Publications of Gerhard Hummer

Journal Article (324)

2008
Journal Article
Köfinger, J.; Hummer, G.; Dellago, C.: Macroscopically ordered water in nanopores. Proceedings of the National Academy of Sciences of the United States of America 105 (36), pp. 13218 - 13222 (2008)
Journal Article
Kim, Y. C.; Tang, C.; Clore, G. M.; Hummer, G.: Replica exchange simulations of transient encounter complexes in protein-protein association. Proceedings of the National Academy of Sciences of the United States of America 105 (35), pp. 12855 - 12860 (2008)
Journal Article
Tikhonova, I. G.; Best, R. B.; Engel, S.; Gershengorn, M. C.; Hummer, G.; Costanzi, S.: Atomistic insights into rhodopsin activation from a dynamic model. Journal of the American Chemical Society 130 (31), pp. 10141 - 10149 (2008)
Journal Article
Kaila, V. R. I.; Verkhovsky, M.; Hummer, G.; Wikström, M.: Prevention of leak in the proton pump of cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - General Subjects 1777 (7-8), pp. 890 - 892 (2008)
Journal Article
Best, R. B.; Buchete, N.-V.; Hummer, G.: Are current molecular dynamics force fields too helical? Biophysical Journal 95 (1), pp. L07 - L09 (2008)
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Eaton, W. A.; Hummer, G.; Zwanzig, R. W.: A tribute to Attila Szabo. The Journal of Physical Chemistry B 112 (19), pp. 5881 - 5882 (2008)
Journal Article
Best, R. B.; Paci, E.; Hummer, G.; Dudko, O. K.: Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. The Journal of Physical Chemistry B 112 (19), pp. 5968 - 5976 (2008)
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Buchete, N.-V.; Hummer, G.: Coarse master equations for peptide folding dynamics. The Journal of Physical Chemistry B 112 (19), pp. 6057 - 6069 (2008)
Journal Article
Canagarajah, B. J.; Hummer, G.; Prinz, W. A.; Hurley, J. H.: Dynamics of cholesterol exchange in the oxysterol binding protein family. Journal of Molecular Biology 378 (3), pp. 737 - 748 (2008)
Journal Article
Kaila, V. R. I.; Verkhovsky, M. I.; Hummer, G.; Wikström, M.: Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America 105 (17), pp. 6255 - 6259 (2008)
Journal Article
Mittal, J.; Truskett, T. M.; Errington, J. R.; Hummer, G.: Layering and position-dependent diffusive dynamics of confined fluids. Physical Review Letters 100 (14), p. 145901 (4) (2008)
Journal Article
Turjanski, A. G.; Gutkind, J. S.; Best, R. B.; Hummer, G.: Binding-induced folding of a natively unstructured transcription factor. PLoS Computational Biology 4 (4), e1000060 (2008)
Journal Article
Best, R. B.; Hummer, G.: Protein folding kinetics under force from molecular simulation. Journal of the American Chemical Society 130 (12), pp. 3706 - 3707 (2008)
Journal Article
Buchete, N.-V.; Hummer, G.: Peptide folding kinetics from replica exchange molecular dynamics. Physical Review E 77 (3 Pt 1), pp. 030902-1 - 030902-4 (2008)
Journal Article
Kim, Y. C.; Hummer, G.: Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. Journal of Molecular Biology (London) 375 (5), pp. 1416 - 1433 (2008)
2007
Journal Article
Milac, A. L.; Buchete, N. V.; Fritz, T. A.; Hummer, G.; Tabak, L. A.: Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2. Journal of Molecular Biology 373 (2), pp. 439 - 451 (2007)
Journal Article
Zheng, W.; Brooks, B. R.; Hummer, G.: Protein conformational transitions explored by mixed elastic network models. Proteins: Structure, Function, and Bioinformatics 69 (1), pp. 43 - 57 (2007)
Journal Article
Hummer, G.: Water pulls the strings in hydrophobic polymer collapse. Proceedings of the National Academy of Sciences of the United States of America 104 (38), pp. 14883 - 14884 (2007)
Journal Article
Tuukkanen, A.; Kaila, V. R. I.; Laakkonen, L.; Hummer, G.; Wikström, M.: Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase. Biochimica et Biophysica Acta: BBA 1767 (9), pp. 1102 - 1106 (2007)
Journal Article
Dudko, O. K.; Mathé, J.; Szabo, A.; Meller, A.; Hummer, G.: Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophysical Journal (Annual Meeting Abstracts) 92 (12), pp. 4188 - 4195 (2007)
Journal Article
