Alexander J. Sodt, Ph.D. - Publications

Affiliations: 
2007 University of California, Berkeley, Berkeley, CA 
Area:
Theoretical Chemistry

26/71 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 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  0.4
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  0.96
2015 Sodt AJ, Pastor RW, Lyman E. Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin. Biophysical Journal. 109: 948-55. PMID 26331252 DOI: 10.1016/j.bpj.2015.07.036  0.96
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  0.96
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: 10.1007/s00232-014-9733-1  0.96
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  0.96
2014 Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophysical Journal. 107: 134-45. PMID 24988348 DOI: 10.1016/j.bpj.2014.05.034  0.96
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  0.96
2014 Sodt AJ, Sandar ML, Gawrisch K, Pastor RW, Lyman E. The molecular structure of the liquid-ordered phase of lipid bilayers. Journal of the American Chemical Society. 136: 725-32. PMID 24345334 DOI: 10.1021/ja4105667  0.96
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  0.96
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  0.96
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  0.96
2012 Pfefferkorn CM, Heinrich F, Sodt AJ, Maltsev AS, Pastor RW, Lee JC. Depth of α-synuclein in a bilayer determined by fluorescence, neutron reflectometry, and computation. Biophysical Journal. 102: 613-21. PMID 22325285 DOI: 10.1016/j.bpj.2011.12.051  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
Low-probability matches
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  0.24
2017 Chlanda P, Mekhedov E, Waters H, Sodt A, Schwartz C, Nair V, Blank PS, Zimmerberg J. Palmitoylation contributes to membrane curvature in Influenza A virus assembly and hemagglutinin-mediated membrane fusion. Journal of Virology. PMID 28794042 DOI: 10.1128/JVI.00947-17  0.04
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  0.04
2020 Dorrell M, Beaven AH, Sodt AJ. A combined molecular/continuum-modeling approach to predict the small-angle neutron scattering of curved membranes. Chemistry and Physics of Lipids. 104983. PMID 33035544 DOI: 10.1016/j.chemphyslip.2020.104983  0.01
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  0.01
2020 Lyman E, Sodt AJ. Differential or Curvature Stress? Modus Vivendi. Biophysical Journal. 118: 535-537. PMID 32023440 DOI: 10.1016/j.bpj.2019.11.3399  0.01
2020 Sapp K, Sodt AJ. Continuum-Modeling Software for Modeling the Dynamics of Arbitrary Topology Membranes Biophysical Journal. 118: 84a. DOI: 10.1016/j.bpj.2019.11.626  0.01
2020 Beaven AH, Sodt AJ. All-Atom Molecular Dynamics Simulations of Ganglioside GM1 and its Degradation Products Biophysical Journal. 118: 83a. DOI: 10.1016/j.bpj.2019.11.623  0.01
2020 Beaven AH, Sapp K, Sodt AJ. Partially Automated Identification of Curvature-Sensitive Collective Lipid Structure Biophysical Journal. 118: 77a-78a. DOI: 10.1016/j.bpj.2019.11.596  0.01
2020 Galimzyanov TR, Beaven AH, Kalutskiy MA, Sodt AJ, Blank PS, Zimmerberg J, Akimov SA, Batishchev OV. Effect of Lipid Structure and Material Properties on the Membrane Stability to Pore Formation Biophysical Journal. 118: 390a. DOI: 10.1016/j.bpj.2019.11.2221  0.01
2020 Leonard A, Sodt AJ, Lyman ER. Lipid Chain Entropy and Exchange in the Vicinity of G-Protein Coupled Receptors Biophysical Journal. 118: 242a. DOI: 10.1016/j.bpj.2019.11.1421  0.01
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  0.01
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  0.01
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  0.01
2019 Smith DJ, Klauda JB, Sodt AJ. Simulation Best Practices for Lipid Membranes [Article v1.0] Living Journal of Computational Molecular Science. 1. DOI: 10.33011/livecoms.1.1.5966  0.01
2019 Allender D, Sodt AJ, Schick M. Cholesterol-Dependent Bending Energies in Both Leaves Play a Significant Role in Determining the Cholesterol Distribution in the Plasma Membrane Biophysical Journal. 116: 88a. DOI: 10.1016/j.bpj.2018.11.518  0.01
2019 Beaven AH, Sodt AJ. Molecular Simulation and Continuum Modeling of N-Bar-Induced Lipid Membrane Deformations Biophysical Journal. 116: 374a. DOI: 10.1016/j.bpj.2018.11.2032  0.01
2019 Sapp K, Sodt AJ, Maibaum L. Modeling Relaxation Timescales of Coupled Membrane/Protein Systems Biophysical Journal. 116: 363a. DOI: 10.1016/J.BPJ.2018.11.1975  0.01
2019 Lessen HJ, Fleming P, Fleming KG, Sodt AJ. Transmembrane Beta-Barrel Proteins Rigidify the Bacterial Outer Membrane Biophysical Journal. 116: 327a. DOI: 10.1016/j.bpj.2018.11.1774  0.01
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  0.01
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  0.01
2018 Sapp K, Sodt A. Exploring Apparent Membrane Stiffness due to the Presence of GM1 using a Continuum Model Biophysical Journal. 114: 95a. DOI: 10.1016/j.bpj.2017.11.561  0.01
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  0.01
2017 Beaven AH, Sodt AJ, Pastor RW, Koeppe RE, Andersen OS, Im W. Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. Journal of Chemical Theory and Computation. PMID 28870079 DOI: 10.1021/acs.jctc.7b00400  0.01
2017 Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W. Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. Biophysical Journal. 112: 1185-1197. PMID 28355546 DOI: 10.1016/j.bpj.2017.01.028  0.01
2017 Gurnev PA, Roark TC, Petrache HI, Sodt AJ, Bezrukov SM. Cation-Selective Channel Regulated by Anions According to Their Hofmeister Ranking. Angewandte Chemie (International Ed. in English). PMID 28198582 DOI: 10.1002/anie.201611335  0.01
2017 Freeman CM, Sodt AJ. Investigating MUC1 Transmembrane Dimer Structure using Replica Exchange Molecular Dynamics Biophysical Journal. 112: 89a. DOI: 10.1016/j.bpj.2016.11.522  0.01
2017 Chlanda P, Mekhedov E, Waters H, Sodt A, Blank PS, Zimmerberg J. Hemagglutinin Palmitoylation Contributes to Membrane Curvature in Influenza a Virus Assembly and Membrane Fusion Biophysical Journal. 112: 80a. DOI: 10.1016/j.bpj.2016.11.477  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
2014 Thompson CL, Ng L, Menon V, Martinez S, Lee CK, Glattfelder K, Sunkin SM, Henry A, Lau C, Dang C, Garcia-Lopez R, Martinez-Ferre A, Pombero A, Rubenstein JL, Wakeman WB, ... ... Sodt AJ, et al. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron. 83: 309-23. PMID 24952961 DOI: 10.1016/j.neuron.2014.05.033  0.01
2014 Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, ... ... Sodt AJ, et al. Transcriptional landscape of the prenatal human brain. Nature. 508: 199-206. PMID 24695229 DOI: 10.1038/nature13185  0.01
2014 Beaven AH, Sodt AJ, Greathouse DV, Koeppe RE, Pastor RW, Andersen OS, Im W. All-Atom Simulation and Continuum Elastic Theory of Gramicidin a in Binary Component Lipid Bilayers Biophysical Journal. 106: 801a. DOI: 10.1016/j.bpj.2013.11.4389  0.01
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  0.01
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  0.01
2013 Sodt AJ, Pastor RW. Lipid Bilayer Curvature Frustration Biophysical Journal. 104: 91a. DOI: 10.1016/j.bpj.2012.11.545  0.01
2012 Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, van de Lagemaat LN, Smith KA, Ebbert A, Riley ZL, Abajian C, Beckmann CF, Bernard A, Bertagnolli D, Boe AF, ... ... Sodt AJ, et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature. 489: 391-9. PMID 22996553 DOI: 10.1038/nature11405  0.01
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  0.01
2012 Sodt AJ, Pastor RW. Lipid Mechanical Properties from Computer Simulation Biophysical Journal. 102: 291a. DOI: 10.1016/j.bpj.2011.11.1611  0.01
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  0.01
2007 Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, ... ... Sodt AJ, et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature. 445: 168-76. PMID 17151600 DOI: 10.1038/nature05453  0.01
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