Escaping free-energy minima

Abstract

We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates.A characteristic feature of this dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the free energy surface, allowing the efficient exploration and accurate determination of the free energy surface as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

3 figures

References in corpus (1)

• Action-derived molecular dynamics in the study of rare events

Cited by in corpus (481)

• PLUMED 2: New feathers for an old bird
• Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
• PLUMED: a portable plugin for free-energy calculations with molecular dynamics
• Ab initio Random Structure Searching
• Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations
• Predicting crystal structures: the Parrinello-Rahman method revisited
• Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems
• From Metadynamics to Dynamics
• Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
• Equilibrium free energies from non-equilibrium metadynamics
• Rethinking Metadynamics: from bias potentials to probability distributions
• i-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations
• Atomistic details of oxide surfaces and surface oxidation: the example of copper and its oxides
• Enhanced sampling methods for molecular dynamics simulations
• A Variational Approach to Enhanced Sampling and Free Energy Calculations
• Metadynamics with adaptive Gaussians
• Crystal structure prediction using the Minima Hopping method
• Enhanced Sampling in the Well-Tempered Ensemble
• Caliber based spectral gap optimization of order parameters (SGOOP) for sampling complex molecular systems
• Hamiltonian replica-exchange in GROMACS: a flexible implementation
• Exploration of Reaction Pathways and Chemical Transformation Networks
• Elucidating the Bimodal Acid-base Behavior of the Water-silica Interface from First Principles
• The Many Faces of Heterogeneous Ice Nucleation: Interplay Between Surface Morphology and Hydrophobicity
• Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration
• Data-Driven Collective Variables for Enhanced Sampling
• Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations
• Ballistic molecular transport through two-dimensional channels
• Anisotropy of Earth's D" layer and stacking faults in the MgSiO3 post-perovskite phase
• The Exploration of Chemical Reaction Networks
• Deep Potentials for Materials Science
• Adaptively Biased Molecular Dynamics for Free Energy Calculations
• A novel superhard tungsten nitride predicted by machine-learning accelerated crystal structure searching
• Unsupervised machine learning in atomistic simulations, between predictions and understanding
• Entropy based fingerprint for local crystalline order
• Evidence for supercritical behavior of high-pressure liquid hydrogen
• Nonlinear Discovery of Slow Molecular Modes using State-Free Reversible VAMPnets
• Single-Sweep Methods for Free Energy Calculations
• A self-learning algorithm for biased molecular dynamics
• Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
• Reconstructing the Density of States by History-Dependent Metadynamics
• Silicon liquid structure and crystal nucleation from ab-initio deep Metadynamics
• A Unified Approach to Enhanced Sampling
• Data-driven parameterization of the generalized Langevin equation
• Neural networks-based variationally enhanced sampling
• Cobalt-Porphyrin Catalyzed Electrochemical Reduction of Carbon Dioxide in Water II: Mechanism from First Principles
• A variational conformational dynamics approach to the selection of collective variables in metadynamics
• Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments
• First Principles Modeling of the Initial Stages of Organic Solvent Decomposition on Li(x)Mn(2)O(4) (100) Surfaces
• Universality of Block Copolymer Melts
• First Principles Modeling of Mn(II) Migration above and Dissolution from Li(x)Mn(2)O(4) (001) Surfaces
• Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
• Folding of guanine quadruplex molecules -- funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies
• Thermodynamically Driven Assemblies and Liquid-liquid Phase Separations in Biology
• Reinforced dynamics for enhanced sampling in large atomic and molecular systems
• Investigating Rare Events by Transition Interface Sampling
• Enhancing entropy and enthalpy fluctuations to drive crystallization in atomistic simulations
• The mold integration method for the calculation of the crystal-fluid interfacial free energy from simulations
• Uncertainty Quantification in Classical Molecular Dynamics
• Accelerated weight histogram method for exploring free energy landscapes
• Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering
• Computation of free energy profiles with parallel adaptive dynamics
• Unraveling the water degradation mechanism of CH${}_3$NH${}_3$PbI${}_3$
• Solid-liquid interface free energy through metadynamics simulations
• Free Energy Landscape of GAGA and UUCG RNA Tetraloops
