SCLab | Publications

Unraveling antibody‐induced mechanical stability of antigen: Insights from single‐molecule studies

Soham Chakraborty, Shivam Pandit, Krishnendu Sinha, Madhu Bhatt, Debojyoti Chowdhury, Suman Chakrabarty, Shubhasis Haldar

Protein Science, 2025

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WeTICA: A directed search weighted ensemble based enhanced sampling method to estimate rare event kinetics in a reduced dimensional space

S Mitra, R Biswas, S Chakrabarty

The Journal of Chemical Physics, 2025

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Mapping conformational landscape in protein folding: Benchmarking dimensionality reduction and clustering techniques on the Trp-Cage mini-protein

S Bhattacharya, S Chakrabarty

Biophysical Chemistry, 2025

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Ion-Pairing Propensity in Guanidinium Salts Dictates Their Protein (De) stabilization Behavior

R Saha, S Chakraborty, K Sinha, P Pyne, S Pal, A Barman, S Chakrabarty, ...

The Journal of Physical Chemistry Letters, 2024

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IceCoder: Identification of Ice phases in molecular simulation using variational autoencoder

D Maity, S Chakrabarty

Journal of Chemical Theory and Computation, 2024

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Molecular Insights into the Conformational and Binding Behaviors of Human Serum Albumin Induced by Surface-Active Ionic Liquids

D Ray, D Chamlagai, S Kumar, S Mukhopadhyay, S Chakrabarty, ...

The Journal of Physical Chemistry B, 2024

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Elucidating the microscopic origin of observed anti-correlation between the protein-protein and protein-water interaction energies

K Sinha, A Kumawat, S Chakrabarty

Chemical Physics Impact 8, 2024

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Leveraging Bidirectional Nature of Allostery To Inhibit Protein–Protein Interactions (PPIs): A Case Study of PCSK9–LDLR Interaction

K Sinha, I Basu, Z Shah, S Shah, S Chakrabarty

Journal of Chemical Information and Modeling, 2024

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Conformational Effects on the Absorption Spectra of Phytochromes

S Santra, RN Manna, S Chakrabarty, D Ghosh

The Journal of Physical Chemistry B, 2024

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Molecular mechanism of regulation of RhoA GTPase by phosphorylation of RhoGDI

K Sinha, A Kumawat, H Jang, R Nussinov, S Chakrabarty

Biophysical Journal, 2024

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Elucidating the molecular mechanism of noncompetitive inhibition of acetylcholinesterase by an antidiabetic drug chlorpropamide: identification of new allosteric sites

A Das, K Sinha, S Chakrabarty

Physical Chemistry Chemical Physics, 2024

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Phosphorylation-Competent Metastable State of Escherichia coli Toxin HipA

B Pandey, K Sinha, A Dev, HK Ganguly, S Polley, S Chakrabarty, G Basu

Biochemistry, 2023

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Molecular Thermodynamic Origin of Substrate Promiscuity in the Enzyme Laccase: Toward a Broad-Spectrum Degrader of Dye Effluents

S Mitra, A Sil, R Biswas, S Chakrabarty

The Journal of Physical Chemistry Letters, 2023

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Design of CO2 Thickeners and Role of Aromatic Rings in Enhanced Oil Recovery Using Molecular Dynamics

KM Tadepalli, S Chakrabarty, P Patil, R Kumar

Langmuir, 2023

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Efficient light harvesting in self-assembled organic luminescent nanotubes

SK Bhaumik, D Maity, I Basu, S Chakrabarty, S Banerjee

Chemical Science, 2023

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Modulation of drug binding ability and augmented enzymatic activity of lysozyme stabilized in presence of surface-active ionic liquids

D Ray, IR Singh, A Bhatta, A Das, S Chakrabarty, S Mitra

Journal of Molecular Liquids, 2022

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Traceless cysteine-linchpin enables precision engineering of lysine in native proteins

NC Reddy, R Molla, PN Joshi, S TK, I Basu, J Kawadkar, N Kalra, ...

Nature Communications, 2022

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Dimer-parity-dependent odd-even effects in photoinduced transitions to cholesteric and twist grain boundary smectic- mesophases: Experiments and simulations

R Sahoo, D Maity, DS Shankar Rao, S Chakrabarty, CV Yelamaggad, ...

