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  • richardmitnick 7:25 pm on January 31, 2013 Permalink | Reply
    Tags: , , Clean Water, ,   

    From SLAC: “Synchrotrons Explore Water’s Molecular Mysteries” 

    Glenn Roberts Jr.
    January 31, 2013

    In experiments at SLAC National Accelerator Laboratory and Lawrence Berkeley National Laboratory, scientists observed a surprisingly dense form of water that remained liquid well beyond its typical freezing point.

    droplets
    Illustration of the first layer of a thin film of water on a barium fluoride crystal surface, showing that the water sample exists in an unexpected, high-density liquid form, with chain-like molecular formations resembling low-density crystalline ice. (Credit: Nature Scientific Reports)

    Researchers applied a superthin coating of water – no deeper than a few molecules – to the surface of a barium fluoride crystal.

    This surface was expected to stimulate ice formation, but even when chilled to a temperature of about 6.5 degrees Fahrenheit – well below water’s normal freezing point – the water remained liquid.

    Further, the molecular structure of the water on the crystal surface unexpectedly transformed to a high-density form in a broad temperature range, mimicking the density water achieves when pressure is applied.

    The research, published Jan. 15 in Nature Scientific Reports, spanned more than three years and included experiments at SLAC’s Stanford Synchrotron Radiation Lightsource and Berkeley Lab’s Advanced Light Source synchrotrons, as well as computer simulations by collaborators in Sweden.

    The work represents a milestone in understanding some of the many exotic properties water exhibits under a range of conditions, said Anders Nilsson, one of the lead authors. He is deputy director of the SUNCAT Center for Interface Science and Catalysis, a Stanford/SLAC institute, and a professor of photon science at SLAC.

    Understanding the effect that certain materials have on water at the molecular scale may help scientists design materials that ‘can steer the water structure and properties,’ he said.

    ‘This can lead to the design of new membranes for water purification,’ Nilsson said. ‘Access to clean water will be the next crisis in the world after energy, and maybe even become more challenging.”

    See the full article here.

    SLAC Campus

    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
    i1


    ScienceSprings is powered by MAINGEAR computers

     
  • richardmitnick 5:17 pm on August 17, 2012 Permalink | Reply
    Tags: , , Clean Water, , Computing For Clean Water (C4CW), , ,   

    From Computing For Clean Water at WCG Status Update 

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    “The Computing for Clean Water (C4CW) project has returned over 90 million results!”

    Mission
    The mission of Computing for Clean Water is to provide deeper insight on the molecular scale into the origins of the efficient flow of water through a novel class of filter materials. This insight will in turn guide future development of low-cost and more efficient water filters.

    Significance
    Lack of access to clean water is one of the major humanitarian challenges for many regions in the developing world. It is estimated that 1.2 billion people lack access to safe drinking water, and 2.6 billion have little or no sanitation. Millions of people die annually – estimates are 3,900 children a day – from the results of diseases transmitted through unsafe water, in particular diarrhea.

    Technologies for filtering dirty water exist, but are generally quite expensive. Desalination of sea water, a potentially abundant source of drinking water, is similarly limited by filtering costs. Therefore, new approaches to efficient water filtering are a subject of intense research. Carbon nanotubes, stacked in arrays so that water must pass through the length of the tubes, represent a new approach to filtering water.

    Approach
    Normally, the extremely small pore size of nanotubes, typically only a few water molecules in diameter, would require very large pressures and hence expensive equipment in order to filter useful amounts of water. However, in 2005 experiments showed that such arrays of nanotubes allow water to flow at much higher rates than expected. This surprising result has spurred many scientists to invest considerable effort in studying the underlying processes that facilitate water flow in nanotubes.

    This project uses large-scale molecular dynamics calculations – where the motions of individual water molecules through the nanotubes are simulated – in order to get a deeper understanding of the mechanism of water flow in the nanotubes. For example, there has been speculation about whether the water molecules in direct contact with the nanotube might behave more like ice. This in turn might reduce the friction felt by the rest of the water, hence increasing the rate of flow. Realistic computer simulations are one way to test such hypotheses.

