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Project Information

Project Information


Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Tenth Round


Project Scope:

At the request of the Pittsburgh Supercomputing Center (PSC) and D.E. Shaw Research (DESRES), the National Academies of Sciences, Engineering, and Medicine will appoint a tenth committee of experts to review proposals for allocations of time to conduct molecular dynamics (MD) simulations of biological molecules using an "Anton" computer housed at PSC. Proposals will be evaluated on the basis of selection criteria in the Request for Proposals including (a) scientific merit, (b) the capabilities, past accomplishments, and/or scientific promise of the applicant, (c) suitability of the targeted biochemical system for simulation on the PSC machine, (d) overall feasibility of the proposed studies, and (e) likely scientific impact. At least 25% of the total allotted time will be reserved for new users who were not principal investigators on proposals selected to receive simulation allotments on the Anton awarded in the previous rounds. The committee will prepare a brief report summarizing its evaluations and identifying proposals that best meet the selection criteria for the project. 

Status: Current

PIN: DELS-BLS-19-04

RSO: Hodgson, Andrea

Board(s)/Committee(s):

Board on Life Sciences

Topic(s):

Biology and Life Sciences



Geographic Focus:

Committee Membership


James Briggs - (Chair)
James Briggs, Ph.D., is a Professor within the Biology and Biochemistry Department at the University of Houston. Dr. Briggs received his Ph.D. in Chemistry from Purdue University. His research focuses on computational studies of protein structure and function, inhibitor design, investigations of possible inhibitor resistance pathways, and development of methods for the above areas. Targets for these studies include those important in the treatment of AIDS, cancer, bacterial infections, and other disease states. In addition, Dr. Briggs has worked on inhibitors to aid in biowarfare defense (botulinum neurotoxins, anthrax toxin, cholera toxin). Dr. James Briggs’ research is focused in the highly interdisciplinary and collaborative area of computational chemistry/biochemistry. He develops and applies computational methods to problems of chemical and biochemical interest. His research falls into two general categories: computer-aided inhibitor design/discovery and computational biophysics. His main target areas in the inhibitor/ligand area are Rho kinase 1 (heart disease), PTEN (cancer), PTEN/5HTC2C (addiction control), BCL2 (cancer), gluconeogenesis and glucose uptake (cancer); those for the computational biophysics area include cholera toxin, biofilm control, RNA structure prediction, protein electrostatics and pKa predictions, and identification of protein/enzyme function from structure only.
Jerome Baudry
Jerome Baudry, Ph.D., is the Pei-Ling Chan Professor of Biological Sciences in the Department of Biological Sciences at the University of Alabama, Huntsville (UAH). Dr. Baudry obtained his Ph.D. in Molecular Biophysics from the University of Paris, UPMC/Sorbonne Universities, France. He subsequently joined the group of Klaus Schulten at the University of Illinois at Urbana-Champaign as a post-doc. After his post-doctoral work, Dr. Baudry worked in the pharmaceutical industry as a Research Scientist, and then accepted a Senior Research Scientist position back in Illinois on a non-tenure track research faculty position. Dr. Baudry joined the University of Tennessee, Knoxville and the UT/ORNL Center for Molecular Biophysics as a tenure track Assistant Professor in 2008. In 2014, he was promoted to Associate Professor with tenure. In August 2017, Dr. Baudry joined UAH as the Pei-Ling Chan Professor. At UAH, Dr. Baudry’s group develops and applies methods and protocols for computational drug discovery, both on small-molecules and biologicals, within academic, national laboratories and industrial collaborations.
Heather Carlson
Heather Carlson, Ph.D., is currently a Professor of Medicinal Chemistry at the University of Michigan College of Pharmacy. She also holds joint appointments with the Biophysics Department in the College of Pharmacy and the Chemistry Department in the College of Literature, Science, and the Arts. Dr. Carlson received both her Masters and Ph.D. in Physical Chemistry from Yale University, and completed her post-doctoral work at the University of California, San Diego. Her expertise is in the area of computer simulations, cheminformatics, bioinformatics, and structure-based drug design. She is a leader in the incorporation of protein flexibility and allosteric control in drug design. She is also well known for her studies of protein-ligand binding and the biophysics of molecular recognition. Dr. Carlson is also the director of two large, online resources for studying protein-ligand interactions: Binding MOAD (www.BindingMOAD.org) and the Community Structure-Activity Resource (www.CSARdock.org). These resources are used by numerous research groups around the world. She also serves the scientific community through NIH review panels and editorial roles for scientific journals.
Linda Columbus