• Neural network based path collective variables for enhanced sampling of phase transformations
• Identification of simple reaction coordinates from complex dynamics
• Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional
• Homogeneous ice nucleation in an ab initio machine learning model of water
• Ice Formation on Kaolinite: Insights from Molecular Dynamics Simulations
• Structure prediction based on ab initio simulated annealing for boron nitride
• The Microscopic Features of Heterogeneous Ice Nucleation May Affect the Macroscopic Morphology of Atmospheric Ice Crystals
• Homogeneous nucleation of ice
• Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks
• Impact of Surface Charging on Catalytic Processes
• SchNetPack 2.0: A neural network toolbox for atomistic machine learning
• Systematic search for low-enthalpy sp3 carbon using evolutionary metadynamics
• Coarse-Grained Kinetic Computations for Rare Events: Application to Micelle Formation
• A Bell-Evans-Polanyi principle for molecular dynamics trajectories and its implications for global optimization
• Studying Rare Events using Forward-Flux Sampling: Recent Breakthroughs and Future Outlook
• The phase diagram of water at high pressures as obtained by computer simulations of the TIP4P/2005 model: the appearance of a plastic crystal phase
• A unified framework for machine learning collective variables for enhanced sampling simulations: $\text{mlcolvar}$
• Exploring High Dimensional Free Energy Landscapes: Temperature Accelerated Sliced Sampling
• Rare Event Kinetics from Adaptive Bias Enhanced Sampling
• The role of water and steric constraints in the kinetics of cavity-ligand unbinding
• Analyzing and biasing simulations with PLUMED
• Unravelling Mg${}^{2+}$-RNA binding with atomistic molecular dynamics
• Tutorial: How to Train a Neural Network Potential
• Metadynamics for Training Neural Network Model Chemistries: a Competitive Assessment
• Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics
• Tuning Chemical Precompression: Theoretical Design and Crystal Chemistry of Novel Hydrides in the Quest for Warm and Light Superconductivity at Ambient Pressures
• Global exploration of the energy landscape of solids on the ab initio level
• Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
• Recognizing molecular patterns by machine learning: an agnostic structural definition of the hydrogen bond
• Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks
• Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids
• The kinetics of homogeneous melting beyond the limit of superheating
• Stochastic resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
• Special Topic: Markov Models of Molecular Kinetics
• From enhanced sampling to reaction profiles
• Frequency adaptive metadynamics for the calculation of rare-event kinetics
• Water regulates the residence time of Benzamidine in Trypsin
• The role of water in host-guest interaction
• Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways
• Navigating at Will on the Water Phase Diagram
• Windowed Carbon Nanotubes for Efficient CO2 Removal from Natural Gas
• Computing Committor Functions for the Study of Rare Events Using Deep Learning
• Topology in full QCD at high temperature: a multicanonical approach
• Computing the Committor with the Committor: an Anatomy of the Transition State Ensemble
• Learning Free Energy Landscapes Using Artificial Neural Networks
• Overcoming the time limitation in Molecular Dynamics simulation of crystal nucleation: a persistent-embryo approach
• Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densities
• Atomistic Mechanism of the Nucleation of Methylammonium Lead Iodide Perovskite from Solution
• Evolutionary Metadynamics: a Novel Method to Predict Crystal Structures
• Folding a Small Protein Using Harmonic Linear Discriminant Analysis
• Unravelling the Origins of Ice Nucleation on Organic Crystals
• Characterizing Structure Through Shape Matching and Applications to Self Assembly
• Empirical corrections to the Amber RNA force field with Target Metadynamics
• Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide
• Unraveling the Crystallization Kinetics of the Ge${}_2$Sb${}_2$Te${}_5$ Phase Change Compound with a Machine-Learned Interatomic Potential
• Pathways to self-organization: crystallization via nucleation and growth
• Liquid-Liquid Critical Point in Phosphorus
• The Search for Superconductivity in High Pressure Hydrides
• Sampling polymorphs of ionic solids using random superlattices
• The quest to simulate excited-state dynamics of transition metal complexes
• Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics
• Puckering Free Energy of Pyranoses: an NMR and Metadynamics--Umbrella Sampling Investigation
• Principal component analysis of nonequilibrium molecular dynamics simulations
• Deep Learning Collective Variables from Transition Path Ensemble
• Gaussian Mixture Based Enhanced Sampling
• A microscopic description of acid-base equilibrium
• Coarse Nonlinear Dynamics and Metastability of Filling-Emptying Transitions: Water in Carbon Nanotubes
