Nov 2016: Congratulations to Matthew Cuffaro for securing a full time position at Vuram Technology Solutions.
Oct 2016: Our simulations provide new molecular-level insight into regulated host invasion by paramyxoviruses, and provide a striking example of how small intra-domain changes are capable of producing large inter-domain rearragements in proteins. (View Biophys. J article)
Sep 2016: New post-doctoral and graduate student positions available. Please contact PI for details.
Jul 2016: Congratulations to Mohsen for winning best poster award at the ISCB 2016 meeting. The poster entitled "Quantifying conformational ensemble changes in proteins using inverse machine learning" can be downloaded here.
Jul 2016: Our simulations recommend a paradigm shift in our understanding of why collagen fibers weaken during fibrillogenesis. (View Biophys. J article)
Jun 2016: Congratulations to Priyanka for successfully defending her PhD thesis. Best wishes to her for her future at Agile SDE.
Jun 2016: Congratulations to Nalvi, Marion and Ahnaf for publishing their first paper. This study makes a novel proposition for making designer supported membranes: surface hydroxylation and surface charge on nanoporous substrates can be made to work against each other in remodeling lipid bilayers (View).
Mar 2016: Our collaborative work with the Steven's group on the effect of phosphatase oxidation appeared in Nature Scientific Reports (View)
Feb 2016: Congratulations to Priyanka for receiving travel award to attend the 2016 Biophysical Sociey Meeting and present findings on the mechanism of paramyxovirus entry.
Jan 2016: We develop a new laser-tweezer based method to measure the Young's modulus of freshly-extracted collagen (View)
Molecular and quantum mechanics simulations are fast becoming powerful alternatives to wet lab experiments for studying the structure, dynamics and function of biomolucules. Our primary goals are to further enhance their reliability and extend their applicability to systems that function through increasingly more complex interactions. Specifically, we are (a) enhancing the reliability of molecular mechanics based methods toward modeling biomolecular ionic interactions, and (b) developing new machine learning inspired methods to describe proteins regulated by dynamic allostery. We also utilize simulations, mostly in collaboration with experimental groups, to address key unresolved biophysical questions in membrane structure, transmembrane ion transport, allosteric signaling and protein-protein interactions.
Sameer Varma, PhD
Assistant Professor, Department of Cell Biology, Microbiology and Molecular Biology
Affiliate Professor, Department of Physics
Office: ISA 6205
ISA-2015, University of South Florida, 4202 E. Fowler Ave., Tampa, FL-33620