Linda Columbus, Ph.D., is a Professor of Chemistry at the University of Virginia. Dr. Columbus received
her Bachelor’s degree in Chemistry from Smith College, and her Ph.D. in Biochemistry and Molecular
Biology from the University of California, Los Angeles. Dr. Columbus’s lab focuses on using biophysical
chemistry to study membrane biophysics and membrane protein structure, function, and dynamics. Her
research specifically looks at the structure and dynamics of membrane proteins involved in bacterial
pathogenesis. To facilitate this research, her lab develops and uses approaches such as site-directed spin
labeling (SDSL), nuclear magnetic resonance (NMR) spectroscopy, and X-ray crystallography.
Brian Dominy
Brian Dominy, Ph.D., is an Associate Professor in the Department of Chemistry at Clemson University. Dr. Dominy earned his B.S. degree from Carnegie Mellon University in the Biological Sciences and Computer Science tracks with a minor in Chemistry. He then joined the Scripps Research Institute as a Ralph M. Parsons Foundation predoctoral fellow, earning his Ph.D. under the direction of Dr. Charles L. Brooks III. Following this, he worked as an NIH postdoctoral fellow at Harvard University with Dr. Eugene Shakhnovich in the department of Chemistry and Chemical Biology. During this time, his research dealt with improving statistical mechanical models, primarily inverse Boltzmann knowledge-based potentials, designed for rapid binding free energy prediction and automated drug design. His current research involves the development and application of molecular mechanics and bioinformatics techniques to explore the physical chemical basis of biological phenomena at the molecular level. Specifically, his group focuses on applications relevant to medicine, including drug design and biomolecular evolution of drug targets (i.e., drug resistance).
James C. Gumbart
James C. (JC) Gumbart, Ph.D., is an Associate Professor of Physics at the Georgia Institute of Technology in Atlanta, Georgia. He obtained his B.S. from Western Illinois University and his PhD in Physics from the University of Illinois, Urbana-Champaign under the mentorship of Klaus Schulten, focusing on the area of computational biophysics. After two years as a postdoctoral fellow at Argonne National Lab working with Benoit Roux, he started his lab at Georgia Tech in early 2013. His lab carries out molecular dynamics simulations aimed primarily at understanding the composition, construction, and function of the Gram-negative bacterial cell envelope.
Ellinor Haglund
Ellinor Haglund, Ph.D., is currently an Assistant Professor in the Department of Chemistry at the University of Hawaii in Manoa. Dr. Haglund received her Masters in Molecular Biology and Chemistry from Umeå University, her Ph.D. at Stockholm University, and completed her post-doctoral work at Rice University and the University of California, San Diego, with the Center for Theoretical Biological Physics. Her research is focused on the folding event in proteins, utilizing both computational and experimental techniques to understand the molecular details of how proteins fold into biologically active molecules. She is inspired by how nature works and utilizes her multidisciplinary training to answer questions at the interface of chemistry, biology, and physics.
Fatemah Khalili-Araghi
Fatemeh Khalili-Araghi, Ph.D., is an Assistant Professor at the University of Illinois at Chicago, specializing in theoretical and computational studies of ion channels. She obtained her B.S. in Physics from Sharif University of Technology, and her Ph.D. from University of Illinois at Urbana-Champaign. She was a postdoctoral scholar at the University of Chicago, where she continued studies of membrane proteins with a focus on the Na/K ATPase using computational modeling techniques, as well as molecular dynamics simulations. She currently works on transport properties of tight junctions and bacterial efflux pumps.
Andrzej Kloczkowski
Andrzej Kloczkowski, Ph.D., is a Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He has a joint appointment as a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in the application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
Themis Lazaridis
Themis Lazaridis, Ph.D., is currently a Professor in the Department of Chemistry and Biochemistry at the City College of New York, affiliated with the CUNY Institute for Macromolecular Assemblies. Dr. Lazaridis earned his Ph.D. in Chemical Engineering from the University of Delaware, followed by post-doctoral work at Harvard University. His research is in the area of Theoretical and Computational Biophysical Chemistry, which aims to understand how biological systems work in terms of the fundamental laws of Physics and Chemistry. One goal of his research is to understand the forces that operate within and between biomolecules and develop quantitative mathematical models for their energy as a function of conformation. Such models are useful in many ways, such as predicting the three-dimensional structure from sequence, characterizing conformational changes involved in biological function, or predicting the binding affinity between two biomolecules. A particular focus in the past several years has been the interaction of proteins with biological membranes and pore formation in lipid bilayers.
