Downhill kinetics of biomolecular interface binding: Globally connected scenario

We study the kinetics of the biomolecular binding process at the interface using energy landscape theory. The global kinetic connectivity case is considered for a downhill funneled energy landscape. By solving the kinetic master equation, the kinetic time for binding is obtained and shown to have a U-shape curve-dependence on the temperature. The kinetic minimum of the binding time monotonically decreases when the ratio of the underlying energy gap between native state and average non-native states versus the roughness or the fluctuations of the landscape increases. At intermediate temperatures,fluctuations measured by the higher moments of the binding time lead to non-Poissonian, non-exponential kinetics. At both high and very low temperatures, the kinetics is nearly Poissonian and exponential.

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Molecular Dynamics Simulation of Microstructure of Nanocrystalline Copper

The microstructure of computer generated nanocrystalline coppers is simulated by using molecular dynamics with the Finnis-Sinclair potential, analysed by means of radial distribution functions, coordination number, atomic energy and local crystalline order. The influence of the grain size on the nanocrystalline structure is studied. The results reveal that as the grain size is reduced, the grain boundary shows no significant structural difference, but the grain interior becomes more disordered, and their structural difference diminishes gradually; however, the density and the atomic average energy of the grain boundary present different tendencies from those of the grain interior.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Forced extension of P-selectin construct using steered molecular dynamics

P-selectin, a 70-nm-long cellular adhesive molecule, possesses elastic and extensible properties when neutrophils roll over the activated endotheliam of blood vessel in inflammatory reaction. Transient formation and dissociation of P-selectin/ligand bond on applied force of blood flow induces the extension of P-selectin and relevant ligands. Steered molecular dynamics simulations were performed to stretch a single P-selectin construct consisting of a lectin (Lec) domain and an epithelial growth factor (EGF)-like domain, where P-selectin construct was forced to extend in water with pulling velocities of 0.005-0.05 nm/ps and with constant forces of 1000-2500 pN respectively. Resulting force-extension profiles exhibited a dual-peak pattern on various velocities, while both plateaus and shoulders appeared in the extension-time profiles on various forces. The force or extension profiles along stretching pathways were correlated to the conformational changes, suggesting that the structural collapses of P-selectin Lec/EGF domains were mainly attributed to the burst of hydrogen bonds within the major beta sheet of EGF domain and the disruptions of two hydrophobic cores of Lee domain. This work furthers the understanding of forced dissociation of P-selectin/ligand bond.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Structural and optical properties of Al1-xInxN epilayers on GaN template grown by metalorganic chemical vapor deposition

This paper reports that Al1-xInxN epilayers were grown on GaN template by metalorganic chemical vapor deposition with an In content of 7%-20%. X-ray diffraction results indicate that all these Al1-xInxN epilayers have a relatively low density of threading dislocations. Rutherford backscattering/channeling measurements provide the exact compositional information and show that a gradual variation in composition of the Al1-xInxN epilayer happens along the growth direction. The experimental results of optical reflection clearly show the bandgap energies of Al1-xInxN epilayers. A bowing parameter of 6.5 eV is obtained from the compositional dependence of the energy gap. The cathodoluminescence peak energy of the Al1-xInxN epilayer is much lower than its bandgap, indicating a relatively large Stokes shift in the Al1-xInxN sample.

Fine structural splitting and exciton spin relaxation in single InAs quantum dots

We have studied the exciton spin dynamics in single InAs quantum dots (QDs) with different exciton fine structural splitting (FSS) by transient luminescence measurements. We have established the correlation between exciton spin relaxation rate and the energy splitting of the FSS when FSS is nonzero and found that the spin relaxation rate in QD increases with a slope of 8.8x10(-4) ns(-1) mu eV(-1). Theoretical analyses based on the phonon-assisted relaxations via the deformation potential give a reasonable interpretation of the experimental results.