• Towards an integrated modeling of the plasma-solid interface
• Free energy surface reconstruction from umbrella samples using Gaussian process regression
• A local order metric for condensed phase environments
• Unfolding Hidden Barriers by Active Enhanced Sampling
• Overcoming timescale and finite-size limitations to compute nucleation rates from small scale Well Tempered Metadynamics simulations
• Variationally Optimized Free Energy Flooding for Rate Calculation
• The structure of CaSO4 nanorods -- the precursor of gypsum
• Importance sampling large deviations in nonequilibrium steady states. I
• Seeding Approach to nucleation in the NVT ensemble: the case of bubble cavitation in overstretched Lennard Jones fluids
• Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
• Forward-Flux Sampling with Jumpy Order Parameters
• Uncertainty-biased molecular dynamics for learning uniformly accurate interatomic potentials
• Conformational free energies of methyl-$\alpha$-L-iduronic and methyl-$\beta$-D-glucuronic acids in water
• RNA/peptide binding driven by electrostatics -- Insight from bi-directional pulling simulations
• Girsanov reweighting for path ensembles and Markov state models
• Efficient Rare Event Simulation by Optimal Nonequilibrium Forcing
• Folding and insertion thermodynamics of the transmembrane WALP peptide
• Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications
• Correlated materials design: prospects and challenges
• Driving and characterizing nucleation of urea and glycine polymorphs in water
• Collective Variables for the Study of Crystallization
• Expansive Quantum Mechanical Exploration of Chemical Reaction Paths
• Optimal Langevin modelling of out-of-equilibrium molecular dynamics simulations
• Making the best of a bad situation: a multiscale approach to free energy calculation
• Multiscale reweighted stochastic embedding (MRSE): Deep learning of collective variables for enhanced sampling
• Finding Multiple Reaction Pathways of Ligand Unbinding
• Accelerated simulation method for charge regulation effects
• Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials
• Efficiency analysis of reaction rate calculation methods using analytical models I: The 2D sharp barrier
• Human learning for molecular simulations: the Collective Variables Dashboard in VMD
• On Machine Learning Force Fields for Metallic Nanoparticles
• Combining Metadynamics and Integrated Tempering Sampling
• Hydrolysis of Cephalexin and Meropenem by New Delhi Metallo $\beta$-Lactamase: Substrate Protonation Mechanism is Drug Dependent
• Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution
• Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
• Weighted Ensemble Milestoning (WEM): A Combined Approach for Rare Event Simulations
• METAGUI 3: a graphical user interface for choosing the collective variables in molecular dynamics simulations
• Predictive Collective Variable Discovery with Deep Bayesian Models
• Topological critical slowing down: variations on a toy model
• Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang-Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics
• Multithermal-multibaric molecular simulations from a variational principle
• Accurate multiple time step in biased molecular simulations
• Finding the structure of phosphorus in the phase IV
• Transformation pathways in high-pressure solid nitrogen: from molecular N${}_2$ to polymeric cg-N
• DNA denaturation bubbles: free-energy landscape and nucleation/closure rates
• Dual-Topology Hamiltonian-Replica-Exchange Overlap Histogramming Method to Calculate Relative Free Energy Difference in Rough Energy Landscape
• Reconstructing the free-energy landscape of Met-enkephalin using dihedral Principal Component Analysis and Well-tempered Metadynamics
• The onset of dehydrogenation in solid Ammonia Borane, an ab-initio metadynamics study
• High-pressure NMR spectroscopy in studies of the conformational composition of small molecules of ibuprofen in supercritical carbon dioxide
• Identification and Analysis of Transition and Metastable Markov States
• Dynamical reweighting methods for Markov models
• Layer-by-layer phase transformation in Ti${}_3$O${}_5$ revealed by machine learning molecular dynamics simulations
• Pushing the limit of molecular dynamics with ab initio accuracy to 100 million atoms with machine learning
• MUSE: Multi-algorithm collaborative crystal structure prediction
• Metadynamics Surfing on Topology Barriers: the $C{P}^{N-1}$ Case
• CO2 packing polymorphism under pressure: mechanism and thermodynamics of the I-III polymorphic transition
• Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators
• ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials
• Blind search for complex chemical pathways using Harmonic Linear Discriminant Analysis
• Dominant Reaction Pathways in High Dimensional Systems
• Riemann metric approach to optimal sampling of multidimensional free-energy landscapes
