Barry Isralewitz
Personal Data
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I work in the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. I received my Ph. D. in Biophysics, here at the University of Illinois, in 2007.
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Current Research Projects
I work in the Theoretical and Computational Biophysics Group at the Beckman Institute. My areas of research include:
Steered Molecular Dynamics (SMD), including simulations of bacteriorhodopsin, titin, and ATP synthase.
Molecular dynamics analysis tools, including methods for interactive visualization of trajectory information.
software for visualization and analysis of neuronal circuit models
Selected Publications
Suresh Marru, Marlon Pierce, Beth Plale, Sudhakar Pamidighantam, Dimuthu Wannipurage, Marcus Christie, Isuru Ranawaka, Eroma Abeysinghe, Rob Quick, Emad Tajkhorshid, Seid Koric, Jim Basney, Mariano Spivak, Barry Isralewitz, Rafael Bernardi, Diego Gomes, Giri Krishnan, Maxim Bazhenov, Shava Smallen, Amit Majumdar, Anton Arkhipov, Kael Dai, Xiao-Ping Liu, and Kenneth Yoshimoto. "Cybershuttle: An End-to-End Cyberinfrastructure Continuum to Accelerate Discovery in Science and Engineering" in PEARC '23: Practice and Experience in Advanced Research Computing, 26 - 34 (2023).
DOI
David J. Hardy, John E. Stone, Barry Isralewitz, and Emad Tajkhorshid. "Lessons learned from responsive molecular dynamics studies of the COVID-19 virus", in IEEE/ACM HPC for Urgent Decision Making 2021. IEEE, 2021.
Melih Sener, Stuart Levy, John E. Stone, AJ Christensen, Barry Isralewitz, Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida Luthey-Schulten, and Donna Cox. "Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales." Parallel Computing, 102 (2021): 102698.
Abhishek Singharoy, Christopher Maffeo, Karelia Delgardo-Magnero, David J.K. Swainsbury, Melih Sener, Ulrich Kleinekathöfer, Barry Isralewitz, Ivan Teo, Danielle Chandler, John Stone, James Phillips, Taras Pogorelov, M. Ilaria Mallus, Christophe Chipot, Zaida Luthey-Schulten, D. Peter Tieleman, C. Neil Hunter, Emad Tajkhorshid, Aleksei Aksimentiev, and Klaus Schulten. "Atoms to phenotypes: Molecular design principles of cellular energy metabolism" Cell, 179:1098-1111, 2019.
John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, João V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. "Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing" J. Parallel Computing, 55:17-27, 2016. (full text)
John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten. "GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting", 2014, Faraday Discussions, vol. 169, 265-283.
John E. Stone, Barry Isralewitz, and Klaus Schulten.
"Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters", in Extreme Scaling Workshop (XSW) 2013, 43-50, 2013.
Ulrich Kleinekathöfer, Barry Isralewitz, Markus Dittrich, and Klaus Schulten. "Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations.", 2011, Journal of Physical Chemistry A, vol. 115 (25), 7267-7274. (abstract)
John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten. "GPU algorithms for molecular modeling." In Jack Dongarra, David A. Bader, and Jakub Kurzak, editors, Scientific Computing with Multicore and Accelerators, chapter 16, 351-371. Chapman & Hall/CRC Press, 2011. (abstract)
Emad Tajkhorshid, Aleksei Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. "Large scale simulation of protein mechanics and function.", 2003, Advances in Protein Chemistry, vol. 66, 195-247.
(abstract) (PDF pre-print)
Barry Isralewitz, Mu Gao, and Klaus Schulten. "Steered molecular dynamics and mechanical functions of proteins.", 2001, Current Opinion in Structural Biology, vol. 11, 224-230. (abstract) (PDF)
Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. "Steered molecular dynamics investigations of protein function", 2001, Journal of Molecular Graphics and Modeling, vol.19, 13-25 ; also in Protein Flexibility and Folding , L. A. Kuhn and M. F. Thorpe, editors , Biological Modeling Series , Elsevier, New York, NY 2001. (abstract) (PDF)
H. Lu, A. Krammer, B. Isralewitz, V. Vogel, and K. Schulten,
"Computer modeling of force-induced titin domain unfolding".
In Jerry Pollack and Henk Granzier, editors. Elastic Filaments of
the Cell, chapter 1. Kluwer Academic/Plenum Publishers, New York, NY,
2000.
(abstract)
(PDF pre-print)
A. Krammer, H. Lu, B. Isralewitz, K. Schulten,
and V. Vogel, "Forced unfolding of the fibronectin type III module
reveals a tensile molecular recognition switch", 1999, Proceedings
of the National Academy of Science, USA, vol. 96, 1351-1356.
(abstract)
(PDF)
H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten,"Unfolding of Titin Immunoglobulin Domains by Steered Molecular Dynamics", 1998,
Biophysical Journal, vol. 75, 662-671
(abstract)
(PDF)
S. Izrailev, S. Stepaniants, B. Isralewitz, D. Kosztin,
H. Lu, F. Molnar, W. Wriggers, K. Schulten,
"Steered molecular dynamics",
In P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, R. D. Skeel,
and S. Reich, editors.
Computational Molecular Dynamics: Challenges, Methods, Ideas
Springer-Verlag, 1999.
(abstract)
(PDF)
B. Isralewitz, S. Izrailev and K. Schulten, "Binding
pathway of retinal to bacterio-opsin: a prediction by
molecular dynamics simulations", 1997,
Biophysical Journal, vol. 73, 2972-2979.
(abstract)
(PDF)
B. Isralewitz and Shalloway, D., Computer assisted recombinant DNA design and analysis with MATILDA. In Microcomputers in
Biochemistry: A Practical Approach. C.F.A. Bryce, ed., IRL Press, Oxford, 1992, 159-188.
Feel free to mail me any time.