Physical Review E, 2022

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Molecular Insight into Dye–Surfactant Interaction at Premicellar Concentrations: A Combined Two-Photon Absorption and Molecular Dynamics Simulation Study

SI Islam, P Pyne, DK Das, S Mukherjee, S Chakrabarty, RK Mitra

Langmuir, 2022

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How Far Is “Bulk Water” from Interfaces? Depends on the Nature of the Surface and What We Measure

VR Hande, S Chakrabarty

The Journal of Physical Chemistry B, 2022

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Size-Dependent Order–Disorder Crossover in Hydrophobic Hydration: Comparison between Spherical Solutes and Linear Alcohols

V Hande, S Chakrabarty

ACS omega, 2022

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Therapeutic opportunities of surface-active ionic liquids: a case study on acetylcholinesterase, citrate synthase and HeLa cell lines

P Baruah, D Ray, I Konthoujam, A Das, S Chakrabarty, K Aguan, S Mitra

New Journal of Chemistry, 2022

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Heterogeneous nucleation in citrate synthesis of AgNPs: Effect of mixing and solvation dynamics

JB Deshpande, S Chakrabarty, AA Kulkarni

Chemical Engineering Journal, 2021

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Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

M Santra, A Seal, K Bhattacharjee, S Chakrabarty

The Journal of Chemical Physics , 2021

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Organoselenium compounds as acetylcholinesterase inhibitors: Evidence and mechanism of mixed inhibition

A Kumawat, S Raheem, F Ali, TA Dar, S Chakrabarty, MA Rizvi

The Journal of Physical Chemistry B, 2021

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Sulfonylurea class of antidiabetic drugs inhibit acetylcholinesterase activity: unexplored auxiliary pharmacological benefit toward Alzheimer’s disease

P Baruah, A Das, D Paul, S Chakrabarty, K Aguan, S Mitra

ACS pharmacology & translational science, 2021

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Morphology and dynamics of self-assembled structures in mixed surfactant systems (SDS+ CAPB) in the context of methane hydrate growth

V Hande, N Choudhary, S Chakrabarty, R Kumar

Journal of Molecular Liquids, 2020

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Macro and Molecular Level Insights on Gas Hydrate Growth in the Presence of Hofmeister Salts

N Choudhary, OS Kushwaha, G Bhattacharjee, S Chakrabarty, R Kumar

Ind. Eng. Chem. Res., 2020

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Hydroxyl Group-Directed Solvation of Excited-State Intramolecular Proton Transfer Probes in Water: A Demonstration from the Fluorescence Anisotropy of Hydroxyflavones

S Das, S Mukherjee, S Chakrabarty, N Chattopadhyay

J. Phys. Chem. A, 2020

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Protonation-induced dynamic allostery in PDZ domain: evidence of perturbation-independent universal response network

A Kumawat, S Chakrabarty

The Journal of Physical Chemistry Letters, 2020

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Support vector regression-based Monte Carlo simulation of flexible water clusters

S Bose, S Chakrabarty, D Ghosh

ACS omega, 2020

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Amino-acid-based ionic liquids for the improvement in stability and activity of cytochrome c: A combined experimental and molecular dynamics study

DK Sahoo, S Jena, KD Tulsiyan, J Dutta, S Chakrabarty, HS Biswal

The Journal of Physical Chemistry B, 2019

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Origin of unusually high fluorescence anisotropy of 3-hydroxyflavone in water: Formation of probe–solvent cage-like cluster

S Das, S Chakrabarty, N Chattopadhyay

The Journal of Physical Chemistry B, 2019

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A comparison of different water models for melting point calculation of methane hydrate using molecular dynamics simulations

N Choudhary, S Chakrabarty, S Roy, R Kumar

Chemical Physics, 2019

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Charge transfer liquid: a stable donor–acceptor interaction in the solvent-free liquid state

VC Wakchaure, LV Pillai, KC Ranjeesh, S Chakrabarty, ...

Chemical Communications, 2019

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Critical assessment of the interaction between DNA and choline amino acid ionic liquids: evidences of multimodal binding and stability enhancement

DK Sahoo, S Jena, J Dutta, S Chakrabarty, HS Biswal

ACS central science, 2018

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Effect of sodium dodecyl sulfate surfactant on methane hydrate formation: a molecular dynamics study

N Choudhary, VR Hande, S Roy, S Chakrabarty, R Kumar

The Journal of Physical Chemistry B, 2018

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Soluble polybenzimidazoles with intrinsic porosity: Synthesis, structure, properties and processability

V Kumar, S Chatterjee, P Sharma, S Chakrabarty, CV Avadhani, ...

