Chaos game representation walk model for the protein sequences

A new chaos game representation of protein sequences based on the detailed hydrophobic--hydrophilic (HP) model has been proposed by Yu et al (Physica A 337 (2004) 171). A CGR-walk model is proposed based on the new CGR coordinates for the protein sequences from complete genomes in the present paper. The new CGR coordinates based on the detailed HP model are converted into a time series, and a long-memory ARFIMA(p, d, q) model is introduced into the protein sequence analysis. This model is applied to simulating real CGR-walk sequence data of twelve protein sequences. Remarkably long-range correlations are uncovered in the data and the results obtained from these models are reasonably consistent with those available from the ARFIMA(p, d, q) model.     

TEMPORAL CHARACTERIZATION OF LASER PULSES FROM JIGUANG-I LASER FACILITY WITH A COMPACT DUAL FUNCTION AUTOCORRELATOR

An optical pulse autocorrelator for rapid and slow scanning is described in this paper. Using an audio loudspeaker on one arm, an interferometric rapid-scanning signal of the output from a high-repetition laser oscillator is obtained. However, by adjusting the positions of the mirrors and using a step-motor on another arm, the intensity autocorrelation function of the output from a low-repetition laser amplifier can be easily measured. Using all-reflecting optics and an adequate nonlinear crystal, the whole instrument is very compact and has been used to measure sub-20 fs light pulses in both configurations with excellent agreement. In the slow-scanning configuration, a pulse train as long as 500ps has been determined. Using this autocorrelator, the home-made JIGUANG-I CPA laser facility was characterized for its pulse duration evolution.     

线性回归模型误差相关的一种诊断方法

本文就线性回归模型的优化问题 ,对误差的自相关性作了一些简单的分析 ,得出了一个对自相关现象的诊断方法 ,从而为模型的进一步诊断和治疗提供了依据和思路     

A trace representation of binary Jacobi sequences

We determine the trace function representation, or equivalently, the Fourier spectral sequences of binary Jacobi sequences of period pq, where p and q are two distinct odd primes. This includes the twin-prime sequences of period p(p+2) whenever both p and p+2 are primes, corresponding to cyclic Hadamard difference sets.     

Temperature dependence of vibrational modes of CH3?CC(ads) and I(ads) coadsorbed on Ag(111): Ab initio molecular dynamics approach

Ab initio molecular dynamics simulations accompanied by a Fourier transform of the dipole moment (aligned perpendicular to the surface) autocorrelation function are implemented to investigate the temperature‐dependent infrared (IR) active vibrational modes of CH₃? C_(β)?C_(α)(ads) and I_(ads) when coadsorbed on an Ag(111) surface at 200 and 400 K, respectively. The analytic scheme of the Fourier transform of a structural coordinate autocorrelation function is used to identify two distinguishable IR active peaks of C_(β)?C_(α) stretching, which are characterized by two types of dynamic motion of adsorbed CH₃? C_(β)?C_(α)(ads) at 200 K, namely, the motion of the tilted ? C? C_(β)?C_(α)? axis and the motion of the stand‐up ? C? C_(β)?C_(α)? axis. These two recognisable IR active peaks of C_(β)?C_(α) stretching are gradually merged into one peak as a result of the dominant motion of the stand‐up ? C? C_(β)?C_(α)? axis as the temperature increases from 200 to 400 K. The calculated intensities of the IR active peaks of the asymmetrical deformation mode of CH₃ and the asymmetrical stretching mode of CH₃, with their dynamic dipole moments nearly perpendicular to the ? C? C_(β)?C_(α)? axis, become relatively weak; however, the symmetrical deformation mode of CH₃ and the symmetrical stretching mode of CH₃, with their dynamic dipole moments randomly directed away from the ? C? C_(β)?C_(α)? axis, will not have direct correspondence between the intensities of their IR active peaks and the angle between the Ag(111) surface and the ? C? C_(β)?C_(α)? axis as the temperature increases from 200 to 400 K. Finally, the increased flipping from the motion of the tilted ? C? C_(β)?C_(α)? axis to the motion of the stand‐up ? C? C_(β)?C_(α)? axis followed by its diffusion, resulting from the increasing temperature from 200 to 400 K or even higher, seems to be the initial event that initiates the alkyne self‐coupling reaction that leads to the final production of H₃C? C?C? C?C? CH₃. © 2012 Wiley Periodicals, Inc.     

