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  • richardmitnick 12:34 pm on November 7, 2017 Permalink | Reply
    Tags: , , Discovering detrimental leaks by developing “smart” paper that can sense the presence of water, , , Smart paper, U Washington   

    From University of Washington: “‘Smart’ paper can conduct electricity, detect water” 

    U Washington

    University of Washington

    November 6, 2017
    Michelle Ma

    1
    Anthony Dichiara, a University of Washington professor in the School of Environmental and Forest Sciences, holds a piece of “smart” paper created in his lab. Mark Stone/University of Washington

    In cities and large-scale manufacturing plants, a water leak in a complicated network of pipes can take tremendous time and effort to detect, as technicians must disassemble many pieces to locate the problem. The American Water Works Association indicates that nearly a quarter-million water line breaks occur each year in the U.S., costing public water utilities about $2.8 billion annually.

    A University of Washington team wants to simplify the process for discovering detrimental leaks by developing “smart” paper that can sense the presence of water. The paper, laced with conductive nanomaterials, can be employed as a switch, turning on or off an LED light or an alarm system indicating the absence or presence of water.

    The researchers described their discovery in a paper appearing in the November issue of the Journal of Materials Chemistry A.

    “Water sensing is very challenging to do due to the polar nature of water, and what is used now is very expensive and not practical to implement,” said lead author Anthony Dichiara, a UW assistant professor of bioresource science and engineering in the School of Environment and Forest Sciences. “That led to the reason to pursue this work.”

    See slide show of images at the full article.

    Along with Dichiara, a team of UW undergraduate students in the Bioresource Science and Engineering program successfully embedded nanomaterials in paper that can conduct electricity and sense the presence of water. Starting with pulp, they manipulated the wood fibers and carefully mixed in nanomaterials using a standard process for papermaking, but never before used to make sensing papers.

    Discovering that the paper could detect the presence of water came by way of a fortuitous accident. Water droplets fell onto the conductive paper the team had created, causing the LED light indicating conductivity to turn off. Though at first they thought they had ruined the paper, the researchers realized they had instead created a paper that was sensitive to water.

    When water hits the paper, its fibrous cells swell to up to three times their original size. That expansion displaces conductive nanomaterials inside the paper, which in turn disrupts the electrical connections and causes the LED indicator light to turn off.

    This process is fully reversible, and as the paper dries, the conductive network re-forms so the paper can be used multiple times.

    The researchers envision an application in which a sheet of conductive paper with a battery could be placed around a pipe or under a complex network of intersecting pipes in a manufacturing plant. If a pipe leaks, the paper would sense the presence of water, then send an electrical signal wirelessly to a central control center so a technician could quickly locate and repair the leak.
    example use around a pipe

    The paper could be wrapped around a pipe, as shown in this example, to detect leaks.Mark Stone/University of Washington

    In addition, the paper is so sensitive that it can also detect trace amounts of water in mixtures of various liquids. This ability to distinguish water from other molecules is particularly valuable for the petroleum and biofuel industries, where water is regarded as an impurity.

    “I believe that for large-scale applications, this is definitely doable,” Dichiara said. “The price for nanomaterials is going to drop, and we’re already using an established papermaking process. You just add what we developed in the right place and time in the process.”

    The nanomaterials added to the paper were engineered in such a way that they can be incorporated during conventional papermaking without having to modify the process. These materials are made of extremely conductive carbon. Because carbon is found in all living things, nearly any natural material can be burned to make charcoal, and then carbon atoms can be extracted to synthesize the materials. The team has experimented with making nanomaterials from banana peels, tree bark and even animal feces.

    They also tried making nanomaterials from wood scraps to show that the entire papermaking process can be completed with cheap, natural materials.

    “Now we have a sustainable process where everything is from pulp and paper, and we can make conductive materials from them,” Dichiara said.

    The paper, stiff and smooth in texture, is a rich black color because of the nanomaterials (carbon from charcoal). The 8-inch disks made in the lab are prototypes; the team hopes to test the process on an industrial-sized papermaking machine next, which will require more nanomaterials and paper pulp.

    Other co-authors are Sheila Goodman, a UW graduate student, and Delong He and Jinbo Bai of Universite Paris-Saclay in France. UW undergraduate students Jimeng Cui, Riley Fitzpatrick, Sydney Fry, Demi Lidorikiotis, Anna Song and Zoie Tisler completed additional lab work.

    Funding for this research came from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, McIntire Stennis project, and from the UW School of Environmental and Forest Sciences.

    ###

    For more information, contact Dichiara at abdichia@uw.edu or 206-543-1581.

    Along with Dichiara, a team of UW undergraduate students in the Bioresource Science and Engineering program successfully embedded nanomaterials in paper that can conduct electricity and sense the presence of water. Starting with pulp, they manipulated the wood fibers and carefully mixed in nanomaterials using a standard process for papermaking, but never before used to make sensing papers.

    Discovering that the paper could detect the presence of water came by way of a fortuitous accident. Water droplets fell onto the conductive paper the team had created, causing the LED light indicating conductivity to turn off. Though at first they thought they had ruined the paper, the researchers realized they had instead created a paper that was sensitive to water.

    When water hits the paper, its fibrous cells swell to up to three times their original size. That expansion displaces conductive nanomaterials inside the paper, which in turn disrupts the electrical connections and causes the LED indicator light to turn off.

    This process is fully reversible, and as the paper dries, the conductive network re-forms so the paper can be used multiple times.

    The researchers envision an application in which a sheet of conductive paper with a battery could be placed around a pipe or under a complex network of intersecting pipes in a manufacturing plant. If a pipe leaks, the paper would sense the presence of water, then send an electrical signal wirelessly to a central control center so a technician could quickly locate and repair the leak.

    3
    The paper could be wrapped around a pipe, as shown in this example, to detect leaks.Mark Stone/University of Washington

    They also tried making nanomaterials from wood scraps to show that the entire papermaking process can be completed with cheap, natural materials.

    “Now we have a sustainable process where everything is from pulp and paper, and we can make conductive materials from them,” Dichiara said.

    The paper, stiff and smooth in texture, is a rich black color because of the nanomaterials (carbon from charcoal). The 8-inch disks made in the lab are prototypes; the team hopes to test the process on an industrial-sized papermaking machine next, which will require more nanomaterials and paper pulp.

    Other co-authors are Sheila Goodman, a UW graduate student, and Delong He and Jinbo Bai of Universite Paris-Saclay in France. UW undergraduate students Jimeng Cui, Riley Fitzpatrick, Sydney Fry, Demi Lidorikiotis, Anna Song and Zoie Tisler completed additional lab work.

