computer video games like Spacewar! and created much of modern hacker slang and culture. Several major computer-related organizations have originated at MIT since the 1980s: Richard Stallman’s GNU Project and the subsequent Free Software Foundation were founded in the mid-1980s at the AI Lab; the MIT Media Lab was founded in 1985 by Nicholas Negroponte and Jerome Wiesner to promote research into novel uses of computer technology; the World Wide Web Consortium standards organization was founded at the Laboratory for Computer Science in 1994 by Tim Berners-Lee; the MIT OpenCourseWare project has made course materials for over 2,000 Massachusetts Institute of Technology classes available online free of charge since 2002; and the One Laptop per Child initiative to expand computer education and connectivity to children worldwide was launched in 2005.

The Massachusetts Institute of Technology was named a sea-grant college in 1976 to support its programs in oceanography and marine sciences and was named a space-grant college in 1989 to support its aeronautics and astronautics programs. Despite diminishing government financial support over the past quarter century, MIT launched several successful development campaigns to significantly expand the campus: new dormitories and athletics buildings on west campus; the Tang Center for Management Education; several buildings in the northeast corner of campus supporting research into biology, brain and cognitive sciences, genomics, biotechnology, and cancer research; and a number of new “backlot” buildings on Vassar Street including the Stata Center. Construction on campus in the 2000s included expansions of the Media Lab, the Sloan School’s eastern campus, and graduate residences in the northwest. In 2006, President Hockfield launched the MIT Energy Research Council to investigate the interdisciplinary challenges posed by increasing global energy consumption.

In 2001, inspired by the open source and open access movements, The Massachusetts Institute of Technology launched OpenCourseWare to make the lecture notes, problem sets, syllabi, exams, and lectures from the great majority of its courses available online for no charge, though without any formal accreditation for coursework completed. While the cost of supporting and hosting the project is high, OCW expanded in 2005 to include other universities as a part of the OpenCourseWare Consortium, which currently includes more than 250 academic institutions with content available in at least six languages. In 2011, The Massachusetts Institute of Technology announced it would offer formal certification (but not credits or degrees) to online participants completing coursework in its “MITx” program, for a modest fee. The “edX” online platform supporting MITx was initially developed in partnership with Harvard and its analogous “Harvardx” initiative. The courseware platform is open source, and other universities have already joined and added their own course content. In March 2009 the Massachusetts Institute of Technology faculty adopted an open-access policy to make its scholarship publicly accessible online.

The Massachusetts Institute of Technology has its own police force. Three days after the Boston Marathon bombing of April 2013, MIT Police patrol officer Sean Collier was fatally shot by the suspects Dzhokhar and Tamerlan Tsarnaev, setting off a violent manhunt that shut down the campus and much of the Boston metropolitan area for a day. One week later, Collier’s memorial service was attended by more than 10,000 people, in a ceremony hosted by the Massachusetts Institute of Technology community with thousands of police officers from the New England region and Canada. On November 25, 2013, The Massachusetts Institute of Technology announced the creation of the Collier Medal, to be awarded annually to “an individual or group that embodies the character and qualities that Officer Collier exhibited as a member of The Massachusetts Institute of Technology community and in all aspects of his life”. The announcement further stated that “Future recipients of the award will include those whose contributions exceed the boundaries of their profession, those who have contributed to building bridges across the community, and those who consistently and selflessly perform acts of kindness”.

In September 2017, the school announced the creation of an artificial intelligence research lab called the MIT-IBM Watson AI Lab. IBM will spend $240 million over the next decade, and the lab will be staffed by MIT and IBM scientists. In October 2018 MIT announced that it would open a new Schwarzman College of Computing dedicated to the study of artificial intelligence, named after lead donor and The Blackstone Group CEO Stephen Schwarzman. The focus of the new college is to study not just AI, but interdisciplinary AI education, and how AI can be used in fields as diverse as history and biology. The cost of buildings and new faculty for the new college is expected to be $1 billion upon completion.

The Caltech/MIT Advanced aLIGO was designed and constructed by a team of scientists from California Institute of Technology , Massachusetts Institute of Technology, and industrial contractors, and funded by the National Science Foundation .

Caltech /MIT Advanced aLigo

It was designed to open the field of gravitational-wave astronomy through the detection of gravitational waves predicted by general relativity. Gravitational waves were detected for the first time by the LIGO detector in 2015. For contributions to the LIGO detector and the observation of gravitational waves, two Caltech physicists, Kip Thorne and Barry Barish, and Massachusetts Institute of Technology physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also a Massachusetts Institute of Technology graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

The mission of The Massachusetts Institute of Technology is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of The Massachusetts Institute of Technology community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

From The College of Engineering At Cornell University Via “The Chronicle”: “Biosensor could lead to new drugs sensory organs on a chip”

From The College of Engineering

At

Cornell University

Via

From “The Chronicle”

2.7.23
Krishna Ramanujan
ksr32@cornell.edu

A synthetic biosensor that mimics properties found in cell membranes and provides an electronic readout of activity could lead to a better understanding of cell biology, development of new drugs, and the creation of sensory organs on a chip capable of detecting chemicals, similar to how noses and tongues work.

A study was published Jan. 18 in the Synthetic Biology journal [below] of the American Chemical Society.

The bioengineering feat described in the paper uses synthetic biology to re-create a cell membrane and its embedded proteins, which are gatekeepers of cellular functions. A conducting sensing platform allows for an electronic readout when a protein is activated. Being able to test if and how a molecule reacts with proteins in a cell membrane could generate a great many applications.

But embedding membrane proteins into sensors had been notoriously difficult until the study’s authors combined bioelectronic sensors with a new approach to synthesize proteins.

“This technology really allows us to study these proteins in ways that would be incredibly challenging, if not impossible, with current technology,” said first author Zachary Manzer, a doctoral student in the lab of senior author Susan Daniel, the Fred H. Rhodes Professor and director of the Robert Frederick Smith School of Chemical and Biomolecular Engineering at Cornell Engineering.

Proteins within cell membranes serve many important functions, including communicating with the environment, catalyzing chemical reactions, and moving compounds and ions across the membranes. When a membrane protein receptor is activated, charged ions move across a membrane channel, triggering a function in the cell. For example, brain neurons or muscle cells fire when cues from nerves signal charged calcium-ion channels to open.

The researchers have created a biosensor that starts with a conducting polymer, which is soft and easy to work with, on top of a support that together act as an electric circuit that is monitored by a computer. A layer of lipid (fat) molecules, which forms the membrane, lies on top of the polymer, and the proteins of interest are placed within the lipids.

In this proof of concept, the researchers have created a cell-free platform that allowed them to synthesize a model protein directly into this artificial membrane. The system has a dual readout technology built in. Since the components of the sensor are transparent, researchers can use optical techniques, such as engineering proteins that fluoresce when activated, which allows scientists to study the fundamentals via microscope, and observe what happens to the protein itself during a cellular process. They can also record electronic activity to see how the protein is functioning through clever circuit design.

“This really is the first demonstration of leveraging cell-free synthesis of transmembrane proteins into biosensors,” Daniel said. “There’s no reason why we wouldn’t be able to express many different kinds of proteins into this general platform.”

Currently, researchers have used proteins grown and extracted from living cells for similar applications, but given this advance, users won’t have to grow proteins in cells and then harvest and embed them in the membrane platform. Instead, they can synthesize them directly from DNA, the basic template for proteins.

“We can bypass the whole process of the cell as the factory that produces the protein,” Daniel said, “and biomanufacture the proteins ourselves.”

With such a system, a drug chemist interested in a particular protein implicated in a disease might flow potentially therapeutic molecules across that protein to see how it responds. Or a scientist looking to create an environmental sensor could place on the platform a particular protein that is sensitive to a chemical or pollutant, such as those found in lake water.

“If you think of your nose, or your tongue, every time you smell or taste something, ion channels are firing,” Manzer said. Scientists may now take the proteins being activated when we smell something and translate the results into this electronic system to sense things that might be undetectable with a chemical sensor.”

The new sensor opens the door for pharmacologists to research how to create non-opioid pain medicines, or drugs to treat Alzheimer’s or Parkinson’s disease, which interact with cell membrane proteins.

Surajit Ghosh, a postdoctoral researcher in Daniel’s lab, is a co-first author. Neha Kamat, assistant professor of biomedical engineering at Northwestern University, is a senior co-author of the paper.

The study was funded by the National Science Foundation, the Air Force Office of Scientific Research, the American Heart Association, the National Institute of General Medical Sciences and the Defense Advanced Research Projects Agency.

Synthetic Biology

See the full article here .

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The Cornell University College of Engineering is a division of Cornell University that was founded in 1870 as the Sibley College of Mechanical Engineering and Mechanic Arts. It is one of four private undergraduate colleges at Cornell that are not statutory colleges.

It currently grants bachelors, masters, and doctoral degrees in a variety of engineering and applied science fields, and is the third largest undergraduate college at Cornell by student enrollment. The college offers over 450 engineering courses, and has an annual research budget exceeding US$112 million.

The College of Engineering was founded in 1870 as the Sibley College of Mechanical Engineering and Mechanic Arts. The program was housed in Sibley Hall on what has since become the Arts Quad, both of which are named for Hiram Sibley, the original benefactor whose contributions were used to establish the program. The college took its current name in 1919 when the Sibley College merged with the College of Civil Engineering. It was housed in Sibley, Lincoln, Franklin, Rand, and Morse Halls. In the 1950s the college moved to the southern end of Cornell’s campus.

The college is known for a number of firsts. In 1889, the college took over electrical engineering from the Department of Physics, establishing the first department in the United States in this field. The college awarded the nation’s first doctorates in both electrical engineering and industrial engineering. The Department of Computer Science, established in 1965 jointly under the College of Engineering and the College of Arts and Sciences, is also one of the oldest in the country.

For many years, the college offered a five-year undergraduate degree program. However, in the 1960s, the course was shortened to four years for a B.S. degree with an optional fifth year leading to a masters of engineering degree. From the 1950s to the 1970s, Cornell offered a Master of Nuclear Engineering program, with graduates gaining employment in the nuclear industry. However, after the 1979 accident at Three Mile Island, employment opportunities in that field dimmed and the program was dropped. Cornell continued to operate its on-campus nuclear reactor as a research facility following the close of the program. For most of Cornell’s history, Geology was taught in the College of Arts and Sciences. However, in the 1970s, the department was shifted to the engineering college and Snee Hall was built to house the program. After World War II, the Graduate School of Aerospace Engineering was founded as a separate academic unit, but later merged into the engineering college.

Cornell Engineering is home to many teams that compete in student design competitions and other engineering competitions. Presently, there are teams that compete in the Baja SAE, Automotive X-Prize (see Cornell 100+ MPG Team), UNP Satellite Program, DARPA Grand Challenge, AUVSI Unmanned Aerial Systems and Underwater Vehicle Competition, Formula SAE, RoboCup, Solar Decathlon, Genetically Engineered Machines, and others.

Cornell’s College of Engineering is currently ranked 12th nationally by U.S. News and World Report, making it ranked 1st among engineering schools/programs in the Ivy League. The engineering physics program at Cornell was ranked as being No. 1 by U.S. News and World Report in 2008. Cornell’s operations research and industrial engineering program ranked fourth in nation, along with the master’s program in financial engineering. Cornell’s computer science program ranks among the top five in the world, and it ranks fourth in the quality of graduate education.

The college is a leader in nanotechnology. In a survey done by a nanotechnology magazine Cornell University was ranked as being the best at nanotechnology commercialization, 2nd best in terms of nanotechnology facilities, the 4th best at nanotechnology research and the 10th best at nanotechnology industrial outreach.

Departments and schools

With about 3,000 undergraduates and 1,300 graduate students, the college is the third-largest undergraduate college at Cornell by student enrollment. It is divided into twelve departments and schools:

School of Applied and Engineering Physics
Department of Biological and Environmental Engineering
Meinig School of Biomedical Engineering
Smith School of Chemical and Biomolecular Engineering
School of Civil & Environmental Engineering
Department of Computer Science
Department of Earth & Atmospheric Sciences
School of Electrical and Computer Engineering
Department of Materials Science and Engineering
Sibley School of Mechanical and Aerospace Engineering
School of Operations Research and Information Engineering
Department of Theoretical and Applied Mechanics
Department of Systems Engineering

Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

On the Ithaca campus alone nearly 20,000 students representing every state and 120 countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

Cornell University is a private, statutory, Ivy League and land-grant research university in Ithaca, New York. Founded in 1865 by Ezra Cornell and Andrew Dickson White, the university was intended to teach and make contributions in all fields of knowledge—from the classics to the sciences, and from the theoretical to the applied. These ideals, unconventional for the time, are captured in Cornell’s founding principle, a popular 1868 quotation from founder Ezra Cornell: “I would found an institution where any person can find instruction in any study.”

The university is broadly organized into seven undergraduate colleges and seven graduate divisions at its main Ithaca campus, with each college and division defining its specific admission standards and academic programs in near autonomy. The university also administers two satellite medical campuses, one in New York City and one in Education City, Qatar, and Jacobs Technion-Cornell Institute 8in New York City, a graduate program that incorporates technology, business, and creative thinking. The program moved from Google’s Chelsea Building in New York City to its permanent campus on Roosevelt Island in September 2017.