Yin, H.; Hummer, G.; Rasaiah, J. C.: Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. Journal of the American Chemical Society 129 (23), pp. 7369 - 7377 (2007)
Journal Article
Prag, G.; Watson, H.; Kim, Y. C.; Beach, B. M.; Ghirlando, R.; Hummer, G.; Bonifacino, J. S.; Hurley, J. H.: The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting. Developmental Cell 12 (6), pp. 973 - 986 (2007)
Journal Article
Buchete, N.-V.; Hummer, G.: Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils. Biophysical Journal (Annual Meeting Abstracts) 92 (9), pp. 3032 - 3039 (2007)
Journal Article
Collins, M. D.; Quillin, M. L.; Hummer, G.; Matthews, B. W.; Gruner, S. M.: Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. Journal of Molecular Biology (London) 367 (3), pp. 752 - 763 (2007)
Journal Article
Chen, Y.-G.; Hummer, G.: Slow conformational dynamics and unfolding of the calmodulin C-terminal domain. Journal of the American Chemical Society 129 (9), pp. 2414 - 2415 (2007)
Journal Article
Kim, Y. C.; Wikström, M.; Hummer, G.: Kinetic models of redox-coupled proton pumping. Proceedings of the National Academy of Sciences of the United States of America 104 (7), pp. 2169 - 2174 (2007)
Journal Article
Hummer, G.: Water, proton, and ion transport: from nanotubes to proteins. Molecular Physics 105 (2-3), pp. 201 - 207 (2007)
2006
Journal Article
Dellago, C.; Hummer, G.: Kinetics and mechanism of proton transport across membrane nanopores. Physical Review Letters 97 (24), 245901 (2006)
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Berezhkovskii, A. M.; Hummer, G.; Bezrukov, S. M.: Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels. Physical Review Letters 97 (2), 020601 (2006)
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Berezhkovskii, A. M.; Hummer, G.; Bezrukov, S. M.: Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels. Physical Review Letters 97 (2), 020601 (2006)
Journal Article
Best, R. B.; Hummer, G.: Diffusive model of protein folding dynamics with Kramers turnover in rate. Physical Review Letters 96 (22), 228104 (2006)
Journal Article
Hassan, S. A.; Hummer, G.; Lee, Y.-S.: Effects of electric fields on proton transport through water chains. The Journal of Chemical Physics 124 (20), 204510 (2006)
Journal Article
Dudko, O. K.; Hummer, G.; Szabo, A.: Intrinsic rates and activation free energies from single-molecule pulling experiments. Physical Review Letters 96 (10), 108101 (2006)
2005
Journal Article
Best, R. B.; Chen, Y.-G.; Hummer, G.: Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure 13 (12), pp. 1755 - 1763 (2005)
Journal Article
Collins, M. D.; Hummer, G.; Quillin, M. L.; Matthews, B. W.; Gruner, S. M.: Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proceedings of the National Academy of Sciences of the United States of America 102 (46), pp. 16668 - 16671 (2005)
Journal Article
Buchete, N.-V.; Tycko, R.; Hummer, G.: Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. Journal of Molecular Biology (London) 353 (4), pp. 804 - 821 (2005)
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Andreev, S.; Reichman, D.; Hummer, G.: Effect of flexibility on hydrophobic behavior of nanotube water channels. The Journal of Chemical Physics 123 (19), 194502 (2005)
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Peter, C.; Hummer, G.: Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations. Biophysical Journal 89 (4), pp. 2222 - 2234 (2005)
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Peter, C.; Hummer, G.: Ion Transport through Membrane-Spanning Nanopores Studiedby Molecular Dynamics Simulations and ContinuumElectrostatics Calculations. Biophysical Journal 89, pp. 2222 - 2234 (2005)
Journal Article
Sriraman, S.; Kevrekidis, I. G.; Hummer, G.: Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Physical Review Letters 95 (13), 130603 (2005)
Journal Article
Sriraman, S.; Kevrekidis, I. G.; Hummer, G.: Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Physical Review Letters 95 (13), 130603 (2005)
Journal Article
Hummer, G.; Szabo, A.: Free energy surfaces from single-molecule force spectroscopy. Accounts of Chemical Research 38 (7), pp. 504 - 513 (2005)
