A one-dimensional dipole lattice model for water in narrow nanopores (2009)
Köfinger, Jürgen, Hummer, Gerhard, Dellago, Christoph
We present a recently developed one-dimensional dipole lattice model that accurately captures the key properties of water in narrow nanopores. For this model, we derive three equivalent...
Exploration of Effective Potential Landscapes using Coarse Reverse Integration (2008)
Frewen, Thomas A., Hummer, Gerhard, Kevrekidis, Ioannis G.
We describe a reverse integration approach for the exploration of low-dimensional effective potential landscapes. Coarse reverse integration initialized on a ring of coarse states enables efficient...
Layering and position-dependent diffusive dynamics of confined fluids (2008)
Mittal, Jeetain, Truskett, Thomas M., Errington, Jeffrey R., Hummer, Gerhard
We study the diffusive dynamics of a hard-sphere fluid confined between parallel smooth hard walls. The position-dependent diffusion coefficient normal to the walls is larger in regions of high local...
Gerhard Hummer, Lawrence R. Pratt, Angel E. García, Shekhar Garde, Bruce J. Berne, Steven W. Rick
Calculation of single-ion free energies of solvation1 requires careful treatment of electrostatic interactions. In computer simulations of ion solvation, only a finite number of solvent molecules are...
Peptide Folding Kinetics from Replica Exchange Molecular Dynamics (2007)
Buchete, Nicolae-Viorel, Hummer, Gerhard
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and...
Kinetics and mechanism of proton transport across membrane nanopores (2006)
Dellago, Christoph, Hummer, Gerhard
We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant...
Sriraman, Saravanapriyan, Kevrekidis, Ioannis G., Hummer, Gerhard
Using a Coarse-grained Molecular Dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling/emptying carbon nanotubes as a function of system parameters. Different...
Hummer, Gerhard, Kevrekidis, Ioannis G.
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized...
The Hydration Number of Li+ in Liquid Water (2000)
Rempe, Susan B., Pratt, Lawrence R., Hummer, Gerhard, Kress, Joel D., Martin, Richard L., Redondo, Antonio
A theoretical treatment based upon the quasi-chemical theory of solutions predicts the most probable number of water neighbors in the inner shell of a Li+ ion in liquid water to be four. The...
Hummer, Gerhard, Grønbech-Jensen, Niels, Neumann, Martin
Ewald summation and physically equivalent methods such as particle-mesh Ewald, kubic-harmonic expansions, or Lekner sums are commonly used to calculate long-range electrostatic interactions in...
Theories of Hydrophobic Effects and the Description of Free Volume in Complex Liquids (1998)
Pratt, Lawrence R., Garde, Shekhar, Hummer, Gerhard
Recent progress on molecular theories of hydration of nonpolar solutes in aqueous solution has led to new ways of thinking about the old issue of free, or "available," volume in liquids. This article...
Molecular theories and simulation of ions and polar molecules in water (1998)
Hummer, Gerhard, Pratt, Lawrence R., Garcia, Angel E.
Recent developments in molecular theories and simulation of ions and polar molecules in water are reviewed. The hydration of imidazole and imidazolium solutes is used to exemplify the theoretical...
Theories Of Hydrophobic Effects And The Description Of Free Volume In Complex Liquids (1998)
Lawrence R. Pratt, Shekhar Garde, Gerhard Hummer
. Recent progress on molecular theories of hydration of nonpolar solutes in aqueous solution has led to new ways of thinking about the old issue of free volume in liquids. This article surveys the...
Gerhard Hummer, Niels Grønbech-Jensen, Martin Neumann
Ewald summation and physically equivalent methods such as particle-mesh Ewald, kubic-harmonic expansions, or Lekner sums are commonly used to calculate long-range electrostatic interactions in...
Ion Sizes and Finite-Size Corrections for Ionic-Solvation Free Energies (1997)
Hummer, Gerhard, Pratt, Lawrence R., Garcia, Angel E.
Free energies of ionic solvation calculated from computer simulations exhibit a strong system size dependence. We perform a finite-size analysis based on a dielectric-continuum model with periodic...
Electrostatic potentials and free energies of solvation of polar and charged molecules (1997)
Hummer, Gerhard, Pratt, Lawrence R., Garcia, Angel E., Berne, Bruce J., Rick, Steven W.
Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on...
Origin of entropy convergence in hydrophobic hydration and protein folding (1996)
Garde, Shekhar, Hummer, Gerhard, Garcia, Angel E., Paulaitis, Michael E., Pratt, Lawrence R.
An information theory model is used to construct a molecular explanation why hydrophobic solvation entropies measured in calorimetry of protein unfolding converge at a common temperature. The entropy...
A closed form of the electrostatic potential of a homogeneously charged cube is derived by integration. The exact result is compared with multipole expansions for the exterior and interior of the...
The hydration free energy of water (1995)
Hummer, Gerhard, Pratt, Lawrence R., Garcia, Angel E.
