Publications of Gerhard Hummer

Journal Article (356)

301.
Journal Article
Hummer, G.: Fast-growth Thermodynamic Integration∶ Results for Sodium Ion Hydration. Molecular Simulation 28 (1-2), pp. 81 - 90 (2002)
302.
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)
303.
Journal Article
Hummer, G.: Fast-growth thermodynamic integration: Error and efficiency analysis. The Journal of Chemical Physics 114 (17), pp. 7330 - 7337 (2001)
304.
Journal Article
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)
305.
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)
306.
Journal Article
Hummer, G.; García, A. E.; Garde, S.: Conformational diffusion and helix formation kinetics. Physical Review Letters 85 (12), pp. 2637 - 2640 (2000)
307.
Journal Article
Hummer, G.; Garde, S.; Garcı́a, A. E.; Pratt, L. R.: New perspectives on hydrophobic effects. Chemical Physics 258 (2), pp. 349 - 370 (2000)
308.
Journal Article
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)
309.
Journal Article
García, A. E.; Hummer, G.: Water penetration and escape in proteins. Proteins: Structure, Function, and Genetics 38 (3), pp. 261 - 272 (2000)
310.
Journal Article
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)
311.
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)
312.
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)
313.
Journal Article
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)
314.
Journal Article
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)
315.
Journal Article
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)
316.
Journal Article
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)
317.
Journal Article
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)
318.
Journal Article
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)
319.
Journal Article
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)
320.
Journal Article
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)
321.
Journal Article
Hummer, G.; Garde, S.: Cavity Expulsion and Weak Dewetting of Hydrophobic Solutes in Water. Physical Review Letters 80 (19), pp. 4193 - 4196 (1998)
322.
Journal Article
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)
323.
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)
324.
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)
325.
Journal Article
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)
326.
Journal Article
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)
327.
Journal Article
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)
328.
Journal Article
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)
329.
Journal Article
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)
330.
Journal Article
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)
331.
Journal Article
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)
332.
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)
333.
Journal Article
Garde, S.; Hummer, G.; García, A. E.; Paulaitis, M. E.; Pratt, L. R.: Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding. Physical Review Letters 77 (24), pp. 4966 - 4968 (1996)
334.
Journal Article
Hummer, G.; Garde, S.; García, A. E.; Pohorille, A.; Pratt, L. R.: An information theory model of hydrophobic interactions. Proceedings of the National Academy of Sciences of the United States of America 93 (17), pp. 8951 - 8955 (1996)
335.
Journal Article
Hummer, G.; Szabo, A.: Calculation of free‐energy differences from computer simulations of initial and final states. The Journal of Chemical Physics 105 (5), pp. 2004 - 2010 (1996)
336.
Journal Article
Tung, C.-S.; Oprea, T. I.; Hummer, G.; García, A. E.: Three-dimensional model of a selective theophylline-binding RNA molecule. Journal of Molecular Recognition 9 (4), pp. 275 - 286 (1996)
337.
Journal Article
Garde, S.; Hummer, G.; García, A. E.; Pratt, L. R.; Paulaitis, M. E.: Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes. Physical Review E 53 (5), pp. R4310 - R4313 (1996)
