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3rd Edition: Advances in Molecular Simulation
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3rd Edition: Advances in Molecular Simulation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (30 August 2023) | Viewed by 8980

Special Issue Editor

Prof. Dr. Małgorzata Borówko

E-Mail Website
Guest Editor
Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
Interests: molecular simulations; theory of fluids; interfacial phenomena; phase transitions; Janus particles; hairy nanoparticles; chromatography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This is a 3rd edition of our successful issues and we would like to keep providing this platform for scientists all over the world. Molecular simulations play an increasingly significant role in science today. The rapid progress in computer technology has given a strong impetus to the development of many statistical–mechanical methods for modeling physical, chemical and biological processes. Among the simulation techniques, molecular dynamics and the Monte Carlo method are the most popular. The simulations provide a tool which allows for interpolation between laboratory experiments and theory, and for a deeper insight into the processes being studied when direct measurements are not possible.  

We are currently observing the explosive development of simulation methods and their applications in fundamental and technological research. The latter range from the design of new smart materials, active materials, through the development of drugs and drug delivery to the fabrication of novel biomaterials for DNA sequencing, and many others.

This Special Issue collects papers devoted to the extension of novel simulation techniques and new methods for the analysis of the results. The other aim is to present applications of computer simulations to explore different phenomena with a focus on the explanation of their molecular mechanism and on the description of potential practical applications in nanotechnology, biotechnology, and medicine.

Prof. Dr. Małgorzata Borówko
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 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 simulation
  • molecular dynamics
  • Monte Carlo method
  • molecular modeling
  • self-assembly
  • phase transitions
  • nanoparticles
  • supramolecular structures
  • biotechnology
  • nanotechnology

Related Special Issues

Published Papers (7 papers)

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Editorial

Jump to: Research, Review

4 pages, 150 KiB  
Editorial
Special Issue “Third Edition: Advances in Molecular Simulation”
by Małgorzata Borówko
Int. J. Mol. Sci. 2024, 25(5), 2709; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25052709 - 27 Feb 2024
Viewed by 498
Abstract
Molecular simulation is one of the fastest growing fields in science [...] Full article
(This article belongs to the Special Issue 3rd Edition: Advances in Molecular Simulation)

