scholarly journals Plasticity through De-Twinning in Twinned BCC Nanowires

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 366 ◽  
Author(s):  
G. Sainath ◽  
Sunil Goyal ◽  
A. Nagesha
Keyword(s):  
Molecular Dynamics ◽  
Shear Stress ◽  
Md Simulation ◽  
Deformation Behaviour ◽  
Compressive Loading ◽  
Md Simulations ◽  
Deformation Mechanisms ◽  
Loading Direction ◽  
Simulation Results ◽  
Oriented Parallel

The deformation behaviour of twinned FCC nanowires has been extensively investigated in recent years. However, the same is not true for their BCC counterparts. Very few studies exist concerning the deformation behaviour of twinned BCC nanowires. In view of this, molecular dynamics (MD) simulations have been performed to understand the deformation mechanisms in twinned BCC Fe nanowires. The twin boundaries (TBs) were oriented parallel to the loading direction [110] and the number of TBs is varied from one to three. MD simulation results indicate that deformation under the compressive loading of twinned BCC Fe nanowires is dominated by a unique de-twinning mechanism involving the migration of a special twin–twin junction. This de-twinning mechanism results in the complete annihilation of pre-existing TBs along with reorientation of the nanowire. Further, it has been observed that the annihilation of pre-existing TBs has occurred through two different mechanisms, one without any resolved shear stress and other with finite and small resolved shear stress. The present study enhances our understanding of de-twinning in BCC nanowires.

STUDY OF AFFINITIES BETWEEN SINGLE-WALLED NANOTUBE AND EPOXY RESIN USING MOLECULAR DYNAMICS SIMULATION

2006 ◽  
Vol 05 (01) ◽  
pp. 131-144 ◽  
Author(s):  
JIHUA GOU ◽  
BIN FAN ◽  
GANGBING SONG ◽  
AURANGZEB KHAN
Keyword(s):  
Molecular Dynamics ◽  
Epoxy Resin ◽  
Md Simulation ◽  
Average Distance ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Repulsive Interaction ◽  
Curing Agent ◽  
Single Walled Nanotubes ◽  
Simulation Results

In the processing of carbon nanotube/polymer composites, the interactions between the nanotube and polymer matrix will occur at the molecular level. Understanding their interactions before curing is crucial for nanocomposites processing. In this study, molecular dynamics (MD) simulations were employed to reveal molecular interactions between (10, 10) single-walled nanotube and two kinds of epoxy resin systems. The two kinds of resin systems were EPON 862/EPI-CURE W curing agent (DETDA) and DGEBA (diglycidylether of bisphenol A)diethylenetriamine (DETA) curing agent. The MD simulation results show that the EPON 862, DETDA and DGEBA molecules had strong attractive interactions with single-walled nanotubes and their molecules changed their conformation to align their aromatic rings parallel to the nanotube surface due to π-stacking effect, whereas the DETA molecule had a repulsive interaction with the single-walled nanotubes. The interaction energies of the molecular systems were also calculated. Furthermore, an affinity index (AI) of the average distance between the atoms of the resin molecule and nanotube surface was defined to quantify the affinities between the nanotubes and resin molecules. The MD simulation results show that the EPON 862/EPI-CURE W curing agent system has good affinities with single-walled nanotubes.

Adsorption behavior of Cs+ ions to vermiculite demonstrated by molecular dynamics simulations

2018 ◽  
Vol 28 (01n02) ◽  
pp. 1-5
Author(s):  
Akira Takeuchi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Constant Pressure ◽  
Md Simulations ◽  
Kinetic Process ◽  
Adsorption Behavior ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Cs Ions

The present paper discusses the simulation results, performed by classical molecular dynamics (MD), for vermiculite. The kinetic process of the [Formula: see text] ions in water that are adsorbed into vermiculite [Formula: see text] was investigated with classical MD simulations utilizing Coulomb and Born–Mayer–Huggins potentials. A monoclinic vermiculite crystal with a [Formula: see text] supercell was placed into 8461 molecules of water to form a rectangular supercell of [Formula: see text]. The water was placed into contact with both sides of the [Formula: see text]–[Formula: see text] planes of the vermiculite crystal, along the [Formula: see text]-axis only. The rectangular supercells, which were prepared with the vermiculite in water with and without an additional 200 [Formula: see text] ions, were simulated. The MD conditions included a constant pressure ensemble for 1 ps at a constant step of 0.1 fs. The results revealed an increase in the distances of the [Formula: see text] layers at the interface between the vermiculite and water. This increase in the separation of the [Formula: see text] layers was suitable for the uptake of [Formula: see text] ions by the vermiculite. The accelerated MD simulation which replaced the interfacial [Formula: see text] ions with [Formula: see text] ions tended to include the [Formula: see text] ions into the vermiculite by excluding the [Formula: see text] ions.