338.
Journal Article
Garde, S.; Hummer, G.; E. Paulaitis, M.: Hydrophobic interactions: conformational equilibria and the association of non-polar molecules in water. Faraday Discussions 103, pp. 125 - 139 (1996)
339.
Journal Article
Garde, S.; Hummer, G.; Paulaitis, M. E.; Garcia, A. E.: Hydration of Biological Macromolecules: From Small Solutes to Proteins and Nucleic Acids. MRS Online Proceedings Library (OPL) 463 (1996)
340.
Journal Article
Hummer, G.: Electrostatic potential of a homogeneously charged square and cube in two and three dimensions. Journal of Electrostatics 36 (3), pp. 285 - 291 (1996)
341.
Journal Article
Hummer, G.; E. García, A.; Soumpasis, D. M.: A statistical mechanical description of biomolecular hydration. Faraday Discussions 103, pp. 175 - 189 (1996)
342.
Journal Article
Hummer, G.; Pratt, L. R.; García, A. E.: Free Energy of Ionic Hydration. The Journal of Physical Chemistry 100 (4), pp. 1206 - 1215 (1996)
343.
Journal Article
Hummer, G.; García, A. E.; Soumpasis, D. M.: Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophysical Journal 68 (5), pp. 1639 - 1652 (1995)
344.
Journal Article
Hummer, G.: The numerical accuracy of truncated Ewald sums for periodic systems with long-range Coulomb interactions. Chemical Physics Letters 235 (3), pp. 297 - 302 (1995)
345.
Journal Article
Hummer, G.; Pratt, L. R.; Garcia, A. E.: Hydration free energy of water. The Journal of Physical Chemistry 99 (38), pp. 14188 - 14194 (1995)
346.
Journal Article
Hummer, G.; Soumpasis, D. M.: Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for B-DNA. Physical Review E 50 (6), pp. 5085 - 5095 (1994)
347.
Journal Article
Pratt, L. R.; Hummer, G.; Garcia´, A. E.: Ion pair potentials-of-mean-force in water. Biophysical Chemistry 51 (2), pp. 147 - 165 (1994)
348.
Journal Article
Hummer, G.; Soumpasis, D. M.; Neumann, M.: Computer simulation of aqueous Na-Cl electrolytes. Journal of Physics: Condensed Matter 6 (23A), pp. A141 - A144 (1994)
349.
Journal Article
Tung, C.-S.; Soumpasis, D. M.; Hummer, G.: An Extension of the Rigorous Base-unit Oriented Description of Nucleic Acid Structures. Journal of Biomolecular Structure and Dynamics 11 (6), pp. 1327 - 1344 (1994)
350.
Journal Article
Hummer, G.; Soumpasis, D. M.; Neumann, M.: Computer simulations do not support Cl-Cl pairing in aqueous NaCl solution. Molecular Physics 81 (5), pp. 1155 - 1163 (1994)
351.
Journal Article
Hummer, G.; Soumpasis, D. M.: Computation of the water density distribution at the ice-water interface using the potentials-of-mean-force expansion. Physical Review E 49 (1), pp. 591 - 596 (1994)
352.
Journal Article
Höfers, C.; Jovin, T. M.; Hummer, G.; Arndt-Jovin, D. J.: The localization of chromosome domains in human interphase nuclei. Semi-automated two-dimensional image acquisition and analysis of fluorescence in situ hybridization signals. Bioimaging 1 (2), pp. 107 - 118 (1993)
353.
Journal Article
Höfers, C.; Baumann, P.; Hummer, G.; Jovin, T. M.; Arndt-Jovin, D. J.: The localization of chromosome domains in human interphase nuclei. Three-dimensional distance determinations of fluorescence in situ hybridization signals from confocal laser scanning microscopy. Bioimaging 1 (2), pp. 96 - 106 (1993)
354.
Journal Article
Hummer, G.; Soumpasis, D. M.: Correlations and free energies in restricted primitive model descriptions of electrolytes. The Journal of Chemical Physics 98 (1), pp. 581 - 591 (1993)
355.
Journal Article
Hummer, G.; Soumpasis, D. M.; Neumann, M.: Pair correlations in an NaCl-SPC water model: Simulations versus extended RISM computations. Molecular Physics 77 (4), pp. 769 - 785 (1992)
356.
Journal Article
Hummer, G.; Soumpasis, D. M.: An extended RISM study of simple electrolytes: pair correlations in a NaCl-SPC water model. Molecular Phylogenetics and Evolution 75 (3), pp. 633 - 651 (1992)

