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  1. J.M. Delgado, G. Schillaci and S. Varma, Structural and energetic insights into lithium binding to nucleotides in the aqueous phase: Predictions from polarizable MM simulations. In preparation.

  2. J.M. Delgado, G. Schillaci and S. Varma, Phosphate and protein phosphorylation parameters for AMOEBA polarizable force field with high field corrections. In preparation.

  3. G. W. Dayhoff II and S. Varma, Machine learning velocities to propagate molecular dynamics simulations. In preparation.

  4. J. G. Guergues, J. Koomen, J. Wohlfahrt, J. Krieger, S. Varma and S. M. Stevens Jr., A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis. Submitted.

  5. P.S. Higbeee, G. W. Dayhoff IIe, A. Anbanandam, S. Varma and G. Daughdrill, Structural adaptation of p53 to secondary binding sites on MDM2 and MDMX. Submitted. (e: equal contribution)

  6. J.M. Delgado, P. Nagy and S. Varma, Polarizable AMOEBA model for simulating Mg2+·Protein·Nucleotide Complexes. J. Chem. Info. Model. 64: 378-392, 2024. View

  7. R.R. Cueny, S. Varma, K.H. Schmidt and J.L. Keck, Biochemical Properties of Naturally Occurring Human Bloom Helicase Variants. PLOS One. 18: e0281524, 2023. View

  8. N. Rogic, S.J. Charbonnier, F.Garin1, G.W. Dayhoff II, E. Gagliano, M. Rodgers, C.B. Connor, S. Varma and D. Shean, Characterizing and Mapping Volcanic Flow Deposits on Mount St. Helens via Dual-band SAR Imagery. Remote Sensing. 5: 2791, 2023. View

  9. J.M. Delgado, V. Wineman-Fisher, S.A. Pandit and S. Varma, Inclusion of high-field target data in AMOEBA’s calibration improves predictions of protein-ion interactions. J. Chem. Info. Model, 62: 4713–4726, 2022. View

  10. M. Saunders, V. Wineman-Fisher, E. Jakobsson, S. Varma and S.A. Pandit, High-dimensional parameter search method to determine force field mixing terms in molecular simulations. Langmuir, 38: 2840–2851, 2022. View

  11. S. Varma, J.P.R.O. Orgel and J.D. Schieber, Contrasting local and macroscopic effects of collagen hydroxylation. Int. J. Mol. Sci. 22: 9068, 2021. View

  12. J.M. Delgado, N. Duro, D.M. Rogers, A. Tkatchenko, S.A. Pandit and S. Varma, Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor. Proteins 89: 1134-1144, 2021. View

  13. S. Rahman, V. Wineman-Fisher, P. Nagy, Y. Al-Hamdani, A. Tkatchenko and S. Varma, Methyl-induced polarization destabilizes non-covalent interactions of N-methylated lysines. Chem. Euro. J. 27: 11005-11014, 2021. View

  14. C.L. Kriss, N. Duro, O.W. Nadeau, J. Guergues, O. Chavez-Chiang, A.E. Culver-Cochran, D. Chaput, S. Varma and S.M. Stevens Jr., Site‐specific identification and validation of hepatic histone nitration in vivo: Implications for alcohol‐induced liver injury. J Mass Spectrom. 56: e4713, 2021 View

  15. S. Rahman, V. Wineman-Fisher, Y. Al-Hamdani, A. Tkatchenko and S. Varma, Predictive QM/MM modeling of modulations in protein-protein binding by lysine methylation. J Mol. Biol. 433: 166745, 2021 View

  16. V. Wineman-Fisher, J.A. Melendez, P. Nagy, E. Jakobsson, S.A. Pandit and S. Varma, Transferable interactions of Li+ and Mg2+ ions in polarizable models. J. Chem. Phys. 153: 104113, 2020. View

  17. V. Wineman-Fisher, Y. Al-Hamdani, P. Nagy, A. Tkatchenko and S. Varma, Improved description of ligand polarization enhances transferability of ion-ligand interactions. J. Chem. Phys. 153:094115, 2020. View

  18. J. Kruczek, S.W. Chiu, S. Varma, E. Jakobsson, S.A. Pandit, Interactions of Monovalent and Divalent Cations at Palmitoyl-Oleoyl-Phosphatidylcholine Interface. Langmuir, 35: 10522–10532, 2019. View
    Dedicated to Dr. Chiu: Mentor, friend and a great scientist -- thank you for teaching us the meaning of rigor!

