Max Planck Institute of Biophysics

Publications of Gerhard Hummer

All genres

Journal Article (372)

201.

Journal Article

Schotte, F.; Cho, H. S.; Kaila, V. R. I.; Kamikubo, H.; Dashdorj, N.; Henry, E. R.; Graber, T. J.; Henning, R.; Wulff, M.; Hummer, G. et al.; Kataoka, M.; Anfinrud, P. A.: Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proceedings of the National Academy of Sciences of the United States of America 109 (47), pp. 19256 - 19261 (2012)

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202.

Journal Article

Zhu, F.; Hummer, G.: Theory and simulation of ion conduction in the pentameric GLIC channel. Journal of Chemical Theory and Computation 8 (10), pp. 3759 - 3768 (2012)

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203.

Journal Article

Różycki, B.; Boura, E.; Hurley, J. H.; Hummer, G.: Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes. PLoS Computational Biology 8 (10), e1002736 (2012)

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204.

Journal Article

Hummer, G.; Eaton, W. A.: Transition path times for DNA and RNA folding from force spectroscopy. Physics 5, 87 (2012)

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205.

Journal Article

Mittal, J.; Hummer, G.: Pair diffusion, hydrodynamic interactions, and available volume in dense fluids. The Journal of Chemical Physics 137 (3), 034110 (2012)

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206.

Journal Article

Zhu, F.; Hummer, G.: Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophysical Journal 103 (2), pp. 219 - 227 (2012)

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207.

Journal Article

Johnson, M. E.; Hummer, G.: Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. The Journal of Physical Chemistry B 116 (29), pp. 8573 - 8583 (2012)

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208.

Journal Article

Waghe, A.; Rasaiah, J. C.; Hummer, G.: Entropy of single-file water in (6,6) carbon nanotubes. The Journal of Chemical Physics 137 (4), 044709 (2012)

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209.

Journal Article

Boura, E.; Różycki, B.; Chung, H. S.; Herrick, D. Z.; Canagarajah, B.; Cafiso, D. S.; Eaton, W. A.; Hummer, G.; Hurley, J. H.: Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission. Structure 20 (5), pp. 874 - 886 (2012)

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210.

Journal Article

Kim, Y. C.; Hummer, G.: Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach. Biochimica et Biophysica Acta: BBA 1817 (4), pp. 526 - 536 (2012)

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211.

Journal Article

Wikström, M.; Hummer, G.: Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proceedings of the National Academy of Sciences of the United States of America 109 (12), pp. 4431 - 4436 (2012)

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212.

Journal Article

Zhu, F.; Hummer, G.: Convergence and error estimation in free energy calculations using the weighted histogram analysis method. Journal of Computational Chemistry 33 (4), pp. 453 - 465 (2012)

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213.

Journal Article

Francis, D. M.; Różycki, B.; Koveal, D.; Hummer, G.; Page, R.; Peti, W.: Structural basis of p38α regulation by hematopoietic tyrosine phosphatase. Nature Chemical Biology 7 (12), pp. 916 - 924 (2011)

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214.

Journal Article

Francis, D. M.; Różycki, B.; Tortajada, A.; Hummer, G.; Peti, W.; Page, R.: Resting and active states of the ERK2:HePTP complex. Journal of the American Chemical Society 133 (43), pp. 17138 - 17141 (2011)

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215.

Journal Article

Kaila, V. R. I.; Hummer, G.: Energetics of direct and water-mediated proton-coupled electron transfer. Journal of the American Chemical Society 133 (47), pp. 19040 - 19043 (2011)

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216.

Journal Article

Best, R. B.; Hummer, G.: Diffusion models of protein folding. Physical Chemistry Chemical Physics 13 (38), pp. 16902 - 16911 (2011)

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217.

Journal Article

Köfinger, J.; Hummer, G.; Dellago, C.: Single-file water in nanopores. Physical Chemistry Chemical Physics 13 (34), pp. 15403 - 15417 (2011)

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218.

