Journal Article (370)
2004
Journal Article
Equation-Free: The Computer-Aided Analysis of Complex Multiscale Systems. AIChE-Journal 50 (7), pp. 1346 - 1355 (2004)
Journal Article
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
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
From transition paths to transition states and rate coefficients. The Journal of Chemical Physics 120 (2), pp. 516 - 523 (2004)
Journal Article
Methane Partitioning and ransport in Hydrated Carbon Nanotubes. The Journal of Physical Chemistry B 108 (2), pp. 544 - 549 (2004)
2003
Journal Article
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
Kinetics from nonequilibrium single-molecule pulling experiments. Biophysical Journal (Annual Meeting Abstracts) 85 (1), pp. 5 - 15 (2003)
Journal Article
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
Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochimica et Biophysica Acta: BBA 1604 (2), pp. 61 - 65 (2003)
Journal Article
Random Walk Model for Single‐File Transport of Water Molecules through Carbon Nanotubes. AIP Conference Proceedings 665 (1), pp. 267 - 272 (2003)
Journal Article
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)
Journal Article
Proton transport through water-filled carbon nanotubes. Physical Review Letters 90 (10), 105902 (2003)
Journal Article
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
Filling and emptying kinetics of carbon nanotubes in water. The Journal of Chemical Physics 117 (23), pp. 10789 - 10795 (2002)
Journal Article
Single-file transport of water molecules through a carbon nanotube. Physical Review Letters 89 (6), 064503 (2002)
Journal Article
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. Journal of the American Chemical Society 124 (23), pp. 6563 - 6568 (2002)
Journal Article
Hydrophobicity maps of the N-peptide coiled coil of HIV-1 gp41. Biochemistry 41 (9), pp. 2956 - 2961 (2002)
Journal Article
Fast-growth Thermodynamic Integration∶ Results for Sodium Ion Hydration. Molecular Simulation 28 (1-2), pp. 81 - 90 (2002)
2001
Journal Article
Water conduction through the hydrophobic channel of a carbon nanotube. Nature 414 (6860), pp. 188 - 190 (2001)
Journal Article
Fast-growth thermodynamic integration: Error and efficiency analysis. The Journal of Chemical Physics 114 (17), pp. 7330 - 7337 (2001)
Journal Article
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
Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins: Structure, Function, and Genetics 42 (1), pp. 77 - 84 (2001)
2000
Journal Article
Conformational diffusion and helix formation kinetics. Physical Review Letters 85 (12), pp. 2637 - 2640 (2000)
Journal Article
New perspectives on hydrophobic effects. Chemical Physics 258 (2), pp. 349 - 370 (2000)
Journal Article
Proton translocation by cytochrome c oxidase can take place without the conserved glutamic acid in subunit I. Biochemistry 39 (27), pp. 7863 - 7867 (2000)
Journal Article
Water penetration and escape in proteins. Proteins: Structure, Function, and Genetics 38 (3), pp. 261 - 272 (2000)
Journal Article
The Hydration Number of Li+ in Liquid Water. Journal of the American Chemical Society 122 (5), pp. 966 - 967 (2000)
Journal Article
Microscopic density fluctuations and solvation in polymeric fluids. The Journal of Chemical Physics 112 (3), pp. 1574 - 1578 (2000)
1999
Journal Article
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)
Journal Article
Conformational dynamics of cytochrome c: Correlation to hydrogen exchange. Proteins: Structure, Function, and Genetics 36 (2), pp. 175 - 191 (1999)
Journal Article
Hydrophobic Force Field as a Molecular Alternative to Surface-Area Models. Journal of the American Chemical Society 121 (26), pp. 6299 - 6305 (1999)
Journal Article
Molecular realism in default models for information theories of hydrophobic effects. The Journal of Physical Chemistry B 103 (18), pp. 3520 - 3523 (1999)
Journal Article
Temperature dependence of the solubility of non-polar gases in water. Biophysical Chemistry 78 (1), pp. 21 - 32 (1999)
1998
Journal Article
Hydrophobic Effects on a Molecular Scale. The Journal of Physical Chemistry B 102, pp. 10469 - 10489 (1998)
Journal Article
Molecular Theories and Simulation of Ions and Polar Molecules in Water. The Journal of Physical Chemistry A 102 (41), pp. 7885 - 7895 (1998)
Journal Article
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)
Journal Article
Structure and dynamics of a proton shuttle in cytochrome c oxidase. Biochimica et Biophysica Acta, Bioenergetics 1365 (1), pp. 255 - 260 (1998)
Journal Article
Cavity Expulsion and Weak Dewetting of Hydrophobic Solutes in Water. Physical Review Letters 80 (19), pp. 4193 - 4196 (1998)
Journal Article
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
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
Lekner summation of Coulomb interactions in partially periodic systems. Molecular Physics 92 (5), pp. 941 - 946 (1997)
Journal Article
Ion sizes and finite-size corrections for ionic-solvation free energies. The Journal of Chemical Physics 107 (21), pp. 9275 - 9277 (1997)
Journal Article
Multi-basin dynamics of a protein in a crystal environment. Physica D: Nonlinear Phenomena 107 (2), pp. 225 - 239 (1997)
Journal Article
Multistate Gaussian Model for Electrostatic Solvation Free Energies. Journal of the American Chemical Society 119 (36), pp. 8523 - 8527 (1997)
Journal Article
Bound water in the proton translocation mechanism of the haem-copper oxidases. FEBS Letters 414 (2), pp. 275 - 280 (1997)
Journal Article
Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules. The Journal of Physical Chemistry B 101 (16), pp. 3017 - 3020 (1997)
Journal Article
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)
Journal Article
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
Boundary integral methods for the Poisson equation of continuum dielectric solvation models. International Journal of Quantum Chemistry 64 (1), pp. 121 - 141 (1997)
1996
Journal Article
Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding. Physical Review Letters 77 (24), pp. 4966 - 4968 (1996)
Journal Article
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)
Journal Article
Calculation of free‐energy differences from computer simulations of initial and final states. The Journal of Chemical Physics 105 (5), pp. 2004 - 2010 (1996)
Journal Article
Three-dimensional model of a selective theophylline-binding RNA molecule. Journal of Molecular Recognition 9 (4), pp. 275 - 286 (1996)
Journal Article
Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes. Physical Review E 53 (5), pp. R4310 - R4313 (1996)
Journal Article
Hydrophobic interactions: conformational equilibria and the association of non-polar molecules in water. Faraday Discussions 103, pp. 125 - 139 (1996)
Journal Article
Hydration of Biological Macromolecules: From Small Solutes to Proteins and Nucleic Acids. MRS Online Proceedings Library (OPL) 463 (1996)
Journal Article
Electrostatic potential of a homogeneously charged square and cube in two and three dimensions. Journal of Electrostatics 36 (3), pp. 285 - 291 (1996)
Journal Article
A statistical mechanical description of biomolecular hydration. Faraday Discussions 103, pp. 175 - 189 (1996)
Journal Article
Free Energy of Ionic Hydration. The Journal of Physical Chemistry 100 (4), pp. 1206 - 1215 (1996)
1995
Journal Article
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)
Journal Article
The numerical accuracy of truncated Ewald sums for periodic systems with long-range Coulomb interactions. Chemical Physics Letters 235 (3), pp. 297 - 302 (1995)
Journal Article
Hydration free energy of water. The Journal of Physical Chemistry 99 (38), pp. 14188 - 14194 (1995)
1994
Journal Article
Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for B-DNA. Physical Review E 50 (6), pp. 5085 - 5095 (1994)
Journal Article
Ion pair potentials-of-mean-force in water. Biophysical Chemistry 51 (2), pp. 147 - 165 (1994)
Journal Article
Computer simulation of aqueous Na-Cl electrolytes. Journal of Physics: Condensed Matter 6 (23A), pp. A141 - A144 (1994)
Journal Article
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)
Journal Article
Computer simulations do not support Cl-Cl pairing in aqueous NaCl solution. Molecular Physics 81 (5), pp. 1155 - 1163 (1994)
Journal Article
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)
1993
Journal Article
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)
Journal Article
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)
Journal Article
Correlations and free energies in restricted primitive model descriptions of electrolytes. The Journal of Chemical Physics 98 (1), pp. 581 - 591 (1993)
1992
Journal Article
Pair correlations in an NaCl-SPC water model: Simulations versus extended RISM computations. Molecular Physics 77 (4), pp. 769 - 785 (1992)
Journal Article
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)
2019
Book Chapter
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)
2012
Book Chapter
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)
2008
Book Chapter
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)
Book Chapter
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)
2007
Book Chapter
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)
2005
Book Chapter
Equation-Free Modeling For Complex Systems. In: Handbook of Materials Modeling: Methods, pp. 1453 - 1475 (Ed. Yip, S.). Springer Netherlands, Dordrecht (2005)
2001
Book Chapter
Theoretical and Computational Methods of Biomolecular Hydration. In: Water in Biomaterials Surface Science, pp. 25 - 52 (Ed. Morra, M.) (2001)
1999
Book Chapter
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)
Book Chapter
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)
1996
Book Chapter
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)
1995
Book Chapter
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)
1999
Proceedings
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.
Proceedings
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)
2020
Conference Paper
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)
2017
Conference Paper
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)
2005
Conference Paper
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)
1996
Conference Paper
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)
Conference Paper
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)
1997
Report
Computer simulation of protein solvation, hydrophobic mapping, and the oxygen effect in radiation biology. Los Alamos National Laboratory, Los Alamos (1997), 22 pp.
1996
Report
Theoretical studies of the interaction of water with DNA oligomers and proteins. Los Alamos National Laboratory, Los Alamos (1996)
1995
Report
Predicting B-DNA structure from sequence. Los Alamos National Lab. (LANL), Los Alamos, NM (United States) (1995), 9 pp.
Report
Diffusion of a protein in configuration space. Los Alamos National Laboratory, Los Alalmos (1995), 29 pp.
1993
Report
A new approach to calculate the hydration of DNA molecules. Los Alamos National Laboratory, Los Alamos (1993), 20 pp.