Eric May
Eric May, Ph.D., is an Associate Professor in the Department of Molecular and Cell Biology at the University of Connecticut. He obtained his Ph.D. from the University of Florida in Chemical Engineering and was an NSF postdoctoral fellow at the University of Michigan. His research interests are in the general area of computational and theoretical biophysics and biochemistry, with emphasis towards understanding conformational/phase transitions and the mechanical and thermodynamic properties of biological materials. His research group works on a variety of biomolecular systems, with particular emphasis on virus and membrane systems and protein dynamics.
Clare McCabe
Clare McCabe, Ph.D., received her bachelors and Ph.D. degrees in Chemistry from Sheffield University. After postdoctoral and research faculty appointments at the University of Tennessee, she joined the Colorado School of Mines faculty as an Assistant Professor of Chemical Engineering. She is currently a Faculty member at Vanderbilt University, where she is the Cornelius Vanderbilt Chair of Engineering and Professor of Chemical and Biomolecular engineering. Dr. McCabe is also Associate Dean of the Graduate School and Director of the Office of Postdoctoral Affairs. Her research interests focus on the use of molecular modeling techniques to understand and predict the thermodynamic and transport properties of complex fluids and materials. She is a fellow of the Royal Society of Chemistry and recently received the American Institute of Chemical Engineers Computational Molecular Science and Engineering Forum Impact Award.
Yinglong Miao
Yinglong Miao, Ph.D., is an Assistant Professor in the Department of Molecular Biosciences and Center for Computational Biology at the University of Kansas. Yinglong obtained his Ph.D. in Computational Chemistry in the lab of Peter Ortoleva at Indiana University. His graduate work was focused on all-atom multiscale modeling of infectious viruses and other bionanosystems. He subsequently began his postdoctoral research with Jeremy Smith and Jerome Baudry at the University of Tennessee and Oak Ridge National Laboratory. There he combined the world-class experimental and supercomputing resources to investigate the structural dynamics and function of protein enzymes that are responsible for drug metabolism. Yinglong then moved to Andy McCammon’s lab at the Howard Hughes Medical Institute and University of California, San Diego, where he worked on both method developments and cutting-edge applications in accelerated biomolecular simulations and drug discovery of the G-protein-coupled receptors. Yinglong develops novel theoretical and computational methods, with applications in protein folding, molecular recognition, cellular signaling and computer-aided drug design.
Vivek Narsimhan
Vivek Narsimhan, Ph.D., is an Assistant Professor of Chemical Engineering at Purdue University. Dr. Narsimhan received his bachelors in Chemical Engineering from the California Institute of Technology, his Master in Advanced Study in Mathematics from the University of Cambridge, his Ph.D. in Chemical Engineering from Stanford University, and completed his Post-doctoral research at MIT. His research uses a mixture of theory, simulations, and experiments to examine problems in the areas of suspensions, complex interfaces, fluid mechanics, and polymers. He has developed mathematical models, performed simulations, and conducted experiments to describe the mechanics of droplets, red blood cells, and vesicles under various flow types and microfluidic geometries. These investigations provide insight into how complex membranes alter the mechanical stability and motion of fluid-filled particles, both individually and as a suspension.
Steven W. Rick
Steven W. Rick, Ph.D., is a Professor in the Chemistry Department at the University of New Orleans. Dr. Rick received his Bachelors from the University of California, Los Angeles, his Ph.D. from the University of California, Berkeley, and completed his postdoctoral research at Columbia University. His research applies theoretical and computational approaches to a variety of chemically interesting systems. His work involves the development of more efficient computer simulation methods and better models for molecular interactions. Dr. Rick’s group is applying these methods to the study of liquid water, interface, aqueous solutions, proteins, and ion transport through various materials.
Christopher Rowley
Christopher Rowley, Ph.D., is an Assistant Professor in the Department of Chemistry at the Memorial University of Newfoundland. Dr. Rowley’s research interests are in computational chemistry, statistical thermodynamics, medicinal chemistry, biophysical chemistry, protein folding, and multi-scale modeling. His research group uses application-driven method development to investigate issues of irreversible enzyme inhibition, ion solvation, and environmental pollutants. Dr. Rowley received his Ph.D. in Chemistry from the University of Ottawa.
Leonor Saiz
