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List of works by Jakub Rydzewski

Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations

scientific article published on 01 November 2015

Conformational sampling of a biomolecular rugged energy landscape.

scientific article

Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

scientific article published on 17 December 2021

Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

scientific article published on 15 December 2021

Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome

scientific article published on 14 April 2022

Finding multiple reaction pathways of ligand unbinding

scientific article published on 01 June 2019

Inferring pathological states in cortical neuron microcircuits

scientific article published on 12 September 2015

Inhibition-mediated changes in prolyl oligopeptidase dynamics possibly related to α-synuclein aggregation

scientific article published in 2022

Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways

scientific article published on 24 May 2018

Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

scientific article

Molecular Dynamics Simulations of Large Systems in Electronic Excited States

Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling

scientific article

Nanomechanics of PCNA: A protein-made DNA sliding clamp

Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations

scientific article published on 04 June 2019

Rare-event sampling in ligand diffusion: Reply to comments on "Ligand diffusion in proteins via enhanced sampling in molecular dynamics".

scientific article

Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations

scientific article published on 11 November 2022

Selecting High-Dimensional Representations of Physical Systems by Reweighted Diffusion Maps

Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations

scientific article published on 10 August 2017

Toward overcoming pyrethroid resistance in mosquito control: the role of sodium channel blocker insecticides

scientific article published on 30 March 2023

maze: Heterogeneous ligand unbinding along transient protein tunnels

article published in 2020

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