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Edward Lyman, Ph.D. - Publications

Affiliations: 
2004 Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
Condensed Matter Physics, Fluid and Plasma Physics
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52 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
2023 Fitzgerald JE, Venable RM, Pastor RW, Lyman ER. Surface viscosities of lipid bilayers determined from equilibrium molecular dynamics simulations. Biophysical Journal. PMID 36739477 DOI: 10.1016/j.bpj.2023.01.038  0.327
2021 Beaven AH, Arnarez C, Lyman E, Bennett WFD, Sodt AJ. Curvature Energetics Determined by Alchemical Simulation on Four Topologically Distinct Lipid Phases. The Journal of Physical Chemistry. B. PMID 33570958 DOI: 10.1021/acs.jpcb.0c09458  0.305
2020 Baral S, Levental I, Lyman E. Composition dependence of cholesterol flip-flop rates in physiological mixtures. Chemistry and Physics of Lipids. 232: 104967. PMID 32888914 DOI: 10.1016/J.Chemphyslip.2020.104967  0.373
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  0.422
2020 Lorent JH, Levental KR, Ganesan L, Rivera-Longsworth G, Sezgin E, Doktorova MD, Lyman E, Levental I. Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape. Nature Chemical Biology. PMID 32367017 DOI: 10.1038/S41589-020-0529-6  0.349
2020 Baral S, Phillips M, Yan H, Avenso J, Gundlach L, Baumeier B, Lyman E. Ultrafast Formation of the Charge-transfer State of Prodan Reveals Unique Aspects of the Chromophore Environment. The Journal of Physical Chemistry. B. PMID 32160469 DOI: 10.1021/Acs.Jpcb.0C00121  0.327
2019 Ghysels A, Krämer A, Venable RM, Teague WE, Lyman E, Gawrisch K, Pastor RW. Permeability of membranes in the liquid ordered and liquid disordered phases. Nature Communications. 10: 5616. PMID 31819053 DOI: 10.1038/S41467-019-13432-7  0.364
2019 Yang L, Lyman E. Local Enrichment of Unsaturated Chains Around the A Adenosine Receptor. Biochemistry. PMID 31496229 DOI: 10.1021/Acs.Biochem.9B00607  0.384
2019 Zgorski A, Lyman E, Pastor RW. Surface Shear Viscosity and Interleaflet Friction from Nonequilibrium Simulations of Lipid Bilayers. Journal of Chemical Theory and Computation. PMID 31476126 DOI: 10.1021/Acs.Jctc.9B00683  0.366
2019 Pinkwart K, Schneider F, Lukoseviciute M, Sauka-Spengler T, Lyman E, Eggeling C, Sezgin E. Nanoscale dynamics of cholesterol in the cell membrane. The Journal of Biological Chemistry. PMID 31270209 DOI: 10.1074/Jbc.Ra119.009683  0.324
2019 McGraw C, Yang L, Levental I, Lyman E, Skaja-Robinson A. Membrane cholesterol depletion reduces downstream signaling activity of the adenosine A receptor. Biochimica Et Biophysica Acta. Biomembranes. PMID 30629951 DOI: 10.1016/J.Bbamem.2019.01.001  0.318
2018 Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, ... ... Lyman E, et al. Neutron scattering in the biological sciences: progress and prospects. Acta Crystallographica. Section D, Structural Biology. 74: 1129-1168. PMID 30605130 DOI: 10.1107/S2059798318017503  0.31
2018 Lyman E, Hsieh CL, Eggeling C. From Dynamics to Membrane Organization: Experimental Breakthroughs Occasion a "Modeling Manifesto". Biophysical Journal. PMID 30075850 DOI: 10.1016/J.Bpj.2018.07.012  0.413
2018 Baral S, Baumeier B, Lyman E. Predicting Spectral Properties of Polarity Sensitive Dyes with QM/MM Simulation Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.1572  0.388
