44 citations · 210 across the 12 of their papers we have counts for
3 papers · 1 filter
Constructing Generalized Sample Transition Probabilities with Biased Simulations
Yanbin Wang, Jakub Rydzewski, Ming Chen
In molecular dynamics (MD) simulations, accessing transition probabilities between states is crucial for understanding kinetic information, such as reaction paths and rates. Howeve…
NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks
Patryk Tajs, Mateusz Skarupski, Jakub Rydzewski
Unsupervised machine learning has recently gained much attention in the field of molecular dynamics (MD). Particularly, dimensionality reduction techniques have been regularly empl…
Illuminating Protein Dynamics: A Review of Computational Methods for Studying Photoactive Proteins
Sylwia Czach, Jakub Rydzewski, Wiesław Nowak
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-ind…