Publications

2024

• J. Rydzewski
  Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles
  J. Chem. Theory Comput. 20, 7775 (2024)
  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 (2024)
  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 (2024)
  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 (2023)
  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 (2023)
  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 (2023)
  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 (2023)
  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 (2022)
  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 (2022)
  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 (2022)
  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 (2021)
  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 (2020)
  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 (2019)
  doi:10.1038/s41592-019-0506-8

• J. Rydzewski, O. Valsson
  Finding Multiple Reaction Pathways of Ligand Unbinding
  J. Chem. Phys. 150, 221101 (2019)
  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 (2019)
  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 (2018)
  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 (2018)
  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 (2018)
  doi:10.1109/tcbb.2016.2634008

2017

• J. Rydzewski, W. Nowak
  Rare-Event Sampling in Ligand Diffusion
  Phys. Life Rev. 22-23, 85 (2017)
  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 (2017)
  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 (2017)
  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 (2016)
  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 (2015)
  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 (2015)
  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 (2015)
  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 (2015)
  doi:10.1016/j.cplett.2015.06.027