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Molecular Dynamics: Application of Computer Simulations in Soft Matter, Nano-Engineering and Biophysics

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Nanotechnology and Applied Nanosciences".

Deadline for manuscript submissions: closed (20 July 2022) | Viewed by 7648

Special Issue Editor


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Guest Editor
Centre for Complex Systems, The University of Sydney, Camperdown 2006, Australia
Interests: statistical physics; complex systems; irreversibility and dissipation; transport processes; interfacial phenomena; nanoporous materials

Special Issue Information

Dear Colleagues,

With the availability of contemporary computational resources, we can now simulate various physical, chemical, and biological processes at a molecular level with realistic temporal and spatial resolutions. Molecular dynamics (MD) views such processes as emergent results of complex collective interactions within a dynamical system comprising of many particles. Using basic Newton’s laws, MD simulates the motion of molecules, atoms, and ions, which are driven by their interactions with each other and the environment. The behavior of matter, produced by microscopic MD simulations, replicates the macroscopic phenomena observed in the real world; this makes MD experiments a viable alternative to sometimes hardly accessible actual experiments.

This Special Issue seeks to provide insights into modern problems in soft matter, nano-engineering, and biophysics, with the help of molecular dynamics simulations. It aims to identify contributions that emphasize the importance of computer simulations for revealing the fundamental phenomena behind the processes in nature, as well as the application of MD simulations to practical engineering questions. This collection targets a wide range of possible utilizations of MD simulations with an equally important focus on both methodological challenges of computational experiments and relevant problems in the surrounding world.

Contributions from any area of soft matter, nano-engineering, and biophysics, are welcomed, including (but not limited to):

  • Complex fluids, colloids, ionic liquids;
  • Glasses, polymers, gels, surfactants;
  • Porous, disordered, and functional materials;
  • Biological membranes and biomolecules;
  • Self-assembling structures, active matter, drug delivery.

We invite original research that addresses computational challenges in systems with non-equilibrium conditions, large fluctuations, strong coupling, non-local effects, active and non-potential interactions, coarse-graining needs, long relaxations, and phase transitions.

Dr. Kirill Glavatskiy
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 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

  • Molecular dynamics
  • molecular simulations
  • statistical physics
  • computational chemistry
  • soft matter
  • biophysics
  • nanoengineering
  • thermodynamics

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Published Papers (3 papers)

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Research

13 pages, 5865 KiB  
Article
Stability of Graphene Oxide Composite Membranes in an Aqueous Environment from a Molecular Point of View
by Chiara Muzzi, Anastasios Gotzias, Enrica Fontananova and Elena Tocci
Appl. Sci. 2022, 12(7), 3460; https://doi.org/10.3390/app12073460 - 29 Mar 2022
Cited by 8 | Viewed by 1972
Abstract
We used molecular dynamics to investigate the stability of graphene oxide (GO) layers supported on three polymeric materials, namely a polyvinylidene fluoride (PVDF), a pristine and a crosslinked polyamide–imide (PAI and PAI-cr). The membrane configurations consisted of a few layers of GO nanosheets [...] Read more.
We used molecular dynamics to investigate the stability of graphene oxide (GO) layers supported on three polymeric materials, namely a polyvinylidene fluoride (PVDF), a pristine and a crosslinked polyamide–imide (PAI and PAI-cr). The membrane configurations consisted of a few layers of GO nanosheets stacked over the specified polymeric supports and submerged in water. We monitored the position, the tilt angle, and the radial distribution function of the individual GO nanosheets in respect to the plane of the supports. We showed that the outermost GO nanosheets were more distorted than those attached directly on the supports. The greatest distortion was observed for the GO nanosheets of the PVDF-supported system. Next, we recorded the density profiles of the water molecules across the distance from the layers to the polymer and discussed the hydrogen bonds between water hydrogens and the oxygen atoms of the GO functional groups. Full article
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17 pages, 15060 KiB  
Article
In Silico Pesticide Discovery for New Anti-Tobacco Mosaic Virus Agents: Reactivity, Molecular Docking, and Molecular Dynamics Simulations
by Hala A. Abdulhassan, Basil A. Saleh, Dalal Harkati, Hadjer Khelfaoui, Natalie L. Hewitt and Gamal A. El-Hiti
Appl. Sci. 2022, 12(6), 2818; https://doi.org/10.3390/app12062818 - 9 Mar 2022
Cited by 8 | Viewed by 2616
Abstract
Considerable data are available regarding the molecular genetics of the tobacco mosaic virus. The disease caused by the tobacco mosaic virus is still out of control due to the lack of an efficient functional antagonist chemical molecule. Extensive research was carried out [...] Read more.
Considerable data are available regarding the molecular genetics of the tobacco mosaic virus. The disease caused by the tobacco mosaic virus is still out of control due to the lack of an efficient functional antagonist chemical molecule. Extensive research was carried out to try to find effective new anti-tobacco mosaic virus agents, however no study could find an effective agent which could completely inhibit the disease caused by the virus. In recent years, molecular docking, combined with molecular dynamics, which is considered to be one of the most important methods of drug discovery and design, were used to evaluate the type of binding between the ligand and its protein enzyme. The aim of the current work was to assess the in silico anti-tobacco mosaic virus activity for a selection of 41 new and 2 reference standard compounds. These compounds were chosen to examine their reactivity and binding efficiency with the tobacco mosaic virus coat protein (PDB ID: 2OM3). A comparison was made between the activity of the selected compounds and that for ningnanmycin and ribavirin, which are common inhibitors of plant viruses. The simulation results obtained from the molecular docking and molecular dynamics showed that two compounds of the antofine analogues could bind with the tobacco mosaic virus coat protein receptor better than ningnanmycin and ribavirin. Full article
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9 pages, 2418 KiB  
Article
A Water/Ion Separation Device: Theoretical and Numerical Investigation
by Filippos Sofos
Appl. Sci. 2021, 11(18), 8548; https://doi.org/10.3390/app11188548 - 14 Sep 2021
Cited by 11 | Viewed by 2126
Abstract
An array of ion separation cells is presented in this work, to propose a novel desalination device. Molecular Dynamics simulations have been incorporated to establish the theoretical background and calculate all parameters that could lead the manufacturing step. The main system component is [...] Read more.
An array of ion separation cells is presented in this work, to propose a novel desalination device. Molecular Dynamics simulations have been incorporated to establish the theoretical background and calculate all parameters that could lead the manufacturing step. The main system component is an ion separation cell, in which water/NaCl solution flows due to an external pressure difference and ions are directed towards the non-permeable walls under the effect of an electric field, with direction perpendicular to the flow. Clean water is gathered from the output, while the remaining, high-concentration water/ion solution is re-cycled in the cells. The strength of the electric field, cell dimensions, and wall/fluid interactions are investigated over a wide range, and shear viscosity and the volumetric flow rate are calculated for each case. Full article
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