Extensions to the likelihood maximization approach for finding reaction coordinates.

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Journal of Chemical Physics

• Publication date

  2007-07-18

• Fields of study

  Mathematics, Chemistry, Medicine

• Identifiers
  DOI 10.1063/1.2748396PMID 17655433
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Surface-mediated nucleation in the solid-state polymorph transformation of terephthalic acid.

  2007cited by this paper
• Forward flux sampling-type schemes for simulating rare events: efficiency analysis.

  2006cited by this paper
• Efficiency analysis of reaction rate calculation methods using analytical models I: The two-dimensional sharp barrier.

  2006cited by this paper
• Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

  2006cited by this paper
• Using the histogram test to quantify reaction coordinate error.

  2006cited by this paper
• String method in collective variables: minimum free energy paths and isocommittor surfaces.

  2006cited by this paper
• Efficiency analysis of reaction rate calculation methods using analytical models I: The two-dimensional sharp barrier

  2006cited by this paper
• Bias annealing: a method for obtaining transition paths de novo.

  2006cited by this paper
• Illustration of transition path theory on a collection of simple examples.

  2006cited by this paper
• Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

  2006cited by this paper
• The Amber biomolecular simulation programs

  2005cited by this paper
• GROMACS: Fast, flexible, and free

  2005cited by this paper
• Scalable molecular dynamics with NAMD

  2005cited by this paper
• Automatic method for identifying reaction coordinates in complex systems.

  2005cited by this paper
• Reaction coordinates and rates from transition paths.

  2005cited by this paper
• Assessing the efficiency of free energy calculation methods.

  2004cited by this paper
• Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS".

  2004cited by this paper
• Rate constants from the reaction path Hamiltonian. I. Reactive flux simulations for dynamically correct rates.

  2004cited by this paper
• From transition paths to transition states and rate coefficients.

  2004cited by this paper
• A growing string method for determining transition states: comparison to the nudged elastic band and string methods.

  2004cited by this paper
• Elaborating transition interface sampling methods

  2004cited by this paper
• Accelerating Monte Carlo Sampling

  2002cited by this paper
• Escaping free-energy minima

  2002cited by this paper
• Transition path sampling: throwing ropes over rough mountain passes, in the dark.

  2002cited by this paper
• Finite temperature string method for the study of rare events.

  2002cited by this paper
• Filling and emptying kinetics of carbon nanotubes in water

  2002cited by this paper
• Understanding Molecular Simulation

  2001cited by this paper
• On the calculation of reaction rate constants in the transition path ensemble

  1999cited by this paper
• On the transition coordinate for protein folding

  1998cited by this paper
• Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events

  1997cited by this paper
• A method for accelerating the molecular dynamics simulation of infrequent events

  1997cited by this paper
• λ‐dynamics: A new approach to free energy calculations

  1996cited by this paper
• THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

  1992cited by this paper
• Reaction-rate theory: fifty years after Kramers

  1990cited by this paper
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

  1983cited by this paper
• Reaction path Hamiltonian for polyatomic molecules

  1980cited by this paper
• Location of saddle points and minimum energy paths by a constrained simplex optimization procedure

  1979cited by this paper
• Generalized transition state theory. Bond energy-bond order method for canonical variational calculations with application to hydrogen atom transfer reactions

  1979cited by this paper
• Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

  1977cited by this paper
• Variational Theory of Chemical Reaction Rates Applied to Three‐Body Recombinations

  1960cited by this paper
• Initial Recombination of Ions

  1938cited by this paper
• Statistical Mechanics of Fluid Mixtures

  1935cited by this paper

• Mechanism of Bacterial Arginine N‑Glycosylation: A Chemically Challenging Post-Translational Modification

  2026cites this paper
• An exact multiple-time-step variational formulation for the committor and the transition rate

  2025cites this paper
• Deep learning of committor for ion dissociation and interpretable analysis of solvent effects using atom-centered symmetry functions.

  2025cites this paper
• The impact of hydration shell inclusion and chain exclusion in the efficacy of reaction coordinates for homogeneous and heterogeneous ice nucleation.