Journal of Polymer Science Part A: Polymer Chemistry 56 (10), 1046-1057, 2018

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Molecular View of CO2 Capture by Polyethylenimine: Role of Structural and Dynamical Heterogeneity

P Sharma, S Chakrabarty, S Roy, R Kumar

Langmuir 34 (17), 5138-5148, 2018

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Partially bio‐based poly (amide imide) s by polycondensation of aromatic diacylhydrazides based on lignin‐derived phenolic acids and aromatic dianhydrides: Synthesis …

SS Kuhire, P Sharma, S Chakrabarty, PP Wadgaonkar

Journal of Polymer Science Part A: Polymer Chemistry 55 (21), 3636-3645, 2017

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Hidden electrostatic basis of dynamic allostery in a PDZ domain

A Kumawat, S Chakrabarty

Proceedings of the National Academy of Sciences 114 (29), E5825-E5834, 2017

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Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach

S Bose, S Chakrabarty, D Ghosh

The Journal of Physical Chemistry B 121 (18), 4790-4798, 2017

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Molecular dynamics simulation and experimental study on the growth of methane hydrate in presence of methanol and sodium chloride

N Choudhary, OS Kushwaha, G Bhattacharjee, S Chakrabarty, R Kumar

Energy Procedia 105, 5026-5033, 2017

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Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics

SM Kashid, GY Jin, S Chakrabarty, YS Kim, S Bagchi

The Journal of Physical Chemistry Letters 8 (7), 1604-1609, 2017

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Nucleotide dependent switching in rho GTPase: conformational heterogeneity and competing molecular interactions

A Kumawat, S Chakrabarty, K Kulkarni

Scientific reports 7 (1), 45829, 2017

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Temperature-induced misfolding in prion protein: evidence of multiple partially disordered states stabilized by non-native hydrogen bonds

NG Chamachi, S Chakrabarty

Biochemistry 56 (6), 833-844, 2017

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Mechanism of unfolding of human prion protein

RK Singh, NG Chamachi, S Chakrabarty, A Mukherjee

The Journal of Physical Chemistry B 121 (3), 550-564, 2017

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Effect of the amino acid l-histidine on methane hydrate growth kinetics

G Bhattacharjee, N Choudhary, A Kumar, S Chakrabarty, R Kumar

Journal of Natural Gas Science and Engineering 35, 1453-1462, 2016

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Replica exchange molecular dynamics study of dimerization in prion protein: multiple modes of interaction and stabilization

NG Chamachi, S Chakrabarty

The Journal of Physical Chemistry B 120 (30), 7332-7345, 2016

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Composition dependence of the glass forming ability in binary mixtures: The role of demixing entropy

UK Nandi, A Banerjee, S Chakrabarty, SM Bhattacharyya

The Journal of chemical physics 145 (3), 2016

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Effect of solvation on electron detachment and excitation energies of a green fluorescent protein chromophore variant

S Bose, S Chakrabarty, D Ghosh

The Journal of Physical Chemistry B 120 (19), 4410-4420, 2016

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Correlating nitrile IR frequencies to local electrostatics quantifies noncovalent interactions of peptides and proteins

P Deb, T Haldar, SM Kashid, S Banerjee, S Chakrabarty, S Bagchi

The Journal of Physical Chemistry B 120 (17), 4034-4046, 2016

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Exploration of the presence of bulk-like water in AOT reverse micelles and water-in-oil nanodroplets: the role of charged interfaces, confinement size and properties of water

VR Hande, S Chakrabarty

Physical Chemistry Chemical Physics 18 (31), 21767-21779, 2016

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Structural order of water molecules around hydrophobic solutes: Length-scale dependence and solute–solvent coupling

VR Hande, S Chakrabarty

The Journal of Physical Chemistry B 119 (34), 11346-11357, 2015

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Bioactive Polymersomes Self-Assembled from Amphiphilic PPO-GlycoPolypeptides: Synthesis, Characterization, and Dual-Dye Encapsulation

S Das, DK Sharma, S Chakrabarty, A Chowdhury, S Sen Gupta

Langmuir 31 (11), 3402-3412, 2015

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Modeling gating charge and voltage changes in response to charge separation in membrane proteins

I Kim, S Chakrabarty, P Brzezinski, A Warshel

Proceedings of the National Academy of Sciences 111 (31), 11353-11358, 2014

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Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces

NV Plotnikov, BR Prasad, S Chakrabarty, ZT Chu, A Warshel

The Journal of Physical Chemistry B 117 (42), 12807-12819, 2013

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Interplay between crystallization and glass transition in binary Lennard-Jones mixtures

A Banerjee, S Chakrabarty, SM Bhattacharyya

The Journal of chemical physics 139 (10), 2013

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Capturing the energetics of water insertion in biological systems: The water flooding approach

S Chakrabarty, A Warshel

Proteins: Structure, Function, and Bioinformatics 81 (1), 93-106, 2013

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Realistic simulation of the activation of voltage-gated ion channels

