Computational Biology

Enhanced Kinetic Sampling Methods for Biomolecular Simulations (TA/FA)

All life processes are based on the fact
that biomolecules can exist in and can switch between different conformations. However,
tracing the structures and the dynamics of proteins and other biomolecules is
expensive and in fact, not possible through experimental means alone in most
cases. Atomistic simulations are playing an increasingly important role in
elucidating molecular processes. However, brute force methods are limited in  read more »

Proposing Faculty
Research Area
  • Computational Biology

State and parameter estimation of ensemble dynamics (TA only)

 read more »

Proposing Faculty
Research Area
  • Computational Biology
  • Data Analysis
  • Identification
  • Modelling
  • Optimisation
  • Systems Biology

Modeling and simulations of anti-HIV protein SAMHD1 (TA/FA)






A human cellular
enzyme, SAMHD1 has recently generated immense interest in its activity and
regulation on account of its role in blocking HIV-1 infection in dendritic
cells. The enzyme has the potential to provide a solution to the pandemic that
has already taken an enormous human and economic toll. However, the functioning  read more »

Proposing Faculty
Research Area
  • Computational Biology

Theoretical models to understand evolutionary processes.

In the story of evolution from a single cell (LUCA: https://en.wikipedia.org/wiki/Last_universal_common_ancestor) to complex eukaryotes, there are several missing links. In this project, we aim to develop theoretical and computational models to analyze these missing aspects in our understanding of evolution of life on Earth.  read more »

Proposing Faculty
Research Area
  • Biochemical Engineering
  • Biomolecular Engineering
  • Computational Biology
  • Enzymology
  • Systems Biology
Swati Bhattacharya

Sympatric speciation experiments in yeast.

New species come into being when an existing species "splits" into two species. This process is called speciation, and is known to occur via two modes - allopatry (literally meaning different place) and sympatry (same place). In allopatry, individuals of a species are separated physically (by a water body, for instance), and thereafter, the two separated groups evolve independently. The precise environmental conditions in the two regions drive these two groups apart with time, and eventually, the two groups speciatte into distinct species.  read more »

Proposing Faculty
Research Area
  • Computational Biology
  • Systems Biology

Modeling and simulation of endoplasmic reticulum stress pathways (TA/FA)

Endoplasmic reticulum (ER) is responsible for many important cellular functions such as
folding of proteins, glycosylation and quality control etc. Many
environmental and genetic perturbations such as hypoxia, glucose deficiency, overload of unfolded protein can lead to ER stress. ER stress has been associated with pathogenesis of many diseases
such as diabetes, neurodegenarative diseases such as Alziemers and
Parkinsons. Further, industrial recombinant mammalian cell lines producting recombinant therapeutics are also subject to ER stress.  read more »

Proposing Faculty
Research Area
  • Biochemical Engineering
  • Biomolecular Engineering
  • Computational Biology
  • Systems Biology
Supreet Saini
Ganesh A Viswanathan

Intel P4 server

This server is used for running of inhouse codes for simulation of materials.

Web links:
http://www.intel.com/p/en_US/products/server/processor
http://www.intel.com/itcenter/system/server/index.htm?cid=apac:ggl|xeon_in_brand|rd12B26|s

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