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Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events
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References needing attention
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Coarse Nonlinear Dynamics and Metastability of Filling-Emptying Transitions: Water in Carbon Nanotubes
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Functional Significance of Hierarchical Tiers in Carbonmonoxy Myoglobin: Conformational Substates and Transitions Studied by Conformational Flooding Simulations
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Local elevation: A method for improving the searching properties of molecular dynamics simulation
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Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States
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Reconstructing the Density of States by History-Dependent Metadynamics
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Unified Approach for Molecular Dynamics and Density-Functional Theory
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Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
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Azulene‐to‐Naphthalene Rearrangement: The Car–Parrinello Metadynamics Method Explores Various Reaction Mechanisms
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Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions
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Microscopic Mechanism of Antibiotics Translocation through a Porin
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Transition state theory: Variational formulation, dynamical corrections, and error estimates
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On the Statistical Mechanical Treatment of the Absolute Rate of Chemical Reaction
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Statistical mechanics of isomerization dynamics in liquids and the transition state approximation
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Statistical theories of chemical reactions. Distributions in the transition region
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Chemical dynamics of the protonated water trimer analyzed by transition path sampling
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Quantum Statistical Mechanical Theory of the Rate of Exchange Chemical Reactions in the Gas Phase
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A formula to compute the microcanonical volume of reactive initial conditions in transition state theory
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A computational procedure to detect a new type of high-dimensional chaotic saddle and its application to the 3D Hill's problem
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Phase space conduits for reaction in multidimensional systems: HCN isomerization in three dimensions
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Transition state theory and dynamical corrections in ergodic systems
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A new algorithm for Monte Carlo simulation of Ising spin systems
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Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table
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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
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Parallel replica dynamics with a heterogeneous distribution of barriers: Application to <i>n</i>-hexadecane pyrolysis
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Accelerated dynamics simulations of interstitial-cluster growth
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Mechanisms and Rates of Interstitial<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi mathvariant="normal">H</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:math>Diffusion in Crystalline<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi mathvariant="normal">C</mml:mi><mml:mn>60</mml:mn></mml:msub></mml:math>
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Parallel replica dynamics for driven systems: Derivation and application to strained nanotubes
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A method for accelerating the molecular dynamics simulation of infrequent events
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Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
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Fast Peptidyl cis−trans Isomerization within the Flexible Gly-Rich Flaps of HIV-1 Protease
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Accelerated molecular dynamics simulation of the thermal desorption of n-alkanes from the basal plane of graphite
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Closing the Gap between Experiment and Theory: Crystal Growth by Temperature Accelerated Dynamics
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Atomistic study of the dissolution of small boron interstitial clusters in c-Si
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Simulation of growth of Cu on Ag(001) at experimental deposition rates
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T<scp>RANSITION</scp>P<scp>ATH</scp>S<scp>AMPLING</scp>: Throwing Ropes Over Rough Mountain Passes, in the Dark
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Equilibrium Time Correlation Functions from Irreversible Transformations in Trajectory Space
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On the calculation of reaction rate constants in the transition path ensemble
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Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference
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Mechanisms of the Wurtzite to Rocksalt Transformation in CdSe Nanocrystals
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An efficient transition path sampling algorithm for nanoparticles under pressure
resolves10.1073/pnas.0606692103
Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
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Simultaneous computation of free energies and kinetics of rare events
resolves10.1063/1.2198827
Forward flux sampling-type schemes for simulating rare events: Efficiency analysis
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Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling
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Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
resolves10.1529/biophysj.106.101899
A Milestoning Study of the Kinetics of an Allosteric Transition: Atomically Detailed Simulations of Deoxy Scapharca Hemoglobin
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Interplay between Structure and Size in a Critical Crystal Nucleus
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Atomistic Mechanisms of Phase Separation and Formation of Solid Solutions: Model Studies of NaCl, NaCl−NaF, and Na(Cl<sub>1-</sub><i><sub>x</sub></i>Br<i><sub>x</sub></i>) Crystallization from the Melt
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Surface-Mediated Nucleation in the Solid-State Polymorph Transformation of Terephthalic Acid
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Competing Evaporation and Condensation Processes during the Boiling of Methane
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Mechanism of the pressure-induced wurtzite to rocksalt transition of CdSe
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Mechanisms and Nucleation Characteristics of the Pressure-Induced B1−B2 Transition in Potassium Halides: A Question of Ion Hardness and Softness
