Related references
Note: Only part of the references are listed.Correlation functions, mean first passage times, and the Kemeny constant
Adam Kells et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Defining, Calculating, and Converging Observables of a Kinetic Transition Network
Thomas D. Swinburne et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Efficient and exact sampling of transition path ensembles on Markovian networks
Daniel J. Sharpe et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Rare events and first passage time statistics from the energy landscape
Thomas D. Swinburne et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Optimal dimensionality reduction of Markov chains using graph transformation
Deepti Kannan et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Committors, first-passage times, fluxes, Markov states, milestones, and all that
Alexander M. Berezhkovskii et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Mean first passage times in variational coarse graining using Markov state models
Adam Kells et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Sampling rare events across dynamical phase transitions
Carlos Perez-Espigares et al.
CHAOS (2019)
Identifying mechanistically distinct pathways in kinetic transition networks
Daniel J. Sharpe et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Computing committor functions for the study of rare events using deep learning
Qianxiao Li et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Elastodiffusion and cluster mobilities using kinetic Monte Carlo simulations: Fast first-passage algorithms for reversible diffusion processes
Manuel Athenes et al.
PHYSICAL REVIEW MATERIALS (2019)
Exact analysis of summary statistics for continuous-time discrete-state Markov processes on networks using graph-automorphism lumping
Jonathan A. Ward et al.
APPLIED NETWORK SCIENCE (2019)
Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems
Konstantin Roder et al.
ADVANCED THEORY AND SIMULATIONS (2019)
Statistical Analysis of the First Passage Path Ensemble of Jump Processes
Max von Kleist et al.
JOURNAL OF STATISTICAL PHYSICS (2018)
Markov State Models: From an Art to a Science
Brooke E. Husic et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)
The computation of the mean first passage times for Markov chains
Jeffrey J. Hunter
LINEAR ALGEBRA AND ITS APPLICATIONS (2018)
Aggregation of Markov flows I: theory
R. S. MacKay et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2018)
Robustness of weighted networks
Michele Bellingeri et al.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS (2018)
VAMPnets for deep learning of molecular kinetics
Andreas Mardt et al.
NATURE COMMUNICATIONS (2018)
First passage events in biological systems with non-exponential inter-event times
Mario Castro et al.
SCIENTIFIC REPORTS (2018)
A Graph-Algorithmic Approach for the Study of Metastability in Markov Chains
Tingyue Gan et al.
JOURNAL OF NONLINEAR SCIENCE (2017)
Mean First Passage Time of Preferential Random Walks on Complex Networks with Applications
Zhongtuan Zheng et al.
MATHEMATICAL PROBLEMS IN ENGINEERING (2017)
Random walks and diffusion on networks
Naoki Masuda et al.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS (2017)
Dynamic patterns of information flow in complex networks
Uzi Harush et al.
NATURE COMMUNICATIONS (2017)
Exploring biomolecular energy landscapes
Jerelle A. Joseph et al.
CHEMICAL COMMUNICATIONS (2017)
Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models
Ernesto Suarez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Multi-scale metastable dynamics and the asymptotic stationary distribution of perturbed Markov chains
Volker Betz et al.
STOCHASTIC PROCESSES AND THEIR APPLICATIONS (2016)
Accurate calculations of Stationary Distributions and Mean First Passage Times in Markov Renewal Processes and Markov Chains
Jeffrey J. Hunter
SPECIAL MATRICES (2016)
Markov State Models Provide Insights into Dynamic Modulation of Protein Function
Diwakar Shukla et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
CONTINUOUS-TIME DISCRETE-SPACE MODELS FOR ANIMAL MOVEMENT
Ephraim M. Hanks et al.
ANNALS OF APPLIED STATISTICS (2015)
Path statistics, memory, and coarse-graining of continuous-time random walks on networks
Michael Manhart et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Protein folding and binding can emerge as evolutionary spandrels through structural coupling
Michael Manhart et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models
Gerhard Hummer et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Markov State Models for Rare Events in Molecular Dynamics
Marco Sarich et al.
ENTROPY (2014)
Characterization of Rare Events in Molecular Dynamics
Carsten Hartmann et al.
ENTROPY (2014)
Communication: Analysing kinetic transition networks for rare events
Jacob D. Stevenson et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network
Maria K. Cameron
JOURNAL OF CHEMICAL PHYSICS (2014)
Flows in Complex Networks: Theory, Algorithms, and Application to Lennard-Jones Cluster Rearrangement
Maria Cameron et al.
JOURNAL OF STATISTICAL PHYSICS (2014)
Steady-state simulation of metastable stochastic chemical systems
Andreas Milias-Argeitis et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Hitting Times of Rare Events in Markov Chains
O. Benois et al.
JOURNAL OF STATISTICAL PHYSICS (2013)
Universality in network dynamics
Baruch Barzel et al.
NATURE PHYSICS (2013)
Random walks on weighted networks
Zhongzhi Zhang et al.