    Funding for this research came from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, McIntire Stennis project, and from the UW School of Environmental and Forest Sciences.

    See the full article here .

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    u-washington-campus
    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.

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  • richardmitnick 9:07 am on October 24, 2017 Permalink | Reply
    Tags: 1700 just over 300 years ago, , , , , Great Subduction Zone earthquakes are the largest earthquakes in the world, Off the Oregon and Washington coast the Juan de Fuca oceanic plate is slowly moving under the North American plate, One of the worst nightmares for many Pacific Northwest residents is a huge earthquake along the offshore which would unleash damaging and likely deadly shaking in coastal Washington Oregon British Col, The CSZ has produced magnitude 9.0 or greater earthquakes in the past and undoubtedly will in the future, The last known megathrust earthquake in the northwest was in January, U Washington   

    From University of Washington: “50 simulations of the ‘Really Big One’ show how a 9.0 Cascadia earthquake could play out” 

    U Washington

    University of Washington

    October 23, 2017
    Hannah Hickey

    One of the worst nightmares for many Pacific Northwest residents is a huge earthquake along the offshore Cascadia Subduction Zone, which would unleash damaging and likely deadly shaking in coastal Washington, Oregon, British Columbia and northern California.

    1

    2
    PacNW_Earthquake2

    At depths shallower than 30 km or so, the CSZ is locked by friction while strain slowly builds up as the subduction forces act, until the fault’s frictional strength is exceeded and the rocks slip past each other along the fault in a “megathrust” earthquake. The fault’s frictional properties change with depth, such that immediately below the locked part is a strip (the “Transition Zone”) that slides in “slow slip events” that slip a few cm every dozen months or so. This relieves the plate boundary stresses there, but adds to the stress on the locked part of the fault. Below the transition zone geodetic evidence suggests that the fault slides continuously and silently at long term plate slip rate. From it’s surface trace offshore to a depth of possibly 5 km, all remote from land, observations are few and it remains unknown whether the fault is stuck or slipping silently.

    Great Subduction Zone earthquakes are the largest earthquakes in the world, and are the only source zones that can produce earthquakes greater than M8.5. The CSZ has produced magnitude 9.0 or greater earthquakes in the past, and undoubtedly will in the future.

    Seismologist Kim Olsen of San Diego State University produced this simulation of what slip in a M9 CSZ earthquake might look like.

    The last known megathrust earthquake in the northwest was in January, 1700, just over 300 years ago. Geological evidence indicates that such great earthquakes have occurred at least seven times in the last 3,500 years, a return interval of 400 to 600 years. To learn more about the history of the Cascadia Subduction Zone and the science that led to the discovery of it, delve into land level changes and turbidites created by the CSZ earthquakes. For more about the Cascadia Subduction Zone, visit the USGS webpage discussing this topic.

    The CSZ may be unique among the worlds subduction zones in that it produces very few (if any) earthquakes unambiguously on the plate interface. Coupled with evident occurrence of great megathrust earthquakes, the CSZ must be much more strongly locked than other subduction faults. The geological evidence has led to different interpretrations, moreover, about whether the entire CSZ always ruptures in great M9 earthquakes, or whether smaller M8 or M8.5-sized events also can break parts of the zone in between the full rupture events.

    The last time this happened was in 1700, before seismic instruments were around to record the event. So what will happen when it ruptures next is largely unknown.

    A University of Washington research project, to be presented Oct. 24 at the Geological Society of America’s annual meeting in Seattle, simulates 50 different ways that a magnitude-9.0 earthquake on the Cascadia subduction zone could unfold.

    “There had been just a handful of detailed simulations of a magnitude-9 Cascadia earthquake, and it was hard to know if they were showing the full range,” said Erin Wirth, who led the project as a UW postdoctoral researcher in Earth and space sciences. “With just a few simulations you didn’t know if you were seeing a best-case, a worst-case or an average scenario. This project has really allowed us to be more confident in saying that we’re seeing the full range of possibilities.”

    Off the Oregon and Washington coast, the Juan de Fuca oceanic plate is slowly moving under the North American plate. Geological clues show that it last jolted and unleashed a major earthquake in 1700, and that it does so roughly once every 500 years. It could happen any day.

    Wirth’s project ran simulations using different combinations for three key factors: the epicenter of the earthquake; how far inland the earthquake will rupture; and which sections of the fault will generate the strongest shaking.

    Results show that the intensity of shaking can be less for Seattle if the epicenter is fairly close to beneath the city. From that starting point, seismic waves will radiate away from Seattle, sending the biggest shakes in the direction of travel of the rupture.

    “Surprisingly, Seattle experiences less severe shaking if the epicenter is located just beneath the tip of northwest Washington,” Wirth said. “The reason is because the rupture is propagating away from Seattle, so it’s most affecting sites offshore. But when the epicenter is located pretty far offshore, the rupture travels inland and all of that strong ground shaking piles up on its way to Seattle, to make the shaking in Seattle much stronger.”

    The research effort began by establishing which factors most influence the pattern of ground shaking during a Cascadia earthquake. One, of course, is the epicenter, or more specifically the “hypocenter,” which locates the earthquake’s starting point in three-dimensional space.

    Another factor they found to be important is how far inland the fault slips. A magnitude-9.0 earthquake would likely give way along the whole north-south extent of the subduction zone, but it’s not well known how far east the shake-producing area would extend, approaching the area beneath major cities such as Seattle and Portland.

    The third factor is a new idea relating to a subduction zone’s stickiness. Earthquake researchers have become aware of the importance of “sticky points,” or areas between the plates that can catch and generate more shaking. This is still an area of current research, but comparisons of different seismic stations during the 2010 Chile earthquake and the 2011 Tohoku earthquake show that some parts of the fault released more strong shaking than others.

    Wirth simulated a magnitude-9.0 earthquake, about the middle of the range of estimates for the magnitude of the 1700 earthquake. Her 50 simulations used variables spanning realistic values for the depth of the slip, and had randomly placed hypocenters and sticky points. The high-resolution simulations were run on supercomputers at the Pacific Northwest National Laboratory and the University of Texas, Austin.

    Overall, the results confirm that coastal areas would be hardest hit, and locations in sediment-filled basins like downtown Seattle would shake more than hard, rocky mountaintops. But within that general framework, the picture can vary a lot; depending on the scenario, the intensity of shaking can vary by a factor of 10. But none of the pictures is rosy.

    “We are finding large amplification of ground shaking by the Seattle basin,” said collaborator Art Frankel, a U.S. Geological Survey seismologist and affiliate faculty member at the UW. “The average duration of strong shaking in Seattle is about 100 seconds, about four times as long as from the 2001 Nisqually earthquake.”

    The research was done as part of the M9 Project, a National Science Foundation-funded effort to figure out what a magnitude-9 earthquake might look like in the Pacific Northwest and how people can prepare. Two publications are being reviewed by the USGS, and engineers are already using the simulation results to assess how tall buildings in Seattle might respond to the predicted pattern of shaking.

    As a new employee of the USGS, Wirth will now use geological clues to narrow down the possible earthquake scenarios.

    “We’ve identified what parameters we think are important,” Wirth said. “I think there’s a future in using geologic evidence to constrain these parameters, and maybe improve our estimate of seismic hazard in the Pacific Northwest.”

    Other co-authors are Nasser Marafi, a UW doctoral student in civil and environmental engineering; John Vidale, a former UW professor now at the University of Southern California; and Bill Stephenson with the USGS.

    For more information, contact Wirth at ewirth@uw.edu.

    Videos and images for two of the simulations are available here.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    u-washington-campus
    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.

     
  • richardmitnick 8:52 am on October 19, 2017 Permalink | Reply
    Tags: , Bio-inspired robot sensor skin, Flexible ‘skin’ can help robots, , prosthetics perform everyday tasks by sensing shear force, U Washington   

    From University of Washington: “Flexible ‘skin’ can help robots, prosthetics perform everyday tasks by sensing shear force” 

    U Washington

    University of Washington

    October 17, 2017
    Jennifer Langston

    1
    The flexible sensor skin wrapped around the robot finger (orange) is the first to measure shear forces with similar sensitivity as a human hand — which is critical for successfully gripping and manipulating objects.UCLA Engineering

    If a robot is sent to disable a roadside bomb — or delicately handle an egg while cooking you an omelet — it needs to be able to sense when objects are slipping out of its grasp.

    Yet to date it’s been difficult or impossible for most robotic and prosthetic hands to accurately sense the vibrations and shear forces that occur, for example, when a finger is sliding along a tabletop or when an object begins to fall.

    Now, engineers from the University of Washington and UCLA have developed a flexible sensor “skin” that can be stretched over any part of a robot’s body or prosthetic to accurately convey information about shear forces and vibration that are critical to successfully grasping and manipulating objects.

    The bio-inspired robot sensor skin, described in a paper published in Sensors and Actuators A: Physical [ScienceDirect], mimics the way a human finger experiences tension and compression as it slides along a surface or distinguishes among different textures. It measures this tactile information with similar precision and sensitivity as human skin, and could vastly improve the ability of robots to perform everything from surgical and industrial procedures to cleaning a kitchen.

    “Robotic and prosthetic hands are really based on visual cues right now — such as, ‘Can I see my hand wrapped around this object?’ or ‘Is it touching this wire?’ But that’s obviously incomplete information,” said senior author Jonathan Posner, a UW professor of mechanical engineering and of chemical engineering.

    “If a robot is going to dismantle an improvised explosive device, it needs to know whether its hand is sliding along a wire or pulling on it. To hold on to a medical instrument, it needs to know if the object is slipping. This all requires the ability to sense shear force, which no other sensor skin has been able to do well,” Posner said.

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    The bio-inspired sensor skin developed by University of Washington and UCLA engineers can be wrapped around a finger or any other part of a robot or prosthetic device to help convey a sense of touch.UCLA Engineering

    Some robots today use fully instrumented fingers, but that sense of “touch” is limited to that appendage and you can’t change its shape or size to accommodate different tasks. The other approach is to wrap a robot appendage in a sensor skin, which provides better design flexibility. But such skins have not yet provided a full range of tactile information.

    “Traditionally, tactile sensor designs have focused on sensing individual modalities: normal forces, shear forces or vibration exclusively. However, dexterous manipulation is a dynamic process that requires a multimodal approach. The fact that our latest skin prototype incorporates all three modalities creates many new possibilities for machine learning-based approaches for advancing robot capabilities,” said co-author and robotics collaborator Veronica Santos, a UCLA associate professor of mechanical and aerospace engineering.

    The new stretchable electronic skin, which was manufactured at the UW’s Washington Nanofabrication Facility, is made from the same silicone rubber used in swimming goggles. The rubber is embedded with tiny serpentine channels — roughly half the width of a human hair — filled with electrically conductive liquid metal that won’t crack or fatigue when the skin is stretched, as solid wires would do.

    When the skin is placed around a robot finger or end effector, these microfluidic channels are strategically placed on either side of where a human fingernail would be.

    As you slide your finger across a surface, one side of your nailbed bulges out while the other side becomes taut under tension. The same thing happens with the robot or prosthetic finger — the microfluidic channels on one side of the nailbed compress while the ones on the other side stretch out.

    When the channel geometry changes, so does the amount of electricity that can flow through them. The research team can measure these differences in electrical resistance and correlate them with the shear forces and vibrations that the robot finger is experiencing.

    3
    As the robot finger slides along a surface, serpentine channels embedded in the skin and filled with electrically conductive liquid metal stretch on one side of the finger and compress on the other. This changes the amount of electricity that can flow through the channels, which can be correlated with shear force and vibration.Reprinted from Sensors and Actuators A: Physical 2017:264:289-297; Yin, J., Santos, V.J., and Posner, J.D. “Bioinspired flexible microfluidic shear force sensor skin,” with permission from Elsevier.

    “It’s really following the cues of human biology,” said lead author Jianzhu Yin, who recently received his doctorate from the UW in mechanical engineering. “Our electronic skin bulges to one side just like the human finger does and the sensors that measure the shear forces are physically located where the nailbed would be, which results in a sensor that performs with similar performance to human fingers.”

    Placing the sensors away from the part of the finger that’s most likely to make contact makes it easier to distinguish shear forces from the normal “push” forces that also occur when interacting with an object, which has been difficult to do with other sensor skin solutions.

    The research team from the UW College of Engineering and the UCLA Henry Samueli School of Engineering and Applied Science has demonstrated that the physically robust and chemically resistant sensor skin has a high level of precision and sensitivity for light touch applications — opening a door, interacting with a phone, shaking hands, picking up packages, handling objects, among others. Recent experiments have shown that the skin can detect tiny vibrations at 800 times per second, better than human fingers.

    “By mimicking human physiology in a flexible electronic skin, we have achieved a level of sensitivity and precision that’s consistent with human hands, which is an important breakthrough,” Posner said. “The sense of touch is critical for both prosthetic and robotic applications, and that’s what we’re ultimately creating.”

    The research was funded by the National Science Foundation.

    For more information, contact Posner at jposner@uw.edu.

    Grant numbers NSF: CBET – 1264046 and NSF: CBET – 1461630.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    u-washington-campus
    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.

     
    • folia przeciwsłoneczna do samochodu 6:47 pm on October 19, 2017 Permalink | Reply

      I’m a third-generation educator, and when I see a piece of teaching this good, all I can do is offer my professional kudos. I hope it’s a lesson you don’t have to re-teach.

      Like

  • richardmitnick 5:07 pm on October 6, 2017 Permalink | Reply
    Tags: A microfluidic approach for hemoglobin detection in whole blood, About one quarter of the world’s population suffers from anemia, AIP Advances, , Blood analyzer, , U Washington   

    From U Washington via AIP: “New portable blood analyzer could improve anemia detection worldwide” 

    U Washington

    University of Washington

    AIP

    October 4, 2017
    AIP News Staff
    Julia Majors
    media@aip.org
    301-209-3090
    @AIPPhysicsNews

    1
    Top: Nikita Taparia stands with a microfluidic card in her hand, next to the optical analyzer.
    Bottom: Close-up view of the optical analyzer
    CREDIT: Nikita Taparia, University of Washington

    About one quarter of the world’s population suffers from anemia, a disease caused by a concentration deficiency of hemoglobin in red blood cells. To reduce the burden of anemia, health officials need a better picture of the disease’s global impact, an understanding made viable by a portable and affordable way to analyze blood.

    Researchers at the University of Washington developed a device smaller than a toaster that can detect the level of hemoglobin in whole blood samples using optical absorbance. The work is published this week in AIP Advances, from AIP Publishing.

    Hemoglobin is a protein found in red blood cells that transports oxygen throughout the body. As the concentration of hemoglobin decreases, the body becomes starved of oxygen, often resulting in dizziness, fatigue, shortness of breath, and abnormal heart rate.

    Blood analyzers currently on the market measure hemoglobin by chemically rupturing the red blood cells in a sample. This technique requires hands-on expertise to prepare and run a sample, limiting the ability to monitor anemia in many parts of the world.

    “The most exciting aspect to this analyzer is that it uses whole blood and does not require the additional steps and reagents to prepare a sample,” said Nathan Sniadecki, associate professor in mechanical engineering at the University of Washington and one of the authors.

    The device only requires a few drops of blood for analysis.

    “You just run blood into the channel and that’s it,” said Nikita Taparia, a doctoral candidate in Snaidecki’s lab and another author. “It can be used anywhere.”

    The analyzer takes advantage of the optical properties of blood, such as absorption and scattering, to measure hemoglobin concentration. Anemic blood transmits more light compared to normal blood, so the severity of anemia can be measured as a ratio of transmitted to original light intensity.

    To simulate anemia, the researchers diluted blood samples with a buffer solution. The blood analyzer was effective at predicting cases of moderate to severe anemia, defined as less than 10 grams per deciliter of hemoglobin in a sample. The analyzer did not produce any false negative results.

    The optical density of samples did not increase linearly, so a higher concentration of hemoglobin defines the upper limit of detection for the device.

    The primary cause of anemia is iron deficiency, but it can co-occur with other conditions, such as malaria and genetic disorders like sickle cell. Severe anemia can lead to increased maternal and child mortality. It also impairs cognitive and physical development in children.

    “It has been really rewarding to be part of a project from start to finish that produced a device that will really help people,” Taparia said. “This analyzer is meant for people who have disease.”

    The current design is a prototype that could be integrated with other microfluidic devices to analyze whole blood samples in parallel to diagnose anemia and other underlying factors that could contribute to the disease.

    The research received support from a Department of Education GAANN Fellowship and a National Science Foundation Grant.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    u-washington-campus
    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.

     
  • richardmitnick 8:25 am on September 22, 2017 Permalink | Reply
    Tags: , , Hacking a pressure sensor to track gradual motion along marine faults, U Washington   

    From U Washington: “Hacking a pressure sensor to track gradual motion along marine faults” 

    U Washington

    University of Washington

    September 21, 2017
    Hannah Hickey

    Deep below the ocean’s surface, shielded from satellite signals, the gradual movement of the seafloor — including along faults that can unleash deadly earthquakes and tsunamis — goes largely undetected. As a result, we know distressingly little about motion along the fault that lies just off the Pacific Northwest coast.

    University of Washington oceanographers are working with a local company to develop a simple new technique that could track seafloor movement in earthquake-prone coastal areas. Researchers began testing the approach this summer in central California, and they plan to present initial results in December at the American Geophysical Union’s annual meeting in New Orleans.

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    The modified pressure sensor is now being tested at the bottom of Monterey Bay.MBARI/University of Washington

    Their approach uses existing water-pressure sensors to cheaply measure gradual swelling of the seafloor over months to years. If successful, the innovative hack could provide new insight into motion along the Cascadia Subduction Zone and similar faults off Mexico, Chile and Japan. The data could provide clues about what types of earthquakes and tsunamis each fault can generate, where and how often.

    The concept began with a workshop in 2012 that brought together Jerry Paros, the founder of Bellevue-based Paroscientific, Inc., with UW geoscientists. Paros’ company manufactures sensors used to measure pressure at the bottom of the ocean with high precision, which are used by the National Oceanographic and Atmospheric Administration for its tsunami sensors.

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    The Paroscientific sensor’s crystal inside this instrument can measure crushing pressures on the seafloor. University of Washington researchers altered the sensor to monitor seismic creep by calibrating its measurements against the pressure inside the silver titanium case.University of Washington

    But an engineering quirk prevents the sensors from measuring the gradual ground motions that build up pressure along earthquake faults. The instruments can measure seafloor pressure, or the weight of water above the sensor, to an extremely precise fraction of a millimeter. But the readings lose accuracy over time, and the error is proportional to the quantity measured. On the ocean floor, where pressures are tens to hundreds of times that on the surface, the readings can change by 10 centimeters (3 inches) per year. In between major earthquakes, this is much more than the seafloor might shift up or down due to tectonic forces.

    “If you want to measure how the seafloor is moving, you don’t want your reading to change by a larger value than the thing that you’re measuring,” said Dana Manalang, an engineer at the UW’s Applied Physics Laboratory who is working on the project.

    Paros proposed an idea that would instead calibrate the pressure sensor against the air pressure inside the metal case that houses the instrument, which is roughly one atmosphere. This would allow existing pressure sensors to autonomously track small bulges and slumps on the seafloor.

    3
    This deep-sea robot, the ROV Ventana operated by Monterey Bay Aquarium Research Institute, in June attached the instrument (lower right) to the Internet-connected observatory at the bottom of Monterey Bay.MBARI/University of Washington

    Last year engineers at the UW Applied Physics Laboratory modified an existing Paros pressure sensor. The sensitive quartz crystal that measures the seafloor pressure can now be connected to measure pressure inside its titanium instrument case, with a known pressure and another barometer to check the value. The prototype instrument was attached in mid-June to the Monterey Accelerated Research System, a cabled seafloor observatory that lets researchers communicate directly with the instrument.

    “That chunk of seafloor actually does not move much. We’re looking for a null result,” Manalang said. “If successful, the next step would be to deploy similar instruments in some more geologically active areas.”

    Those areas include the Cascadia Subduction Zone, the fault that could unleash the Really Big One at any time on the Pacific Northwest.

    4
    http://www.zerohedge.com/news/2016-05-30/fema-preparing-magnitude-90-cascadia-subduction-zone-earthquake-tsunami

    Geologists studying the small rise and fall of this section of seafloor, around 1 centimeter per year, have instead been forced to develop complicated workarounds.

    “We are trying to find a pattern of which areas are going up and which areas are going down, and how quickly, which can potentially tell us where the subduction zone fault is locked,” said William Wilcock, a UW oceanography professor who holds the Paros endowed chair. “But we can’t yet do that with a conventional pressure sensor.”

    Wilcock and seismologists at Scripps Institution of Oceanography have been monitoring seafloor movement off central Oregon, where the Cascadia Fault displays behavior that suggests it may gradually slip, releasing strain along that section of the fault. Once a year, the partners go to sea with a research ship, deep-sea robot and specialized equipment to calibrate six seafloor pressure sensors. By monitoring exactly how the seafloor has moved in this way from one summer to the next, they can compare sections of the fault and learn which zones are fully locked, building up potentially dangerous energy, and which aren’t.

    “The approach we are using appears to work, but it’s expensive, and you can’t do it very often,” Wilcock said.

    If Paros’ modified sensors can do the job, future work might place a network of them along Cascadia or other subduction zones, in which a seafloor plate plunges beneath a continental plate. Measuring motion along different parts of these faults might answer longstanding questions about how and where a fault ruptures.

    From her Seattle office, Manalang now communicates with the prototype sensor in Monterey and flips the crystal about once each weekday to recalibrate it against the instrument housing pressure. She will flip it less often as the test continues, while remotely monitoring the change in pressure readings.

    “We’re still close to the starting line on this one, and have some initial, really promising results,” Manalang said. Observations so far show that the shift in measurements is predictable, and similar at both ends of the instrument’s range. “We’re at the very beginning of what we hope is a fairly long-term test,” she said.

    If the method proves reliable, future pressure sensors could be programmed to pivot periodically on their own and gather observations over months or years. Precise long-term measurements of water pressure could not only help seismologists, but also researchers who study how sea level changes over decades.

    “If you can make very accurate observations, and routinely, it would interest both the people studying what’s happening beneath and what’s happening above,” Wilcock said. “These data would open up a whole bunch of new studies.”

    The research is funded by Jerry Paros and the University of Washington.

    See the full article here .

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    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.

     
  • richardmitnick 1:12 pm on September 8, 2017 Permalink | Reply
    Tags: Anthropocene epoch, Earth as hybrid planet, Nikolai Kardashev, Non-equilibrium thermodynamics, U Washington   

    From U Washington: “Earth as hybrid planet” 

    U Washington

    University of Washington

    New classification scheme places Anthropocene era in astrobiological context.

    September 6, 2017
    Peter Kelley

    For decades, as astronomers have imagined advanced extraterrestrial civilizations, they categorized such worlds by the amount of energy their inhabitants might conceivably be able to harness and use.

    They sorted the hypothetical worlds into three types according to a scheme named in 1964 for Soviet astronomer Nikolai Kardashev. A Type 1 civilization could manipulate all the energy resources of its home planet (a distant goal yet for Earth) and Type 2 all the energy in its star/planetary system. A super-advanced Type 3 civilization would command the energy of its whole home galaxy. The Kardashev Scale has since become a sort of gold standard for dreaming about possible civilizations beyond Earth.

    Now, a team of researchers including Marina Alberti of the University of Washington has devised a new classification scheme for the evolutionary stages of worlds based on “non-equilibrium thermodynamics” — a planet’s energy flow being out of synch, as the presence of life could cause. The categories range from imagined planets with no atmosphere whatsoever to those with an “agency-dominated biosphere” or even a “technosphere,” reflecting the achievements of a vastly advanced, “energy-intensive technological species.”

    Their paper, Earth as a Hybrid Planet: The Anthropocene in an Evolutionary Astrobiological Context, was published Sept. 6 in the journal Anthropocene. Lead author is Adam Frank, professor of physics and astronomy at the University of Rochester. Alberti is a professor of urban design and planning in the UW College of Built Environments, and director of the college’s Urban Ecology Research Lab.

    The new classification system, the researchers say, is a way of thinking about sustainability on a planetary scale in what is being recognized as the Anthropocene epoch — the geological period of humanity’s significant impact on Earth and its ecosystems. Alberti contends in her research that humans and the urban areas we create are having a strong, planetwide effect on evolution.

    “Our premise is that Earth’s entry into the Anthropocene represents what might, from an astrobiological perspective, be a predictable planetary transition,” they write. “We explore this problem from the perspective of our own solar system and exoplanet studies.

    “In our perspective, the beginning of the Anthropocene can be seen as the onset of the hybridization of the planet — a transitional stage from one class of planetary systems to another.”

    That would be, in their scheme, Earth’s possible transition from Class IV — marked by a thick biosphere and life having some effect on the planet — to the final Class V, where a planet is profoundly affected by the activity of an advanced, energy-intensive species.

    The classification scheme, the researchers write, is based on “the magnitude by which different planetary processes — abiotic, biotic and technologic — generate free energy, i.e. energy that can perform work within the system.”

    Class I represents worlds with no atmosphere at all, such as the planet Mercury and the Earth’s moon.
    Class II planets have a thin atmosphere containing greenhouse gases, but no current life, such as the current states of planets Mars and Venus.
    Class III planets have perhaps a thin biosphere and some biotic activity, but much too little to “affect planetary drivers and alter the evolutionary state of the planet as a whole.” No current examples exist in the solar system, but early Earth may have represented such a world — and possibly early Mars, if life ever flickered there in the distant past.
    Class IV planets have a thick biosphere sustained by photosynthetic activity and life has begun strongly affecting the planetary energy flow.

