Publications
Recent Publications
Google Scholar Profile

Theoretical insights into the binding interaction of Nirmatrelvir with SARSCoV2 Mpro mutants (C145A and C145S): MD simulations and binding freeenergy calculation to understand drug resistance.
P Purohit, M Panda, JT Muya, P Bandyopadhyay, BR Meher  Journal of Biomolecular Structure and Dynamics, 120, 2023.

Nested Monte Carlo simulation of ionic systems with the primitive model using DebyeHückel (DH) potential as an importance function and optimizing the DH potential with KullbackLeibler divergence minimization.
R Srivastava, P Bandyopadhyay  Journal of Chemical Sciences 135 (2), 51, 2023.

Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein.
Umesh C. Roy and P Bandyopadhyay  The Journal of Chemical Physics, 2023.

Crustwater: Modeling Hydrophobic Solvation.
AK Yadav, P Bandyopadhyay, EA Coutsias, KA Dill  The Journal of Physical Chemistry B, 2022.

Tests of a generalized BarkerHenderson perturbation theory for the phase coexistence diagram of an anisotropic potential.
B Kumari, SK Sarkar, P Bandyopadhyay  Chemical Physics 559, 111533, 2022.

Calcium ion binding to the mutants of calmodulin: a structurebased computational predictive model of binding affinity using a charge scaling approach in molecular dynamics simulation.
A Basit, AK Yadav, P Bandyopadhyay  Journal of Chemical Information and Modeling, 2022.

A strategy to optimize the peptidebased inhibitors against different mutants of the spike protein of SARSCoV2.
P Priya, A Basit, P Bandyopadhyay  Journal of Biomolecular Structure and Dynamics, 2022.

Analytical 2Dimensional Model of Nonpolar and Ionic Solvation in Water.
AK Yadav, P Bandyopadhyay, T Urbic, KA Dill  The Journal of Physical Chemistry B, 2021.

Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics PoissonBoltzmann surface area (MMPBSA) method by incorporating implicit polarization.
A Basit, RK Mishra, P Bandyopadhyay  Journal of Biomolecular Structure and Dynamics, 2021.

Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters.
N Tiwari, RK Mishra, S Gupta, R Srivastava…  Langmuir, 2021.

A look inside the black box: Using graphtheoretical descriptors to interpret a ContinuousFilter Convolutional Neural Network (CFCNN) trained on the global and local minimum energy structures of neutral water clusters.
JA Bilbrey, JP Heindel, M Schram, P Bandyopadhyay…  The Journal of Chemical Physics, 2020.

Calculation of saltdependent free energy of binding of βlactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and threedimensional reference interaction site model (3DRISM): diffuse salt ions and nonpolar interactions between the monomers favor the dimer formation.
R Srivastava, M Chattopadhyaya, P Bandyopadhyay  Physical Chemistry Chemical Physics, 2020.

Optimising the parameters of the Gibbs Ensemble Monte Carlo simulation of phase separation: the role of multiple relaxation times.
B Kumari, P Bandyopadhyay, SK Sarkar  Molecular Simulation, 2020.

Atlas of putative minima and lowlying energy networks of water clusters n = 325.
A Rakshit, P Bandyopadhyay, JP Heindel…  The Journal of chemical physics, 2019

A comparative evaluation of pair correlation functions for a highly asymmetric electrolyte with mono and divalent counterions from integral equation theory in hypernetted chain (HNC) approximation and Monte Carlo simulation.
P Bandyopadhyay, P GuptaBhaya  Chemical Physics Letters, 2019.
Publications topic wise
Calcium Binding Proteins

Calcium ion binding to the mutants of calmodulin: a structurebased computational predictive model of binding affinity using a charge scaling approach in molecular dynamics simulation.
A Basit, AK Yadav, P Bandyopadhyay  Journal of Chemical Information and Modeling, 2022.

Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics PoissonBoltzmann surface area (MMPBSA) method by incorporating implicit polarization.
A Basit, RK Mishra, P Bandyopadhyay  Journal of Biomolecular Structure and Dynamics, 2021.
Solvation Models
DNAion Interactions
Cytoplasm, molecular crowding, diffusion

Microscopic picture of waterethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics.
Atul Kumar Jaiswal, Rakesh Srivastava, Preeti Pandey and Pradipta Bandyopadhyay, PloS one, 13 (11), e0206359 (2018).