• Statistically optimal continuous free energy surfaces from biased simulations and multistate reweighting
• Adaptively accelerating reactive molecular dynamics using boxed molecular dynamics in energy space
• NENCI-2021 Part I: A Large Benchmark Database of Non-Equilibrium Non-Covalent Interactions Emphasizing Close Intermolecular Contacts
• A unifying framework for amyloid-mediated membrane damage: The lipid-chaperon hypothesis
• Strain-rate and temperature dependence of yield stress of amorphous solids via self-learning metabasin escape algorithm
• Identification of structural motifs as tunneling two-level systems in amorphous alumina at low temperatures
• Metadynamics of paths
• Materials under high pressure: A chemical perspective
• Temperature Accelerated Monte Carlo (TAMC): a method for sampling the free energy surface of non-analytical collective variables
• Strain-rate and temperature-driven transition in the shear transformation zone for two-dimensional amorphous solids
• Descriptors-free Collective Variables From Geometric Graph Neural Networks
• Time-independent free energies from metadynamics via Mean Force Integration
• Approaching a parameter-free metadynamics
• Can High-Temperature Reactions Be Described by a Minimum Energy Path Model? Steric Hindrance Matters
• Computer Simulation of the Early Stages of Self-Assembly and Thermal Decomposition of ZIF-8
• Finite-temperature materials modeling from the quantum nuclei to the hot electrons regime
• Practical guide to replica exchange transition interface sampling and forward flux sampling
• Efficient estimation of rare-event kinetics
• Detecting stable adsorbates of (1S)-camphor on Cu(111) with Bayesian optimization
• Local and Global Perspectives on Diffusion Maps in the Analysis of Molecular Systems
• Reaction coordinates and rate constants for liquid droplet nucleation: quantifying the interplay between driving force and memory
• From Free-Energy Profiles to Activation Free Energies
• Enhanced sampling of transition states
• Metadynamics sampling in atomic environment space for collecting training data for machine learning potentials
• I. Dissociation free energies in drug-receptor systems via non equilibrium alchemical simulations: theoretical framework
• Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials
• Heterogeneous Seeded Molecular Dynamics as a Tool to Probe the Ice Nucleating Ability of Crystalline Surfaces
• Towards fully ab initio simulation of atmospheric aerosol nucleation
• Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways
• Modeling molecular and ionic absolute solvation free energies with quasi-chemical theory bounds
• Free energy reconstruction from steered dynamics without post-processing
• xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states
• A Deep Autoencoder Framework for Discovery of Metastable Ensembles in Biomacromolecules
• Accelerated ab-initio Molecular Dynamics: probing the weak dispersive forces in dense liquid hydrogen
• Contour forward flux sampling: Sampling rare events along multiple collective variables
• Adding alchemical variables to metadynamics to enhance sampling in free energy calculations
• Hybrid deterministic and stochastic approach for efficient atomistic simulations at long time scales
• Neural Canonical Transformation with Symplectic Flows
• Equivalence between condensation and boiling in a Lennard Jones fluid
• Size-Dependent Nucleation in Crystal Phase Transition from Machine Learning Metadynamics
• Diffusion of large particles through small pores: from entropic to enthalpic transport
• Superposition Enhanced Nested Sampling
• Nucleating a Different Coordination in a Crystal under Pressure: A Study of the B1-B2 Transition in NaCl by Metadynamics
• On the Calculation of Puckering Free Energy Surfaces
• Everything everywhere all at once: a probability-based enhanced sampling approach to rare events
• Estimation of the infinitesimal generator by square-root approximation
• Conformational Entropy as Collective Variable for Proteins
• Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d
• Target search of active agents crossing high energy barriers
• Probing the unfolded configurations of a $\beta$-hairpin using sketch-map
• Diffusion and desorption of SiH3 on hydrogenated H:Si(100)-(2x1) from first principles
• Computing committors via Mahalanobis diffusion maps with enhanced sampling data
• Kinetics of aqueous media reactions via ab initio enhanced molecular dynamics: the case of urea decomposition
• Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk
• A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models
• Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting
• Identifying rare chaotic and regular trajectories in dynamical systems with Lyapunov weighted path sampling
• Construction of coarse-grained molecular dynamics with many-body non-Markovian memory
• PySAGES: flexible, advanced sampling methods accelerated with GPUs
• Methods to locate Saddle Points in Complex Landscapes
• Equilibrium Sampling in Biomolecular Simulation
