Master's Thesis Projects

Capturing Intra-molecular Vibrational Energy Flow

Vibrational energy flow dictates the reactivity of a molecule. Despite great progress in this area, most available methods operate on model Hamiltonians, restricting the pathways for energy transfer. We propose a computational method (extending the work of Srihari Keshavamurthy), that can track vibrational energy flow from full-dimensional on-the-fly trajectory simulations. We use this method to understand non-statistical dynamics of guanidine isomerization and thermal deazetization reactions.

Methanol Photodissociation Dynamics

We modelled a unified picture of methanol photo-dissociation. The photo-dissociation pathways were mapped using multi-reference methods (CASSCF and CASPT2) and the excited-state dynamics was investigated using trajectory surface hopping algorithm.

Undergraduate Research Projects

1. Enhanced Sampling Protein-Surface Complexes

Rational design of protein-surface complexes has received considerable attention since their use in biomedical applications. However, one needs to know what all conformations a protein can attain in contact with the surface to prevent forming disease-causing forms!! In this project with Prof. Sapna Sarupria (UMN), we extended the molecular enhanced sampling with autoencoders (MESA) algorithm, proposed by Andrew Ferguson and coworkers to do a exhaustive sampling of the conformational landscape of peptide-surface complexes and tested it on a trp-cage protein on graphene surface.

Science, 338(6110), 1042-1046 (2012)

2. vdW-corrected PB Theory of Electrical Double Layers

Electrical double layers (EDLs) arise when an electrolyte is in contact with a charged surface, and can be found in batteries and many more devices!! Over the last century, the development of Poisson-Boltzmann (PB) models have provided significant physical insight into the EDL structure and dynamics. However, a prominent knowledge gap has been the exclusion of van der Waals (vdW) interactions, which brings in the chemical specificity. With Prof. Ananth Govind Rajan (IISc Bengaluru), we developed an analytical extension to Gupta-Stone PB theory with the vdW interactions treated using Lennard-Jones potential.

ADF-STEM images from Warner Group, UT Austin 

3. Atomistic Modelling of Defects on 2D Materials

Defects are ubiquitous in nanomaterials, yet their role in modulating fluid flow is not well understood and often ignored in computational modelling. In this project, we developed a self-consistent protocol to model vacancy defects on 2D materials that involve transferring plane-wave density to partial charges. Combining this with classical MD simulations, the effect of defect composition and concentration on the structure and dynamics of interfacial fluid was studied at the hexagonal boron nitride (hBN)-water interface.

4. Molecular Basis of Membrane Domain Registration

Biological membrane is a complex self-assembly of lipids, sterols and proteins organized as a fluid bilayer of two closely stacked lipid leaflets. Differential molecular interactions among its constituents give rise to heterogeneities in the membrane lateral organization. Under certain conditions, heterogeneities in the two leaflets can be spatially synchronised and exist as registered domains across the bilayer. With Prof. Anand Srivastava (IISc Bengaluru), we developed an analytical theory to elucidate the driving forces that create and maintain domain registry across leaflets. A workflow was also developed to parametrize artificial lipid molecules for all-atom simulations.

Nat. Rev. Mol. Cell Biol, 18, 361–374 (2017)

5. Role of Water in Rhodopsin Ion Conduction

With Prof. Suman Chakrabarty (SNBNCBS), we studied the the localisation, structure, dynamics and energetics of the water molecules along the channel of the sodium-pumping KR2 rhodopsin. We identified the movement of the trapped water molecules to be gated by protein side-chains which controls ion-pumping, suggesting a water-mediated pathway.