Molecular Modeling and Simulations, Biological Self-Assembly, Aqueous Solutions, Gas Hydrates and Ice Nucleation, Coarse-Grained Simulations of Polymer Systems
Office: 208 Earle Hall
Ph. D., Rensselaer Polytechnic Institute, 2009
M. E., Texas A&M University, 2004
B. Tech., Chaitanya Bharathi Institute of Technology (affiliated to Osmania University, India), 2002
The goal of our research is to understand how materials behave at the molecular level. The research is motivated by the fact that if we can understand the molecular behavior of materials, we can engineer them to have specific properties. We study various systems including water and aqueous solutions, thermoresponsive polymers and biological systems using state-of-the-art tools of molecular modeling, computer simulations and statistical mechanics. We are currently focused on four specific problems that are motivated by the 21st century challenges in fields of energy, environment and bioengineering.
Virus Capsid Assembly: Our group interested in understanding the assembly of virus particles and exploring scenarios that either promote or inhibit their assembly. Various aspects of capsid assembly such as capsid nucleation, stability, growth, and role of water in and effect of solution conditions on the assembly process are being probed. Insights from these studies will contribute towards the development of capsid targeting therapeutic strategies and virus-based approaches of gene therapy and drug delivery.
Ice Nucleation and Growth: Ice nucleation is important in various scientific disciplines. The essence of cloud physics is in the phase transitions of water, which are affected by the various components like pollen, mineral dusts, soot and different gases present in the atmosphere. Heterogeneous ice nucleation also forms the core of cloud seeding, and is involved in icing-related issues in power gridlines, and transport vehicles like ships and airplanes. Our group is investigating the relative importance of various surface properties on the kinetics of ice nucleation using state-of-the-art computer simulation techniques. Such a thorough investigation will provide guidelines for a priori estimation of the 'ice nucleation propensity' of a surface.
Gas Hydrates: Minimal understanding of the nucleation and growth of hydrates hinders the development of hydrate-based technologies. To this end, our research efforts are focused on using computer simulations to obtain detailed molecular-level picture of hydrate formation kinetics. Kinetics of hydrate formation for different hydrate structures, and the influence of the type of guest molecule, kinetics of mixed hydrates formation, effect of additives on hydrate nucleation and growth are being studied. Our studies will contribute towards advancing the proposed hydrate applications for energy recovery, water desalination, gas storage and transportation, and carbon dioxide sequestration to working technologies.
We are currently actively recruiting one graduate student on an exciting project focused on using coarse-grained simulations to study nanoparticle assembly and nanotoxicology. This work will be pursued in collaborations with experimental groups at Clemson University.
We are always seeking talented and interested undergraduate students to join our group. We have several exciting projects in our group and I will work with you to design a project that appeals to your interests. Projects may involve performing molecular dynamics simulations of proteins, water, and polymers, researching literature, and testing and identifying techniques and codes. If you are interested, contact Dr. Sarupria (firstname.lastname@example.org) for further details and we will design your project together.
B. Sengupta, W. Gregory, J. Zhu, S. Dasetty, M. Karakaya, J. Brown, A. Rao, J. Barrows, S. Sarupria and R. Podilla, “Influence of carbon nanomaterial defects on the formation of protein corona,” rsc, Advances, 5, 82395-82402, (2015)
R. DeFever and S. Sarupria, “Association of small aromatic molecules with PAMAM dendrimers,” Phys. Chem. Chem. Phys., 17, 29548-29557, (2015)
C. Bodenschatz, S. Sarupria and R. Getman, “Molecular-Level Details about Liquid H2O Interactions with CO and Sugar Alcohol Adsorbates on Pt(111) Calculated Using Density Functional Theory and Molecular Dynamics,” J. Phys. Chem. C, 119, 13642-13651, (2015)
R. DeFever, N. Geitner, P. Bhattacharya, F.Ding, P.C. Ke, and S. Sarupria, “PAMAM dendrimers and graphene: Materials for removing aromatic contaminants from water,” Environ. Sci. Technol., 49, 4490-7, (2015)
A. Haji-Akbari, R. DeFever, S. Sarupria and P. Debenedetti, “Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water,” Phys. Chem. Chem. Phys., 16, 25916–25927, (2014)
O. Kaunwi, *C. Baldwin, *G. Greisheimer, S. Sarupria and A. Guiseppi-Elie, “Molecular dynamics simulations of peptide-SWCNT interactions related to enzyme conjugates for biosensors and biofuel cells”, Nano LIFE, 03, 1343007 (2013)
S. Vembanur, A. J. Patel, S. Sarupria and S. Garde, “On the thermodynamics and kinetics of hydrophobic interactions at interfaces”, Journal of Physical Chemistry B, 117 (35), 10261–10270 (2013)
P. Xuan, Y. Zheng, S. Sarupria, and A. Apon, "SciFlow: A Dataflow-Driven Model Architecture for Scientific Computing using Hadoop", IEEE BigData Conference: Big Data and Science Workshop Proceedings, (2013)
P. Bhattacharya, N.K. Geitner, S. Sarupria, and P.C. Ke, *Exploiting the Physicochemical Properties of Dendritic Polymers for Environmental and Biological Applications, Physical Chemistry Chemical Physics 15 (2013), 4477. *Featured as Cover Art of PCCP.
S. Sarupria and P. Debenedetti, “Homogeneous nucleation of methane hydrate in microsecond molecular dynamics simulations”, Journal of Physical Chemistry Letters, 3: 2942-2947 (2012)
S. Sarupria and P. G. Debenedetti, “Molecular dynamics study of dissociation of carbon dioxide hydrates”, Journal of Physical Chemistry A, 115: 6102 (2011)
P. G. Debenedetti and S. Sarupria, “Hydrate molecular ballet”, Science, 326: 1070 (2009)
S. Sarupria, T. Ghosh, A. E. Garcia and S. Garde, “Studying pressure denaturation of a protein by molecular dynamics simulations”, Proteins: Structure, Function and Bioinformatics, 78:1641-1651 (2010)
S. Sarupria and S. Garde, “Quantifying water density fluctuations and compressibility of hydration shells of hydrophobic solutes and proteins”, Physical Review Letters. 103:037803 (2009). Featured in Virtual Journal of Biological Physics Research (24 citations as of April 4, 2011).
C. J. Fennell, A. Bizjak, V. Vlachy, K. A. Dill, S. Sarupria, S. Rajamani, and S. Garde, “Ion pairing in molecular simulations of aqueous alkali halide solutions”, Journal of Physical Chemistry B, 113: 14837 (2009)
M. Athawale, S. Sarupria and S. Garde, “Enthalpy-entropy contributions to salt and osmolyte effects on molecular-scale hydrophobic hydration and interactions”, Journal of Physical Chemistry B, 112: 5661 (2008)
B. Pereira, S. Jain, S. Sarupria, L. Yang and S. Garde, “Pressure dependence of the compressibility of a micelle and a protein: insights from cavity formation analysis”, Molecular Physics, 105: 189-199 (2007)