Alexander J. Sodt, Ph.D. - Publications

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

26 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
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