• On the hierarchical parallelization of ab initio simulations
• Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
• Mechanistic insights into water autoionization
• Assessing models of force-dependent unbinding rates via infrequent metadynamics
• Ab initio mass tensor molecular dynamics
• Bayesian Calibration of Force-fields from Experimental Data: TIP4P Water
• Sampling, rates, and reaction currents through reverse stochastic quantization on quantum computers
• Learning Clustered Representation for Complex Free Energy Landscapes
• A framework of nonequilibrium statistical mechanics. II. Coarse-graining
• Dominant Reaction Pathways by Quantum Computing
• Multimap targeted free energy estimation
• Accelerating Langevin Sampling with Birth-death
• Homogeneous nucleation rate of carbon dioxide hydrate formation under experimental condition from Seeding simulations
• Polymorph selection during crystallization of a model colloidal fluid with a free energy landscape containing a metastable solid
• Kinetics and Free Energy of Ligand Dissociation Using Weighted Ensemble Milestoning
• A variational approach to nucleation simulation
• Data-driven construction of stochastic reduced dynamics encoded with non-Markovian features
• Manifold Learning in Atomistic Simulations: A Conceptual Review
• PLUMED-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts
• A perturbative solution to metadynamics ordinary differential equation
• Xsorb: a software for identifying the most stable adsorption configuration and energy of a molecule on a crystal surface
• Theoretical investigation of methane under pressure
• Collective Variable for Metadynamics Derived from AlphaFold Output
• Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks
• Accelerating molecular dynamics simulations with population annealing
• Deep learning the slow modes for rare events sampling
• Estimating thermodynamic expectations and free energies in expanded ensemble simulations: systematic variance reduction through conditioning
• Free Energy Landscapes, Diffusion Coefficients, and Kinetic Rates from Transition Paths
• First principles approaches and concepts for electrochemical systems
• Self-learning hybrid Monte Carlo method for isothermal-isobaric ensemble: Application to liquid silica
• Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces
• Atomistic simulation of the Coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface
• Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems
• Sampling Rare Conformational Transitions with a Quantum Computer
• 3BrY nucleation: from dimers to needle-like clusters
• Quantifying the impact of vibrational nonequilibrium in plasma catalysis: Insights from a molecular dynamics model of dissociative chemisorption
• Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study
• Finding reaction pathways with optimal atomic index mappings
• Waste-recycling Monte Carlo with optimal estimates: application to free energy calculations in alloys
• Variational Umbrella Seeding for Calculating Nucleation Barriers
• Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: Performance in pose prediction in the D3R-GC4
• Estimation of microscopic averages from metadynamics
• Simulated Tempering Method in the Infinite Switch Limit with Adaptive Weight Learning
• Exploration of Effective Potential Landscapes using Coarse Reverse Integration
• Free energy landscape of sodium solvation into graphite
• Computing the Tolman length for solid-liquid interfaces
• Hyperdynamics for entropic systems: time-space compression and pair correlation function approximation
• maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels
• Facile implementation of integrated tempering sampling method to enhance the sampling over a broad range of temperatures
• Tautomeric equilibrium in condensed phases
• Crystal Structure Prediction Supported by Incomplete Experimental Data
• Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification
• Integrated Reaction Path Processing from Sampled Structure Sequences
• First-principles calculations that clarify energetics and reactions of oxygen adsorption and carbon desorption on 4H-SiC ($11\bar{2}0$) surface
• Supervised Learning and the Finite-Temperature String Method for Computing Committor Functions and Reaction Rates
• Statistical mechanics of a single active slider on a fluctuating interface
• Physics-informed active learning for accelerating quantum chemical simulations
• Calculating the free energy of 2D materials on substrates
• Quantum symmetry from enhanced sampling methods
• Learning Collective Variables with Synthetic Data Augmentation through Physics-Inspired Geodesic Interpolation
• Efficient determination of alloy ground-state structures
• Unsupervised learning of representative local atomic arrangements in molecular dynamics data
• Autoencoders for dimensionality reduction in molecular dynamics: collective variable dimension, biasing and transition states
• Multi-replica biased sampling for photoswitchable pi-conjugated polymers
