Dr. Sudipta Kumar Sinha

Profile Image: 
Dr. Sudipta Kumar Sinha
Room & Contact: 

Office: Room 315 (Transit campus)

Phone: 01881-242238

Designation: 

Assistant Professor

Department: 

Department of Chemistry

Email: 

sudipta@iitrpr.ac.in

Biography: 

Sudipta has been quite active over the last ten years in theoretical and computational biophysical chemistry, which primarily addresses molecular modeling of soft materials and have important applications in chemical and biological sciences. He is experienced with state-of the-art computer simulation techniques such as Molecular dynamics (MD), Monte Carlo (MC), Density Functional Theory (DFT), hydrodynamics and statistical mechanics to study complex biochemical and biophysical processes those occur in cellular environment. His current research focuses on the control of gene regulation, Epithelial-Mesenchymal Transition (EMT), and computational nanofluidics.

Areas of Research: 

Statistical mechanical modeling of gene regulation

Dynamics of Complex Biochemical Networks

Computational Nanofluidics

Molecular dynamics and Monte-Carlo Simulations

Education: 

Ph.D. (Chemistry): Indian Institute of Technology Kharagpur (2011)

M.Sc. (Chemistry): University of Calcutta (2005)

B.Sc. (Chemistry): University of Calcutta (2003)

Selected Publications/Patents: 

Group Members

Ph.D. Scholars

  1. Pankaj Gautam (Aug 2017 - present)
  2. Vishal Kumar (Aug 2019 - present)

M.Sc. Project Students

  1. Naresh (2019)
  2. Vishal (ongoing)
  3. Anjli (ongoing)

 

Selected Publications

1. Anticipating critical transitions in epithelial-hybrid-mesenchymal cell-fate determination S. Sarkar, S. K. Sinha, H. Levine, M. K. Jolly, P. S. Dutta bioRxiv: 733006 PNAS (accepted)

2. Dynamic environment-induced multistability and critical transition in a metacommunity ecosystem R. Arumugam, S. Sarkar, T. Banerjee, S. Sinha, P. S. Dutta Physical Review E 2019, 99, 032216.

3. Drop deformation and emulsion rheology under the combined influence of uniform electric field and linear flow S. Mandal, S. Sinha, A. Bandopadhyay, S. Chakraborty Journal of Fluid Mechanics 2018, 841, 408-433.

4. Size-Dependent Conformational Features of A1742 Protofilaments from Molecular Simulation Studies, P. Khatua, S. K. Sinha, S. Bandyopadhyay, Journal of Chemical Information and Modeling 2017, 57, 2378-2392.

5. A charge equilibration formalism for treating charge transfer effects in MD simulations: Application to water clusters S Kumar Sinha, M Mehta, S Patel Journal of computational chemistry 2017 38, 1389-1409.

6. Insights into thiol aromatic interactions: A stereoelectronic basis for SH/ interactions,C. R. Forbes, S. K. Sinha, H. K. Ganguly, S. Bai, G. P. A. Yap, S. Patel, N. J. Zondlo, Journal of the American Chemical Society 2017, 139, 1842-1855.

7. Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein, K. Chakraborty, S. K. Sinha, S. Bandyopadhyay, The Journal of Chemical Physics 2016, 144, 205105.

8. Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics, Y. Hu, S. K. Sinha, S. Patel, Langmuir 2015, 31, 6615-6631.

9. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation Into DMPC Bilayers Y. Hu, S. K. Sinha, and S. Patel J. Phys. Chem. B 2014, 118 11973-92.

10. In silico studies of the properties of water hydrating a small protein SK Sinha, M Jana, K Chakraborty, S Bandyopadhyay The Journal of chemical physics, 2014 141 (22), 12B602_1.

10. In silico studies of the properties of water hydrating a small protein SK Sinha, M Jana, K Chakraborty, S Bandyopadhyay The Journal of chemical physics, 2014 141 (22), 12B602_1.

11. Secondary structure specific entropy change of a partially unfolded protein molecule SK Sinha, S Chakraborty, S Bandyopadhyay Langmuir, 2010, 26 (12), 9911-9916.

Sponsored Project

Ongoing
        
1. Multi-scale Computational Model of Gene Regulation: Exploiting the Phenomenon of Self Assembly, ISIRD(IIT Ropar); 2017-2020; INR 5500000
 
2. Controlled Molecular Transportation Through Engineered Nanopores: Design and Applications in Biomedical Sciences, Early Career Research Award(DST-SERB), 2019-2022; INR 2700000
Work Experience: 

Assistant Professor (Dec 2016 - present): IIT Ropar

Postdoctoral Fellow (2013 - 2015): University of Delaware, Newark

Postdoctoral Fellow (2011 - 2013): University of California, Davis