We study the chemical potential of water as a function of charge based on perturbation theory. By calculating the electrostatic-energy fluctuations of two states (fully charged and uncharged) we are...
On the free energy of ionic hydration (1995)
Hummer, Gerhard, Pratt, Lawrence R., Garcia, Angel E.
The hydration free energies of ions exhibit an approximately quadratic dependence on the ionic charge, as predicted by the Born model. We analyze this behavior using second-order perturbation theory....
Ewald summation is widely used to calculate electrostatic interactions in computer simulations of condensed-matter systems. We present an analysis of the errors arising from truncating the infinite...
Ion Pair Potentials-of-Mean-Force in Water (1994)
Pratt, Lawrence R., Hummer, Gerhard, Garcia, Angel E.
Recent molecular simulation and integral equation results alkali-halide ion pair potentials-of-mean-force in water are discussed. Dielectric model calculations are implemented to check that these...
Hummer, Gerhard, Garde, Shekhar, García, Angel E., Paulaitis, Michael E., Pratt, Lawrence R.
Proteins can be denatured by pressures of a few hundred MPa. This finding apparently contradicts the most widely used model of protein stability, where the formation of a hydrophobic core drives...
Identification of a functional water channel in cytochrome P450 enzymes
Oprea, Tudor I., Hummer, Gerhard, García, Angel E.
Cytochrome P450 enzymes are monooxygenases that contain a functional heme b group linked to a conserved cysteine with a thiolate bond. In the native state, the central iron atom is hexacoordinated...
Free energy reconstruction from nonequilibrium single-molecule pulling experiments
Hummer, Gerhard, Szabo, Attila
Laser tweezers and atomic force microscopes are increasingly used to probe the interactions and mechanical properties of individual molecules. Unfortunately, using such time-dependent perturbations...
Osmotic water transport through carbon nanotube membranes
Kalra, Amrit, Garde, Shekhar, Hummer, Gerhard
We use molecular dynamics simulations to study osmotically driven transport of water molecules through hexagonally packed carbon nanotube membranes. Our simulation setup comprises two such...
Nucleic acid transport through carbon nanotube membranes
We study the electrophoretic transport of single-stranded RNA molecules through 1.5-nm-wide pores of carbon nanotube membranes by molecular dynamics simulations. From ≈170 individual RNA...
Hummer, Gerhard, Schotte, Friedrich, Anfinrud, Philip A.
A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved x-ray structures was performed to gain single-molecule insights into mechanisms of protein function....
Water clusters in nonpolar cavities
Vaitheeswaran, Subramanian, Yin, Hao, Rasaiah, Jayendran C., Hummer, Gerhard
We explore the structure and thermodynamics of water clusters confined in nonpolar cavities. By calculating the grand-canonical partition function term by term, we show that small nonpolar cavities...
Reaction coordinates and rates from transition paths
Best, Robert B., Hummer, Gerhard
The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles...
Kinetics from Nonequilibrium Single-Molecule Pulling Experiments
Hummer, Gerhard, Szabo, Attila
Mechanical forces exerted by laser tweezers or atomic force microscopes can be used to drive rare transitions in single molecules, such as unfolding of a protein or dissociation of a ligand. The...
Diffusion and Electrophoretic Mobility of Single-Stranded RNA from Molecular Dynamics Simulations
Hydrodynamic properties of small single-stranded RNA homopolymers with three and six nucleotides in free solution are determined from molecular dynamics simulations in explicit solvent. We find that...
Zweckstetter, Markus, Hummer, Gerhard, Bax, Ad
Alignment of macromolecules in nearly neutral aqueous lyotropic liquid-crystalline media such as bicelles, commonly used in macromolecular NMR studies, can be predicted accurately by a steric...
Collins, Marcus D., Hummer, Gerhard, Quillin, Michael L., Matthews, Brian W., Gruner, Sol M.
Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in “hydrophobic” cavities is...
Peter, Christine, Hummer, Gerhard
Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic...
Hummer, Gerhard, Garde, Shekhar, García, Angel E., Paulaitis, Michael E., Pratt, Lawrence R.
Proteins can be denatured by pressures of a few hundred MPa. This finding apparently contradicts the most widely used model of protein stability, where the formation of a hydrophobic core drives...
Identification of a functional water channel in cytochrome P450 enzymes
Oprea, Tudor I., Hummer, Gerhard, García, Angel E.
Cytochrome P450 enzymes are monooxygenases that contain a functional heme b group linked to a conserved cysteine with a thiolate bond. In the native state, the central iron atom is hexacoordinated...
Free energy reconstruction from nonequilibrium single-molecule pulling experiments
Hummer, Gerhard, Szabo, Attila
Laser tweezers and atomic force microscopes are increasingly used to probe the interactions and mechanical properties of individual molecules. Unfortunately, using such time-dependent perturbations...
Osmotic water transport through carbon nanotube membranes
Kalra, Amrit, Garde, Shekhar, Hummer, Gerhard
We use molecular dynamics simulations to study osmotically driven transport of water molecules through hexagonally packed carbon nanotube membranes. Our simulation setup comprises two such...