Cornell is one of the few private land-grant universities in the United States. Of its seven undergraduate colleges, three are state-supported statutory or contract colleges through the SUNY – The State University of New York system, including its Agricultural and Human Ecology colleges as well as its Industrial Labor Relations school. Of Cornell’s graduate schools, only the veterinary college is state-supported. As a land grant college, Cornell operates a cooperative extension outreach program in every county of New York and receives annual funding from the State of New York for certain educational missions. The Cornell University Ithaca Campus comprises 745 acres, but is much larger when the Cornell Botanic Gardens (more than 4,300 acres) and the numerous university-owned lands in New York City are considered.

Alumni and affiliates of Cornell have reached many notable and influential positions in politics, media, and science. As of January 2021, 61 Nobel laureates, four Turing Award winners and one Fields Medalist have been affiliated with Cornell. Cornell counts more than 250,000 living alumni, and its former and present faculty and alumni include 34 Marshall Scholars, 33 Rhodes Scholars, 29 Truman Scholars, 7 Gates Scholars, 55 Olympic Medalists, 10 current Fortune 500 CEOs, and 35 billionaire alumni. Since its founding, Cornell has been a co-educational, non-sectarian institution where admission has not been restricted by religion or race. The student body consists of more than 15,000 undergraduate and 9,000 graduate students from all 50 American states and 119 countries.

History

Cornell University was founded on April 27, 1865; the New York State (NYS) Senate authorized the university as the state’s land grant institution. Senator Ezra Cornell offered his farm in Ithaca, New York, as a site and $500,000 of his personal fortune as an initial endowment. Fellow senator and educator Andrew Dickson White agreed to be the first president. During the next three years, White oversaw the construction of the first two buildings and traveled to attract students and faculty. The university was inaugurated on October 7, 1868, and 412 men were enrolled the next day.

Cornell developed as a technologically innovative institution, applying its research to its own campus and to outreach efforts. For example, in 1883 it was one of the first university campuses to use electricity from a water-powered dynamo to light the grounds. Since 1894, Cornell has included colleges that are state funded and fulfill statutory requirements; it has also administered research and extension activities that have been jointly funded by state and federal matching programs.

Cornell has had active alumni since its earliest classes. It was one of the first universities to include alumni-elected representatives on its Board of Trustees. Cornell was also among the Ivies that had heightened student activism during the 1960s related to cultural issues; civil rights; and opposition to the Vietnam War, with protests and occupations resulting in the resignation of Cornell’s president and the restructuring of university governance. Today the university has more than 4,000 courses. Cornell is also known for the Residential Club Fire of 1967, a fire in the Residential Club building that killed eight students and one professor.

Since 2000, Cornell has been expanding its international programs. In 2004, the university opened the Weill Cornell Medical College in Qatar. It has partnerships with institutions in India, Singapore, and the People’s Republic of China. Former president Jeffrey S. Lehman described the university, with its high international profile, a “transnational university”. On March 9, 2004, Cornell and Stanford University laid the cornerstone for a new ‘Bridging the Rift Center’ to be built and jointly operated for education on the Israel–Jordan border.

Research

Cornell, a research university, is ranked fourth in the world in producing the largest number of graduates who go on to pursue PhDs in engineering or the natural sciences at American institutions, and fifth in the world in producing graduates who pursue PhDs at American institutions in any field. Research is a central element of the university’s mission; in 2009 Cornell spent $671 million on science and engineering research and development, the 16th highest in the United States.
Cornell is a member of the Association of American Universities and is classified among “R1: Doctoral Universities – Very high research activity”.

For the 2016–17 fiscal year, the university spent $984.5 million on research. Federal sources constitute the largest source of research funding, with total federal investment of $438.2 million. The agencies contributing the largest share of that investment are the Department of Health and Human Services and the National Science Foundation, accounting for 49.6% and 24.4% of all federal investment, respectively. Cornell was on the top-ten list of U.S. universities receiving the most patents in 2003, and was one of the nation’s top five institutions in forming start-up companies. In 2004–05, Cornell received 200 invention disclosures; filed 203 U.S. patent applications; completed 77 commercial license agreements; and distributed royalties of more than $4.1 million to Cornell units and inventors.

Since 1962, Cornell has been involved in unmanned missions to Mars. In the 21st century, Cornell had a hand in the Mars Exploration Rover Mission. Cornell’s Steve Squyres, Principal Investigator for the Athena Science Payload, led the selection of the landing zones and requested data collection features for the Spirit and Opportunity rovers. NASA-JPL/Caltech engineers took those requests and designed the rovers to meet them. The rovers, both of which have operated long past their original life expectancies, are responsible for the discoveries that were awarded 2004 Breakthrough of the Year honors by Science. Control of the Mars rovers has shifted between National Aeronautics and Space Administration’s JPL-Caltech and Cornell’s Space Sciences Building.

Further, Cornell researchers discovered the rings around the planet Uranus, and Cornell built and operated the telescope at Arecibo Observatory located in Arecibo, Puerto Rico until 2011, when they transferred the operations to SRI International, the Universities Space Research Association and the Metropolitan University of Puerto Rico [Universidad Metropolitana de Puerto Rico].

The Automotive Crash Injury Research Project was begun in 1952. It pioneered the use of crash testing, originally using corpses rather than dummies. The project discovered that improved door locks; energy-absorbing steering wheels; padded dashboards; and seat belts could prevent an extraordinary percentage of injuries.

In the early 1980s, Cornell deployed the first IBM 3090-400VF and coupled two IBM 3090-600E systems to investigate coarse-grained parallel computing. In 1984, the National Science Foundation began work on establishing five new supercomputer centers, including the Cornell Center for Advanced Computing, to provide high-speed computing resources for research within the United States. As an National Science Foundation center, Cornell deployed the first IBM Scalable Parallel supercomputer.

In the 1990s, Cornell developed scheduling software and deployed the first supercomputer built by Dell. Most recently, Cornell deployed Red Cloud, one of the first cloud computing services designed specifically for research. Today, the center is a partner on the National Science Foundation XSEDE-Extreme Science Engineering Discovery Environment supercomputing program, providing coordination for XSEDE architecture and design, systems reliability testing, and online training using the Cornell Virtual Workshop learning platform.

Cornell scientists have researched the fundamental particles of nature for more than 70 years. Cornell physicists, such as Hans Bethe, contributed not only to the foundations of nuclear physics but also participated in the Manhattan Project. In the 1930s, Cornell built the second cyclotron in the United States. In the 1950s, Cornell physicists became the first to study synchrotron radiation.

During the 1990s, the Cornell Electron Storage Ring, located beneath Alumni Field, was the world’s highest-luminosity electron-positron collider. After building the synchrotron at Cornell, Robert R. Wilson took a leave of absence to become the founding director of DOE’s Fermi National Accelerator Laboratory, which involved designing and building the largest accelerator in the United States.

Cornell’s accelerator and high-energy physics groups are involved in the design of the proposed ILC-International Linear Collider(JP) and plan to participate in its construction and operation. The International Linear Collider(JP), to be completed in the late 2010s, will complement the The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][Organisation européenne pour la recherche nucléaire] [Europäische Organisation für Kernforschung](CH)[CERN] <a href="http://“>Large Hadron Collider(CH) and shed light on questions such as the identity of dark matter and the existence of extra dimensions.

As part of its research work, Cornell has established several research collaborations with universities around the globe. For example, a partnership with the University of Sussex(UK) (including the Institute of Development Studies at Sussex) allows research and teaching collaboration between the two institutions.

From The School of Medicine At The University of Washington: “Protein scientists share Frontiers of Knowledge Award”

From The School of Medicine

At

The University of Washington

1.25.23

Leila Gray
UW Medicine
leilag@uw.edu

BBVA Foundation honors UW Medicine’s David Baker and British scientists Demis Hassabis and John Jumper for artificial intelligence in protein design.

U Washington, Dr. David Baker, Baker Lab, University of Washington Institute for Protein Design.

David Baker’s Rosetta@home project, a project running on BOINC software from University of California-Berkeley

BOINC-Berkeley Open Infrastructure for Network Computing from University of California-Berkeley

BOINC-Berkeley Open Infrastructure for Network Computing from University of California-Berkeley.

Rosetta@home BOINC project screen saver

My BOINC stats

UW Medicine biochemist David Baker is among three scientists named to receive The Frontiers of Knowledge Award in Biology and Biomedicine. The BBVA Foundation is honoring Baker and British scientists Demis Hassabis and John Jumper, both at AI company Deep Mind, for leading parallel efforts that are revolutionizing artificial intelligence for protein design.

Protein molecules are the workhorses of biology and are involved in almost every cellular activity in all living things. The ability to analyze their structure, understand their functions and interactions, and engineer brand new, highly useful proteins not found in nature opens avenues to many medical and other advances.

Baker, who directs the UW Medicine Institute for Protein Design, oversaw the development of RoseTTAFold.

Researchers used artificial intelligence to generate hundreds of new protein structures, including this 3D view of human interleukin-12 bound to its receptor. Credit: Ian Haydon.

Deep learning hallucinating a protein design. Image: Ian Haydon.

It is a “deep learning” system that can quickly and accurately decipher the three-dimensional structure of proteins. It can accomplish in a just a few seconds what used to take years of laboratory work. This technology also supports the design of new proteins, created to carry out specific functions. This holds promise for the engineering of new therapies against a variety of diseases, including cancer and infectious illness, as well as applications in energy, environmental, nanotech and other fields.

DeepMind’s CEO Hassabis and chief research scientist Jumper headed the creation of the AlphaFold2 tool, which brought artificial intelligence and deep learning to protein structure prediction and design, and which is powering protein research a variety of medical areas and other bioscientific fields.

The BBVA Foundation promotes world-class scientific research and cultural creation, and the recognition of talent. It is assisted in evaluating nominees for the Frontiers Award in Biology and Biomedicine by the Spanish National Research Council, the country’s premier public research organization. They were joined by an international jury for this category.

According to the selection committee, as reported in the BBVA Foundation news announcement on the work being honored by this year’s award, “Both computer methods rely on a sophisticated machine-learning technique known as deep learning to predict the shape of proteins with unprecedented accuracy, similar to that of experimentally determined structures, and with exceptional speed.”

They added, “This breakthrough is revolutionizing our understanding of how the amino acid sequence of proteins leads to uniquely ordered three-dimensional structures. Scientists are now using these new methods.”

This is an advance, the announcement noted, with huge potential for the development of new treatments against multiple conditions, from combatting the flu virus or COVID-19, cancer cell growth, or malaria parasites, as a few examples.

Baker was born in Seattle. He earned his Ph.D. in biochemistry from the University of California-Berkeley. He is currently a Howard Hughes Medical Institute Investigator and the Henrietta and Aubrey Davis Endowed Professor in Biochemistry at the University of Washington School of Medicine, in addition to directing the Institute for Protein Design. He is also an adjunct professor of genome sciences, bioengineering, chemical engineering, computer science and physics at the UW. He has authored more than 570 research papers, holds more than 100 patents, co-founded 11 tech firms, and directs Rosetta Commons, a consortium of labs and researchers working on biomolecular structure predictions and design software. He and his colleagues are also know for their longstanding citizen scientist effort to involve people from a variety of backgrounds and locations in protein design through Rosetta@Home.

In the BBVA Foundation award announcement, Baker described the revolution in purpose-designed proteins to advance the creation of new drugs and vaccines. He said that the latest RoseTTAFold version even allows for the design of proteins from simple descriptions, similar to the DALL-E system that generates images from text prompts.

“So, for example, you can tell RoseTTAFold: design a protein which blocks this flu virus protein, or design a protein which will block these cancer cells,” he said in the BBVA Foundation news release. “RoseTTAFold will then make those proteins. We’ve made them in the lab, and we find that they have exactly those functions.”

An anti-coronavirus vaccine created with RoseTTAFold has been clinically tested and distributed in South Korea. New purpose-designed anti-cancer medicines are being evaluated in human clinical trials. There are plans for a nasal spray that protects against COVID-19 and work underway on an RSV vaccine, a universal flu vaccine, and ideas for a vaccine against a family of viruses related to SARS-CoV-2.

“We believe that almost all of medicine will be transformed by the protein design revolution,” said Baker. “Most medicines today are made by making small modifications to the proteins which already exist in nature. Now that we can design completely new proteins, we can develop much more improved, more sophisticated medicines that, for example, can treat cancer without the side effects, be made very quickly upon the outbreak of a new pandemic, and in general will be more precise and more robust.”

RoseTTAFold and AlphaFold2 are freely available to the scientific community. Upgrades have practically equalized the computing times required by each.

Although these AI tools have not entirely supplanted experimental methods, they are starting to transform both the field of protein design and biological research more generally.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

The University of Washington School of Medicine (UWSOM) is a large public medical school in the northwest United States, located in Seattle and affiliated with the University of Washington. According to U.S. News & World Report’s 2022 Best Graduate School rankings, University of Washington School of Medicine ranked #1 in the nation for primary care education, and #7 for research.

UWSOM is the first public medical school in the states of Washington, Wyoming, Alaska, Montana, and Idaho. The school maintains a network of teaching facilities in more than 100 towns and cities across the five-state region. As part of this “WWAMI” partnership, medical students from Wyoming, Alaska, Montana, and Idaho spend their first year and a half at The University of Wyoming , The University of Alaska-Anchorage , Montana State University , or The University of Idaho , respectively. In addition, sixty first-year students and forty second-year students from Washington are based at Gonzaga University in Spokane. Preference is given to residents of the WWAMI states.