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Best, R. B.; Hummer, G.: Reaction coordinates and rates from transition paths. Proceedings of the National Academy of Sciences of the United States of America 102 (19), pp. 6732 - 6737 (2005)
Journal Article
Gustchina, E.; Hummer, G.; Bewley, C. A.; Clore, G. M.: Differential inhibition of HIV-1 and SIV envelope-mediated cell fusion by C34 peptides derived from the C-terminal heptad repeat of gp41 from diverse strains of HIV-1, HIV-2, and SIV. Journal of Medicinal Chemistry 48 (8), pp. 3036 - 3044 (2005)
Journal Article
Sriraman, S.; Kevrekidis, I. G.; Hummer, G.: Coarse master equation from Bayesian analysis of replica molecular dynamics simulations. The Journal of Physical Chemistry B 109 (14), pp. 6479 - 6484 (2005)
Journal Article
Hummer, G.: Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New Journal of Physics 7, 34 (2005)
2004
Journal Article
Vaitheeswaran, S.; Yin, H.; Rasaiah, J. C.; Hummer, G.: Water clusters in nonpolar cavities. Proceedings of the National Academy of Sciences of the United States of America 101 (49), pp. 17002 - 17005 (2004)
Journal Article
Hummer, G.; Schotte, F.; Anfinrud, P. A.: Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 101 (43), pp. 15330 - 15334 (2004)
Journal Article
Vaitheeswaran, S.; Rasaiah, J. C.; Hummer, G.: Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes. The Journal of Chemical Physics 121 (16), pp. 7955 - 7965 (2004)
Journal Article
Yeh, I.-C.; Hummer, G.: System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions. The Journal of Physical Chemistry B 108 (40), pp. 15873 - 15879 (2004)
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Yeh, I.-C.; Hummer, G.: Nucleic acid transport through carbon nanotube membranes. Proceedings of the National Academy of Sciences of the United States of America 101 (33), pp. 12177 - 12182 (2004)
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Kevrekidis, I. G.; Gear, C. W.; Hummer, G.: Equation-Free: The Computer-Aided Analysis of Complex Multiscale Systems. AIChE-Journal 50 (7), pp. 1346 - 1355 (2004)
Journal Article
Zweckstetter, M.; Hummer, G.; Bax, A.: Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophysical Journal (Annual Meeting Abstracts) 86 (6), pp. 3444 - 3460 (2004)
Journal Article
Yeh, I.-C.; Hummer, G.: Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophysical Journal (Annual Meeting Abstracts) 86 (2), pp. 681 - 689 (2004)
Journal Article
Hummer, G.: From transition paths to transition states and rate coefficients. The Journal of Chemical Physics 120 (2), pp. 516 - 523 (2004)
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Kalra, A.; Hummer, G.; Garde, S.: Methane Partitioning and ransport in Hydrated Carbon Nanotubes. The Journal of Physical Chemistry B 108 (2), pp. 544 - 549 (2004)
2003
Journal Article
Kalra, A.; Garde, S.; Hummer, G.: Osmotic water transport through carbon nanotube membranes. Proceedings of the National Academy of Sciences of the United States of America 100 (18), pp. 10175 - 10180 (2003)
Journal Article
Hummer, G.; Szabo, A.: Kinetics from nonequilibrium single-molecule pulling experiments. Biophysical Journal (Annual Meeting Abstracts) 85 (1), pp. 5 - 15 (2003)
Journal Article
Hummer, G.; Kevrekidis, I. G.: Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations. The Journal of Chemical Physics 118 (23), pp. 10762 - 10773 (2003)
Journal Article
Wikström, M.; Verkhovsky, M. I.; Hummer, G.: Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochimica et Biophysica Acta: BBA 1604 (2), pp. 61 - 65 (2003)
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Berezhkovskii, A.; Hummer, G.: Random Walk Model for Single‐File Transport of Water Molecules through Carbon Nanotubes. AIP Conference Proceedings 665 (1), pp. 267 - 272 (2003)
Journal Article
Taraphder, S.; Hummer, G.: Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam. Journal of the American Chemical Society 125 (13), pp. 3931 - 3940 (2003)
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Dellago, C.; Naor, M. M.; Hummer, G.: Proton transport through water-filled carbon nanotubes. Physical Review Letters 90 (10), 105902 (2003)
