9 citations · 19 across the 8 of their papers we have counts for
8 papers
Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning
Mariia Ivonina, Jakub Rydzewski
The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through 1 programmed ribosomal frameshifting ( PRF), a mechanism that allo…
Decoding Binding Pathways of Ligands in Prolyl Oligopeptidase
Katarzyna Walczewska-Szewc, Jakub Rydzewski
Neurodegenerative diseases, such as Alzheimer's and Parkinson's, pose a growing global health burden. Prolyl oligopeptidase (PREP) has emerged as a potential therapeutic target in…
Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques
Tuğçe Gökdemir, Jakub Rydzewski
Understanding the long-time dynamics of complex physical processes depends on our ability to recognize patterns. To simplify the description of these processes, we often introduce…
A Note on Spectral Map
Tuğçe Gökdemir, Jakub Rydzewski
In molecular dynamics (MD) simulations, transitions between states are often rare events due to energy barriers that exceed the thermal temperature. Because of their infrequent occ…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles
Jakub Rydzewski
Understanding the behavior of complex molecular systems is a fundamental problem in physical chemistry. To describe the long-time dynamics of such systems, which is responsible for…
Learning Markovian Dynamics with Spectral Maps
Jakub Rydzewski, Tuğçe Gökdemir
The long-time behavior of many complex molecular systems is often governed by slow relaxation dynamics that can be described by a few reaction coordinates referred to as collective…
Spectral Maps for Learning Reduced Representations of Molecular Systems
Tuğçe Gökdemir, Jakub Rydzewski
Investigating processes in complex molecular systems, which are characterized by many variables, is a crucial problem in computational physics. These systems can be reduced to a fe…