We are a theoretical and computational group interested in understanding structure and dynamics of complex systems using classical statistical mechanics and electronic structure methods. Our research program has an equal emphasis on development of new simulation methods and application of existing/new methods to important problems in chemistry, molecular biophysics, bioinorganic chemistry and soft matter systems.
Our study employs MD simulations to investigate how peptide sequences and external factors influence assembly, leading to diverse nanostructures.
Understanding the orientational behavior of particles in the self-assembled crystal of hard polyhedra and correlation of shape attributes with the thermodynamic phases.
Understanding molecular mechanism of biological copper trafficking. We study the copper ion transfer mechanism between a pair proteins and the role of protein motions on the preorganization of the reaction center as well as second sphere effect on the electronic rearrangement accompanying the chemical reaction.
The primary objective is to venture new enhanced rare event sampling approaches to handle the complex hierarchical assembly to understand microscopic pictures and morphological arrangements of different interactions in the self-assembly process and endeavor the emergent phenomena from rare fluctuations.
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*
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*
Phase behaviors of a family of hard sheared cubes Kaustav Chakraborty, Sumitava Kundu 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*
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)
We are looking for PhD students with background in chemistry, physics, materials science and chemical engineering for our research projects in soft matter science. The work will involve understanding mechanisms of complex molecular and colloidal self-assemblies, phase transitions in colloidal systems and development of novel algorithms. Please send me an email with your CV research interests. Candidates must have their own fellowship through CSIR/UGC NET, DST-INSPIRE
If you are interested in a postdoctoral positions in our group please contact me directly. Candidates with backgrounds in theoretical/computational chemistry, condensed matter/statistical/computational physics are particularly encouraged to apply.