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Multicenter multidomain<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>B</mml:mi><mml:mn>1</mml:mn><mml:mtext>−</mml:mtext><mml:mi>B</mml:mi><mml:mn>2</mml:mn></mml:mrow></mml:math>pressure-induced reconstructive phase transition in potassium fluoride
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Molecular dynamics investigation of the pressure induced B1 to B2 phase transitions of RbBr
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Putting the squeeze on NaCl: modelling and simulation of the pressure driven B1-B2 phase transition
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Mechanism of the pressure induced reconstructive transformation of KCl from the NaCl type to the CsCl type structure
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Nucleation and Growth in Pressure-Induced Phase Transitions from Molecular Dynamics Simulations: Mechanism of the Reconstructive Transformation of NaCl to the CsCl-Type Structure
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Atomistic Mechanism of NaCl Nucleation from an Aqueous Solution
resolves10.1016/j.cattod.2005.04.005
Application of transition path sampling methods in catalysis: A new mechanism for CC bond formation in the methanol coupling reaction in chabazite
resolves10.1016/j.chemphys.2004.01.016
Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations
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Atomistic Simulation Study of the Pressure Induced Incorporation of Helium into C<sub>60</sub>
resolves10.1021/jp025833l
Reaction Path Sampling of the Reaction between Iron(II) and Hydrogen Peroxide in Aqueous Solution
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Thermal effects on the Cl−+ClCH2CN reaction by Car-Parrinello molecular dynamics
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Stochastic transition pathways in the aqueous sodium chloride dissociation process
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Dynamical Aspects of Isomerization and Melting Transitions in [H<sub>2</sub>O]<sub>8</sub>
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Transition pathways in a many-body system: Application to hydrogen-bond breaking in water
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The aqueous solvation of sodium chloride: A Monte Carlo transition path sampling study
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Transition Path Sampling Study of the Local Molecular Structure in the Aqueous Solvation of Sodium Chloride
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Transition path sampling of cavitation between molecular scale solvophobic surfaces
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Conformational kinetics in liquid <i>n</i>-butane by transition path sampling
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Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase β's closing
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Biomolecular free energy profiles by a shooting/umbrella sampling protocol, “BOLAS”
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Grid−Flux Method for Learning the Solvent Contribution to the Mechanisms of Reactions
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Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA
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A Transition Path Sampling Study of the Reaction Catalyzed by the Enzyme Chorismate Mutase
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Fidelity Discrimination in DNA Polymerase β: Differing Closing Profiles for a Mismatched (G:A) versus Matched (G:C) Base Pair
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How Enzyme Dynamics Helps Catalyze a Reaction in Atomic Detail: A Transition Path Sampling Study
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Transition path sampling study of flip-flop transitions in model lipid bilayer membranes
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A molecular dynamics transition path sampling study of model lipid bilayer membranes in aqueous environments
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Activation Mechanism of a Signaling Protein at Atomic Resolution from Advanced Computations
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resolves10.1103/PhysRevE.64.026109
Efficient transition path sampling for nonequilibrium stochastic dynamics
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Importance sampling and theory of nonequilibrium solvation dynamics in water
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Equilibrium free energies from path sampling of nonequilibrium trajectories
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Single-ensemble nonequilibrium path-sampling estimates of free energy differences
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Biased Sampling of Nonequilibrium Trajectories: Can Fast Switching Simulations Outperform Conventional Free Energy Calculation Methods?
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On the efficiency of path sampling methods for the calculation of free energies from non-equilibrium simulations
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A path-sampling scheme for computing thermodynamic properties of a many-body system in a generalized ensemble
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The distribution function of entropy flow in stochastic systems
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Work and heat probability distributions in out-of-equilibrium systems
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Kinetic analysis of discrete path sampling stationary point databases
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Real-Space Imaging of Nucleation and Growth in Colloidal Crystallization
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On the eigenfunctions of the Fokker-Planck operator and of its adjoint
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Perturbation theory of Φ-value analysis of two-state protein folding: Relation between pfold and Φ values
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The Kramers Problem in the Turnover Regime: The Role of the Stochastic Separatrix
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Activated rate processes: A relation between Hamiltonian and stochastic theories
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Finite barrier corrections for the Kramers rate problem in the spatial diffusion regime
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One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions
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Reaction coordinate of an enzymatic reaction revealed by transition path sampling
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Evolutionary Optimization in Quantitative Structure−Activity Relationship: An Application of Genetic Neural Networks
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Extensions to the likelihood maximization approach for finding reaction coordinates
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Simplified and improved string method for computing the minimum energy paths in barrier-crossing events
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Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide
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Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain
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