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.

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

scholarly journals Energy transfer and gas diffusion at gas-liquid interfaces

2015 ◽  
Author(s):  
◽  
Daniel J. Shaughnessy
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Energy Transfer ◽  
Dipole Moment ◽  
Surface Temperature ◽  
Vapor Phase ◽  
Incident Energy ◽  
Incidence Angle ◽  
Surface Scattering ◽  
Increasing Temperature

The interactions of gasses and liquids play an important role in many systems in chemistry. Gas-liquid surface scattering techniques are a useful tool towards the investigation of energy transfer resulting from gas-liquid collisions. We use molecular dynamics to simulate surface scattering in order to investigate the effects of incident energy, incidence angle, and surface temperature on energy transfer of a CO2 molecule scattering from a liquid indium surface modeled as a simple Lennard-Jones liquid. We focus our investigation on the two-channel theory of gas-liquid scattering with a primary focus on the trapping-desorption scattering channel. We use a novel technique to investigate the average trajectory of the scattering gas species to determine the effects of energy transfer on this channel. We find species scattering via this channel are unaffected by incident energy and incidence angle in agreement with experimental trends. We find our gas species scattered by the trapping desorption channel emerge with four degrees of freedom thermalized to the surface temperature, with substantial variance in the translational degree of freedom in the surface normal direction which we attribute to both the enthalpy of desorption and interactions with vapor-phase indium atoms. We observe a substantial increase in interactions with vapor-phase indium with increasing temperature. Our second simulation uses molecular dynamics to examine the diffusion of various gas species through a room temperature ionic liquid at standard pressure conditions. We were able to replicate the bulk properties of the bmim PF6 ionic liquid with reasonable accuracy compared with other experimental and theoretical work. We varied the gas species mass, the gas species dipole moment, and the ionic liquid temperature to examine the effects of each variable on gas diffusivity. We find a general trend of increased diffusivity with increasing temperature; however, we are unable to discern a definite trend relating to gas species mass or dipole moment. We observe significant short-time trapping effects on our diffusing gas species, particularly at low temperatures, that make examining the diffusivity of our gases problematic.

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.

Electron Channeling Patterns

1977 ◽  
Vol 35 ◽  
pp. 12-13
Author(s):  
David C. Joy
Keyword(s):  
Electron Diffraction ◽  
Incidence Angle ◽  
Photographic Plate ◽  
Diffraction Effect ◽  
Angle Of Incidence ◽  
Bulk Single Crystal ◽  
Time Resolved ◽  
Electron Channeling ◽  
Spatially Resolved ◽  
Large Bulk

Electron channeling patterns (ECP) were first found by Coates (1967) while observing a large bulk, single crystal of silicon in a scanning electron microscope. The geometric pattern visible was shown to be produced as a result of the changes in the angle of incidence, between the beam and the specimen surface normal, which occur when the sample is examined at low magnification (Booker, Shaw, Whelan and Hirsch 1967).A conventional electron diffraction pattern consists of an angularly resolved intensity distribution in space which may be directly viewed on a fluorescent screen or recorded on a photographic plate. An ECP, on the other hand, is produced as the result of changes in the signal collected by a suitable electron detector as the incidence angle is varied. If an integrating detector is used, or if the beam traverses the surface at a fixed angle, then no channeling contrast will be observed. The ECP is thus a time resolved electron diffraction effect. It can therefore be related to spatially resolved diffraction phenomena by an application of the concepts of reciprocity (Cowley 1969).

Atomic force microscopy (AFM) of the topography of silicon surfaces exposed to ion beams

1992 ◽  
Vol 50 (2) ◽  
pp. 1132-1133
Author(s):  
Mark Denker ◽  
Jennifer Wall ◽  
Mark Ray ◽  
Richard Linton
Keyword(s):  
Secondary Ion Mass Spectrometry ◽  
Incidence Angle ◽  
Ion Beam ◽  
Depth Profiling ◽  
Depth Resolution ◽  
Ion Beams ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Trace Impurities ◽  
Energy Dose

Reactive ion beams such as O2+ and Cs+ are used in Secondary Ion Mass Spectrometry (SIMS) to analyze solids for trace impurities. Primary beam properties such as energy, dose, and incidence angle can be systematically varied to optimize depth resolution versus sensitivity tradeoffs for a given SIMS depth profiling application. However, it is generally observed that the sputtering process causes surface roughening, typically represented by nanometer-sized features such as cones, pits, pyramids, and ripples. A roughened surface will degrade the depth resolution of the SIMS data. The purpose of this study is to examine the relationship of the roughness of the surface to the primary ion beam energy, dose, and incidence angle. AFM offers the ability to quantitatively probe this surface roughness. For the initial investigations, the sample chosen was <100> silicon, and the ion beam was O2+.Work to date by other researchers typically employed Scanning Tunneling Microscopy (STM) to probe the surface topography.

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