    Ultimately, the scientists hope to use the insights they glean from the simulations in order to optimize the underlying process that is enabling water to flow much more rapidly through nanotubes and other nanoporous materials. This optimization process will allow water to flow even more easily, while retaining sources of contamination. The simulations may also reveal under what conditions such filters can best assist in a desalination process.”

    C4CF had its origin in the Center for Nano and Micro Mechanics at Tsinghua University, Beijing, China

    From CNMM

    “The Computing for Clean Water (C4CW) project is a joint project between CNMM and several international research institutions [The University of Sydney, Monash University, The National Centre of Nanoscience and Technology, Chinese Academy of Sciences, Institute of High Energy Physics, The Citizen Cyberscience Centre, with the support of IBM’s World Community Grid, and thousands of volunteers.

    The team at CNMM is investigating how water flows in nanotubes, using a computer-based simulation technique known as molecular dynamics. The ultimate goal of this research is deeper insight into how nanotubes and other porous nanomaterials can be used to build a new generation of cheap water filters, to alleviate the pressing demand for clean water in large parts of China and many other parts of the developing world.

    To do these simulations with the sort of accuracy we need takes a lot of computing power, far more than is accessible to us currently. Volunteers provide this computing power by allowing some simulations to run using the idle time of the processor chips in their laptops and PCs, for example while they are writing emails or surfing the web. Indeed, when doing these common tasks, the processor is idle often more than 90% of the time, and using some of that idle time turns out to be energetically very efficient, since it only adds a few percent extra power to what the computer would otherwise consume.

    The results from each simulation, when combined together statistically for millions of runs, help us create a pool of necessary data that can be analyzed to understand why recent experiments show that water flows much more easily in nanotubes than standard hydrodynamical considerations would normally lead us to believe. Understanding this process is a first step to optimizing it for practical purposes, in particular to make cheaper filters that do not require so much pressue to filter water through them.
    This is an exciting project, but it is also complicated and will run over some time. World Community Grid enables scientists and volunteers to co-operate in a very simple and powerful way. We are grateful for the continuing support of every one of our volunteers and will post our progress here to keep you updated.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma
    sch

    GO Fight Against Malaria
    mal

    Drug Search for Leishmaniasis
    lish

    Computing for Clean Water
    c4cw

    The Clean Energy Project
    cep2

    Discovering Dengue Drugs – Together
    dengue

    Help Cure Muscular Dystrophy
    md

    Help Fight Childhood Cancer
    hccf

    Help Conquer Cancer
    hcc

    Human Proteome Folding
    hpf

    FightAIDS@Home
    faah

    Computing for Sustainable Water

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp


    ScienceSprings is powered by MAINGEAR computers

     
    • richardmitnick 12:16 pm on September 5, 2012 Permalink | Reply

      Jefferson- Thanks for the vote of confidence. WCG projects are direct ed at immediate problems for life around the globe.

      Like

  • richardmitnick 6:10 pm on August 6, 2012 Permalink | Reply
    Tags: , Clean Water,   

    From Livermore Labs: “New desalination technique uses flow-through electrodes for faster desalination and lower cost” 


    Lawrence Livermore National Laboratory

    08/03/2012
    Anne M Stark

    Lawrence Livermore National Laboratory researchers have developed a new capacitive desalination technique that could ultimately lower the cost and time of desalinating seawater.

    image
    Flow-through electrode capacitive desalination uses a new hierarchical porous carbon material to create a new device geometry in which the feed stream passes directly through the electrodes, resulting in significant improvements to salt removal and desalination rate.

    The new technique, called flow-through electrode capacitive desalination (FTE CD), uses new porous carbon materials with a hierarchical pore structure, which allows the saltwater to easily flow through the electrodes themselves.

    ‘By leveraging innovative porous carbon materials recently developed at LLNL, our new method removes the diffusion limitations afflicting traditional CD cells. The desalination process now only takes as long as it takes to charge the electrodes, on the order of minutes or less,’ said Matthew Suss, a Lawrence scholar and first author of a recent paper in Energy & Environmental Science. ‘The new method currently removes salt five to 10 times faster than previous CD systems, and can be further optimized for increased speed. It also reduces the concentration of the feed up to three times as much per charge.'”

    See the full article here.