  19. N. Duro, and S. Varma, Role of Structural Fluctuations in Allosteric Stimulation of Paramyxovirus Hemagglutinin-Neuraminidase. Structure. 27: 1-11, 2019. View

  20. V. Wineman-Fisher, Y. Al-Hamdani, I. Addou, A. Tkatchenko and S. Varma, Ion-hydroxyl interactions: From high-level quantum benchmarks to transferable polarizable force fields. J Chem. Theory and Comput. 15: 2444−2453, 2019. View

  21. M. Saunders, M. Steele, W. Lavigne, S. Varma and S.A. Pandit, Interactions of salt with ether- and ester-linked phospholipid bilayers. BBA biomembranes. 1861: 907-915, 2019. View

  22. M. Botlani, A. Siddiqui and S. Varma, Machine learning approaches to evaluate correlation patterns in allosteric signaling: a case study of the PDZ2 domain. J Chem. Phys. 148. 2018. Featured Article View Press Release

  23. P. Dutta, A. Siddiqui, M. Botlani and S. Varma, Stimulation of Nipah Fusion: Small Intradomain Changes Trigger Extensive Interdomain Rearrangements. Biophys. J. 111: 1621–1630, 2016. View

  24. N. Duroe, M. Gjikae, A. Siddiqui, H.L. Scott and S. Varma, POPC bilayers supported on nanoporous substrates: specific effects of silica-type surface hydroxylation and charge density. Langmuir. 32: 6766–6774, 2016. View (e: equal contribution)

  25. S. Varma, J.P.R.O. Orgel and J.D. Schieber, Nanomechanics of Type I collagen. Biophys. J. 111: 50-56, 2016. View

  26. P.K. Bahia, T.A. Parks, K.R. Stanford, D.A. Mitchell, S. Varma, S.M. Stevens Jr. amd T.E. Taylor-Clark, The exceptionally high reactivity of Cys 621 is critical for electrophilic activation of the sensory nerve ion channel TRPA1. J Gen. Physiol. 147: 451-465, 2016. View

  27. D. Martin, P. Dutta, S. Mahajan, S. Varma and S. M. Stevens Jr., Structural and activity characterization of human PHPT1 after oxidative modification. Scientific Reports. 6:23658, 2016. View

  28. P.M. Dutov, O. Antipova, S. Varma, J.P.R.O. Orgel and J.D. Schieber, Measurement of elastic modulus of collagen type I single fiber. PLoS ONE. 11: e0145711, 2016. View

  29. S. Varma, M. Botlani, J. Hammond, H.L. Scott, J.P.R.O Orgel and J.D. Schieber, Effect of intrinsic and extrinsic factors on the simulated D-band length of Type I collagen. Proteins. 83: 1800–1812, 2015. View

  30. C. N. Krute, R. K. Carroll, F. E. Rivera, A. Weiss, R. M. Young, M. Botlani, S. Varma, B. J. Baker, L. N. Shaw. The Disruption of Prenylation Leads to Pleiotropic Rearrangements in Cellular Behavior and Virulence in Staphylococcus aureus. Molecular Microbiology. 95:819-32, 2015. View

  31. P. Dutta, M. Botlani and S. Varma, Water dynamics at protein-protein interfaces: A molecular dynamics study of virus-host receptor complexes. J Phys. Chem. B. 118: 14795-14807, 2014. View

  32. S. Varma, M. Botlani and R.E. Leighty, Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning. Proteins. 82: 3241-3254, 2014. View

  33. M. Rossi, A. Tkatchenko, S.B. Rempe and S. Varma, Role of methyl-induced polarization in ion binding. Proc. Natl. Acad. Sci. U.S.A. 110: 12978-12983, 2013. View

