Seminar


Department of Chemistry
Indian Institute of Technology Delhi

Molecular Dynamics Simulations under Realistic Conditions - A Constant Chemical Potential and Enhanced Sampling Approach


Dr. Tarak Karmakar

Department of Chemistry and Applied Biosciences, ETH Zurich

Institute of Computational Science, Switzerland

Date: February 12th 2020 (Wednesday)
Time: 4:00 PM
Venue: Committee Room (MS710), Department of Chemistry, IIT Delhi

Abstract: Computer simulations have shown prowess to provide atomistic details of many complex physical and biological processes, however, they are stymied by two significant limitations; the short time scale accessible by the regular simulations which is often not sufficient to sample slow transitions, and the finite-size effects that arise due to the small system size. While the first one has been circumvented by several enhanced sampling methods, the second has received much less attention. In my presentation, I will discuss both of these aspects in the context of simulations of crystallization from solution. During crystallization, the solute molecules are continuously extracted from the solution to the solid phase. This leads to the solution depletion, and the finite-size system thus fails to maintain a steady thermodynamic driving force for further growth of the crystal. We have developed a method, constant chemical potential molecular dynamics (CμMD), in which the solution concentration in the vicinity of a growing crystal surface or a nucleus is maintained at a constant value throughout the simulation time mimicking realistic experiments. This method is not only effective in crystallization simulations but can also be applied in the study of the molecular separation, gas adsorption, and self-assembly processes. In the last part, I will discuss some of the latest enhanced sampling methods that we utilize to explore the phase diagram of molecular systems and calculate free energy associated with the first-order phase transitions. The CμMD method in combination with several enhanced sampling and multiscale simulation techniques provides a solid platform to study complex processes.

    References:
  1. T. Karmakar, P. M. Piaggi, C. Perego, and M. Parrinello, J. Chem. Theory Comput. 2018, 14, 2678–2683
  2. D. Han, T. Karmakar, Z. Bjelobrk, J. Gong, and M. Parrinello, Chem. Eng. Sci . 2019, 204, 320–328
  3. Z. Bjelobrk, P. M. Piaggi, T. Weber, T. Karmakar, M. Mazzotti, and M. Parrinello, CrystEngComm , 2019, 21, 3280-3288
  4. T. Karmakar, P. M. Piaggi, and M. Parrinello, J. Chem. Theory Comput. 2019, 15, 6923-6930

    All are cordially invited to attend.
    Convener (Seminar)