  2025cites this paper
• Molecular-Level Mechanistic Insights into PETase-Catalyzed Plastics Hydrolysis from Accurate QM/MM Free Energy Calculations

  2025cites this paper
• Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications

  2025cites this paper
• Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach.

  2024cites this paper
• Harvesting nucleating structures in nanoparticle crystallization: The example of gold, silver, and iron.

  2024cites this paper
• Investigating the hyperparameter space of deep neural network models for reaction coordinates

  2024cites this paper
• Reaction Coordinates Are Optimal Channels of Energy Flow.

  2024cites this paper
• The reaction mechanism of the Ideonella sakaiensis PETase enzyme

  2024cites this paper
• RSeeds: Rigid Seeding Method for Studying Heterogeneous Crystal Nucleation.

  2023cites this paper
• Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction.

  2023cites this paper
• Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models.

  2023cites this paper
• Optimal Reaction Coordinates and Kinetic Rates from the Projected Dynamics of Transition Paths.

  2023cites this paper
• Resolving Temperature-Dependent Hydrate Nucleation Pathway: The Role of "Transition Layer".

  2023cites this paper
• Variational deep learning of equilibrium transition path ensembles.

  2023cites this paper
• An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions.

  2023cites this paper
• Heterogeneous nucleation in the random field Ising model.

  2023cites this paper
• Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling.

  2023cites this paper
• Time-lagged Flux in the Transition Path Ensemble: Flux Maximization and Relation to Transition Path Theory

  2022cites this paper
• Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI).

  2022cites this paper
• ATESA: An Automated Aimless Shooting Workflow.

  2022cites this paper
• The role of pressure and defects in the wurtzite to rock salt transition in cadmium selenide.

  2022cites this paper
• Potential Energy Weighted Reactive Flux and Total Rate of Change of Potential Energy: Theory and Illustrative Applications

  2022cites this paper
• Energy Decomposition along the Reaction Coordinate: Theory and Applications to Nonequilibrium Ensembles of Trajectories.

  2022cites this paper
• Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.

  2022cites this paper
• Critical Assessment of Data-Driven versus Heuristic Reaction Coordinates in Solution Chemistry.

  2022cites this paper
• Reaction coordinates in complex systems-a perspective

  2021cites this paper
• Exact non-Markovian permeability from rare event simulations

  2021cites this paper
• Reaction Coordinate and Thermodynamics of Base Flipping in RNA.

  2021cites this paper
• From Enhanced Sampling to Reaction Profiles.

  2021cites this paper
• Free Energy Landscapes, Diffusion Coefficients, and Kinetic Rates from Transition Paths.

  2021cites this paper
• Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook

  2021cites this paper
• QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase

  2021cites this paper
• Transition Path Sampling Study of the Feruloyl Esterase Mechanism.

  2021cites this paper
• Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA

  2021cites this paper
• Optimizing reaction coordinate by flux maximization in the transition path ensemble

  2021cites this paper
• Ligand Recognition in Viral RNA Necessitates Rare Conformational Transitions.

  2020cites this paper
• Using metadynamics to explore complex free-energy landscapes

  2020cites this paper
• The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function

  2020cites this paper
• Deep Reinforcement Learning of Transition States

  2020cites this paper
• Effect of Collective Dynamics and Anharmonicity on Entropy in Heterogenous Catalysis: Building the Case for Advanced Molecular Simulations

  2020cites this paper
• The value of temporal information when analyzing reaction coordinates.

  2020cites this paper
• Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange Between Membranes

  2020cites this paper
• Solvent reaction coordinate for an SN2 reaction.

  2020cites this paper
• Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation

  2020cites this paper
• Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II.

  2020cites this paper
• Using metadynamics to explore complex free-energy landscapes

  2020cites this paper
• Identification of a multi-dimensional reaction coordinate for crystal nucleation in Ni3Al.

  2020cites this paper
• Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide.

  2020influential citation
• Hierarchical phenomena in multicomponent liquids: simulation methods, analysis, chemistry.

