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Nanomaterials
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Nanomaterials Investigation by Molecular Dynamics Simulation
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Nanomaterials Investigation by Molecular Dynamics Simulation

A special issue of Nanomaterials (ISSN 2079-4991). This special issue belongs to the section "Theory and Simulation of Nanostructures".

Deadline for manuscript submissions: closed (15 May 2023) | Viewed by 31121

Special Issue Editor

Dr. Vladimir S. Bystrov

E-Mail Website
Guest Editor
Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences (IMPB RAS—Branch of KIAM RAS), 142290 Pushchino, Moscow Region, Russia
Interests: computational molecular modeling; molecular dynamics (MD) simulations; molecular mechanics, quantum-chemical calculations (ab initio, semi-empirical methods, density functional theory (DFT) methods, including, DFT with combined hybrid functionals); computational materials science and bionanomaterials; nanomaterials; surface; interface; self-assembly; amino acids and peptides; nanotubes; nanoparticles; polymers; piezoelectrics; pyroelectrics; ferroelectrics and bioferroelectrics; two-dimensional materials; carbons, graphene and graphene oxide; composite nanomaterials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fast progress in the nanomaterials sciences is closely related to the development and application of computer methods in this field—computational materials sciences. Today, more and more attention is being paid to a universal method for modeling the properties of nanomaterials—the method of molecular dynamics (MD). MD simulation is a method of computer simulation, where time evolution of an ensemble of interacting atoms is determined by integrating the equations of their motion. The interaction between objects in any system can be described by classical molecular dynamics using molecular mechanics (MM) force field methods, by quantum-mechanical (QM) methods or using mixed approaches containing both (QM/MM).

This Special Issue focuses on nanomaterials computational studies using MD simulation methods in various applications for simulation and calculations of the structures and properties of different nanomaterials (nanocrystals, nanoparticles, nanolayers, nanofibers, nanotubes, etc.) based on various components and compounds, including organic and biological ones.

For many practical applications in nanoelectronics, biomedicine self-assembled and specific nanostructures, with switched order parameters (such as polarization in ferroelectrics), are highly demanded, and MD simulation of its switching dynamic behavior is an especially important task. Another important task is MD simulation of the dynamics of 2D structures and composites: thin film polymeric ferroelectrics, transition metals dichalcogenides, and graphene/graphene-like structures.

Recent developments in large-scale MD simulation have increased the likelihood of successful deposition of the various thin films. The use of high-performance supercomputer calculations makes it possible to investigate molecular clusters and film thicknesses with sizes of several nanometers. Using quantum molecular dynamics and supercomputer technology makes it possible to simulate the production of amorphous states of different materials.

These new approaches are of great importance today, and our aim is for this Special Issue to publish high-level achievements in this fast-growing scientific field.

Dr. Vladimir S. Bystrov
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. Nanomaterials is an international peer-reviewed open access semimonthly 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 2900 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 (MD)
  • molecular mechanics (MM)
  • quantum-mechanics (QM)
  • density functional theory (DFT)
  • nanomaterials
  • two-dimensional materials
  • thin films
  • polymers
  • graphene and graphene oxide
  • biomolecular structures

Published Papers (16 papers)