The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

The University of Washington is a public research university in Seattle, Washington, United States. Founded in 1861, University of Washington is one of the oldest universities on the West Coast; it was established in downtown Seattle approximately a decade after the city’s founding to aid its economic development. Today, the university’s 703-acre main Seattle campus is in the University District above the Montlake Cut, within the urban Puget Sound region of the Pacific Northwest. The university has additional campuses in Tacoma and Bothell. Overall, University of Washington encompasses over 500 buildings and over 20 million gross square footage of space, including one of the largest library systems in the world with more than 26 university libraries, as well as the UW Tower, lecture halls, art centers, museums, laboratories, stadiums, and conference centers. The university offers bachelor’s, master’s, and doctoral degrees through 140 departments in various colleges and schools, sees a total student enrollment of roughly 46,000 annually, and functions on a quarter system.

University of Washington is a member of the Association of American Universities and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation, UW spent $1.41 billion on research and development in 2018, ranking it 5th in the nation. As the flagship institution of the six public universities in Washington state, it is known for its medical, engineering and scientific research as well as its highly competitive computer science and engineering programs. Additionally, University of Washington continues to benefit from its deep historic ties and major collaborations with numerous technology giants in the region, such as Amazon, Boeing, Nintendo, and particularly Microsoft. Paul G. Allen, Bill Gates and others spent significant time at Washington computer labs for a startup venture before founding Microsoft and other ventures. The University of Washington’s 22 varsity sports teams are also highly competitive, competing as the Huskies in the Pac-12 Conference of the NCAA Division I, representing the United States at the Olympic Games, and other major competitions.

The university has been affiliated with many notable alumni and faculty, including 21 Nobel Prize laureates and numerous Pulitzer Prize winners, Fulbright Scholars, Rhodes Scholars and Marshall Scholars.

In 1854, territorial governor Isaac Stevens recommended the establishment of a university in the Washington Territory. Prominent Seattle-area residents, including Methodist preacher Daniel Bagley, saw this as a chance to add to the city’s potential and prestige. Bagley learned of a law that allowed United States territories to sell land to raise money in support of public schools. At the time, Arthur A. Denny, one of the founders of Seattle and a member of the territorial legislature, aimed to increase the city’s importance by moving the territory’s capital from Olympia to Seattle. However, Bagley eventually convinced Denny that the establishment of a university would assist more in the development of Seattle’s economy. Two universities were initially chartered, but later the decision was repealed in favor of a single university in Lewis County provided that locally donated land was available. When no site emerged, Denny successfully petitioned the legislature to reconsider Seattle as a location in 1858.

In 1861, scouting began for an appropriate 10 acres (4 ha) site in Seattle to serve as a new university campus. Arthur and Mary Denny donated eight acres, while fellow pioneers Edward Lander, and Charlie and Mary Terry, donated two acres on Denny’s Knoll in downtown Seattle. More specifically, this tract was bounded by 4th Avenue to the west, 6th Avenue to the east, Union Street to the north, and Seneca Streets to the south.

John Pike, for whom Pike Street is named, was the university’s architect and builder. It was opened on November 4, 1861, as the Territorial University of Washington. The legislature passed articles incorporating the University, and establishing its Board of Regents in 1862. The school initially struggled, closing three times: in 1863 for low enrollment, and again in 1867 and 1876 due to funds shortage. University of Washington awarded its first graduate Clara Antoinette McCarty Wilt in 1876, with a bachelor’s degree in science.

19th century relocation

By the time Washington state entered the Union in 1889, both Seattle and the University had grown substantially. University of Washington’s total undergraduate enrollment increased from 30 to nearly 300 students, and the campus’s relative isolation in downtown Seattle faced encroaching development. A special legislative committee, headed by University of Washington graduate Edmond Meany, was created to find a new campus to better serve the growing student population and faculty. The committee eventually selected a site on the northeast of downtown Seattle called Union Bay, which was the land of the Duwamish, and the legislature appropriated funds for its purchase and construction. In 1895, the University relocated to the new campus by moving into the newly built Denny Hall. The University Regents tried and failed to sell the old campus, eventually settling with leasing the area. This would later become one of the University’s most valuable pieces of real estate in modern-day Seattle, generating millions in annual revenue with what is now called the Metropolitan Tract. The original Territorial University building was torn down in 1908, and its former site now houses the Fairmont Olympic Hotel.

The sole-surviving remnants of Washington’s first building are four 24-foot (7.3 m), white, hand-fluted cedar, Ionic columns. They were salvaged by Edmond S. Meany, one of the University’s first graduates and former head of its history department. Meany and his colleague, Dean Herbert T. Condon, dubbed the columns as “Loyalty,” “Industry,” “Faith”, and “Efficiency”, or “LIFE.” The columns now stand in the Sylvan Grove Theater.

20th century expansion

Organizers of the 1909 Alaska-Yukon-Pacific Exposition eyed the still largely undeveloped campus as a prime setting for their world’s fair. They came to an agreement with Washington’s Board of Regents that allowed them to use the campus grounds for the exposition, surrounding today’s Drumheller Fountain facing towards Mount Rainier. In exchange, organizers agreed Washington would take over the campus and its development after the fair’s conclusion. This arrangement led to a detailed site plan and several new buildings, prepared in part by John Charles Olmsted. The plan was later incorporated into the overall University of Washington campus master plan, permanently affecting the campus layout.

Both World Wars brought the military to campus, with certain facilities temporarily lent to the federal government. In spite of this, subsequent post-war periods were times of dramatic growth for the University. The period between the wars saw a significant expansion of the upper campus. Construction of the Liberal Arts Quadrangle, known to students as “The Quad,” began in 1916 and continued to 1939. The University’s architectural centerpiece, Suzzallo Library, was built in 1926 and expanded in 1935.

After World War II, further growth came with the G.I. Bill. Among the most important developments of this period was the opening of the School of Medicine in 1946, which is now consistently ranked as the top medical school in the United States. It would eventually lead to the University of Washington Medical Center, ranked by U.S. News and World Report as one of the top ten hospitals in the nation.

In 1942, all persons of Japanese ancestry in the Seattle area were forced into inland internment camps as part of Executive Order 9066 following the attack on Pearl Harbor. During this difficult time, university president Lee Paul Sieg took an active and sympathetic leadership role in advocating for and facilitating the transfer of Japanese American students to universities and colleges away from the Pacific Coast to help them avoid the mass incarceration. Nevertheless, many Japanese American students and “soon-to-be” graduates were unable to transfer successfully in the short time window or receive diplomas before being incarcerated. It was only many years later that they would be recognized for their accomplishments during the University of Washington’s Long Journey Home ceremonial event that was held in May 2008.

From 1958 to 1973, the University of Washington saw a tremendous growth in student enrollment, its faculties and operating budget, and also its prestige under the leadership of Charles Odegaard. University of Washington student enrollment had more than doubled to 34,000 as the baby boom generation came of age. However, this era was also marked by high levels of student activism, as was the case at many American universities. Much of the unrest focused around civil rights and opposition to the Vietnam War. In response to anti-Vietnam War protests by the late 1960s, the University Safety and Security Division became the University of Washington Police Department.

Odegaard instituted a vision of building a “community of scholars”, convincing the Washington State legislatures to increase investment in the University. Washington senators, such as Henry M. Jackson and Warren G. Magnuson, also used their political clout to gather research funds for the University of Washington. The results included an increase in the operating budget from $37 million in 1958 to over $400 million in 1973, solidifying University of Washington as a top recipient of federal research funds in the United States. The establishment of technology giants such as Microsoft, Boeing and Amazon in the local area also proved to be highly influential in the University of Washington’s fortunes, not only improving graduate prospects but also helping to attract millions of dollars in university and research funding through its distinguished faculty and extensive alumni network.

21st century

In 1990, the University of Washington opened its additional campuses in Bothell and Tacoma. Although originally intended for students who have already completed two years of higher education, both schools have since become four-year universities with the authority to grant degrees. The first freshman classes at these campuses started in fall 2006. Today both Bothell and Tacoma also offer a selection of master’s degree programs.

In 2012, the University began exploring plans and governmental approval to expand the main Seattle campus, including significant increases in student housing, teaching facilities for the growing student body and faculty, as well as expanded public transit options. The University of Washington light rail station was completed in March 2015, connecting Seattle’s Capitol Hill neighborhood to the University of Washington Husky Stadium within five minutes of rail travel time. It offers a previously unavailable option of transportation into and out of the campus, designed specifically to reduce dependence on private vehicles, bicycles and local King County buses.

University of Washington has been listed as a “Public Ivy” in Greene’s Guides since 2001, and is an elected member of the American Association of Universities. Among the faculty by 2012, there have been 151 members of American Association for the Advancement of Science, 68 members of the National Academy of Sciences, 67 members of the American Academy of Arts and Sciences, 53 members of the National Academy of Medicine, 29 winners of the Presidential Early Career Award for Scientists and Engineers, 21 members of the National Academy of Engineering, 15 Howard Hughes Medical Institute Investigators, 15 MacArthur Fellows, 9 winners of the Gairdner Foundation International Award, 5 winners of the National Medal of Science, 7 Nobel Prize laureates, 5 winners of Albert Lasker Award for Clinical Medical Research, 4 members of the American Philosophical Society, 2 winners of the National Book Award, 2 winners of the National Medal of Arts, 2 Pulitzer Prize winners, 1 winner of the Fields Medal, and 1 member of the National Academy of Public Administration. Among UW students by 2012, there were 136 Fulbright Scholars, 35 Rhodes Scholars, 7 Marshall Scholars and 4 Gates Cambridge Scholars. UW is recognized as a top producer of Fulbright Scholars, ranking 2nd in the US in 2017.

The Academic Ranking of World Universities has consistently ranked University of Washington as one of the top 20 universities worldwide every year since its first release. In 2019, University of Washington ranked 14th worldwide out of 500 by the ARWU, 26th worldwide out of 981 in the Times Higher Education World University Rankings, and 28th worldwide out of 101 in the Times World Reputation Rankings. Meanwhile, QS World University Rankings ranked it 68th worldwide, out of over 900.

U.S. News & World Report ranked University of Washington 8th out of nearly 1,500 universities worldwide for 2021, with University of Washington’s undergraduate program tied for 58th among 389 national universities in the U.S. and tied for 19th among 209 public universities.

In 2019, it ranked 10th among the universities around the world by SCImago Institutions Rankings. In 2017, the Leiden Ranking, which focuses on science and the impact of scientific publications among the world’s 500 major universities, ranked University of Washington 12th globally and 5th in the U.S.

In 2019, Kiplinger Magazine’s review of “top college values” named University of Washington 5th for in-state students and 10th for out-of-state students among U.S. public colleges, and 84th overall out of 500 schools. In the Washington Monthly National University Rankings University of Washington was ranked 15th domestically in 2018, based on its contribution to the public good as measured by social mobility, research, and promoting public service.

From The School of Engineering and Applied Science At The University of Pennsylvania: “Glassy Discovery Offers Computational Windfall to Researchers Across Disciplines”

From The School of Engineering and Applied Science

At

The University of Pennsylvania

12.5.22
Devorah Fischler

Penn Engineers used a counterintuitive algorithmic strategy called “metadynamics” to find rare low-energy canyons in glassy materials. Their breakthrough suggests the algorithm may have a wide range of useful scientific applications, potentially speeding up the pace of computational protein folding and eliminating the need for large data sets in machine learning. (Image credit: Dariusz Jemielniak)

John Crocker had expected to see a flat line — a familiar horizontal track with some slight peaks and valleys — but the plot of energy in front of him dove sharply downward.

“It’s a once-in-a-lifetime finding,” says Crocker. “It was as if the simulation had unexpectedly fallen into a deep canyon on an energy surface. This was lucky for two reasons. Firstly, it turned out to be a game changer for our study of glassy materials. And secondly, similar canyons have the potential to help others grappling with the same computational obstacles we face in our field, from computer scientists working on machine learning algorithms to bioengineers studying protein folding. We ended up with significant results because we were curious enough to try a method that shouldn’t have worked. But it did.”

The method is metadynamics, a computational approach to exploring energy landscapes. Its counterintuitive application is the subject of a recent publication in PNAS [below] from a group of Penn Engineers at the University of Pennsylvania led by Crocker, Professor and Graduate Group Chair in the Department of Chemical and Biomolecular Engineering (CBE), along with Robert Riggleman, Associate Professor in CBE, and Amruthesh Thirumalaiswamy, Ph.D. student in CBE.

Most solids are glasses (or glassy). We categorize the rest as crystals. These categorizations are not limited to glass or crystal as we might imagine them, but instead indicate how atoms in any solid are arranged. Crystals have neat, repetitive atomic structures. Glasses, however, are amorphous. Their atoms and molecules take on a vast number of disordered configurations.

Glassy and crystal solids.

Glassy configurations get stuck while pursuing — as all systems do — their most stable, lowest energy states. Given enough time, glasses will still very slowly relax in energy, but their disordered atoms make it a slow and difficult process.

Low-energy, stable glasses, or “ideal glasses,” are the key to a storehouse of knowledge that researchers are keen to unlock.

