A Molecular Dynamics Study of the Effect of Incident Angle on Dissociation Probability of H2/D2 - Pt(111) System

2019 ◽  
Vol 25 (23) ◽  
pp. 59-68
Author(s):  
Tetsuya Koido ◽  
Daigo Ito ◽  
Takashi Tokumasu ◽  
Kou Tomarikawa ◽  
Shigeru Yonemura
Keyword(s):  
Molecular Dynamics ◽  
Incident Angle ◽  
Dissociation Probability

Sputtering of Graphite by Hydrogen Isotopes in the Fusion Environment: A Molecular Dynamics Simulation Study

2018 ◽  
Vol 4 (4) ◽  
Author(s):  
Qiang Zhao ◽  
Yang Li ◽  
Zheng Zhang ◽  
Xiaoping Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Incident Energy ◽  
Large Scale ◽  
Incident Angle ◽  
Hydrogen Isotopes ◽  
Dynamics Simulation ◽  
Calculation Results ◽  
Sputtering Yield ◽  
Increasing Temperature ◽  
Sputtering Yields

The sputtering of graphite due to the bombardment of hydrogen isotopes is crucial to successfully using graphite in the fusion environment. In this work, we use molecular dynamics to simulate the sputtering using the large-scale atomic/molecular massively parallel simulator (lammps). The calculation results show that the peak values of the sputtering yield are between 25 eV and 50 eV. When the incident energy is greater than the energy corresponding to the peak value, a lower carbon sputtering yield is obtained. The temperature that is most likely to sputter is approximately 800 K for hydrogen, deuterium, and tritium. Below the 800 K, the sputtering yields increase with temperature. By contrast, above the 800 K, the yields decrease with increasing temperature. Under the same temperature and incident energy, the sputtering rate of tritium is greater than that of deuterium, which in turn is greater than that of hydrogen. When the incident energy is 25 eV, the sputtering yield at 300 K increases below an incident angle at 30 deg and remains steady after that.

scholarly journals A Molecular Dynamics Study of the Effect of the Incidence Angle on the Dissociation Probability of H2 on Pt(111)

2011 ◽  
Vol 6 (3) ◽  
pp. 333-343
Author(s):  
Tetsuya KOIDO ◽  
Daigo ITO ◽  
Takashi TOKUMASU ◽  
Ko TOMARIKAWA ◽  
Shigeru YONEMURA
Keyword(s):  
Molecular Dynamics ◽  
Incidence Angle ◽  
Dissociation Probability

scholarly journals Biphasic Force-Regulated Phosphorylation Site Exposure and Unligation of ERM Bound with PSGL-1: A Novel Insight into PSGL-1 Signaling via Steered Molecular Dynamics Simulations

2020 ◽  
Vol 21 (19) ◽  
pp. 7064
Author(s):  
Jingjing Feng ◽  
Yan Zhang ◽  
Quhuan Li ◽  
Ying Fang ◽  
Jianhua Wu
Keyword(s):  
Molecular Dynamics ◽  
Tensile Force ◽  
Complex Structure ◽  
Phosphorylation Site ◽  
Steered Molecular Dynamics ◽  
Structural Basis ◽  
Quasi Equilibrium ◽  
Dissociation Probability ◽  
Transition Mechanism ◽  
Insight Into

The PSGL-1-actin cytoskeleton linker proteins ezrin/radixin/moesin (ERM), an adaptor between P-selectin glycoprotein ligand-1 (PSGL-1) and spleen tyrosine kinase (Syk), is a key player in PSGL-1 signal, which mediates the adhesion and recruitment of leukocytes to the activated endothelial cells in flow. Binding of PSGL-1 to ERM initials intracellular signaling through inducing phosphorylation of Syk, but effects of tensile force on unligation and phosphorylation site exposure of ERM bound with PSGL-1 remains unclear. To answer this question, we performed a series of so-called “ramp-clamp” steered molecular dynamics (SMD) simulations on the radixin protein FERM domain of ERM bound with intracellular juxtamembrane PSGL-1 peptide. The results showed that, the rupture force of complex pulled with constant velocity was over 250 pN, which prevented the complex from breaking in front of pull-induced exposure of phosphorylation site on immunoreceptor tyrosine activation motif (ITAM)-like motif of ERM; the stretched complex structure under constant tensile forces <100 pN maintained on a stable quasi-equilibrium state, showing a high mechano-stabilization of the clamped complex; and, in consistent with the force-induced allostery at clamped stage, increasing tensile force (<50 pN) would decrease the complex dissociation probability but facilitate the phosphorylation site exposure, suggesting a force-enhanced biophysical connectivity of PSGL-1 signaling. These force-enhanced characters in both phosphorylation and unligation of ERM bound with PSGL-1 should be mediated by a catch-slip bond transition mechanism, in which four residue interactions on binding site were involved. This study might provide a novel insight into the transmembrane PSGL-1 signal, its biophysical connectivity and molecular structural basis for cellular immune responses in mechano-microenvironment, and showed a rational SMD-based computer strategy for predicting structure-function relation of protein under loads.