An analytical correlated random walk model and its application to understand subdiffusion in crowded environment.
Sabeeha Hasnain and Pradipta Bandyopadhyay, J.Chem.Phys, 143 (11), 114104 (2015).

A New CoarseGrained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion.
Sabeeha Hasnain, Christopher L. McClendon, Monica T. Hsu, Matthew P. Jacobson and Pradipta Bandyopadhyay, PloS one, 9(9), e106466 (2014).

A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA.
Sabeeha Hasnain, Matthew P. Jacobson and Pradipta Bandyopadhyay, Chem. Phys. Lett., 591, 253  258 (2014).
Monte Carlo based optimization and water clusters

A look inside the black box: Using graphtheoretical descriptors to interpret a ContinuousFilter Convolutional Neural Network (CFCNN) trained on the global and local minimum energy structures of neutral water clusters.
JA Bilbrey, JP Heindel, M Schram, P Bandyopadhyay…  The Journal of Chemical Physics, 2020.

Optimising the parameters of the Gibbs Ensemble Monte Carlo simulation of phase separation: the role of multiple relaxation times.
B Kumari, P Bandyopadhyay, SK Sarkar  Molecular Simulation, 2020.

Atlas of putative minima and lowlying energy networks of water clusters n = 325.
A Rakshit, P Bandyopadhyay, JP Heindel…  The Journal of chemical physics, 2019

A comparative evaluation of pair correlation functions for a highly asymmetric electrolyte with mono and divalent counterions from integral equation theory in hypernetted chain (HNC) approximation and Monte Carlo simulation.
P Bandyopadhyay, P GuptaBhaya  Chemical Physics Letters, 2019.

Understanding the structure and hydrogen bonding network of (H_{2}O)_{32} and (H_{2}O)_{33}: an improved Monte Carlo temperature basin paving (MCTBP) method and quantum theory of atoms in molecules (QTAIM) analysis.
Avijit Rakshit, Takamasa Yamaguchi, Toshio Asada and Pradipta Bandyopadhyay, RSC Advances, 7 (30), 1840118417 (2017).

A combination of Monte Carlo Temperature Basin Paving and graph theory: water cluster low energy structures and completeness of search.
Rajan Srivastava, Sudhanshu Shanker, Avijit Rakshit, Lovekesh Vig and Pradipta Bandyopadhyay, J.Chem.Sci., 128(9), 15071516 (2016).

Low energy isomers of (H_{2}O)_{25} from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations.
Nityananda Sahu, Shridhar R. Gadre, Avijit Rakshit, Pradipta Bandyopadhyay, Evangelos Miliordos and Sotiris S. Xantheas, J. Chem. Phys., 141(16), 164304 (2014).

Finding low energy minima of (H_{2}O)_{25} and (H_{2}O)_{30} with temperature basin paving Monte Carlo method with effective fragment potential: New 'global minimum' and graph theoretical characterization of low energy structures.
Avijit Rakshit, Pradipta Bandyopadhyay, Theoretical and Computational Chemistry, 1021, 206214 (2013).

Cooperative Roles of Charge Transfer and Dispersion Terms in HydrogenBonded Networks of (H_{2}O)_{n}, n = 6, 11, and 16.
Suehiro Iwata, Pradipta Bandyopadhyay, and Sotiris S. Xantheas, J.Phys.Chem. A, 2013, 117 (30), 66416651. 141 (2013).

Facilitating Minima Search for Large Water Clusters at MP2 level via Molecular Tailoring.
Jonathan P. Furtado, Anuja P. Rahalkar, Sudhanshu Shanker, Pradipta Bandyopadhyay and Shridhar R. Gadre, J. Phys. Chem. Lett., 3(16), 2253  2258 (2012).

Monte Carlo Temperature Basin Paving with Effective Fragment Potential: An Efficient and Fast Method for Finding Low Energy Structures of Water Clusters (H_{2}O)_{20} and (H_{2}O)_{25}.
Sudhanshu Shanker and Pradipta Bandyopadhyay, J. Phys. Chem. A, 115(42), 1186611875 (2011).

Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H_{2}O)_{20} and (H_{2}O)_{50}.
Pradipta Bandyopadhyay, Chem. Phys. Lett., 487, 133138 (2010).
Enhanced sampling and WangLandau method

Foldingunfolding transition in the miniprotein villin headpiece (HP35): An equilibrium study using the WangLandau algorithm.
Priya Singh, S. K. Sarkar and P. Bandyopadhyay, Chem. Phys., 468, 18 (2016).

WangLandau density of states based study of the foldingunfolding transition in the miniprotein Trpcage (TC5b).
Priya Singh, S. K. Sarkar and P. Bandyopadhyay, J. Chem. Phys., 141(1), 015103 (2014).

Increasing the efficiency of Monte Carlo simulation with sampling from an approximate potential.
Pradipta Bandyopadhyay, Chem. Phys. Lett. 556, 341345 (2013).

Accurate calculation of the Density of states near the ground state energy of the peptides Metenkephalin and (Alanine)5 with the WangLandau method: Lessons learned.
Priya Singh and Pradipta Bandyopadhyay, J. Atom. Mol. Opt. Phys., (2012).

Understanding the applicability and limitations of WangLandau method for biomolecules: Metenkephalin and Trpcage.
Priya Singh, Subir K. Sarkar, Pradipta Bandyopadhyay, Chem. Phys. Lett., 514 (4), 357  361 (2011).

Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H_{2}O)_{20} and (H_{2}O)_{50}.
Pradipta Bandyopadhyay, Chem. Phys. Lett., 487, 133138 (2010).

Two surface Monte Carlo with Basin Hopping: quantum mechanical trajectory and multiple stationary points of water clusters.
Pradipta Bandyopadhyay, J. Chem. Phys., 128(13), 134103 (2008).

Accelerating QM/MM sampling using pure MM potential: the case of effective fragment potential.
Pradipta Bandyopadhyay, Journal of Chemical Physics, 122, 2005 (1st March issue).
RNA

How Mg^{2+} ion and water network affect the stability and structure of nonWatsonCrick base pairs in E. coli Loop E of 5S rRNA: A Molecular Dynamics and Reference Interaction Site Model (RISM) study.
Sudhanshu Shanker and Pradipta Bandyopadhyay, Journal of Biomolecular Structure and Dynamics, 35(10), 21032122 (2016).

Determination of low energy structures of a small RNA hairpin using Monte Carlo based techniques.
Sudhanshu Shanker and Pradipta Bandyopadhyay, J. Biosciences, 37(3), 533  538 (2012).

Monte Carlo Energy Landscape Paving and Basin Paving simulation of RNA Tloop hairpin.
Pradipta Bandyopadhyay, Hungyo Kharerin, Chem. Phys. Lett., 502, 130 (2011).
Application to biological systems

A strategy to optimize the peptidebased inhibitors against different mutants of the spike protein of SARSCoV2.
P Priya, A Basit, P Bandyopadhyay  Journal of Biomolecular Structure and Dynamics, 2022.

Calculation of saltdependent free energy of binding of βlactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and threedimensional reference interaction site model (3DRISM): diffuse salt ions and nonpolar interactions between the monomers favor the dimer formation.
R Srivastava, M Chattopadhyaya, P Bandyopadhyay  Physical Chemistry Chemical Physics, 2020.

Computational approach for molecular design using free energy contribution analysis.
Toshio Asada, Pradipta Bandyopadhyay and Shiro Koseki, AIP Conference Proceedings, 2040(1),020016 (2018).

Free Energy Contribution Analysis Using Response Kernel Approximation: Insights into the Acylation Reaction of a BetaLactamase.
Toshio Asada, Kanta Ando, Pradipta Bandyopadhyay and Shiro Koseki, J. Phys. Chem. B, 120(35), 93389346 (2016).

Molecular dynamics simulations indicate that tyrosineB10 limits motions of distal histidine to regulate CO binding in soybean leghemoglobin.
Smriti Sharma, Amit Kundu, Suman Kundu and Pradipta Bandyopadhyay, Proteins: Structure, Function, and Bioinformatics, 83(10), 18361848 (2015).

