Sameer Varma - Publications

Biophysics University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 

27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Kruczek J, Chiu SW, Varma S, Jakobsson E, Pandit S. Interactions of Mono and Di-valent cations at Palmitoyl-Oleoyl-Phosphatidylcholine Interface. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 31337218 DOI: 10.1021/acs.langmuir.9b01275  1
2016 Duro N, Gjika M, Siddiqui A, Scott HL, Varma S. POPC bilayers supported on nanoporous substrates: specific effects of silica-type surface hydroxylation and charge density. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 27283467 DOI: 10.1021/acs.langmuir.6b01155  1
2016 Martin DR, Dutta P, Mahajan S, Varma S, Stevens SM. Structural and activity characterization of human PHPT1 after oxidative modification. Scientific Reports. 6: 23658. PMID 27034094 DOI: 10.1038/srep23658  1
2016 Dutov P, Antipova O, Varma S, Orgel JP, Schieber JD. Measurement of Elastic Modulus of Collagen Type I Single Fiber. Plos One. 11: e0145711. PMID 26800120 DOI: 10.1371/journal.pone.0145711  1
2015 Varma S, Botlani M, Hammond JR, Scott HL, Orgel JP, Schieber JD. Effect of Intrinsic and Extrinsic Factors on the Simulated D-band Length of Type I Collagen. Proteins. PMID 26214145 DOI: 10.1002/prot.24864  1
2014 Dutta P, Botlani M, Varma S. Water Dynamics at Protein-Protein Interfaces: Molecular Dynamics Study of Virus-Host Receptor Complexes. The Journal of Physical Chemistry. B. PMID 25420132 DOI: 10.1021/jp5089096  1
2014 Varma S, Botlani M, Leighty RE. Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning. Proteins. 82: 3241-54. PMID 24615845 DOI: 10.1002/prot.24541  1
2013 Leighty RE, Varma S. Quantifying Changes in Intrinsic Molecular Motion Using Support Vector Machines. Journal of Chemical Theory and Computation. 9: 868-75. PMID 26588730 DOI: 10.1021/ct300694e  1
2013 Rossi M, Tkatchenko A, Rempe SB, Varma S. Role of methyl-induced polarization in ion binding. Proceedings of the National Academy of Sciences of the United States of America. 110: 12978-83. PMID 23878238 DOI: 10.1073/pnas.1302757110  1
2013 Sabo D, Jiao D, Varma S, Pratt LR, Rempe SB. Case study of Rb+(aq), quasi-chemical theory of ion hydration, and the no split occupancies rule Annual Reports On the Progress of Chemistry - Section C. 109: 266-278. DOI: 10.1039/c3pc90009f  1
2012 Varma S, Teng M, Scott HL. Nonintercalating nanosubstrates create asymmetry between bilayer leaflets. Langmuir : the Acs Journal of Surfaces and Colloids. 28: 2842-8. PMID 22239169 DOI: 10.1021/la204623u  1
2011 Varma S, Rogers DM, Pratt LR, Rempe SB. Perspectives on: ion selectivity: design principles for K+ selectivity in membrane transport. The Journal of General Physiology. 137: 479-88. PMID 21624944 DOI: 10.1085/jgp.201010579  1
2011 Varma S, Rogers DM, Pratt LR, Rempe SB. Perspectives on: Ion selectivity Design principles for K + selectivity in membrane transport Journal of General Physiology. 138: 279. DOI: 10.1085/jgp.2010105791382c  1
2010 Varma S, Rempe SB. Multibody effects in ion binding and selectivity. Biophysical Journal. 99: 3394-401. PMID 21081088 DOI: 10.1016/j.bpj.2010.09.019  1
2010 Asthagiri D, Dixit PD, Merchant S, Paulaitis ME, Pratt LR, Rempe SB, Varma S. Ion selectivity from local configurations of ligands in solutions and ion channels Chemical Physics Letters. 485: 1-7. DOI: 10.1016/j.cplett.2009.12.013  1
2008 Varma S, Rempe SB. Structural transitions in ion coordination driven by changes in competition for ligand binding. Journal of the American Chemical Society. 130: 15405-19. PMID 18954053 DOI: 10.1021/ja803575y  1
2008 Varma S, Sabo D, Rempe SB. K+/Na+ selectivity in K channels and valinomycin: over-coordination versus cavity-size constraints. Journal of Molecular Biology. 376: 13-22. PMID 18155244 DOI: 10.1016/j.jmb.2007.11.059  1
2008 Sabo D, Varma S, Martin MG, Rempe SB. Studies of the thermodynamic properties of hydrogen gas in bulk water. The Journal of Physical Chemistry. B. 112: 867-76. PMID 18154326 DOI: 10.1021/jp075459v  1
2007 Whitfield TW, Varma S, Harder E, Lamoureux G, Rempe SB, Roux B. A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. Journal of Chemical Theory and Computation. 3: 2068-2082. PMID 21785577 DOI: 10.1021/ct700172b  1
2007 Varma S, Rempe SB. Tuning ion coordination architectures to enable selective partitioning. Biophysical Journal. 93: 1093-9. PMID 17513348 DOI: 10.1529/biophysj.107.107482  1
2007 Varma S, Jakobsson E. The cPLA2 C2alpha domain in solution: structure and dynamics of its Ca2+-activated and cation-free states. Biophysical Journal. 92: 966-76. PMID 17085504 DOI: 10.1529/biophysj.106.091850  1
2006 Varma S, Rempe SB. Coordination numbers of alkali metal ions in aqueous solutions. Biophysical Chemistry. 124: 192-9. PMID 16875774 DOI: 10.1016/j.bpc.2006.07.002  1
2006 Varma S, Chiu SW, Jakobsson E. The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF. Biophysical Journal. 90: 112-23. PMID 16183883 DOI: 10.1529/biophysj.105.059329  1
2004 Malmberg NJ, Varma S, Jakobsson E, Falke JJ. Ca2+ activation of the cPLA2 C2 domain: ordered binding of two Ca2+ ions with positive cooperativity. Biochemistry. 43: 16320-8. PMID 15610026 DOI: 10.1021/bi0482405  1
2004 Varma S, Jakobsson E. Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues. Biophysical Journal. 86: 690-704. PMID 14747308 DOI: 10.1016/S0006-3495(04)74148-X  1
2004 Natarajan S, Varma S, Tang Y, Parker S, Mashl J, Jakobsson E. Toward an integrated computational environment for multiscale computational design of nanoscale Ion Channel semiconductors 2004 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2004. 1: 147-150.  1
2002 Van Der Straaten T, Varma S, Chiu SW, Tang J, Aluru N, Eisenberg R, Ravaioli U, Jakobsson E. Combining computational chemistry and computational electronics to understand protein ion channels 2002 International Conference On Computational Nanoscience and Nanotechnology - Iccn 2002. 60-63.  1
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