2017 Rouviere E, Arnarez C, Yang L, Lyman E. Identification of Two New Cholesterol Interaction Sites on the A2A Adenosine Receptor. Biophysical Journal. 113: 2415-2424. PMID 29211995 DOI: 10.1016/J.Bpj.2017.09.027  0.352
2017 Zgorski A, Lyman E. STRD MARTINI: Simulating Quasi-2D Hydrodynamics with Chemically Detailed Lipid Models Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.763  0.419
2017 Rouviere E, Arnarez C, Lyman E. Automated Identification of Cholesterol Interaction Sites on G-Protein Coupled Receptors by Coarse-Grained Simulation Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.2128  0.385
2017 Webb A, Arnarez C, Lyman E. Hysteresis and the Cholesterol-Dependent Melting Transition of the Martini Model Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.2088  0.366
2016 Zgorski A, Lyman E. Toward Hydrodynamics with Solvent Free Lipid Models: STRD Martini. Biophysical Journal. 111: 2689-2697. PMID 28002745 DOI: 10.1016/J.Bpj.2016.11.010  0.44
2016 Arnarez C, Webb A, Rouvière E, Lyman E. Hysteresis and the Cholesterol Dependent Phase Transition in Binary Lipid Mixtures with the Martini Model. The Journal of Physical Chemistry. B. PMID 27976582 DOI: 10.1021/Acs.Jpcb.6B09728  0.37
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  0.355
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  0.343
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  0.325
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  0.366
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  0.351
2013 Lee JY, Patel R, Lyman E. Ligand-dependent cholesterol interactions with the human A(2A) adenosine receptor. Chemistry and Physics of Lipids. 169: 39-45. PMID 23454349 DOI: 10.1016/J.Chemphyslip.2013.02.002  0.328
2013 Cui H, Mim C, Vázquez FX, Lyman E, Unger VM, Voth GA. Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling. Biophysical Journal. 104: 404-11. PMID 23442862 DOI: 10.1016/J.Bpj.2012.12.006  0.313
2012 Lai CL, Jao CC, Lyman E, Gallop JL, Peter BJ, McMahon HT, Langen R, Voth GA. Membrane binding and self-association of the epsin N-terminal homology domain. Journal of Molecular Biology. 423: 800-17. PMID 22922484 DOI: 10.1016/J.Jmb.2012.08.010  0.352
2012 Lee JY, Lyman E. Agonist dynamics and conformational selection during microsecond simulations of the A(2A) adenosine receptor. Biophysical Journal. 102: 2114-20. PMID 22824275 DOI: 10.1016/J.Bpj.2012.03.061  0.317
2012 Mim C, Cui H, Gawronski-Salerno JA, Frost A, Lyman E, Voth GA, Unger VM. Structural basis of membrane bending by the N-BAR protein endophilin. Cell. 149: 137-45. PMID 22464326 DOI: 10.1016/J.Cell.2012.01.048  0.349
2012 Simunovic M, Lyman E, Voth GA. Relating Molecular Interactions with N-BAR Domains to the Mesoscopic Nature of Membrane Remodeling Biophysical Journal. 102: 296a. DOI: 10.1016/J.Bpj.2011.11.1638  0.421
2012 Lee JY, Lyman E. Ligand Dynamics during Microsecond Simulations of the A2a Adenosine Receptor Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.1346  0.3
2011 Lyman E, Cui H, Voth GA. Reconstructing protein remodeled membranes in molecular detail from mesoscopic models. Physical Chemistry Chemical Physics : Pccp. 13: 10430-6. PMID 21503332 DOI: 10.1039/C0Cp02978E  0.394
2011 Cui H, Lyman E, Voth GA. Mechanism of membrane curvature sensing by amphipathic helix containing proteins. Biophysical Journal. 100: 1271-9. PMID 21354400 DOI: 10.1016/J.Bpj.2011.01.036  0.329
