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Potential Energy and Free Energy Landscapes
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics
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Effective energy function for proteins in solution
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Protein Folding: A Perspective from Theory and Experiment
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Structure and Dynamics of Simple Microclusters
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Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation
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Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first‐order phase transition
inferredcites →https://doi.org/10.1002/bip.360281004openalex-snapshot
Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution
inferredcites →https://doi.org/10.1002/bip.360300117openalex-snapshot
A simple statistical field theory of heteropolymer collapse with application to protein folding
inferredcites →https://doi.org/10.1002/bip.360321216openalex-snapshot
Conformational analysis of met‐enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling
inferredcites →https://doi.org/10.1002/bip.360350114openalex-snapshot
Nucleation mechanism for protein folding and theoretical predictions for hydrogen‐exchange labeling experiments
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/jcc.540141110openalex-snapshot
Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple‐minima problem
inferredcites →https://doi.org/10.1002/pro.5560030413openalex-snapshot
Protein folding dynamics: The diffusion‐collision model and experimental data
inferredcites →https://doi.org/10.1002/prot.340210302openalex-snapshot
Funnels, pathways, and the energy landscape of protein folding: A synthesis
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The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding
inferredcites →https://doi.org/10.1006/jmbi.2000.3693openalex-snapshot
Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? an investigation for small globular proteins
inferredcites →https://doi.org/10.1007/bf01386390openalex-snapshot
A note on two problems in connexion with graphs
inferredcites →https://doi.org/10.1007/bf01589116openalex-snapshot
On the limited memory BFGS method for large scale optimization
inferredcites →https://doi.org/10.1007/bf02189229openalex-snapshot
Monte carlo study of the interacting self-avoiding walk model in three dimensions
inferredcites →https://doi.org/10.1007/s004600050192openalex-snapshot
Surveying a potential energy surface by eigenvector-following
inferredcites →https://doi.org/10.1016/0021-9991(75)90060-1openalex-snapshot
A new algorithm for Monte Carlo simulation of Ising spin systems
inferredcites →https://doi.org/10.1016/0021-9991(76)90041-3openalex-snapshot
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
inferredcites →https://doi.org/10.1016/0166-1280(88)80040-xopenalex-snapshot
Potential energy hypersurfaces
inferredcites →https://doi.org/10.1016/0301-4622(89)80058-4openalex-snapshot
Formation of unique structure in polypeptide chains
inferredcites →https://doi.org/10.1016/0959-440x(95)80012-popenalex-snapshot
Characterizing transition states in protein folding: an essential step in the puzzle
inferredcites →https://doi.org/10.1016/b978-0-444-52965-7.x5000-4openalex-snapshot
Stochastic Processes in Physics and Chemistry
inferredcites →https://doi.org/10.1016/s0006-3495(02)75530-6openalex-snapshot
Long Time Dynamics of Met-Enkephalin: Comparison of Explicit and Implicit Solvent Models
inferredcites →https://doi.org/10.1016/s0009-2614(01)00334-7openalex-snapshot
Transition states and rearrangement mechanisms from hybrid eigenvector-following and density functional theory.
inferredcites →https://doi.org/10.1016/s0009-2614(03)00668-7openalex-snapshot
Ab initio study of rearrangements between C60 fullerenes
inferredcites →https://doi.org/10.1016/s0009-2614(97)01198-6openalex-snapshot
Parallel tempering algorithm for conformational studies of biological molecules
inferredcites →https://doi.org/10.1016/s0009-2614(98)00431-xopenalex-snapshot
An investigation of two approaches to basin hopping minimization for atomic and molecular clusters
inferredcites →https://doi.org/10.1016/s0009-2614(99)01123-9openalex-snapshot
Replica-exchange molecular dynamics method for protein folding
inferredcites →https://doi.org/10.1016/s0959-440x(97)80002-4openalex-snapshot
Nucleation mechanisms in protein folding
inferredcites →https://doi.org/10.1016/s0959-440x(98)80012-2openalex-snapshot
Pathways for protein folding: is a new view needed?
inferredcites →https://doi.org/10.1016/s1359-0278(97)00002-3openalex-snapshot
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties
inferredcites →https://doi.org/10.1016/s1359-0278(97)00016-3openalex-snapshot
Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold
inferredcites →https://doi.org/10.1021/bi00009a038openalex-snapshot
Is Burst Hydrophobic Collapse Necessary for Protein Folding?