Journal Article
Taraphder, S.; Hummer, G.: Dynamic proton transfer pathways in proteins: role of sidechain conformational fluctuations. Physica A: Statistical and Theoretical Physics 318 (1), pp. 293 - 301 (2003)
2002
Journal Article
Waghe, A.; Rasaiah, J. C.; Hummer, G.: Filling and emptying kinetics of carbon nanotubes in water. The Journal of Chemical Physics 117 (23), pp. 10789 - 10795 (2002)
Journal Article
Berezhkovskii, A.; Hummer, G.: Single-file transport of water molecules through a carbon nanotube. Physical Review Letters 89 (6), 064503 (2002)
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Yeh, I.-C.; Hummer, G.: Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. Journal of the American Chemical Society 124 (23), pp. 6563 - 6568 (2002)
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Siebert, X.; Hummer, G.: Hydrophobicity maps of the N-peptide coiled coil of HIV-1 gp41. Biochemistry 41 (9), pp. 2956 - 2961 (2002)
Journal Article
Hummer, G.: Fast-growth Thermodynamic Integration∶ Results for Sodium Ion Hydration. Molecular Simulation 28 (1-2), pp. 81 - 90 (2002)
2001
Journal Article
Hummer, G.; Rasaiah, J. C.; Noworyta, J. P.: Water conduction through the hydrophobic channel of a carbon nanotube. Nature 414 (6860), pp. 188 - 190 (2001)
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Hummer, G.: Fast-growth thermodynamic integration: Error and efficiency analysis. The Journal of Chemical Physics 114 (17), pp. 7330 - 7337 (2001)
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Hummer, G.; Szabo, A.: Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proceedings of the National Academy of Sciences of the United States of America 98 (7), pp. 3658 - 3661 (2001)
Journal Article
Hummer, G.; García, A. E.; Garde, S.: Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins: Structure, Function, and Genetics 42 (1), pp. 77 - 84 (2001)
2000
Journal Article
Hummer, G.; García, A. E.; Garde, S.: Conformational diffusion and helix formation kinetics. Physical Review Letters 85 (12), pp. 2637 - 2640 (2000)
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Hummer, G.; Garde, S.; Garcı́a, A. E.; Pratt, L. R.: New perspectives on hydrophobic effects. Chemical Physics 258 (2), pp. 349 - 370 (2000)
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Backgren, C.; Hummer, G.; Wikström, M.; Puustinen, A.: Proton translocation by cytochrome c oxidase can take place without the conserved glutamic acid in subunit I. Biochemistry 39 (27), pp. 7863 - 7867 (2000)
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García, A. E.; Hummer, G.: Water penetration and escape in proteins. Proteins: Structure, Function, and Genetics 38 (3), pp. 261 - 272 (2000)
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Rempe, S. B.; Pratt, L. R.; Hummer, G.; Kress, J. D.; Martin, R. L.; Redondo, A.: The Hydration Number of Li+ in Liquid Water. Journal of the American Chemical Society 122 (5), pp. 966 - 967 (2000)
Journal Article
Garde, S.; Khare, R.; Hummer, G.: Microscopic density fluctuations and solvation in polymeric fluids. The Journal of Chemical Physics 112 (3), pp. 1574 - 1578 (2000)
1999
Journal Article
Ashbaugh, H. S.; Garde, S.; Hummer, G.; Kaler, E. W.; Paulaitis, M. E.: Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes. Biophysical Journal (Annual Meeting Abstracts) 77 (2), pp. 645 - 654 (1999)
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García, A. E.; Hummer, G.: Conformational dynamics of cytochrome c: Correlation to hydrogen exchange. Proteins: Structure, Function, and Genetics 36 (2), pp. 175 - 191 (1999)
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Hummer, G.: Hydrophobic Force Field as a Molecular Alternative to Surface-Area Models. Journal of the American Chemical Society 121 (26), pp. 6299 - 6305 (1999)
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Gomez, M. A.; Pratt, L. R.; Hummer, G.; Garde, S.: Molecular realism in default models for information theories of hydrophobic effects. The Journal of Physical Chemistry B 103 (18), pp. 3520 - 3523 (1999)