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Research

Jump to: Review

16 pages, 2180 KiB  
Article
Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality
by Vladimir Bystrov, Ilya Likhachev, Sergey Filippov and Ekaterina Paramonova
Nanomaterials 2023, 13(13), 1905; https://doi.org/10.3390/nano13131905 - 21 Jun 2023
Cited by 2 | Viewed by 1123
Abstract
In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of [...] Read more.
In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of a phenylalanine helical nanotube. Now, a new application of the algorithm has been developed for implementing a similar molecular dynamic self-assembly into helical structures of peptide nanotubes (PNTs) based on other peptide molecules—namely diphenylalanine (FF) molecules of different chirality L-FF and D-FF. In this work, helical nanotubes were assembled from linear sequences of FF molecules with these initially different chiralities. The chirality of the obtained nanotubes was calculated by various methods, including calculation by dipole moments. In addition, a statistical analysis of the results obtained was performed. A comparative analysis of the structures of nanotubes was also performed using the method of visual differential analysis. It was found that FF PNTs obtained by the MD self-assembly method form helical nanotubes of different chirality. The regimes that form nanotubes of right chirality D from initial L-FF dipeptides and nanotubes of left chirality L from D-FF dipeptides are revealed. This corresponds to the law of changing the sign of the chirality of molecular helical structures as the level of their hierarchical organization becomes more complicated. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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24 pages, 36418 KiB  
Article
Structural Evolution and Transitions of Mechanisms in Creep Deformation of Nanocrystalline FeCrAl Alloys
by Huan Yao, Tianzhou Ye, Pengfei Wang, Junmei Wu, Jing Zhang and Ping Chen
Nanomaterials 2023, 13(4), 631; https://doi.org/10.3390/nano13040631 - 05 Feb 2023
Viewed by 1280
Abstract
FeCrAl alloys have been suggested as one of the most promising fuel cladding materials for the development of accident tolerance fuel. Creep is one of the important mechanical properties of the FeCrAl alloys used as fuel claddings under high temperature conditions. This work [...] Read more.
FeCrAl alloys have been suggested as one of the most promising fuel cladding materials for the development of accident tolerance fuel. Creep is one of the important mechanical properties of the FeCrAl alloys used as fuel claddings under high temperature conditions. This work aims to elucidate the deformation feature and underlying mechanism during the creep process of nanocrystalline FeCrAl alloys using atomistic simulations. The creep curves at different conditions are simulated for FeCrAl alloys with grain sizes (GS) of 5.6–40 nm, and the dependence of creep on temperature, stress and GS are analyzed. The transitions of the mechanisms are analyzed by stress and GS exponents firstly, and further checked not only from microstructural evidence, but also from a vital comparison of activation energies for creep and diffusion. Under low stress conditions, grain boundary (GB) diffusion contributes more to the overall creep deformation than lattice diffusion does for the alloy with small GSs. However, for the alloy with larger GSs, lattice diffusion controls creep. Additionally, a high temperature helps the transition of diffusional creep from the GB to the dominant lattice. Under medium- and high-stress conditions, GB slip and dislocation motion begin to control the creep mechanism. The amount of GB slip increases with the temperature, or decreases with GS. GS and temperature also have an impact on the dislocation behavior. The higher the temperature or the smaller the GS is, the smaller the stress at which the dislocation motion begins to affect creep. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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19 pages, 4585 KiB  
Article
Molecular Dynamics Simulation of the Thermal Behavior of Hydroxyapatite
by Ilya Likhachev, Nikolay Balabaev, Vladimir Bystrov, Ekaterina Paramonova, Leon Avakyan and Natalia Bulina
Nanomaterials 2022, 12(23), 4244; https://doi.org/10.3390/nano12234244 - 29 Nov 2022
Cited by 4 | Viewed by 1510
Abstract
Hydroxyapatite (HAP) is the main mineral component of bones and teeth. Due to its biocompatibility, HAP is widely used in medicine as a filler that replaces parts of lost bone and as an implant coating that promotes new bone growth. The modeling and [...] Read more.
Hydroxyapatite (HAP) is the main mineral component of bones and teeth. Due to its biocompatibility, HAP is widely used in medicine as a filler that replaces parts of lost bone and as an implant coating that promotes new bone growth. The modeling and calculations of the structure and properties of HAP showed that various structural defects have a significant effect on the properties of the material. By varying these structural heterogeneities, it is possible to increase the biocompatibility of HAP. An important role here is played by OH group vacancies, which are easily formed when these hydroxyl groups leave OH channels of HAP. In this case, the temperature dependence of the concentration of OH ions, which also determines the thermal behavior of HAP, is important. To study the evaporation of OH ions from HAP structures with increasing temperatures, molecular dynamics simulation (MDS) methods were used in this work. As a program for MDS modeling, we used the PUMA-CUDA software package. The initial structure of HAP, consisting of 4 × 4 × 2 = 32 unit cells of the hexagonal HAP phase, surrounded by a 15-Å layer of water was used in the modelling. Multiple and statistically processed MDS, running calculations in the range of 700–1400 K, showed that active evaporation of OH ions begins at the temperature of 1150 K. The analysis of the obtained results in comparison with those available in the literature data shows that these values are very close to the experiments. Thus, this MDS approach demonstrates its effective applicability and shows good results in the study of the thermal behavior of HAP. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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22 pages, 4334 KiB  
