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Alexander J. Sodt, Ph.D. - Publications

Affiliations: 
2007 University of California, Berkeley, Berkeley, CA, United States 
Area:
Theoretical Chemistry
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44 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
2022 Guo SK, Sodt AJ, Johnson ME. Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins. Plos Computational Biology. 18: e1009969. PMID 35312692 DOI: 10.1371/journal.pcbi.1009969  0.432
2020 Dorrell MW, Heberle FA, Katsaras J, Maibaum L, Lyman E, Sodt AJ. Laterally resolved small-angle scattering intensity from lipid bilayer simulations: an exact and a limited-range treatment. Journal of Chemical Theory and Computation. PMID 32579370 DOI: 10.1021/Acs.Jctc.0C00132  0.377
2020 Fu Y, Sodt AJ, Johnson ME. An Implicit Lipid Model for Efficient Reaction Diffusion Simulations of Proteins Binding to Arbitrary Surfaces Biophysical Journal. 118: 240a. DOI: 10.1016/J.Bpj.2019.11.1412  0.464
2019 Sapp K, Maibaum L, Sodt AJ. Simple differences in the protein-membrane attachment mechanism have functional consequences for surface mechanics. The Journal of Chemical Physics. 151: 164116. PMID 31675881 DOI: 10.1063/1.5119088  0.333
2019 Fu Y, Yogurtcu ON, Kothari R, Thorkelsdottir G, Sodt AJ, Johnson ME. An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology. The Journal of Chemical Physics. 151: 124115. PMID 31575182 DOI: 10.1063/1.5120516  0.519
2019 Allender DW, Sodt AJ, Schick M. Cholesterol-Dependent Bending Energy Is Important in Cholesterol Distribution of the Plasma Membrane. Biophysical Journal. 116: 2356-2366. PMID 31023537 DOI: 10.1016/J.Bpj.2019.03.028  0.306
2019 Sodt A, Sapp K, Dorrell M, Beaven AH. Deciphering Nanometer-Scale Lipid Structure and Physics to Model Membrane Reshaping Biophysical Journal. 116: 7a. DOI: 10.1016/J.Bpj.2018.11.070  0.303
2018 Lessen HJ, Fleming PJ, Fleming KG, Sodt AJ. Building Blocks of the Outer Membrane: Calculating a general elastic energy model for β-barrel membrane proteins. Journal of Chemical Theory and Computation. PMID 29979594 DOI: 10.1021/Acs.Jctc.8B00377  0.322
2018 Freeman CM, Sodt AJ. Computationally Determined Free Energy Profiles of the Mucin-1 Transmembrane Homodimer Biophysical Journal. 114: 73a. DOI: 10.1016/J.Bpj.2017.11.445  0.345
2017 Sodt AJ, Beaven AH, Andersen OS, Im W, Pastor RW. Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model. Biophysical Journal. 112: 1198-1213. PMID 28355547 DOI: 10.1016/J.Bpj.2017.01.035  0.32
2017 Beaven AH, Sodt AJ, Pastor RW, Im W. Protocol and Validation of CHARMM-GUI Hex Phase Builder Biophysical Journal. 112: 73a-74a. DOI: 10.1016/J.Bpj.2016.11.442  0.315
2016 Sodt AJ, Venable RM, Lyman E, Pastor RW. Nonadditive Compositional Curvature Energetics of Lipid Bilayers. Physical Review Letters. 117: 138104. PMID 27715135 DOI: 10.1103/Physrevlett.117.138104  0.32
2016 Lyman E, Sodt AJ. Amphipathic Helices-Wedge? Or Nae Nae? Biophysical Journal. 110: 1-2. PMID 26745402 DOI: 10.1016/J.Bpj.2015.11.3513  0.305
2016 Sodt AJ, Soubias O, Gawrisch K, Pastor RW. Lipid-Lipid Coupling to Membrane Curvature by Simulation and NMR Biophysical Journal. 110: 243a. DOI: 10.1016/J.Bpj.2015.11.1340  0.354