Nucleic acid transport through carbon nanotube membranes
We study the electrophoretic transport of single-stranded RNA molecules through 1.5-nm-wide pores of carbon nanotube membranes by molecular dynamics simulations. From ≈170 individual RNA...
Hummer, Gerhard, Schotte, Friedrich, Anfinrud, Philip A.
A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved x-ray structures was performed to gain single-molecule insights into mechanisms of protein function....
Water clusters in nonpolar cavities
Vaitheeswaran, Subramanian, Yin, Hao, Rasaiah, Jayendran C., Hummer, Gerhard
We explore the structure and thermodynamics of water clusters confined in nonpolar cavities. By calculating the grand-canonical partition function term by term, we show that small nonpolar cavities...
Reaction coordinates and rates from transition paths
Best, Robert B., Hummer, Gerhard
The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles...
Collins, Marcus D., Hummer, Gerhard, Quillin, Michael L., Matthews, Brian W., Gruner, Sol M.
Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in “hydrophobic” cavities is...
Kinetics from Nonequilibrium Single-Molecule Pulling Experiments
Hummer, Gerhard, Szabo, Attila
Mechanical forces exerted by laser tweezers or atomic force microscopes can be used to drive rare transitions in single molecules, such as unfolding of a protein or dissociation of a ligand. The...
Diffusion and Electrophoretic Mobility of Single-Stranded RNA from Molecular Dynamics Simulations
Hydrodynamic properties of small single-stranded RNA homopolymers with three and six nucleotides in free solution are determined from molecular dynamics simulations in explicit solvent. We find that...
Zweckstetter, Markus, Hummer, Gerhard, Bax, Ad
Alignment of macromolecules in nearly neutral aqueous lyotropic liquid-crystalline media such as bicelles, commonly used in macromolecular NMR studies, can be predicted accurately by a steric...
Peter, Christine, Hummer, Gerhard
Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic...
Kinetic models of redox-coupled proton pumping
Kim, Young C., Wikström, Mårten, Hummer, Gerhard
Cytochrome c oxidase, the terminal enzyme of the respiratory chain, pumps protons across the inner mitochondrial membrane against an opposing electrochemical gradient by reducing oxygen to water. To...
Binding-Induced Folding of a Natively Unstructured Transcription Factor
Turjanski, Adrian Gustavo, Gutkind, J. Silvio, Best, Robert B., Hummer, Gerhard
Transcription factors are central components of the intracellular regulatory networks that control gene expression. An increasingly recognized phenomenon among human transcription factors is the...
Structure and Dynamics of Parallel β-Sheets, Hydrophobic Core, and Loops in Alzheimer's Aβ Fibrils
Buchete, Nicolae-Viorel, Hummer, Gerhard
We explore the relative contributions of different structural elements to the stability of Aβ fibrils by molecular-dynamics simulations performed over a broad range of temperatures (298 K to 398 K)....
Extracting Kinetics from Single-Molecule Force Spectroscopy: Nanopore Unzipping of DNA Hairpins
Dudko, Olga K., Mathé, Jérôme, Szabo, Attila, Meller, Amit, Hummer, Gerhard
Single-molecule force experiments provide powerful new tools to explore biomolecular interactions. Here, we describe a systematic procedure for extracting kinetic information from force-spectroscopy...
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
Kaila, Ville R. I., Verkhovsky, Michael I., Hummer, Gerhard, Wikström, Mårten
Aerobic life is based on a molecular machinery that utilizes oxygen as a terminal electron sink. The membrane-bound cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water in...
Replica exchange simulations of transient encounter complexes in protein–protein association
Kim, Young C., Tang, Chun, Clore, G. Marius, Hummer, Gerhard
Recent paramagnetic relaxation enhancement (PRE) studies on several weakly interacting protein complexes have unequivocally demonstrated the existence of transient encounter complexes. Here, we...
Macroscopically ordered water in nanopores
Köfinger, Jürgen, Hummer, Gerhard, Dellago, Christoph
Water confined into the interior channels of narrow carbon nanotubes or transmembrane proteins forms collectively oriented molecular wires held together by tight hydrogen bonds. Here, we explore the...
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments
Dudko, Olga K., Hummer, Gerhard, Szabo, Attila
Dynamic force spectroscopy probes the kinetic and thermodynamic properties of single molecules and molecular assemblies. Here, we propose a simple procedure to extract kinetic information from such...
Static and dynamic correlations in water at hydrophobic interfaces
Mittal, Jeetain, Hummer, Gerhard
We study the static and dynamic properties of the water-density fluctuations in the interface of large nonpolar solutes. With the help of extensive molecular dynamics simulations of TIP4P water near...
Are Current Molecular Dynamics Force Fields too Helical?
Best, Robert B., Buchete, Nicolae-Viorel, Hummer, Gerhard
Accurate force fields are essential for the success of molecular dynamics simulations. In apparent contrast to the conformational preferences of most force fields, recent NMR experiments suggest that...