Seminar in Chemistry: Molecular Modeling and Simulation of Complex Systems: From Biology to Materials

Seminar Title : Molecular Modeling and Simulation of Complex Systems: From Biology to Materials

Speaker : Dr. Sudip Chakraborty (Post Doctoral Research Associate at Colorado State University, Colorado, USA)

Venue : L3

Date & Time : 12 September, 2012: 3.00 pm - 4:00 pm

Abstract:

Molecular Modeling and Simulation of Complex Systems: From Biology to Materials

Sudip Chakraborty

The goal of my presentation is to provide a brief overview of computer simulation techniques and its use to tackle computationally challenging problems in chemistry /biology, with special emphasis on protein hydration, role of water in the protein folding/unfolding process, biomembrane, drug modeling, surfactant aggregation, and ionic liquids. In the first part of my presentation, I will present my research work based on two main objectives. The first objective is to explore in detail the dynamical coupling that exists between a protein and its hydration layer water (biological water) by performing atomistic Molecular Dynamics (MD) simulations of an aqueous solution of a small 36-residue globular protein (HP-36). Attempts are also made to understand the correlation between the unfolding of a protein molecule and the dynamics of water around it. The second objective involves investigating the microscopic properties of self- assembled surfactant monolayers (Langmuir films) adsorbed at the air/water interface by using MD simulation techniques. The structure and dynamics of the adsorbed monolayer films as well as that of the interfacial water molecules are investigated in detail at an atomic level resolution. In the second part of my presentation, I will present another important work based on the topic “a many-body polarizable force field development for ionic liquids”, a potential solvent for the pretreatment of lignocellulosic biomass. The description of the electrostatic interactions for this model requires a contribution from polarizable atomic multipole. The multipole moments up through the quadrupole are assigned on each atomic center, based on a Distributed Multipole Analysis (DMA) derived from large basic set molecular orbital calculations on small molecules and relevant molecular fragments. The vdW parameters of the hydrogen atoms on the heterocyclic ring are adjusted to agree with the ab initio optimized geometries of isolated ion pairs. Classical MD simulations are performed for a wide range of temperatures to validate our many- body polarizable force field. The liquid density, heat of vaporization, and ion self- diffusion coefficient are found in a good agreement with available experimental data. Finally, I will conclude my presentation with my future research plans and an invitation for any queries or any valuable suggestions.