  34. D. Sabo, D. Jiao, S. Varma, L.R. Pratt and S.B. Rempe, Case study of Rb+(aq), quasi-chemical theory of ion hydration, and the no split occupancies rule. Ann. Rep. Prog. Chem. Sect. C. 109: 266-278, 2013. View

  35. R.E. Leighty and S. Varma, Quantifying changes in intrinsic molecular motion using support vector machines. J Chem. Theory and Comput. 9: 868–875, 2013. View

  36. S. Varma, M. Teng and H. Larry Scott, Non-intercalating nanosubstrates create asymmetry between bilayer leaflets. Langmuir 28: 2842-2848, 2012. View

  37. S. Varma, D.M. Rogers, L.R. Pratt and S.B. Rempe, Perspectives on: Ion selectivity Design principles for K+ selectivity in membrane transport. J Gen. Physiol. 137: 479-488, 2011. Invited Review View

  38. S. Varma and S.B. Rempe, Multi-body effects in ion binding and selectivity. Biophys. J, 99: 3394-3401, 2010. View

  39. D. Asthagiri, P.D. Dixit, S. Merchant, M.E. Paulaitis, L.R. Pratt, S.B. Rempe and S. Varma, Ion selectivity from local configuration of ligands in solutions and ion channels. Chem. Phys. Letts. 485: 1-7, 2010 Cover Article View

  40. S. Varma and S.B. Rempe, Structural transitions in ion coordination driven by changes in competition for ligand binding. J Amer. Chem. Soc. 130, 15405-15419, 2008. View

  41. D. Sabo, S. Varma, M. Martin and S.B. Rempe, Studies of the thermodynamic properties of hydrogen gas in bulk water. J Phys. Chem. B.112, 867-876, 2008. View

  42. S. Varma, D. Sabo and S.B. Rempe, K+/Na+ selectivity in K-channels and Valinomycin: Over-coordination Vs Cavity-size constraints. J Mol. Biol. 376, 13-22, 2008. View

  43. T. Whitfield, S. Varma, E. Harder, G. Lamoureux, S.B. Rempe and B. Roux, Theoretical Study of Aqueous solvation of K+: Comparison of ab initio, polarizable and fixed charge models. J Chem. Theo. Comput. 3, 2068-2082, 2007. View

  44. S. Varma and S.B. Rempe, Tuning ion coordination architectures to enable selective partitioning. Biophys J. 93, 1093-1099, 2007. New and Notable article View

  45. S. Varma and E. Jakobsson, The cPLA2 C2α Domain in Solution: Structure and Dynamics of its Ca2+-activated and Cation-free States. Biophys. J., 92, 966-976, 2007.View

  46. S. Varma and S.B. Rempe, Coordination numbers of alkali metal ions in aqueous solutions. J Biophys. Chem., 124, 192-199, 2006. Invited Review View

  47. S. Varma, S. W. Chiu and E. Jakobsson, The influence of amino acid protonation states on molecular dynamics simulations of a bacterial porin OmpF. Biophys. J., 90, 112-123, 2006. View

  48. N.J. Malmberg, S. Varma, E. Jakobsson and J.J. Falke, Ca2+ Activation of the cPLA2 C2 Domain: Ordered Binding of Two Ca2+ Ions with Positive Cooperativity. Biochemistry, 43, 16320-16328, 2004. View

  49. S. Natarajan, S. Varma, Y. Tang, S. Parker, J. Mashl and E. Jakobsson, Toward an Integrated Computational Environment for Multiscale Computational Design of Nanoscale Ion Channel Semiconductors, ICCN, 1, 147-150, 2004. View

  50. S. Varma and E. Jakobsson, Ionization states of residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions between Residues. Biophys. J, 86, 690-704, 2004. View

  51. T. van der Straaten., S. Varma, C-W Chiu, Y. Tang, N.R. Aluru, R. Eisenberg, U. Ravaioli and E. Jakobsson, Combining Computational Chemistry and Computational Electronics to Understand Protein Ion Channels. ICCN, 2, 60-63, 2002. View