230 citations · 407 across the 3 of their papers we have counts for
6 papers
Reconstruction of Protein Structures from Single-Molecule Time Series
Maximilian Topel, Andrew L. Ferguson
Single-molecule experimental techniques track the real-time dynamics of molecules by recording a small number of experimental observables. Following these observables provides a co…
Molecular Latent Space Simulators
Hythem Sidky, Wei Chen, Andrew L. Ferguson
Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales. Markov state models (MSMs) and equation-free approaches learn low-dimensional kin…
Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
Paraskevi Gkeka, Gabriel Stoltz, Amir Barati Farimani +14
Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as…
High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets
Hythem Sidky, Wei Chen, Andrew L. Ferguson
State-free reversible VAMPnets (SRVs) are a neural network-based framework capable of learning the leading eigenfunctions of the transfer operator of a dynamical system from trajec…
Capabilities and Limitations of Time-lagged Autoencoders for Slow Mode Discovery in Dynamical Systems
Wei Chen, Hythem Sidky, Andrew L. Ferguson
Time-lagged autoencoders (TAEs) have been proposed as a deep learning regression-based approach to the discovery of slow modes in dynamical systems. However, a rigorous analysis of…
Nonlinear Discovery of Slow Molecular Modes using State-Free Reversible VAMPnets
Wei Chen, Hythem Sidky, Andrew L Ferguson
The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables coincident with the slow coll…