scholarly journals Fully Atomistic Molecular Dynamics Computation of Physico-Mechanical Properties of PB, PS, and SBS

Nanomaterials ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 1088 ◽  
Author(s):  
Yang Kang ◽  
Dunhong Zhou ◽  
Qiang Wu ◽  
Fuyan Duan ◽  
Rufang Yao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strain Rate ◽  
Strain Hardening ◽  
Md Simulation ◽  
Md Simulations ◽  
Strain Rates ◽  
Young’S Moduli ◽  
Plastic Modulus ◽  
Styrene Butadiene ◽  
Butadiene Styrene

The physical properties—including density, glass transition temperature (Tg), and tensile properties—of polybutadiene (PB), polystyrene (PS) and poly (styrene-butadiene-styrene: SBS) block copolymer were predicted by using atomistic molecular dynamics (MD) simulation. At 100 K, for PB and SBS under uniaxial tension with strain rate ε ˙ = 1010 s−1 and 109 s−1, their stress–strain curves had four features, i.e., elastic, yield, softening, and strain hardening. At 300 K, the tensile curves of the three polymers with strain rates between 108 s−1 and 1010 s−1 exhibited strain hardening following elastic regime. The values of Young’s moduli of the copolymers were independent of strain rate. The plastic modulus of PS was independent of strain rate, but the Young’s moduli of PB and SBS depended on strain rate under the same conditions. After extrapolating the Young’s moduli of PB and SBS at strain rates of 0.01–1 s−1 by the linearized Eyring-like model, the predicted results by MD simulations were in accordance well with experimental results, which demonstrate that MD results are feasible for design of new materials.

A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase

2020 ◽  
Vol 36 (18) ◽  
pp. 4714-4720
Author(s):  
Farzin Sohraby ◽  
Mostafa Javaheri Moghadam ◽  
Masoud Aliyar ◽  
Hassan Aryapour
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
Md Simulation ◽  
Src Kinase ◽  
Deep Understanding ◽  
Md Simulations ◽  
Binding Mode ◽  
Supplementary Information ◽  
Computational Resources ◽  
Binding Mechanisms

Abstract Summary Small molecules such as metabolites and drugs play essential roles in biological processes and pharmaceutical industry. Knowing their interactions with biomacromolecular targets demands a deep understanding of binding mechanisms. Dozens of papers have suggested that discovering of the binding event by means of conventional unbiased molecular dynamics (MD) simulation urges considerable amount of computational resources, therefore, only one who holds a cluster or a supercomputer can afford such extensive simulations. Thus, many researchers who do not own such resources are reluctant to take the benefits of running unbiased MD simulation, in full atomistic details, when studying a ligand binding pathway. Many researchers are impelled to be content with biased MD simulations which seek its validation due to its intrinsic preconceived framework. In this work, we have presented a workable stratagem to encourage everyone to perform unbiased (unguided) MD simulations, in this case a protein–ligand binding process, by typical desktop computers and so achieve valuable results in nanosecond time scale. Here, we have described a dynamical binding’s process of an anticancer drug, the dasatinib, to the c-Src kinase in full atomistic details for the first time, without applying any biasing force or potential which may lead the drug to artificial interactions with the protein. We have attained multiple independent binding events which occurred in the nanosecond time scales, surprisingly as little as ∼30 ns. Both the protonated and deprotonated forms of the dasatinib reached the crystallographic binding mode without having any major intermediate state during induction. Availability and implementation The links of the tutorial and technical documents are accessible in the article. Supplementary information Supplementary data are available at Bioinformatics online.