2011 Cui H, Lyman E, Voth GA. Coarse-Grained Simulations of Membrane Remodeling by Bar Domains Biophysical Journal. 100: 405a. DOI: 10.1016/J.Bpj.2010.12.2404  0.409
2010 Ayton GS, Lyman E, Voth GA. Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discussions. 144: 347-57; discussion 4. PMID 20158037 DOI: 10.1039/B901996K  0.414
2010 Pfaendtner J, Lyman E, Pollard TD, Voth GA. Structure and dynamics of the actin filament. Journal of Molecular Biology. 396: 252-63. PMID 19931282 DOI: 10.1016/J.Jmb.2009.11.034  0.329
2009 Lyman E, Higgs C, Kim B, Lupyan D, Shelley JC, Farid R, Voth GA. A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor. Structure (London, England : 1993). 17: 1660-8. PMID 20004169 DOI: 10.1016/J.Str.2009.10.010  0.314
2009 Ayton GS, Lyman E, Krishna V, Swenson RD, Mim C, Unger VM, Voth GA. New insights into BAR domain-induced membrane remodeling. Biophysical Journal. 97: 1616-25. PMID 19751666 DOI: 10.1016/J.Bpj.2009.06.036  0.371
2009 Lyman E, Zuckerman DM. Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol. The Journal of Chemical Physics. 130: 081102. PMID 19256587 DOI: 10.1063/1.3081626  0.58
2009 Lyman ER, Ayton GS, Voth GA. Membrane Remodeling By N-bar Domains At All Scales: Theory And Simulation Of The Ensemble Effect Biophysical Journal. 96: 453a. DOI: 10.1016/J.Bpj.2008.12.2328  0.311
2008 Liu P, Shi Q, Lyman E, Voth GA. Reconstructing atomistic detail for coarse-grained models with resolution exchange. The Journal of Chemical Physics. 129: 114103. PMID 19044946 DOI: 10.1063/1.2976663  0.419
2008 Lyman E, Pfaendtner J, Voth GA. Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophysical Journal. 95: 4183-92. PMID 18658214 DOI: 10.1529/Biophysj.108.139733  0.346
2007 Lyman E, Zuckerman DM. On the structural convergence of biomolecular simulations by determination of the effective sample size. The Journal of Physical Chemistry. B. 111: 12876-82. PMID 17935314 DOI: 10.1021/Jp073061T  0.614
2007 Lyman E, Zuckerman DM. Annealed importance sampling of peptides. The Journal of Chemical Physics. 127: 065101. PMID 17705625 DOI: 10.1063/1.2754267  0.614
2006 Zuckerman DM, Lyman E. A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]. Journal of Chemical Theory and Computation. 2: 1693. PMID 26627040 DOI: 10.1021/Ct600297Q  0.588
2006 Lyman E, Zuckerman DM. Resolution Exchange Simulation with Incremental Coarsening. Journal of Chemical Theory and Computation. 2: 656-66. PMID 26626672 DOI: 10.1021/Ct050337X  0.62
2006 Zuckerman DM, Lyman E. A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation. Journal of Chemical Theory and Computation. 2: 12001202. PMID 19043602 DOI: 10.1021/Ct0600464  0.639
2006 Lyman E, Zuckerman DM. Ensemble-based convergence analysis of biomolecular trajectories. Biophysical Journal. 91: 164-72. PMID 16617086 DOI: 10.1529/Biophysj.106.082941  0.601
2006 Lyman E, Ytreberg FM, Zuckerman DM. Resolution exchange simulation. Physical Review Letters. 96: 028105. PMID 16486650 DOI: 10.1103/Physrevlett.96.028105  0.625
2005 Lyman E, Schmittmann B. Steady states of a nonequilibrium lattice gas. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 036127. PMID 16241535 DOI: 10.1103/Physreve.72.036127  0.561
2002 Lyman E, Schmittmann B. Phase diagram of a driven interacting three-state lattice gas Journal of Physics a: Mathematical and General. 35. DOI: 10.1088/0305-4470/35/16/102  0.576
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