  2020cites this paper
• The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function

  2020cites this paper
• A deep learning framework for mesh relaxation in arbitrary Lagrangian-Eulerian simulations

  2019cites this paper
• Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems

  2019cites this paper
• Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers

  2019cites this paper
• Phase space and collective variable based simulation methods for studies of rare events

  2019cites this paper
• Following the nucleation pathway from disordered liquid to gyroid mesophase.

  2019cites this paper
• Advancing Molecular Simulations of Crystal Nucleation: Applications to Clathrate Hydrates

  2019influential citation
• Estimating reciprocal partition functions to enable design space sampling.

  2019cites this paper
• Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide

  2019cites this paper
• Orthogonal order parameters to model the reaction coordinate of an enzyme catalyzed reaction.

  2019cites this paper
• Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide.

  2018cites this paper
• Nonlinear machine learning in simulations of soft and biological materials

  2018cites this paper
• Recovery of Protein Folding Funnels from Single-Molecule Time Series by Delay Embeddings and Manifold Learning.

  2018cites this paper
• Thermal cis-trans isomerization of azobenzene studied by path sampling and QM/MM stochastic dynamics

  2018cites this paper
• Reaction coordinates and transition states in enzymatic catalysis

  2018cites this paper
• Unbiased Atomistic Insight into the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation

  2018influential citation
• Reaction Coordinate, Free Energy, and Rate of Intramolecular Proton Transfer in Human Carbonic Anhydrase II.

  2018cites this paper
• Maximum Likelihood Analysis of Reaction Coordinates during Solidification in Ni.

  2018cites this paper
• Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.

  2017cites this paper
• Foundations and latest advances in replica exchange transition interface sampling.

  2017cites this paper
• Reaction coordinates and mechanisms

  2017cites this paper
• Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead

  2017cites this paper
• Role of stacking disorder in ice nucleation

  2017cites this paper
• Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration

  2017cites this paper
• Reaction Coordinate for Ice Crystallization on a Soft Surface.

  2017cites this paper
• Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning

  2017cites this paper
• Pre-ordering of interfacial water in the pathway of heterogeneous ice nucleation does not lead to a two-step crystallization mechanism.

  2016cites this paper
• Reaction mechanism and reaction coordinates from the viewpoint of energy flow.

  2016cites this paper
• Nonadiabatic transition path sampling.

  2016cites this paper
• A benchmark for reaction coordinates in the transition path ensemble.

  2016cites this paper
• Analyzing Complex Reaction Mechanisms Using Path Sampling.

  2016cites this paper
• Reaction Coordinates and Mechanistic Hypothesis Tests.

  2016cites this paper
• Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases

  2016cites this paper
• A Supervised Learning Framework for Arbitrary Lagrangian-Eulerian Simulations

  2016cites this paper
• Identification of simple reaction coordinates from complex dynamics.

  2016cites this paper
• Pathways to self-organization: Crystallization via nucleation and growth

  2016cites this paper
• Easy transition path sampling methods: flexible-length aimless shooting and permutation shooting.

  2015cites this paper
• Common features of extraordinary rate theories.

  2015cites this paper
• Reducing the cost of evaluating the committor by a fitting procedure.

  2015cites this paper
• Determination of the Reaction Coordinate for a Key Conformational Fluctuation in Human Carbonic Anhydrase II.

  2015cites this paper
• Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape.

  2015cites this paper
• Fungal cellulases.

  2015cites this paper
• Kinetic distance and kinetic maps from molecular dynamics simulation.

  2015cites this paper
• Machine Learning and Understanding for Intelligent Extreme Scale Scientific Computing and Discovery DOE Workshop Report

  2015cites this paper
• Transition state ensemble optimization for reactions of arbitrary complexity.

  2015cites this paper
• Competitive Nucleation in Nanoclusters

  2015cites this paper
• Machine Learning and Understanding for Intelligent Extreme Scale Scientifc Computing and Discovery

  2015cites this paper
• Solute Precipitate Nucleation: A Review of Theory and Simulation Advances

  2014cites this paper