Book Chapter (11)

357.
Book Chapter
Köfinger, J.; Rózycki, B.; Hummer, G.: Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods. In: Methods in Molecular Biology, Vol. 2022, pp. 341 - 352. Springer (2019)
358.
Book Chapter
Hummer, G.: Non-equilibrium molecular dynamics for biomolecular systems using fluctuation theorems. In: Hierarchical Methods for Dynamics in Complex Molecular Systems: IAS Winter School, 5 – 9 March 2012 Forschungszentrum Jülich GmbH Lecture Notes, pp. 269 - 279 (Ed. Grotendorst, J.). Forschungszentrum Jülich, Jülich (2012)
359.
Book Chapter
Hummer, G.; Szabo, A.: Thermodynamics and kinetics of single-molecule force spectroscopy. In: Theory and Evaluation of Single-molecule Signals, pp. 139 - 178 (Eds. Barkai, E.; Brown, F.; Orrit, M.; Yang, H.). World Scientific, New Jersey (2008)
360.
Book Chapter
Rasaiah, J. C.; Garde, S.; Hummer, G.: Water in nonpolar confinement: from nanotubes to proteins and beyond. In: Annual Review of Physical Chemistry, Vol. 59, pp. 713 - 740. Annual Reviews., Palo Alto, Calif. [etc.] (2008)
361.
Book Chapter
Hummer, G.: Nonequilibrium Methods for Equilibrium Free Energy Calculations. In: Free Energy Calculations: Theory and Applications in Chemistry and Biology, pp. 171 - 198 (Eds. Chipot, C.; Pohorille, A.). Springer, Berlin, Heidelberg (2007)
362.
Book Chapter
Kevrekidis, I. G.; Gear, C. W.; Hummer, G.: Equation-Free Modeling For Complex Systems. In: Handbook of Materials Modeling: Methods, pp. 1453 - 1475 (Ed. Yip, S.). Springer Netherlands, Dordrecht (2005)
363.
Book Chapter
Garcia, C. A.; Hummer, G.; Soumpasis, D. M.: Theoretical and Computational Methods of Biomolecular Hydration. In: Water in Biomaterials Surface Science, pp. 25 - 52 (Ed. Morra, M.) (2001)
364.
Book Chapter
Pratt, L. R.; Garde, S.; Hummer, G.: Theories of Hydrophobic Effects and the Description of Free Volume in Complex Liquids. In: New Approaches to Problems in Liquid State Theory: Inhomogeneities and Phase Separation in Simple, Complex and Quantum Fluids, pp. 407 - 420 (Eds. Caccamo, C.; Hansen, J.-P.; Stell, G.). Springer Netherlands, Dordrecht (1999)
365.
Book Chapter
Wikström, M.; Morgan, J. E.; Hummer, G.; Woodruff, W. H.; Verkhovsky, M. I.: Oxygen Reduction and Proton Translocation by the Heme-Copper Oxidases. In: Frontiers of Cellular Bioenergetics: Molecular Biology, Biochemistry, and Physiopathology, Vol. 2, pp. 193 - 217 (Eds. Papa, S.; Guerrieri, F.; Tager, J. M.). Springer, New York (1999)
366.
Book Chapter
García, A. E.; Hummer, G.; Soumpasis, D. M.: Theoretical Description of Biomolecular Hydration. In: Neutrons in Biology, Vol. 64, pp. 299 - 308 (Eds. Schoenborn, B. P.; Knott, R. B.). Springer, Boston, MA (1996)
367.
Book Chapter
Hummer, G.; Soumpasis, D. M.; García, A. E.: Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems. In: Nonlinear Excitations in Biomolecules, pp. 83 - 99 (Ed. Peyrard, M.). Springer, Berlin (1995)

Proceedings (2)

368.
Proceedings
Pratt, L. R.; Hummer, G. (Eds.): Simulation and theory of electrostatic interactions in solution: computational chemistry, biophysics, and aqueous solutions. AIP Conference Proceedings; 492, Sante Fe, New Mexico (USA, June 23, 1999 - June 25, 1999. American Institute of Physics, Melville (1999), 534 pp.
369.
Proceedings
Frauenfelder, H.; Hummer, G.; Garcia, R. (Eds.): Biological physics: third international symposium. AIP Conference Proceedings; 487, Sante Fe, New Mexico (USA, 1999-09. American Institute of Physics, Melville (1999), 290 pp.