Interchain hydrophobic clustering promotes rigidity in HIV1 protease flap dynamics: New insights from Molecular Dynamics.
Biswa Ranjan Meher, Mattaparthi Venkata Satish Kumar and Pradipta Bandyopadhyay, Journal of Biomolecular Structure & Dynamics, 32(6), 899915 (2013).

Conformational Dynamics of HIV1 protease: a comparative molecular dynamics simulation study with multiple amber force fields.
Biswa Ranjan Meher, Mattaparthi Venkata Satish Kumar, Smriti Sharma and Pradipta Bandyopadhyay, Journal of Bioinformatics and Computational Biology, 10(06), 1250018 (2012).

Investigation of the acylation mechanism of class C betalactamase: pKa calculation, Molecular Dynamics simulation and quantum mechanical calculation.
Smriti Sharma and Pradipta Bandyopadhyay, Journal of Molecular Modeling, 18(2), 481  492 (2012).

Molecular Dynamics simulation of HIVprotease with polarizable and nonpolarizable force fields.
B. R. Meher, M. V. Satish Kumar and Pradipta Bandyopadhyay, Indian Journal of Physics, 83, 81 (2009).

Drug resistance of HIV1 Protease against JE2147: I47V mutation investigated by molecular dynamics simulation.
Pradipta Bandyopadhyay and B. R. Meher, Chemical Biology and Drug Design, 67(2), 155161 (2006).
Others

Computational approach for molecular design using free energy contribution analysis.
T Asada, P Bandyopadhyay, S Koseki  AIP Conference Proceedings, 2018.

Comparison of molecular mechanicsPoissonBoltzmann surface area (MMPBSA) and molecular mechanicsthreedimensional reference interaction site model (MM3DRISM) method to calculate the binding free energy of proteinligand complexes: Effect of metal ion and advance statistical test.
P Pandey, R Srivastava, P Bandyopadhyay  Chemical Physics Letters, 2018.

Identification of inhibitors against αIsopropylmalate Synthase of Mycobacterium tuberculosis using dockingMM/PBSA hybrid approach.
Preeti Pandey, Andrew M Lynn, Pradipta Bandyopadhyay, Bioinformation, 13 (5), 144148 (2017).

Computational investigation of kinetics of crosslinking reactions in proteins: importance in structure prediction.
Pradipta Bandyopadhyay, Irwin D. Kuntz, Biopolymers, 91, 68 (2009). *Corresponding author.

Riboswitch detection using profile hidden markov models.
Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, A Krishnamachari, Supratim Sengupta, BMC Bioinformatics, 10(1), 325 (2009).

Partial Acetylation of Lysine Residues Improves IntraProtein Crosslinking.
Xin Gao, Pradipta Bandyopadhyay, Birgit Schilling, Malin M. Young, Naoaki Fujii, Tiba Aynechi, R. Kiplin Guy, Irwin D. Kuntz and Bradford W. Gibson, Analytical Chemistry, 80(4), 951960 (2008).
Selected publications from Ph.D. and Postdoc days

Direct Hydroxide attack is a plausible mechanism for amidase antibody 43C9.
L. T. Chong, P. Bandyopadhyay, T. S. Scanlan, I. D. Kuntz, P. A. Kollman. 24, 1371, 2003. J. Comp. Chem.

An integrated Effective FragmentPolarizable Continuum approach to solvation: Theory and Application to Glycine.
P. Bandyopadhyay, M. S. Gordon, B. Mennucci, J. Tomasi. J. Chem. Phys., 2002, 116, 5023.

The effective fragment potential method: a QMbased MM approach to modeling environmental effects in chemistry.
M. S. Gordon, M. Freitag, P. Bandyopadhyay, J. H. Jensen, V. Kairys and W. J. Stevens. J. Phys. Chem. A (feature article), 2001, 105, 293307.

A combined discrete continuum solvation model: application to glycine.
P. Bandyopadhyay and M. S. Gordon J. Chem. Phys., 2000, 113, 1104.

Ab initio Monte Carlo simulation using multicanonical algorithm: temperature dependence of the average structure of water dimer.
P. Bandyopadhyay, S. Tenno, S. Iwata. Molecular Physics, 1999, 96, 349.