概周期系统的一个重要性质

将概周期序列与系统相联系,给出了概周期系统这一特殊的时变系统的一个重要性质,并说明了此性质住一般的时变系统中是不成立的．     

A hybrid formalism combining fluctuating hydrodynamics and generalized Langevin dynamics for the simulation of nanoparticle thermal motion in an incompressible fluid medium

A novel hybrid scheme based on Markovian fluctuating hydrodynamics of the fluid and a non-Markovian Langevin dynamics with the Ornstein-Uhlenbeck noise perturbing the translational and rotational equations of motion of the nanoparticle is employed to study the thermal motion of a nanoparticle in an incompressible Newtonian fluid medium. A direct numerical simulation adopting an arbitrary Lagrangian-Eulerian (ALE) based finite element method (FEM) is employed in simulating the thermal motion of a particle suspended in the fluid confined in a cylindrical vessel. The results for thermal equilibrium between the particle and the fluid are validated by comparing the numerically predicted temperature of the nanoparticle with that obtained from the equipartition theorem. The nature of the hydrodynamic interactions is verified by comparing the velocity autocorrelation function (VACF) and mean squared displacement (MSD) with well-known analytical results. For nanoparticle motion in an incompressible fluid, the fluctuating hydrodynamics approach resolves the hydrodynamics correctly but does not impose the correct equipartition of energy based on the nanoparticle mass because of the added mass of the displaced fluid. In contrast, the Langevin approach with an appropriate memory is able to show the correct equipartition of energy, but not the correct short- and long-time hydrodynamic correlations. Using our hybrid approach presented here, we show for the first time, that we can simultaneously satisfy the equipartition theorem and the (short- and long-time) hydrodynamic correlations. In effect, this results in a thermostat that also simultaneously preserves the true hydrodynamic correlations. The significance of this result is that our new algorithm provides a robust computational approach to explore nanoparticle motion in arbitrary geometries and flow fields, while simultaneously enabling us to study carrier adhesion mediated by biological reactions (receptor-ligand interactions) at the vessel wall at a specified finite temperature.     

Angle-resolved X-ray photoemission electron microscopy

Synchrotron based photoemission electron microscopy with energy filter combines real space imaging with microprobe diffraction (μ-ARPES), giving access to the local electronic structure of laterally inhomogeneous materials. We present here an overview of the capabilities of this technique, illustrating selected applications of angle resolved photoemission electron microscopy and related microprobe methods. In addition, we report the demonstration of a darkfield XPEEM (df-XPEEM) imaging method for real space mapping of the electronic structure away from Γ at a lateral resolution of few tens of nm. The application of df-XPEEM to the (1 × 12)-O/W(1 1 0) model oxide structure shows the high sensitivity of this technique to the local electronic structure, allowing to image domains with inequivalent adsorption site symmetry. Perspectives of angle-resolved PEEM are discussed.     

Soft X-ray ARPES and Fermiology of strongly correlated electron systems and PES by hard X-ray and extremely low energy photons

Bulk sensitivity is inevitable for photoelectron spectroscopy (PES) when one studies bulk electronic structures of strongly correlated electron systems, which are often much different from surface electronic structures. Combination of soft and hard X-ray PES (SXPES and HAXPES) is a promising approach for this purpose by quantitatively evaluating the contribution of the surface in the observed angle integrated PES spectra. Even in the angle resolved PES studies (ARPES), the bulk sensitivity of the SX-ARPES is required to get the real bulk band dispersions and Fermi surface topology, which may be noticeably modified in the surface region as seen in several materials studied in this paper.Although hard X-ray ARPES is feasible, deep attention is required for the discussion of the possible recoil effects for the valence band. Besides, extremely low energy PES (ELEPES) by use of microwave excited Xe, Kr and Ar lamps will be as useful as those by synchrotron radiation and laser to realize a very high resolution of better than 5 meV with bulk sensitivity under certain conditions.     

A note on the sum of the sample autocorrelation function

It is shown that the sum of the sample autocorrelation function at lag h≥1 is always for any stationary time series with arbitrary length T≥2 (Hassani, 2009 [1]). In this paper, the distribution of a set of the sample autocorrelation function using the properties of this quantity is considered. It is found that the distribution of a set of the sample autocorrelation estimates is not independent and identically distributed. This finding implies that the result of diagnostic check and model building using the traditional assumption of iid can be quite misleading.