inferredcites →https://doi.org/10.1021/bi00199a029openalex-snapshot
Specific Nucleus as the Transition State for Protein Folding: Evidence from the Lattice Model
inferredcites →https://doi.org/10.1021/j100356a007openalex-snapshot
Intermediates and barrier crossing in a random energy model (with applications to protein folding)
inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
inferredcites →https://doi.org/10.1021/jp026994sopenalex-snapshot
Computer Simulation of Met-Enkephalin Using Explicit Atom and United Atom Potentials: Similarities, Differences, and Suggestions for Improvement
inferredcites →https://doi.org/10.1021/jp046448uopenalex-snapshot
Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/jp0549632openalex-snapshot
Novel Structural Motifs in Clusters of Dipolar Spheres: Knots, Links, and Coils
inferredcites →https://doi.org/10.1021/jp970984nopenalex-snapshot
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
inferredcites →https://doi.org/10.1038/340122a0openalex-snapshot
Mapping the transition state and pathway of protein folding by protein engineering
inferredcites →https://doi.org/10.1038/379096a0openalex-snapshot
Conserved residues and the mechanism of protein folding
inferredcites →https://doi.org/10.1038/nsb0197-10openalex-snapshot
From Levinthal to pathways to funnels
inferredcites →https://doi.org/10.1039/a701489iopenalex-snapshot
Rearrangements of bulk face-centred-cubic nickel modelled by a Sutton[ndash ]Chen potential
inferredcites →https://doi.org/10.1039/ft9928800653openalex-snapshot
Basins of attraction for stationary points on a potential-energy surface
inferredcites →https://doi.org/10.1039/ft9969202505openalex-snapshot
Rearrangements of the water trimer
inferredcites →https://doi.org/10.1039/tf9686400371openalex-snapshot
Symmetries of activated complexes
inferredcites →https://doi.org/10.1063/1.1323224openalex-snapshot
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
inferredcites →https://doi.org/10.1063/1.1329672openalex-snapshot
A climbing image nudged elastic band method for finding saddle points and minimum energy paths
inferredcites →https://doi.org/10.1063/1.1343486openalex-snapshot
Energy landscapes, global optimization and dynamics of the polyalanine Ac(ala)8NHMe
inferredcites →https://doi.org/10.1063/1.1415500openalex-snapshot
Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table
inferredcites →https://doi.org/10.1063/1.1484389openalex-snapshot
Energy landscapes of model polyalanines
inferredcites →https://doi.org/10.1063/1.1517606openalex-snapshot
Free energy disconnectivity graphs: Application to peptide models
inferredcites →https://doi.org/10.1063/1.1531612openalex-snapshot
Hydration structure of met-enkephalin: A molecular dynamics study
inferredcites →https://doi.org/10.1063/1.1540099openalex-snapshot
Free energy landscapes of model peptides and proteins
inferredcites →https://doi.org/10.1063/1.1545096openalex-snapshot
Energy landscapes of model glasses. II. Results for constant pressure
inferredcites →https://doi.org/10.1063/1.1562614openalex-snapshot
A novel path sampling method for the calculation of rate constants
inferredcites →https://doi.org/10.1063/1.1566951openalex-snapshot
Theoretical study of finite-temperature spectroscopy in van der Waals clusters. II. Time-dependent absorption spectra
inferredcites →https://doi.org/10.1063/1.1616515openalex-snapshot
The free energy landscape and dynamics of met-enkephalin
inferredcites →https://doi.org/10.1063/1.1625644openalex-snapshot
Stationary points and dynamics in high-dimensional systems
inferredcites →https://doi.org/10.1063/1.1636455openalex-snapshot
A doubly nudged elastic band method for finding transition states
inferredcites →https://doi.org/10.1063/1.1675790openalex-snapshot
Vapor Phase Homogeneous Nucleation and the Thermodynamic Properties of Small Clusters of Argon Atoms
inferredcites →https://doi.org/10.1063/1.1677650openalex-snapshot
Vibrational Frequencies and Entropies of Small Clusters of Atoms
inferredcites →https://doi.org/10.1063/1.1738640openalex-snapshot
Computing time scales from reaction coordinates by milestoning
inferredcites →https://doi.org/10.1063/1.1738647openalex-snapshot
Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin
inferredcites →https://doi.org/10.1063/1.1759317openalex-snapshot
Folding of the GB1 hairpin peptide from discrete path sampling
inferredcites →https://doi.org/10.1063/1.1854123openalex-snapshot
How many dimensions are required to approximate the potential energy landscape of a model protein?
inferredcites →https://doi.org/10.1063/1.1874832openalex-snapshot
Free energy profile along a discretized reaction path via the hyperplane constraint force and torque
inferredcites →https://doi.org/10.1063/1.1931587openalex-snapshot
Finding pathways between distant local minima
inferredcites →https://doi.org/10.1063/1.2135783openalex-snapshot
Global optimization and folding pathways of selected α-helical proteins
inferredcites →https://doi.org/10.1063/1.2138030openalex-snapshot
Basin hopping simulations for all-atom protein folding
inferredcites →https://doi.org/10.1063/1.2140273openalex-snapshot
Simulating rare events in equilibrium or nonequilibrium stochastic systems
inferredcites →https://doi.org/10.1063/1.2148958openalex-snapshot
Equilibrium thermodynamics from basin-sampling
inferredcites →https://doi.org/10.1063/1.2198806openalex-snapshot
Graph transformation method for calculating waiting times in Markov chains
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.457790openalex-snapshot
Exploring potential energy surfaces with transition state calculations
inferredcites →https://doi.org/10.1063/1.458491openalex-snapshot
Reaction path study of conformational transitions in flexible systems: Applications to peptides
inferredcites →https://doi.org/10.1063/1.461138openalex-snapshot
Theoretical foundations of dynamical Monte Carlo simulations
inferredcites →https://doi.org/10.1063/1.462802openalex-snapshot
Computer simulation study of free energy barriers in crystal nucleation
inferredcites →https://doi.org/10.1063/1.464070openalex-snapshot
The structure of small clusters: Multiple normal-modes model
inferredcites →https://doi.org/10.1063/1.465277openalex-snapshot
Energy landscapes and the collapse dynamics of homopolymers
inferredcites →https://doi.org/10.1063/1.466677openalex-snapshot
Transition states and folding dynamics of proteins and heteropolymers
inferredcites →https://doi.org/10.1063/1.467771openalex-snapshot
Free energy barriers to melting in atomic clusters
inferredcites →https://doi.org/10.1063/1.467775openalex-snapshot
Folding kinetics of proteinlike heteropolymers
inferredcites →https://doi.org/10.1063/1.468786openalex-snapshot
An order parameter approach to coexistence in atomic clusters
inferredcites →https://doi.org/10.1063/1.469714openalex-snapshot
Statistical interpretation of topographies and dynamics of multidimensional potentials
inferredcites →https://doi.org/10.1063/1.471317openalex-snapshot
Diffusive dynamics of the reaction coordinate for protein folding funnels
inferredcites →https://doi.org/10.1063/1.472697openalex-snapshot
On potential energy surfaces and relaxation to the global minimum
inferredcites →https://doi.org/10.1063/1.473299openalex-snapshot
The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
inferredcites →https://doi.org/10.1063/1.473525openalex-snapshot
