Postdoctoral Research:

Analysis of large scale human genomic data [August 2017-Onwards]

Advisor: Prof. Jeff Wall, Institute for Human Genetics, University of California, San Francisco

Currently, with large scale human genomic sequencing, a wealth of information has become available for use in genetic analysis like GWAS, or inferring demographic histories of populations. However, the quality of this information varies across different reference databases. Also, population specific databases are being generated to be able to obtain more specific information for these studies. Generation of these reference databases is important for performing analysis. In addition, assessing these databases for quality is important to understand which applications a particular dataset can be used for, and the corresponding reliablity of any analysis carried out in this manner.

I am working on the generation and analysis of such databases, in collaboration with various experimental groups in academia and industry. In particular, my work is focussed on the the public 1000 Genomes database, as well as the GenomeAsia 100K Consortium, which is a project to sequence 100,000 Asian individuals to help study of medical questions specific to the Asian population, also from the perspective of addressing demographic questions related to Asian populations.

Graduate Research:

Studying dynamics of small biomolecules and enzymes, and their interactions with solvent [July 2012-June 2017]

Advisor: Prof. Teresa Head-Gordon, Department of Bioengineering, University of California, Berkeley

  • Developing computational methods to analyze dynamics of biomolecules
  • Implemented codes in Fortran within existing simulation packages to enable calculations of dynamic observables
  • Developing an understanding of the influence of specific residue modification on protein function
  • Understanding the influence of solvent on biomolecule behavior
  • Developed scripts in python and matlab for determining observables from simulation data

Research Collaborations:

Studying entropic contributions to enzyme solvation using a polarizable force field [May 2016-June 2017]

Advisors: Prof. Teresa Head-Gordon, Department of Bioengineering, University of California, Berkeley Prof. Matthias Heyden, Max Planck Institut fur Kohlenforschung, Mulheim

  • Performed molecular dynamics simulations of Kemp Eliminase artificial enzymes and MMP enzyme using the AMOEBA polarizable force field
  • Analyzed the solvation entropy trends over evolved variants in Kemp Eliminase to explain solvent contribution to improved catalytic activity
  • Analyzed solvation around MMP active site with zinc cofactor, to understand influence of polarization and solvation in entropic contribution to MMP activitya

Studying small molecule dynamic modes via classical simulations [May 2015-January 2017]

Advisors: Prof. Teresa Head-Gordon, Department of Bioengineering, University of California, Berkeley, Prof. Dominik Marx, Institute for Theoretical Chemistry, Ruhr University Bochum

  • Modified existing classical simulation approaches to compare with Ab-Initio Simulation approaches
  • Developed a formulation for localizing charges to allow mode decomposition
  • Obtained significantly improved agreement of classical simulations with Ab-Initio methods

Research Internship:

Protein Structure Prediction using a homology based approach [May-July 2010]

Supervisor: Dr. Michael Lappe, Structural Proteomics Group, Max Planck Institute for Molecular Genetics, Berlin

  • Explored various computational tools available for protein structure prediction and developed an efficient prediction pipeline for this task
  • Was part of the team from the Structural Proteomics Group that participated in the international CASP 9 (Critical Assessment of tertiary Structure Prediction) competition
  • Predicted structures for 18 out of 60 target proteins released for structure prediction
  • Developed a scoring function in Java to assess the quality of predicted structures based on the favorability of the spatial location of a residue with respect to its neighbors

Undergraduate Thesis:

Computational Prediction of Loop Structures in GPCR proteins [Aug 2010-May 2011]

Advisor: Prof. Santosh Noronha, IIT Bombay

  • Reviewed existing ab-initio transmembrane protein folding and packing methods in in literature and identified the most suitable method for loop structure prediction
  • Implemented a kinematic loop closure algorithm method to predict loop structure for proteins.
  • Good loop closure was observed for test system beta adrenoceptor

Undergraduate Thesis:

Computational Prediction of Loop Structures in GPCR proteins [Aug 2010-May 2011]

Advisor: Prof. Santosh Noronha, IIT Bombay

  • Reviewed existing ab-initio transmembrane protein folding and packing methods in in literature and identified the most suitable method for loop structure prediction
  • Implemented a kinematic loop closure algorithm method to predict loop structure for proteins.
  • Good loop closure was observed for test system beta adrenoceptor

Undergraduate Technical Project:

Project BioSynth: Student initiative for setting up a test scale biodiesel production facility on IIT Bombay Campus [Oct 2008-May 2011]

Advisor: Prof. Sanjay Mahajani, IIT Bombay

Overall Coordinator, Project BioSynth [May 2010-May 2011]

  • Leading a two-tier team of 11 core members and 17 organizers in setting up a biodiesel production plant in IIT Bombay campus with a budget of INR 5 million
  • Managing the installation and commissioning of a 200 lt capacity facility on campus
  • Supervised the integration of the biodiesel process as a part of the 4th year undergraduate lab curriculum in the Department of Chemical Engineering

    In-charge R&D Team, Project BioSynth [May 2009-April 2010]

  • Experimentally tuned the process parameters for synthesis of biodiesel from multiple raw materials
  • Performed quality control of final product using prescribed standards and carried out testing of fuel in vehicles and proved the product to be meeting ASTM criteria for biodiesel
  • Proposed a model to implement a virtual lab experiment based on the biodiesel process