A combined statistical model for multiple motifs search

Transcription factor binding sites (TFBS) play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with de¯nite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite di®erent from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for ¯nding over- represented short sequence segments in di®erent kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from di®erent species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite di®erent, the results show that this model is rather general and sensible.

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.

Plasma channeling by multiple short-pulse lasers

Channeling by a train of laser pulses into homogeneous and inhomogeneous plasmas is studied using particle-in-cell simulation. When the pulse duration and the interval between the successive pulses are appropriate, the laser pulse train can channel into the plasma deeper than a single long-pulse laser of similar peak intensity and total energy. The increased penetration distance can be attributed to the repeated actions of the ponderomotive force, the continuous between-pulse channel lengthening by the inertially evacuating ions, and the suppression of laser-driven plasma instabilities by the intermittent laser-energy cut-offs.

Electron acceleration by an intense short-pulse laser in underdense plasma

Electron acceleration from the interaction of an intense short-pulse laser with low density plasma is considered. The relation between direct electron acceleration within the laser pulse and that in the wake is investigated analytically. The magnitude and location of the ponderomotive-force-caused charge separation field with respect to that of the pulse determine the relative effectiveness of the two acceleration mechanisms. It is shown that there is an optimum condition for acceleration in the wake. Electron acceleration within the pulse dominates as the pulse becomes sufficiently short, and the latter directly drives and even traps the electrons. The latter can reach ultrahigh energies and can be extracted by impinging the pulse on a solid target. (C) 2003 American Institute of Physics.

Short-pulse laser absorption in very steep plasma density gradients

An analytical fluid model for resonance absorption during the oblique incidence by femtosecond laser pulses on a small-scale-length density plasma [k(0)L is an element of(0.1,10)] is proposed. The physics of resonance absorption is analyzed more clearly as we separate the electric field into an electromagnetic part and an electrostatic part. It is found that the characteristics of the physical quantities (fractional absorption, optimum angle, etc.) in a small-scale-length plasma are quite different from the predictions of classical theory. Absorption processes are generally dependent on the density scale length. For shorter scale length or higher laser intensity, vacuum heating tends to be dominant. It is shown that the electrons being pulled out and then returned to the plasma at the interface layer by the wave field can lead to a phenomenon like wave breaking. This can lead to heating of the plasma at the expanse of the wave energy. It is found that the optimum angle is independent of the laser intensity while the absorption rate increases with the laser intensity, and the absorption rate can reach as high as 25%. (c) 2006 American Institute of Physics.

Short-pulse laser absorption via J x B heating in ultrahigh intensity laser plasma interaction

An analytical fluid model for JxB heating during the normal incidence by a short ultraintense linearly polarized laser on a solid-density plasma is proposed. The steepening of an originally smooth electron density profile as the electrons are pushed inward by the laser is included self-consistently. It is shown that the JxB heating includes two distinct coupling processes depending on the initial laser and plasma conditions: for a moderate intensity (a <= 1), the ponderomotive force of the laser light can drive a large plasma wave at the point n(e)=4 gamma(0)n(c) resonantly. When this plasma wave is damped, the energy is transferred to the plasma. At higher intensity, the electron density is steepened to a high level by the time-independent ponderomotive force, n(e)> 4 gamma(0)n(c), so that no 2 omega resonance will occur, but the longitudinal component of the oscillating ponderomotive field can lead to an absorption mechanism similar to "vacuum heating." (c) 2006 American Institute of Physics.

Generation of strong quasistatic magnetic fields in interactions of ultraintense and short laser pulses with overdense plasma targets

An analytical fluid model is proposed for the generation of strong quasistatic magnetic fields during normal incidence of a short ultraintense Gaussian laser pulse with a finite spot size on an overdense plasma. The steepening of the electron density profile in the originally homogeneous overdense plasma and the formation of electron cavitation as the electrons are pushed inward by the laser are included self-consistently. It is shown that the appearance of the cavitation plays an important role in the generation of quasistatic magnetic fields: the strong plasma inhomogeneities caused by the formation of the electron cavitation lead to the generation of a strong axial quasistatic magnetic field B-z. In the overdense regime, the generated quasistatic magnetic field increases with increasing laser intensity, while it decreases with increasing plasma density. It is also found that, in a moderately overdense plasma, highly intense laser pulses can generate magnetic fields similar to 100 MG and greater due to the transverse linear mode conversion process.

Spectroscopic and thermal properties of short wavelength metal (II) complexes containing alpha-isoxazolylazo-beta-diketones as co-ligands

Two new azo dyes of alpha-isoxazolylazo-beta-dilcetones and their Ni(II) and Cu(II) complexes with blue-violet light wavelength were synthesized using a coupling component, different diazo components and metal (II) ions (Ni2+ and Cu2+). Based on the elemental analysis, MS spectra and FT-IR spectral analyses, azo dyes were unequivocally shown to exist as hydrazoketo and azoenol forms which were respectively obtained from the solution forms and from the solid forms. The action of sodium methoxide (NaOMe) on azo dyes in solutions converts hydrazoketo form into azoenol form, so azo dyes are coordinated with metal (II) ions as co-ligands in the azoenol forms. The solubility of all the compounds in common organic solvents such as 2,2,3,3-tetrafluoro-1-propanol (TFP) or chloroform (CHCl3) and absorption properties of spin-coating thin films were measured. The difference of absorption maxima from the complexes to their ligands was discussed. In addition, the TG analysis of the complexes was also determined, and their thermal stability was evaluated. It is found that these new metal (II) complexes had potential application for high-density digital versatile disc-recordable (HD-DVD-R) system due to their good solubility in organic solvents, reasonable and controllable absorption spectra in blue-violet light region and high thermal stability. (c) 2004 Elsevier B.V. All rights reserved.