Molecular dynamics study of the effects of translational energy and incident angle on dissociation probability of hydrogen/deuterium molecules on Pt(111)

2011 ◽  
Vol 110 (2) ◽  
pp. 024301 ◽  
Author(s):  
Tetsuya Koido ◽  
Ko Tomarikawa ◽  
Shigeru Yonemura ◽  
Takashi Tokumasu
Keyword(s):  
Molecular Dynamics ◽  
Incident Angle ◽  
Translational Energy ◽  
Dissociation Probability ◽  
Hydrogen Deuterium

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

Scattering of Low-Energy (5-12 eV) C2D4•+ Ions from Room-Temperature Carbon Surfaces

2008 ◽  
Vol 73 (6-7) ◽  
pp. 755-770 ◽  
Author(s):  
Andriy Pysanenko ◽  
Ján Žabka ◽  
Zdeněk Herman
Keyword(s):  
Survival Probability ◽  
Room Temperature ◽  
Incident Angle ◽  
Pyrolytic Graphite ◽  
Carbon Surface ◽  
Translational Energy ◽  
Energy Distributions ◽  
Surface Mass ◽  
Fragment Ions ◽  
Product Ions

The scattering of the hydrocarbon radical cation C2D4•+ from room-temperature carbon (highly oriented pyrolytic graphite, HOPG) surface was investigated at low incident energies of 6-12 eV. Mass spectra, angular and translational energy distributions of product ions were measured. From these data, information on processes at surfaces, absolute ion survival probability, and kinematics of the collision was obtained. The projectile ion showed both inelastic, dissociative and reactive scattering, namely the occurrence of H-atom transfer reaction with hydrocarbons present on the room-temperature carbon surface. The absolute survival probability of the ions for the incident angle of 30° (with respect to the surface) decreased from about 1.0% (16 eV) towards zero at incident energies below 10 eV. Estimation of the effective surface mass involved in the collision process led to m(S)eff of about 57 a.m.u. for inelastic non-dissociative collisions of C2D4•+ and of about 115 a.m.u. for fragment ions (C2D3+, C2D2•+) and ions formed in reactive surface collisions (C2D4H+, C2D2H+, contributions to C2D3+ and C2D2•+). This suggested a rather complex interaction between the projectile ion and the hydrocarbon-covered surface during the collision.

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.

Molecular Dynamics Simulation of the Sputtering of Graphite due to Bombardment With Deuterium and Tritium in Fusion Environment

2017 ◽  
Author(s):  
Qiang Zhao ◽  
Yang Li ◽  
Zheng Zhang ◽  
Xiaoping Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Temperature Increase ◽  
Incident Energy ◽  
Dynamics Simulation ◽  
Critical Issues ◽  
Calculation Results ◽  
Hydrogen Deuterium ◽  
Sputtering Yield ◽  
Dynamics Method ◽  
Lower Carbon

The sputtering of graphite due to the bombardment of hydrogen isotopes is one of the critical issues in successfully using graphite in the fusion environment. In this work, we use molecular dynamics method to simulate the sputtering by using the LAMMPS. Calculation results show that the peak values of the sputtering yield are located between 25 eV to 50 eV. After the energy of 25 eV, the higher incident energy cause the lower carbon sputtering yield. The temperature which is most likely to sputter is about 800 K for hydrogen, deuterium and tritium. Before the 800 K, the sputtering rates increase when the temperature increase. After the 800 K, they decrease with the temperature increase. Under the same temperature and energy, the sputtering rate of tritium is bigger than that of deuterium, the sputtering rate of deuterium is bigger than that of hydrogen.

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 Conservation of the conformational dynamics and ligand binding within M49 enzyme family

RSC Advances ◽  
2018 ◽  
Vol 8 (24) ◽  
pp. 13310-13322 ◽  
Author(s):  
Saša Kazazić ◽  
Zrinka Karačić ◽  
Igor Sabljić ◽  
Dejan Agić ◽  
Marko Tomin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Ligand Binding ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Dipeptidyl Peptidase ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Enzyme Family ◽  
Hydrogen Deuterium

The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family).

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