A Dryga, S Chakrabarty, S Vicatos, A Warshel

Proceedings of the National Academy of Sciences 109 (9), 3335-3340, 2012

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Coarse grained model for exploring voltage dependent ion channels

A Dryga, S Chakrabarty, S Vicatos, A Warshel

Biochimica et Biophysica Acta (BBA)-Biomembranes 1818 (2), 303-317, 2012

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Understanding Nucleation Phenomena at Large Metastability: From Gas Liquid to Metastable Solids and Polymers

M Santra, RS Singh, S Chakrabarty, B Bagchi

Nanoparticle Assembly: From Fundamentals to Applications, 15, 2011

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Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects

AL Johansson, S Chakrabarty, CL Berthold, M Högbom, A Warshel, ...

Biochimica et Biophysica Acta (BBA)-Bioenergetics 1807 (9), 1083-1094, 2011

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Anomalous behavior of linear hydrocarbon chains in water–DMSO binary mixture at low DMSO concentration

R Ghosh, S Banerjee, S Chakrabarty, B Bagchi

The Journal of Physical Chemistry B 115 (23), 7612-7620, 2011

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Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects

S Chakrabarty, I Namslauer, P Brzezinski, A Warshel

Biochimica et Biophysica Acta (BBA)-Bioenergetics 1807 (4), 413-426, 2011

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Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

S Chakrabarty, B Bagchi

The Journal of chemical physics 133 (21), 2010

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Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

S Chakrabarty, B Bagchi

The Journal of Physical Chemistry B 113 (25), 8446-8448, 2009

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Gas-liquid nucleation in a two dimensional system

M Santra, S Chakrabarty, B Bagchi

The Journal of chemical physics 129 (23), 2008

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Chakrabarty, Santra, and Bagchi Reply

S Chakrabarty, M Santra, B Bagchi

Physical Review Letters 101 (1), 019602, 2008

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Elucidating the mechanism of nucleation near the gas-liquid spinodal

P Bhimalapuram, S Chakrabarty, B Bagchi

Physical review letters 98 (20), 206104, 2007

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Power law relaxation and glassy dynamics in Lebwohl-Lasher model near the isotropic-nematic phase transition

S Chakrabarty, D Chakrabarti, B Bagchi

Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 73 (6 …, 2006

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Universal power law in the orientational relaxation in thermotropic liquid crystals

D Chakrabarti, PP Jose, S Chakrabarty, B Bagchi

Physical review letters, 2005

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Publications

Publications

Recently published papers

Unraveling antibody‐induced mechanical stability of antigen: Insights from single‐molecule studies

WeTICA: A directed search weighted ensemble based enhanced sampling method to estimate rare event kinetics in a reduced dimensional space

Mapping conformational landscape in protein folding: Benchmarking dimensionality reduction and clustering techniques on the Trp-Cage mini-protein

Ion-Pairing Propensity in Guanidinium Salts Dictates Their Protein (De) stabilization Behavior

IceCoder: Identification of Ice phases in molecular simulation using variational autoencoder

Molecular Insights into the Conformational and Binding Behaviors of Human Serum Albumin Induced by Surface-Active Ionic Liquids

Elucidating the microscopic origin of observed anti-correlation between the protein-protein and protein-water interaction energies

Leveraging Bidirectional Nature of Allostery To Inhibit Protein–Protein Interactions (PPIs): A Case Study of PCSK9–LDLR Interaction

Conformational Effects on the Absorption Spectra of Phytochromes

Molecular mechanism of regulation of RhoA GTPase by phosphorylation of RhoGDI

Elucidating the molecular mechanism of noncompetitive inhibition of acetylcholinesterase by an antidiabetic drug chlorpropamide: identification of new allosteric sites

Phosphorylation-Competent Metastable State of Escherichia coli Toxin HipA

Molecular Thermodynamic Origin of Substrate Promiscuity in the Enzyme Laccase: Toward a Broad-Spectrum Degrader of Dye Effluents

Design of CO2 Thickeners and Role of Aromatic Rings in Enhanced Oil Recovery Using Molecular Dynamics

Efficient light harvesting in self-assembled organic luminescent nanotubes

Modulation of drug binding ability and augmented enzymatic activity of lysozyme stabilized in presence of surface-active ionic liquids

Traceless cysteine-linchpin enables precision engineering of lysine in native proteins

Dimer-parity-dependent odd-even effects in photoinduced transitions to cholesteric and twist grain boundary smectic- mesophases: Experiments and simulations

Molecular Insight into Dye–Surfactant Interaction at Premicellar Concentrations: A Combined Two-Photon Absorption and Molecular Dynamics Simulation Study