A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain. I. Formulation and test on a hexadecapeptide
inferredcites →https://doi.org/10.1063/1.474546openalex-snapshot
Folding a 20 amino acid αβ peptide with the diffusion process-controlled Monte Carlo method
inferredcites →https://doi.org/10.1063/1.477520openalex-snapshot
Realistic master equation modeling of relaxation on complete potential energy surfaces: Partition function models and equilibrium results
inferredcites →https://doi.org/10.1063/1.477521openalex-snapshot
Realistic master equation modeling of relaxation on complete potential energy surfaces: Kinetic results
inferredcites →https://doi.org/10.1063/1.478067openalex-snapshot
Structural relaxation in Morse clusters: Energy landscapes
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The double-funnel energy landscape of the 38-atom Lennard-Jones cluster
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Dynamics on statistical samples of potential energy surfaces
inferredcites →https://doi.org/10.1063/1.480097openalex-snapshot
A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives
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Evolution of the potential energy surface with size for Lennard-Jones clusters
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The dynamics of structural transitions in sodium chloride clusters
inferredcites →https://doi.org/10.1063/1.481671openalex-snapshot
Phase changes in 38-atom Lennard-Jones clusters. I. A parallel tempering study in the canonical ensemble
inferredcites →https://doi.org/10.1063/1.481672openalex-snapshot
Phase changes in 38-atom Lennard-Jones clusters. II. A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical ensembles
inferredcites →https://doi.org/10.1073/pnas.122076099openalex-snapshot
Topological determinants of protein folding
inferredcites →https://doi.org/10.1073/pnas.162268099openalex-snapshot
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation
inferredcites →https://doi.org/10.1073/pnas.84.19.6611openalex-snapshot
Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
inferredcites →https://doi.org/10.1073/pnas.84.21.7524openalex-snapshot
Spin glasses and the statistical mechanics of protein folding.
inferredcites →https://doi.org/10.1073/pnas.89.11.4918openalex-snapshot
Optimal protein-folding codes from spin-glass theory.
inferredcites →https://doi.org/10.1073/pnas.89.18.8721openalex-snapshot
Protein folding funnels: a kinetic approach to the sequence-structure relationship.
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Simple model of protein folding kinetics.
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Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.
inferredcites →https://doi.org/10.1073/pnas.92.5.1282openalex-snapshot
Evolution-like selection of fast-folding model proteins.
inferredcites →https://doi.org/10.1073/pnas.92.8.3626openalex-snapshot
Toward an outline of the topography of a realistic protein-folding funnel.
inferredcites →https://doi.org/10.1073/pnas.94.12.6170openalex-snapshot
Folding funnels and energy landscapes of larger proteins within the capillarity approximation
inferredcites →https://doi.org/10.1073/pnas.94.16.8545openalex-snapshot
Ultrafast signals in protein folding and the polypeptide contracted state
inferredcites →https://doi.org/10.1073/pnas.95.11.5921openalex-snapshot
Folding funnels and frustration in off-lattice minimalist protein landscapes
inferredcites →https://doi.org/10.1080/00268970410001703363openalex-snapshot
Some further applications of discrete path sampling to cluster isomerization
inferredcites →https://doi.org/10.1080/00268970600556659openalex-snapshot
Kinetic analysis of discrete path sampling stationary point databases
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Coexistence in small inert gas clusters
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Stochastic Processes in Physics and Chemistry
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Updating Quasi-Newton Matrices with Limited Storage
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The energy landscape as a unifying theme in molecular science
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Complete statistical thermodynamics of the cluster solid-liquid transition
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Bond-orientational order in liquids and glasses
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Computer simulation of local order in condensed phases of silicon
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Rearrangements in model face-centered-cubic solids
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Defect migration in crystalline silicon
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Energy landscapes of some model glass formers
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Crystals of binary Lennard-Jones solids
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Structural relaxation in atomic clusters: Master equation dynamics
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Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
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Small-world view of the amino acids that play a key role in protein folding
inferredcites →https://doi.org/10.1103/physrevlett.57.2607openalex-snapshot
Replica Monte Carlo Simulation of Spin-Glasses
inferredcites →https://doi.org/10.1103/physrevlett.65.1567openalex-snapshot
Statistical thermodynamics of the cluster solid-liquid transition
inferredcites →https://doi.org/10.1103/physrevlett.80.1357openalex-snapshot
Thermodynamics of Global Optimization
inferredcites →https://doi.org/10.1103/physrevlett.81.5237openalex-snapshot
Variational Theory for Site Resolved Protein Folding Free Energy Surfaces
inferredcites →https://doi.org/10.1103/physrevlett.86.2050openalex-snapshot
Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States
inferredcites →https://doi.org/10.1103/physrevlett.87.108302openalex-snapshot
Action-Derived Molecular Dynamics in the Study of Rare Events
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A dense non-crystallographic packing of equal spheres
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A new approach to Monte Carlo simulations in statistical physics: Wang-Landau sampling
inferredcites →https://doi.org/10.1126/science.1120177openalex-snapshot
Evidence for Macromolecular Protein Rings in the Absence of Bulk Water
inferredcites →https://doi.org/10.1126/science.1749933openalex-snapshot
The Energy Landscapes and Motions of Proteins
inferredcites →https://doi.org/10.1126/science.208.4442.355openalex-snapshot
Computer Models of Crystal Growth
inferredcites →https://doi.org/10.1126/science.225.4666.983openalex-snapshot
Packing Structures and Transitions in Liquids and Solids
inferredcites →https://doi.org/10.1126/science.278.5345.1928openalex-snapshot
"New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations
inferredcites →https://doi.org/10.1126/science.285.5432.1368openalex-snapshot
Global Optimization of Clusters, Crystals, and Biomolecules
inferredcites →https://doi.org/10.1143/jpsj.65.1604openalex-snapshot
Exchange Monte Carlo Method and Application to Spin Glass Simulations
inferredcites →https://doi.org/10.1146/annurev.bb.12.060183.001151openalex-snapshot
Theoretical Studies of Protein Folding
