Publications

• Role of explicit solvation 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*

          (Under review)     

• Correlated disorder in entropic crystals

          Sumitava Kundu, Kaustav Chakraborty and Avisek Das*

          (Under review)

• Atomistic pictures of self-assembled helical peptide nanofibers

  Rumela Adhikary and Avisek Das*

  The Journal of Physical Chemistry B 126, 9476 (2022)

Manuscripts under preparation

• Predictive orientational phase behaviors in entropic crystals

          Sumitava Kundu and Avisek Das*

• Phase behaviors of a family of hard sheared cubes

          Kaustav Chakraborty, Sumitava Kundu and Avisek Das*

• Event Tracking: A systematic approach to analyze complex nucleation and growth phenomena in dynamical simulations of self-assembly processes

          Argha Chakraborty†, Sangeeta Das†, Rumela Adhikary† and Avisek Das*

• How small changes in molecular structure influence structure and mechanism of spontaneous self-assembly?: Insights from fully atomistic molecular dynamics simulations via clustering in multidimensional order parameter space

          Sangeeta Das†, Rumela Adhikary†, Argha Chakraborty and Avisek Das*

• Crucial role of solvation in hierarchical mechanism of self-assembled helical peptide nanofiber formation

          Rumela Adhikary, Argha Chakraborty†, Sangeeta Das† and Avisek Das*

• Heuristic algorithms for detecting crystal class and unit cell information from computer simulation data

          Sumitava Kundu, Kaustav Chakraborty and Avisek Das*

• Self-assembly of hard convex spheropolyhedra I: Crystalline assembled states of underlying sharp polyhedra

          Sumitava Kundu, Kaustav Chakraborty and Avisek Das*

Publications before joining IACS

• Proton contertransport 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 po- tentials 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. VIII. Multiresolution hierarchical basis functions and basis function selection in the construction of coarse-grained force fields.

  Avisek Das and Hans C. Andersen

  Journal of Chemical Physics 136, 194113 (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. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation.

  Avisek Das and Hans C. Andersen

  Journal of Chemical Physics 131, 034102 (2009)

• 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. Andersen

  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)