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Research on Molecular Dynamics 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 30 May 2024 | Viewed by 471

Special Issue Editors

Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Republic of Korea
Interests: protein structure and dynamics; protein conformational disorders; drug design; protein–protein interaction; neurodegenerative diseases; molecular modeling
Special Issues, Collections and Topics in MDPI journals
Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Republic of Korea
Interests: computational biology; molecular modeling; drug design; protein structure and dynamics; protein conformational disorders
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular dynamics (MD) simulation has emerged as a fundamental research methodology in biology, material sciences, and chemical physics as a way to understand the physical basis of any molecular motion at the atomic level. This science of simulating motion allows the visualization and dynamic characterization of any expensive or empirically challenging system of particles. Many advanced tools, including cryo-electron microscopy, X-ray crystallography, solid-state nuclear magnetic resonance, and fiber diffraction, have been developed to determine molecular structure and function. Still, these tools only provide a static picture, while dynamic properties are essential for a complete understanding of molecular functionality.

Recent advances in computational platforms, algorithms, analysis tools, software, and high-performance computing have made molecular simulations useful for investigating more complicated and large systems. In hypotheses and experiments, MD data may often be complementary to experimental studies since they can assist in analyzing and interpreting both in vivo and in vitro findings.

We warmly welcome your contributions to this Special Issue, “Research on Molecular Dynamics”. This Special Issue will cover all aspects of MD simulation, including theory, techniques, and computational or methodological developments for result analysis. Original research papers and review articles addressing MD simulation applications in diverse biomolecular systems, interactions, and functions are welcome. Submissions of combined simulation and experimental studies are also encouraged.

Prof. Dr. II Soo Moon
Dr. Raju Dash
Guest Editors

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 submissions that pass pre-check are 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • molecular dynamics
  • quantum mechanics/molecular mechanics approaches
  • conformational change
  • dynamic changes of intermolecular interactions
  • protein–ligand interactions
  • nucleic acid ligand interactions
  • computational modeling of molecular systems
  • drug design and delivery
  • structure–function relationships in proteins
  • simulation of drug-like molecules and lipid membranes

Published Papers (1 paper)

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Research

27 pages, 1076 KiB  
Article
Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments
Int. J. Mol. Sci. 2024, 25(3), 1547; https://doi.org/10.3390/ijms25031547 - 26 Jan 2024
Viewed by 381
Abstract
Molecular Dynamics simulations study material structure and dynamics at the atomic level. X-ray and neutron scattering experiments probe exactly the same time- and length scales as the simulations. In order to benchmark simulations against measured scattering data, a program is required that computes [...] Read more.
Molecular Dynamics simulations study material structure and dynamics at the atomic level. X-ray and neutron scattering experiments probe exactly the same time- and length scales as the simulations. In order to benchmark simulations against measured scattering data, a program is required that computes scattering patterns from simulations with good single-core performance and support for parallelization. In this work, the existing program Sassena is used as a potent solution to this requirement for a range of scattering methods, covering pico- to nanosecond dynamics, as well as the structure from some Ångströms to hundreds of nanometers. In the case of nanometer-level structures, the finite size of the simulation box, which is referred to as the finite size effect, has to be factored into the computations for which a method is described and implemented into Sassena. Additionally, the single-core and parallelization performance of Sassena is investigated, and several improvements are introduced. Full article
(This article belongs to the Special Issue Research on Molecular Dynamics 2.0)
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