    Alberti said, “The discovery of seven new exoplanets orbiting the relatively close star TRAPPIST-1 forces us to rethink life on Earth. It opens the possibility to broaden our understanding of coupled system dynamics and lay the foundations to explore a path to long-term sustainability by entering into a cooperative ecological-evolutionary dynamic with the coupled planetary systems.”

    The researchers write, “Our thesis is that the development of long-term sustainable, versions of an energy-intensive civilization must be seen on a continuum of interactions between life and its host planet.”

    The classifications lay the groundwork, they say, for future research on the “co-evolution” of planets along that continuum.

    “Any world hosting a long-lived energy-intensive civilization must share at least some similarities in terms of the thermodynamic properties of the planetary system,” they write. “Understanding these properties, even in the broadest outlines, can help us understand which direction we must aim our efforts in developing a sustainable human civilization.”

    In other words, they added, “If one does not know where one is going, it’s hard to get there.”

    Co-author on the paper is Axel Kleidon of the Max Planck Institute for Biogeochemistry in Jena, Germany.

    See the full article here .

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    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.

     
  • richardmitnick 8:13 am on August 28, 2017 Permalink | Reply
    Tags: , , , Tsewone Melaku, U Washington,   

    From U Washington: Women in STEM – “Undaunted passion: Making STEM education accessible” Tsewone Melaku 

    U Washington

    University of Washington

    August 16, 2017 [U Wash took their sweet time getting this into social media.]
    Chelsea Yates

    1
    HCDE major Tsewone Melaku. Photo by Dennis Wise / University of Washington.

    Tsewone Melaku discovered engineering in high school through a UW mentorship program. Now a UW student majoring in HCDE [Human Centered Design & Engineering], she is aligning her interests in engineering with her passion to make STEM education accessible to underrepresented high school students.

    Melaku benefited from many of the same UW college access programs in which she now holds leadership roles, such as the Dream Project and the Women’s Center Making Connections program. She shares with us why it’s important to prioritize social justice issues and how she balances volunteering with her engineering studies.

    What led you to the UW?

    I attended high school here in Seattle, first at Ingraham and then at Chief Sealth. I struggled with math during my sophomore year to the point that I nearly failed. A friend was involved with Making Connections, a college readiness program offered through the UW Women’s Center. The program prepares Seattle-area high school girls from low-income communities for success in STEM fields in college. It offers everything from one-on-one tutoring and mentoring to college tours, job shadowing opportunities and college application workshops.

    I got involved with Making Connections because I needed a tutor, but it opened my eyes to so much more! I’m the first in my family to go to college; my parents are from Ethiopia, and the higher education system here was completely unfamiliar to us. After Making Connections, I sought out all the admissions support programs I could. I passed my math class and attended Young, Gifted and Black, a UW conference on social consciousness, cultural awareness and the importance of higher education for Black high school students. I signed up for the Dream Project, a program that partners UW students with first-generation and underrepresented high school students to assist in the college admissions process. I also joined UW’s Young Executives of Color program, certain that I’d major in business.

    Why did you decide to study HCDE?

    I first learned about HCDE through a Making Connections networking event, where a panel of Seattle-area women engineers talked to us about their careers. One woman — an employee at Boeing — was an HCDE alumna. I’d never heard of HCDE, but as she described it, I just kept thinking how cool it sounded. HCDE focuses on end users; it’s a field of engineering that’s all about helping people, and that really aligned with my personal interests.

    Not long after enrolling at the UW, I switched from being a pre-business major to majoring in HCDE. It’s been a great fit. I love the way it’s trained me to think creatively and solve problems.

    Tell us more about how HCDE and your academic goals overlap with your interests in creating awareness, access and exposure to opportunities for underrepresented high school students.

    I want to use my engineering background to help transform education, so I’m also minoring in the UW’s Education, Learning & Society program. My research interests involve the lack of diversity in higher education, particularly in STEM. I want to figure out ways to create better technology — and technical literacy — for underserved K-12 classrooms. There are huge gaps between technology, access and underrepresented communities. I hope to apply HCDE’s approach to user-centered problem solving and design to create technologies that meet the needs of low-income and underserved students.

    I want to put my degree to work after graduating, but I also want to go to graduate school and study human-computer interaction. My ultimate goal is a Ph.D. in engineering education.

    You continue to be involved with Making Connections and the Dream Project as an engineering student. Why?

    2
    “I love the way HCDE has trained me to think creatively and solve problems,” says Melaku. Here she constructs an affinity diagram with classmates Tsuki Kaneko-Hall and Jason Chen. Photo by Dennis Wise / University of Washington

    Making Connections is my second family, and I help anytime I can. I want kids to believe that higher education is an option, even if it seems impossible. I’ve been there; I know how tough it can be when you’re fifteen and asked to think about your college aspirations, yet the idea of going to college seems like something beyond your world. If I can share my experiences and skills in ways that help high schoolers see themselves as part of this world, then count me in. Especially for girls of color. If we want girls of color to pursue STEM, they need to see women of color being successful in STEM fields.

    I got involved with the Dream Project primarily to help transform it. I valued what the program was trying to do but from my high school experience, I saw ways it could be improved. I was invited to join the Dream Project’s leadership team and teach UW students how to be mentors in high schools after serving as a mentor myself. We’ve reshaped the course curriculum to include — and prioritize — topics like power, privilege, oppression, racism and social awareness. Many of the Dream Project’s student mentors are white or come from privileged backgrounds, and most of the high school students they’re mentoring aren’t, and we felt that it was crucial to overhaul our training practices. We’ve also updated the program’s mission statement and introduced racial equity workshops for leaders and mentors.

    You’re also involved with the UW chapter of National Society of Black Engineers (NSBE) and Women in Science & Engineering (WiSE). Tell us about your roles with these organizations.

    I started working with WiSE this summer as the program assistant for WiSE UP BRIDGE, a first-year academic program for women engineering students. Last year, I served as UW NSBE’s Pre-College Initiative (PCI) Chair and am now serving as the regional PCI Chair. In this role, I work with Black high school students who want to pursue engineering in college. This year we’ll be starting two NSBE Jr. high school chapters in Seattle! In addition to helping them and the other UW chapter leaders, I’ll also be planning the regional PCI conference for NSBE.

    3
    “I want kids to believe that higher education is an option, even if it seems impossible,” says Melaku, who mentors high school students through access programs like Making Connections at the UW Women’s Center. Photo courtesy of the UW Women’s Center.

    How do you balance your engineering studies with your commitments to UW access programs?

    I’m involved in a lot of campus activities, but they’re activities that I’m passionate about. I never feel like, “Oh great, I have to go do X.” It’s always more like, “Cool, I get to go do X.” I try to make time for the things that make me happy. I’m fortunate that engineering is one of those things. Helping people makes me happy, and through HCDE I’m learning all sorts of new ways to help.