scholarly journals MD Simulations on a Well-Built Docking Model Reveal Fine Mechanical Stability and Force-Dependent Dissociation of Mac-1/GPIbα Complex

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaoyan Jiang ◽  
Xiaoxi Sun ◽  
Jiangguo Lin ◽  
Yingchen Ling ◽  
Ying Fang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Basis ◽  
Mechanical Stability ◽  
Inflammatory Responses ◽  
Bond Number ◽  
Complex Model ◽  
Platelet Glycoprotein ◽  
Regulation Mechanism ◽  
Dissociation Probability ◽  
Docking Model

Interaction of leukocyte integrin macrophage-1 antigen (Mac-1) to platelet glycoprotein Ibα (GPIbα) is critical for platelet–leukocyte crosstalk in hemostasis and inflammatory responses to vessel injuries under hemodynamic environments. The mechano-regulation and its molecular basis for binding of Mac-1 to GPIbα remain unclear, mainly coming from the lack of crystal structure of the Mac-1/GPIbα complex. We herein built a Mac-1/GPIbα complex model through a novel computer strategy, which included a flexible molecular docking and system equilibrium followed by a “force-ramp + snapback” molecular dynamics (MD) simulation. With this model, a series of “ramp-clamp” steered molecular dynamics (SMD) simulations were performed to examine the GPIbα–Mac-1 interaction under various loads. The results demonstrated that the complex was mechano-stable for both the high rupture force (&gt;250 pN) at a pulling velocity of 3 Å/ns and the conformational conservation under various constant tensile forces (≤75 pN); a catch-slip bond transition was predicted through the dissociation probability, examined with single molecular AFM measurements, reflected by the interaction energy and the interface H-bond number, and related to the force-induced allostery of the complex; besides the mutation-identified residues D222 and R218, the residues were also dominant in the binding of Mac-1 to GPIbα. This study recommended a valid computer strategy for building a likely wild-type docking model of a complex, provided a novel insight into the mechanical regulation mechanism and its molecular basis for the interaction of Mac-1 with GPIbα, and would be helpful for understanding the platelet–leukocyte interaction in hemostasis and inflammatory responses under mechano-microenvironments.

scholarly journals A Study on Sputtering of Copper Seed Layer for Interconnect Metallization via Molecular Dynamics Simulation

2021 ◽  
Vol 11 (20) ◽  
pp. 9702
Author(s):  
Cheng-Hsuan Ho ◽  
Cha’o-Kuang Chen ◽  
Chieh-Li Chen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Substrate Temperature ◽  
Deposition Rate ◽  
Process Parameters ◽  
Seed Layer ◽  
Incident Energy ◽  
Incident Angle ◽  
Dynamics Simulation ◽  
Copper Seed Layer

Interconnects are significant elements in integrated circuits (ICs), as they connect individual components of the circuit into a functioning whole. To form a void-free interconnect, a thin and uniform copper seed layer must be deposited as a basis for electroplating. In this paper, process parameters of sputtering including incident energy, incident angle, substrate temperature, and deposition rate were studied to form a uniform copper seed layer. Different liner/barrier materials and properties including crystal planes were also studied to enhance the quality of the copper seed layer. The study was carried out by molecular dynamics simulation. It revealed that increasing the incident energy and substrate temperature during the sputtering process increases their diffusivity but results in poorer uniformity and larger alloy percentage. By decreasing the deposition rate, the Ostwald ripening effect becomes dominant and increases the uniformity. An adequate incident angle could increase necking and uniformity. Among the sputtering process parameters and material properties discussed in this study, surface diffusion barrier energy of different crystal planes is the most decisive factor, which leads to good uniformity.

A Molecular Dynamics Study for Dissociation of H2 Molecule on Pt(111) Surface

2012 ◽  
Vol 452-453 ◽  
pp. 1144-1148
Author(s):  
Takashi Tokumasu
Keyword(s):  
Molecular Dynamics ◽  
Atomic Motion ◽  
Embedded Atom Method ◽  
Dissociation Probability ◽  
Embedded Atom ◽  
Gas Molecule ◽  
H2 Molecule

The dissociation phenomena of H2 molecule on Pt(111) surface was simulated by Molecular Dynamics (MD) method and the effect of motion of the gas molecule or surface atoms on dissociation phenomena was analyzed in detail. The Embedded Atom Method (EAM) was used to model the interaction between an H2 molecule and Pt(111) surface. Using this potential, simulations of an H2 molecule impinging on a Pt(111) surface were performed and the characteristics of the collision were observed. Using MD data the dynamic dissociation probability were obtained and compared with the static dissociation probability to analyze the effect of atomic motion on dissociation phenomena.

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