Molecular Dynamics Modeling of Buckling Behavior of Hydrogenated Graphyne

NANO ◽  
2015 ◽  
Vol 10 (07) ◽  
pp. 1550105 ◽  
Author(s):  
A. Montazeri ◽  
S. Ebrahimi ◽  
A. Rajabpour ◽  
H. Rafii-Tabar
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Adsorption ◽  
Graphene Nanoribbons ◽  
Dynamics Simulation ◽  
Dynamics Modeling ◽  
Stability Behavior ◽  
Molecular Dynamics Modeling ◽  
Buckling Behavior ◽  
Out Of Plane ◽  
The Stability

Molecular dynamics simulation is employed to explore the influence of hydrogen adsorption on the stability behavior of graphyne (GY) as a new allotrope of carbon. The strain for the onset of buckling is determined for pristine GY and the results are compared with those for perfect graphene nanoribbons under identical conditions. The results reveal that due to the presence of triple C–C bonds in the GY structure, which are harder to rotate and bend in compression compared to single bonds, the new allotrope is stiffer than graphene during buckling phenomenon. In addition, the effect of hydrogen adsorption on the stability behavior of GY is examined with different H coverage in the range 0–50%. It is concluded that this adsorption promotes a rapid buckling which is attributed to the conversion of the stiff in-plane carbon bonding in the GY structure to the out-of-plane bonding which is weaker and easier to bend in compression. Finally, a critical value of adsorption is found above in which such a trend is not observed.

scholarly journals A Molecular Dynamics Study on Rotational Nanofluid and Its Application to Desalination

Membranes ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 117
Author(s):  
Qingsong Tu ◽  
Wice Ibrahimi ◽  
Steven Ren ◽  
James Wu ◽  
Shaofan Li
Keyword(s):  
Molecular Dynamics ◽  
Angular Velocity ◽  
Large Scale ◽  
Salt Water ◽  
Dynamics Simulation ◽  
Dynamics Modeling ◽  
Molecular Dynamics Modeling ◽  
Desalination Technology ◽  
Nanofluidic Device ◽  
Fluid Hydrodynamics

In this work, we systematically study a rotational nanofluidic device for reverse osmosis (RO) desalination by using large scale molecular dynamics modeling and simulation. Moreover, we have compared Molecular Dynamics simulation with fluid mechanics modeling. We have found that the pressure generated by the centrifugal motion of nanofluids can counterbalance the osmosis pressure developed from the concentration gradient, and hence provide a driving force to filtrate fresh water from salt water. Molecular Dynamics modeling of two different types of designs are performed and compared. Results indicate that this novel nanofluidic device is not only able to alleviate the fouling problem significantly, but it is also capable of maintaining high membrane permeability and energy efficiency. The angular velocity of the nanofluids within the device is investigated, and the critical angular velocity needed for the fluids to overcome the osmotic pressure is derived. Meanwhile, a maximal angular velocity value is also identified to avoid Taylor-Couette instability. The MD simulation results agree well with continuum modeling results obtained from fluid hydrodynamics theory, which provides a theoretical foundation for scaling up the proposed rotational osmosis device. Successful fabrication of such rotational RO membrane centrifuge may potentially revolutionize the membrane desalination technology by providing a fundamental solution to the water resource problem.

STUDY ON NANOMETRIC CUTTING MECHANISM AND BURR FORMATION USING MOLECULAR DYNAMICS SIMULATION

2006 ◽  
Vol 05 (04n05) ◽  
pp. 547-551 ◽  
Author(s):  
H. WU ◽  
F. Z. FANG ◽  
Q. X. PEI
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Burr Formation ◽  
Work Piece ◽  
Dynamics Modeling ◽  
Modeling And Analysis ◽  
Nanometric Cutting ◽  
Molecular Dynamics Modeling ◽  
Elastic Rebound

Since no physical approach can be employed to study the mechanism in micro cutting, the molecular dynamics simulation is becoming more and more important. In this study, the results of molecular dynamics modeling and analysis on the nanometric machining on silicon surface are presented. According to the simulation, some phenomena in the nanometric cutting process are found. First, surface elastic rebound happens on the cut surface after cutter moving away. The value of the surface elastic rebound is calculated in the simulation. Second, the atoms near the corner of work piece swirl up following the cutter moving direction at the initial stage of removing atoms from the work piece. Third, the simulation results show that no matter how small material removal is, the burr is always formed at the edge of work piece.

scholarly journals Molecular dynamics modeling of the Vibrio cholera Na+-translocating NADH:quinone oxidoreductase NqrB–NqrD subunit interface

2021 ◽  
Author(s):  
Alexander Dibrov ◽  
Muntahi Mourin ◽  
Pavel Dibrov ◽  
Grant N. Pierce
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Modeling ◽  
Nadh:Quinone Oxidoreductase ◽  
Molecular Dynamics Modeling ◽  
Subunit Interface ◽  
Manual Methods ◽  
The Stability ◽  
Dynamics Simulations

AbstractThe Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) is the major Na+ pump in aerobic pathogens such as Vibrio cholerae. The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na+-NQR. While the mechanisms underlying Na+-NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na+-NQR. An in silico model of the NqrB–D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published V. cholerae Na+-NQR crystal structure. Results from one 1 µs, three 150 ns and two 50 ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1 µs. However, the NqrB–D interface underwent a non-physiological transition after 350 ns.