    Operated by Lawrence Livermore National Security, LLC, for the Department of Energy’s National Nuclear Security
    Administration

    i2

     
  • richardmitnick 3:17 am on April 21, 2012 Permalink | Reply
    Tags: , , , Clean Water, Computing for Sustainable Water,   

    BOINC Announces a New Project at WCG: Computing for Sustainable Water 

    “The Computing for Sustainable Water (CFSW) project is one of three water-related projects selected to run on the IBM World Community Grid. This project evolved from the UVa Bay Game as a very detailed, simulation-only model of the Chesapeake Bay. Not a game, the CFSW model simulates over 34,000 spatial areas; 1,069 river and stream segments; and 4 million households over a 20-year period on a monthly basis. The model explores the potential outcomes of various practices (“Best Management Practices”) on the nutrient loads reaching and impacting Bay health.

    The CFSW project launched publicly on April 17, 2012 and is available for execution on the World Community Grid…

    Mission
    The mission of the Computing for Sustainable Water project is to study the effects of human activity on a large watershed and gain deeper insights into what actions can lead to restoration, health and sustainability of this important water resource. The extensive computing power of World Community Grid will be used to perform millions of computer simulations to better understand the effects that result from a variety of human activity patterns in the Chesapeake Bay area. The researchers hope to be able to apply what is learned from this project across the globe to other regions which face challenges of sustainable water.

    Significance
    Water is the most abundant resource on Earth, yet the world faces many challenging water-related problems. Among them is the management of its freshwater resources. More than 1.2 billion people lack access to clean, safe water. This problem is becoming more critical in the world as the proportion of people living in dense urban environments rises. The resulting demands for water contend with increasing human activities which degrade the quality of available water. A complex set of interrelated forces makes the problem difficult to address, much less to solve effectively via coordinated policy.

    Approach
    The University of Virginia developed a participatory simulation model of the Chesapeake Bay, the UVa Bay Game® (www.virginia.edu/baygame), incorporating natural elements and human activity using game players representing crop farmers, land developers, watermen, and assorted regulators. The UVa Bay Game has been successful in providing a learning platform for conveying the issues of complex watershed behavior and management. But to better understand the complex natural and human dynamics at work in this complex system, a much more detailed simulation model was developed to run on World Community Grid. Each of many millions of computer simulations, using unique combinations of a wide variety of assumptions about the natural and human actions at play, will calculate the resulting effects on the watershed. Exploring these many results, the researchers expect to develop insight into how these assumptions affect the overall health of the Chesapeake Bay. With these insights, the researchers will be able to better inform policy makers and suggest how prudent actions can lead to water restoration and sustainability. The ultimate goal is to eventually apply this knowledge and the techniques learned with the Computing for Sustainable Water project to other watersheds around the world.”

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

    Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

    MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

    SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

    Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

    Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”


    SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

    seti
    The famous SET@home screen saver, a beauteous thing to behold.

    einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

    MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

    Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

    World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

    Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

    GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

    These projects are just the oldest and most prominent projects. There are many others from which you can choose.

    There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

     
  • richardmitnick 8:02 am on April 14, 2012 Permalink | Reply
    Tags: , , Clean Water, , ,   

    New Project at WCG: “Computing for Sustainable Water” 

    Computing for Sustainable Water

    The Computing for Sustainable Water (CFSW) project is one of three water-related projects selected to run on the IBM World Community Grid. This project evolved from the UVa Bay Game as a very detailed, simulation-only model of the Chesapeake Bay. Not a game, the CFSW model simulates over 34,000 spatial areas; 1,069 river and stream segments; and 4 million households over a 20-year period on a monthly basis. The model explores the potential outcomes of various practices (“Best Management Practices”) on the nutrient loads reaching and impacting Bay health.

    The CFSW project will launch publicly on April 16, 2012 and will be available for execution on the World Community Grid, a network of nearly 2 million contributed computers [Currently 95,000 active users]. The model runs in the background of these volunteered computers using otherwise idle cycles and not interfering with the owner’s applications. There will be over 1.3 million experiments[work umits] distributed to computers on the World Community Grid, each requiring approximately 7 hours of computing time. If this work were done on the UVa Cross-Campus Computing Grid (XCG), it would take about 90 years to complete; with the power of the IBM World Community Grid, it will require less than one year.