• Searching for the optimum conditions for silicene growth by calculations of the free energy
• Atomistic View of Homogeneous Nucleation of Water into Polymorphic Ices
• Simulated Tempering and Magnetizing: An Application of Two-Dimensional Simulated Tempering to Two-Dimensional Ising Model and Its Crossover
• Efficient Rare Event Sampling with Unsupervised Normalising Flows
• Prospects of Transition Interface Sampling simulations for the theoretical study of zeolite synthesis
• Nucleation rates from small scale atomistic simulations and transition state theory
• Efficiently Sampling Conformations and Pathways Using the Concurrent Adaptive Sampling (CAS) Algorithm
• Combining Enhanced Sampling with Experiment Directed Simulation of the GYG peptide
• Implementing Dimer Metadynamics using GROMACS
• Computing Transition Rates for Rare Event: When Kramers Theory meets Free Energy Landscape
• A "parallel universe" scheme for crack nucleation in the phase field approach to fracture
• Birth-death dynamics for sampling: Global convergence, approximations and their asymptotics
• Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer
• Understanding In-line Probing Experiments by Modeling Cleavage of Non-reactive RNA Nucleotides
• Multistate metadynamics for automatic exploration of conical intersections
• Data-driven Langevin modeling of nonequilibrium processes
• Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters
• Enhancing the formation of ionic defects to study the ice Ih/XI transition with molecular dynamics simulations
• Extending \textit{ab initio} plasma-surface simulations to experimentally relevant scales
• Mechanisms of DNA Hybridization: Transition Path Analysis of a Simulation-Informed Markov Model
• Enhanced Sampling for Free Energy Profiles with Post-Transition-State Bifurcations
• A structural optimization algorithm with stochastic forces and stresses
• An Efficient Simulation Protocol for Determining the Density of States: Combination of Replica-Exchange Wang-Landau Method and Multicanonical Replica-Exchange Method
• High-pressure phase diagram, structural transitions, and persistent non-metallicity of BaBiO${}_3$: theory and experiment
• Towards an optimal flow: Density-of-states-informed replica-exchange simulations
• Out-of-equilibrium Polymorph Selection in Nanoparticle Freezing
• Flow Matching for Optimal Reaction Coordinates of Biomolecular System
• Weighted Active Space Protocol for Multireference Machine-Learned Potentials
• First Principles Prediction of Amorphous Phases Using Evolutionary Algorithms
• Free-energy landscapes in magnetic systems from metadynamics
• Machine Learning Enhanced Calculation of Quantum-Classical Binding Free Energies
• Crystal-Structure Matches in Solid-Solid Phase Transitions
• Coarse molecular-dynamics analysis of stress-induced structural transitions in crystals
• MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development
• Sampling a rare protein transition with a hybrid classical-quantum computing algorithm
• Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm
• $\mu$-tempered metadynamics: Artifact independent convergence times for wide hills
• Rotationally invariant local bond order parameters for accurate determination of hydrate structures
• Nanostars planarity modulates the elasticity of DNA hydrogels
• Quantum Diffusive Dynamics of Macromolecular Transitions
• Calculation of the Residual Entropy of Ice Ih by Monte Carlo simulation with the Combination of the Replica-Exchange Wang-Landau algorithm and Multicanonical Replica-Exchange Method
• Nonequilibrium thermodynamics of DNA nanopore unzipping
• Exploring canyons in glassy energy landscapes using metadynamics
• A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
• Parallel Tempered Metadynamics: Overcoming potential barriers without surfing or tunneling
• The topological properties of QCD at high temperature: problems and perspectives
• A Noise-Robust Data Assimilation Method for Crystal Structure Prediction Using Powder Diffraction Intensity
• Funnel Hopping Monte Carlo: An efficient method to overcome broken ergodicity
• Coarse Molecular-Dynamics Determination of the Onset of Structural Transitions: Melting of Crystalline Solids
• Maxwell's demon and the management of ignorance in stochastic thermodynamics
• Interplay of Physically Different Properties Leading to Challenges in Separating Lanthanide Cations -- an Ab Initio Molecular Dynamics and Experimental Study
• Microscopically Computing Free-energy Profiles and Transition Path Time of Rare Macromolecular Transitions
• Equilibrium sampling by re-weighting non-equilibrium simulation trajectories
• Metashooting: A Novel Tool for Free Energy Reconstruction from Polymorphic Phase Transition Mechanisms
• Prediction of Novel High Pressure H2O-NaCl and Carbon Oxide Compounds with Symmetry-Driven Structure Search Algorithm
• Compressing and forecasting atomic material simulations with descriptors
• Can molecular dynamics be used to simulate biomolecular recognition?
