scholarly journals Nonlinear thermal vibration of a nanoplate attached to a cavity

2021 ◽  
Author(s):  
Yuhe Bai ◽  
Rumeng Liu ◽  
Lifeng Wang
Keyword(s):  
Md Simulation ◽  
Md Simulations ◽  
Good Prediction ◽  
Nonlinear Phenomenon ◽  
Plate Model ◽  
Dynamic Problems ◽  
Helium Atoms ◽  
Nonlinear Plate ◽  
Cavity System ◽  
Increasing Temperature

Abstract Dynamic problems of a nanocircular plate-cavity system are investigated using molecular dynamics (MD) method. A nonlinear plate model considering gas action is developed. The results of the MD simulation show that the helium atoms adsorb on the wall of the cavity at low temperature, resulting in a negative deflection of the molybdenum disulfide (MoS2) plate. As the temperature increases, the pressure in the cavity increases, leading to a gradual rise in the deflection of the plate. A nonlinear phenomenon of stiffness hardening is shown with increasing temperature. The nonlinear plate model can give a relatively good prediction compared with the results of MD simulations. The natural frequency of the plate is affected by temperature and the presence of gas in the cavity. The phenomenon of stiffness hardening and softening can be well simulated by the nonlinear plate model and MD method. The present study provides a reference for vibration experiments of two-dimensional nanostructures.

Study of Helium Bubble Induced Hardening in BCC-Fe by Molecular Dynamics Simulation

2019 ◽  
Vol 944 ◽  
pp. 378-386
Author(s):  
Li Xia Jia ◽  
Xin Fu He ◽  
Shi Wu ◽  
Dong Jie Wang ◽  
Han Cao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Edge Dislocation ◽  
Reasonable Agreement ◽  
Md Simulation ◽  
Md Simulations ◽  
Defect Size ◽  
Dynamics Simulation ◽  
Helium Bubble ◽  
Increasing Temperature ◽  
Critical Resolved Shear Stress

The interaction between an moving edge dislocation and helium bubble was studied in BCC-Fe using Molecular dynamics（MD）simulation. Edge dislocation passed the bubble via cut mechanism. A step with a length of b is left on both sides of the bubble after dislocation left away. The influence of simulation temperature, defect size and He/V ratio in bubble on critical resolved shear stress (CRSS) for dislocation to shear bubble were investigated. The CRSS increases with increasing defect sizes, and decreases with increasing temperature. When He/V ratio is at the range of 0-1, CRSS depends weakly on the He/V ratio. The estimated obstacle strength of helium bubble based on MD simulations is acceptable and reasonable agreement with one deduced from the dispersion barrier-hardening model applied to experimental results.

A comprehensive in silico study towards understanding the inhibitory mechanism of Lactoperoxidase by Dapsone and Propofol

2020 ◽  
Vol 16 ◽  
Author(s):  
Rameez Jabeer Khan ◽  
Rajat Kumar Jha ◽  
Gizachew Muluneh Amera ◽  
Jayaraman Muthukumaran ◽  
Rashmi Prabha Singh ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Protoporphyrin Ix ◽  
Md Simulations ◽  
Prosthetic Group ◽  
Drug Molecules ◽  
Group A ◽  
Complex Forms ◽  
Covalently Linked

Introduction: Lactoperoxidase (LPO) is a member of mammalian heme peroxidase family and is an enzyme of innate immune system. It possesses a covalently linked heme prosthetic group (a derivative of protoporphyrin IX) in its active site. LPO catalyzes the oxidation of halides and pseudohalides in the presence of hydrogen peroxide (H2O2) and shows a broad range of antimicrobial activity. Methods: In this study, we have used two pharmaceutically important drug molecules, namely dapsone and propofol, which are earlier reported as potent inhibitors of LPO. Whereas the stereochemistry and mode of binding of dapsone and propofol to LPO is still not known because of the lack of the crystal structure of LPO with these two drugs. In order to fill this gap, we utilized molecular docking and molecular dynamics (MD) simulation studies of LPO in native and complex forms with dapsone and propofol. Results: From the docking results, the estimated binding free energy (ΔG) of -9.25 kcal/mol (Ki = 0.16 μM) and -7.05 kcal/mol (Ki = 6.79 μM) was observed for dapsone, and propofol, respectively. The standard error of Auto Dock program is 2.5 kcal/mol; therefore, molecular docking results alone were inconclusive. Conclusion: To further validate the docking results, we performed MD simulation on unbound, and two drugs bounded LPO structures. Interestingly, MD simulations results explained that the structural stability of LPO-Propofol complex was higher than LPO-Dapsone complex. The results obtained from this study establish the mode of binding and interaction pattern of the dapsone and propofol to LPO as inhibitors.

scholarly journals Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sensen Zhang ◽  
Baolei Yuan ◽  
Jordy Homing Lam ◽  
Jun Zhou ◽  
Xuan Zhou ◽  
...  
Keyword(s):  
Md Simulation ◽  
Potential Role ◽  
Md Simulations ◽  
Full Length ◽  
Inflammasome Activation ◽  
Simulation Studies ◽  
Cryo Electron Microscopy ◽  
Gating Mechanism ◽  
Atp Efflux

AbstractPannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.

