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Research on Molecular Dynamics: 2nd Edition
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Research on Molecular Dynamics: 2nd Edition

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: closed (20 June 2025) | Viewed by 5050

Special Issue Editors

Prof. Dr. II Soo Moon

E-Mail Website
Guest Editor
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
Dr. Raju Dash

E-Mail Website
Guest Editor
Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, 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

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Published Papers (4 papers)

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Research

24 pages, 5811 KiB  
Article
Thermodynamics of Molecular Transport Through a Nanochannel: Evidence of Energy–Entropy Compensation
by Changsun Eun
Int. J. Mol. Sci. 2025, 26(15), 7277; https://doi.org/10.3390/ijms26157277 - 28 Jul 2025
Viewed by 206
Abstract
In this work, the thermodynamics of molecular transport between two compartments connected by a nanochannel is investigated through an analysis of internal energy and entropy changes, with a focus on how these changes depend on intermolecular interaction strength. When interactions are weak, resembling [...] Read more.
In this work, the thermodynamics of molecular transport between two compartments connected by a nanochannel is investigated through an analysis of internal energy and entropy changes, with a focus on how these changes depend on intermolecular interaction strength. When interactions are weak, resembling gas-like behavior, entropy dominates and favors configurations in which molecules are evenly distributed between the two compartments, despite an increase in internal energy. In contrast, strong interactions, characteristic of liquid-like behavior, lead to dominant energetic contributions that favor configurations with molecules localized in a single compartment, despite entropy loss. Intermediate interaction strengths yield comparable entropic and energetic contributions that cancel each other out, resulting in oscillatory behavior between evenly distributed and localized configurations, as observed in previous work. This thermodynamic analysis reveals energy–entropy compensation, in which entropic and energetic contributions offset each other across different interaction strengths; notably, this compensatory relationship exhibits a linear trend. These findings provide insight into the thermodynamic origins of molecular transport behavior and highlight fundamental parallels between molecular transport and molecular binding, the latter being particularly relevant to molecular recognition and drug design. Full article
(This article belongs to the Special Issue Research on Molecular Dynamics: 2nd Edition)
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19 pages, 19033 KiB  
Article
Disclosing Pathogenic Variant Effects on the Structural Dynamics of the VAPB MSP Domain Causing Familial ALS
by Md Abul Bashar, Nayan Dash, Sarmistha Mitra and Raju Dash
Int. J. Mol. Sci. 2025, 26(13), 6489; https://doi.org/10.3390/ijms26136489 - 5 Jul 2025
Viewed by 527
Abstract
Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB) serves as a tethering factor that interacts with various proteins and recruits these proteins to the ER surface, exerting multiple functions, such as organelle membrane tethering, lipid transfer between organelles, regulation of calcium homeostasis, autophagy, and [...] Read more.
Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB) serves as a tethering factor that interacts with various proteins and recruits these proteins to the ER surface, exerting multiple functions, such as organelle membrane tethering, lipid transfer between organelles, regulation of calcium homeostasis, autophagy, and the unfolded protein response (UPR). Its interaction is often mediated by its MSP (major sperm) domain, which binds with FFAT (two phenylalanines in an acidic tract)-motif-containing proteins. However, pathogenic variations, such as P56S, P56H, and T46I, in the VAPB MSP domain lead to the familial form of amyotrophic lateral sclerosis (ALS8). Still, the underlying pathophysiology of ALS8 due to pathogenic variations in the VAPB MSP domain remains elusive. In this study, we conducted molecular dynamics (MD) simulations to understand the pathogenic-variant-derived changes in the structural dynamics of the VAPB MSP domain. We found that pathogenic variants altered the fluctuations and conformational dynamics of the VAPB protein. Analyzing the organizations of the secondary structure revealed that pathogenic variants changed the composition of secondary structure elements, especially increasing the proportion of α-helix while reducing β-sheet formation, which might affect the organelle tethering and other functions of VAPB, as well as VAPB homodimer and heterodimer formation. Taken together, these findings can be further investigated through in vivo and/or in vitro studies to not only clarify the pathophysiology of ALS8 resulting from VAPB MSP domain pathogenic variants but also develop novel therapeutics for the disease that restore the native structural organizations as well as fluctuations and motions. Full article
(This article belongs to the Special Issue Research on Molecular Dynamics: 2nd Edition)
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16 pages, 2284 KiB  
Article
Local Strain Effects on Lattice Defect Dynamics and Interstitial Dislocation Loop Formation in Irradiated Tungsten–Molybdenum Alloys: A Molecular Dynamics Study
by Marzoqa M. Alnairi and Mosab Jaser Banisalman
Int. J. Mol. Sci. 2024, 25(19), 10777; https://doi.org/10.3390/ijms251910777 - 7 Oct 2024
Cited by 1 | Viewed by 1254
Abstract
In this study, molecular dynamics (MD) simulations were used to investigate how alloying tungsten (W) with molybdenum (Mo) and local strain affect the primary defect formation and interstitial dislocation loops (IDLs) in W–Mo alloys. While the number of Frenkel pairs (FPs) in the [...] Read more.
In this study, molecular dynamics (MD) simulations were used to investigate how alloying tungsten (W) with molybdenum (Mo) and local strain affect the primary defect formation and interstitial dislocation loops (IDLs) in W–Mo alloys. While the number of Frenkel pairs (FPs) in the W–Mo alloy is similar to pure W, it is half that of pure Mo. The W–20% Mo alloy, chosen for further analysis, showed minimal FP variance after collision cascades induced by primary knock-on atoms (PKAs) at 10 to 80 keV. The research examined hydrostatic strains from −1.4% to 1.6%, finding that higher strains correlated with increased FP counts and cluster formation, including IDLs. The following two types of IDLs were identified: majority ½ <111> loops as well as <100> IDLs that formed within the initial picoseconds of the simulations under higher tensile strain (1.6%) and larger PKA energies (80 keV). The strain effects also correlated with changes in threshold displacement energy (TDE), with higher FP formation under tensile strain. This study highlights the impact of strain and alloying on radiation damage, particularly in low-temperature, high-energy environments. Full article
(This article belongs to the Special Issue Research on Molecular Dynamics: 2nd Edition)
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27 pages, 1076 KiB  
Article
Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments
by Arnab Majumdar, Martin Müller and Sebastian Busch
Int. J. Mol. Sci. 2024, 25(3), 1547; https://doi.org/10.3390/ijms25031547 - 26 Jan 2024
Cited by 1 | Viewed by 2140
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: 2nd Edition)
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