2016 Soubias O, Sodt AJ, Teague WE, Hines KG, Gawrisch K. Controlling GPCR Rhodopsin Function by Small, Physiologically Relevant Changes in Bilayer Hydrophobic Thickness Biophysical Journal. 110: 205a. DOI: 10.1016/J.Bpj.2015.11.1142  0.301
2015 Sodt AJ, Mei Y, König G, Tao P, Steele RP, Brooks BR, Shao Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. The Journal of Physical Chemistry. A. 119: 1511-23. PMID 25321186 DOI: 10.1021/Jp5072296  0.714
2015 Perrin BS, Sodt AJ, Cotten ML, Pastor RW. The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length. The Journal of Membrane Biology. 248: 455-67. PMID 25292264 DOI: 10.1016/J.Bpj.2014.11.2723  0.309
2015 Beaven AH, Sodt AJ, Andersen OS, Pastor RW, Im W. Ion Channel Regulation by Lipid Bilayers: Theory & Simulation of Deformed Membranes around Gramicidin A Biophysical Journal. 108: 209a. DOI: 10.1016/J.Bpj.2014.11.1155  0.333
2015 Sodt AJ, Venable RM, Lyman E, Pastor RW. Lipid-Lipid Interactions Determine the Membrane Spontaneous Curvature Biophysical Journal. 108: 181a. DOI: 10.1016/J.Bpj.2014.11.1002  0.317
2014 Tao P, Sodt AJ, Shao Y, König G, Brooks BR. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics. Journal of Chemical Theory and Computation. 10: 4198-4207. PMID 25328492 DOI: 10.1021/Ct500342H  0.56
2014 Sodt AJ, Pastor RW. Molecular modeling of lipid membrane curvature induction by a peptide: more than simply shape. Biophysical Journal. 106: 1958-69. PMID 24806928 DOI: 10.1016/J.Bpj.2014.02.037  0.35
2014 Lyman ER, Sodt A, Gawrisch K, Pastor R. The Molecular Structure of the Liquid Ordered Phase Biophysical Journal. 106: 634a. DOI: 10.1016/J.Bpj.2013.11.3505  0.308
2014 Sodt AJ, Pastor RW. Quantitative Molecular Modeling of Membrane Curvature Induction by an Amphipathic Helix Biophysical Journal. 106: 505a. DOI: 10.1016/J.Bpj.2013.11.2828  0.313
2013 Sodt AJ, Pastor RW. Bending free energy from simulation: correspondence of planar and inverse hexagonal lipid phases. Biophysical Journal. 104: 2202-11. PMID 23708360 DOI: 10.1016/J.Bpj.2013.03.048  0.318
2013 Zhang L, Sodt AJ, Venable RM, Pastor RW, Buck M. Prediction, refinement, and persistency of transmembrane helix dimers in lipid bilayers using implicit and explicit solvent/lipid representations: microsecond molecular dynamics simulations of ErbB1/B2 and EphA1. Proteins. 81: 365-76. PMID 23042146 DOI: 10.1002/Prot.24192  0.337
2013 Sodt AJ, Pastor RW. Lipid Bilayer Curvature Frustration Biophysical Journal. 104: 91a. DOI: 10.1016/J.Bpj.2012.11.545  0.342
2012 Sodt AJ, Pastor RW. The tension of a curved surface from simulation. The Journal of Chemical Physics. 137: 234101. PMID 23267465 DOI: 10.1063/1.4769880  0.336
2012 Zhang L, Sodt A, Venable R, Pastor RW, Buck M. Molecular Dynamics Prediction and Refinement of Transmembrane Helix Dimers Biophysical Journal. 102: 497a-498a. DOI: 10.1016/J.Bpj.2011.11.2723  0.33
2012 Sodt AJ, Pastor RW. Lipid Mechanical Properties from Computer Simulation Biophysical Journal. 102: 291a. DOI: 10.1016/J.Bpj.2011.11.1611  0.353
2011 Sodt AJ, Pastor RW. The Lateral Stress Profiles of Lipid Bilayers Compared with Spontaneous Lipid Curvature Using Computer Simulations Biophysical Journal. 100: 333a. DOI: 10.1016/J.Bpj.2010.12.2019  0.307