Conference Paper (5)

370.
Conference Paper
Karathanasis, C.; Baldering, T. N.; Boeger, C.; Harwardt, M.-L. I. E.; Li, Y.; Schroeder, M. S.; Deussner-Helfmann, N. S.; Glaesmann, M.; Malkusch, S.; Dietz, M. S. et al.; Hafner, A.-S.; Schuman, E.; Hummer, G.; Heilemann, M.: Quantitative single-molecule localization microscopy reports on protein numbers in signaling protein complexes. In: Proceedings of SPIE: Single molecule spectroscopy and superresolution imaging XIII, Vol. 11246, UNSP 112460N (Eds. Gregor, I.; Koberling, F.; Erdmann, R.). SPIE BIOS, San Francisco, Carlifornia, United States, February 01, 2020 - February 02, 2020. Spie-Int Soc Optical Engineering, Bellingham (2020)
371.
Conference Paper
Krüger, C.; Fricke, F.; Karathanasis, C.; Dietz, M. S.; Malkusch, S.; Hummer, G.; Heilemann, M.: Molecular counting of membrane receptor subunits with single-molecule localization microscopy. In: Proceedings SPIE 10071, Single Molecule Spectroscopy and Superresolution Imaging X, Vol. 10071, 100710K. SPIE BiOS, 2017, San Francisco, California, United States, January 28, 2017 - February 02, 2017. (2017)
372.
Conference Paper
Hummer, G.: Simulations of nanoscale flow: water, proton, and biopolymer transport through carbon nanotube membranes. In: Nanofabrication: Technologies, Devices, and Applications, Vol. 5592, pp. 214 - 219. International Society for Optics and Photonics (2005)
373.
Conference Paper
Pratt, L. R.; Tawa, G. J.; Hummer, G.; Garcia, A. E.; Corcelli, S. A.: Hydrophobic & hydrophilic: Theoretical models of solvation for molecular biophysics. In: 2. International Congress on Theoretical Chemical Physics, New Orleans, LA (United States), 9-13 Mar 1996. (1996)
374.
Conference Paper
Pratt, L.R.; Tawa, G.J.; Hummer, G.; Garcia, A.E.; Corcelli, S.A.: Hydrophobic ampersand hydrophilic: Theoretical models of solvation for molecular biophysics. In: Second international congress on theoretical chemical physics - ICTCP II; New Orleans, LA (United States); 9-13 Mar 1996. (1996)

Report (5)

375.
Report
Pratt, L. R.; Garcia, A. E.; Hummer, G.; Berne, B. J.; Corcelli, S. A.; Garde, S.; Paulaitis, M. E.; Pohorille, A.; Rick, S. W.; Tawa, G. J.: Computer simulation of protein solvation, hydrophobic mapping, and the oxygen effect in radiation biology. Los Alamos National Laboratory, Los Alamos (1997), 22 pp.
376.
Report
Garcia, A. E.; Hummer, G.: Theoretical studies of the interaction of water with DNA oligomers and proteins. Los Alamos National Laboratory, Los Alamos (1996)
377.
Report
Tung, C.-S.; Hummer, G.; Soumpasis, D. M.: Predicting B-DNA structure from sequence. Los Alamos National Lab. (LANL), Los Alamos, NM (United States) (1995), 9 pp.
378.
Report
Garcia, A. E.; Blumenfeld, R.; Hummer, G.; Sobehart, J.: Diffusion of a protein in configuration space. Los Alamos National Laboratory, Los Alalmos (1995), 29 pp.
379.
Report
Hummer, G.; Soumpasis, D. M.: A new approach to calculate the hydration of DNA molecules. Los Alamos National Laboratory, Los Alamos (1993), 20 pp.
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