• An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
• Topology changing update algorithms for SU(3) gauge theory
• Spin reorientation transition in an ultrathin Fe film on W(110) induced by Dzyaloshinsky-Moriya interactions
• Stein Self-Repulsive Dynamics: Benefits From Past Samples
• Activated sampling in complex materials at finite temperature: the properly-obeying-probability activation-relaxation technique
• Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations
• An observable for vacancy characterization and diffusion in crystals
• GANs and Closures: Micro-Macro Consistency in Multiscale Modeling
• Application of Simulated Tempering and Magnetizing to a Two-Dimensional Potts Model
• How to Differentiate Collective Variables in Free Energy Codes: Computer-Algebra Code Generation and Automatic Differentiation
• Applying the Wang-Landau Algorithm to Lattice Gauge Theory
• LeaPP: Learning Pathways to Polymorphs through machine learning analysis of atomic trajectories
• Machine-learning-based sampling method for exploring local energy minima of interstitial species in a crystal
• Self-Organizing Maps of Unbiased Ligand-Target Binding Pathways and Kinetics
• Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations
• Deriving effective electrode-ion interactions from free-energy profiles at electrochemical interfaces
• Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics
• On Committor Functions in Milestoning
• Collapse/expansion dynamics and actuation of pH-responsive nanogels
• A critical comparison of general-purpose collective variables for crystal nucleation
• Diffusive vs. non-diffusive paths to interstellar hydrogen peroxide. A machine learning-based molecular dynamics study
• Free energy profiles for chemical reactions in solution from high-dimensional neural network potentials: The case of the Strecker synthesis
• Properties of low-dimensional collective variables in the molecular dynamics of biopolymers
• Metadynamics for Automatic Sampling of Quantum Property Manifolds: Exploration of Molecular Biradicality Landscapes
• Flat histogram method comparison on 2D Ising Model
• An efficient time-stepping scheme for ab initio molecular dynamics simulations
• A permutation invariant collective variable to track and drive vacancy dynamics in simulations of solids
• Metadynamics study of the temperature dependence of magnetic anisotropy and spin-reorientation transitions in ultrathin films
• Determining Free Energy Differences Through Variational Morphing
• Continuously tempered Hamiltonian Monte Carlo
• Unraveling the Atomic-Scale Pathways Driving Pressure-Induced Phase Transitions in Silicon
• Transition-path sampling for Run-and-Tumble particles
• Relative Resolution: A Multipole Approximation at Appropriate Distances
• Energy-Based Coarse-Graining in Molecular Dynamics: A Flow-Based Framework without Data
• A Generalized Nucleation Theory for Ice Crystallization
• Stochastic formalism for thermally driven distribution frontier: A nonempirical approach to the potential escape problem
• Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling
• Harmonic Order Parameters for Characterizing Complex Particle Morphologies
• Unveiling ZIF-8 nucleation mechanisms through molecular simulation: role of temperature, solvent and reactant concentration
• High-Throughput Computation of Anharmonic Low-Frequency Protein Vibrations
• Fokker-Planck Score Learning: Efficient Free-Energy Estimation under Periodic Boundary Conditions
• Kinetic pathways of coesite densification from metadynamics
• The Impact of Hydration Shell Inclusion and Chain Exclusion in the Efficacy of Reaction Coordinates for Homogeneous and Heterogeneous Ice Nucleation
• Pressure-induced structural transformation of clathrate Ge${}_{136}$ via an ultrafast recrystallization of an amorphous intermediate
• Coarse-graining strategy for molecular pair interactions: A reaction coordinate study for two- and three-dimensional systems
• Quantum Momentum Distribution and Quantum Entanglement in the Deep Tunneling Regime
• Accelerating the convergence of replica exchange simulations using Gibbs sampling and adaptive temperature sets
• A Sinking Approach to Explore Arbitrary Areas in Free Energy Landscapes
• A particle-based Ising model
• Predicting the unobserved: a statistical mechanics framework for non-equilibrium material response with quantified uncertainty
• Fast estimation of ion-pairing for screening electrolytes: A cluster can approximate a bulk liquid
• Staying the course: Locating equilibria of dynamical systems on Riemannian manifolds defined by point-clouds
• Configurational entropy, transition rates, and optimal interactions for rapid folding in coarse-grained model proteins