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.
    CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma
    sch

    GO Fight Against Malaria
    mal

    Drug Search for Leishmaniasis
    lish

    Computing for Clean Water
    c4cw

    The Clean Energy Project
    cep2

    Discovering Dengue Drugs – Together
    dengue

    Help Cure Muscular Dystrophy
    md

    Help Fight Childhood Cancer
    hccf

    Help Conquer Cancer
    hcc

    Human Proteome Folding
    hpf

    FightAIDS@Home
    faah

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 2:49 pm on November 18, 2011 Permalink | Reply
    Tags: , , , , , , Clean Water,   

    From the WCG Clean Energy Project at Harvard 

    Take a look at the video, get excited, go to World Community Grid (WCG), sign up, download the BOINC software agent, and attach to this terrific project and any others about which you are enthusiastic. We have projects in AIDS, Cancer, Malaria(new), Leishmaniasis, Clean Water, Dengue Fever, Muscular Dystrophy.

    You can also visit BOINC, view the projects running the software that are not tied to WCG, and lend a hand.

    When you view the video, discount the business about only running when your screen saver is running. That is a long time ago. The BOINC software runs all of the time; but the project work never interferes with your normal computing activities.

    All of BOINC is pretty impressive. We are currently at 6.34 PetaFLOPS of computation. That is bigger than almost all of the supercomputers in the world today.

     
  • richardmitnick 12:33 pm on June 23, 2011 Permalink | Reply
    Tags: , , Clean Water, , ,   

    From CNN Money: “A supercomputer made of unused PCs” 

    i1

    David Goldman
    June 23, 2011

    “Buying a supercomputer costs millions of dollars, then thousands more each year to maintain it. That’s not to mention the hefty electric bill to keep the massive system running.

    So it goes without saying that average Joes can’t just get themselves a supercomputer. But many scientific researchers also don’t have access to them, even if they work at a university that owns one…But if you link millions of ordinary PCs together and split the calculations across them, you get a virtual supercomputer. That’s exactly what some people are doing…Multiplied a thousand or even million times, the combined processing power of all of those PCs is formidable.

    The concept is called volunteer grid computing, and it’s being used by projects like World Community Grid (WCG).

    SETI@home is perhaps the most well-known of the projects. It was set up by University of Berkeley researchers in 1999 with the goal of finding radio signals indicative of intelligent life outside of Earth.

    Folding@home is a Stanford project for researching protein folds, and Einstein@home is a Max Planck Institute research program to study gravitational waves. Of the university projects, Folding@home is the largest, with about 350,000 donated PCs.”

    The article does severely overstate the size of WCG. Active users are about 98,000 “crunchers”. You can visit the WCG page at BOINCStats to see the current statistics.

    Also, the article does not mention that the software on which WCG runs originated at the Space Science Labs, UC Berkeley, being birthed out of the afore mentioned seti@home project.

    Suffice it to say we are at 240 TeraFLOPS at WCG, which is pretty darn big. But, even our 98,000 “crunchers” and 195,000 machines is a drop in the bucket of over a billion computers in the world. Please visit the WCG web site and look at the projects in AIDS, Cancer, Dengue Fever, Clean Energy, Clean Water, and the Human Proteome Project. With very little effort, you could help on any or all with your unused CPU cycles.

    See the full article here.

     
  • richardmitnick 4:06 pm on April 10, 2011 Permalink | Reply
    Tags: , , , , Clean Water, , , , ,   

    WCG: An Overview 

    World Community Grid

    WCG tells us: “World Community Grid brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    “We are now partnering with People for a Smarter Planet, a collective of communities that let you make a personal difference in solving some of the world’s toughest challenges. Please show your support by clicking the Like button on their Facebook page.

    i1

    World Community Grid operates under the watchful eye and with the financial support of IBM Corporation.

    ibm

    Here is what IBM says: “Our World Community Grid initiative utilizes grid computing technology to harness the tremendous power of idle computers to perform specific computations related to critical research around complex biological, environmental and health-related issues. The current projects include Help Fight Childhood Cancer, Clean Energy, and Nutritious Rice for the World, FightAIDS@Home, Help Conquer Cancer, AfricanClimate@Home, and a genomics initiative and research on Dengue Fever.