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THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
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T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Energy Landscapes of Spin Models on the Snub Archimedean (32,4,3,4) Lattice
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Extending the Time Scale in Atomically Detailed Simulations
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Energy Landscapes and Structure Prediction Using Basin‐Hopping
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Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems
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Predicting Solubility of Small Molecules in Macromolecular Compounds for Nanomedicine Application from Atomistic Simulations
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Driving Protein Conformational Cycles in Physiology and Disease: “Frustrated” Amino Acid Interaction Networks Define Dynamic Energy Landscapes
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Computational investigation of the conformational profile of the four stereomers of Ac‐L‐Pro‐c3Phe‐NHMe (c3Phe= 2,3‐methanophenylalanine)
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Synthesis of Metastable Inorganic Solids with Extended Structures
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Calculation of free energy landscapes: A histogram reweighted metadynamics approach
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Efficiency of tabu‐search‐based conformational search algorithms
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Visualizing energy landscapes with metric disconnectivity graphs
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An automated method to find transition states using chemical dynamics simulations
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Conformational ensembles and sampled energy landscapes: Analysis and comparison
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Predicting stability limits for pure and doped dicationic noble gas clusters undergoing coulomb explosion: A parallel tempering based study
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Development of a Conformational Sampling Method for Transition State Structures With Diverse Active Bond Lengths
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A theoretical investigation to understand the difference in reactivities of secondary and tertiary propargylic alcohols with 1,3,5‐trimethoxybenzene in presence of Brnøsted acid
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Investigation into the effect of phenylalanine gating on anaerobic haem breakdown using the energy landscape approach
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Global optimization of clusters using electronic structure methods
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Intrinsic reaction coordinate: Calculation, bifurcation, and automated search
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Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach
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An investigation on the structure, spectroscopy, and thermodynamic aspects of clusters: A combined Parallel tempering and DFT based study
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AI‐Organized Multiscale Battery Modeling: Linking Structure and Property from Quantum to Device Scales
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Methods for exploring reaction space in molecular systems
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Simulation of Metal Clusters and Nanostructures
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Exploring the potential energy landscape over a large parameter-space
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The antioxidant activity of N-E-caffeoyl and N-E-feruloyl tyramine conformers and their sulfured analogs contribution: density functional theory studies
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Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory
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Generating conformational transition paths with low potential-energy barriers for proteins
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Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation
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Constructing a bunch of paths for conformational changes in size specific noble gas cluster: a study using a stochastic procedure
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The Global Optimization of Pt13 Cluster Using the First-Principle Molecular Dynamics with the Quenching Technique
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An integrated computational strategy for profiling terpenoid for dual-target leads against Klebsiella pneumoniae penicillin-binding protein 3 and beta-lactamase
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Mapping out reaction paths for conformational changes in (M g O) n clusters: a study based on a stochastic procedure
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Construction of elementary reaction paths of pure and mixed Argon-Xenon clusters : a parallel tempering based study
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Impurity effects on phase change in Lennard-Jones atomic clusters
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Structure Prediction in Solid-State Chemistry as an Approach to Rational Synthesis Planning
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Energy landscapes in inorganic chemistry
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Potential energy surfaces and dynamics
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The R337C mutation in the p53 oligomerization domain affects the regulatory domain and its ability to bind response elements: Evidence based on structural and biophysical studies
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Modelling proteins: Conformational sampling and reconstruction of folding kinetics
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Energy landscapes for proteins described by the UNRES coarse-grained potential
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Membrane lateral organization from potential energy disconnectivity graph
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Exploring the Energy Landscapes of Protein Folding Simulations with Bayesian Computation
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Exploring the Energy Landscapes of Protein Folding Simulations with Bayesian Computation
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A Nonquiescent “Idling” Population State in Drug-Treated, BRAF-Mutated Melanoma
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Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences
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Multi-step binding-unbinding pathways govern properties of biomolecular condensates
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A generalized recipe to construct elementary or multi-step reaction paths via a stochastic formulation: Application to the conformational change in noble gas clusters
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On potential energy landscape and combustion chemistry modeling
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Genetic algorithm optimization of defect clusters in crystalline materials
