Welcome
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Objective
Computational biology and simulations can lead the sciences to decipher the elemental processes and help alleviate human suffering. The methods developed in our lab allow for the precise prediction of how chemical reactions in enzymes and solutions can lead to more efficient chemical processes and the development of new and effective drugs.
"As one of the pioneers of using computer simulations for complex molecular systems, I learned since the late 60s to use very limited resources to capture the main physics of biological systems, without consuming enormous computer power." Arieh Warshel.
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Method
Professor Warshel and his research team leverage their knowledge of chemistry, biology and computer science to simulate biological systems to better understand their structure and function. This methodology has pioneered highly effective models for computer simulations of biological molecules, chemical reactions, and interactive drug therapies.
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Evaluation
The Warshel research group operates 38 dedicated compute nodes on The University of Southern California HPC, all based on Intel CPU architecture and capable of achieving a benchmark of 12.2 trillion floating-point calculations per second. Our lab operates 5 home-based dedicated compute servers (also based on Intel CPU architecture) that can add another 5.18 trillion floating-point calculations per second to the total compute capacity available to group's members.
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HONORS & DISTINCTIONS
Dr. Dibyendu Mondal, PhD
RESEARCH ASSISTANT EDUCATION PhD , University of Southern California, June 2020 MS , Indian Institute of Technology, India, 2015 BS , University of Calcutta, India, 2013 Warshel Group member recipient of The 2020 Kenneth Nobutoshi Wachi Award
The USC Department of Chemistry today awarded The 2020 Kenneth Nobutoshi Wachi Award to Mr. Dibyendu Mondal, in recognition of his outstanding graduate research and excellent service. Mr. Mondal, who will recieve his PhD this July, was nominated for the Award based on his paper EF-Tu and EF-G are activated by allosteric effects, D. Mondal and A. Warshel, Proc. Natl.Acad. Sci. USA, 115, 3386-91 (2018).
Dibyendu is a 4th year graduate student in the Warshel Group. Dr. Arieh Warshel stated that, in Dibyendu's first year, he progressed rapidly and mastered various simulation approaches including EVB and water flooding methods as well as our binding calculations. He took on several challenging projects including comparing EF-Tu and EF-G clarifying the allosteric activation of these systems and also contributed greatly to a study of drug resistance as well as studies of drug resistance the Hepatitis C virus Protease. He also conducted a very systematic study of the ability of alchemical FEP calculations in obtaining converging binding free energies of a series of thrombin ligands. Most impressively, he designed a combinatorial approach of protein side chain conformation analysis and activation free energy calculation to understand the molecular basis of protein design and performed in-silico directed evolution which has just been published in ACS Catalysis. In parallel he studied the activation pathway and selective coupling of Gi (inhibitory G-protein) by μ-opioid receptor (GPCR) from an energy-based picture, using homology modelling and Coarse-Grained based free energy calculations.
The EF-Tu PNAS paper is one excellent example of Dibyendu’s outstanding work. In fact, it is perhaps the most authoritative paper on the role of elongation factor on the activation of the ribosome. This paper’s influence on the field of ribosome activation is clearly deserving of The Kenneth Nobutoshi Wachi Award.
Congratulations Dibyendu!
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