Surface Tension Evaluation Via Thermodynamic Analysis of Statistical Data From Molecular Dynamics Simulations

Volume 4 ◽  
2004 ◽  
Author(s):  
Aaron P. Wemhoff ◽  
Van P. Carey
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Density Profile ◽  
Md Simulation ◽  
Md Simulations ◽  
Bulk Liquid ◽  
Interfacial Region ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones

Surface tension determination of liquid-vapor interfaces of polyatomic fluids using traditional methods has shown to be difficult due to the requirement of evaluating complex intermolecular potentials. However, analytical techniques have recently been developed that determine surface tension solely by means of the characteristics of the interfacial region between the bulk liquid and vapor regions. A post-simulation application of the excess free energy density integration (EFEDI) method was used for analysis of the resultant density profile of molecular dynamics (MD) simulations of argon using a simple Lennard-Jones potential and diatomic nitrogen using a two-center Lennard-Jones potential. MD simulations were also run for an approximation of nitrogen using the simple Lennard-Jones potential. In each MD simulation, a liquid film was initialized between vapor regions and NVE-type simulations were run to equilibrium. The simulation domain was divided into bins across the interfacial region for fluid density collection, and the resultant interfacial region density profile was used for surface tension evaluation. Application of the EFEDI method to these MD simulation results exhibited good approximations to surface tension as a function of temperature for both a simple and complex potential.

scholarly journals Nanoindentation simulations for large atomic systems : an analysis of molecular dynamics and bridged finite element - molecular dynamics methodologies

2021 ◽  
Author(s):  
Jonathan Vandersluis
Keyword(s):  
Molecular Dynamics ◽  
Finite Element ◽  
Md Simulation ◽  
Computational Simulation ◽  
Md Simulations ◽  
Single Step ◽  
Depth Interval ◽  
Simulation Tool ◽  
Custom Made ◽  
Computational Resources

This thesis develops a molecular dynamics (MD) custom made computational tool to perform nanoindentation simulations on copper nanomaterials, a Face Centred Cubic (FCC) metal. The Embedding Atom Method (EAM) is used to model the interatomic forces with the substrate. Further, a bridged finite element - molecular dynamics (FE-MD) simulation tool is also adapted to perform nanoindentation experimentation. Using this bridged FE-MD simulation tool, nanoindentations are performed much more effectively than the MD simulations while saving substantial computational simulation time. While the MD simulation experienced difficulties capturing the behaviour of the system during indentation especially at faster indentation speeds, the bridged FE-MD method is capable of reaching a state of equilibrium within a single step for each indentation depth interval analyzed throughout the nanoindentation. Although the hardness values for these simulations cannot be obtained without larger scale simulations using more powerful computational resources, the simulations provide insight into the behaviour of the copper nanomaterial during nanoindentation. As a result, it is clear that the bridged FE-MD nanoindentation tool is much more effective for executing nanoindentation simulations than the traditional MD methodologies.

scholarly journals Neural relational inference to learn allosteric long-range interactions in proteins from molecular dynamics simulations

2021 ◽  
Author(s):  
Jingxuan Zhu ◽  
Juexin Wang ◽  
Weiwei Han ◽  
Dong Xu
Keyword(s):  
Molecular Dynamics ◽  
Long Range ◽  
Md Simulation ◽  
Biological Process ◽  
Dynamic Networks ◽  
Md Simulations ◽  
Amino Acid Mutation ◽  
Long Range Interactions ◽  
Decoder Architecture ◽  
Dynamics Simulations

Abstract Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid mutation at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allosteric effect. However, current MD simulations cannot reach the time scales of whole allosteric processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference (NRI) model based on a graph neural network (GNN), which adopts an encoder-decoder architecture to simultaneously infer latent interactions to probe protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between the two distant sites in the Pin1, SOD1, and MEK1 systems.

Adhesion and Interface Properties of Polydopamine and Polytetrafluoroethylene Thin Films

2020 ◽  
Vol 87 (12) ◽  
Author(s):  
Matthew Brownell ◽  
Arun K. Nair
Keyword(s):  
Thin Films ◽  
Molecular Dynamics ◽  
Wear Rate ◽  
Density Functional ◽  
Md Simulations ◽  
Deformation Mechanisms ◽  
Adhesive Properties ◽  
Functional Theory ◽  
Ptfe Film ◽  
Scratch Tests

