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Publikacje

Typ publikacji:Wszystko Książka Artykuł Rozdział
Lista filadelfijska:Wszystko Tak Nie  


2024
  • J. Rydzewski, T. Gökdemir,
    " Learning Markovian dynamics with spectral maps "
    J. Chem. Phys. 160 (2024), 091102-
    DOI: 10.1063/5.0189241

  • J. Rydzewski,
    "Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles"
    J. Chem. Theory Comput. 20 (2024), 7775-7784
    DOI: 10.1021/acs.jctc.4c00428




2023
  • J. Rydzewski,
    "Selecting High-Dimensional Representations of Physical Systems by Reweighted Diffusion Maps"
    J. Phys. Chem. Lett. 14 (2023), 2778-2783
    DOI: 10.1021/acs.jpclett.3c00265

  • J. Rydzewski,
    "Spectral Map: Embedding Slow Kinetics in Collective Variables"
    J. Phys. Chem. Lett. 14 (2023), 5216-5220
    DOI: https://doi.org/10.1021/acs.jpclett.3c01101

  • B. Niklas, J. Rydzewski, Bruno Lapied, W. Nowak,
    "Toward Overcoming Pyrethroid Resistance in Mosquito Control: The Role of Sodium Channel Blocker Insecticides"
    Int. J. Mol. Sci. 24(12) (2023), 10334
    DOI: https://doi.org/10.3390/ijms241210334




2022
  • J. Rydzewski, K. Walczewska-Szewc, S. Czach, W. Nowak, Kuczera Krzysztof,
    "Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome"
    J. Phys. Chem. B 126 (2022), 2647-2657
    DOI: 10.1021/acs.jpcb.2c00131

  • K. Walczewska-Szewc, J. Rydzewski, Lewkowicz Aneta,
    "Inhibition-mediated changes in prolyl oligopeptidase dynamics possibly related to a-synuclein aggregation"
    Phys. Chem. Chem. Phys. 24 (2022), 4366 -4373
    DOI: 10.1039/D1CP05238A

  • J. Rydzewski, Chen Ming, Ghosh Tushar, Valsson Omar,
    "Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations"
    J. Chem. Theory Comput. 18 (2022), 7179-7192
    DOI: 10.1021/acs.jctc.2c00873




2021
  • J. Rydzewski, Valsson Omar,
    "Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling"
    J. Phys. Chem. A 125 (2021), 6286-6302
    DOI: 10.1021/acs.jpca.1c02869




2019
  • J. Rydzewski, Omar Valsson,
    "Finding Multiple Reaction Pathways of Ligand Unbinding"
    J. Chem. Phys. 150 (2019), 221101-
    DOI: 10.1063/1.5108638

  • J. Rydzewski,
    "maze: Heterogeneous ligand unbinding along transient protein tunnels"
    Comp. Phys. Commun. (2019), 106865-106873
    DOI: 10.1016/j.cpc.2019.106865

  • Juan Francisco Carrascoza Mayén, J. Rydzewski, Natalia Szostak, Jacek Blazewicz, W. Nowak,
    "Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations"
    Life 9 (2019), 46-54
    DOI: doi:10.3390/life9020046

  • Pavel Banáš, Alessandro Barducci, Mattia Bernetti, Peter G. Bolhuis, Max Bonomi, Sandro Bottaro, Davide Branduardi, Giovanni Bussi, Carlo Camilloni, Riccardo Capelli, Paolo Carloni, Michele Ceriotti, Andrea Cesari, Haochuan Chen, Wei Chen, Francesco Colizzi, Sandip De, Marco DeLaPierre, Davide Donadio, Viktor Drobot, Bernd Ensing, Andrew Ferguson, Marta Filizola, James Fraser, Haohao Fu, Piero Gasparotto, Francesco Luigi Gervasio, Federico Giberti, Alejandro Gil-Ley, Toni Giorgino, Gabriella T. Heller, Glen M. Hocky, Marcella Iannuzzi, Michele Invernizzi, Kim Jelfs, Alexander Jussupow, Evgeny Kirilin, Alessandro Laio, Vittorio Limongelli, Kresten Lindorff-Larsen, Thomas Löhr, Fabrizio Marinelli, Layla Martin-Samos, Matteo Masetti, Ralf Meyer, Angelos Michaelides, Carla Molteni, Tetsuya Morishita, Marco Nava, Cristina Paissoni, Elena Papaleo, Michele Parrinello, Jim Pfaendtner, Pablo Piaggi, GiovanniMaria Piccini, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Davide Provasi, David Quigley, Paolo Raiteri, Stefano Raniolo, J. Rydzewski, Matteo Salvalaglio, Gabriele Cesare Sosso, Vojtech Spiwok, Jiří Šponer, David W. H. Swenson, Pratyush Tiwary, Gareth Tribello, Omar Valsson, Michele Vendruscolo, Gregory A. Voth, Andrew White,
    "Promoting transparency and reproducibility in enhanced molecular simulations"
    Nat. Methods 16 (2019), 670-673
    DOI: https://doi.org/10.1038/s41592-019-0506-8