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Mixed Cayley and Cartesian sampling for fast and accurate coverage and configurational entropy computation
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Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide
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Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling
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Unveiling the mechanism of core–shell formation by counting the relative occurrence of microstates
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A Frank-Kasper polyhedral structure of 17-atom vanadium clusters
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Free energy reconstruction from steered dynamics without post-processing
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A study involving stochastic principle in elucidating discrete and average transformation paths in Xenon doped Argon cluster
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Bayesian inference of the spatial distributions of material properties
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The interaction between nanoscale MIL-53(Fe) and Fzd6 protein drives enhanced bone regeneration
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Computational profiling of terpenoids for putative dual-target leads against Staphylococcus aureus penicillin binding protein 2a and beta-lactamase: An integrated structure-activity-relationship-based study
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Density of states of the X Y model: An energy landscape approach
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Energy landscapes of spin glasses on triangular Archimedean lattices
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Energy landscapes of spin models on the Snub Archimedean ( 32 , 4, 3, 4) lattice
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Energy landscapes of spin glasses on the dice lattice
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Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective
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Growth of epitaxial graphene: Theory and experiment
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Energy landscapes: some new horizons
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Chapter 2 Extending Atomistic Time Scale Simulations by Optimization of the Action
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A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope
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Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00648openalex-snapshot
Efficient Amino Acid Conformer Search with Bayesian Optimization
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Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations
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Molecular Conformer Search with Low-Energy Latent Space
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100 Years of the Lennard-Jones Potential
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00316openalex-snapshot
GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00588openalex-snapshot
Replica Exchange Nested Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01005openalex-snapshot
Energy Landscapes of Model Knotted Polymers
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An Accurate and Efficient Reaction Path Search with Iteratively Trained Neural Network Potential: Answering the Passerini Mechanism Controversy
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00398openalex-snapshot
Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00480openalex-snapshot
Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b01211openalex-snapshot
Defining, Calculating, and Converging Observables of a Kinetic Transition Network
inferred← citeshttps://doi.org/10.1021/acs.jpca.6b03467openalex-snapshot
Ethanol and Water Adsorption on Transition-Metal 13-Atom Clusters: A Density Functional Theory Investigation within van der Waals Corrections
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c00859openalex-snapshot
Energy Landscapes of a Pair of Adsorbed Peptides
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c02424openalex-snapshot
Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c00919openalex-snapshot
Crystal Growth Rates from Molecular Liquids: The Kinetics of Entropy Loss
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c00104openalex-snapshot
Multilevel Framework for Analysis of Protein Folding Involving Disulfide Bond Formation
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c01794openalex-snapshot
Energy Landscapes and Structural Ensembles of Glucagon-like Peptide-1 Monomers
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b12172openalex-snapshot
Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics
inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b10568openalex-snapshot
Energy Landscape Mapping and Replica Exchange Molecular Dynamics of an Adsorbed Peptide
inferred← citeshttps://doi.org/10.1021/acs.jpclett.2c01258openalex-snapshot
Dynamical Signatures of Multifunnel Energy Landscapes
inferred← citeshttps://doi.org/10.1021/acs.jpclett.6c02032openalex-snapshot
Quantum Enhancement of Microcanonical Negative Heat Capacity Features in the Melting of Water Clusters
inferred← citeshttps://doi.org/10.1021/acschemneuro.6c00097openalex-snapshot
Machine Learning-Driven Ensemble Screening of Multitarget Kinase Inhibitors for Tauopathy-Associated Neurodegeneration Using All-Atom and Steered MD Simulations
inferred← citeshttps://doi.org/10.1021/acsnano.5b03299openalex-snapshot
Nanomanufacturing: A Perspective
inferred← citeshttps://doi.org/10.1021/acsnano.5b05309openalex-snapshot
The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex
inferred← citeshttps://doi.org/10.1021/ci400224zopenalex-snapshot
Revised Basin-Hopping Monte Carlo Algorithm for Structure Optimization of Clusters and Nanoparticles
inferred← citeshttps://doi.org/10.1021/cs5011426openalex-snapshot
Rutile-Deposited Pt–Pd clusters: A Hypothesis Regarding the Stability at 50/50 Ratio
inferred← citeshttps://doi.org/10.1021/ct300494qopenalex-snapshot
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/ct400403yopenalex-snapshot
Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules
inferred← citeshttps://doi.org/10.1021/ct500136xopenalex-snapshot
Efficient Basin-Hopping Sampling of Reaction Intermediates through Molecular Fragmentation and Graph Theory
inferred← citeshttps://doi.org/10.1021/ct5009729openalex-snapshot
Time Recovery for a Complex Process Using Accelerated Dynamics
inferred← citeshttps://doi.org/10.1021/ct800236dopenalex-snapshot
A Multiscale Treatment of Angeli’s Salt Decomposition
inferred← citeshttps://doi.org/10.1021/ja507981popenalex-snapshot
Structural Melting of an Amino Acid Dimer upon Intersystem Crossing
inferred← citeshttps://doi.org/10.1021/jacs.5c23300openalex-snapshot
Secondary Structure-Encoded Control of Lipid Assembly by Radially Amphiphilic Peptides
inferred← citeshttps://doi.org/10.1021/jacs.8b01804openalex-snapshot
Multiple Pathways in Capsid Assembly
inferred← citeshttps://doi.org/10.1021/jm0704090openalex-snapshot
Natural Products as Leads to Potential Drugs: An Old Process or the New Hope for Drug Discovery?
