Molecular Dynamics Simulation of the Bio-Adhesion in Molecular Motors

Molecular dynamics (MD) simulation is employed to study the bio-adhesion in F1 ATP molecular motor. Histidine-peptide is widely used as linkage in micro systems because of its strong binding strength to metals. This paper focuses on the adhesion between a synthetic peptide containing 6xHis-tag (Gly-Gly-Lys-Gly-Gly-Lys-Gly-Gly-His-His-His-His-His-His) and metal substrate, which is used to define the position of the F1 ATP molecular motor on the metal substrate. It is shown that the binding strength between histidine and nickel substrate is the strongest, while that of copper is smaller and that of gold substrate is the smallest. From the result of simulation, we find that the stability of adhesion between histidine and the metal substate result of the ringed structure in histidine.

Diffusive waves in a channel with concentrated lateral inflow

In the current paper an analytical solution for diffusive wave equation with the concentrate-distributed lateral inflow is yielded. Finite-difference numerical method is also employed to validate this model. The backwater effects drawn from lateral inflow on the mainstream are examined finally.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Recent progress in femtosecond holography

The recent advancements of femtosecond (fs) holography are introduced. The experimental requirements and the time resolution are presented. Applications of femtosecond holography to signal processing, and other femtosecond holographic techniques such as femtosecond holographic imaging and microprocessing are detailed. A potential alternative of femtosecond holography is proposed, based on the sectional interference of reference pulse with the time stretched signal pulse. (c) 2005 Elsevier B.V. All rights reserved.

Evolution of InAs/GaAs(001) islands during the two- to three-dimensional growth mode transition in molecular-beam epitaxy

A detailed observation was made using atomic force microscopy on the two- to three-dimensional (2D-3D) growth mode transition in the molecular-beam epitaxy of InAs/GaAs(001). The evolution of the 3D InAs islands during the 2D-3D mode transition was divided into two successive phases. The first phase may be explained in terms of a critical phenomenon of the second-order phase transition.

REDUCTION OF CRYSTALLINE DISORDER IN MOLECULAR-BEAM EPITAXY GAAS ON SI BY MEV ION-IMPLANTATION AND SUBSEQUENT ANNEALING

Molecular beam epitaxy GaAs films on Si, with thicknesses ranging from 0.9-2.0-mu-m, were implanted with Si ions at 1.2-2.6 MeV to doses in the range 10(15)-10(16) cm-2. Subsequent rapid infrared thermal annealing was carried out at 850-degrees-C for 15 s in a flowing N2 atmosphere. Crystalline quality was analyzed by using Rutherfold backscattering/channeling technique and Raman scattering spectrometry. The experimental results show that the recrystallization process greatly depends on the dose and energy of implanted ions. Complete recrystallization with better crystalline quality can be obtained under proper implantation and subsequent annealing. In the improved layer the defect density was much lower than in the as-grown layer, especially near the interface.

IMPLANTATION ENERGY SELECTION IN MOLECULAR-BEAM EPITAXY GAAS FILMS ON SI SUBSTRATES

GaAs films made by molecular beam epitaxy with thicknesses ranging from 0.9 to 1.25-mu-m on Si have been implanted with Si ions at 1.2 MeV to dose of 1 x 10(15)/cm2. A rapid infrared thermal annealing and white light annealing were then used for recrystallization. Crystalline quality was analysed by using backscattering channeling technique with Li ion beam of 4.2 MeV. The experimental results show that energy selection is important for obtaining better and uniform recrystallized GaAs epilayers.

Donor acceptor pair in molecular beam epitaxy grown GaN

We have recently found evidence of new donor acceptor pair (DAP) luminescence in molecular beam epitaxy (MBE) grown films. A variety of nominally undoped samples have been studied by photoluminescence (PL) over a temperature range of 5-300 K. The samples show intensive luminescence al energies of 3.404-3.413 eV varying with different sample at 5 K, as well as a fairly strong (DX)-X-0 line at low temperature. We attribute the Line at 3.404-3.413 eV to DAP recombination which is over 0.1 eV different from the well known DAP caused by ME-doping in GaN. The DAP line shows fine structure. it even predominates in one particular sample. The peak position shifts to higher energy with temperature increasing from 5 up to 70 K, and as the excitation laser intensity increases. The data are consistent with DAP luminescence involving an acceptor level of about 90 meV (presumably carbon) above the valence band edge in GaN. It is much shallower than the acceptor level of 250 meV produced by the p-type dopant Mg which is commonly used at present. (C) 1997 Elsevier Science S.A.