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Emad Tajkhorshid

University of Illinois at Urbana-Champaign

Biophysics

2018

Marcelo C R Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C Phillips, Julio D C Maia, Gerd B Rocha, Jo\ ao V Ribeiro, John E Stone, Frank Neese, Klaus Schulten, and Zaida Luthey-Schulten (2018): NAMD Goes Quantum: An Integrative Suite for Hybrid Simulations, Nature Methods, Springer Nature

2017

Tao Jiang, Kuai Yu, H Criss Hartzell, and Emad Tajkhorshid (2017): Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the nhTMEM16 Scramblase, eLife, eLife Sciences Organisation, Ltd., Vol 6

2016

Amir Barati Farimani, Narayana R. Aluru, Emad Tajkhorshid, and Eric Jakobsson (2016): Computational Approach to Designing Antibody for Ebola Virus, Biophysical Journal, Elsevier BV, Vol 110, Num 3, pp537a

2015

Jing Li, Po-Chao Wen, Mahmoud Moradi, and Emad Tajkhorshid (2015): Computational Characterization of Structural Dynamics Underlying Function in Active Membrane Transporters, Current Opinion in Structural Biology, Elsevier BV, Vol 31, pp96-105
Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid (2015): Atomic-Level Characterization of Transport Cycle Thermodynamics in the Glycerol-3-Phosphate:phosphate Antiporter, Nature Communications, Nature Publishing Group, Vol 6, pp8393

2014

Mahmoud Moradi, and Emad Tajkhorshid (2014): Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 10, Num 7, pp2866--2880

2013

M. Moradi, and E. Tajkhorshid (2013): Mechanistic Picture for Conformational Transition of a Membrane Transporter at Atomic Resolution, Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 110, Num 47, pp18916--18921

2017

Emad Tajkhorshid and Klaus Schulten (2017): Studying Cellular Processes through the Computational Microscope, 2017 Blue Waters Annual Report, pp234-235

2015

Emad Tajkhorshid (2015): Characterizing Structural Transitions of Membrane Transport Proteins at Atomic Detail, 2015 Blue Waters Annual Report, pp172-173
Emad Tajkhorshid: Characterizing Structural Transitions of Membrane Transport Proteins at Atomic Details
Blue Waters Symposium 2014, May 15, 2014

18 general, 9 exploratory allocations on Blue Waters awarded to Illinois researchers


Nov 24, 2014

Eighteen researchers at the University of Illinois at Urbana-Champaign received allocations on the Blue Waters petascale supercomputer at the National Center for Supercomputing Applications (NCSA). A portion of available time on Blue Waters is reserved for University faculty and staff projects like these that require the system’s unique capabilities. Ten of the awards will continue projects already running on Blue Waters, related to a wide variety of topics like tornadoes, steel casting, and cell function, among others. Eight allocations are for new projects.


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NSF awards time on Blue Waters to seven new projects


Oct 1, 2014

The National Science Foundation (NSF) has awarded 14 new allocations on the Blue Waters petascale supercomputer at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Seven of the awards are for new projects.


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Blue Waters Illinois allocations awarded to 26 research teams


Mar 7, 2017

Twenty-six research teams at the University of Illinois at Urbana-Champaign have been allocated computation time on the National Center for Supercomputing Application's (NCSA) sustained-petascale Blue Waters supercomputer after applying in Fall 2016. These allocations range from 25,000 to 600,000 node-hours of compute time over a time span of either six months or one year. The research pursuits of these teams are incredibly diverse, ranging anywhere from physics to political science.


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6 science teams begin using Blue Waters Early Science System


Mar 20, 2012

Six research teams have begun using the first phase of the Blue Waters sustained-petascale supercomputer to study some of the most challenging problems in science and engineering, from supernovae to climate change to the molecular mechanism of HIV infection. The Blue Waters Early Science System, which is made up of 48 Cray XE6 cabinets, represents about 15 percent of the total Blue Waters computational system and is currently the most powerful computing resource available through the National Science Foundation.


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What will scientists do with Blue Waters?