Research

Jump to: Editorial, Review

15 pages, 5524 KiB  
Article
Free Energy Profile for the Complete Transport of Nonpolar Molecules through a Carbon Nanotube
by Changsun Eun
Int. J. Mol. Sci. 2023, 24(19), 14565; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241914565 - 26 Sep 2023
Viewed by 543
Abstract
Gas molecules or weakly interacting molecules are commonly observed to diffuse through and fill space. Therefore, when the molecules initially confined in one compartment are allowed to move through a channel into another empty compartment, we expect that some molecules will be transported [...] Read more.
Gas molecules or weakly interacting molecules are commonly observed to diffuse through and fill space. Therefore, when the molecules initially confined in one compartment are allowed to move through a channel into another empty compartment, we expect that some molecules will be transported into the initially empty compartment. In this work, we thermodynamically analyze this transport process using a simple model consisting of graphene plates, a carbon nanotube (CNT), and nonpolar molecules that are weakly interacting with each other. Specifically, we calculate the free energy change, or the potential of mean force (PMF), as the molecules are transported from one compartment to another compartment. The PMF profile clearly exhibits a global minimum, or a free energy well, at the state wherein the molecules are evenly distributed over the two compartments. To better understand the thermodynamic origin of the well, we calculate the energetic and entropic contributions to the formation of the well, and we show that the entropic change is responsible for it and is the driving force for transport. Our work not only enables a fundamental understanding of the thermodynamic nature of the transport of weakly interacting molecules with molecular details, but also provides a method for calculating the free energy change during transport between two separate spaces connected by a nanochannel. Full article
(This article belongs to the Special Issue 3rd Edition: Advances in Molecular Simulation)
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14 pages, 3499 KiB  
Article
Interaction, Insensitivity and Thermal Conductivity of CL-20/TNT-Based Polymer-Bonded Explosives through Molecular Dynamics Simulation
by Shenshen Li, Qiaoli Li and Jijun Xiao
Int. J. Mol. Sci. 2023, 24(15), 12067; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241512067 - 27 Jul 2023
Viewed by 966
Abstract
Binders mixed with explosives to form polymer-bonded explosives (PBXs) can reduce the sensitivity of the base explosive by improving interfacial interactions. The interface formed between the binder and matrix explosive also affects the thermal conductivity. Low thermal conductivity may result in localized heat [...] Read more.
Binders mixed with explosives to form polymer-bonded explosives (PBXs) can reduce the sensitivity of the base explosive by improving interfacial interactions. The interface formed between the binder and matrix explosive also affects the thermal conductivity. Low thermal conductivity may result in localized heat concentration inside the PBXs, causing the detonation of the explosive. To investigate the binder–explosive interfacial interactions and thermal conductivity, PBXs with polyurethane as the binder and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT) co-crystal as the matrix explosive were investigated through molecular dynamics (MD) simulations and reverse non-equilibrium molecular dynamics (rNEMD) simulation. The analysis of the pair correlation function revealed that there are hydrogen bonding interactions between Estane5703 and CL-20/TNT. The length of the trigger bonds was adopted as a theoretical criterion of sensitivity, and the effect of polymer binders on the sensibility of PBXs was correlated by analyzing the interfacial trigger bonds and internal trigger bonds of PBXs for the first time. The results indicated that the decrease in sensitivity of CL-20/TNT mainly comes from the CL-20/TNT contact with Estane5703. Therefore, the sensitivity of CL-20/TNT-based PBXs can be further reduced by increasing the contact area between CL-20/TNT and Estane5703. The thermal conductivity of PBXs composed of Estane5703 and CL-20/TNT (0 0 1), (0 1 0) and (1 0 0) crystal planes, respectively, were calculated through rNEMD simulations, and the results showed that only the addition of Estane5703 to the (1 0 0) crystal plane can improve the thermal conductivity of PBX100. Full article
(This article belongs to the Special Issue 3rd Edition: Advances in Molecular Simulation)
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20 pages, 2844 KiB  
Article
Impact of Semiochemicals Binding to Fel d 1 on Its 3D Conformation and Predicted B-Cell Epitopes Using Computational Approaches
by Rajesh Durairaj, Patrick Pageat and Cécile Bienboire-Frosini
Int. J. Mol. Sci. 2023, 24(14), 11685; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241411685 - 20 Jul 2023
Cited by 1 | Viewed by 955
Abstract
The major cat allergen Fel d 1 is a tetrameric glycoprotein from the secretoglobin superfamily. Fel d 1’s biological role is unknown, but it has been previously shown that it participates in semiochemical binding/transportation. Fel d 1 has linear epitopes, but its conformational [...] Read more.
The major cat allergen Fel d 1 is a tetrameric glycoprotein from the secretoglobin superfamily. Fel d 1’s biological role is unknown, but it has been previously shown that it participates in semiochemical binding/transportation. Fel d 1 has linear epitopes, but its conformational epitope sites remain unclear. In this study, we predicted the B-cell epitopes of Fel d 1 and explored semiochemical dynamics with epitopes using bioinformatics tools. The epitope residues were tabulated for chains 1 and 2 and the heterodimers of Fel d 1. The residual interactions of Fel d 1 with IgE were evaluated, and the prominent epitope sites were predicted. The molecular dynamics simulation (MDS) of Fel d 1 was performed with seven reported semiochemicals to evaluate the Fel d 1–ligand complex stability and decipher the semiochemical effect on Fel d 1 conformational epitopes. Fel d 1–lauric acid, Fel d 1–oleic acid, and Fel d 1–progesterone showed more stability and less fluctuation than other compounds. Fel d 1–linoleic acid and Fel d 1–pregnenolone displayed the most unstable complex with fluctuations. The effects of conformational changes on epitopes are discussed. All the ligand complexes drive substantial fluctuation towards the functionally exposed IgE-binding epitopes. Fel d 1 could be examined for its ligand-binding and conformational changes caused by mutations of B-cell epitopes. Full article
(This article belongs to the Special Issue 3rd Edition: Advances in Molecular Simulation)
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20 pages, 3313 KiB  
Article
Multiscale Model of CVD Growth of Graphene on Cu(111) Surface
by Meysam Esmaeilpour, Patrick Bügel, Karin Fink, Felix Studt, Wolfgang Wenzel and Mariana Kozlowska
Int. J. Mol. Sci. 2023, 24(10), 8563; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24108563 - 10 May 2023
Cited by 2 | Viewed by 2279
Abstract
Due to its outstanding properties, graphene has emerged as one of the most promising 2D materials in a large variety of research fields. Among the available fabrication protocols, chemical vapor deposition (CVD) enables the production of high quality single-layered large area graphene. To [...] Read more.
Due to its outstanding properties, graphene has emerged as one of the most promising 2D materials in a large variety of research fields. Among the available fabrication protocols, chemical vapor deposition (CVD) enables the production of high quality single-layered large area graphene. To better understand the kinetics of CVD graphene growth, multiscale modeling approaches are sought after. Although a variety of models have been developed to study the growth mechanism, prior studies are either limited to very small systems, are forced to simplify the model to eliminate the fast process, or they simplify reactions. While it is possible to rationalize these approximations, it is important to note that they have non-trivial consequences on the overall growth of graphene. Therefore, a comprehensive understanding of the kinetics of graphene growth in CVD remains a challenge. Here, we introduce a kinetic Monte Carlo protocol that permits, for the first time, the representation of relevant reactions on the atomic scale, without additional approximations, while still reaching very long time and length scales of the simulation of graphene growth. The quantum-mechanics-based multiscale model, which links kinetic Monte Carlo growth processes with the rates of occurring chemical reactions, calculated from first principles makes it possible to investigate the contributions of the most important species in graphene growth. It permits the proper investigation of the role of carbon and its dimer in the growth process, thus indicating the carbon dimer to be the dominant species. The consideration of hydrogenation and dehydrogenation reactions enables us to correlate the quality of the material grown within the CVD control parameters and to demonstrate an important role of these reactions in the quality of the grown graphene in terms of its surface roughness, hydrogenation sites, and vacancy defects. The model developed is capable of providing additional insights to control the graphene growth mechanism on Cu(111), which may guide further experimental and theoretical developments. Full article
(This article belongs to the Special Issue 3rd Edition: Advances in Molecular Simulation)
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19 pages, 4279 KiB  
Article
Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions
by German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke and Lan Li
Int. J. Mol. Sci. 2023, 24(4), 4059; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24044059 - 17 Feb 2023
Cited by 4 | Viewed by 1502
Abstract
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between [...] Read more.
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye–DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye–DNA interactions on aggregate orientation and excitonic coupling. Full article
(This article belongs to the Special Issue 3rd Edition: Advances in Molecular Simulation)
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Review

