Publications

2020

J. Rydzewski, and O. Valsson
Multiscale reweighted stochastic embedding (MRSE): Deep learning of collective variables for enhanced sampling
Submitted (2020)
arXiv

J. Rydzewski
maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels
Comp. Phys. Commun. 247, 106865 (2020)
DOI arXiv Github plumID:19.056

2019

J. Rydzewski
Machine Learning for Enhanced Sampling Methods (in Polish)
Głos Uczelni UMK 77, 7–10 (2019)
PDF

The PLUMED Consortium
Promoting Transparency and Reproducibility in Enhanced Molecular Simulations
Nat. Methods 16, 670 (2019)
DOI

J. Rydzewski, and O. Valsson
Communication: Finding Multiple Reaction Pathways of Ligand Unbinding
J. Chem. Phys. 150, 221101 (2019)
DOI arXiv Github plumID:19.066

J. F. Carrascoza Mayén, J. Rydzewski, N. Szostak, J. Blazewicz, and W. Nowak
Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations
Life 9, 46 (2019)
Special Issue DOI

2018

J. Rydzewski, R. Jakubowski, W. Nowak, and H. Grubmüller
Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways
J. Chem. Theory Comput. 14, 2843 (2018)
DOI Figshare plumID:19.067

J. Rydzewski, and W. Nowak
Photoinduced Transport in an H64Q Neuroglobin Antidote for Carbon Monoxide Poisoning
J. Chem. Phys. 148, 115101 (2018)
DOI

J. Rydzewski, R. Jakubowski, G. Nicosia, and W. Nowak
Conformational Sampling of a Biomolecular Rugged Energy Landscape
IEEE/ACM Trans. Comput. Biol. Bioinformatics 15, 732 (2018)
DOI

2017

J. Rydzewski, and W. Nowak
Rare-Event Sampling in Ligand Diffusion
Phys. Life Rev. 22-23, 85 (2017)
DOI

J. Rydzewski, and W. Nowak
Ligand Diffusion in Proteins via Enhanced Sampling in Molecular Dynamics
Phys. Life Rev. 22-23, 58 (2017)
DOI

J. Rydzewski, and W. Nowak
Thermodynamics of Camphor Migration in Cytochrome P450cam by Atomistic Simulations
Sci. Rep. 7, 7736 (2017)
DOI

2016

J. Rydzewski, and W. Nowak
Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam
J. Chem. Theory Comput. 12, 2110 (2016)
DOI Figshare

J. Rydzewski, and W. Nowak
Molecular Dynamics Simulations of Large Systems in Electronic Excited States
Handbook of Computational Chemistry (Vol. I)
Second Edition (2016) (Editior: J. Leszczynski)
DOI

2015

J. Rydzewski, W. Nowak, and G. Nicosia
Inferring Pathological States in Cortical Neuron Microcircuits
J. Theor. Biol. 386, 34 (2015)
DOI

J. Rydzewski, R. Jakubowski, and W. Nowak
Communication: Entropic Measure to Prevent Energy Over-Minimization in Molecular Dynamics Simulations
J. Chem. Phys. 143, 171103 (2015)
DOI arXiv

J. Rydzewski, and W. Nowak
Memetic Algorithms for Ligand Expulsion from Protein Cavities
J. Chem. Phys. 143, 124101 (2015)
DOI arXiv

J. Rydzewski, W. Strzałka, and W. Nowak
Nanomechanics of PCNA: A Protein-Made DNA Sliding Clamp
Chem. Phys. Lett. 634, 236 (2015)
DOI