Article
Digital Twins Solve the Mystery of Raman Spectra of Parental and Reduced Graphene Oxides
by Elena F. Sheka
Nanomaterials 2022, 12(23), 4209; https://doi.org/10.3390/nano12234209 - 26 Nov 2022
Cited by 5 | Viewed by 1439
Abstract
Digital Twins concept presents a new trend in virtual material science, common to all computational techniques. Digital twins, virtual devices and intellectual products, presenting the main constituents of the concept, are considered in detail on the example of a complex problem, which concerns [...] Read more.
Digital Twins concept presents a new trend in virtual material science, common to all computational techniques. Digital twins, virtual devices and intellectual products, presenting the main constituents of the concept, are considered in detail on the example of a complex problem, which concerns an amazing identity of the D-G-doublet Raman spectra of parental and reduced graphene oxides. Digital twins, presenting different aspects of the GO and rGO structure and properties, were virtually synthesized using a spin-density algorithm emerging from the Hartree-Fock approximation. Virtual device presents AM1 version of the semi-empirical unrestricted HF approximation. The equilibrium structure of the twins as well as virtual one-phonon harmonic spectra of IR absorption and Raman scattering constitute a set of intellectual products. It was established that in both cases the D-G doublets owe their origin to the sp3 and sp2 C-C stretchings, respectively. This outwardly similar community reveals different grounds. Thus, multilayer packing of individual rGO molecules in stacks provides the existence of the sp3 D band in addition to sp2 G one. The latter is related to stretchings of the main pool of sp2 C-C bonds, while the sp3 constituent presents out-of-plane stretchings of dynamically stimulated interlayer bonds. In the GO case, the sp3 D component, corresponding to stretchings of the main pool of sp3 C-C bonds, is accompanied by an sp2 G component, which is related to stretchings of the remaining sp2 C-C bonds provided with the spin-influenced prohibition of the 100% oxidative reaction in graphene domain basal plane. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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9 pages, 3141 KiB  
Article
Atomistic Simulation of the Ion-Assisted Deposition of Silicon Dioxide Thin Films
by F. V. Grigoriev, V. B. Sulimov and A. V. Tikhonravov
Nanomaterials 2022, 12(18), 3242; https://doi.org/10.3390/nano12183242 - 19 Sep 2022
Cited by 4 | Viewed by 1447
Abstract
A systematic study of the most significant parameters of the ion-assisted deposited silicon dioxide films is carried out using the classical molecular dynamics method. The energy of the deposited silicon and oxygen atoms corresponds to the thermal evaporation of the target; the energy [...] Read more.
A systematic study of the most significant parameters of the ion-assisted deposited silicon dioxide films is carried out using the classical molecular dynamics method. The energy of the deposited silicon and oxygen atoms corresponds to the thermal evaporation of the target; the energy of the assisting oxygen ions is 100 eV. It is found that an increase in the flow of assisting ions to approximately 10% of the flow of deposited atoms leads to an increase in density and refractive index by 0.5 g/cm3 and 0.1, respectively. A further increase in the flux of assisting ions slightly affects the film density and density profile. The concentration of point defects, which affect the optical properties of the films, and stressed structural rings with two or three silicon atoms noticeably decrease with an increase in the flux of assisting ions. The film growth rate somewhat decreases with an increase in the assisting ions flux. The dependence of the surface roughness on the assisting ions flux is investigated. The anisotropy of the deposited films, due to the difference in the directions of motion of the deposited atoms and assisting ions, is estimated using the effective medium approach. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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16 pages, 3014 KiB  
Article
Influence of Asphaltene Modification on Structure of P3HT/Asphaltene Blends: Molecular Dynamics Simulations
by Natalia Borzdun, Artyom Glova, Sergey Larin and Sergey Lyulin
Nanomaterials 2022, 12(16), 2867; https://doi.org/10.3390/nano12162867 - 20 Aug 2022
Cited by 2 | Viewed by 1423
Abstract
Further development and commercialization of bulk heterojunction (BHJ) solar cells require the search for novel low-cost materials. The present study addresses the relations between the asphaltenes’ chemical structure and the morphology of the poly(3-hexylthiohene) (P3HT)/asphaltene blends as potential materials for the design of [...] Read more.
Further development and commercialization of bulk heterojunction (BHJ) solar cells require the search for novel low-cost materials. The present study addresses the relations between the asphaltenes’ chemical structure and the morphology of the poly(3-hexylthiohene) (P3HT)/asphaltene blends as potential materials for the design of BHJ solar cells. By means of all-atom molecular dynamics simulations, the formation of heterophase morphology is observed for the P3HT-based blends with carboxyl-containing asphaltenes, as well as the aggregation of the asphaltenes into highly ordered stacks. Although the π–π interactions between the polyaromatic cores of the asphaltenes in solutions are sufficient for the molecules to aggregate into ordered stacks, in a blend with a conjugated polymer, additional stabilizing factors are required, such as hydrogen bonding between carboxyl groups. It is found that the asphaltenes’ aliphatic side groups may improve significantly the miscibility between the polymer and the asphaltenes, thereby preventing the formation of heterophase morphology. The results also demonstrate that the carboxyl-containing asphaltenes/P3HT ratio should be at least 1:1, as a decrease in concentration of the asphaltenes leads to the folding of the polymer chains, lower ordering in the polymer phase and the destruction of the interpenetrating 3D structure formed by P3HT and the asphaltene phases. Overall, the results of the present study for the first time reveal the aggregation behavior of the asphaltenes of varying chemical structures in P3HT, as well the influence of their presence and concentration on the polymer phase structure and blend morphology, paving the way for future development of BHJ solar cells based on the conjugated polymer/asphaltene blends. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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14 pages, 1566 KiB  