    Lets look at some of these projects. All of the text for each project comes from the project’s page at WCG.

    Computing for Clean Water

    cw

    Mission
    The mission of Computing for Clean Water is to provide deeper insight on the molecular scale into the origins of the efficient flow of water through a novel class of filter materials. This insight will in turn guide future development of low-cost and more efficient water filters.

    Significance
    Lack of access to clean water is one of the major humanitarian challenges for many regions in the developing world. It is estimated that 1.2 billion people lack access to safe drinking water, and 2.6 billion have little or no sanitation. Millions of people die annually – estimates are 3,900 children a day – from the results of diseases transmitted through unsafe water, in particular diarrhea.

    Technologies for filtering dirty water exist, but are generally quite expensive. Desalination of sea water, a potentially abundant source of drinking water, is similarly limited by filtering costs. Therefore, new approaches to efficient water filtering are a subject of intense research. Carbon nanotubes, stacked in arrays so that water must pass through the length of the tubes, represent a new approach to filtering water.”

    This projects partners with CNMM, the Center for Nano and Micro Mechanics at Tsinghua University in Beijing, China

    cnmm

    The Clean Energy Project

    ce

    Mission
    The mission of The Clean Energy Project is to find new materials for the next generation of solar cells and later, energy storage devices. By harnessing the immense power of World Community Grid, researchers can calculate the electronic properties of hundreds of thousands of organic materials – thousands of times more than could ever be tested in a lab – and determine which candidates are most promising for developing affordable solar energy technology.

    Significance
    We are living in the Age of Energy. The fossil fuel based economy of the present must give way to the renewable energy based economy of the future, but getting there is one of the greatest challenge humanity faces. Chemistry can help meet this challenge by discovering new materials that efficiently harvest solar radiation, store energy for later use, and reconvert the stored energy when needed.

    The Clean Energy Project uses computational chemistry and the willingness of people to help look for the best molecules possible for: organic photovoltaics to provide inexpensive solar cells, polymers for the membranes used in fuel cells for electricity generation, and how best to assemble the molecules to make those devices. By helping search combinatorially among thousands of potential systems, World Community Grid volunteers are contributing to this effort.”

    Discovering Dengue Drugs – Together

    mos

    Mission
    The mission of Discovering Dengue Drugs – Together – Phase 2 is to identify promising drug candidates to combat the Dengue, Hepatitis C, West Nile, Yellow Fever, and other related viruses. The extensive computing power of World Community Grid will be used to complete the structure-based drug discovery calculations required to identify these drug candidates.

    Significance
    This project will discover promising drug candidates that stop the replication of viruses within the Flaviviridae family. Members of this family, including dengue, hepatitis C, West Nile, and yellow fever viruses, pose significant health threats throughout the developed and developing world. More than 40% of the world’s population is at risk for infection by dengue virus. Annually, ~1.5 million people are treated for dengue fever and dengue hemorrhagic fever. Hepatitis C virus has infected ~2% of the world’s population. Yellow fever and West Nile viruses also have had significant global impact. Unfortunately, there are no drugs that effectively treat these diseases. Consequently, the supportive care necessary to treat these infections and minimize mortality severely strains already burdened health facilities throughout the world. The discovery of both broad-spectrum and specific antiviral drugs is expected to significantly improve global health.”

    Help Cure Muscular Dystrophy

    md

    Mission
    The mission of Discovering Dengue Drugs – Together – Phase 2 is to identify promising drug candidates to combat the Dengue, Hepatitis C, West Nile, Yellow Fever, and other related viruses. The extensive computing power of World Community Grid will be used to complete the structure-based drug discovery calculations required to identify these drug candidates.

    Significance
    This project will discover promising drug candidates that stop the replication of viruses within the Flaviviridae family. Members of this family, including dengue, hepatitis C, West Nile, and yellow fever viruses, pose significant health threats throughout the developed and developing world. More than 40% of the world’s population is at risk for infection by dengue virus. Annually, ~1.5 million people are treated for dengue fever and dengue hemorrhagic fever. Hepatitis C virus has infected ~2% of the world’s population. Yellow fever and West Nile viruses also have had significant global impact. Unfortunately, there are no drugs that effectively treat these diseases. Consequently, the supportive care necessary to treat these infections and minimize mortality severely strains already burdened health facilities throughout the world. The discovery of both broad-spectrum and specific antiviral drugs is expected to significantly improve global health.”

    Help Conquer Cancer

    hcc

    Mission
    The mission of Help Conquer Cancer is to improve the results of protein X-ray crystallography, which helps researchers not only annotate unknown parts of the human proteome, but importantly improves their understanding of cancer initiation, progression and treatment.

    Significance
    In order to significantly impact the understanding of cancer and its treatment, novel therapeutic approaches capable of targeting metastatic disease (or cancers spreading to other parts of the body) must not only be discovered, but also diagnostic markers (or indicators of the disease), which can detect early stage disease, must be identified.

    Researchers have been able to make important discoveries when studying multiple human cancers, even when they have limited or no information at all about the involved proteins. However, to better understand and treat cancer, it is important for scientists to discover novel proteins involved in cancer, and their structure and function.

    Scientists are especially interested in proteins that may have a functional relationship with cancer. These are proteins that are either over-expressed or repressed in cancers, or proteins that have been modified or mutated in ways that result in structural changes to them.

    Improving X-ray crystallography will enable researchers to determine the structure of many cancer-related proteins faster. This will lead to improving our understanding of the function of these proteins and enable potential pharmaceutical interventions to treat this deadly disease.”

    Human Proteome Folding

    hpf

    “Human Proteome Folding Phase 2 (HPF2) continues where the first phase left off. The two main objectives of the project are to: 1) obtain higher resolution structures for specific human proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta software structure prediction. Thus, the project will address two very important parallel imperatives, one biological and one biophysical.

    The project, which began at the Institute for Systems Biology and now continues at New York University’s Department of Biology and Computer Science, will refine, using the Rosetta software in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the project. The goal of the first phase was to understand protein function. The goal of the second phase is to increase the resolution of the predictions for a select subset of human proteins. Better resolution is important for a number of applications, including but not limited to virtual screening of drug targets with docking procedures and protein design. By running a handful of well-studied proteins on World Community Grid (like proteins from yeast), the second phase also will serve to improve the understanding of the physics of protein structure and advance the state-of-the-art in protein structure prediction. This also will help the Rosetta developers community to further develop the software and the reliability of its predictions.

    HPF2 will focus on human-secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the proteins). Examples of human secreted proteins turned into therapeutics are insulin and the human growth hormone. Understanding the function of human secreted proteins may help researchers discover the function of proteins of unknown function in the blood and other interstitial fluids.”

    FightAIDS@Home

    HAAH

    What is AIDS?
    UNAIDS, the Joint United Nations Program on HIV/AIDS, estimated that in 2004 there were more than 40 million people around the world living with HIV, the Human Immunodeficiency Virus. The virus has affected the lives of men, women and children all over the world. Currently, there is no cure in sight, only treatment with a variety of drugs.

    Prof. Arthur J. Olson’s laboratory at The Scripps Research Institute (TSRI) is studying computational ways to design new anti-HIV drugs based on molecular structure. It has been demonstrated repeatedly that the function of a molecule — a substance made up of many atoms — is related to its three-dimensional shape. Olson’s target is HIV protease (“pro-tee-ace”), a key molecular machine of the virus that when blocked stops the virus from maturing. These blockers, known as “protease inhibitors”, are thus a way of avoiding the onset of AIDS and prolonging life. The Olson Laboratory is using computational methods to identify new candidate drugs that have the right shape and chemical characteristics to block HIV protease. This general approach is called “Structure-Based Drug Design”, and according to the National Institutes of Health’s National Institute of General Medical Sciences, it has already had a dramatic effect on the lives of people living with AIDS.

    Even more challenging, HIV is a “sloppy copier,” so it is constantly evolving new variants, some of which are resistant to current drugs. It is therefore vital that scientists continue their search for new and better drugs to combat this moving target.

    Scientists are able to determine by experiment the shapes of a protein and of a drug separately, but not always for the two together. If scientists knew how a drug molecule fit inside the active site of its target protein, chemists could see how they could design even better drugs that would be more potent than existing drugs.