inferred← citeshttps://doi.org/10.1021/jp076628eopenalex-snapshot
Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling
inferred← citeshttps://doi.org/10.1021/jp1012973openalex-snapshot
Efficient Sampling of Atomic Configurational Spaces
inferred← citeshttps://doi.org/10.1021/jp103950mopenalex-snapshot
Agent-Based Modeling for the 2D Molecular Self-Organization of Realistic Molecules
inferred← citeshttps://doi.org/10.1021/jp206430zopenalex-snapshot
Calculation of Partition Functions for the Self-Assembly of Patchy Particles
inferred← citeshttps://doi.org/10.1021/jp207246mopenalex-snapshot
Energy Landscape and Global Optimization for a Frustrated Model Protein
inferred← citeshttps://doi.org/10.1021/jp308589bopenalex-snapshot
Chemical Unfolding of Chicken Villin Headpiece in Aqueous Dimethyl Sulfoxide Solution: Cosolvent Concentration Dependence, Pathway, and Microscopic Mechanism
inferred← citeshttps://doi.org/10.1021/jp312457aopenalex-snapshot
Visualizing Basins of Attraction for Different Minimization Algorithms
inferred← citeshttps://doi.org/10.1021/jp409300jopenalex-snapshot
Coarse-Grained Model for Colloidal Protein Interactions, B22, and Protein Cluster Formation
inferred← citeshttps://doi.org/10.1021/jp5037348openalex-snapshot
Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting
inferred← citeshttps://doi.org/10.1021/jp801777popenalex-snapshot
Folding Pathways and Rates for the Three-Stranded β-Sheet Peptide Beta3s using Discrete Path Sampling
inferred← citeshttps://doi.org/10.1021/jp8104425openalex-snapshot
Conformations and Coherences in Structure Determination by Ultrafast Electron Diffraction
inferred← citeshttps://doi.org/10.1021/jp810659uopenalex-snapshot
Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins
inferred← citeshttps://doi.org/10.1021/jp9030442openalex-snapshot
An Artificial Intelligence Approach for Modeling Molecular Self-assembly: Agent-based Simulations of Rigid Molecules
inferred← citeshttps://doi.org/10.1021/nl3013659openalex-snapshot
Nanoparticle Clusters with Lennard-Jones Geometries
inferred← citeshttps://doi.org/10.1038/s41467-019-10947-xopenalex-snapshot
Magnetic origami creates high performance micro devices
inferred← citeshttps://doi.org/10.1038/s41467-019-12700-wopenalex-snapshot
Topology, landscapes, and biomolecular energy transport
inferred← citeshttps://doi.org/10.1038/s41467-024-53138-zopenalex-snapshot
Design principles for energy transfer in the photosystem II supercomplex from kinetic transition networks
inferred← citeshttps://doi.org/10.1038/s41467-025-62866-9openalex-snapshot
Dynamic pathways in energy landscapes guiding supramolecular Janus dendrimer self-assemblies between lamellar and cubic architectures
inferred← citeshttps://doi.org/10.1038/s41467-026-68637-4openalex-snapshot
Protein folding stability estimation with explicit consideration of unfolded states
inferred← citeshttps://doi.org/10.1038/s41524-026-01985-3openalex-snapshot
A general optimization framework for mapping local transition-state networks
inferred← citeshttps://doi.org/10.1038/s41598-017-01283-5openalex-snapshot
Pronounced Plasticity Caused by Phase Separation and β-relaxation Synergistically in Zr–Cu–Al–Mo Bulk Metallic Glasses
inferred← citeshttps://doi.org/10.1038/s41598-023-33024-2openalex-snapshot
MasitinibL shows promise as a drug-like analog of masitinib that elicits comparable SARS-Cov-2 3CLpro inhibition with low kinase preference
inferred← citeshttps://doi.org/10.1038/s43586-022-00121-xopenalex-snapshot
Nested sampling for physical scientists
inferred← citeshttps://doi.org/10.1039/b719792fopenalex-snapshot
Description of pentacoordinated phosphorus under an external electric field: which basis sets and semi-empirical methods are needed?