Atomistic study of the mechanical stability of multi-layered graphene nanobridges

2011 ◽  
Vol 1297 ◽  
Author(s):  
T. Nakajima ◽  
K. Shintani
Keyword(s):  
Mechanical Stability ◽  
Graphene Nanoribbons ◽  
Electronic Devices ◽  
Dynamics Simulation ◽  
Surface Areas ◽  
Out Of Plane ◽  
The Stability ◽  
Atomistic Study ◽  
The Relationship ◽  
Plane Deformations

ABSTRACTThe stability of elongated single- and multi-layered graphene nanoribbons (GNRs) are investigated by molecular-dynamics simulation. In order that GNRs are to be modeled as nanobridges connecting two terminals of electronic devices, the short edges of the GNRs are constrained. The distances between the two constrained edges are gradually increased, and the GNRs are uniaxially strained. The energies and out-of-plane deformations of such uniaxially strained GNRs are examined. The energies of multi-layered GNRs will be lower than those of isolated GNRs because the surface areas of multi-layered GNRs are smaller than the total area of the isolated GNRs. Understanding the relationship between the out-of-plane deformations and strain will lead to the control of the ripple structures of GNRs.

scholarly journals Molecular Dynamics Simulation of Fracture Strength and Morphology of Defective Graphene

2013 ◽  
Vol 25 ◽  
pp. 181-187
Author(s):  
Ming Chao Wang ◽  
Cheng Yan ◽  
Dilini Galpaya ◽  
Zheng Bo Lai ◽  
Lin Ma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fracture Strength ◽  
Graphene Nanoribbons ◽  
Minimum Energy ◽  
Dynamics Simulation ◽  
Structural Defects ◽  
Minimization Principle ◽  
Edge Reconstruction ◽  
Out Of Plane ◽  
Dynamics Simulations

Different types of defects can be introduced into graphene during material synthesis, and significantly influence the properties of graphene. In this work, we investigated the effects of structural defects, edge functionalisation and reconstruction on the fracture strength and morphology of graphene by molecular dynamics simulations. The minimum energy path analysis was conducted to investigate the formation of Stone-Wales defects. We also employed out-of-plane perturbation and energy minimization principle to study the possible morphology of graphene nanoribbons with edge-termination. Our numerical results show that the fracture strength of graphene is dependent on defects and environmental temperature. However, pre-existing defects may be healed, resulting in strength recovery. Edge functionalization can induce compressive stress and ripples in the edge areas of graphene nanoribbons. On the other hand, edge reconstruction contributed to the tensile stress and curved shape in the graphene nanoribbons.

scholarly journals Molecular Dynamics Simulation of Fracture Strength and Morphology of Defective Graphene

2013 ◽  
Vol 23 ◽  
pp. 43-49 ◽  
Author(s):  
Ming Chao Wang ◽  
Cheng Yan ◽  
Dilini Galpaya ◽  
Zheng Bo Lai ◽  
Lin Ma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fracture Strength ◽  
Graphene Nanoribbons ◽  
Minimum Energy ◽  
Dynamics Simulation ◽  
Structural Defects ◽  
Minimization Principle ◽  
Edge Reconstruction ◽  
Out Of Plane ◽  
Dynamics Simulations

Different types of defects can be introduced into graphene during material synthesis, and significantly influence the properties of graphene. In this work, we investigated the effects of structural defects, edge functionalisation and reconstruction on the fracture strength and morphology of graphene by molecular dynamics simulations. The minimum energy path analysis was conducted to investigate the formation of Stone-Wales defects. We also employed out-of-plane perturbation and energy minimization principle to study the possible morphology of graphene nanoribbons with edge-termination. Our numerical results show that the fracture strength of graphene is dependent on defects and environmental temperature. However, pre-existing defects may be healed, resulting in strength recovery. Edge functionalization can induce compressive stress and ripples in the edge areas of graphene nanoribbons. On the other hand, edge reconstruction contributed to the tensile stress and curved shape in the graphene nanoribbons.

scholarly journals Molecular Dynamics Modeling of the Mechanical Behavior of Metallic Multilayers

1993 ◽  
Vol 308 ◽  
Author(s):  
James Belak ◽  
David B. Boercker
Keyword(s):  
Molecular Dynamics ◽  
Poisson Ratio ◽  
Uniaxial Stress ◽  
Interlayer Spacing ◽  
Metallic Multilayers ◽  
Dynamics Modeling ◽  
Equal Concentration ◽  
Molecular Dynamics Modeling ◽  
Out Of Plane ◽  
Dynamics Simulations

ABSTRACTConstant-stress molecular dynamics simulations are used to study the mechanical properties of equal concentration Cu-Ni (111) metallic multilayers of repeat lengths 0.4–5.0 nm. Uniaxial stress is applied along the close-packed [110] and perpendicular to the close-packed [112] directions within the (111) plane. The observed elastic modulus does not display a super-modulus effect as observed in experimental bulge tests for the biaxial modulus. However, both the average interlayer spacing and the out-of-plane Poisson ratio display anomalous effects for multilayer repeat lengths below about two nanometers.

scholarly journals Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

2020 ◽  
Vol 7 ◽  
Author(s):  
Alex Bunker ◽  
Tomasz Róg
Keyword(s):  
Drug Delivery ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Drug Loading ◽  
Pharmaceutical Research ◽  
Design Tool ◽  
Dynamics Simulation ◽  
Strong Impact ◽  
Dynamics Modeling ◽  
Molecular Dynamics Modeling

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

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