    I wanted to be an engineer to prove that I could do it and to show other Black girls that they could, too. Being an engineering student — as well as a mentor, teacher and advocate on campus — is a lot of work, but it’s work that I care about and that I want to do. That makes a huge difference, I think.

    Learn about the UW’s commitment to diversity and access programs for engineering students.

    See the full article here .

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    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.

     
  • richardmitnick 10:47 am on August 15, 2017 Permalink | Reply
    Tags: , , , , , Tidally locked exoplanets, U Washington   

    From U Washington: “Tidally locked exoplanets may be more common than previously thought” 

    U Washington

    University of Washington

    August 14, 2017
    Peter Kelley

    1
    Tidally locked bodies such as the Earth and moon are in synchronous rotation, each taking as long to rotate around its own axis as it does to revolve around its host star or gravitational partner. New research from UW astronomer Rory Barnes indicates that many exoplanets to be found by coming high-powered telescopes also will probably be tidally locked — with one side permanently facing their host star, as one side of the moon forever faces the Earth. NASA.

    Many exoplanets to be found by coming high-powered telescopes will probably be tidally locked — with one side permanently facing their host star — according to new research by astronomer Rory Barnes of the University of Washington.

    Barnes, a UW assistant professor of astronomy and astrobiology, arrived at the finding by questioning the long-held assumption that only those stars that are much smaller and dimmer than the sun could host orbiting planets that were in synchronous orbit, or tidally locked, as the moon is with the Earth. His paper, “Tidal Locking of Habitable Exoplanets,” has been accepted for publication by the journal Celestial Mechanics and Dynamical Astronomy.

    Tidal locking results when there is no side-to-side momentum between a body in space and its gravitational partner and they become fixed in their embrace. Tidally locked bodies such as the Earth and moon are in synchronous rotation, meaning that each takes exactly as long to rotate around its own axis as it does to revolve around its host star or gravitational partner. The moon takes 27 days to rotate once on its axis, and 27 days to orbit the Earth once.

    The moon is thought to have been created by a Mars-sized celestial body slamming into the young Earth at an angle that set the world spinning initially with approximately 12-hour days.

    3
    Artist’s conception of the hypothetical impact of Theia and young Earth.
    Credit: NASA/GSFC

    “The possibility of tidal locking is an old idea, but nobody had ever gone through it systematically,” said Barnes, who is affiliated with the UW-based Virtual Planetary Laboratory.

    In the past, he said, researchers tended to use that 12-hour estimation of Earth’s rotation period to model exoplanet behavior, asking, for example, how long an Earthlike exoplanet with a similar orbital spin might take to become tidally locked.

    “What I did was say, maybe there are other possibilities — you could have slower or faster initial rotation periods,” Barnes said. “You could have planets larger than Earth, or planets with eccentric orbits — so by exploring that larger parameter space, you find that in fact the old ideas were very limited, there was just one outcome there.”

    “Planetary formation models, however, suggest the initial rotation of a planet could be much larger than several hours, perhaps even several weeks,” Barnes said. “And so when you explore that range, what you find is that there’s a possibility for a lot more exoplanets to be tidally locked. For example, if Earth formed with no moon and with an initial ‘day’ that was four days long, one model predicts Earth would be tidally locked to the sun by now.”

    Barnes writes: “These results suggest that the process of tidal locking is a major factor in the evolution of most of the potentially habitable exoplanets to be discovered in the near future.”

    Being tidally locked was once thought to lead to such extremes of climate as to eliminate any possibility of life, but astronomers have since reasoned that the presence of an atmosphere with winds blowing across a planet’s surface could mitigate these effects and allow for moderate climates and life.

    Barnes said he also considered the planets that will likely be discovered by NASA’s next planet-hunting satellite, the Transiting Exoplanet Survey Satellite or TESS, and found that every potentially habitable planet it will detect will likely be tidally locked.

    NASA/TESS

    Even if astronomers discover the long-sought Earth “twin” orbiting a virtual twin of the sun, that world may be tidally locked.

    “I think the biggest implication going forward,” Barnes said, “is that as we search for life on any exoplanets we need to know if a planet is tidally locked or not.”

    The research was funded by a NASA grant through the Virtual Planetary Laboratory.

    See the full article here .

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    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.

     
  • richardmitnick 9:07 am on August 14, 2017 Permalink | Reply
    Tags: Researchers and students on annual expedition to maintain internet-connected deep-sea observatory, U Washington   

    From U Washinton: “Researchers, students on annual expedition to maintain internet-connected deep-sea observatory” 

    U Washington

    University of Washington

    August 10, 2017
    Hannah Hickey

    University of Washington oceanography researchers, engineers, and students are working off the coast of Oregon on the yearly cruise to maintain the deep-ocean observatory, the Cabled Array, which brings power and broadband Internet to the seafloor and water above.

    1
    Deborah Kelley (left) and undergraduate students in Newport, Oregon, on Aug. 9 at the end of the first leg of the cruise. Mitch Elend/University of Washington.

    The cruise, funded by the National Science Foundation, left July 25 from Newport, Oregon, and will be back Aug. 29. The group is on the California-based research vessel Roger Revelle, since the UW’s large research vessel, the Thomas G. Thompson, is completing its major midlife overhaul.

    Deborah Kelley, UW professor of oceanography, is chief scientist on the cruise that recently began its second leg.

    While at sea a deep-sea robot will brave the crushing pressures and cold temperatures, while the team works day and night to direct the dives and prepare equipment above water. The researchers will be cleaning some instruments from marine life, and swapping out sensors that collect hot spring fluids and DNA samples over their year-long missions.

    2
    One of the shallowest pieces of the observatory lives about a tenth of a mile (200 meters) beneath the water’s surface. After a year it is coated in large anemones, small pink sea urchins, feathery brown crinoids , and small crustaceans. UW/NSF-OOI/Jason.

    The team is posting regular updates from the ship. On Aug. 1, members reported seeing pyrosomes, the bioluminescent tube-shaped tropical animals that have been seen this year off the Pacific Northwest. They are also posting highlights of the robot-captured dive videos, including one showing how marine creatures are getting cozy on the UW-built technology.

    In addition to the maintenance work, two new instruments from William Chadwick at Oregon State University will be added. The first will monitor tilting and the rise and fall of the seafloor to detect inflation and deflation at Axial Seamount, an underwater volcano that is part of the cabled observatory. A second instrument, to be placed in a nearby hydrothermal vent field, will measure the temperature and salinity of fluids that waft around the vents and in the Axial caldera. More than 120 instruments — including seismometers, high-definition video and digital still camera, and underwater chemical mass spectrometers — will be recovered and reinstalled during the cruise. Data from all instruments is accessible in real time from shore through the Ocean Observatories Initiative Data Portal.