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.

Atomistic Level Molecular Dynamics Analysis and its Integrity in the Interim of Irradiation

2021 ◽  
Vol 318 ◽  
pp. 39-47
Author(s):  
Ahli K.D. Willie ◽  
Hong Tao Zhao ◽  
M. Annor-Nyarko
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Mixed Oxide ◽  
Md Simulation ◽  
Lattice Thermal Conductivity ◽  
Gas Diffusion ◽  
Mixed Oxide Fuel ◽  
Fission Gas ◽  
Increasing Temperature ◽  
End Members

In this work, molecular dynamics (MD) simulation was utilized in relation to access the thermal conductivity of UO2, PuO2 and (U, Pu)O2 in temperature range of 500–3000 K. Diffusion study on mixed oxide (MOX) was also performed to assess the effect of radiation damage by heavy ions at burnup temperatures. Analysis of the lattice thermal conductivity of irradiated MOX to its microstructure was carried out to enhance the irradiation defects with how high burnup hinders fuel properties and its pellet-cladding interaction. Fission gas diffusion as determined was mainly modelled by main diffusion coefficient. Degradation of diffusivity is predicted in MOX as composition deviate from the pure end members. The concentration of residual anion defects is considerably higher than that of cations in all oxides. Depending on the diffusion behavior of the fuel lattice, there was decrease in the ratio of anion to cation defects with increasing temperature. Besides, the modern mixed oxide fuel releases fission gas compared to that of UO2 fuel at moderate burnups.

scholarly journals Dislocations in Grain Boundary Regions: The Origin of Heterogeneous Microstrains in Nanocrystalline Materials

2019 ◽  
Vol 51 (1) ◽  
pp. 513-530 ◽  
Author(s):  
Zhenbo Zhang ◽  
Éva Ódor ◽  
Diana Farkas ◽  
Bertalan Jóni ◽  
Gábor Ribárik ◽  
...  
Keyword(s):  
Grain Size ◽  
Grain Boundary ◽  
Nanocrystalline Materials ◽  
Md Simulation ◽  
High Pressure Torsion ◽  
Md Simulations ◽  
Line Profile Analysis ◽  
Misfit Dislocations ◽  
X Ray ◽  
Average Grain Size

Abstract Nanocrystalline materials reveal excellent mechanical properties but the mechanism by which they deform is still debated. X-ray line broadening indicates the presence of large heterogeneous strains even when the average grain size is smaller than 10 nm. Although the primary sources of heterogeneous strains are dislocations, their direct observation in nanocrystalline materials is challenging. In order to identify the source of heterogeneous strains in nanocrystalline materials, we prepared Pd-10 pct Au specimens by inert gas condensation and applied high-pressure torsion (HPT) up to γ ≅ 21. High-resolution transmission electron microscopy (HRTEM) and molecular dynamic (MD) simulations are used to investigate the dislocation structure in the grain interiors and in the grain boundary (GB) regions in the as-prepared and HPT-deformed specimens. Our results show that most of the GBs contain lattice dislocations with high densities. The average dislocation densities determined by HRTEM and MD simulation are in good correlation with the values provided by X-ray line profile analysis. Strain distribution determined by MD simulation is shown to follow the Krivoglaz–Wilkens strain function of dislocations. Experiments, MD simulations, and theoretical analysis all prove that the sources of strain broadening in X-ray diffraction of nanocrystalline materials are lattice dislocations in the GB region. The results are discussed in terms of misfit dislocations emanating in the GB regions reducing elastic strain compatibility. The results provide fundamental new insight for understanding the role of GBs in plastic deformation in both nanograin and coarse grain materials of any grain size.

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.

First Principles Molecular Simulations of Soda-Lime-Silica Glass

2008 ◽  
Vol 39-40 ◽  
pp. 85-88 ◽  
Author(s):  
Jan Macháček ◽  
Soňa Charvátová ◽  
Ondrej Gedeon ◽  
Marek Liška
Keyword(s):  
First Principles ◽  
Md Simulation ◽  
Soda Lime ◽  
Md Simulations ◽  
Distribution Functions ◽  
Basis Set ◽  
Ab Initio Molecular Dynamics ◽  
Radial Distribution Functions ◽  
Coordination Numbers ◽  
Soda Lime Silica Glass

This work aims to explore possible applications of the ab initio molecular dynamics (MD) in modeling of the soda-lime-silica (NCS) glass and melt doped with admixtures. Preparation of the basic glass (15.8 wt.% Na2O, 10.5 wt.% CaO, and 73.7 wt.% SiO2) by the MD simulation from scratch is described. The structure analysis of the NCS glass is presented in the form of total and partial radial distribution functions (RDF), coordination numbers, and fractions of Qn units. The reasonable first neighbor distances were obtained, even if a rather small basis set of electronic wavefunctions and softer pseudopotentials for atomic core regions were applied. All major discrepancies in the first neighbor distances can be easily explained, and the results can be improved if needed. The Qn distribution shows higher disproportionation of Q3 than NMR and Raman experimental data, however, it is lower than previous classical MD simulations.

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.

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