Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.

Spin-dependent current noises in transport through coupled quantum dots

Current fluctuations can provide additional insight into quantum transport in mesoscopic systems. The present work is carried out for the fluctuation properties of transport through a pair of coupled quantum dots which are connected with ferromagnetic electrodes. Based on an efficient particle-number-resolved master equation approach, we are concerned with not only fluctuations of the total charge and spin currents, but also of each individual spin-dependent component. As a result of competition among the spin polarization, Coulomb interaction, and dot-dot tunnel coupling, rich behaviors are found for the self- and mutual-correlation functions of the spin-dependent currents.

Correlation effects for semiconducting single-wall carbon nanotubes: A density matrix renormalization group study

In this paper we report the applicability of the density matrix renormalization group (DMRG) approach to the cylindrical single wall carbon nanotube (SWCN) for the purpose of its correlation effect. By applying the DMRG approach to the t+U+V model, with t and V being the hopping and Coulomb energies between the nearest neighboring sites, respectively, and U the on-site Coulomb energy, we calculate the phase diagram for the SWCN with chiral numbers (n(1)=3, n(2)=2), which reflects the competition between the correlation energy U and V. Within reasonable parameter ranges, we investigate possible correlated ground states, the lowest excitations, and the corresponding correlation functions in which the connection with the excitonic insulator is particularly addressed.

Entrance channel dependence of the correlation function of IMFs in Ar-36+Sn-112,Sn-124 at 35MeV/u

The reduced velocity correlation functions of the Intermediate Mass Fragments (IMFs) were measured in the reactions of Ar-36+ Sn-112,Sn-124 at 35MeV/u. The anti-correlation at small reduced velocities is more pronounced in Ar-36+ Sn-124 system than that in Ar-36+ Sn-112 system. The difference of the correlation functions between the two reactions is mainly contributed by the particle pairs with high momenta. A three-body Coulomb repulsive trajectory code (MENEKA) is employed to calculate the emission time scale of IMFs for-the both systems. The time scale is 150fm/c in the Ar-36+ Sn-112 system and 120fm/c in the Ar-36+ Sn-124 system, respectively. A calculation based on an Isospin dependence Quantum Molecular Dynamics code (IQMD) reveals that the emission time spectrum of IMFs is shifted slightly leftwards in Ar-36+ Sn-124 compared with that in the Ar-16+ Sn-112 system, indicating a shorter emission time scale. Correspondingly, the central density of the hot nuclei decreases faster in Ar-36+ Sn-124 than in Ar-36+ Sn-112

MEASUREMENT OF THE PROTON-PROTON CORRELATION FUNCTION FROM THE BREAK-UP OF Mg-22 AND Ne-20

An experiment of Mg-22 and Ne-20 beams bombarding on a C-12 target at an energy of 60 similar to 70 A MeV has been performed at the RIKEN projectile fragment separator (RIPS)in the RIKEN Ring Cyclotron Facility to study the two-proton correlated emission from Mg-22 and Ne-20 excited states. The two-protons momentum correlation functions have been obtained for Mg-22 and Ne-20, respectively. The trajectories of the Mg-22 decayed products (Ne-20 + p + p) were also measured to get the angular correlations between the two protons in Center of Mass of decaying system by relativistic-kinematics reconstruction. The results exhibit that Mg-22 has the features of He-2 cluster decay mechanism.

On the computation of space-time correlations by large-eddy simulation

The effect of subgrid-scale (SGS) modeling on velocity (space-) time correlations is investigated in decaying isotropic turbulence. The performance of several SGS models is evaluated, which shows superiority of the dynamic Smagorinsky model used in conjunction with the multiscale large-eddy simulation (LES) procedure. Compared to the results of direct numerical simulation, LES is shown to underpredict the (un-normalized) correlation magnitude and slightly overpredict the decorrelation time scales. This can lead to inaccurate solutions in applications such as aeroacoustics. The underprediction of correlation functions is particularly severe for higher wavenumber modes which are swept by the most energetic modes. The classic sweeping hypothesis for stationary turbulence is generalized for decaying turbulence and used to analyze the observed discrepancies. Based on this analysis, the time correlations are determined by the wavenumber energy spectra and the sweeping velocity, which is the square root of the total energy. Hence, an accurate prediction of the instantaneous energy spectra is most critical to the accurate computation of time correlations. (C) 2004 American Institute of Physics.

