66 resultados para Molecular Dynamic Simulations


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The reduction of CO2 on copper electrodes has attracted great attentions in the last decades, since it provides a sustainable approach for energy restore. During the CO2 reduction process, the electron transfer to COads is experimentally suggested to be the crucial step. In this work, we examine two possible pathways in CO activation, i.e. to generate COHads and CHOads, respectively, by performing the state-of-the-art constrained ab initio molecular dynamics simulations on the charged Cu(100) electrode under aqueous conditions, which is close to the realistic electrochemical condition. The free energy profile in the formation of COHads via the coupled proton and electron transfer is plotted. Furthermore, by Bader charge analyses, a linear relationship between C-O bond distance and the negative charge in CO fragment is unveiled. The formation of CHOads is identified to be a surface catalytic reaction, which requires the adsorption of H atom on the surface first. By comparing these two pathways, we demonstrate that kinetically the formation of COHads is more favored than that of CHOads, while CHOads is thermodynamically more stable. This work reveals that CO activation via COHads intermediate is an important pathway in electrocatalysis, which could provide some insights into CO2 electroreduction over Cu electrodes.

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We study the nonequilibrium dynamics of the linear to zigzag structural phase transition exhibited by an ion chain confined in a trap with periodic boundary conditions. The transition is driven by reducing the transverse confinement at a finite quench rate, which can be accurately controlled. This results in the formation of zigzag domains oriented along different transverse planes. The twists between different domains can be stabilized by the topology of the trap and under laser cooling the system has a chance to relax to a helical chain with nonzero winding number. Molecular dynamics simulations are used to obtain a large sample of possible trajectories for different quench rates. The scaling of the average winding number with different quench rates is compared to the prediction of the Kibble-Zurek theory, and a good quantitative agreement is found.

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Bin/Amphiphysin/Rvs (BAR) domain proteins control the curvature of lipid membranes in endocytosis, trafficking, cell motility, the formation of complex sub-cellular structures, and many other cellular phenomena. They form three-dimensional assemblies, which act as molecular scaffolds to reshape the membrane and alter its mechanical properties. It is unknown, however, how a protein scaffold forms and how BAR domains interact in these assemblies at protein densities relevant for a cell. In this work, we employ various experimental, theoretical and simulation approaches to explore how BAR proteins organize to form a scaffold on a membrane nanotube. By combining quantitative microscopy with analytical modeling, we demonstrate that a highly curving BAR protein endophilin nucleates its scaffolds at the ends of a membrane tube, contrary to a weaker curving protein centaurin, which binds evenly along the tube’s length. Our work implies that the nature of local protein-membrane interactions can affect the specific localization of proteins on membrane-remodeling sites. Furthermore, we show that amphipathic helices are dispensable in forming protein scaffolds. Finally, we explore a possible molecular structure of a BAR-domain scaffold using coarse-grained molecular dynamics simulations. Together with fluorescence microscopy, the simulations show that proteins need only to cover 30–40% of a tube’s surface to form a rigid assembly. Our work provides mechanical and structural insights into the way BAR proteins may sculpt the membrane as a high-order cooperative assembly in important biological processes. 

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A dynamical method for simulating steady-state conduction in atomic and molecular wires is presented which is both computationally and conceptually simple. The method is tested by calculating the current-voltage spectrum of a simple diatomic molecular junction, for which the static Landauer approach produces multiple steady-state solutions. The dynamical method quantitatively reproduces the static results and provides information on the stability of the different solutions. (c) 2006 American Institute of Physics.

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We present results of wavepacket simulations for multiphoton ionization in argon. A single active electron model is applied to estimate the single-electron ionization rates and photoelectron energy distributions for lambda = 390 nm light with intensities up to I = 2 x 10(14) W cm(-2). The multiphoton ionization rates are compared with R-matrix Floquet calculations and found to be in very good agreement. The photoelectron energy distribution is used to study the nature of ionization at the higher intensities. Our results are consistent with recent calculations and experiments which show the imprint of the tunnelling process in the multiphoton regime. For few-cycle intense pulses, we find that the strong modulation of intensity and increased bandwidth leads to dynamic mixing of the 3d and 5s resonances.

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The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signalling pathway a GPCR promotes intracellular signals though ß-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signalling through the G protein and ß-arrestin. Here we report on the dynamics of the ß2 adrenergic receptor bound to the ß-arrestin and G protein biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring the transition within the nanosecond timescale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the ß-arrestin biased agonist, N-cyclopentylbutanepherine we observe a different pattern of motions in helix 7 when compared to simulations with the G protein biased agonist, Salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs. © 2013 American Chemical Society