Journal Article

Kaila, V. R. I.; Hummer, G.: Energetics and dynamics of proton transfer reactions along short water wires. Physical Chemistry Chemical Physics 13 (29), pp. 13207 - 13215 (2011)

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219.

Journal Article

Boura, E.; Rózycki, B.; Herrick, D. Z.; Chung, H. S.; Vecer, J.; Eaton, W. A.; Cafiso, D. S.; Hummer, G.; Hurley, J. H.: Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 108 (23), pp. 9437 - 9442 (2011)

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220.

Journal Article

Rosta, E.; Nowotny, M.; Yang, W.; Hummer, G.: Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. Journal of the American Chemical Society 133 (23), pp. 8934 - 8941 (2011)

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221.

Journal Article

Różycki, B.; Kim, Y. C.; Hummer, G.: SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure 19 (1), pp. 109 - 116 (2011)

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222.

Journal Article

Johnson, M. E.; Hummer, G.: Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proceedings of the National Academy of Sciences of the United States of America 108 (2), pp. 603 - 608 (2011)

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223.

Journal Article

Leonard, T. A.; Różycki, B.; Saidi, L. F.; Hummer, G.; Hurley, J. H.: Crystal structure and allosteric activation of protein kinase C βII. Cell 144 (1), pp. 55 - 66 (2011)

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224.

Journal Article

Yin, H.; Feng, G.; Clore, G. M.; Hummer, G.; Rasaiah, J. C.: Water in the polar and nonpolar cavities of the protein interleukin-1β. The Journal of Physical Chemistry B 114 (49), pp. 16290 - 16297 (2010)

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225.

Journal Article

Hummer, G.; Szabo, A.: Free energy profiles from single-molecule pulling experiments. Proceedings of the National Academy of Sciences of the United States of America 107 (50), pp. 21441 - 21446 (2010)

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226.

Journal Article

Zhu, F.; Hummer, G.: Pore opening and closing of a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America 107 (46), pp. 19814 - 19819 (2010)

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227.

Journal Article

Hummer, G.: Under water's influence. Nature Chemistry 2 (11), pp. 906 - 907 (2010)

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228.

Journal Article

Kalra, A.; Garde, S.; Hummer, G.: Lubrication by molecularly thin water films confined between nanostructured membranes. The European Physical Journal Special Topics 189 (1), pp. 147 - 154 (2010)

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229.

Journal Article

Hummer, G.: Catching a protein in the act. Proceedings of the National Academy of Sciences of the United States of America 107 (6), pp. 2381 - 2382 (2010)

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230.

Journal Article

Rosta, E.; Hummer, G.: Error and efficiency of simulated tempering simulations. The Journal of Chemical Physics 132 (3), 034102 (2010)

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231.

Journal Article

Best, R. B.; Hummer, G.: Coordinate-dependent diffusion in protein folding. Proceedings of the National Academy of Sciences of the United States of America 107 (3), pp. 1088 - 1093 (2010)

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232.

Journal Article

Mittal, J.; Hummer, G.: Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discussions 146, pp. 341 - 352 (2010)

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233.

Journal Article

Kim, Y. C.; Furchtgott, L. A.; Hummer, G.: Biological proton pumping in an oscillating electric field. Physical Review Letters 103 (26), 268102 (2009)

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234.

Journal Article

Zhu, F.; Hummer, G.: Gating transition of pentameric ligand-gated ion channels. Biophysical Journal (Annual Meeting Abstracts) 97 (9), pp. 2456 - 2463 (2009)

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235.

Journal Article

Rosta, E.; Hummer, G.: Error and efficiency of replica exchange molecular dynamics simulations. The Journal of Chemical Physics 131 (16), 165102 (2009)

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236.

Journal Article

Frewen, T. A.; Hummer, G.; Kevrekidis, I. G.: Exploration of effective potential landscapes using coarse reverse integration. The Journal of Chemical Physics 131 (13), 134104 (2009)

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237.

Journal Article

Kaila, V. R. I.; Verkhovsky, M. I.; Hummer, G.; Wikström, M.: Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - General Subjects 1787 (10), pp. 1205 - 1214 (2009)

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238.