How Far Is “Bulk Water” from Interfaces? Depends on the Nature of the Surface and What We Measure

Size-Dependent Order–Disorder Crossover in Hydrophobic Hydration: Comparison between Spherical Solutes and Linear Alcohols

Therapeutic opportunities of surface-active ionic liquids: a case study on acetylcholinesterase, citrate synthase and HeLa cell lines

Heterogeneous nucleation in citrate synthesis of AgNPs: Effect of mixing and solvation dynamics

Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

Organoselenium compounds as acetylcholinesterase inhibitors: Evidence and mechanism of mixed inhibition

Sulfonylurea class of antidiabetic drugs inhibit acetylcholinesterase activity: unexplored auxiliary pharmacological benefit toward Alzheimer’s disease

Morphology and dynamics of self-assembled structures in mixed surfactant systems (SDS+ CAPB) in the context of methane hydrate growth

Macro and Molecular Level Insights on Gas Hydrate Growth in the Presence of Hofmeister Salts

Hydroxyl Group-Directed Solvation of Excited-State Intramolecular Proton Transfer Probes in Water: A Demonstration from the Fluorescence Anisotropy of Hydroxyflavones

Protonation-induced dynamic allostery in PDZ domain: evidence of perturbation-independent universal response network

Support vector regression-based Monte Carlo simulation of flexible water clusters

Amino-acid-based ionic liquids for the improvement in stability and activity of cytochrome c: A combined experimental and molecular dynamics study

Origin of unusually high fluorescence anisotropy of 3-hydroxyflavone in water: Formation of probe–solvent cage-like cluster

A comparison of different water models for melting point calculation of methane hydrate using molecular dynamics simulations

Charge transfer liquid: a stable donor–acceptor interaction in the solvent-free liquid state

Critical assessment of the interaction between DNA and choline amino acid ionic liquids: evidences of multimodal binding and stability enhancement

Effect of sodium dodecyl sulfate surfactant on methane hydrate formation: a molecular dynamics study

Soluble polybenzimidazoles with intrinsic porosity: Synthesis, structure, properties and processability

Molecular View of CO2 Capture by Polyethylenimine: Role of Structural and Dynamical Heterogeneity

Partially bio‐based poly (amide imide) s by polycondensation of aromatic diacylhydrazides based on lignin‐derived phenolic acids and aromatic dianhydrides: Synthesis …

Hidden electrostatic basis of dynamic allostery in a PDZ domain

Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach

Molecular dynamics simulation and experimental study on the growth of methane hydrate in presence of methanol and sodium chloride

Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics

Nucleotide dependent switching in rho GTPase: conformational heterogeneity and competing molecular interactions

Temperature-induced misfolding in prion protein: evidence of multiple partially disordered states stabilized by non-native hydrogen bonds

Mechanism of unfolding of human prion protein

Effect of the amino acid l-histidine on methane hydrate growth kinetics

Replica exchange molecular dynamics study of dimerization in prion protein: multiple modes of interaction and stabilization

Composition dependence of the glass forming ability in binary mixtures: The role of demixing entropy

Effect of solvation on electron detachment and excitation energies of a green fluorescent protein chromophore variant

Correlating nitrile IR frequencies to local electrostatics quantifies noncovalent interactions of peptides and proteins

Exploration of the presence of bulk-like water in AOT reverse micelles and water-in-oil nanodroplets: the role of charged interfaces, confinement size and properties of water

Structural order of water molecules around hydrophobic solutes: Length-scale dependence and solute–solvent coupling

Bioactive Polymersomes Self-Assembled from Amphiphilic PPO-GlycoPolypeptides: Synthesis, Characterization, and Dual-Dye Encapsulation

Modeling gating charge and voltage changes in response to charge separation in membrane proteins

Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces

Interplay between crystallization and glass transition in binary Lennard-Jones mixtures

Capturing the energetics of water insertion in biological systems: The water flooding approach

Realistic simulation of the activation of voltage-gated ion channels

Coarse grained model for exploring voltage dependent ion channels

Understanding Nucleation Phenomena at Large Metastability: From Gas Liquid to Metastable Solids and Polymers

Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects

Anomalous behavior of linear hydrocarbon chains in water–DMSO binary mixture at low DMSO concentration

Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects

Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

Gas-liquid nucleation in a two dimensional system

Chakrabarty, Santra, and Bagchi Reply

Elucidating the mechanism of nucleation near the gas-liquid spinodal

Power law relaxation and glassy dynamics in Lebwohl-Lasher model near the isotropic-nematic phase transition

Universal power law in the orientational relaxation in thermotropic liquid crystals

Under active development