Special Issue "Nonequilibrium Dynamics and Molecular Simulation in Living Systems"

A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Non-equilibrium Phenomena".

Deadline for manuscript submissions: closed (7 December 2021).

Special Issue Editor

Dr. Pablo Campomanes
E-Mail Website
Guest Editor
Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
Interests: molecular dynamics; enhanced sampling techniques; free energy methods; machine learning; multiscale modeling

Special Issue Information

Living organisms use energy to drive physicochemical processes uphill, against energy gradients, escaping from the corresponding minima. Thus, many biophysical and biochemical processes of interest in biology, ranging from protein–ligand binding or protein unfolding to electron transfer or enzymatic reactivity, are activated events. This nonequilibrium nature manifests at the nanoscale, at the molecular level. Therefore, to interpret experimental findings and assist rational design, these so-called rare events are commonly investigated using molecular dynamics simulations, relying on the use of enhanced sampling techniques.

Many methodological advances, including the use of machine and deep learning to increase the performance of computational protocols, have been made in the last few years. This Special Issue, dedicated to the computational study of out-of-equilibrium processes occurring in complex systems, aims to collect both novel theoretical developments in the field of nonequilibrium molecular simulations as well as applications of well-established techniques to sample rare events occurring in biologically relevant systems in order to shed light on their physicochemical mechanisms and dynamics. To this end, both unpublished original papers and comprehensive reviews focused on, but not restricted to, the research areas listed below will be considered.

  • Novel applications of enhanced sampling techniques to protein folding/unfolding and aggregation;
  • Computational studies on active conduction in ion channels;
  • Modeling and interpretation of single-molecule pulling experiments;
  • Nonequilibrium molecular dynamics simulations on energy transport and protein allosteric communication;
  • New developments and applications of Markov state models to describe activated events;
  • Multiscale modeling studies on electron transfer and enzymatic reactivity;
  • Computational modeling of photoinduced conformational changes and intramolecular signaling in biomolecules;
  • Applications of machine and deep learning to predict nonequilibrium structures and properties;
  • Approaches to learn Markov models from data;
  • Novel computational techniques to investigate rare events.

Dr. Pablo Campomanes
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Entropy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • nonequilibrium processes
  • rare events
  • molecular dynamics
  • enhance sampling
  • machine learning
  • deep learning
  • biomolecules
  • multiscale modeling

Published Papers

There is no accepted submissions to this special issue at this moment.
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