    To address these challenges, World Community Grid’s FightAIDS@Home project runs a software program called AutoDock developed in Prof. Olson’s laboratory. AutoDock is a suite of tools that predicts how small molecules, such as drug candidates, might bind or “dock” to a receptor of known 3D structure.”

    ——————————————–

    There are currently about 98,000 members of this crunching community. We are called crunchers because that is what our computers do. Once having installed the software and chosen our projects, we are sent small work units to process. The finished data is sent back to WCG and we get new work units. How are we rewarded for our efforts? Really, just with the satisfactiuon of knowing that we might be helping to save lives. But, we do get little gifts, badges based upon our completed work. Some crunchers have organized themselves into teams. The teams compete for points or credits. There are al;l sorts of teams, from a few people organizing in a church or synagogue, to mega teams of techies building mroe and more Linux boxes.

    So, 98,000. That is a lot of people; but not in a world with one billion computers. We want and need your help. I am personally crunching 24/7 on five machines – yesterday the sixth, an older PC died.
    The cost in electricity? About the same as a 100-150 watt light bulb as long as you have your monitor on a power save setting.

    All WCG projects run on software developed and continually upgraded by At UC Berkeley, The Berkeley Open Infrastructure for Network Computing.You can download the little piece of BOINC software that makes this all happen either at WCG or http://boinc.berkeley.edu/.

    If you choose to download the software at the BOINC page, there you will see a link to a whole other list of wonderful projects which are running independently of WCG.

    So, please, won’t you give us a look?

     
  • richardmitnick 2:32 pm on January 26, 2011 Permalink | Reply
    Tags: , , Clean Water, , ,   

    Project Update from WCG’s Fight AIDS At Home Project 

    From World Community Grid’s (WCG) Fight Aids At Home Project (FAAH)

    YOU ARE PROBABLY NOT GOING TO UNDERSTAND A SINGLE TECHNICAL TERM IN THIS UPDATE FROM THE FIGHT AIDS AT HOME PROJECT. BUT, READ THE ACCOUNT ANYWAY. THESE GUYS IN THE OLSON LABORATORY AT THE SCRIPPS RESEARCH INSTITUTE HAVE BEEN IN THE FOREFRONT OF AIDS RESEARCH FOR A VERY LONG TIME.

    “Experiment 35 involves screening the full NCI library of ~ 316,000 compounds against the active site of 8 different versions of HIV protease. Thus, this experiment is similar to Exp. 32, but a different library of compounds is being screened, and one new target has been added. All but two of these target conformations were generated by Dr. Alex L. Perryman’s Molecular Dynamics (MD) simulations of 5 different variants of HIV protease. These 8 targets include 2 snapshots of the V82F/I84V mutant from ALP’s 2004 paper in Protein Science. These 2 snapshots of a multi-drug-resistant “superbug” have semi-open conformations of the flaps, which makes these models good targets for the “eye site” that is located between the tip of a semi-open flap and the top of the wall of the active site. The 3rd target is the equilibration MD (EqMD) output for 1HSI.pdb, which is a semi-open conformation of HIV-2 protease. HIV-2 is the group of strains of HIV that are most common in Africa. We’ll be targeting the “eye site” of 1HSI, as well. The 4th target is the EqMD output from 1MSN.pdb, which was created using a different crystal structure of the V82F/I84V superbug. This model has a closed conformation of the flaps, which means that we’ll be targeting the floor of the active site. The 5th target also has a closed conformation of the flaps, but this EqMD output is from 2R5P.pdb, which is the wild type HIV-1c protease. HIV-1c is the group of strains of HIV that are most commonly found in Asia. The 6th target has semi-open flaps, and it is the EqMD output from 1TW7.pdb, which is a superbug with the mutations L10I/D25N/M36V/M46L/I54V/I62V/L63P/A71V/V82A/I84V/L90M. We’ll be targeting the eye site of this superbug, too.

    The 7th target is a crystal structure of the wild type HIV protease with 5-nitroindole bound in the eye site. This new crystal structure from Prof. C. David Stout’s lab was presented in the Supporting Information for our recent article in Chemical Biology and Drug Design, vol. 75: 257-268 (March 2010). This new research article of ours was recently discussed in a press release on Science Daily and in a news story on KPBS-FM. This paper was recently listed as one of the “most read papers” from Chemical Biology and Drug Design this year! I deleted the 5-nitroindole fragment from this structure before generating the AutoDock input file for this target. We’ll be screening new fragments against this crystal structure’s eye site, as well.

