Publications


Role of Explicit Eolvation in Computational Modeling of Chemical Reactions: Mechanism of Cu(I) Transfer between Thiolate-based Chelators in Water

Soumak Ghosh†, Sk Hasibo Hassan† and Avisek Das*
Submitted


Correlated Disorder in Entropic Crystals

Sumitava Kundu, Kaustav Chakraborty and Avisek Das*
Submitted


Atomistic Pictures of Self-Assembled Helical Peptide Nanofibers.

Rumela Adhikary and Avisek Das
Journal of Physical Chemistry B, 126, 46, 9476-9492 (2022)


Proton countertransport and coupled gating in the sarcoplasmic reticulum calcium pump.

Huan Rui†, Avisek Das†, Robert Nakamoto and Benoît Roux
Journal of Molecular Biology 430, 5050 (2018)


Conformational transitions and alternating-access mechanism in the sarcoplasmic reticulum calcium pump.

Avisek Das, Huan Rui, Robert Nakamoto and Benoît Roux
Journal of Molecular Biology 429, 647 (2017)


Mechanism of potassium ions uptake by the Na+/K+-ATPase.

Juan Pablo Castillo, Huan Rui, Daniel Basilio, Avisek Das, Benoît Roux, Ramon Latorre, Francisco Bezanilla and Miguel Holmgren
Nature Communications 6, 7622 (2015)


Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.

Avisek Das, Mert Gur†, Mary Hongying Cheng†, Sunhwan Jo, Ivet Bahar and Benoît Roux
PLoS Computational Biology 10, e1003521 (2014)


The multiscale coarse-graining method. X: Improved algorithms for constructing coarse-grained potentials for molecular systems.

Avisek Das†, Lanyuan Lu†, Hans C. Andersen and Gregory A. Voth
Journal of Chemical Physics 136, 194115 (2012)


The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields.

Avisek Das and Hans C. Andersen
Journal of Chemical Physics 136, 194114 (2012)


The multiscale coarse-graining method. V. Isothermal-isobaric ensemble.

Avisek Das and Hans C. Andersen
Journal of Chemical Physics 132, 164106 (2010)


Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining.

Lanyuan Lu, Sergei Izvekov, Avisek Das, Hans C. Andersen, and Gregory A. Voth
Journal of Chemical Theory and Computation 6, 954 (2010)


The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.

W. G. Noid, Jhih-Wei Chu, Gary S. Ayton, Vinod Krishna, Sergei Izvekov, Gregory A. Voth, Avisek Das, and Hans C. Andersenn
Journal of Chemical Physics 128, 244114 (2008)


Keggin Ion Mediated Synthesis of Hydrophobized Pd Nanoparticles for Multifunctional Catalysis.

Saikat Mandal, Avisek Das, Rajendra Srivastava, and Murali Sastry
Langmuir 21, 2408 (2005)