Last modified: August 23 2016.

Research: Active user groups

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  1. Computer Services Centre
    Dr. Manish Agarwal:
    1. Classical Molecular Dynamics:
      • Simulations of substituted polyethylene using LAMMPS in collaboration with Gourav Shrivastav (Late Prof. Chakravarty's Lab, Department of Chemistry).
      • Simulations of Double Pervoskite materials in collaboration with Uzma Anjum (Dr. Ali Haider's lab, Department of Chemical Engineering)
      • Simulations of Amino acids near metal surfaces in collboration with Madhulika Gupta (Late Prof. Chakravarty's Lab, Department of Chemistry) and Shelaka Gupta (Dr. Haider Ali's Lab, Department of Chemical Engineering)
    2. Improving analysis of trajectories of Molecular Dynamics Simulations using GPU accelerated computing. In collaboration with Gourav Shrivastav of Department of Chemistry (Late Prof. Chakravarty's Lab) , we use CUDA to accelerate calculation of typical dynamical and static properties from molecular dynamics trajectories
    3. Improving acceleration of Direct Numerical Simulation programs in collaboration with Nishant Prashar from Dr. Sawan Suman's lab (Department of Applied Mechanics)
  2. Kusuma School of Biological Sciences
    1. Dr. Manidipa Banerjee's Group

      Dr. Manidipa Banerjee's group is using both experimental and computational approaches to understand the mechanisms and dynamicity of various processes of viruses, including virus assembly and disassembly, and virus interaction with host-cell receptors and membranes. We intend to use these studies to design virus-based macromolecular complexes for various biomedical applications like vaccines and drug delivery systems.

      We have been utilizing the HPC cluster at IIT for our computational work, which falls under two broad categories:

      • Molecular dynamics simulation studies to understand how viral peptides interact with biological membranes at the atomic scale: Simulation software packages like GROMACS and AMBER are being used for this purpose.
      • Cryo-electron microscopy-single particle reconstruction for near-atomic structure determination of virus-like particles: For this we have been using the image processing suites EMAN2, RELION and Scipion.

  3. Department of Physics
    Dr. Saswata Bhattacharya
    Research Application Area: Clusters and catalysis, hydrogen storage, electronic, optical, mechanical and vibrational properties of graphene like 2D materials, Thermoelectric materials, etc.
  4. Department of Chemistry
    1. Late Prof. C. Chakravarty's Group
      Molecular Simulations of Liquids: Water-like fluids, Aqueous and Non-aqueous Solutions, Biomolecular Hydration, Nanoparticle Self-Assembly
    2. Dr. Hemant Kashyap's Group:
      Molecular Simulations using Gromacs and NAMD
    3. Dr. Shashank Deep's Group
      Molecular Simulations:
      Investigation of the mechanism of protein stabilization and aggregation.
      • (Nidhi Katyal and Nidhi Kaur Bhatia)

        The malfunctioning of proteins is a root cause of various diseases. It is widely accepted that this behaviour is intimately tied to protein instability and aggregation. Thus, understanding the mechanism by which known external agents (eg. Trehalose) stabilizes the native state of protein and/or decelerates aggregation is of paramount importance in the design of new therapeutic stabilizers. In this perspective, our group examines the behaviour of different model proteins/peptides in the absence and presence of additives under broad temperature and concentration regime with the help of molecular dynamics simulations with Gromacs software available on HPCA.

        Recently, we have published an article entitled ‚ÄúRevisiting the conundrum of trehalose stabilization‚ÄĚ in PCCP with simulations partially carried out on the HPCA cluster. The system consisted of 50000-70000 atoms and utilized 1 node, 2 GPUs and 16 processes with the performance of 13ns/12hrs. In this study, we have focused on the effect of trehalose against thermal denaturation on Lysozyme. We have monitored the structural properties of protein both in the absence and presence of trehalose under different temperature and hence constructed the free energy landscape using property space approach. An attempt towards dissecting the parameters crucial in orchestrating the stabilization process was carried out using principal component analysis. The clustering tendency of trehalose and its entrapment around lysozyme was viewed at a deeper level under different concentration ranges. We have also looked at effect of trehalose on water by calculating properties like tetrahedral order parameter, diffusion coefficients, radial distribution functions etc. All the calculations were done either using in-house codes or using gromacs analysis commands. Currently, we are trying understand the mechanism of protein self assembly.

  5. Department of Chemical Engineering
    1. Dr. Gaurav Goel's Group:
      Molecular Simulations using Gromacs
    2. Dr. Haider Ali's Group
      Calculations using Materials Studio and VASP
    3. Dr. Sudip Pattanayek's Group
      Uses computational tools for three different areas, Polymer nano-composite, adsorption of protein and rheology of shear thickening fluid.
    4. Dr. Vivek Buwa's Group:
      Flow simulations using OpenFOAM and Ansys Fluent.
      (Arpit Jindal) Simulating liquid distribution in Trickle bed using commercial solver Fluent and verifying the results with corresponding experiments.
  6. Department of Applied Mechanics
    1. Dr. Sawan Suman's group:
      Direct numercial simulations.
    2. Prof. Anupam Dewan Group:
      (Pritanshu Ranjan) Use of Variable Resolution turbulence modelling to study heat transfer over rectangular prisms which involves all complex flow phenomenon, for e.g, stagnation, local acceleration, separation, reattachment and vortex shedding. Use of Large Eddy Simulation to study the buoyancy driven flow.
  7. Centre for Industrial Tribilogy
    Dr. R. K. Pandey(Department of Mechanical Engineering) and Prof. V. K. Agarwal
    Elastohydrodynamic Lubrication of Concentrated contacts e.g. ball bearings using an in-house code.(Vivek Bharadwaj)
  8. Department of Mechanical Engineering
    1. Dr. B. Premachandran's group
      An in-house code has been developed to investigate boiling flow problems with sharp interfaces.
    2. Dr. Devendra K. Dubey
      Molecular Simulations using NAMD
  9. Department of Computer Science
  10. Department of Electrical Engineering
    1. Finding consistent patterns of information flow in Human Brain using fMRI
      Dushyant Sahoo with Dr. Rahul Garg(CSE) Functional Magnetic Resonance Imaging (fMRI) is being used to find functional connectivity and information flow in human brain. We aim to find all the networks of information flow when a person is at rest. In order to find consistent networks we are using granger causality analysis and hypothesis testing. The analysis is done on 500 subjects from 1000 functional connectome project.
    2. Convolutional Neural Networks for Image Classification
    3. Dr. Manik Verma (Department of Computer Science and Engineering)
      Object detection and classification in images using Convolutional Neural Network (Rahul Kumar)
      Softwares Used: Intel MKL, Matlab CPU or CUDA 5.5/6.0
      Experimenting with Convolution Neural Network on ImageNet dataset to detect and classify objects in images. Details of ImageNet dataset are available here.
  11. Department of Civil Engineering
    1. Dr. Dhanya C. T.'s group
      Regional scale hydrologic modelling for climate change impact assessment using Variable Infiltration Capacity (VIC) Macroscale Hydrologic Model
  12. Department of Biochemical Engineering and Biotechnology
    1. Dr. D. Sundar's group
      Long term goal of Dr. D Sundar's group is to understand DNA-protein interactions to evolve DNA-binding specificity in proteins and to make highly specific custom-designed proteins for various applications in Genome Engineering. The current areas of focus include: (a) rational design of zinc finger proteins (ZFPs) for genome editing (b) Biological activity of natural drugs (c) Metabolic Engineering. We use both computational and wet-lab experimental approaches in close collaboration with several groups in India and abroad.