Dec 9, 2009

Many scientists are working now with the Blue Waters team so they are ready to use the massive sustained-petaflop supercomputer when it comes online in 2011. These teams will use Blue Waters to improve our understanding of tornadoes, earthquakes, the spread of contagious diseases, the formation of galaxies, the behavior of molecules and more.


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Celebrating Blue Waters


Apr 7, 2015

On April 6, U.S. Sen. Mark Kirk (R-IL) convened a celebration in honor of the second birthday of NCSA’s Blue Waters supercomputer, which is used by scientists and engineers across the country to tackle challenging research for the benefit of science and society. In kicking off the event, Kirk highlighted the importance of Blue Waters—and of continuing investment in high-performance computing. ... A panel of Blue Waters users—four from among the 200 teams across the country that have used the system—then briefly described how the supercomputer accelerates their research:


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The Top Supercomputing Led Discoveries of 2013


Jan 2, 2014

2013 has been an incredible year for the entire ecosystem around supercomputing; from vendors pushing new technologies to boost performance, capacity, and programmability to researchers turning over new insights with fresh techniques. While exascale has taken more of a backseat than we might have predicted at the year’s end of 2010, there are plenty of signs that production HPC environments are blazing plenty of new trails. ...


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Making history


Sep 24, 2012

A brief but tantalizing test run of the Blue Waters sustained petascale supercomputer earlier this year has left researchers eagerly awaiting full deployment. The Blue Waters Early Science System (BW-ESS) was only about 15 percent of the full machine as it consisted of 48 cabinets with 4,512 XE6 compute nodes and 96 service nodes and a Sonexion Lustre Storage Appliance provided two petabytes of disk storage. But that was enough to allow researchers to test the technology used in Blue Waters and identify and fix software bugs and other issues that prevented some codes from successfully scaling.


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Blue Waters petascale supercomputer now in friendly user phase


Nov 6, 2012

The full Blue Waters petascale computing system is now available in "friendly-user" mode to the National Science Foundation-approved science and engineering teams. These groups from across the country will use Blue Waters for challenging research in weather and climate, astrophysics, biomolecular systems, and other fields. ... Selected "friendly users" will have access to the entire system during this window in order to help the Blue Waters team test and evaluate the full system and to expedite the Petascale Computing Resource Allocation (PRAC) teams' ability to use the full Blue Waters system productively as soon as it is in full production status.


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Titan Helps Researchers Suck Mystery Out of Cell's 'Vacuum Cleaners'


Sep 20, 2017

In the fight against cancer, cancer cells often find ways to fight back. One means is by stocking the cell membrane with proteins that pump foreign substances—including anticancer drugs—out of the cell. This trait can result in multidrug resistance that undermines the effectiveness of cancer treatment. To combat this defense mechanism, scientists are turning to supercomputers and molecular dynamics to better understand the function of a membrane transport protein called P-glycoprotein, or Pgp. ... Recently, a team led by computational biophysicist Emad Tajkhorshid from the University of Illinois at Urbana-Champaign (UIUC) uncovered new details about Pgp that could help the drug discovery community.


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Supercomputer Visualization Shows 1.2 Microseconds in the Life of a 4-Million-Atom HIV Capsid


Jul 21, 2017

While some researchers look for drugs to treat HIV, other scientists delve deep into the virus itself for answers on how it causes infections. Using two supercomputers, University of Illinois research scientist Juan R. Perilla and late physics professor Klaus Schulten simulated 1.2 microseconds of the life of the HIV capsid, the structure that contains the virus's genetic material. The simulation, which took two years to complete, gives us a view of the virus on a molecular level and provides us with insight into how HIV senses its environment and becomes infective.


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A cure for HIV takes a step closer after supercomputers reveal how the virus moves


Jul 19, 2017

A brief glimpse into how HIV travels through the body has been simulated for the first time on supercomputers in the US. For two years, multiple supercomputers at the University of Illinois modelled the behaviour of 64 million atoms to capture 1.2 microseconds of the life of an HIV capsid, a protein cage that transports the HIV virus to the nucleus of a human cell. The capsid simulation was performed on the Department of Energy's Titan supercomputer, while analysis was made using the Blue Waters supercomputer at the National Center for Supercomputing Applications at the university.


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Rock Stars of HPC: James Phillips


Apr 27, 2017

Recipient of a Gordon Bell Award in 2002, James Phillips has been a full-time research programmer for almost 20 years. Since 1998, he has been the lead developer of NAMD, a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales beyond 200,000 cores, and is undoubtedly a Rock Star of HPC. ... InsideHPC: That advice led you to Professor Klaus Schulten – what impact did he have on your career? When Schulten came here from Germany he had a couple of grad students and a home-built parallel computer that they used to run the first simulation of a membrane back in early 1990s. He was very much dedicated to the idea that we can use parallel computing to do science and he largely dedicated his life to running this place. In fact he rarely slept – I remember at one point I was working on something and I sent him an email at 3am to try and impress him, and he wrote back.


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First atomic-scale view of interaction between HIV capsid and host protein cyclophilin A


Mar 7, 2016

A new study offers the first atomic-scale view of an interaction between the HIV capsid - the protein coat that shepherds HIV into the nucleus of human cells - and a host protein known as cyclophilin A. This interaction is key to HIV infection, researchers say. A paper describing the research appears in the journal Nature Communications. ... "We have known for some time that cyclophilin A plays a role in HIV infection," said University of Illinois physics professor Klaus Schulten, who led the new study with postdoctoral researcher Juan R. Perilla and University of Pittsburgh professor Peijun Zhang and postdoctoral researcher Chuang Liu.


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Researchers resolve structure of a key component of bacterial decision-making


Dec 8, 2015

For bacteria that swim, determining whether to stay the course or head in a new direction is vital to survival. A new study offers atomic-level details of the molecular machinery that allows swimming bacteria to sense their environment and change direction when needed. The study, reported in the journal eLife, represents a major step in understanding the "bacterial brain," said University of Illinois physics professor Klaus Schulten, who led the new research.


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Researchers Construct Atomic Model of an Immature Retrovirus


Aug 12, 2015

Using molecular modeling and large-scale molecular dynamic simulation, University of Illinois researchers constructed an atomic model of an immature retrovirus. The researchers, from the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology at Illinois, published their work in the journal Structure.


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Attacking HIV with Titan and Blue Waters


May 13, 2015

In this video from the GPU Technology Conference, James Phillips Senior Research Programmer from the University of Illinois at Urbana-Champaign presents: Attacking HIV with Petascale Molecular Dynamics Simulations on Titan and Blue Waters.


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Bolstering Extreme Scale Computational Biology


Jul 31, 2014

According to Dr. Klaus Schulten from the University of Illinois, the molecular dynamics and visualization programs NAMD and VMD, which serve over 300,000 registered users in many fields of biology and medicine, are pushing the limits of extreme scale computational biology. Schulten says these programs can operate on a wide variety of hardware and offer new inroads to medical discovery. In addition to outlining NAMD and VMD on ARM and GPU developments over the last several years that led to the programs’ extreme performance on Blue Waters, Titan and Stampede, Schulten is known for shedding light on how these fields and programs are enabled by petascale computing.


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NCSA Receives Honors in 2013 HPCwire Readers’ and Editors’ Choice Awards


Nov 18, 2013

NCSA announced today that it received the HPCwire Editors’ Choice Award for Best Use of HPC in Life Sciences for the use of the Blue Waters supercomputer to achieve a significant breakthrough in the understanding of HIV. The 2013 HPCwire Readers’ and Editors’ Choice Awards were announced at the start of the Opening Reception at the 2013 International Conference for High Performance Computing, Networking, Storage and Analysis (SC13), in Denver, Colorado. The award recognizes research conducted by biophysicist Klaus Schulten of the University of Illinois at Urbana-Champaign and his collaborators.


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Wit, grit and a supercomputer yield chemical structure of HIV capsid


May 29, 2013

Researchers report that they have determined the precise chemical structure of the HIV capsid, a protein shell that protects the virus's genetic material and is a key to its virulence. The capsid has become an attractive target for the development of new antiretroviral drugs. ... "This is a big structure, one of the biggest structures ever solved," said U. of I. physics professor Klaus Schulten, who, with postdoctoral researcher Juan R. Perilla, conducted the molecular simulations that integrated data from laboratory experiments performed by colleagues at the University of Pittsburgh and Vanderbilt University. "It was very clear that it would require a huge amount of simulation - the largest simulation ever published - involving 64 million atoms."


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Virus unmasked


Feb 1, 2013

Simulations carried out using the Blue Waters petascale supercomputer have determined the structure of the rabbit hemorrhagic disease virus (RHDV), which causes a highly infectious and often fatal illness in domestic and wild rabbits. This research, carried out collaboratively by researchers at the University of Illinois, the University of California-San Diego and several Chinese research institutions, has been published in PLOS Pathogens. ... University of Illinois biophysicist Klaus Schulten, a co-author of the published study, says the computational power of Blue Waters and the NAMD molecular dynamics code developed at the University of Illinois were vital to achieving this result.


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Massive Simulation Shows HIV Capsid Interacting with its Environment


Jul 20, 2017

It took two years on a supercomputer to simulate 1.2 microseconds in the life of the HIV capsid, a protein cage that shuttles the HIV virus to the nucleus of a human cell. The 64-million-atom simulation offers new insights into how the virus senses its environment and completes its infective cycle. The findings are reported in the journal Nature Communications. "We are learning the details of the HIV capsid system, not just the structure but also how it changes its environment and responds to its environment," said University of Illinois research scientist Juan R. Perilla, who led the study with U. of I. physics professor Klaus Schulten. Such details could help scientists find new ways to defeat the virus, Perilla said.


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Computing a Cure for HIV: 9 Ways Supercomputers Help Scientists Understand and Treat the Virus


Jun 20, 2014

The tendency of HIV to mutate and resist drugs has made it particularly difficult to eradicate. Some treatments have shown progress in slowing or even stopping the progress of the virus, but no cure or vaccine has been discovered that can truly stamp out the disease. In the last decade scientists have begun using a new weapon in the fight against HIV: supercomputers. ... Among the researchers using supercomputers to study HIV is Klaus Schulten, the keynote speaker at the 2014 International Supercomputing Conference in Leipzig, Germany. Schulten, a professor of physics at the University of Illinois at Urbana-Champaign, invented the Nanoscale Molecular Dynamics (NAMD) software program, one of the most widely used tools for understanding diseases at a molecular level.


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Advances in Computational Research Transform Scientific Process and Discovery


Mar 25, 2013

Not every scientific discovery originates in the lab, or from the field. Scientists increasingly are turning to powerful new computers to perform calculations they couldn't do with earlier generation machines, and at breathtaking speed, resulting in groundbreaking computational insights across a range of research fields. .... Last October, NSF inaugurated Yellowstone, one of the world's most powerful computers, based at NCAR in Cheyenne, Wyo., and later this month will dedicate two additional supercomputers, Blue Waters, located at the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign, and Stampede, headquartered at the Texas Advanced Computing Center 9TACC) at The University of Texas at Austin. ... "The computer is excellent in permitting us to test a hypothesis," says Klaus Schulten, a professor of physics at the University of Illinois at Urbana-Champaign, who uses large-scale computing to study the molecular assembly of biological cells, most recently HIV, the virus that causes AIDS. "But if you want to test a hypothesis, you need to have a hypothesis."


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Team brings subatomic resolution to computational microscope


Mar 26, 2018

Scientists have built a “computational microscope” that can simulate the atomic and subatomic forces that drive molecular interactions. This tool will streamline efforts to understand the chemistry of life, model large molecular systems and develop new pharmaceutical and industrial agents, the researchers say. They report their findings in the journal Nature Methods. ... Both molecular mechanics and quantum mechanics programs have been available for years, and other teams have worked to combine them, said University of Illinois chemistry professor Zaida (Zan) Luthey-Schulten, who led the new research with her husband, U. of I. physics professor Klaus Schulten. But the new effort streamlines the process of setting up, performing and analyzing the simulations.


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