Ensuring thermodynamic consistency with invertible coarse-graining

Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces

(2023) Jonas Köhler et al.   Journal of Chemical Theory and Computation

Coarse-Grained Density Functional Theory Predictions via Deep Kernel Learning

(2022) Ganesh Sivaraman et al.   Journal of Chemical Theory and Computation

Accurate Sampling of Macromolecular Conformations Using Adaptive Deep Learning and Coarse-Grained Representation

(2022) Amr H. Mahmoud et al.   Journal of Chemical Information and Modeling

Adaptive Monte Carlo augmented with normalizing flows

(2022) Marylou Gabrié et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trainability and Accuracy of Artificial Neural Networks: An Interacting Particle System Approach

(2022) Grant Rotskoff et al.   COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS

From data to noise to data for mixing physics across temperatures with generative artificial intelligence

(2022) Yihang Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bypassing backmapping: Coarse-grained electronic property distributions using heteroscedastic Gaussian processes

(2022) J. Charlie Maier et al.   JOURNAL OF CHEMICAL PHYSICS

Bottom-up Coarse-Graining: Principles and Perspectives

(2022) Jaehyeok Jin et al.   Journal of Chemical Theory and Computation

Data-driven reaction coordinate discovery in overdamped and non-conservative systems: application to optical matter structural isomerization

(2021) Shiqi Chen et al.   Nature Communications

A microcanonical approach to temperature-transferable coarse-grained models using the relative entropy

(2021) Evan Pretti et al.   JOURNAL OF CHEMICAL PHYSICS

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

(2021) Marco Giulini et al.   Frontiers in Molecular Biosciences

A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level

(2020) Jürgen Walther et al.   NUCLEIC ACIDS RESEARCH

Exploring the landscape of model representations

(2020) Thomas T. Foley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse graining molecular dynamics with graph neural networks

(2020) Brooke E. Husic et al.   JOURNAL OF CHEMICAL PHYSICS

Predictive collective variable discovery with deep Bayesian models

(2019) Markus Schöberl et al.   JOURNAL OF CHEMICAL PHYSICS

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

(2019) Jiang Wang et al.   ACS Central Science

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

(2019) Aleksander E. P. Durumeric et al.   JOURNAL OF CHEMICAL PHYSICS

Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

(2019) Frank Noé et al.   SCIENCE

Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability

(2019) Kathryn M. Lebold et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-graining auto-encoders for molecular dynamics

(2019) Wujie Wang et al.   npj Computational Materials

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

(2018) João Marcelo Lamim Ribeiro et al.   JOURNAL OF CHEMICAL PHYSICS

SchNet – A deep learning architecture for molecules and materials

(2018) K. T. Schütt et al.   JOURNAL OF CHEMICAL PHYSICS

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

(2018) Rafael Gómez-Bombarelli et al.   ACS Central Science

Advances in coarse-grained modeling of macromolecular complexes

(2018) Alexander J Pak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Encoding and selecting coarse-grain mapping operators with hierarchical graphs

(2018) Maghesree Chakraborty et al.   JOURNAL OF CHEMICAL PHYSICS

Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization

(2018) Zachary Smith et al.   JOURNAL OF CHEMICAL PHYSICS

Graph-Based Approach to Systematic Molecular Coarse-Graining

(2018) Michael A. Webb et al.   Journal of Chemical Theory and Computation

Modeling the mechanism of CLN025 beta-hairpin formation

(2017) Keri A. McKiernan et al.   JOURNAL OF CHEMICAL PHYSICS

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

On the representability problem and the physical meaning of coarse-grained models

(2016) Jacob W. Wagner et al.   JOURNAL OF CHEMICAL PHYSICS

The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

(2015) Evangelia Kalligiannaki et al.   JOURNAL OF CHEMICAL PHYSICS

Connecting Free Energy Surfaces in Implicit and Explicit Solvent: An Efficient Method To Compute Conformational and Solvation Free Energies

(2015) Nanjie Deng et al.   Journal of Chemical Theory and Computation

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

(2014) David A. Sivak et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Density estimation by dual ascent of the log-likelihood

(2013) Esteban G. Tabak et al.   Communications in Mathematical Sciences

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

Coarse-graining of multiprotein assemblies

(2012) Marissa G Saunders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules

(2008) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

Crystal Structure of a Ten-Amino Acid Protein

(2008) Shinya Honda et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY