1. F. Mahto, I. Hamid and S. Bhattacharya, “Molecular dynamics study of monomeric chorismate mutase shows large reduction in conformational diversity of loops upon binding of the transition state analog”, J.Mol. Graphics and Model 138, 109059 (2025) . https://doi.org/10.1016/j.jmgm.2025.109059
2. G. Thapa, A. Bhattacharya and S. Bhattacharya, "Dynamics of AKAP/Calmodulin complex is largely driven by ionic occupancy state.", J.Mol. Graphics and Model, 134, 108904 (2025), doi:https://www.sciencedirect.com/science/article/pii/S1093326324002043
3. N. Fazeel, A. Chatterjee and S. Bhattacharya, "Quantifying Disorder in a Protein by Mapping its Locally Correlated Structure and Kinetics", J. Phys. Chem. B, 128 (5), 1179-1187, (2024). doi:https://doi.org/10.1021/acs.jpcb.3c06251
4. G. Thapa, A. Bhattacharya and S. Bhattacharya, "Molecular dynamics investigation of DNA fragments bound to the anti-HIV protein SAMHD1 reveals alterations in allosteric communications ". J.Mol. Graphics and Model (2024). https://doi.org/10.1016/j.jmgm.2024.108748
5. F. Mahto, A. Bhattacharya and S. Bhattacharya,"Molecular dynamics simulations shows real-time lid opening in Hsp70 chaperone" ,129, 108726 J.Mol. Graphics and Model (2024), https://doi.org/10.1016/j.jmgm.2024.108726
6. V. Saravanan, I. Ahammed, A. Bhattacharya and S. Bhattacharya, “Uncovering allostery and regulation in SORCIN through molecular dynamics simulations”, J. Biomol Struct Dyn, 26,1-14, (2023). DOI: 10.1080/07391102.2023.2202772
7. F. K. Mahto, A. Bhattacharya and S. Bhattacharya, “Molecular Dynamics Simulations suggest novel allosteric modes in the Hsp70 chaperone protein ”, J. Biomol Struct Dyn. (2023)
8. G. Thapa, A. Bhattacharya and S. Bhattacharya, “Dimeric hold-states of anti-HIV-1 protein SAMHD1 are redox tunable.”, J Chem Inf Model. 60(12), 6377-6391,(2020). doi: 10.1021/acs.jcim.0c00629, (2020).
9. S. Bhattacharya and A. Chatterjee.”Uncertainty Quantification in Markov State Models constructed using rare events acceleration techniques”, J. Chem. Phys, 150, 044106 (2019).
10. S. Ghosh, A. Chatterjee and S. Bhattacharya,” Accelerated construction of kinetic network model of biomolecules using steered molecular dynamics”, J. Chem Theory Comput., 14, 5393-5405 (2018).
11. K.K. Patra, A. Bhattacharya and S. Bhattacharya. “Allosteric Signal transduction in HIV-1 Restriction Factor SAMHD1 proceeds via Reciprocal Handshake Across Monomers”, J. Chem. Inf. Modeling, 57(10), 2523-2538, (2017).
12. A. Bhoutekar, S. Ghosh, S. Bhattacharya, and A. Chatterjee, “ A New Class of Enhanced Kinetic Sampling Methods for Building Markov State Models”, J. Chem. Phys, 147, 152702 (2017) DOI: 10.1063/1.4984932
13. K.K. Patra, A. Bhattacharya and S. Bhattacharya. “Uncovering allostery and regulation in SAMHD1 through molecular dynamics simulations”. Proteins: Structure, Function and Bioinformatics, 85(7), 1266-1275 (2017). This was the cover article for the journal. https://doi.org/10.1002/prot.25287
14. S. Ghosh, A. Chatterjee and S. Bhattacharya, “Time Dependent Markov State Models for Single Molecule Force Spectroscopy”, J. Chem Theory Comput., 13, 957-962 (2017).
15. S. Bhattacharya, J. Yoo and A. Aksimentiev. “Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore”. ACS Nano, 10(4), 4644-4651, (2016).
16. A. Chatterjee and S. Bhattacharya. “Uncertainty in a Markov State model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics” J. Chem. Phys. 143, 114109 (2015).
17. K. K. Patra, A. Bhattacharya and S. Bhattacharya. “Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations” J. Phys.: Conf. Ser. 759 012026 (2016).
18. A. Chatterjee and S. Bhattacharya. “Probing the energy landscape of alanine dipeptide and deca-alanine using temperature as a tunable parameter” J. Phys.: Conf. Ser. 759 012024 (2016).
1. C. Maffeo, S. Bhattacharya, J. Yoo and A. Aksimentiev. “ Modeling and Simulations of Ion Channels”. Chemical Reviews 112 (12) 6250-6284 (2012). DOI: 10.1021/cr3002609
2. S. Bhattacharya, I. Derrington, M. Pavlenok, M. Niederweis, J. Gundlach and A. Aksimentiev. “Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence” ACS Nano. 6(8) 6969-6968 (2012). DOI: 10.1021/nn3019943
3. M. Wanunu, S. Bhattacharya, Y. Xie, Y.Tor, A. Aksimentiev and M. Drndic. “Nanopore analysis of individual RNA/antibiotic complexes.” ACS Nano, 5(12), 9345, (2011). DOI: 10.1021/nn203764j Highlighted in Chemical and Engineering News. http://cen.acs.org/articles/89/i47/Nanopores-Analyze-RNA-Drug-Complexes.html
4. S. Bhattacharya, J. Muzard, L. Payet, U. Bockelman, A. Aksimentiev, and V. Viasnoff. “Rectification of the current in α-hemolysin pore depends on the cation type: The alkali series probed by molecular dynamics simulations and experiments”. J. Phys. Chem C. 115 (10) 4255-4264 (2011). DOI: 10.1021/jp111441p
5. A. Milchev, V. Rostiashvili, S. Bhattacharya, T. Vilgis. “Polymer desorption under pulling a 1st - order phase transition without phase coexistence” Physics Procedia 3 (3) 1459-1474 (2010). DOI :10.1016/j.phpro.2010.01.207
6. S. Bhattacharya, V.G. Rostiashvili, A. Milchev, A. and T.A. Vilgis. “Force induced desorption of a polymer chain adsorbed on an attractive surface: Theory and Computer Experiment”. Macromolecules, 42 (6) 2236 (2009). DOI: 10.1021/ma8024392
7. S. Bhattacharya, V.G. Rostiashvili, A. Milchev, A. and T.A. Vilgis. “Polymer desorption under pulling: A dichotomic phase transition”. Phys. Rev. E 79 (3) 030802 (2009). DOI: http://dx.doi.org/10.1103/PhysRevE.79.030802
8. S. Bhattacharya, A. Milchev, V.G. Rostiashvili, A. and T.A. Vilgis. “Pulling an adsorbed polymer chain off a solid surface”. Eur. Phys. J. E 29 (3) 285-297 (2009). DOI: 10.1140/epje/i2009-10492-8
9. S. Bhattacharya, A. Y. Grosberg, A. Milchev, V.G. Rostiashvili, and T.A. Vilgis “Adsorption kinetics of a single polymer on a solid plane”. Phys. Rev. E. 77 (6) 061603 (2008). DOI: http://dx.doi.org/10.1103/PhysRevE.77.061603
10. S. Bhattacharya, H.-P. Hsu, A. Milchev, V.G. Rostiashvili, and T.A. Vilgis. “Adsorption of Multiblock and Random Copolymer on a Solid Surface: Critical Behaviour and Phase Diagram”. Macromolecules 41 (8) 2920-2930 (2008). DOI: 10.1021/ma702608j
11. S. Bhattacharya “Galerkin model for Turing patterns on a sphere” Phys. Rev. E, 72 (3) 036208 (2005). DOI: http://dx.doi.org/10.1103/PhysRevE.72.036208
12. S. Bhattacharya and J. K. Bhattacherjee. “Pattern Formation in Convection and Reaction Diffusion Systems” Proc. Indian Natn. Sci. Acad. Part A 71 (1-2) 1-16 (2005)
Book Chapters
1. A. Milchev, V. Rostiashvili, S. Bhattacharya, T. Vilgis. “Polymer chain adsorption on a solid surface: Scaling arguments and computer simulations” Springer Series in Surface Sciences 47 (1) 185-204 (2011).
2. D. B. Wells, S. Bhattacharya, R. C. Carr, C. Maffeo , A. Ho, J. Comer and A.
Aksimentiev, “Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores.” Nanopore-based technology: single molecule characterization and DNA sequencing. Springer Protocols: Methods in Molecular Biology, 870 165 (2012).