inferred← citeshttps://doi.org/10.1039/b820649jopenalex-snapshot
Refined kinetic transition networks for the GB1 hairpin peptide
inferred← citeshttps://doi.org/10.1039/b919148hopenalex-snapshot
Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease
inferred← citeshttps://doi.org/10.1039/bk9781849731331-00058openalex-snapshot
Self-Assembly of Nanoclusters: An Energy Landscape Perspective
inferred← citeshttps://doi.org/10.1039/c0cp01402hopenalex-snapshot
Origin of chiral selectivity in gas-phase serine tetramers
inferred← citeshttps://doi.org/10.1039/c0sc00425aopenalex-snapshot
Universal characteristics of chemical synthesis and property optimization
inferred← citeshttps://doi.org/10.1039/c0sm01289kopenalex-snapshot
Self-assembly of anisotropic particles
inferred← citeshttps://doi.org/10.1039/c1nr10679aopenalex-snapshot
Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms
inferred← citeshttps://doi.org/10.1039/c3cp53537aopenalex-snapshot
A conformational factorisation approach for estimating the binding free energies of macromolecules
inferred← citeshttps://doi.org/10.1039/c3ra41813hopenalex-snapshot
A left-handed building block self-assembles into right- and left-handed helices
inferred← citeshttps://doi.org/10.1039/c6cp08807dopenalex-snapshot
Polymorphs of two dimensional phosphorus and arsenic: insight from an evolutionary search
inferred← citeshttps://doi.org/10.1039/c7cp03346jopenalex-snapshot
Properties of kinetic transition networks for atomic clusters and glassy solids
inferred← citeshttps://doi.org/10.1039/c7cp08372fopenalex-snapshot
Efficient structural elucidation of microhydrated biomolecules through the interrogation of hydrogen bond networks
inferred← citeshttps://doi.org/10.1039/c7sc03628kopenalex-snapshot
Efficient prediction of reaction paths through molecular graph and reaction network analysis
inferred← citeshttps://doi.org/10.1039/d1ra03395fopenalex-snapshot
Mining hydroformylation in complex reaction network via graph theory
inferred← citeshttps://doi.org/10.1039/d2dd00050dopenalex-snapshot
Free energy predictions for crystal stability and synthesisability
inferred← citeshttps://doi.org/10.1039/d3cp00082fopenalex-snapshot
Theoretical and computational methodologies for understanding coordination self-assembly complexes
inferred← citeshttps://doi.org/10.1039/d3cp03897aopenalex-snapshot
Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins
inferred← citeshttps://doi.org/10.1039/d3cp04199aopenalex-snapshot
Analysis and interpretation of first passage time distributions featuring rare events
inferred← citeshttps://doi.org/10.1039/d3dd00078hopenalex-snapshot
Computational and data-driven modelling of solid polymer electrolytes
inferred← citeshttps://doi.org/10.1039/d4cp01891eopenalex-snapshot
Digital nets conformational sampling (DNCS) – an enhanced sampling technique to explore the conformational space of intrinsically disordered peptides
inferred← citeshttps://doi.org/10.1039/d4sm01405gopenalex-snapshot
Collective motion and its connection to the energy landscape in 2D soft crystals
inferred← citeshttps://doi.org/10.1039/d5cp03734dopenalex-snapshot
Terahertz-induced conformational dynamics of synaptotagmin III
inferred← citeshttps://doi.org/10.1063/1.2794032openalex-snapshot
Determination of structural transitions of atomic clusters from local and global bond orientational order parameters
inferred← citeshttps://doi.org/10.1063/1.2897982openalex-snapshot
Exploring a free energy landscape by means of multidimensional infrared and terahertz spectroscopies
inferred← citeshttps://doi.org/10.1063/1.2899020openalex-snapshot
Two-surface Monte Carlo with basin hopping: Quantum mechanical trajectory and multiple stationary points of water cluster
inferred← citeshttps://doi.org/10.1063/1.3152121openalex-snapshot
Funnel hopping: Searching the cluster potential energy surface over the funnels
inferred← citeshttps://doi.org/10.1063/1.3628669openalex-snapshot
Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation
inferred← citeshttps://doi.org/10.1063/1.3673318openalex-snapshot
Energy landscapes of ion clusters in isotropic quadrupolar and octupolar traps
inferred← citeshttps://doi.org/10.1063/1.4810884openalex-snapshot
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics
inferred← citeshttps://doi.org/10.1063/1.4813627openalex-snapshot
Energy landscapes and global thermodynamics for alanine peptides
inferred← citeshttps://doi.org/10.1063/1.4819172openalex-snapshot
Interactions of twin boundaries with intrinsic point defects and carbon in silicon
inferred← citeshttps://doi.org/10.1063/1.4825404openalex-snapshot
A parallel tempering based study of Coulombic explosion and identification of dissociating fragments in charged noble gas clusters
inferred← citeshttps://doi.org/10.1063/1.4830400openalex-snapshot
Potential energy landscapes for the 2D XY model: Minima, transition states, and pathways
inferred← citeshttps://doi.org/10.1063/1.4890743openalex-snapshot
A coarse-grained method based on the analysis of short molecular dynamics trajectories for the simulation of non-Markovian dynamics of molecules adsorbed in microporous materials
inferred← citeshttps://doi.org/10.1063/1.4935574openalex-snapshot
A network of discrete events for the representation and analysis of diffusion dynamics
inferred← citeshttps://doi.org/10.1063/1.4955105openalex-snapshot
