Publications

2026

• B. Niklas, E. Moreau, C. Deshayes, J. Rydzewski, M. Jankowska, J. Kesy, A. J. Martins, P. Mueller, V. Corbel, W. Nowak, B. Lapied
  Cytochrome P450 Inhibition Impedes Pyrethroid Effects on Insects through Nav Channel Regulation
  BMC Biol. 24, 141
  doi:10.1186/s12915-026-02611-w / biorxiv:10.1101/2025.02.03.636193

• S. Alinejad, J. Rydzewski, O. Valsson
  Spectral Autoencoders: Machine Learning Slow Modes for Enhanced Sampling
  Upcoming

• T. Shah, S. Heidari, J. Rydzewski, H. Torabifard
  Decoding the Conformational Dynamics and Hyperactivity of Histone H3K36 N-Methyltransferase in Oncogenic Mutations via tICA and Markov State Modeling
  biorxiv:10.64898/2026.06.03.730013v1

• S. Czach, J. Rydzewski
  Understanding Mechanistic Transitions in Photoactive Yellow Protein with Machine Learning
  Upcoming

• M. Ivonina, J. Rydzewski
  Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning
  Accepted in J. Comput. Chem.
  arxiv:2604.14906 / codeberg:spectre

• K. Walczewska-Szewc, J. Rydzewski
  Decoding Binding Pathways of Ligands in Prolyl Oligopeptidase
  Phys. Chem. Chem. Phys. 28, 829–840
  doi:10.1039/D5CP02804C / arxiv:2503.15139 / github:plumed2-maze

2025

• Y. Wang, J. Rydzewski, M. Chen
  Constructing Generalized Sample Transition Probabilities with Biased Simulations
  J. Chem. Theory Comput. 21, 23, 11920–11930
  doi:10.1021/acs.jctc.5c01307 / arxiv:2508.03977 / github:gstp

• P. Tajs, M. Skarupski, J. Rydzewski
  NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks
  J. Chem. Inf. Model. 65, 14, 7347
  doi:10.1021/acs.jcim.5c01107 / arxiv:2505.1676 / code

• S. Czach, J. Rydzewski, W. Nowak
  Illuminating Protein Dynamics: A Review of Computational Methods for Studying Photoactive Proteins
  arxiv:2503.21418

• T. Gökdemir, J. Rydzewski
  Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques (Featured)
  Chem. Phys. Rev. 6, 011304
  Special Collection: AI and Machine Learning in Chemical and Materials Science
  doi:10.1063/5.0245177 / arxiv:2412.20868

• G.A. Tribello, M. Bonomi, G. Bussi, C. Camilloni, et al.
  PLUMED Tutorials: A Collaborative, Community-Driven Learning Ecosystem
  J. Chem. Phys. 162, 092501
  Special Collection: Michele Parrinello Festschrift
  doi:10.1063/5.0251501 / arxiv:2412.03595

• T. Gökdemir, J. Rydzewski
  A Note on Spectral Map
  Ensemble Journal of the Molecular Simulation Society of Japan (MSSJ), 27, 1
  doi:xyz / arxiv:2412.04011

2024

• J. Rydzewski
  Correction to “Spectral Map: Embedding Slow Kinetics in Collective Variables”
  J. Phys. Chem. Lett. 16, 103
  doi:10.1021/acs.jpclett.4c03457

• J. Rydzewski
  Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles
  J. Chem. Theory Comput. 20, 7775
  Special Issue: Machine Learning and Statistical Mechanics: Shared Synergies for Next Generation of Chemical Theory and Computation
  doi:10.1021/acs.jctc.4c00428 / arxiv:2409.06428

• J. Rydzewski, T. Gökdemir
  Learning Markovian Dynamics with Spectral Maps
  J. Chem. Phys. 160, 091102
  doi:10.1063/5.0189241 / arxiv:2311.16411 / zenodo:10678142 / plumID:24.005

• K. Walczewska-Szewc, J. Rydzewski
  Structural Visualization of Inhibitor Binding in Prolyl Oligopeptidase
  Biophys. Rev. 5, 032105
  doi:10.1063/5.0226428

• T. Gökdemir, J. Rydzewski
  Spectral Maps for Learning Reduced Representations of Molecular Systems
  CCP2023 - 34th IUPAP Conference on Computational Physics
  arxiv:2311.03641

2023

• J. Rydzewski, M. Chen, O. Valsson
  Manifold Learning in Atomistic Simulations: A Conceptual Review
  Mach. Learn.: Sci. Technol. 4, 031001
  doi:10.1088/2632-2153/ace81a / arxiv:2303.08486

• J. Rydzewski
  Spectral Map: Embedding Slow Kinetics in Collective Variables
  J. Phys. Chem. Lett. 14, 5216
  doi:10.1021/acs.jpclett.3c01101 / arxiv:2404.01809

• J. Rydzewski
  Selecting High-Dimensional Representations of Physical Systems by Reweighted Diffusion Maps
  J. Phys. Chem. Lett. 14, 2778
  doi:10.1021/acs.jpclett.3c00265 / arxiv:2404.02639

