Indian Association for the Cultivation of Science

Name : Avisek Das

Department : School of Chemical Sciences
Designation : Assistant Professor
Contact : +91 33 2473 4971 (Ext:2136)
Email : mcsad@iacs.res.in


Home

We are a theoretical and computational group interested in understanding structure and dynamics of complex systems using methods and ideas rooted in classical statistical mechanics and molecular electronic strucutre. Our research program has an equal emphasis on development of new methods and application of existing/new methods to important problems in chemistry, soft condensed matter physics, molecular biophysics and bioinorganic chemistry. Our current research interests involve the following topics.

Please visit our external group website for details: click here

  • Soft Matter
    • Peptide self-assembly
    • Self-assembly of hard particles
    • Orientational disorders in crystals
    •  
  • Molecular Biophysics / Bioinorganic chemistry
    • Molecular mechanism of cellular copper trafficking
    • Computer simulations of protein-protein interactions
    •  
  • Theoretical Chemistry
    • Improved treatment of solvation in computational studies of chemical reaction mechanisms
    • Rare event simulations on complex systems
    • Development of efficeint sampling and free energy methods for self-assembly problems

 


News

Argha Chakraborty has won the best poster prize at MD@60 conference, jointly organised by CECAM and JNCASR.


Academic Profile

  • Assistant Professor, School of Chemical Sciences, IACS, Kolkata  (August 2019 - present)
  • Faculty Fellow, Center for Mathematical, Computational and Data Science and School of Mathematical and Computational Sciences, IACS, Kolkata (December 2017 - August 2019)
  • Postdoctoral fellow. Department of Chemical Engineering, University of Michigan, Ann Arbor, USA. Advisor: Prof. Sharon Glotzer (January 2017 - December 2017)
  • Postdoctoral fellow. Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, USA. Advisor: Prof. Benoit Roux (2011 - 2016)
  • Graduate student. Department of Chemistry, Stanford University, USA. Advisor: Prof. Hans C. Andersen (2005 - 2011)
  • M. Sc. in Chemistry. Indian Institue of Technology, Kanpur, India (2003 - 2005)
  • B. Sc. in Chemistry. Jadavpur University, Kolkata, India (2000 - 2003)

                             


Group

Soumak Ghosh

Senior Research Fellow
Institute Fellow
M.Sc. Chemistry
IIT Bombay
Molecular Mechanism of Copper Trafficking
cssg2202@iacs.res.in
Rumela Adhikary

Senior Research Fellow
Institute Fellow
M.Sc. Chemistry
University of Calcutta
Molecular Self-assembly
mcsra@iacs.res.in
Sumitava Kundu

Senior Research Fellow
INSPIRE Fellow
M.Sc. Physics
RKMVERI
Phase Transition in Hard Particle Systems
mcssk2@iacs.res.in
Sangeeta Das

Senior Research Fellow
Integrated PhD
M.Sc. Mathematical and Computational Sciences IACS, Kolkata
Rare Event Simulations
intsd@iacs.res.in
Sk Hasibo Hasan

Senior Research Fellow
Institute Fellow
M.Sc. Chemistry IIEST, Shibpur
Mechanisn of Copper Trafficking
cshh2343@iacs.res.in
Kaustav Chakraborty

Senior Research Fellow
Integrated PhD
M.Sc. Physics IACS, Kolkata
Phase Transition in Hard Particle Systems
pskc2187@iacs.res.in
Argha Chakraborty

Junior Research Fellow
Integrated PhD
M.Sc. Chemistry IACS, Kolkata
Molecular Self-assembly
csac2388@iacs.res.in
Snehamay Bagchi

Junior Research Fellow
INSPIRE Fellow
M.Sc. Chemistry IIT, Kharagpur
Peptide Assembly
scssb2852@iacs.res.in


Publication

 
 

     Soumak Ghosh, Sk Hasibo Hassan and Avisek Das*

     The Journal of Physical Chemistry B, 128, 12, 2905-2921  

            

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

     ChemRxiv         

 

      Sumitava Kundu, Kaustav Chakraborty and Avisek Das*

      (Under review)

 

 

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*

 

 

  • 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)

 

 


Teaching

  • Stochastic Simulation Practical (Spring, 2019)
  • Computer Programming and Numerical Analysis Practical (Autumn, 2020, 2022, 2023)
  • Advanced Statistical Mechanics (Spring, 2021,2022,2023,2024)

 


Honors/Awards

  • Ramanujan fellowship. Department of  Science and Technology, Government of India (2017 - 2022)
  • General proficiency medal. Indian Institue of Technology, Kanpur, India (2005)
  • University medal. Jadavpur University, Kolkata, India (2003)
  • KVPY fellowship. Department of  Science and Technology, Government of India (2001 - 2005)

 


Open Positions

PhD positions

Students with M.Sc. degrees in physical chemistry, physics, materials science and chemical engineering and are interested in pursuing a PhD in theoretical/computational chemistry/biophysics or computational soft condensed matter physics can directly contact the PI for open positions. In addition to this, interested students must apply formally to the IACS PhD program in the School of Chemical Sciences. Please check IACS website for the next advertisement. 

Postdoctoral positions

If you are interested in a postdoctoral position in our group, please contact the PI directly. Candidates with PhDs in theoretical/computational chemistry, condensed matter/statistical/computational physics are particularly encouraged to apply. 


Alumni

Project Student Alumni

4. Argha Chakraborty (2021-2022), Current position : IACS, Kolkata (PhD)

3. Archy Triphati (2020), Current position : Ruhr-Universitat Bochum, Germany (PhD)

2. Sangeeta Das (2019), Current position : IACS, Kolkata (PhD)

1. Atreyi Chakraborty (2018), Current position : IISER Pune (PhD)

 

 


Contact Us

Avisek Das

School of Chemical Sciences

Indian Association for the Cultivation of Science

Room C-318/C, Centenary Building

2A & 2B Raja S. C. Mullick Road

Kolkata 700032, India

 

Email: mcsad.AT.iacs.res.in

Phone: +91 33 2473 4971 (Ext. 2136)