Related references
Note: Only part of the references are listed.RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics
Hanlin Gu et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)
Elucidation of the key role of Pt-Pt interactions in the directional self-assembly of platinum(II) complexes
Xiaoyan Zheng et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)
Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation
Chu Li et al.
NATURE COMMUNICATIONS (2021)
Variational Approach for Learning Markov Processes from Time Series Data
Hao Wu et al.
JOURNAL OF NONLINEAR SCIENCE (2020)
Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State Models
Hongbin Wan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Dynamical reweighting methods for Markov models
Stefanie Kieninger et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)
Learning molecular dynamics with simple language model built upon long short-term memory neural network
Sun-Ting Tsai et al.
NATURE COMMUNICATIONS (2020)
Coarse graining molecular dynamics with graph neural networks
Brooke E. Husic et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Revealing Thermodynamics and Kinetics of Lipid Self-Assembly by Markov State Model Analysis
Jingwei Weng et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)
Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly
Ushnish Sengupta et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets
Wei Chen et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Graph dynamical networks for unsupervised learning of atomic scale dynamics in materials
Tian Xie et al.
NATURE COMMUNICATIONS (2019)
Rapid Calculation of Molecular Kinetics Using Compressed Sensing
Florian Litzinger et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Markov State Models: From an Art to a Science
Brooke E. Husic et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)
Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways
Xiangze Zeng et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2018)
Harnessing complexity in molecular self-assembly using computer simulations
Xiangze Zeng et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2018)
VAMPnets for deep learning of molecular kinetics
Andreas Mardt et al.
NATURE COMMUNICATIONS (2018)
An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling
Wei Wang et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems
Luming Meng et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations
Hao Wu et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Kinetics-Controlled Amphiphile Self-Assembly Processes
Xiaoyan Zheng et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2017)
Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
Fabian Paul et al.
NATURE COMMUNICATIONS (2017)
Chemical and entropic control on the molecular self-assembly process
Daniel M. Packwood et al.
NATURE COMMUNICATIONS (2017)
The construction and application of Markov state models for colloidal self-assembly process control
Xun Tang et al.
MOLECULAR SYSTEMS DESIGN & ENGINEERING (2017)
Optimal Feedback Controlled Assembly of Perfect Crystals
Xun Tang et al.
ACS NANO (2016)
Peptide self-assembly: thermodynamics and kinetics
Juan Wang et al.
CHEMICAL SOCIETY REVIEWS (2016)
Elucidating dominant pathways of the nano-particle self-assembly process
Xiangze Zeng et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2016)
Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach
Simone Conti et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2016)
Multiensemble Markov models of molecular thermodynamics and kinetics
Hao Wu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Allostery through the computational microscope: cAMP activation of a canonical signalling domain
Robert D. Malmstrom et al.
NATURE COMMUNICATIONS (2015)
A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation
Lin-Tai Da et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
Edina Rosta et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
A Supramolecular Strategy to Leverage the Liquid-Phase Exfoliation of Graphene in the Presence of Surfactants: Unraveling the Role of the Length of Fatty Acids
Sebastien Haar et al.
SMALL (2015)
Using Markov state models to study self-assembly
Matthew R. Perkett et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Variational Approach to Molecular Kinetics
Feliks Nueske et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Kai J. Kohlhoff et al.
NATURE CHEMISTRY (2014)
Millisecond dynamics of RNA polymerase II translocation at atomic resolution
Daniel-Adriano Silva et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Clustering by fast search and find of density peaks
Alex Rodriguez et al.
SCIENCE (2014)
Quantitative comparison of alternative methods for coarse-graining biological networks
Gregory R. Bowman et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Hierarchical Nystrom methods for constructing Markov state models for conformational dynamics
Yuan Yao et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Identification of slow molecular order parameters for Markov model construction
Guillermo Perez-Hernandez et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
Christian R. Schwantes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
A fast parallel clustering algorithm for molecular simulation trajectories
Yutong Zhao et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Fuzzy spectral clustering by PCCA plus : application to Markov state models and data classification
Susanna Roeblitz et al.
ADVANCES IN DATA ANALYSIS AND CLASSIFICATION (2013)
Predicting self-assembly: from empirism to determinism
Carlos-Andres Palma et al.
CHEMICAL SOCIETY REVIEWS (2012)
Self-assembly of block copolymers
Yiyong Mai et al.
CHEMICAL SOCIETY REVIEWS (2012)
Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II
Lin-Tai Da et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Colloids with valence and specific directional bonding
Yufeng Wang et al.
NATURE (2012)
Design and elaboration of colloidal molecules: an overview
Etienne Duguet et al.
CHEMICAL SOCIETY REVIEWS (2011)
Taming the complexity of protein folding
Gregory R. Bowman et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach
Wei Zhuang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
Brownian Molecular Dynamics Simulation on Self-Assembly Behavior of Diblock Copolymers: Influence of Chain Conformation
Shaoliang Lin et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
TRANSITION PATH THEORY FOR MARKOV JUMP PROCESSES
Philipp Metzner et al.
MULTISCALE MODELING & SIMULATION (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)
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
John D. Chodera et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Stable signal recovery from incomplete and inaccurate measurements
Emmanuel J. Candes et al.
COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS (2006)
Towards a theory of transition paths
Weinan E et al.
JOURNAL OF STATISTICAL PHYSICS (2006)
Compressed sensing
DL Donoho
IEEE TRANSACTIONS ON INFORMATION THEORY (2006)
Robust Perron cluster analysis in conformation dynamics
P Deuflhard et al.
LINEAR ALGEBRA AND ITS APPLICATIONS (2005)
Coarse grain models and the computer simulation of soft materials
SO Nielsen et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2004)
Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains
P Deuflhard et al.
LINEAR ALGEBRA AND ITS APPLICATIONS (2000)