• Scalable Bayesian reduced-order models for high-dimensional multiscale dynamical systems
• Sampling Rare Event Energy Landscapes via Birth-Death Augmented Dynamics
• Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
• Simulating bistable current-induced switching of metallic atomic contacts by electron-vibration scattering
• Multi-Hill Strategy in Metadynamics for Interstitial Diffusion in Crystals
• Free energy computations by minimization of Kullback-Leibler divergence: an efficient adaptive biasing potential method for sparse representations
• Density Estimation via Binless Multidimensional Integration
• Combining multiple interface set path ensembles with MBAR reweighting
• Quantum Chemistry Driven Molecular Inverse Design with Data-free Reinforcement Learning
• Homogeneous nucleation mechanism of NaCl in aqueous solutions
• Self-Healing Umbrella Sampling: Convergence and efficiency
• Non-empirical weighted Langevin mechanics for the potential escape problem: parallel algorithm and application to the Argon clusters
• Topology and geometry of molecular conformational spaces and energy landscapes
• Elucidating Ion Capture and Transport Mechanisms of Preyssler Anions in Aqueous Solutions Using Biased MACE-Accelerated MD Simulations
• Determination of protein structural ensembles using cryo-electron microscopy
• Discrete state model of a self-aggregating colloidal system with directional interactions
• Automatic learning of hydrogen-bond fixes in an AMBER RNA force field
• Reweighted Jarzynski sampling: Acceleration of rare events and free energy calculation with a bias potential learned from nonequilibrium work
• A splitting Hamiltonian Monte Carlo method for efficient sampling
• Stochastic Approximation Monte Carlo with a Dynamic Update Factor
• Fast and accurate multidimensional free energy integration
• Scalable Community Detection Using Quantum Hamiltonian Descent and QUBO Formulation
• Global Convergence of Triangularized Orthogonalization-free Method
• Scaling Limit for the Diffusion Exit Problem, a Survey
• From diamond to BC8 to simple cubic and back: kinetic pathways to post-diamond carbon phases from metadynamics
• Deep learning of committor and explainable artificial intelligence analysis for identifying reaction coordinates
• Computational Estimates of Binding Affinities for Estrogen Receptor Isoforms in Rainbow Trout
• Adaptive tensor train metadynamics for high-dimensional free energy exploration
• Sampling metastable systems using collective variables and Jarzynski-Crooks paths
• Rare transition event with self-consistent theory of large-amplitude collective motion
• Dissociation of Liquid Water on Defective Rutile TiO2 (110) Surfaces Using Ab-Initio Molecular Dynamics Simulations
• Exploring the Protein G Helix Free Energy Surface by Solute Tempering Metadynamics
• Exploring the Potential of Parallel Biasing in Flat Histogram Methods
• Global free energy landscapes as a smoothly joined collection of local maps
• Enhanced Sampling Algorithms
• Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes
• Improving the Exploration of High Dimensional Free Energy Landscape by a Combination of Temperature Accelerated Sliced Sampling and Parallel Biasing
• Mean Force Based Temperature Accelerated Sliced Sampling: Efficient Reconstruction of High Dimensional Free Energy Landscapes
• Active learning potentials for first-principles phase diagrams using replica-exchange nested sampling
• Optimal estimation of free energies and stationary densities from multiple biased simulations
• Multiscale Gentlest Ascent Dynamics for Saddle Point in Effective Dynamics of Slow-Fast System
• Computing rates and understanding unbinding mechanism in host-guest systems
• A Bayesian approach for extracting free energy profiles from cryo-electron microscopy experiments using a path collective variable
• Neural Mode Jump Monte Carlo
• AtomREM: Non-empirical seeker of the minimum energy escape paths on many-dimensional potential landscapes without coarse graining
• Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
• Neural-Network Assisted Study of Nitrogen Atom Dynamics on Amorphous Solid Water -- II. Diffusion
• Accelerated Simulations of Molecular Systems through Learning of their Effective Dynamics
• Ge${}_{136}$ type-II clathrate as precursor for the synthesis of metastable germanium polymorphs: a computational study
• Using data-reduction techniques to analyse biomolecular trajectories
• Simulations of Crystal Nucleation from Solution at Constant Chemical Potential
• Comparison of Sampling Methods via Robust Free Energy Inference: Application to Calmodulin
• Neural Network Surrogates for Free Energy Computation of Complex Chemical Systems
• Accelerated Atomistic Simulations of a Supramolecular Polymer in Water