Article
Diameter-Change-Induced Transition in Buckling Modes of Defective Zigzag Carbon Nanotubes
by Yoshitaka Umeno, Atsushi Kubo, Chutian Wang and Hiroyuki Shima
Nanomaterials 2022, 12(15), 2617; https://doi.org/10.3390/nano12152617 - 29 Jul 2022
Cited by 3 | Viewed by 1238
Abstract
In general, the insertion of Stone-Wales (SW) defects into single-walled carbon nanotubes (SWNTs) reduces the buckling resistance of SWNTs under axial compression. The magnitude of reduction is more noticeable in zigzag-type SWNTs than armchair- or chiral-type SWNTs; however, the relation between the magnitude [...] Read more.
In general, the insertion of Stone-Wales (SW) defects into single-walled carbon nanotubes (SWNTs) reduces the buckling resistance of SWNTs under axial compression. The magnitude of reduction is more noticeable in zigzag-type SWNTs than armchair- or chiral-type SWNTs; however, the relation between the magnitude of reduction and aspect ratio of the zigzag SWNTs remains unclear. This study conducted molecular dynamics (MD) simulation to unveil the buckling performance of zigzag SWNTs exhibiting SW defects with various tube diameter. The dependencies of energetically favorable buckling modes and the SW-defect induced reduction in the critical buckling point on the tube diameter were investigated in a systematic manner. In particular, an approximate expression for the critical buckling force as a function of the tube diameter was formulated based on the MD simulation data. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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14 pages, 6487 KiB  
Article
Adsorption Free Energy of Cellulose Nanocrystal on Water–Oil Interface
by Kenya Ito and Mitsuhiro Matsumoto
Nanomaterials 2022, 12(8), 1321; https://doi.org/10.3390/nano12081321 - 12 Apr 2022
Cited by 2 | Viewed by 1399
Abstract
To investigate the amphiphilicity of cellulose, a series of molecular dynamics simulations were performed with a cellulose nanocrystal and a water–octane interfacial system. Assuming that the axis of cellulose is parallel to the water–octane interface, the freedoms of motion of the nanocrystal were [...] Read more.
To investigate the amphiphilicity of cellulose, a series of molecular dynamics simulations were performed with a cellulose nanocrystal and a water–octane interfacial system. Assuming that the axis of cellulose is parallel to the water–octane interface, the freedoms of motion of the nanocrystal were restricted to two, the distance from the interface and the orientation around the axis. The mean force and the mean torque on the nanocrystal were evaluated with sufficiently long simulation at each crystal configuration, and their numerical integration gave a smooth free energy surface as the potential of mean force. The cellulose sample used here was found to be much more hydrophilic than oleophilic with the free energy difference ΔFw→o=318 kcal/mol. Three adsorption states with local minimum of adsorption free energy are distinguished in the free energy surface—the direct contact type which is similar to previously reported one, the hydrophilic-surface/water/octane type where a thin water layer is sandwiched between the surface and the octane phase, and the oleophilic/water/octane type where a thin water layer also exists. Water molecules in these water layers contribute to stabilize the adsorption states by taking a special orientational order and slow self-diffusion. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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15 pages, 5641 KiB  
Article
Revisiting the Rate-Dependent Mechanical Response of Typical Silicon Structures via Molecular Dynamics
by Yi Liu, Wei Wan, Quan Li, Zhenkang Xiong, Changxin Tang and Lang Zhou
Nanomaterials 2022, 12(7), 1203; https://doi.org/10.3390/nano12071203 - 03 Apr 2022
Cited by 1 | Viewed by 1899
Abstract
Strain rate is a critical parameter in the mechanical application of nano-devices. A comparative atomistic study on both perfect monocrystalline silicon crystal and silicon nanowire was performed to investigate how the strain rate affects the mechanical response of these silicon structures. Using a [...] Read more.
Strain rate is a critical parameter in the mechanical application of nano-devices. A comparative atomistic study on both perfect monocrystalline silicon crystal and silicon nanowire was performed to investigate how the strain rate affects the mechanical response of these silicon structures. Using a rate response model, the strain rate sensitivity and the critical strain rate of two structures were given. The rate-dependent dislocation activities in the fracture process were also discussed, from which the dislocation nucleation and motion were found to play an important role in the low strain rate deformations. Finally, through the comparison of five equivalent stresses, the von Mises stress was verified as a robust yield criterion of the two silicon structures under the strain rate effects. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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16 pages, 7730 KiB  
Article
Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes
by Vladimir Bystrov, Ilya Likhachev, Alla Sidorova, Sergey Filippov, Aleksey Lutsenko, Denis Shpigun and Ekaterina Belova
Nanomaterials 2022, 12(5), 861; https://doi.org/10.3390/nano12050861 - 03 Mar 2022
Cited by 5 | Viewed by 2272
Abstract
In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics [...] Read more.
In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector–scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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13 pages, 269 KiB  