Leonor Saiz, Ph.D., is a Professor in the Biomedical Engineering Department at the University of California, Davis. Dr. Saiz received her Ph.D. in Physics from the University of Barcelona. Her research involves the study of the dynamics of biological networks at the cellular and molecular level. Her lab combines computational and theoretical approaches together with experimental data to (1) understand how cellular behavior arises from the physical properties and interactions of the cellular components; and to (2) infer detailed molecular properties, such as the in vivo DNA mechanics, from the cellular physiology. By developing novel methodologies that consider multiple spatial and temporal scales and multiple levels of biological organization, including atomic, molecular, and cellular, their work has provided new avenues to integrate the molecular properties of cellular components directly into the dynamics of cellular networks. The ultimate goal of her work is to understand and follow the impact of molecular perturbations in the cellular components, such as a mutation in a protein or interventions with small molecules or drugs, through the different cellular processes up to the cellular behavior; one of the major challenges of modern biomedical sciences.
Markus Seeliger
Markus Seeliger, Ph.D., is an Associate Professor for Pharmacological Sciences and Associate Faculty of the Laufer Center for Computational and Physical Biology at Stony Brook University’s School of Medicine. Dr. Seeliger received his Ph.D. in Biophysical Chemistry from Cambridge University. The research in his group circles around the questions, how can we help small molecule inhibitors become clinically successful drugs, and what can we learn about the molecular regulation of drug targets through their interaction with small molecule drugs? He combines X-ray crystallography, NMR and other biophysical methods with computational tools.
Jeffrey Skolnick
Jeffrey Skolnick, Ph.D., is Professor and Mary and Maisie Gibson Chair and GRA Eminent Scholar in Computational Systems Biology at Georgia Institute of Technology. He received his B.A. in Chemistry, from Washington University, St. Louis in 1975, his M. Phil. in Chemistry from Yale University in 1977, and his Ph.D. in Chemistry from Yale University in 1978. His research interests include using systems and computational biology approaches to solve health problems. He uses these tools to better understand important areas of study such as cancer metabolomics, drug design, and protein evolution. An additional area of research includes the prediction of protein structure from DNA sequences to better characterize human genes.
Juan Vanegas
Juan Vanegas, Ph.D., is currently an Assistant Professor at the University of Vermont in the Department of Physics with appointments in the Materials Science and Cellular, Molecular, and Biomedical Sciences Graduate Programs. Dr. Vanegas received his masters in Biochemistry and Biophysics from Oregon State University, and his Ph.D. in Biophysics from the University of California, Davis. His research uses coarsegrained, atomistic, and ab initio molecular simulation methods to understand how chemical structure determines mechanical properties of biomolecules and their response to mechanical stimuli. Some applications of this research include understanding elastic properties of lipid biomembranes and force transduction mechanisms in mechanosensitive channels. His lab leads the development of computational tools for local stress calculations from molecular dynamics simulations.
Troy Wymore
Troy Wymore, Ph.D., is an Assistant Research Scientist and Lecturer in the Chemistry Department at the University of Michigan. He received his B.S. and Ph.D. in Chemistry from the University of Missouri-Columbia. His research leverages molecular phylogenetic analyses and ancestral sequence reconstruction to help frame questions and develop hypotheses directed towards understanding sequence-structure-function relationships. His lab is particularly interested in the impact that residues outside the active site have on the evolution of new enzyme functions and how this information can be leveraged to redesign enzymes for alternative purposes. To test the lab’s hypotheses, atomistic models of enzymes are constructed and often molecular dynamics (MD) simulations are performed first to understand fluctuations in the structure and ligand-binding to an allosteric or active site.
Yaroslava G. Yingling
Yaroslava G. Yingling, Ph.D., is Professor of Materials Science and Engineering at North Carolina State University. She received her University Diploma in Computer Science and Engineering from St. Petersburg State Technical University of Russia and her Ph.D. in Materials Engineering and High Performance Computing from the Pennsylvania State University. She carried out postdoctoral research at Penn State University’s Chemistry Department and at the National Institutes of Health-National Cancer Institute prior to joining North Carolina State University in 2007. Research interests in Prof. Yingling’s group are focused on the development of soft materials informatics tools, advanced computational models, and algorithms for multiscale molecular modeling of soft and biological materials. These tools aim to provide a fundamental understanding of the structure-property relations of a variety of soft materials systems that are formed through the process of self-assembly.
Andrea Hodgson - (Staff Officer)