    This year’s cruise includes 24 undergraduate and graduate students from the UW, Peninsula College in Port Angeles, Western Washington University in Bellingham and Queens College in New York. They are posting student blogs. For many undergraduates this will be their first experience at sea.

    Other cruise participants include a teacher from Kingston Middle School in Kitsap County, faculty members from Grays Harbor College in Aberdeen and UW Tacoma, and a postdoctoral researcher from the UW Applied Physics Laboratory.

    Follow along on Twitter at @VISIONSops, or tune in during one of the robot’s dives for live video from the deep sea.

    See the full article here .

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    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.

     
  • richardmitnick 11:12 am on July 17, 2017 Permalink | Reply
    Tags: , , , Synthetic DNA technology and high throughput screening permit large-scale testing of structural stability of multitudes of computationally designed proteins, U Washington   

    From U Washington: “Feedback from 1000s of designs could transform protein engineering” 

    U Washington

    University of Washington

    07.12.2017
    Leila Gray
    206.685.0381
    leilag@uw.edu

    1
    A model of a computationally designed mini-protein from a large-scale study to test structural stability. Institute for Protein Design.

    The stage is set for a new era of data-driven protein molecular engineering as advances in DNA synthesis technology merge with improvements in computational design of new proteins.

    This week’s Science reports the largest-scale testing of folding stability for computationally designed proteins, made possible by a new high-throughput approach.

    The scientists are from the UW Medicine Institute for Protein Design at the University of Washington in Seattle and the University of Toronto in Ontario.

    The lead author of the paper is Gabriel Rocklin, a postdoctoral fellow in biochemistry at the University of Washington School of Medicine. The senior authors are Cheryl Arrowsmith, of the Princess Margaret Cancer Center, the Structural Genomics Consortium and the Department of Medical Biophysics at the University of Toronto, and David Baker, UW professor of biochemistry and a Howard Hughes Medical Institute investigator.

    Proteins are biological workhorses. Researchers want to build new molecules, not found naturally, that can perform tasks in preventing or treating disease, in industrial applications, in energy production, and in environmental cleanups.

    “However, computationally designed proteins often fail to form the folded structures that they were designed to have when they are actually tested in the lab,” Rocklin said.

    In the latest study, the researchers tested more than 15,000 newly designed mini-proteins that do not exist in nature to see whether they form folded structures. Even major protein design studies in the past few years have generally examined only 50 to 100 designs.

    “We learned a huge amount at this new scale, but the taste has given us an even larger appetite,” said Rocklin. “We’re eager to test hundreds of thousands of designs in the next few years.”

    The most recent testing led to the design of 2,788 stable protein structures and could have many bioengineering and synthetic biology applications. Their small size may be advantageous for treating diseases when the drug needs to reach the inside of a cell.

    2
    Design model structures from a comprehensive mutational analysis of stability in natural and designed proteins. UW Institute for Protein Design.

    Proteins are made of amino acid chains with specific sequences, and natural protein sequences are encoded in cellular DNA. These chains fold into 3-dimensional conformations. The sequence of the amino acids in the chain guide where it will bend and twist, and how parts will interact to hold the structure together.

    For decades, researchers have studied these interactions by examining the structures of naturally occurring proteins. However, natural protein structures are typically large and complex, with thousands of interactions that collectively hold the protein in its folded shape. Measuring the contribution of each interaction becomes very difficult.

    The scientists addressed this problem by computationally designing their own, much simpler proteins. These simpler proteins made it easier to analyze the different types of interactions that hold all proteins in their folded structures.

    “Still, even simple proteins are so complicated that it was important to study thousands of them to learn why they fold,” Rocklin said. “This had been impossible until recently, due to the cost of DNA. Each designed protein requires its own customized piece of DNA so that it can be made inside a cell. This has limited previous studies to testing only tens of designs.”

    To encode their designs of short proteins in this project, the researchers used what is called DNA oligo library synthesis technology. It was originally developed for other laboratory protocols, such as large gene assembly. One of the companies that provided their DNA is CustomArray in Bothell, Wash. They also used DNA libraries made by Agilent in Santa Clara, Calif., and Twist Bioscience in San Francisco.

    By repeating the cycle of computation and experimental testing over several iterations, the researchers learned from their design failures and progressively improved their modeling. Their design success rate rose from 6 percent to 47 percent. They also produced stable proteins in shapes where all of their first designs failed.

    Their large set of stable and unstable mini-proteins enabled them to quantitatively analyze which protein features correlated with folding. They also compared the stability of their designed proteins to similarly sized, naturally occurring proteins.

    The most stable natural protein the researchers identified was a much-studied protein from the bacteria Bacillus stearothermophilus.

    3
    The researchers compared the stability of some of their designed proteins to a natural protein found in a bacteria that withstands the high temperatures of hot springs like those in Yellowstone. Alice C. Gray.

    This organism basks in high temperatures, like those in hot springs and ocean thermal vents. Most proteins lose their folded structures under such high temperature conditions. Organisms that thrive there have evolved highly stable proteins that stay folded even when hot.

    “A total of 774 designed proteins had higher stability scores than this most protease-resistant monomeric protein,” the researchers noted. Proteases are enzymes that break down proteins, and were essential tools the researchers used to measure stability for their thousands of proteins.

    The researchers predict that, as DNA synthesis technology continues to improve, high-throughput protein design will become possible for larger, more complex protein structures.

    “We are moving away from the old style of protein design, which was a mix of computer modeling, human intuition, and small bits of evidence about what worked before.” Rocklin said. “Protein designers were like master craftsmen who used their experience to hand-sculpt each piece in their workshop. Sometimes things worked, but when they failed it was hard to say why. Our new approach lets us collect an enormous amount of data on what makes proteins stable. This data can now drive the design process.”

    Their study was supported by the Howard Hughes Medical Institute and the Natural Sciences and Research Council of Canada. Rocklin is a Merck Fellow of the Life Sciences Research Foundation. Arrowsmith holds a Canadian Research Chair in Structural Genomics.

    This work was facilitated by the Hyak supercomputer at the University of Washington and by donations of computing time from Rosetta@home participants.

    Rosetta@home project, a project running on BOINC software from UC Berkeley

    Dr. David Baker, Baker Lab, U Washington

    4
    Hyak supercomputer at the University of Washington

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

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    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.

     
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