Sri Vembanur Ranganathan
Sri Vembanur Ranganathan
- Molecular modeling and simulations of biomolecules
- Thermodynamics of interfacial phenomena
- Advanced sampling techniques and free-energy calculations
Sri has joined the Advanced Computational center of the RNA institute as a molecular modeling research scientist. He is trained in the molecular modeling and simulations of biological systems. Specifically, his graduate research focused on water behavior and water-mediated interactions at interfaces towards understanding structure, stability and dynamics of interfacially-active biomolecules. His research work yielded a framework to understand biomolecule stability and self-assembly at interfaces. He is applying his knowledge and skill-set in modeling and simulations to study nucleic acids and is currently involved in a number of collaborations with RNA biologists and biochemists.
B. Tech in Chemical Engineering, Anna University, Chennai, India
PhD in Chemical Engineering, Rensselaer Polytechnic Institute
- DNA & RNA structure through IMS-MS (Dan Fabris) – We are developing an integrated approach using modeling and experiments to characterize structural changes undergone by nucleic acids when they form complexes with ions, small molecules and proteins.
- Dynamic RNA regulation for germline development (Prashanth Rangan) – We are working to understand how the structure of the 3’ untranslated region in a specific gene relates to its expression, and how RNA binding proteins react to structural rearrangement. Ken Halvorsen is also a collaborator on this project.
- Thermodynamics of nucleic acid-graphene interactions (Mehmet Yigit) – As part of an effort in Dr. Yigit’s lab to create novel nanoparticle based therapeutics and diagnostics, we are characterizing the binding of nucleic acids to graphene, which is a promising new material in biomedicine. Ken Halvorsen is also a collaborator on this project.
- Modeling 5-hydroxy-methyl-cystine (5hmC) modification (Jia Sheng) – We are performing molecular modeling of 5hmC modification in DNA to investigate the factors that influence the oxidation of the modification by TET proteins.
- Understanding the role of modifications in the anticodon stemloop (ASL) of tRNA (Paul Agris) – The modifications in the anticodon stem-loop of tRNA are shown to play an important role in translation leading to protein synthesis. We are currently studying the role of 2-thiocytidine modification on the structure and dynamics of the ASL of tRNAArg. Maria Basanta-Sanchez is also a collaborator on this project.
- V. Venkateshwaran, S. Vembanur, S. Garde “On the enhancement of water-mediated ion-ion interactions at the water vapor-liquid interface” Proc. Natl. Acad. Sci. USA, 111(24):8729-8734, 2014.
- S. Vembanur, V. Venkateshwaran, S. Garde “Structure and dynamics of single hydrophobic/ionic polymers at the vapor-liquid interface of water” Langmuir, 2014, 30(16):4654-4661.
- S. Vembanur, A.J. Patel, S.Sarupria, S. Garde “On the thermodynamics and kinetics of hydrophobic interactions at interfaces” J. Phys. Chem. B, 2013, 117(35):10261:10270.
- H. Acharya, S. Vembanur, S.N. Jamadagni, S. Garde “Mapping hydrophobicity at the nanoscale: Applications to heterogeneous surfaces and proteins” Faraday Discussions, 2010,146:353-365.
- S. Vembanur Ranganathan, S. Lakshmi Narasimhan, K. Muthukumar “An overview of enzymatic production of biodiesel” Bioresource Technology, 2007,99(10):3975-3981.