PHYSICAL REVIEW E (2013)
Path-Based Approach to Random Walks on Networks Characterizes How Proteins Evolve New Functions
Michael Manhart et al.
PHYSICAL REVIEW LETTERS (2013)
Markovian dynamics on complex reaction networks
J. Goutsias et al.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS (2013)
Optimal and suboptimal networks for efficient navigation measured by mean-first passage time of random walks
Zhongzhi Zhang et al.
CHAOS (2012)
Rare Event Simulation of Small Noise Diffusions
Eric Vanden-Eijnden et al.
COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS (2012)
First Passage Time for Random Walks in Heterogeneous Networks
S. Hwang et al.
PHYSICAL REVIEW LETTERS (2012)
Mean first-passage time for random walks on undirected networks
Zhongzhi Zhang et al.
EUROPEAN PHYSICAL JOURNAL B (2011)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
On the Relation Between Projections of the Reweighted Path Ensemble
Peter G. Bolhuis et al.
JOURNAL OF STATISTICAL PHYSICS (2011)
EFFICIENT COMPUTATION, SENSITIVITY, AND ERROR ANALYSIS OF COMMITTOR PROBABILITIES FOR COMPLEX DYNAMICAL PROCESSES
Jan-Hendrik Prinz et al.
MULTISCALE MODELING & SIMULATION (2011)
Bounding the equilibrium distribution of Markov population models
Tugrul Dayar et al.
NUMERICAL LINEAR ALGEBRA WITH APPLICATIONS (2011)
Cascaded failures in weighted networks
Baharan Mirzasoleiman et al.
PHYSICAL REVIEW E (2011)
Physical time scale in kinetic Monte Carlo simulations of continuous-time Markov chains
Santiago A. Serebrinsky
PHYSICAL REVIEW E (2011)
Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
Weinan E et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61 (2010)
Tunneling and Metastability of Continuous Time Markov Chains
J. Beltran et al.
JOURNAL OF STATISTICAL PHYSICS (2010)
Everything you wanted to know about Markov State Models but were afraid to ask
Vijay S. Pande et al.
METHODS (2010)
Reactive flux and folding pathways in network models of coarse-grained protein dynamics
Alexander Berezhkovskii et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Calculating rate constants and committor probabilities for transition networks by graph transformation
David J. Wales
JOURNAL OF CHEMICAL PHYSICS (2009)
TRANSITION PATH THEORY FOR MARKOV JUMP PROCESSES
Philipp Metzner et al.
MULTISCALE MODELING & SIMULATION (2009)
Quantifying the connectivity of a network: The network correlation function method
Baruch Barzel et al.
PHYSICAL REVIEW E (2009)
First-passage kinetic Monte Carlo method
Tomas Oppelstrup et al.
PHYSICAL REVIEW E (2009)
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Frank Noe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Universal robustness characteristic of weighted networks against cascading failure
Wen-Xu Wang et al.
PHYSICAL REVIEW E (2008)
Optimal partition and effective dynamics of complex networks
E. Weinan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Path ensembles and path sampling in nonequilibrium stochastic systems
Ben Harland et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Illustration of transition path theory on a collection of simple examples
Philipp Metzner et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Graph transformation method for calculating waiting times in Markov chains
Semen A. Trygubenko et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Kinetic analysis of discrete path sampling stationary point databases
SA Trygubenko et al.
MOLECULAR PHYSICS (2006)
Towards a theory of transition paths
Weinan E et al.
JOURNAL OF STATISTICAL PHYSICS (2006)
Stationary distributions and mean first passage times of perturbed Markov chains
JJ Hunter
LINEAR ALGEBRA AND ITS APPLICATIONS (2005)
Transition pathways in complex systems: Reaction coordinates, isocommittor surfaces, and transition tubes
E Weinan et al.
CHEMICAL PHYSICS LETTERS (2005)
Reaction coordinates and rates from transition paths
RB Best et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Eigenvalue bounds on restrictions of reversible nearly uncoupled Markov chains
E Meerbach et al.
LINEAR ALGEBRA AND ITS APPLICATIONS (2005)
Computing moments of first passage times to a subset of states in Markov chains
T Dayar et al.
SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS (2005)
From transition paths to transition states and rate coefficients
G Hummer
JOURNAL OF CHEMICAL PHYSICS (2004)
Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin
N Singhal et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Reaction paths based on mean first-passage times
S Park et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Metastability and low lying spectra in reversible Markov chains
A Bovier et al.
COMMUNICATIONS IN MATHEMATICAL PHYSICS (2002)
Fast simulation of Markov chains with small transition probabilities
S Juneja et al.
MANAGEMENT SCIENCE (2001)
Metastability and small eigenvalues in Markov chains
A Bovier et al.
JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL (2000)
Stable computation with the fundamental matrix of a Markov chain
JL Barlow
SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS (2000)
The many proofs and applications of Perron's theorem
CR MacCluer
SIAM REVIEW (2000)