Article
Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations
by Alexey Sulimov, Danil Kutov, Ivan Ilin and Vladimir Sulimov
Nanomaterials 2022, 12(2), 274; https://doi.org/10.3390/nano12020274 - 15 Jan 2022
Cited by 5 | Viewed by 1527
Abstract
The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the [...] Read more.
The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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9 pages, 1785 KiB  
Article
Molecular Dynamics Simulation of Laser Induced Heating of Silicon Dioxide Thin Films
by Fedor Vasilievich Grigoriev, Vladimir Borisovich Sulimov and Alexander Vladimirovich Tikhonravov
Nanomaterials 2021, 11(11), 2986; https://doi.org/10.3390/nano11112986 - 06 Nov 2021
Cited by 3 | Viewed by 1651
Abstract
The full-atomistic classical molecular dynamics simulation of the laser heating of silicon dioxide thin films is performed. Both dense isotropic films and porous anisotropic films are investigated. It is assumed that heating occurs due to nodal structural defects, which are currently considered one [...] Read more.
The full-atomistic classical molecular dynamics simulation of the laser heating of silicon dioxide thin films is performed. Both dense isotropic films and porous anisotropic films are investigated. It is assumed that heating occurs due to nodal structural defects, which are currently considered one of the possible causes of laser induced damage. It is revealed that heating to a temperature of 1000 K insignificantly affects the structure of the films and the concentration of point defects responsible for the radiation absorption. An increase in the heating temperature to 2000 K leads to the growth of the concentration of these defects. For “as deposited” films, this growth is greater in the case of a porous film deposited at a high deposition angle. Annealing of film reduces the difference in the concentration of laser induced defects in dense and porous films. The possible influence of optical active defects arising due to heating on the laser induced damage threshold is discussed. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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17 pages, 12199 KiB  
Article
General Molecular Dynamics Approach to Understand the Mechanical Anisotropy of Monocrystalline Silicon under the Nanoscale Effects of Point Defect
by Wei Wan, Changxin Tang, Jianjie Zhang and Lang Zhou
Nanomaterials 2021, 11(8), 1965; https://doi.org/10.3390/nano11081965 - 30 Jul 2021
Cited by 8 | Viewed by 2513
Abstract
Mechanical anisotropy and point defects would greatly affect the product quality while producing silicon wafers via diamond-wire cutting. For three major orientations concerned in wafer production, their mechanical performances under the nanoscale effects of a point defect were systematically investigated through molecular dynamics [...] Read more.
Mechanical anisotropy and point defects would greatly affect the product quality while producing silicon wafers via diamond-wire cutting. For three major orientations concerned in wafer production, their mechanical performances under the nanoscale effects of a point defect were systematically investigated through molecular dynamics methods. The results indicated anisotropic mechanical performance with fracture phenomena in the uniaxial deformation process of monocrystalline silicon. Exponential reduction caused by the point defect has been demonstrated for some properties like yield strength and elastic strain energy release. Dislocation analysis suggested that the slip of dislocations appeared and created hexagonal diamond structures with stacking faults in the [100] orientation. Meanwhile, no dislocation was observed in [110] and [111] orientations. Visualization of atomic stress proved that the extreme stress regions of the simulation models exhibited different geometric and numerical characteristics due to the mechanical anisotropy. Moreover, the regional evolution of stress concentration and crystal fracture were interrelated and mutually promoted. This article contributes to the research towards the mechanical and fracture anisotropy of monocrystalline silicon. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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15 pages, 7446 KiB  
Article
Interaction between Graphene-Based Materials and Small Ag, Cu, and CuO Clusters: A Molecular Dynamics Study
by Isabel Lado-Touriño and Alicia Páez-Pavón
Nanomaterials 2021, 11(6), 1378; https://doi.org/10.3390/nano11061378 - 23 May 2021
Cited by 4 | Viewed by 2790
Abstract
The excessive use of antibiotics has contributed to the rise in antibiotic-resistant bacteria, and thus, new antibacterial compounds must be developed. Composite materials based on graphene and its derivatives doped with metallic and metallic oxide nanoparticles, particularly Ag, Cu, and Cu oxides, hold [...] Read more.
The excessive use of antibiotics has contributed to the rise in antibiotic-resistant bacteria, and thus, new antibacterial compounds must be developed. Composite materials based on graphene and its derivatives doped with metallic and metallic oxide nanoparticles, particularly Ag, Cu, and Cu oxides, hold great promise. These materials are often modified with polyethylene glycol (PEG) to improve their pharmacokinetic behavior and their solubility in biological media. In this work, we performed molecular dynamics (MD) simulations to study the interaction between small Ag, Cu, and CuO clusters and several graphene-based materials. These materials include pristine graphene (PG) and pristine graphene nanoplatelets (PGN) as well as PEGylated graphene oxide (GO_PEG) and PEGylated graphene oxide nanoplatelets (GO-PEG_N). We calculated the adsorption energies, mean equilibrium distances between the nanoparticles and graphene surfaces, and mean square displacement (MSD) of the nanoclusters. The results show that PEGylation favors the adsorption of the clusters on the graphene surfaces, causing an increase in adsorption energies and a decrease in both distances and MSD values. The strengthening of the interaction could be crucial to obtain effective antibacterial compounds. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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Review