First principles prediction of amorphous phases using evolutionary algorithms
inferred← citeshttps://doi.org/10.1063/1.4974838openalex-snapshot
Atomic clusters with addressable complexity
inferred← citeshttps://doi.org/10.1063/1.4982252openalex-snapshot
Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures
inferred← citeshttps://doi.org/10.1063/1.5036677openalex-snapshot
A spin-1 representation for dual-funnel energy landscapes
inferred← citeshttps://doi.org/10.1063/1.5125689openalex-snapshot
Thermodynamic properties of 55-atom Pt-based nanoalloys: Phase changes and structural effects on the electronic properties
inferred← citeshttps://doi.org/10.1063/5.0016244openalex-snapshot
Rare events and first passage time statistics from the energy landscape
inferred← citeshttps://doi.org/10.1063/5.0074677openalex-snapshot
A symmetry-orientated divide-and-conquer method for crystal structure prediction
inferred← citeshttps://doi.org/10.1063/5.0159367openalex-snapshot
Exploring energy landscapes for solid-state systems with variable cells at the extended tight-binding level
inferred← citeshttps://doi.org/10.1063/5.0212867openalex-snapshot
Energy landscapes—Past, present, and future: A perspective
inferred← citeshttps://doi.org/10.1063/5.0289549openalex-snapshot
The energy landscape of folding in n -C14H30 described by a machine-learned potential
inferred← citeshttps://doi.org/10.1063/5.0333811openalex-snapshot
Structure-resolved free energy estimation of the 38-atom Lennard Jones cluster via population annealing
inferred← citeshttps://doi.org/10.1073/pnas.0801850105openalex-snapshot
Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions
inferred← citeshttps://doi.org/10.1073/pnas.1610437113openalex-snapshot
Evidence from mixed hydrate nucleation for a funnel model of crystallization
inferred← citeshttps://doi.org/10.1080/07391102.2023.2252071openalex-snapshot
Flavonoids as potential reactivators of structural mutation p53Y220C by computational and cell-based studies
inferred← citeshttps://doi.org/10.1080/08927020903536382openalex-snapshot
Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics
inferred← citeshttps://doi.org/10.1080/14786430903270668openalex-snapshot
Global minima of transition metal clusters described by Finnis–Sinclair potentials: A comparison with semi-empirical molecular orbital theory
inferred← citeshttps://doi.org/10.1088/0953-8984/22/10/104101openalex-snapshot
Modelling the self-assembly of virus capsids
inferred← citeshttps://doi.org/10.1088/0953-8984/27/29/293201openalex-snapshot
Computer simulations of glasses: the potential energy landscape
inferred← citeshttps://doi.org/10.1088/1742-6596/1913/1/012083openalex-snapshot
The nature of catalytic species in the Wacker oxidation process-A review
inferred← citeshttps://doi.org/10.1088/2632-2153/ac8f1bopenalex-snapshot
Subaging in underparametrized deep neural networks
inferred← citeshttps://doi.org/10.1093/nsr/nwad128openalex-snapshot
MAGUS: machine learning and graph theory assisted universal structure searcher
inferred← citeshttps://doi.org/10.1098/rsos.170175openalex-snapshot
Machine learning landscapes and predictions for patient outcomes
inferred← citeshttps://doi.org/10.1098/rsta.2011.0208openalex-snapshot
Decoding the energy landscape: extracting structure, dynamics and thermodynamics
inferred← citeshttps://doi.org/10.1101/2022.11.29.517349openalex-snapshot
Adaptive collective motions: a hybrid method to improve conformational sampling with molecular dynamics and normal modes
inferred← citeshttps://doi.org/10.1101/2023.08.09.552573openalex-snapshot
Searching deeply into the conformational space of glycoprotein hormone receptors. Molecular dynamics of the human follitropin and lutropin receptors within a bilayer of (SDPC) poly-unsaturated lipids
inferred← citeshttps://doi.org/10.1101/683466openalex-snapshot
Dancing Molecules: Rewiring Cooperative Communications within 14-3-3 ζ Docking Proteins
inferred← citeshttps://doi.org/10.1103/physrevb.107.184407openalex-snapshot
Theory of the collective behavior of two-dimensional periodic ensembles of dipole-coupled magnetic nanoparticles
inferred← citeshttps://doi.org/10.1103/physrevb.75.085420openalex-snapshot
Comprehensive study of the potential energy surface minima of a monolayer on (111) surface
inferred← citeshttps://doi.org/10.1103/physrevb.77.172410openalex-snapshot
Dynamically relevant structural properties of short-range spin glasses and disordered ferromagnets
inferred← citeshttps://doi.org/10.1103/physrevb.79.075430openalex-snapshot
Self-assembly of s p 2 -bonded carbon nanostructures from amorphous precursors
inferred← citeshttps://doi.org/10.1103/physreve.102.062153openalex-snapshot
Visualizing free-energy landscapes for four hard disks
inferred← citeshttps://doi.org/10.1103/physreve.110.024120openalex-snapshot
Variational time reversal for free-energy estimation in nonequilibrium steady states
inferred← citeshttps://doi.org/10.1103/physreve.79.051117openalex-snapshot
Energy landscape of a spin-glass model: Exploration and characterization
inferred← citeshttps://doi.org/10.1103/physreve.88.022104openalex-snapshot
Solid-liquid transition in polydisperse Lennard-Jones systems
inferred← citeshttps://doi.org/10.1103/physreve.93.020901openalex-snapshot
Modifying self-assembly and species separation in three-dimensional systems of shape-anisotropic particles
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