Journal Article

Rosta, E.; Woodcock, H. L.; Brooks, B. R.; Hummer, G.: Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. Journal of Computational Chemistry 30 (11), pp. 1634 - 1641 (2009)

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239.

Journal Article

Kim, Y. C.; Wikström, M.; Hummer, G.: Kinetic gating of the proton pump in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America 106 (33), pp. 13707 - 13712 (2009)

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240.

Journal Article

Best, R. B.; Hummer, G.: Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. The Journal of Physical Chemistry B 113 (26), pp. 9004 - 9015 (2009)

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241.

Journal Article

Berezhkovskii, A.; Hummer, G.; Szabo, A.: Reactive flux and folding pathways in network models of coarse-grained protein dynamics. The Journal of Chemical Physics 130 (20), 205102 (2009)

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242.

Journal Article

Turjanski, A. G.; Hummer, G.; Gutkind, J. S.: How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study. Journal of the American Chemical Society 131 (17), pp. 6141 - 6148 (2009)

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243.

Journal Article

Köfinger, J.; Hummer, G.; Dellago, C.: A one-dimensional dipole lattice model for water in narrow nanopores. The Journal of Chemical Physics 130 (15), 154110 (2009)

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244.

Journal Article

Ren, X.; Kloer, D. P.; Kim, Y. C.; Ghirlando, R.; Saidi, L. F.; Hummer, G.; Hurley, J. H.: Hybrid structural model of the complete human ESCRT-0 complex. Structure 17 (3), pp. 406 - 416 (2009)

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245.

Journal Article

Best, R. B.; Hummer, G.: Unfolding the secrets of calmodulin. Science 323 (5914), pp. 593 - 594 (2009)

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246.

Journal Article

Rosta, E.; Buchete, N.-V.; Hummer, G.: Thermostat artifacts in replica exchange molecular dynamics simulations. Journal of Chemical Theory and Computation 5 (5), pp. 1393 - 1399 (2009)

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247.

Journal Article

Mittal, J.; Hummer, G.: Static and dynamic correlations in water at hydrophobic interfaces. Proceedings of the National Academy of Sciences of the United States of America 105 (51), pp. 20130 - 20135 (2008)

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248.

Journal Article

Dudko, O. K.; Hummer, G.; Szabo, A.: Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proceedings of the National Academy of Sciences of the United States of America 105 (41), pp. 15755 - 15760 (2008)

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249.

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)

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250.

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)

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251.

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)

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252.

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)

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253.

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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254.

Journal Article

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)

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255.

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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256.

Journal Article

Buchete, N.-V.; Hummer, G.: Coarse master equations for peptide folding dynamics. The Journal of Physical Chemistry B 112 (19), pp. 6057 - 6069 (2008)

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257.

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)

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258.

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)

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259.

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)

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260.

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)

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261.

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)

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262.

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)

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263.

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)

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264.

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)

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265.

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)

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266.

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)

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267.

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)

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268.

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)

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269.

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)

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270.

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)

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271.

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)

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272.

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)

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273.

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)

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274.

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)

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275.

Journal Article

Hummer, G.: Water, proton, and ion transport: from nanotubes to proteins. Molecular Physics 105 (2-3), pp. 201 - 207 (2007)

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276.

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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277.

Journal Article

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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278.

Journal Article

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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279.

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)

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280.

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)

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281.

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)

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282.

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)

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283.

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)

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284.

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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285.

Journal Article

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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286.

Journal Article

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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287.

Journal Article

Peter, C.; Hummer, G.: Ion Transport through Membrane-Spanning Nanopores Studiedby Molecular Dynamics Simulations and ContinuumElectrostatics Calculations. Biophysical Journal 89, pp. 2222 - 2234 (2005)

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288.

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)

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289.

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)

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290.

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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291.

Journal Article

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)

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292.

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)

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293.

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)

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294.

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)

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295.

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)

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296.

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)

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297.

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)

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298.

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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299.

Journal Article

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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300.

Journal Article

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)

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