Quantum and variational monte-carlo interaction potentials for li2 (x1-sigma-g+)

Optimized trial functions are used in quantum Monte Carlo and variational Monte Carlo calculations of the Li₂(X ¹Σ⁺_g) potential curve. The trial functions used are a product of a Slater determinant of molecular orbitals multiplied by correlation functions of electron—nuclear and electron—electron separation. The parameters of the determinant and correlation functions are optimized simultaneously by reducing the deviations of the local energy E_L (E_L  Ψ⁻¹_THΨ_T, where Ψ_T denotes a trial function) over a fixed sample. At the equilibrium separation, the variational Monte Carlo and quantum Monte Carlo methods recover 68% and 98% of the correlation energy, respectively. At other points on the curves, these methods yield similar accuracies.

Analytical calculations of Eulerian and Lagrangian time correlations in turbulent shear flows

The Taylor series expansion method is used to analytically calculate the Eulerian and Lagrangian time correlations in turbulent shear flows. The short-time behaviors of those correlation functions can be obtained from the series expansions. Especially, the propagation velocity and sweeping velocity in the elliptic model of space-time correlation are analytically calculated and further simplified using the sweeping hypothesis and straining hypothesis. These two characteristic velocities mainly determine the space-time correlations.

Space-time correlations of fluctuating velocities in turbulent shear flows

Space-time correlations or Eulerian two-point two-time correlations of fluctuating velocities are analytically and numerically investigated in turbulent shear flows. An elliptic model for the space-time correlations in the inertial range is developed from the similarity assumptions on the isocorrelation contours: they share a uniform preference direction and a constant aspect ratio. The similarity assumptions are justified using the Kolmogorov similarity hypotheses and verified using the direct numerical simulation DNS of turbulent channel flows. The model relates the space-time correlations to the space correlations via the convection and sweeping characteristic velocities. The analytical expressions for the convection and sweeping velocities are derived from the Navier-Stokes equations for homogeneous turbulent shear flows, where the convection velocity is represented by the mean velocity and the sweeping velocity is the sum of the random sweeping velocity and the shearinduced velocity. This suggests that unlike Taylor’s model where the convection velocity is dominating and Kraichnan and Tennekes’ model where the random sweeping velocity is dominating, the decorrelation time scales of the space-time correlations in turbulent shear flows are determined by the convection velocity, the random sweeping velocity, and the shear-induced velocity. This model predicts a universal form of the spacetime correlations with the two characteristic velocities. The DNS of turbulent channel flows supports the prediction: the correlation functions exhibit a fair good collapse, when plotted against the normalized space and time separations defined by the elliptic model.

Monte Carlo Simulation Of Thermal Fluctuations Below The Onset Of Rayleigh-Benard Convection

The density fluctuations below the onset of convection in the Rayleigh-Benard problem are studied with the direct simulation Monte Carlo method. The particle simulation results clearly show the connection between the static correlation functions of fluctuations below the critical Rayleigh number and the flow patterns above the onset of convection for small Knudsen number flows (Kn=0.01 and Kn=0.005). Furthermore, the physical nature for no convection in the Rayleigh-Benard problem under large Knudsen number conditions (Kn>0.028) is explained based on the dynamics of fluctuations.

Simulation of growth process of thin film on non-planar substrate

In (2 + 1) dimension, growth process of thin film on non-planar substrate in Kuramoto-Sivashinsky model is studied with numerical simulation approach. 15 x 15 semi-ellipsoids arranged orderly on the surface of substrate are used to represent initial rough surface. The results show that at the initial stage of growth process, the surface morphology of thin film appears to be grid-structure, and the interface width constantly decreases with the growth time, then reaches minimum. However, the grid-structure becomes ambiguous, and granules of different sizes distribute evenly on the surface of thin film with the increase of growth time. Thereafter, the average size of granules and the interface width gradually increase, and the surface morphology of thin film presents fractal properties. The numerical results of height-height correlation functions of thin film verify the surface morphology of thin film to be fractal for a longer growth time. By fitting of the height-height correlation functions of thin film with different growth times, the growth process is described quantitatively. (c) 2004 Elsevier B.V. All rights reserved.

Energy spectra of two-electron two-dimensional quantum dots confined by elliptical and bowl-like potentials

The laterally confining potential of quantum dots (QDs) fabricated in semiconductor heterostructures is approximated by an elliptical two-dimensional harmonic-oscillator well or a bowl-like circular well. The energy spectrum of two interacting electrons in these potentials is calculated in the effective-mass approximation as a function of dot size and characteristic frequency of the confining potential by the exact diagonalization method. Energy level crossover is displayed according to the ratio of the characteristic frequencies of the elliptical confinement potential along the y axis and that along the x axis. Investigating the rovibrational spectrum with pair-correlation function and conditional probability distribution, we could see the violation of circular symmetry. However, there are still some symmetries left in the elliptical QDs. When the QDs are confined by a "bowl-like" potential, the removal of the degeneracy in the energy levels of QDs is found. The distribution of energy levels is different for the different heights of the barriers. (C) 2003 American Institute of Physics.

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.