Abstract Polytetrafluoroethylene (PTFE) has been studied as a low friction surface coating since its discovery. The high wear-rate of PTFE reduces the usefulness of the polymer for mechanical purposes; however, combining PTFE with polydopamine (PDA) has been shown to greatly reduce the film wear-rate. During rubbing tests involving PDA/PTFE thin films, a tenacious layer of PTFE remains intact after substantial testing even though pure PTFE film layers are destroyed quickly. Understanding the interface mechanics that allow PTFE and PDA to adhere so well during experimental rubbing tests is necessary to improve the wear-rate of PDA/PTFE thin films. In this study, we use density functional theory (DFT) and molecular dynamics (MD) simulations to investigate the adhesive properties and interface deformation mechanisms between PDA and PTFE molecules. Steered molecular dynamics (SMD) is then performed on isolated pairs of PDA and PTFE molecules to investigate different modes of deformation from equilibrium. PDA trimer oligomers were identified as the most adhesive to PTFE and selected to use in a PDA/PTFE thin film, where nano-indentation and scratch tests are performed. Our results indicate that a combination of the unique deformation mechanisms of PDA molecules and the penetration of PTFE molecules into the PDA substrate provide the PTFE/PDA interface with its wear resistance.

Effect of w/c ratio and cement content on diffusivity of chloride ion in concrete: A molecular dynamics study

2019 ◽  
Vol 10 (4) ◽  
pp. 83
Author(s):  
Rokonuzzaman Rokon ◽  
Md. Shafiqul Islam ◽  
Nusrat E. Mursalin
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Diffusion Coefficients ◽  
Md Simulation ◽  
Cement Content ◽  
Chloride Ion ◽  
Simulation Method ◽  
Chloride Induced Corrosion ◽  
Simulation Results ◽  
And Performance

When a reinforced structure is exposed to marine environments, chloride-induced corrosion occurs and it decreases the durability and performance of the structure. The degree of humidity, the presence of cracks, environmental conditions, w/c ratio, and cement content are the influencing factors for chloride ion ingress into concrete. All of them, w/c ratio and cement content are treated as the most crucial factors on diffusion. This paper focus on Molecular Dynamics (MD) simulation method to determine the diffusion coefficient of chloride ion in concrete. The effect of w/c ratio and cement content on the diffusivity of chloride ion is also evaluated. The diffusion coefficients are obtained 2.88x10-12 m2/s, 3.13x10-12 m2/s, and 3.61x10-12 m2/s respectively for different w/c ratio of 0.40, 0.45 and 0.50 with constant cement content. Again the diffusion coefficient are calculated 4.6x10-12 m2/s, 3.13x10-12 m2/s, 2.78x10-12 m2/s respectively for different cement content of 300 kg/m3, 350 kg/m3 and 400 kg/m3 with constant w/c ratio. The simulation results clearly indicate that the diffusion coefficient of chlorine was affected by w/c ratio and cement content significantly.

scholarly journals Molecular Dynamics Simulation-Based Study on Enhancing Thermal Properties of Graphene-Reinforced Thermoplastic Polyurethane Nanocomposite for Heat Exchanger Materials

2020 ◽  
Author(s):  
Animesh Talapatra ◽  
Debasis Datta
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Glass Transition ◽  
Thermal Properties ◽  
Transition Temperature ◽  
Glass Transition Temperature ◽  
Md Simulation ◽  
Thermoplastic Polyurethane ◽  
Simulation Based ◽  
Simulation Results

Molecular dynamics (MD) simulation-based development of heat resistance nanocomposite materials for nanoheat transfer devices (like nanoheat exchanger) and applications have been studied. In this study, MD software (Materials Studio) has been used to know the heat transport behaviors of the graphene-reinforced thermoplastic polyurethane (Gr/TPU) nanocomposite. The effect of graphene weight percentage (wt%) on thermal properties (e.g., glass transition temperature, coefficient of thermal expansion, heat capacity, thermal conductivity, and interface thermal conductance) of Gr/TPU nanocomposites has been studied. Condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field which is incorporated in both amorphous and forcite plus atomistic simulation modules within the software are used for this present study. Layer models have been developed to characterize thermal properties of the Gr/TPU nanocomposites. It is seen from the simulation results that glass transition temperature (Tg) of the Gr/TPU nanocomposites is higher than that of pure TPU. MD simulation results indicate that addition of graphene into TPU matrix enhances thermal conductivity. The present study provides effective guidance and understanding of the thermal mechanism of graphene/TPU nanocomposites for improving their thermal properties. Finally, the revealed enhanced thermal properties of nanocomposites, the interfacial interaction energy, and the free volume of polymer nanocomposites are examined and discussed.

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