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Garde, S.; Garcı́a, A. E.; Pratt, L. R.; Hummer, G.: Temperature dependence of the solubility of non-polar gases in water. Biophysical Chemistry 78 (1), pp. 21 - 32 (1999)
1998
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Hummer, G.; Garde, S.; Garcia, A. E.; Paulaitis, M. E.; Pratt, L. R.: Hydrophobic Effects on a Molecular Scale. The Journal of Physical Chemistry B 102, pp. 10469 - 10489 (1998)
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Hummer, G.; Pratt, L. R.; García, A. E.: Molecular Theories and Simulation of Ions and Polar Molecules in Water. The Journal of Physical Chemistry A 102 (41), pp. 7885 - 7895 (1998)
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Hummer, G.; Grønbech-Jensen, N.; Neumann, M.: Pressure calculation in polar and charged systems using Ewald summation: Results for the extended simple point charge model of water. The Journal of Chemical Physics 109 (7), pp. 2791 - 2797 (1998)
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Pomès, R.; Hummer, G.; Wikström, M.: Structure and dynamics of a proton shuttle in cytochrome c oxidase. Biochimica et Biophysica Acta, Bioenergetics 1365 (1), pp. 255 - 260 (1998)
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Hummer, G.; Garde, S.: Cavity Expulsion and Weak Dewetting of Hydrophobic Solutes in Water. Physical Review Letters 80 (19), pp. 4193 - 4196 (1998)
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Hummer, G.; Garde, S.; García, A. E.; Paulaitis, M. E.; Pratt, L. R.: The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proceedings of the National Academy of Sciences of the United States of America 95 (4), pp. 1552 - 1555 (1998)
Journal Article
Garde, S.; Hummer, G.; Paulaitis, M. E.: Free energy of hydration of a molecular ionic solute: Tetramethylammonium ion. The Journal of Chemical Physics 108 (4), pp. 1552 - 1561 (1998)
1997
Journal Article
Grøbech-Jensen, N.; Hummer, G.; Beardmore, K. M.: Lekner summation of Coulomb interactions in partially periodic systems. Molecular Physics 92 (5), pp. 941 - 946 (1997)
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Hummer, G.; Pratt, L. R.; García, A. E.: Ion sizes and finite-size corrections for ionic-solvation free energies. The Journal of Chemical Physics 107 (21), pp. 9275 - 9277 (1997)
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García, A. E.; Blumenfeld, R.; Hummer, G.; Krumhansl, J. A.: Multi-basin dynamics of a protein in a crystal environment. Physica D: Nonlinear Phenomena 107 (2), pp. 225 - 239 (1997)
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Hummer, G.; Pratt, L. R.; García, A. E.: Multistate Gaussian Model for Electrostatic Solvation Free Energies. Journal of the American Chemical Society 119 (36), pp. 8523 - 8527 (1997)
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Riistama, S.; Hummer, G.; Puustinen, A.; Brian Dyer, R.; Woodruff, W. H.; Wikström, M.: Bound water in the proton translocation mechanism of the haem-copper oxidases. FEBS Letters 414 (2), pp. 275 - 280 (1997)
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Hummer, G.; Pratt, L. R.; García, A. E.; Berne, B. J.; Rick, S. W.: Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules. The Journal of Physical Chemistry B 101 (16), pp. 3017 - 3020 (1997)
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Oprea, T. I.; Hummer, G.; Garcia, A. E.: Identification of a functional water channel in cytochrome P450 enzymes. Proceedings of the National Academy of Sciences of the United States of America 94 (6), pp. 2133 - 2138 (1997)
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García, A. E.; Hummer, G.; Soumpasis, D. M.: Hydration of an α-Helical peptide: comparison of theory and molecular dynamics simulation. Proteins: Structure, Function, and Bioinformatics 27 (4), pp. 471 - 480 (1997)
Journal Article
Pratt, L. R.; Tawa, G. J.; Hummer, G.; García, A. E.; Corcelli, S. A.: Boundary integral methods for the Poisson equation of continuum dielectric solvation models. International Journal of Quantum Chemistry 64 (1), pp. 121 - 141 (1997)
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