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34 pages, 17635 KiB  
Review
Hybrid Nanoparticles at Fluid–Fluid Interfaces: Insight from Theory and Simulation
by Małgorzata Borówko and Tomasz Staszewski
Int. J. Mol. Sci. 2023, 24(5), 4564; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24054564 - 26 Feb 2023
Cited by 6 | Viewed by 1737
Abstract
Hybrid nanoparticles that combine special properties of their different parts have numerous applications in electronics, optics, catalysis, medicine, and many others. Of the currently produced particles, Janus particles and ligand-tethered (hairy) particles are of particular interest both from a practical and purely cognitive [...] Read more.
Hybrid nanoparticles that combine special properties of their different parts have numerous applications in electronics, optics, catalysis, medicine, and many others. Of the currently produced particles, Janus particles and ligand-tethered (hairy) particles are of particular interest both from a practical and purely cognitive point of view. Understanding their behavior at fluid interfaces is important to many fields because particle-laden interfaces are ubiquitous in nature and industry. We provide a review of the literature, focusing on theoretical studies of hybrid particles at fluid–fluid interfaces. Our goal is to give a link between simple phenomenological models and advanced molecular simulations. We analyze the adsorption of individual Janus particles and hairy particles at the interfaces. Then, their interfacial assembly is also discussed. The simple equations for the attachment energy of various Janus particles are presented. We discuss how such parameters as the particle size, the particle shape, the relative sizes of different patches, and the amphiphilicity affect particle adsorption. This is essential for taking advantage of the particle capacity to stabilize interfaces. Representative examples of molecular simulations were presented. We show that the simple models surprisingly well reproduce experimental and simulation data. In the case of hairy particles, we concentrate on the effects of reconfiguration of the polymer brushes at the interface. This review is expected to provide a general perspective on the subject and may be helpful to many researchers and technologists working with particle-laden layers. Full article
(This article belongs to the Special Issue 3rd Edition: Advances in Molecular Simulation)
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