    The 8th target has never been used on FightAIDS@Home before. It is a brand new crystal structure from Assoc. Prof. C. David Stout’s lab of the chimeric “FIV 6s98S” protease, which was developed by our collaborators Ying-Chuan Lin, Prof. Bruce E. Torbett, and Prof. John H. Elder. A paper on this new crystal structure of FIV 6s98S protease is currently being peer-reviewed. This protease enzyme is “chimeric,” because it contains 5 residues from HIV protease that were substituted into the corresponding positions in FIV protease. The 6th residue was also substituted from HIV protease, but it changed into a different residue during serial passage experiments (i.e., during directed evolution studies performed with the presence of different HIV protease drugs). This 6s98S FIV protease has HIV-like drug sensitivity profiles and is a new model system for multi-drug-resistant HIV protease.”

    You can help in this vital project and other very worthwhile projects which are a part of World Community Grid (WCG). Visit WCG, download the BOINC software application and attach to the WCG project. Build your own “profile” at WCG, selecting which projects you find to be of interest. There are some 97,000 of us “crunching” data for these projects on out home and/or work computers. Most of these projects are in the fields of medical or biological research.

    While you are at it, visit the BOINC site where you will find a whole host of other projects in biology, chemistry, cosmology, mathematics and physics.

    Visit the project home pages, read about the work, and maybe you will also find other attractive projects on which you might wish to lend a hand. All in all, about 303,000 people “crunch” data for all of the BOINC projects combined, including the projects at WCG. Together, we have saved lab scientists literally thousands of hours of research time. Current over all statistics: 303,045 volunteers, 486,047 computers. 24-hour average: 5,150.82 TeraFLOPS. So, we have just under a half million computers on all of the projects. Think that’s a goodly number? Well, there are close to a billion computers in use in the world. So that means we have 0.0003, that’s 0.03%, 3 one hundredths of one percent. If you add just one computer to this total, it means a lot.

    The process uses the idle CPU cycles of your computer(s) while they are running. After you attach to projects, you have really no work to do. The BOINC software takes care of everything, downloading “work units” (WU’s), processing the WU’s, uploading the finished results. You can if you wish become active in the forums maintained by WCG, BOINC, and each project. You can join a team, say at your alma mater, or your company; or you can start a team in your company, church, mosque, temple or synagogue, whatever. Some of the projects have really cool screen savers which you can use.

    I am personally running three Win 7 machines and two Vista machines, 24/7. The cost of running a computer is about the same as a 100-150 watt light bulb, so it is quite cheap.

    I consider this to be the most meaningful thing that I have ever done with my computers. I urge you to take a look, give us a shot.

     
  • richardmitnick 3:51 pm on December 15, 2010 Permalink | Reply
    Tags: Clean Water,   

    From Pacific Northwest National Labs: “Seeing Diffusion from the Atom’s Perspective” 

    December 2010
    A new approach to calculating uranium diffusion challenges traditional equation

    “Uranium contamination may move much slower in groundwater than previously believed, according to scientists at Pacific Northwest National Laboratory. Around the nation, sediments and groundwater are contaminated with uranium from discharges at mining and processing sites. Knowing how uranium spreads out or diffuses in water is critical to predicting its movement and removing the contamination. But previous estimates may have significantly overestimated the radionuclide’s ability to move with the groundwater…

    “With a better understanding of uranium diffusion at the molecular level, scientists can build more accurate models of uranium movement in groundwater. Being able to accurately predict how quickly uranium moves with groundwater will help regulators and other decision makers prioritize cleanup decisions. It will also allow engineers to design better cleanup approaches…

    “Pacific Northwest National Laboratory scientists Dr. Sebastien Kerisit and Dr. Chongxuan Liu used molecular dynamics techniques and EMSL’s Chinook supercomputer to calculate diffusion trajectories of uranium-containing species based on a set of equations describing the way atoms interact….”

    i2
    Diffusion coefficients calculated using EMSL’s supercomputer show that uranium-containing species may move slower in groundwater than originally thought.

    See the full article here.

     
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