2010 Sodt AJ, Head-Gordon T. Driving forces for transmembrane α-helix oligomerization Biophysical Journal. 99: 227-237. PMID 20655851 DOI: 10.1016/J.Bpj.2010.03.071  0.521
2010 Sodt AJ, Head-Gordon T. An implicit solvent coarse-grained lipid model with correct stress profile. The Journal of Chemical Physics. 132: 205103. PMID 20515115 DOI: 10.1063/1.3408285  0.546
2010 Subotnik JE, Vura-Weis J, Sodt AJ, Ratner MA. Predicting accurate electronic excitation transfer rates via marcus theory with Boys or Edmiston-Ruedenberg localized diabatization. The Journal of Physical Chemistry. A. 114: 8665-75. PMID 20446743 DOI: 10.1021/Jp101235A  0.592
2010 Sodt AJ, Head-Gordon T. An implicit solvent coarse-grained lipid model with correct stress profile Journal of Chemical Physics. 132. DOI: 10.1063/1.3408285  0.447
2008 Sodt A, Head-Gordon M. Hartree-Fock exchange computed using the atomic resolution of the identity approximation. The Journal of Chemical Physics. 128: 104106. PMID 18345876 DOI: 10.1063/1.2828533  0.513
2008 Subotnik JE, Sodt A, Head-Gordon M. The limits of local correlation theory: electronic delocalization and chemically smooth potential energy surfaces. The Journal of Chemical Physics. 128: 034103. PMID 18205484 DOI: 10.1063/1.2821124  0.705
2007 Subotnik JE, Sodt A, Head-Gordon M. Localized orbital theory and ammonia triborane. Physical Chemistry Chemical Physics : Pccp. 9: 5522-30. PMID 17957308 DOI: 10.1039/B709171K  0.679
2006 Sodt A, Subotnik JE, Head-Gordon M. Linear scaling density fitting. The Journal of Chemical Physics. 125: 194109. PMID 17129091 DOI: 10.1063/1.2370949  0.653
2006 Subotnik JE, Sodt A, Head-Gordon M. A near linear-scaling smooth local coupled cluster algorithm for electronic structure. The Journal of Chemical Physics. 125: 074116. PMID 16942331 DOI: 10.1063/1.2336426  0.72
2006 Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA, Lochan RC, Wang T, Beran GJ, Besley NA, ... ... Sodt A, et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics : Pccp. 8: 3172-91. PMID 16902710 DOI: 10.1039/B517914A  0.475
2006 Sodt A, Beran GJO, Jung Y, Austin B, Head-Gordon M. A fast implementation of perfect pairing and imperfect pairing using the resolution of the identity approximation Journal of Chemical Theory and Computation. 2: 300-305. DOI: 10.1021/ct050239b  0.589
2005 Beran GJ, Austin B, Sodt A, Head-Gordon M. Unrestricted perfect pairing: the simplest wave-function-based model chemistry beyond mean field. The Journal of Physical Chemistry. A. 109: 9183-92. PMID 16332028 DOI: 10.1021/Jp053780C  0.759
2005 Jung Y, Sodt A, Gill PM, Head-Gordon M. Auxiliary basis expansions for large-scale electronic structure calculations. Proceedings of the National Academy of Sciences of the United States of America. 102: 6692-7. PMID 15845767 DOI: 10.1073/Pnas.0408475102  0.636
2005 Head-Gordon M, Beran GJO, Sodt A, Jung Y. Fast electronic structure methods for strongly correlated molecular systems Journal of Physics: Conference Series. 16: 233-242. DOI: 10.1088/1742-6596/16/1/031  0.693
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