171 citations · 389 across the 6 of their papers we have counts for
7 papers
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…
Discovery of Self-Assembling -Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation
Kirill Shmilovich, Rachael A. Mansbach, Hythem Sidky +4
Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from -c…
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…
Automatic Determination of -Cyanobiphenyl Elastic Constants from Molecular Simulation
Hythem Sidky, Jonathan K. Whitmer
New applications of liquid crystalline materials have increased the need for precise engineering of elastic properties. Recently, Sidky et al. presented methods by which the elasti…
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…
Learning Free Energy Landscapes Using Artificial Neural Networks
Hythem Sidky, Jonathan K. Whitmer
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis…