Daipayan Sarkar

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Professional summary: My research interests are in computational biophysics and bioinformatics using principles of thermodynamics (statistical mechanics), programming and applied mathematics. My goals are to understand the relation between structure and function of bio-molecular systems and multiscale biophysical simulations. I like to develop algorithms and write computer code to be used in biophysics and bioinformatics applications.


Research Interests: Free-energy calculations, molecular dynamics flexible fitting (MDFF), protein-protein interactions (protein docking), ab-initio structure prediction and refinement, machine learning.

Selected peer-reviewed publications (in reverse chronological order):

1. John W. Vant*, Daipayan Sarkar*, Chitrak Gupta*, Mrinal Shekhar, Sumit Mittal and Abhishek Singharoy, Molecular Dynamics Flexible Fitting: All you want to know about flexible fitting, Methods in Molecular Biology, Protein Structure Prediction, 4th Ed - in press, 2019 (role: equal contribution) 

 
2. Eric Wilson, John W. Vant, Jacob Layton, Ryan Boyd, Hyungro Lee, Matteo Turilli, Benjamin Hernandez, Sean Wilkinson, Shantenu Jha, Chitrak Gupta, Daipayan Sarkar and Abhishek Singharoy, All You Want to Know About Large System Simulations, Methods in Molecular Biology -submitted, 2019 (role: corresponding author)
 
3. Daipayan Sarkar*, Peiyuan Kang*, Steven O. Nielsen, Zhenpeng Qin, Non-Arrhenius Reaction-Diffusion Kinetics for Protein Unfolding over a Large Temperature Range, ACS Nano, 2019, 13, 8, 8669-8679. 
 
4. Mrinal Shekhar, Genki Terashi, Chitrak Gupta, Gaspard Debussche, Nicholas J. Sisco, Jonathan Nguyen, James Zook, John Vant, Daipayan Sarkar, Petra Fromme, Wade D. Van Horn, Ken Dill, Daisuke Kihara, Emad Tajkhor- shid, Alberto Perez, Abhishek Singharoy, CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics, bioRxiv 687087; doi: https://doi.org/10.1101/687087 
 

 

 

Selected invited talks and presentations (in reverse chronological order):
 
1. Daipayan Sarkar, Robert D. Skeel and Abhishek Singharoy, String like simulations outside the friction dominated regime, 4th NAMD Developers Meeting, Beckman Institute, University of Illinois Urbana-Champaign, Champaign, IL, 2019.
 
2. John W. Vant, Daipayan Sarkar, Robert D. Skeel and Abhishek Singharoy, MDFF Error Analysis, 4th NAMD Developers Meeting, Beckman Institute, University of Illinois Urbana-Champaign, Champaign, IL, 2019.
 
3. Daipayan Sarkar, Peiyuan Kang, Zhenpeng Qin, Examining Arrhenius Kinetics over a Large Temperature Range, Summer Biomechanics, Bioengineering, and Biotransport (SB3C) Conference, June 2019, Seven Springs, Pennsylvania, USA - Invited talk for John Pearce 70th Birthday. 
 
4. Daipayan Sarkar, John W. Vant, Mrinal Shekhar, Jane. S. Richardson, Robert D. Skeel, Abhishek Singharoy, MDFF Error Analysis: A Tool for Determining Stereochemical and Thermodynamic Correct Structures, Biophysical Journal, 116, 3, supp. 1, 140A-141A (694-Pos) Annual Biophysical Society Meeting 2019, Baltimore, MD. 
 
Notable awards: 
1. Summer Research Fellow, Dept. of Mechanical Engineering, Indian Institute of Science, Bengauru.
2. Doctoral Dissertation Fellowship, College of Engineering, The University of Texas at Arlington.