Seeking to understand and eventually replicate the conditions of glassy materials that overcome the obstacles of their own atomic quirks, scientists use both experimental and theoretical approaches.

Labs have, for example, melted and re-cooled fossilized amber to develop processes for recreating the encouraging effects that millions of years have had on its glassy pursuit of low-energy states. Crocker’s team, affiliated with the cross-disciplinary Penn Institute for Computational Science (PICS), explores physical structures with mathematical models.

“We use computational models to simulate the positions and movements of atoms in different glasses,” says Thirumalaiswamy. “In order to keep track of a material’s particles, which are so numerous and dynamic they are impossible to visualize in three dimensions, we need to represent them mathematically in high-dimensional virtual spaces. If we have 300 atoms, for example, we need to represent them in 900 dimensions. We call these energy landscapes. We then investigate the landscapes, navigating them almost like explorers.”

In these computational models, single configuration points, digests of atomic movement, tell the story of a glass’ energy levels. They show where a glass has gotten stuck and where it might have achieved a low-energy state.

The problem is that until now, researchers have not been able to navigate landscapes efficiently enough to find these rare instances of stability.

“Most studies do random walks around high-dimensional landscapes at enormous computational cost. It would take an infinite amount of time to find anything of interest. The landscapes are immense, and these walks are repetitive, wasting large amounts of time fixed in a single state before moving on to the next one,” says Riggleman.

And so, they took a chance in trying metadynamics, a method that seemed destined to fail.

Metadynamics is an algorithmic strategy developed to explore the entire landscape and avoid repetition. It assigns a penalty for going back to the same place twice. Metadynamics never works in high-dimensional spaces, however, because it takes too long to construct the penalties, canceling out the strategy’s potential for efficiency.

Yet as the researchers watched their configuration energy trend downward, they realized it had succeeded.

“We couldn’t have guessed it, but the landscapes proved to have these canyons with floors that are only two- or three-dimensional,” says Crocker. “Our algorithm literally fell right in. We found regularly occurring low-energy configurations in several different glasses with a method we think could be revolutionary for other disciplines as well.”

The potential applications of the Crocker Lab canyons are wide-ranging.

In the two decades since the Human Genome Project finished its mapping, scientists have been using computational models to fold peptide sequences into proteins. Proteins that fold well in nature have, through evolution, found ways to explore low-energy states analogous to those of ideal glasses.

Theoretical studies of proteins use energy landscapes to learn about the folding processes that create the functional (or dysfunctional) foundations for biological health. Yet measuring these structures takes time, money and energy that scientists and the populations they aim to serve don’t have to spare. Bogged down by the same computational inefficiencies that glassy materials researchers face, genomic scientists may find similar successes with metadynamics-based approaches, accelerating the pace of medical research.

Machine learning processes have a lot in common with random walks in high-dimensional space. Training artificial intelligence takes an enormous amount of computational time and power and has a long way to go in terms of predictive accuracies.

A neural net needs to “see,” for example, thousands to millions of faces in order to acquire enough skill for facial recognition. With a more strategic computational process, machine learning could become faster, cheaper and more accessible. The metadynamics algorithm may have the potential to overcome the need for the huge and costly datasets typical of the process.

Not only would this provide solutions for industry efficiency, but it could also democratize AI, allowing people with modest resources to do their own training and development.

“We’re conjecturing that the landscapes in these different fields have similar geometric structures to ours,” says Crocker. “We suspect there might be a deep mathematical reason for why these canyons exist, and they may be present in these other related systems. This is our invitation; we look forward to the dialogue it begins.”

This work was supported by NSF-Division of Material Research 1609525 and 1720530 and computational resources provided by XSEDE (Extreme Science and Engineering Discovery Environment) through TG-DMR150034.

Science paper:
PNAS

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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The University of Pennsylvania School of Engineering and Applied Science.

The School of Engineering and Applied Science is an undergraduate and graduate school of The University of Pennsylvania. The School offers programs that emphasize hands-on study of engineering fundamentals (with an offering of approximately 300 courses) while encouraging students to leverage the educational offerings of the broader University. Engineering students can also take advantage of research opportunities through interactions with Penn’s School of Medicine, School of Arts and Sciences and the Wharton School.

Penn Engineering offers bachelors, masters and Ph.D. degree programs in contemporary fields of engineering study. The nationally ranked bioengineering department offers the School’s most popular undergraduate degree program. The Jerome Fisher Program in Management and Technology, offered in partnership with the Wharton School, allows students to simultaneously earn a Bachelor of Science degree in Economics as well as a Bachelor of Science degree in Engineering. SEAS also offers several masters programs, which include: Executive Master’s in Technology Management, Master of Biotechnology, Master of Computer and Information Technology, Master of Computer and Information Science and a Master of Science in Engineering in Telecommunications and Networking.

History

The study of engineering at The University of Pennsylvania can be traced back to 1850 when the University trustees adopted a resolution providing for a professorship of “Chemistry as Applied to the Arts”. In 1852, the study of engineering was further formalized with the establishment of the School of Mines, Arts and Manufactures. The first Professor of Civil and Mining Engineering was appointed in 1852. The first graduate of the school received his Bachelor of Science degree in 1854. Since that time, the school has grown to six departments. In 1973, the school was renamed as the School of Engineering and Applied Science.

The early growth of the school benefited from the generosity of two Philadelphians: John Henry Towne and Alfred Fitler Moore. Towne, a mechanical engineer and railroad developer, bequeathed the school a gift of $500,000 upon his death in 1875. The main administration building for the school still bears his name. Moore was a successful entrepreneur who made his fortune manufacturing telegraph cable. A 1923 gift from Moore established the Moore School of Electrical Engineering, which is the birthplace of the first electronic general-purpose Turing-complete digital computer, ENIAC, in 1946.

During the latter half of the 20th century the school continued to break new ground. In 1958, Barbara G. Mandell became the first woman to enroll as an undergraduate in the School of Engineering. In 1965, the university acquired two sites that were formerly used as U.S. Army Nike Missile Base (PH 82L and PH 82R) and created the Valley Forge Research Center. In 1976, the Management and Technology Program was created. In 1990, a Bachelor of Applied Science in Biomedical Science and Bachelor of Applied Science in Environmental Science were first offered, followed by a master’s degree in Biotechnology in 1997.

The school continues to expand with the addition of the Melvin and Claire Levine Hall for computer science in 2003, Skirkanich Hall for Bioengineering in 2006, and the Krishna P. Singh Center for Nanotechnology in 2013.

Academics

Penn’s School of Engineering and Applied Science is organized into six departments:

Bioengineering
Chemical and Biomolecular Engineering
Computer and Information Science
Electrical and Systems Engineering
Materials Science and Engineering
Mechanical Engineering and Applied Mechanics

The school’s Department of Bioengineering, originally named Biomedical Electronic Engineering, consistently garners a top-ten ranking at both the undergraduate and graduate level from U.S. News & World Report. The department also houses the George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace (aka Biomakerspace) for training undergraduate through PhD students. It is Philadelphia’s and Penn’s only Bio-MakerSpace and it is open to the Penn community, encouraging a free flow of ideas, creativity, and entrepreneurship between Bioengineering students and students throughout the university.

Founded in 1893, the Department of Chemical and Biomolecular Engineering is “America’s oldest continuously operating degree-granting program in chemical engineering.”

The Department of Electrical and Systems Engineering is recognized for its research in electroscience, systems science and network systems and telecommunications.

Originally established in 1946 as the School of Metallurgical Engineering, the Materials Science and Engineering Department “includes cutting edge programs in nanoscience and nanotechnology, biomaterials, ceramics, polymers, and metals.”

The Department of Mechanical Engineering and Applied Mechanics draws its roots from the Department of Mechanical and Electrical Engineering, which was established in 1876.

Each department houses one or more degree programs. The Chemical and Biomolecular Engineering, Materials Science and Engineering, and Mechanical Engineering and Applied Mechanics departments each house a single degree program.

Bioengineering houses two programs (both a Bachelor of Science in Engineering degree as well as a Bachelor of Applied Science degree). Electrical and Systems Engineering offers four Bachelor of Science in Engineering programs: Electrical Engineering, Systems Engineering, Computer Engineering, and the Networked & Social Systems Engineering, the latter two of which are co-housed with Computer and Information Science (CIS). The CIS department, like Bioengineering, offers Computer and Information Science programs under both bachelor programs. CIS also houses Digital Media Design, a program jointly operated with PennDesign.

Research

Penn’s School of Engineering and Applied Science is a research institution. SEAS research strives to advance science and engineering and to achieve a positive impact on society.

Academic life at University of Pennsylvania is unparalleled, with 100 countries and every U.S. state represented in one of the Ivy League’s most diverse student bodies. Consistently ranked among the top 10 universities in the country, Penn enrolls 10,000 undergraduate students and welcomes an additional 10,000 students to our world-renowned graduate and professional schools.

Penn’s award-winning educators and scholars encourage students to pursue inquiry and discovery, follow their passions, and address the world’s most challenging problems through an interdisciplinary approach.

The University of Pennsylvania is a private Ivy League research university in Philadelphia, Pennsylvania. The university claims a founding date of 1740 and is one of the nine colonial colleges chartered prior to the U.S. Declaration of Independence. Benjamin Franklin, Penn’s founder and first president, advocated an educational program that trained leaders in commerce, government, and public service, similar to a modern liberal arts curriculum.

Penn has four undergraduate schools as well as twelve graduate and professional schools. Schools enrolling undergraduates include the College of Arts and Sciences; the School of Engineering and Applied Science; the Wharton School; and the School of Nursing. Penn’s “One University Policy” allows students to enroll in classes in any of Penn’s twelve schools. Among its highly ranked graduate and professional schools are a law school whose first professor wrote the first draft of the United States Constitution, the first school of medicine in North America (Perelman School of Medicine, 1765), and the first collegiate business school (Wharton School, 1881).

Penn is also home to the first “student union” building and organization (Houston Hall, 1896), the first Catholic student club in North America (Newman Center, 1893), the first double-decker college football stadium (Franklin Field, 1924 when second deck was constructed), and Morris Arboretum, the official arboretum of the Commonwealth of Pennsylvania. The first general-purpose electronic computer (ENIAC) was developed at Penn and formally dedicated in 1946. In 2019, the university had an endowment of $14.65 billion, the sixth-largest endowment of all universities in the United States, as well as a research budget of $1.02 billion. The university’s athletics program, the Quakers, fields varsity teams in 33 sports as a member of the NCAA Division I Ivy League conference.

As of 2018, distinguished alumni and/or Trustees include three U.S. Supreme Court justices; 32 U.S. senators; 46 U.S. governors; 163 members of the U.S. House of Representatives; eight signers of the Declaration of Independence and seven signers of the U.S. Constitution (four of whom signed both representing two-thirds of the six people who signed both); 24 members of the Continental Congress; 14 foreign heads of state and two presidents of the United States, including Donald Trump. As of October 2019, 36 Nobel laureates; 80 members of the American Academy of Arts and Sciences; 64 billionaires; 29 Rhodes Scholars; 15 Marshall Scholars and 16 Pulitzer Prize winners have been affiliated with the university.

History

The University of Pennsylvania considers itself the fourth-oldest institution of higher education in the United States, though this is contested by Princeton University and Columbia University. The university also considers itself as the first university in the United States with both undergraduate and graduate studies.

In 1740, a group of Philadelphians joined together to erect a great preaching hall for the traveling evangelist George Whitefield, who toured the American colonies delivering open-air sermons. The building was designed and built by Edmund Woolley and was the largest building in the city at the time, drawing thousands of people the first time it was preached in. It was initially planned to serve as a charity school as well, but a lack of funds forced plans for the chapel and school to be suspended. According to Franklin’s autobiography, it was in 1743 when he first had the idea to establish an academy, “thinking the Rev. Richard Peters a fit person to superintend such an institution”. However, Peters declined a casual inquiry from Franklin and nothing further was done for another six years. In the fall of 1749, now more eager to create a school to educate future generations, Benjamin Franklin circulated a pamphlet titled Proposals Relating to the Education of Youth in Pensilvania, his vision for what he called a “Public Academy of Philadelphia”. Unlike the other colonial colleges that existed in 1749—Harvard University, William & Mary, Yale Unversity, and The College of New Jersey—Franklin’s new school would not focus merely on education for the clergy. He advocated an innovative concept of higher education, one which would teach both the ornamental knowledge of the arts and the practical skills necessary for making a living and doing public service. The proposed program of study could have become the nation’s first modern liberal arts curriculum, although it was never implemented because Anglican priest William Smith (1727-1803), who became the first provost, and other trustees strongly preferred the traditional curriculum.

Franklin assembled a board of trustees from among the leading citizens of Philadelphia, the first such non-sectarian board in America. At the first meeting of the 24 members of the board of trustees on November 13, 1749, the issue of where to locate the school was a prime concern. Although a lot across Sixth Street from the old Pennsylvania State House (later renamed and famously known since 1776 as “Independence Hall”), was offered without cost by James Logan, its owner, the trustees realized that the building erected in 1740, which was still vacant, would be an even better site. The original sponsors of the dormant building still owed considerable construction debts and asked Franklin’s group to assume their debts and, accordingly, their inactive trusts. On February 1, 1750, the new board took over the building and trusts of the old board. On August 13, 1751, the “Academy of Philadelphia”, using the great hall at 4th and Arch Streets, took in its first secondary students. A charity school also was chartered on July 13, 1753 by the intentions of the original “New Building” donors, although it lasted only a few years. On June 16, 1755, the “College of Philadelphia” was chartered, paving the way for the addition of undergraduate instruction. All three schools shared the same board of trustees and were considered to be part of the same institution. The first commencement exercises were held on May 17, 1757.