Structural and optical properties of InAlGaN films grown directly on low-temperature buffer layer with (0001)sapphire substrate

Quaternary InAlGaN film has been grown directly on top of low-temperature-deposited GaN buffer layer by low-pressure metalorganic vapor phase epitaxy. High-resolution X-ray diffraction and photoluminescence (PL) results show that the film has good crystal quality and optical property. Temperature-dependent PL and time-resolved PL (TRPL) have been employed to study the carriers recombination dynamics in the film. The TRPL signals can be well fitted as a stretched exponential function exp[-(t/tau)(beta)] from 14 to 250 K, indicating that the emission is attributed to the radiative recombination of excitons localized in disorder quantum nanostructures such as quantum disks originating from indium (In) clusters or In composition fluctuation. The cross-sectional high-resolution electron microscopy measurement further proves that there exist the disorder quantum nanostructures in the quaternary. By investigating the dependence of the exponential parameter beta on the temperature, it is shown that the multiple trapping-detrapping mechanism dominates the diffusion among the localized states. The localized states are considered to have two-dimensional density of states (DOS) at 250 K, since radiative recombination lifetime tau(r) increases linearly with increasing temperature. (C) 2002 Elsevier Science B.V. All rights reserved.

Effects of multistage coupling and disk flexibility on mistuned bladed disk dynamics

The effects ofdisk flexibility and multistage coupling on the dynamics of bladed disks with and without blade mistuning are investigated. Both free and forced responses are examined using finite element representations of example single and two-stage rotor models. The reported work demonstrates the importance of proper treatment of interstage (stage-to-stage) boundaries in order to yield adequate capture of disk-blade modal interaction in eigenfrequency veering regions. The modified disk-blade modal interactions resulting from interstage-coupling-induced changes in disk flexibility are found to have a significant impact on (a) tuned responses due to excitations passing through eigenfrequency veering regions, and (b) a design's sensitivity to blade mistuning. Hence, the findings in this paper suggest that multistage analyses may be required when excitations are expected to fall in or near eigenfrequency veering regions or when the sensitivity to blade mistuning is to be accounted for Conversely, the observed sensitivity to disk flexibility also indicates that the severity of unfavorable structural interblade coupling may be reduced significantly by redesigning the disk(s) and stage-to-stage connectivity. The relatively drastic effects of such modifications illustrated in this work indicate that the design modifications required to alleviate veering-related response problems may be less comprehensive than what might have been expected.

Dynamics of formation of defects in annealed InP

Dynamics of formation of defects in the annealed nominally undoped semi-insulating InP obtained by high pressure, high temperature annealing of high purity materials is proposed. Incorporated hydrogen passivates vacancy at indium site from annihilation forming fully hydrogenated indium vacancy which dissociates leaving large lattice relaxation behind, deep donors, mainly larger complexes involving phosphorus at indium site and isolated hydrogen defects are created in nominally undoped InP after annealing. Also created are acceptor levels such as vacancy at indium site. Carrier charge compensation mechanism in nominally undoped InP upon annealing at high temperature is given. Microscopic models of hydrogen related defects are given. Structural, electronic and vibrational properties of LVMs related to hydrogen as well as their temperature effect are discussed.

Pressure Effects on the Structural, Electronic, and Optical Properties of Si-n@SWCNTs

Well-ordered single, double/four parallel, three/four-strands helical chains, and five-strand helical chain with a single atom chain at the center of Si nanowires (NWs) inside single-walled carbon nanotubes (Si-n@SWCNTs) are obtained by means of molecular dynamics. On the basis of these optimized structures, the structural evolution of Si-n@SWCNTs subjected to axial stress at low temperature is also investigated. Interestingly, the double parallel chains depart at the center and transform into two perpendicular parts, the helical shell transformed into chain, and the strand number of Si NWs increases during the stress load. Through analyzis of pair correlation function (PCF), the density of states (DOS), and the z-axis polarized absorption spectra of Si-n@SWCNTs, we find that the behavior of Si-n@SWCNTs under stress strongly depends on SWCNTs' symmetry, diameter, as well as the shape of Nws, which provide valuable information for potential application in high pressure cases such as seabed cable.