• B. Niklas, J. Rydzewski, B. Lapied, W. Nowak
  Toward Overcoming Pyrethroid Resistance in Mosquito Control: The Role of Sodium Channel Blocker Insecticides
  Int. J. Mol. Sci. 24, 10334
  doi:10.3390/ijms241210334 / biorxiv:10.1101/2023.03.29.534712

2022

• J. Rydzewski, M. Chen, T. K. Ghosh, O. Valsson
  Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
  J. Chem. Theory Comput. 18, 7179
  doi:10.1021/acs.jctc.2c00873 / arxiv:2207.14554 / plumID:21.023

• J. Rydzewski, K. Walczewska-Szewc, S. Czach, W. Nowak, K. Kuczera
  Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome
  J. Phys. Chem. B 126, 2647
  doi:10.1021/acs.jpcb.2c00131 / chemrxiv:n8hlc / plumID:22.015

• K. Walczewska-Szewc, J. Rydzewski, A. Lewkowicz
  Inhibition-Mediated Changes in Prolyl Oligopeptidase Dynamics Possibly Related to α-Synuclein Aggregation
  Phys. Chem. Chem. Phys. 24, 4366
  doi:10.1039/D1CP05238A

2021

• J. Rydzewski, O. Valsson
  Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling
  J. Phys. Chem. A 125, 6286
  doi:10.1021/acs.jpca.1c02869 / arxiv:2007.06377 / zenodo:4756093 / plumID:21.023

2020

• J. Rydzewski
  maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels
  Comp. Phys. Commun. 247, 106865
  doi:10.1016/j.cpc.2019.106865 / arxiv:1904.03929 / plumID:19.056

2019

• J. Rydzewski as part of PLUMED Consortium
  Promoting Transparency and Reproducibility in Enhanced Molecular Simulations
  Nat. Methods 16, 670
  doi:10.1038/s41592-019-0506-8

• J. Rydzewski, O. Valsson
  Finding Multiple Reaction Pathways of Ligand Unbinding
  J. Chem. Phys. 150, 221101
  doi:10.1063/1.5108638 / arxiv:1808.08089 / plumID:19.066

• J. F. Carrascoza Mayén, J. Rydzewski, N. Szostak, J. Blazewicz, W. Nowak
  Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations
  Life 9, 46
  doi:10.3390/life9020046

2018

• J. Rydzewski, R. Jakubowski, W. Nowak, H. Grubmüller
  Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways
  J. Chem. Theory Comput. 14, 2843
  doi:10.1021/acs.jctc.8b00173 / plumID:19.067

• J. Rydzewski, W. Nowak
  Photoinduced Transport in an H64Q Neuroglobin Antidote for Carbon Monoxide Poisoning
  J. Chem. Phys. 148, 115101
  doi:10.1063/1.5013659

• J. Rydzewski, R. Jakubowski, G. Nicosia, W. Nowak
  Conformational Sampling of a Biomolecular Rugged Energy Landscape
  IEEE/ACM Trans. Comput. Biol. Bioinformatics 15, 732
  doi:10.1109/tcbb.2016.2634008

2017

• J. Rydzewski, W. Nowak
  Rare-Event Sampling in Ligand Diffusion
  Phys. Life Rev. 22-23, 85
  doi:10.1016/j.plrev.2017.08.011

• J. Rydzewski, W. Nowak
  Ligand Diffusion in Proteins via Enhanced Sampling in Molecular Dynamics
  Phys. Life Rev. 22-23, 58
  doi:10.1016/j.plrev.2017.03.003

• J. Rydzewski, W. Nowak
  Thermodynamics of Camphor Migration in Cytochrome P450cam by Atomistic Simulations
  Sci. Rep. 7, 7736
  doi:10.1038/s41598-017-07993-0

2016

• J. Rydzewski, W. Nowak
  Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam
  J. Chem. Theory Comput. 12, 2110
  doi:10.1021/acs.jctc.6b00212

• J. Rydzewski, 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:10.1007/978-94-007-6169-8_49-1

2015

• J. Rydzewski, W. Nowak, G. Nicosia
  Inferring Pathological States in Cortical Neuron Microcircuits
  J. Theory Biol. 386, 34
  doi:10.1016/j.jtbi.2015.09.004

• J. Rydzewski, R. Jakubowski, W. Nowak
  Entropic Measure to Prevent Energy Over-Minimization in Molecular Dynamics Simulations
  J. Chem. Phys. 143, 171103
  doi:10.1063/1.4935370 / arxiv:1507.01118

• J. Rydzewski, W. Nowak
  Memetic Algorithms for Ligand Expulsion from Protein Cavities
  J. Chem. Phys. 143, 124101
  doi:10.1063/1.493118 / arxiv:1507.00150

• J. Rydzewski, W. Strzałka, W. Nowak
  Nanomechanics of PCNA: A Protein-Made DNA Sliding Clamp
  Chem. Phys. Lett. 634, 236
  doi:10.1016/j.cplett.2015.06.027