The institution of higher learning was known as the College of Philadelphia from 1755 to 1779. In 1779, not trusting then-provost the Reverend William Smith’s “Loyalist” tendencies, the revolutionary State Legislature created a University of the State of Pennsylvania. The result was a schism, with Smith continuing to operate an attenuated version of the College of Philadelphia. In 1791, the legislature issued a new charter, merging the two institutions into a new University of Pennsylvania with twelve men from each institution on the new board of trustees.

Penn has three claims to being the first university in the United States, according to university archives director Mark Frazier Lloyd: the 1765 founding of the first medical school in America made Penn the first institution to offer both “undergraduate” and professional education; the 1779 charter made it the first American institution of higher learning to take the name of “University”; and existing colleges were established as seminaries (although, as detailed earlier, Penn adopted a traditional seminary curriculum as well).

After being located in downtown Philadelphia for more than a century, the campus was moved across the Schuylkill River to property purchased from the Blockley Almshouse in West Philadelphia in 1872, where it has since remained in an area now known as University City. Although Penn began operating as an academy or secondary school in 1751 and obtained its collegiate charter in 1755, it initially designated 1750 as its founding date; this is the year that appears on the first iteration of the university seal. Sometime later in its early history, Penn began to consider 1749 as its founding date and this year was referenced for over a century, including at the centennial celebration in 1849. In 1899, the board of trustees voted to adjust the founding date earlier again, this time to 1740, the date of “the creation of the earliest of the many educational trusts the University has taken upon itself”. The board of trustees voted in response to a three-year campaign by Penn’s General Alumni Society to retroactively revise the university’s founding date to appear older than Princeton University, which had been chartered in 1746.

Research, innovations and discoveries

Penn is classified as an “R1” doctoral university: “Highest research activity.” Its economic impact on the Commonwealth of Pennsylvania for 2015 amounted to $14.3 billion. Penn’s research expenditures in the 2018 fiscal year were $1.442 billion, the fourth largest in the U.S. In fiscal year 2019 Penn received $582.3 million in funding from the National Institutes of Health.

In line with its well-known interdisciplinary tradition, Penn’s research centers often span two or more disciplines. In the 2010–2011 academic year alone, five interdisciplinary research centers were created or substantially expanded; these include the Center for Health-care Financing; the Center for Global Women’s Health at the Nursing School; the $13 million Morris Arboretum’s Horticulture Center; the $15 million Jay H. Baker Retailing Center at Wharton; and the $13 million Translational Research Center at Penn Medicine. With these additions, Penn now counts 165 research centers hosting a research community of over 4,300 faculty and over 1,100 postdoctoral fellows, 5,500 academic support staff and graduate student trainees. To further assist the advancement of interdisciplinary research President Amy Gutmann established the “Penn Integrates Knowledge” title awarded to selected Penn professors “whose research and teaching exemplify the integration of knowledge”. These professors hold endowed professorships and joint appointments between Penn’s schools.

Penn is also among the most prolific producers of doctoral students. With 487 PhDs awarded in 2009, Penn ranks third in the Ivy League, only behind Columbia University and Cornell University (Harvard University did not report data). It also has one of the highest numbers of post-doctoral appointees (933 in number for 2004–2007), ranking third in the Ivy League (behind Harvard and Yale University) and tenth nationally.

In most disciplines Penn professors’ productivity is among the highest in the nation and first in the fields of epidemiology, business, communication studies, comparative literature, languages, information science, criminal justice and criminology, social sciences and sociology. According to the National Research Council nearly three-quarters of Penn’s 41 assessed programs were placed in ranges including the top 10 rankings in their fields, with more than half of these in ranges including the top five rankings in these fields.

Penn’s research tradition has historically been complemented by innovations that shaped higher education. In addition to establishing the first medical school; the first university teaching hospital; the first business school; and the first student union Penn was also the cradle of other significant developments. In 1852, Penn Law was the first law school in the nation to publish a law journal still in existence (then called The American Law Register, now the Penn Law Review, one of the most cited law journals in the world). Under the deanship of William Draper Lewis, the law school was also one of the first schools to emphasize legal teaching by full-time professors instead of practitioners, a system that is still followed today. The Wharton School was home to several pioneering developments in business education. It established the first research center in a business school in 1921 and the first center for entrepreneurship center in 1973 and it regularly introduced novel curricula for which BusinessWeek wrote, “Wharton is on the crest of a wave of reinvention and change in management education”.

Several major scientific discoveries have also taken place at Penn. The university is probably best known as the place where the first general-purpose electronic computer (ENIAC) was born in 1946 at the Moore School of Electrical Engineering.

ENIAC UPenn

It was here also where the world’s first spelling and grammar checkers were created, as well as the popular COBOL programming language. Penn can also boast some of the most important discoveries in the field of medicine. The dialysis machine used as an artificial replacement for lost kidney function was conceived and devised out of a pressure cooker by William Inouye while he was still a student at Penn Med; the Rubella and Hepatitis B vaccines were developed at Penn; the discovery of cancer’s link with genes; cognitive therapy; Retin-A (the cream used to treat acne), Resistin; the Philadelphia gene (linked to chronic myelogenous leukemia) and the technology behind PET Scans were all discovered by Penn Med researchers. More recent gene research has led to the discovery of the genes for fragile X syndrome, the most common form of inherited mental retardation; spinal and bulbar muscular atrophy, a disorder marked by progressive muscle wasting; and Charcot–Marie–Tooth disease, a progressive neurodegenerative disease that affects the hands, feet and limbs.

Conductive polymer was also developed at Penn by Alan J. Heeger, Alan MacDiarmid and Hideki Shirakawa, an invention that earned them the Nobel Prize in Chemistry. On faculty since 1965, Ralph L. Brinster developed the scientific basis for in vitro fertilization and the transgenic mouse at Penn and was awarded the National Medal of Science in 2010. The theory of superconductivity was also partly developed at Penn, by then-faculty member John Robert Schrieffer (along with John Bardeen and Leon Cooper). The university has also contributed major advancements in the fields of economics and management. Among the many discoveries are conjoint analysis, widely used as a predictive tool especially in market research; Simon Kuznets’s method of measuring Gross National Product; the Penn effect (the observation that consumer price levels in richer countries are systematically higher than in poorer ones) and the “Wharton Model” developed by Nobel-laureate Lawrence Klein to measure and forecast economic activity. The idea behind Health Maintenance Organizations also belonged to Penn professor Robert Eilers, who put it into practice during then-President Nixon’s health reform in the 1970s.

International partnerships

Students can study abroad for a semester or a year at partner institutions such as the London School of Economics(UK), University of Barcelona [Universitat de Barcelona](ES), Paris Institute of Political Studies [Institut d’études politiques de Paris](FR), University of Queensland(AU), University College London(UK), King’s College London(UK), Hebrew University of Jerusalem(IL) and University of Warwick(UK).

From The DOE’s Sandia National Laboratories: “Burping bacteria – Identifying Arctic microbes that produce greenhouse gases”

From The DOE’s Sandia National Laboratories

10.17.22
Mollie Rappe
mrappe@sandia.gov
505-228-6123

Sandia scientists study soil and gas samples to improve climate models.

As greenhouse gases bubble up across the rapidly thawing Arctic, Sandia National Laboratories researchers are trying to identify other trace gases from soil microbes that could shed some light on what is occurring biologically in melting permafrost in the Arctic.

Sandia bioengineer Chuck Smallwood and his team recently spent five days collecting lakebed soil and gas samples. They were joined by international collaborators led by professor Katey Walter Anthony from the University of Alaska, Fairbanks, including researchers from the University of Colorado Boulder, University of Quebec in Rimouski and Ben-Gurion University of the Negev in Israel.

Sandia National Laboratories technologist Jenna Schambach working with a sample of Alaska lakebed soil. By studying the microbes in the soil, and the gases they emit, Schambach and project lead Chuck Smallwood hope to improve our understanding of the rapidly melting Arctic permafrost and improve computer models of climate change. (Photo by Craig Fritz)

“The Arctic is rapidly changing, releasing large amounts of greenhouse gases; we just don’t know how much greenhouse gases are released every year,” Smallwood said. “Our work at Sandia seeks to improve our understanding of how much greenhouse gases soil microbes are producing, without going out and destructively sampling permafrost soils. The goal is to use sensitive gas detection devices to sample microbial volatile compounds coming out with the methane and CO2 gases instead.”

Both methane and CO2 are greenhouse gases, and methane actually traps more heat in the atmosphere than the commonly discussed CO2. In fact, it is 30 times more potent than CO2, Smallwood said.

Collecting samples of soil and microbes

To measure rates of microbial activity in permafrost soil systems, Smallwood’s team partnered with the University of Alaska, Fairbanks team to collect their first permafrost samples in late March at two frozen lakes formed from thawing permafrost about 20 minutes north of Fairbanks, Alaska. They also collected samples this September. Next year, they plan to collect samples from thawing coastal marshlands near Oliktok Point on the North Slope of Alaska.

To collect a soil sample from a lakebed, first a member of the University of Alaska, Fairbanks team would put on a harness connected to a rope and walk out onto the frozen lake to clear snow from the frozen lake surface and check for signs of thin ice, Smallwood said. Then the researchers prepared the site by using a chainsaw to cut down through three- or four-foot-thick ice to remove huge ice cubes.

The team then positioned one of two coring apparatuses over and around the hole in the ice, Smallwood said. One apparatus provided by University of Alaska, Fairbanks scientist Chris Maio, called a hammer corer, collects 3-foot-long samples while another, called a Vibracore sampler, collects deeper samples, up to 13 feet.

The Vibracore drilling apparatus contains a long 3-inch diameter tube that would rapidly vibrate through the lake, down into the lakebed. Using suction — similar to a child playing around with a straw and their finger to suck up soda — the researchers removed 3- to 10-foot-long cylindrical “cores” of lakebed soil containing microbes that have lived there for hundreds to thousands of years.

These core samples were frozen and shipped to New Mexico for Sandia technologists Jenna Schambach and Bryce Ricken to extract microbes, including bacteria and archaea. Archaea are single-celled organisms similar to bacteria, but they have many biological similarities to the nuclei-possessing eukaryotes that comprise multicellular organisms like humans and trees. Many archaea can thrive in extreme environments such as geysers, very salty lakes and sulfureous deep sea vents. Archaea are of particular interest to Smallwood and his team because evidence suggests they are the primary methane producers.

During their March field expedition, the research team also measured greenhouse gas emissions from their various field sites. With most of the lake frozen, they didn’t expect to measure much methane release. However, at a bore hole site located at the lake rim, they measured methane concentrations of 500-800 parts per million, which is roughly 400 times the normal atmospheric level of methane.

Using Sandia equipment, the team collected gas from this methane “chimney” and is working with scientists at the University of Colorado-Boulder to determine how old and how deep the carbon being converted into methane by microbes is, Smallwood said.

The Sandia team is currently conducting laboratory experiments to study microbial populations found in the methane chimney to look for other gases indicative of microbial methane metabolism, Schambach said.

“We believe that we have underestimated the amount of methane release during winter and early spring and that there are likely many more methane chimneys than anyone has considered,” Smallwood said. “It’s a scary thought, imagining hundreds of chimneys pumping out methane at remote Alaska sites. We don’t know how much is really occurring, and that contributes to the uncertainty in our climate models.

Growing Arctic microbes

Schambach and Ricken are processing lakebed soil samples and dividing them into temperature- and moisture-controlled bioreactors. These containers can simulate what is happening in the thawing-permafrost lake system in the lab, Smallwood said.

Jenna Schambach, Sandia National Laboratories technologist, preparing a sampling core on an Arctic microbe sampling trip in Alaska. “One of the worries we had going in was it being really, really cold,” Schambach said. “Thankfully it wasn’t; we weren’t cold the whole trip. It was sad too because March in Alaska should be near zero degrees Fahrenheit and it was 35 degrees.”

The researchers will sequence DNA from the samples to identify the types of microorganisms present in different layers of the lakebed before being grown in the bioreactors. They will also use similar sequencing approaches to track how microbe populations change over time during temperature and nutrient changes. The goal of these experiments is to connect microbes to the release of methane and other volatile gases.

“As we do these evolutions in controlled bioreactors, we will be sampling every so often to characterize how the microbe populations change over time,” Schambach said. “The questions we’re trying to answer: Who is in these incubations and when are they becoming prevalent in the community? We’ll also be doing microbiology experiments to isolate strains of these very unusual organisms of interest.”

The team will also be measuring what particular microbes are doing in the community by examining the RNA present. This will connect each microbe with an activity and perhaps even suggest which microbes are chiefly responsible for producing methane and their allies, the microbes that provide vitamins or other indirect assistance to the methane producers, Smallwood said.

Detecting digestion gases

From the bouquet of a fine wine to the musk of aging compost, the activities of single-celled organisms produce distinct scents caused by a complex mix of gases. Philip Miller, a Sandia biological engineer, is spearheading the analysis of the gas samples collected on the trip to try to tease apart specific gases tied to specific biological activities in thawing permafrost.

During the trip, Smallwood’s team collected gas samples in small adsorption tubes. Miller compared these tubes to chemical sponges, able to “suck up” a lot of interesting gases without taking up a lot of space. Like the lakebed samples, these tubes were also frozen and shipped from Alaska to New Mexico. Now, Miller is beginning to see what kinds of gases they collected using an advanced piece of equipment called a comprehensive two-dimensional gas chromatograph with mass spectrometry.

“The name of the game for biomarker hunting of volatile compounds is separation,” Miller said. “The second gas chromatography column allows for better separation of gases that have similar chemical backgrounds. We’re able to see more, and it becomes easier to identify gases of interest. It’s a starting point on understanding if we can use a similar tool to monitor a fragile ecosystem over a long period of time.”

Miller will use the same advanced system to analyze the gases produced in real-time from the microbes grown in the bioreactors.

The goal for the team is to identify gases that are markers for important biological activity or the presence of important microbes. By the end of the three-year project, they hope to have the information needed to design a portable detector that looks for those specific gases in the thawing Arctic, improving scientists’ ability to monitor the rapidly changing environment, Smallwood said.

“I feel like this type of research to define how living organisms and climate impact each other is really taking off,” Smallwood said. “People are finally paying attention not just to what is happening above ground but how things are changing underneath our feet. For a long time, scientists only viewed soils as a source of carbon, but now we’ve realized that soils can produce or remove greenhouse gases. We are working with computational modelers such as Umakant Mishra at Sandia to ultimately model how soil microbes are contributing to greenhouse gas emissions to reduce the uncertainties in our climate change predictions.”

See the full article here .

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Please help promote STEM in your local schools.

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Sandia Campus.

Sandia National Laboratories managed and operated by the National Technology and Engineering Solutions of Sandia (a wholly owned subsidiary of Honeywell International), is one of three National Nuclear Security Administration research and development laboratories in the United States. Their primary mission is to develop, engineer, and test the non-nuclear components of nuclear weapons and high technology. Headquartered in Central New Mexico near the Sandia Mountains, on Kirtland Air Force Base in Albuquerque, Sandia also has a campus in Livermore, California, next to DOE’s Lawrence Livermore National Laboratory, and a test facility in Waimea, Kauai, Hawaii.

It is Sandia’s mission to maintain the reliability and surety of nuclear weapon systems, conduct research and development in arms control and nonproliferation technologies, and investigate methods for the disposal of the United States’ nuclear weapons program’s hazardous waste.

Other missions include research and development in energy and environmental programs, as well as the surety of critical national infrastructures. In addition, Sandia is home to a wide variety of research including computational biology; mathematics (through its Computer Science Research Institute); materials science; alternative energy; psychology; MEMS; and cognitive science initiatives.

Sandia formerly hosted ASCI Red, one of the world’s fastest supercomputers until its recent decommission, and now hosts ASCI Red Storm supercomputer, originally known as Thor’s Hammer.

ASCI Red Storm Cray superrcomputer at DOE’s Sandia National Laboratory.

Sandia is also home to the Z Machine.

Sandia Z machine

The Z Machine is the largest X-ray generator in the world and is designed to test materials in conditions of extreme temperature and pressure. It is operated by Sandia National Laboratories to gather data to aid in computer modeling of nuclear guns. In December 2016, it was announced that National Technology and Engineering Solutions of Sandia, under the direction of Honeywell International, would take over the management of Sandia National Laboratories starting on May 1, 2017.

From Michigan State University: “Michigan State University researchers help reveal a ‘blueprint’ for photosynthesis”

From Michigan State University

8.31.22
Matt Davenport

MSU researchers helped reveal, with nearly atomic precision, the biological structure of an “antenna” used by cyanobacteria for photosynthesis. Knowing the position of different proteins and pigments (shown in different colors) helps researchers better understand this natural process and can inspire future applications in areas such as renewable energy. Credit: Domínguez-Martín et al., Nature (2022)

New findings in microbes called cyanobacteria present new opportunities for plant science, bioengineering and environmental protection.

Michigan State University researchers and colleagues at the University of California-Berkeley, the University of South Bohemia and The DOE’s Lawrence Berkeley National Laboratory have helped reveal the most detailed picture to date of important biological “antennae.”

Nature has evolved these structures to harness the sun’s energy through photosynthesis, but these sunlight receivers don’t belong to plants. They’re found in microbes known as cyanobacteria, the evolutionary descendants of the first organisms on Earth capable of taking sunlight, water and carbon dioxide and turning them into sugars and oxygen.

Published Aug. 31 in the journal Nature [below], the findings immediately shed new light on microbial photosynthesis — specifically, how light energy is captured and sent to where it’s needed to power the conversion of carbon dioxide into sugars. Going forward, the insights could also help researchers remediate harmful bacteria in the environment, develop artificial photosynthetic systems for renewable energy and enlist microbes in sustainable manufacturing that starts with the raw materials of carbon dioxide and sunlight.

“There’s a lot of interest in using cyanobacteria as solar-powered factories that capture sunlight and convert it into a kind of energy that can be used to make important products,” said Cheryl Kerfeld, Hannah Distinguished Professor of structural bioengineering in the College of Natural Science. “With a blueprint like the one we’ve provided in this study, you can start thinking about tuning and optimizing the light-harvesting component of photosynthesis.”

“Once you see how something works, you have a better idea of how you can modify it and manipulate it. That’s a big advantage,” said Markus Sutter, a senior research associate in the Kerfeld Lab, which operates at MSU and Berkeley Lab in California.

For decades, researchers have been working to visualize the different building blocks of phycobilisomes to try to understand how they’re put together. Phycobilisomes are fragile, necessitating this piecemeal approach. Historically, researchers have been unable to get the high-resolution images of intact antennae needed to understand how they capture and conduct light energy.

Now, thanks to an international team of experts and advances in a technique known as cryo-electron microscopy, the structure of a cyanobacterial light harvesting antenna is available with nearly atomic resolution. The team included researchers from Michigan State University, Berkeley Lab, the University of California, Berkeley and the University of South Bohemia in the Czech Republic.

“We were fortunate to be a team made up of people with complementary expertise, people who worked well together,” said Kerfeld, who is also a member of the MSU-DOE Plant Research Laboratory, which is supported by the U.S. Department of Energy. “The group had the right chemistry.”

‘A long journey full of nice surprises’

“This work is a breakthrough in the field of photosynthesis,” said Paul Sauer, a postdoctoral researcher in Professor Eva Nogales’ cryogenic electron microscopy lab at The DOE’s Lawrence Berkeley National Laboratory and The University of California-Berkeley.

“The complete light-harvesting structure of a cyanobacteria’s antenna has been missing until now,” Sauer said. “Our discovery helps us understand how evolution came up with ways to turn carbon dioxide and light into oxygen and sugar in bacteria, long before any plants existed on our planet.”

Along with Kerfeld, Sauer is a corresponding author of the new article. The team documented several notable results, including finding a new phycobilisome protein and observing two new ways that the phycobilisome orients its light-capturing rods that hadn’t been resolved before.

“It is 12 pages of discoveries,” said María Agustina Domínguez-Martín of the Nature report. As a postdoctoral researcher in the Kerfeld Lab, Domínguez-Martín initiated the study at Michigan State University and brought it to completion at the Berkeley Lab. She is currently at the University of Cordoba in Spain as part of the Marie Skłowdoska-Curie Postdoctoral Fellowship. “It’s been a long journey full of nice surprises.”

One surprise, for example, came in how a relatively small protein can act as a surge protector for the massive antenna. Before this work, researchers knew the phycobilisome could corral molecules called orange carotenoid proteins, or OCPs, when the phycobilisome had absorbed too much sunlight. The OCPs release the excess energy as heat, protecting a cyanobacterium’s photosynthetic system from burning up.

Until now, there’s been debate about how many OCPs the phycobilisome could bind and where those binding sites were. The new research answers these fundamental questions and offers potentially practical insights.

This kind of surge-protecting system — which is called photoprotection and has analogs in the plant world — naturally tends to be wasteful. Cyanobacteria are slow to turn their photoprotection off after it has done its job. Now, with the complete picture of how the surge protector works, researchers can design ways to engineer “smart,” less wasteful photoprotection, Kerfeld said.

MSU researchers helped uncover an unparalleled level of detail in phycobilisomes, the green and blue assemblies in this illustration. These structures work as antennae that cyanobacteria use in photosynthesis. The blue and green colors represent different proteins and pigments in the phycobilisome. OCPs, the occasional orange hangers-on, help dissipate excess captured energy as heat. Credit: Janet Iwasa/University of Utah.

And, despite helping make the planet habitable for humans and countless other organisms that need oxygen to survive, cyanobacteria have a dark side. Cyanobacteria blooms in lakes, ponds and reservoirs can produce toxins that are deadly to native ecosystems as well as humans and their pets. Having a blueprint of how the bacteria not only collect the sun’s energy, but also protect themselves from too much of it could inspire new ideas to attack harmful blooms.

Beyond the new answers and potential applications this work offers, the researchers are also excited about the new questions it raises and the research it could inspire.

“If you think of this like Legos, you can keep building up, right? The proteins and pigments are like blocks making the phycobilisome, but then that’s part of the photosystem, which is in the cell membrane, which is part of the entire cell,” Sutter said. “We’re climbing up the ladder of scale in a way. We’ve found something new on our rung, but we can’t say we’ve got the system settled.”

“We’ve answered some questions, but we’ve opened the doors on others and, to me, that’s what makes it a breakthrough,” Domínguez-Martín said. “I’m excited to see how the field develops from here.”

This work was supported by the U.S. Department of Energy Office of Science, the National Institutes of Health, the Czech Science Foundation and the European Union’s Horizon 2020 research and innovation program.

Science paper:
Nature

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Michigan State University is a public research university located in East Lansing, Michigan, United States. Michigan State University was founded in 1855 and became the nation’s first land-grant institution under the Morrill Act of 1862, serving as a model for future land-grant universities.

The university was founded as the Agricultural College of the State of Michigan, one of the country’s first institutions of higher education to teach scientific agriculture. After the introduction of the Morrill Act, the college became coeducational and expanded its curriculum beyond agriculture. Today, Michigan State University is one of the largest universities in the United States (in terms of enrollment) and has approximately 634,300 living alumni worldwide.

U.S. News & World Report ranks its graduate programs the best in the U.S. in elementary teacher’s education, secondary teacher’s education, industrial and organizational psychology, rehabilitation counseling, African history (tied), supply chain logistics and nuclear physics in 2019. Michigan State University pioneered the studies of packaging, hospitality business, supply chain management, and communication sciences. Michigan State University is a member of the Association of American Universities and is classified among “R1: Doctoral Universities – Very high research activity”. The university’s campus houses the National Superconducting Cyclotron Laboratory, the W. J. Beal Botanical Garden, the Abrams Planetarium, the Wharton Center for Performing Arts, the Eli and Edythe Broad Art Museum, the Facility for Rare Isotope Beams, and the country’s largest residence hall system.

Research

The university has a long history of academic research and innovation. In 1877, botany professor William J. Beal performed the first documented genetic crosses to produce hybrid corn, which led to increased yields. Michigan State University dairy professor G. Malcolm Trout improved the process for the homogenization of milk in the 1930s, making it more commercially viable. In the 1960s, Michigan State University scientists developed cisplatin, a leading cancer fighting drug, and followed that work with the derivative, carboplatin. Albert Fert, an Adjunct professor at Michigan State University, was awarded the 2007 Nobel Prize in Physics together with Peter Grünberg.

Today Michigan State University continues its research with facilities such as the Department of Energy -sponsored Plant Research Laboratory and a particle accelerator called the National Superconducting Cyclotron Laboratory [below]. The Department of Energy Office of Science named Michigan State University as the site for the Facility for Rare Isotope Beams (FRIB). The $730 million facility will attract top researchers from around the world to conduct experiments in basic nuclear science, astrophysics, and applications of isotopes to other fields.

Michigan State University FRIB [Facility for Rare Isotope Beams] .

In 2004, scientists at the Cyclotron produced and observed a new isotope of the element germanium, called Ge-60 In that same year, Michigan State University, in consortium with the University of North Carolina at Chapel Hill and the government of Brazil, broke ground on the 4.1-meter Southern Astrophysical Research Telescope (SOAR) in the Andes Mountains of Chile.

NSF NOIRLab NOAO Southern Astrophysical Research [SOAR] telescope, operated by a consortium including the countries of Brazil and Chile, Michigan State University, the Cerro Tololo Inter-American Observatory (CTIO) (part of the National Optical Astronomy Observatory, NOAO), and the University of North Carolina at Chapel Hill situated on Cerro Pachón, just to the southeast of Cerro Tololo, on the NOIRLab NOAO AURA site at an altitude of 2,700 meters (8,775 feet) above sea level.

The consortium telescope will allow the Physics & Astronomy department to study galaxy formation and origins. Since 1999, Michigan State University has been part of a consortium called the Michigan Life Sciences Corridor, which aims to develop biotechnology research in the State of Michigan. Finally, the College of Communication Arts and Sciences’ Quello Center researches issues of information and communication management.

NSCL Nuclear research at Michigan State University National Superconducting Cyclotron Laboratory S800 Spectrograph schematic.

The Michigan State University Spartans compete in the NCAA Division I Big Ten Conference. Michigan State Spartans football won the Rose Bowl Game in 1954, 1956, 1988 and 2014, and the university claims a total of six national football championships. Spartans men’s basketball won the NCAA National Championship in 1979 and 2000 and has attained the Final Four eight times since the 1998–1999 season. Spartans ice hockey won NCAA national titles in 1966, 1986 and 2007. The women’s cross country team was named Big Ten champions in 2019. In the fall of 2019, MSU student-athletes posted all-time highs for graduation success rates and federal graduation rates, according to NCAA statistics.

From Stanford University: “Stanford Hopkins Marine Station’s new biodiversity mission”

From Stanford University

August 15, 2022
Tara Roberts

Improved facilities and equipment at the Monterey Bay station will open the door for researchers to study more of the Pacific’s diverse species, gain a deeper understanding of fundamental biology, and develop new biotechnologies.

Nabor Vázquez Martínez had never been tidepooling until he spent a month at the Stanford Hopkins Marine Station in Monterey Bay this summer. On the beach near the station, he climbed across slippery rocks and beds of mussels, touched starfish, observed sea urchins, and searched for sea worms. But just as exciting was going back to the lab to study the specimens he gathered.

“I got to be submerged in the ocean for a couple hours, then took samples back to the laboratory to explore under a microscope,” he said. “It was amazing seeing life happen before my own eyes.”

Vázquez Martínez, who is working toward his PhD in biology, was a student in Developmental Biology in the Ocean: Comparative Embryology and Larval Development, which brings graduate students and faculty in biology, developmental biology, and bioengineering to Hopkins. The students spent the month of June exploring the incredible biodiversity in the nearby beaches and waters, then applying the station’s advanced tools to explore questions related to invertebrate embryology.

The class, which Hopkins has offered since 2015, is indicative of the station’s future. With funding from the School of Humanities and Sciences dean’s office and the Chan Zuckerberg Biohub, Hopkins is adding a research and teaching mission focused on mining biodiversity – delving into the genomes and molecular characteristics of the multitudes of species that live along the Pacific Coast to search for answers to important biological questions.

Christopher Lowe, an associate professor of biology at Hopkins who co-teaches the class, is leading the effort to form a center of cell and molecular biodiversity in service of this new mission. The dean’s office funding will help create a functional genomics center and a biological imaging center, while CZ Biohub is providing financial and scientific support for the mission of the center.

“If you want to understand any kind of animal diversity in any meaningful way, every animal phylum – and in fact any phylum, whether it’s plant, algae, fungi, whatever – started out their evolutionary journey in the ocean,” Lowe said. “So the ocean really is the crucible of creation.”

The people to apply biodiversity

In the past five to 10 years, improved tools have dramatically reduced the cost and increased the effectiveness of genomic and genetic research. Applying these technologies to diverse species will lead to new discoveries, Lowe said. And, in turn, asking new questions about marine life can lead to novel technologies and techniques.

David Booth, an assistant professor of biochemistry and biophysics from The University of California-San Francisco, shows students in Developmental Biology in the Ocean: Comparative Embryology and Larval Development how to collect Choanoflagellates, an important unicellular group for exploring the origins of multicellularity. (Image credit: Christopher Lowe)

“The opportunities are out there, and all it requires is a bold and industrious postdoc or graduate student to come up with a really interesting biological question, and then look for the right animal that matches that question,” Lowe said.

For example, Lowe’s colleague, Stanford bioengineer Manu Prakash, developed a new microscope that allows for high-resolution, real-time imaging of larvae swimming and behavior, thanks to his time at Hopkins. Before, the only way to study how the larvae of common intertidal animals like starfish or sea anemones behave in the ocean was to squish them on a microscope slide. Such research is important, said Lowe, because “marine plankton play incredibly important roles in marine ecosystems, but because of their tiny size, our understanding of their biology is rudimentary.”

The summer course students also learned how working in marine biodiversity can enrich many areas of research.

With his mind opened to other species, Vázquez Martínez – who usually studies a common model organism, the roundworm C. elegans – achieved a scientific first.

“No one has ever done an in situ hybridization chain reaction to visualize the nuclei and muscle on a juvenile mud worm – and then actually getting to do it for the first time and image our worms with colleagues in this class was an unbelievable experience,” he said.

Azalia Martínez Jaimes, a PhD student in developmental biology, studied stem cell transplantation among colonies of Botryllus schlosseri, or star tunicates, during the course. The experience will come in handy when she returns to her stem cell-focused lab on the main campus, but it also had a more profound effect – clarifying a biological truth she knew before, but never really understood until witnessing the biodiversity at Hopkins.

“One of the biggest things I learned, that continues to blow my mind, is when you’re comparing species, you’re looking back in time,” she said.

Nelson Hall, a PhD student in bioengineering, used his month at Hopkins to practice microinjection protocols – injections involving tiny needles, which Hall performed on eggs from a variety of organisms. This technique is the first step to gene editing with tools like CRISPR. Like his classmates, Hall was in awe of the number of organisms he could find and study. He urged other researchers to consider spending time at Hopkins.

“The biodiversity of the area is just through the roof,” he said. “If you’re interested in genetic engineering across a broad spectrum, you want to be able to sample a wide array of animals. If your environment happens to provide that to you on a silver platter, all the better.”

The tools to mine biodiversity

Fundamental biological challenges span every species: How do we fight off disease? How do we communicate? How do we adapt to new environments?

As Lowe and other scientists like to say, evolution has already done those experiments for us.

In the early 20th century, for example, researchers gained basic understandings of neurobiology by studying the enormous axons found in squid. As a current example, investigations of immune response beyond what’s seen in vertebrates could reveal previously undiscovered methods of protection from pathogens, explained Lowe. By exploring those differences, biologists could gain a deeper understanding of immunity in general, and apply it to other questions.

With the added benefit of more advanced equipment and application of novel genomic technologies, Lowe sees the future work at Hopkins as continuing this long tradition in biodiversity science of embracing the unknown and pursuing big questions.

“Curiosity-driven basic research can provide some incredibly valuable insights into major biological questions,” Lowe said. “A center for cellular and molecular biodiversity at Hopkins provides a portal to the incredible range of biodiversity and the opportunity to experimentally investigate the solutions to biological challenges that have evolved independently in organisms separated by hundreds of millions of years.”

Alongside offering more opportunities for the graduate students who visit each summer, the new updates at Hopkins aim to draw more researchers and students from the main campus. Lowe expects the renovations will be ready for researchers by summer 2023.

“My mission,” said Lowe, “is to persuade people at Stanford who work on these really cool technologies that have been developed – that are strongly focused on either stem cells or on mammalian development – to think about how we can apply these new tools to address really basic biological questions by diving into the diversity in the marine realm.”

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Stanford University campus

Leland and Jane Stanford founded Stanford University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members.

Stanford University, officially Leland Stanford Junior University, is a private research university located in Stanford, California. Stanford was founded in 1885 by Leland and Jane Stanford in memory of their only child, Leland Stanford Jr., who had died of typhoid fever at age 15 the previous year. Stanford is consistently ranked as among the most prestigious and top universities in the world by major education publications. It is also one of the top fundraising institutions in the country, becoming the first school to raise more than a billion dollars in a year.

Leland Stanford was a U.S. senator and former governor of California who made his fortune as a railroad tycoon. The school admitted its first students on October 1, 1891, as a coeducational and non-denominational institution. Stanford University struggled financially after the death of Leland Stanford in 1893 and again after much of the campus was damaged by the 1906 San Francisco earthquake. Following World War II, provost Frederick Terman supported faculty and graduates’ entrepreneurialism to build self-sufficient local industry in what would later be known as Silicon Valley.

The university is organized around seven schools: three schools consisting of 40 academic departments at the undergraduate level as well as four professional schools that focus on graduate programs in law, medicine, education, and business. All schools are on the same campus. Students compete in 36 varsity sports, and the university is one of two private institutions in the Division I FBS Pac-12 Conference. It has gained 126 NCAA team championships, and Stanford has won the NACDA Directors’ Cup for 24 consecutive years, beginning in 1994–1995. In addition, Stanford students and alumni have won 270 Olympic medals including 139 gold medals.

As of October 2020, 84 Nobel laureates, 28 Turing Award laureates, and eight Fields Medalists have been affiliated with Stanford as students, alumni, faculty, or staff. In addition, Stanford is particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups. Stanford alumni have founded numerous companies, which combined produce more than $2.7 trillion in annual revenue, roughly equivalent to the 7th largest economy in the world (as of 2020). Stanford is the alma mater of one president of the United States (Herbert Hoover), 74 living billionaires, and 17 astronauts. It is also one of the leading producers of Fulbright Scholars, Marshall Scholars, Rhodes Scholars, and members of the United States Congress.

Stanford University was founded in 1885 by Leland and Jane Stanford, dedicated to Leland Stanford Jr, their only child. The institution opened in 1891 on Stanford’s previous Palo Alto farm.

Jane and Leland Stanford modeled their university after the great eastern universities, most specifically Cornell University. Stanford opened being called the “Cornell of the West” in 1891 due to faculty being former Cornell affiliates (either professors, alumni, or both) including its first president, David Starr Jordan, and second president, John Casper Branner. Both Cornell and Stanford were among the first to have higher education be accessible, nonsectarian, and open to women as well as to men. Cornell is credited as one of the first American universities to adopt this radical departure from traditional education, and Stanford became an early adopter as well.

Despite being impacted by earthquakes in both 1906 and 1989, the campus was rebuilt each time. In 1919, The Hoover Institution on War, Revolution and Peace was started by Herbert Hoover to preserve artifacts related to World War I. The Stanford Medical Center, completed in 1959, is a teaching hospital with over 800 beds. The DOE’s SLAC National Accelerator Laboratory (originally named the Stanford Linear Accelerator Center), established in 1962, performs research in particle physics.

DOE’s SLAC National Accelerator Laboratory campus with world’s first x-ray laser- the Linac Coherent Light Source (LCLS) unveiled in 2009.

Land

Most of Stanford is on an 8,180-acre (12.8 sq mi; 33.1 km^2) campus, one of the largest in the United States. It is located on the San Francisco Peninsula, in the northwest part of the Santa Clara Valley (Silicon Valley) approximately 37 miles (60 km) southeast of San Francisco and approximately 20 miles (30 km) northwest of San Jose. In 2008, 60% of this land remained undeveloped.

Stanford’s main campus includes a census-designated place within unincorporated Santa Clara County, although some of the university land (such as the Stanford Shopping Center and the Stanford Research Park) is within the city limits of Palo Alto. The campus also includes much land in unincorporated San Mateo County (including the SLAC National Accelerator Laboratory and the Jasper Ridge Biological Preserve), as well as in the city limits of Menlo Park (Stanford Hills neighborhood), Woodside, and Portola Valley.

Non-central campus

Stanford currently operates in various locations outside of its central campus.

On the founding grant:

Jasper Ridge Biological Preserve is a 1,200-acre (490 ha) natural reserve south of the central campus owned by the university and used by wildlife biologists for research.

SLAC National Accelerator Laboratory is a facility west of the central campus operated by the university for the Department of Energy. It contains the longest linear particle accelerator in the world, 2 miles (3.2 km) on 426 acres (172 ha) of land.

Golf course and a seasonal lake: The university also has its own golf course and a seasonal lake (Lake Lagunita, actually an irrigation reservoir), both home to the vulnerable California tiger salamander. As of 2012 Lake Lagunita was often dry and the university had no plans to artificially fill it.

Off the founding grant:

Hopkins Marine Station, in Pacific Grove, California, is a marine biology research center owned by the university since 1892.

Study abroad locations: unlike typical study abroad programs, Stanford itself operates in several locations around the world; thus, each location has Stanford faculty-in-residence and staff in addition to students, creating a “mini-Stanford”.

Redwood City campus for many of the university’s administrative offices located in Redwood City, California, a few miles north of the main campus. In 2005, the university purchased a small, 35-acre (14 ha) campus in Midpoint Technology Park intended for staff offices; development was delayed by The Great Recession. In 2015 the university announced a development plan and the Redwood City campus opened in March 2019.

The Bass Center in Washington, DC provides a base, including housing, for the Stanford in Washington program for undergraduates. It includes a small art gallery open to the public.

China: Stanford Center at Peking University, housed in the Lee Jung Sen Building, is a small center for researchers and students in collaboration with Beijing University [北京大学](CN) (Kavli Institute for Astronomy and Astrophysics at Peking University(CN) (KIAA-PKU).

Administration and organization

Stanford is a private, non-profit university that is administered as a corporate trust governed by a privately appointed board of trustees with a maximum membership of 38. Trustees serve five-year terms (not more than two consecutive terms) and meet five times annually.[83] A new trustee is chosen by the current trustees by ballot. The Stanford trustees also oversee the Stanford Research Park, the Stanford Shopping Center, the Cantor Center for Visual Arts, Stanford University Medical Center, and many associated medical facilities (including the Lucile Packard Children’s Hospital).

The board appoints a president to serve as the chief executive officer of the university, to prescribe the duties of professors and course of study, to manage financial and business affairs, and to appoint nine vice presidents. The provost is the chief academic and budget officer, to whom the deans of each of the seven schools report. Persis Drell became the 13th provost in February 2017.