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36 pages, 3685 KiB  
Review
Atomistic Simulation of Physical Vapor Deposition of Optical Thin Films
by Fedor Vasilievich Grigoriev and Vladimir Borisovich Sulimov
Nanomaterials 2023, 13(11), 1717; https://doi.org/10.3390/nano13111717 - 24 May 2023
Cited by 2 | Viewed by 1928
Abstract
A review of the methods and results of atomistic modeling of the deposition of thin optical films and a calculation of their characteristics is presented. The simulation of various processes in a vacuum chamber, including target sputtering and the formation of film layers, [...] Read more.
A review of the methods and results of atomistic modeling of the deposition of thin optical films and a calculation of their characteristics is presented. The simulation of various processes in a vacuum chamber, including target sputtering and the formation of film layers, is considered. Methods for calculating the structural, mechanical, optical, and electronic properties of thin optical films and film-forming materials are discussed. The application of these methods to studying the dependences of the characteristics of thin optical films on the main deposition parameters is considered. The simulation results are compared with experimental data. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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27 pages, 2185 KiB  
Review
Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review
by Philipp S. Orekhov, Marine E. Bozdaganyan, Natalia Voskoboynikova, Armen Y. Mulkidjanian, Maria G. Karlova, Anna Yudenko, Alina Remeeva, Yury L. Ryzhykau, Ivan Gushchin, Valentin I. Gordeliy, Olga S. Sokolova, Heinz-Jürgen Steinhoff, Mikhail P. Kirpichnikov and Konstantin V. Shaitan
Nanomaterials 2022, 12(3), 361; https://doi.org/10.3390/nano12030361 - 23 Jan 2022
Cited by 11 | Viewed by 3774
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without [...] Read more.
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency. Full article
(This article belongs to the Special Issue Nanomaterials Investigation by Molecular Dynamics Simulation)
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