Events



Location:

Keck Center
500 5th St NW, Washington, DC 20001
Event Type :  
Meeting

Description :   

Meeting to discuss proposals and finalize details on the amount of awards to be given.


Registration for Online Attendance :   
NA

Registration for in Person Attendance :   
NA


If you would like to attend the sessions of this event that are open to the public or need more information please contact

Contact Name:  Steven Moss
Contact Email:  smoss@nas.edu
Contact Phone:  -

Agenda
-
Supporting File(s)
-
Is it a Closed Session Event?
Yes

Publication(s) resulting from the event:

-

Event Type :  
TeleConference

Description :   

Committee call to discuss proposal review template, review timeline, system tutorial, conflict of interest, and meeting logistics.


Registration for Online Attendance :   
NA

Registration for in Person Attendance :   
NA


If you would like to attend the sessions of this event that are open to the public or need more information please contact

Contact Name:  Steven Moss
Contact Email:  smoss@nas.edu
Contact Phone:  -

Agenda
-
Supporting File(s)
-
Is it a Closed Session Event?
Yes

Closed Session Summary Posted After the Event

The following committee members were present at the closed sessions of the event:

Clare McCabe
Eric May
Themis Lazaridis
Brian Dominy
Leonor Saiz
Steven W. Rick
Christopher Rowley
Fatemeh Khalili-Araghi
James C. Gumbart
Juan M. Vanegas
Linda Columbus
Markus Seeliger
James Briggs
Troy Wymore
Vivek Narsimhan

The following topics were discussed in the closed sessions:

The proposal review template, review timeline, system tutorial, conflict of interest, and meeting logistics.

Date of posting of Closed Session Summary:
July 24, 2019
Publication(s) resulting from the event:

-

Publications

Publications

No data present.