As of 2018, the university was organized into seven academic schools. The schools of Humanities and Sciences (27 departments), Engineering (nine departments), and Earth, Energy & Environmental Sciences (four departments) have both graduate and undergraduate programs while the Schools of Law, Medicine, Education and Business have graduate programs only. The powers and authority of the faculty are vested in the Academic Council, which is made up of tenure and non-tenure line faculty, research faculty, senior fellows in some policy centers and institutes, the president of the university, and some other academic administrators, but most matters are handled by the Faculty Senate, made up of 55 elected representatives of the faculty.

The Associated Students of Stanford University (ASSU) is the student government for Stanford and all registered students are members. Its elected leadership consists of the Undergraduate Senate elected by the undergraduate students, the Graduate Student Council elected by the graduate students, and the President and Vice President elected as a ticket by the entire student body.

Stanford is the beneficiary of a special clause in the California Constitution, which explicitly exempts Stanford property from taxation so long as the property is used for educational purposes.

Endowment and donations

The university’s endowment, managed by the Stanford Management Company, was valued at $27.7 billion as of August 31, 2019. Payouts from the Stanford endowment covered approximately 21.8% of university expenses in the 2019 fiscal year. In the 2018 NACUBO-TIAA survey of colleges and universities in the United States and Canada, only Harvard University, the University of Texas System, and Yale University had larger endowments than Stanford.

In 2006, President John L. Hennessy launched a five-year campaign called the Stanford Challenge, which reached its $4.3 billion fundraising goal in 2009, two years ahead of time, but continued fundraising for the duration of the campaign. It concluded on December 31, 2011, having raised a total of $6.23 billion and breaking the previous campaign fundraising record of $3.88 billion held by Yale. Specifically, the campaign raised $253.7 million for undergraduate financial aid, as well as $2.33 billion for its initiative in “Seeking Solutions” to global problems, $1.61 billion for “Educating Leaders” by improving K-12 education, and $2.11 billion for “Foundation of Excellence” aimed at providing academic support for Stanford students and faculty. Funds supported 366 new fellowships for graduate students, 139 new endowed chairs for faculty, and 38 new or renovated buildings. The new funding also enabled the construction of a facility for stem cell research; a new campus for the business school; an expansion of the law school; a new Engineering Quad; a new art and art history building; an on-campus concert hall; a new art museum; and a planned expansion of the medical school, among other things. In 2012, the university raised $1.035 billion, becoming the first school to raise more than a billion dollars in a year.

Research centers and institutes

DOE’s SLAC National Accelerator Laboratory
Stanford Research Institute, a center of innovation to support economic development in the region.

Hoover Institution, a conservative American public policy institution and research institution that promotes personal and economic liberty, free enterprise, and limited government.

Hasso Plattner Institute of Design, a multidisciplinary design school in cooperation with the Hasso Plattner Institute of University of Potsdam [Universität Potsdam](DE) that integrates product design, engineering, and business management education).
Martin Luther King Jr. Research and Education Institute, which grew out of and still contains the Martin Luther King Jr.

Papers Project.

John S. Knight Fellowship for Professional Journalists

Center for Ocean Solutions

Together with University of California-Berkeley and UC San Francisco, Stanford is part of the Biohub, a new medical science research center founded in 2016 by a $600 million commitment from Facebook CEO and founder Mark Zuckerberg and pediatrician Priscilla Chan.

Discoveries and innovation

Natural sciences

Biological synthesis of deoxyribonucleic acid (DNA) – Arthur Kornberg synthesized DNA material and won the Nobel Prize in Physiology or Medicine 1959 for his work at Stanford.
First Transgenic organism – Stanley Cohen and Herbert Boyer were the first scientists to transplant genes from one living organism to another, a fundamental discovery for genetic engineering. Thousands of products have been developed on the basis of their work, including human growth hormone and hepatitis B vaccine.
Laser – Arthur Leonard Schawlow shared the 1981 Nobel Prize in Physics with Nicolaas Bloembergen and Kai Siegbahn for his work on lasers.
Nuclear magnetic resonance – Felix Bloch developed new methods for nuclear magnetic precision measurements, which are the underlying principles of the MRI.

Computer and applied sciences

ARPANET – Stanford Research Institute, formerly part of Stanford but on a separate campus, was the site of one of the four original ARPANET nodes.

Internet—Stanford was the site where the original design of the Internet was undertaken. Vint Cerf led a research group to elaborate the design of the Transmission Control Protocol (TCP/IP) that he originally co-created with Robert E. Kahn (Bob Kahn) in 1973 and which formed the basis for the architecture of the Internet.

Frequency modulation synthesis – John Chowning of the Music department invented the FM music synthesis algorithm in 1967, and Stanford later licensed it to Yamaha Corporation.

Google – Google began in January 1996 as a research project by Larry Page and Sergey Brin when they were both PhD students at Stanford. They were working on the Stanford Digital Library Project (SDLP). The SDLP’s goal was “to develop the enabling technologies for a single, integrated and universal digital library” and it was funded through the National Science Foundation, among other federal agencies.

Klystron tube – invented by the brothers Russell and Sigurd Varian at Stanford. Their prototype was completed and demonstrated successfully on August 30, 1937. Upon publication in 1939, news of the klystron immediately influenced the work of U.S. and UK researchers working on radar equipment.

RISC – ARPA funded VLSI project of microprocessor design. Stanford and The University of California-Berkeley are most associated with the popularization of this concept. The Stanford MIPS would go on to be commercialized as the successful MIPS architecture, while Berkeley RISC gave its name to the entire concept, commercialized as the SPARC. Another success from this era were IBM’s efforts that eventually led to the IBM POWER instruction set architecture, PowerPC, and Power ISA. As these projects matured, a wide variety of similar designs flourished in the late 1980s and especially the early 1990s, representing a major force in the Unix workstation market as well as embedded processors in laser printers, routers and similar products.
SUN workstation – Andy Bechtolsheim designed the SUN workstation for the Stanford University Network communications project as a personal CAD workstation, which led to Sun Microsystems.

Businesses and entrepreneurship

Stanford is one of the most successful universities in creating companies and licensing its inventions to existing companies; it is often held up as a model for technology transfer. Stanford’s Office of Technology Licensing is responsible for commercializing university research, intellectual property, and university-developed projects.

The university is described as having a strong venture culture in which students are encouraged, and often funded, to launch their own companies.

Companies founded by Stanford alumni generate more than $2.7 trillion in annual revenue, equivalent to the 10th-largest economy in the world.

Some companies closely associated with Stanford and their connections include:

Hewlett-Packard, 1939, co-founders William R. Hewlett (B.S, PhD) and David Packard (M.S).
Silicon Graphics, 1981, co-founders James H. Clark (Associate Professor) and several of his grad students.
Sun Microsystems, 1982, co-founders Vinod Khosla (M.B.A), Andy Bechtolsheim (PhD) and Scott McNealy (M.B.A).
Cisco, 1984, founders Leonard Bosack (M.S) and Sandy Lerner (M.S) who were in charge of Stanford Computer Science and Graduate School of Business computer operations groups respectively when the hardware was developed.[163]
Yahoo!, 1994, co-founders Jerry Yang (B.S, M.S) and David Filo (M.S).
Google, 1998, co-founders Larry Page (M.S) and Sergey Brin (M.S).
LinkedIn, 2002, co-founders Reid Hoffman (B.S), Konstantin Guericke (B.S, M.S), Eric Lee (B.S), and Alan Liu (B.S).
Instagram, 2010, co-founders Kevin Systrom (B.S) and Mike Krieger (B.S).
Snapchat, 2011, co-founders Evan Spiegel and Bobby Murphy (B.S).
Coursera, 2012, co-founders Andrew Ng (Associate Professor) and Daphne Koller (Professor, PhD).

Student body

Stanford enrolled 6,996 undergraduate and 10,253 graduate students as of the 2019–2020 school year. Women comprised 50.4% of undergraduates and 41.5% of graduate students. In the same academic year, the freshman retention rate was 99%.

Stanford awarded 1,819 undergraduate degrees, 2,393 master’s degrees, 770 doctoral degrees, and 3270 professional degrees in the 2018–2019 school year. The four-year graduation rate for the class of 2017 cohort was 72.9%, and the six-year rate was 94.4%. The relatively low four-year graduation rate is a function of the university’s coterminal degree (or “coterm”) program, which allows students to earn a master’s degree as a 1-to-2-year extension of their undergraduate program.

As of 2010, fifteen percent of undergraduates were first-generation students.

Athletics

As of 2016 Stanford had 16 male varsity sports and 20 female varsity sports, 19 club sports and about 27 intramural sports. In 1930, following a unanimous vote by the Executive Committee for the Associated Students, the athletic department adopted the mascot “Indian.” The Indian symbol and name were dropped by President Richard Lyman in 1972, after objections from Native American students and a vote by the student senate. The sports teams are now officially referred to as the “Stanford Cardinal,” referring to the deep red color, not the cardinal bird. Stanford is a member of the Pac-12 Conference in most sports, the Mountain Pacific Sports Federation in several other sports, and the America East Conference in field hockey with the participation in the inter-collegiate NCAA’s Division I FBS.

Its traditional sports rival is the University of California, Berkeley, the neighbor to the north in the East Bay. The winner of the annual “Big Game” between the Cal and Cardinal football teams gains custody of the Stanford Axe.

Stanford has had at least one NCAA team champion every year since the 1976–77 school year and has earned 126 NCAA national team titles since its establishment, the most among universities, and Stanford has won 522 individual national championships, the most by any university. Stanford has won the award for the top-ranked Division 1 athletic program—the NACDA Directors’ Cup, formerly known as the Sears Cup—annually for the past twenty-four straight years. Stanford athletes have won medals in every Olympic Games since 1912, winning 270 Olympic medals total, 139 of them gold. In the 2008 Summer Olympics, and 2016 Summer Olympics, Stanford won more Olympic medals than any other university in the United States. Stanford athletes won 16 medals at the 2012 Summer Olympics (12 gold, two silver and two bronze), and 27 medals at the 2016 Summer Olympics.

Traditions

The unofficial motto of Stanford, selected by President Jordan, is Die Luft der Freiheit weht. Translated from the German language, this quotation from Ulrich von Hutten means, “The wind of freedom blows.” The motto was controversial during World War I, when anything in German was suspect; at that time the university disavowed that this motto was official.
Hail, Stanford, Hail! is the Stanford Hymn sometimes sung at ceremonies or adapted by the various University singing groups. It was written in 1892 by mechanical engineering professor Albert W. Smith and his wife, Mary Roberts Smith (in 1896 she earned the first Stanford doctorate in Economics and later became associate professor of Sociology), but was not officially adopted until after a performance on campus in March 1902 by the Mormon Tabernacle Choir.
“Uncommon Man/Uncommon Woman”: Stanford does not award honorary degrees, but in 1953 the degree of “Uncommon Man/Uncommon Woman” was created to recognize individuals who give rare and extraordinary service to the University. Technically, this degree is awarded by the Stanford Associates, a voluntary group that is part of the university’s alumni association. As Stanford’s highest honor, it is not conferred at prescribed intervals, but only when appropriate to recognize extraordinary service. Recipients include Herbert Hoover, Bill Hewlett, Dave Packard, Lucile Packard, and John Gardner.
Big Game events: The events in the week leading up to the Big Game vs. UC Berkeley, including Gaieties (a musical written, composed, produced, and performed by the students of Ram’s Head Theatrical Society).
“Viennese Ball”: a formal ball with waltzes that was initially started in the 1970s by students returning from the now-closed Stanford in Vienna overseas program. It is now open to all students.
“Full Moon on the Quad”: An annual event at Main Quad, where students gather to kiss one another starting at midnight. Typically organized by the Junior class cabinet, the festivities include live entertainment, such as music and dance performances.
“Band Run”: An annual festivity at the beginning of the school year, where the band picks up freshmen from dorms across campus while stopping to perform at each location, culminating in a finale performance at Main Quad.
“Mausoleum Party”: An annual Halloween Party at the Stanford Mausoleum, the final resting place of Leland Stanford Jr. and his parents. A 20-year tradition, the “Mausoleum Party” was on hiatus from 2002 to 2005 due to a lack of funding, but was revived in 2006. In 2008, it was hosted in Old Union rather than at the actual Mausoleum, because rain prohibited generators from being rented. In 2009, after fundraising efforts by the Junior Class Presidents and the ASSU Executive, the event was able to return to the Mausoleum despite facing budget cuts earlier in the year.
Former campus traditions include the “Big Game bonfire” on Lake Lagunita (a seasonal lake usually dry in the fall), which was formally ended in 1997 because of the presence of endangered salamanders in the lake bed.

Award laureates and scholars

Stanford’s current community of scholars includes:

19 Nobel Prize laureates (as of October 2020, 85 affiliates in total)
171 members of the National Academy of Sciences
109 members of National Academy of Engineering
76 members of National Academy of Medicine
288 members of the American Academy of Arts and Sciences
19 recipients of the National Medal of Science
1 recipient of the National Medal of Technology
4 recipients of the National Humanities Medal
49 members of American Philosophical Society
56 fellows of the American Physics Society (since 1995)
4 Pulitzer Prize winners
31 MacArthur Fellows
4 Wolf Foundation Prize winners
2 ACL Lifetime Achievement Award winners
14 AAAI fellows
2 Presidential Medal of Freedom winners