2018
  • J. Rydzewski, dr inż. Rafał Jakubowski, W. Nowak, prof. Helmut Grubmueller,
    "Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways"
    J. Chem. Theory Comput. 14 (6) (2018), 2843- 2851
    DOI: DOI: 10.1021/acs.jctc.8b00173

  • J. Rydzewski, W. Nowak,
    "Photoinduced Transport in an H64Q Neuroglobin Antidote for Carbon Monoxide Poisoning"
    J. Chem. Phys. 148(11) (2018), 115101-
    DOI: https://doi.org/10.1063/1.5013659




2017
  • J. Rydzewski, W. Nowak,
    "Ligand diffusion in proteins via enhanced sampling in molecular dynamics"
    Phys. Life Rev. 22-23 (2017), 58- 74
    DOI: 10.1016/j.plrev.2017.03.003

  • J. Rydzewski, W. Nowak,
    "Rare-event sampling in ligand diffusion: Reply to comments on “Ligand diffusion in proteins via enhanced sampling in molecular dynamics”"
    Phys. Life Rev. 22-23 (2017), 82- 85
    DOI: 10.1016/j.plrev.2017.08.011

  • J. Rydzewski, W. Nowak,
    "Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations"
    Sci. Rep. 7 (2017), 7736- 7746
    DOI: https://www.nature.com/articles/s41598-017-07993-0




2016
  • J. Rydzewski, R. Jakubowski, prof. Giuseppe Nicosia, W. Nowak,
    "Conformational sampling of a biomolecular rugged energy landscape"
    IEEE/ACM Trans. Comput. Biol. (2016), -
    DOI: 10.1109/TCBB.2016.2634008

  • J. Rydzewski, W. Nowak,
    "Machine learning based dimensionality reduction facilitates ligand diffusion paths assessment: a case of cytochrome P450cam"
    J. Chem. Theory Comput. (2016), -
    DOI: 10.1021/acs.jctc.6b00212

  • J. Rydzewski, W. Nowak,
    "Molecular Dynamics Simulations of Large Systems in Electronic Excited States"
    in (editor), Handbook of Computational Chemistry, Springer, Netherlands (2016), pp. 1917-1941
    ISBN: 978-94-007-6169-8




2015
  • J. Rydzewski, R. Jakubowski, W. Nowak,
    "Entropic measure to prevent energy over-minimization in molecular dynamics simulations"
    J. Chem. Phys. 143(19) (2015), 171103
    DOI: 10.1063/1.4935370

  • J. Rydzewski, W. Nowak, Giussepe Nicosia,
    "Inferring pathological states in cortical neuron microcircuits"
    J. Theor. Biol. 386 (2015), 34-43
    DOI: doi:10.1016/j.jtbi.2015.09.004

  • J. Rydzewski, W. Nowak,
    "Memetic algorithms for ligand expulsion from protein cavities"
    J. Chem. Phys. 143(12) (2015), 124101-
    DOI: 10.1063/1.4931181

  • J. Rydzewski, Wojciech Strzałka, W. Nowak,
    "Nanomechanics of PCNA: A protein-made DNA sliding clamp"
    Chem. Phys. Lett. 634 (2015), 236-242
    DOI: doi:10.1016/j.cplett.2015.06.027

  • R. Jakubowski, J. Rydzewski, W. Nowak,
    "On the role of metal ions in synaptic proteins assembly"
    Protein Sci. 24 (2015), 161-162