Genetic algorithm based indicator sequence method for exon prediction

Considerable research effort has been devoted in predicting the exon regions of genes. The binary indicator (BI), Electron ion interaction pseudo potential (EIIP), Filter method are some of the methods. All these methods make use of the period three behavior of the exon region. Even though the method suggested in this paper is similar to above mentioned methods , it introduces a set of sequences for mapping the nucleotides selected by applying genetic algorithm and found to be more promising

Electron/ion energy loss to discharge walls revised : a case study in low-temperature, thermally nonequilibrium plasmas

Reliable calculations of the electron/ion energy losses in low-pressure thermally nonequilibrium low-temperature plasmas are indispensable for predictive modeling related to numerous applications of such discharges. The commonly used simplified approaches to calculation of electron/ion energy losses to the chamber walls use a number of simplifying assumptions that often do not account for the details of the prevailing electron energy distribution function (EEDF) and overestimate the contributions of the electron losses to the walls. By direct measurements of the EEDF and careful calculation of contributions of the plasma electrons in low-pressure inductively coupled plasmas, it is shown that the actual losses of kinetic energy of the electrons and ions strongly depend on the EEDF. It is revealed that the overestimates of the total electron/ion energy losses to the walls caused by improper assumptions about the prevailing EEDF and about the ability of the electrons to pass through the repulsive potential of the wall may lead to significant overestimates that are typically in the range between 9 and 32%. These results are particularly important for the development of power-saving strategies for operation of low-temperature, low-pressure gas discharges in diverse applications that require reasonably low power densities. © 2008 American Institute of Physics.

The dynamics of solvation of an electron in the image potential state by a layer of polar adsorbates

Recently, ultrafast two-photon photoemission has been used to study electron solvation at a two-dimensional metal/polar adsorbate interfaces [A. Miller , Science 297, 1163 (2002)]. The electron is bound to the surface by the image interaction. Earlier we have suggested a theoretical description of the states of the electron interacting with a two-dimensional layer of the polar adsorbate [K. L. Sebastian , J. Chem. Phys. 119, 10350 (2003)]. In this paper we have analyzed the dynamics of electron solvation, assuming a trial wave function for the electron and the solvent polarization and then using the Dirac-Frenkel variational method to determine it. The electron is initially photoexcited to a delocalized state, which has a finite but large size, and causes the polar molecules to reorient. This reorientation acts back on the electron and causes its wave function to shrink, which will cause further reorientation of the polar molecules, and the process continues until the electron gets self-trapped. For reasonable values for the parameters, we are able to obtain fair agreement with the experimental observations. (c) 2005 American Institute of Physics.

Relativistic theory for localized electrostatic excitations in degenerate electron-ion plasmas

A self-consistent relativistic two-fluid model is proposed for electron-ion plasma dynamics. A one-dimensional geometry is adopted. Electrons are treated as a relativistically degenerate fluid, governed by an appropriate equation of state. The ion fluid is also allowed to be relativistic, but is cold, nondegenerate, and subject only to an electrostatic potential. Exact stationary-profile solutions are sought, at the ionic scale, via the Sagdeev pseudopotential method. The analysis provides the pulse existence region, in terms of characteristic relativistic parameters, associated with the (ultrahigh) particle density.

Kinetics of photo-induced electron transfer from high-potential iron-sulfur protein to the photosynthetic reaction center of the purple phototroph Rhodoferax fermentans.

The kinetics of photo-induced electrontransfer from high-potential iron-sulfur protein (HiPIP) to the photosynthetic reaction center (RC) of the purple phototroph Rhodoferarfermentans were studied. The rapid photooxidation of heme c-556 belonging to RC is followed, in the presence of HiPIP, by a slower reduction having a second-order rate constant of 4.8 x 10(7) M(-1) x s(-1). The limiting value of kobs at high HiPIP concentration is 95 s(-1). The amplitude of this slow process decreases with increasing HiPIP concentration. The amplitude of a faster phase, observed at 556 and 425 nm and involving heme c-556 reduction, increases proportionately. The rate constant of this fast phase, determined at 425 and 556 nm, is approximately 3 x 10(5) s(-1). This value is not dependent on HiPIP concentration, indicating that it is related to a first-order process. These observations are interpreted as evidence for the formation of a HiPIP-RC complex prior to the excitation flash, having a dissociation constant of -2.5 microM. The fast phase is absent at high ionic strength, indicating that the complex involves mainly electrostatic interactions. The ionic strength dependence of kobs for the slow phase yields a second-order rate constant at infinite ionic strength of 5.4 x 10(6) M(-1) x s(-1) and an electrostatic interaction energy of -2.1 kcal/mol (1 cal = 4.184 J). We conclude that Rhodoferar fermentans HiPIP is a very effective electron donor to the photosynthetic RC.

Ribosome-RNA interaction: a potential target for developing antiviral against hepatitis C virus

Hepatitis C virus (HCV), a member of Flaviviridae, encoding a positive-sense single-stranded RNA translates by cap-independent mechanism using the internal ribosome entry site (IRES) present in the 5' UTR of the virus. The IRES has complex stem loop structures and is capable of recruiting the 40S ribosomal subunit in a factor-independent fashion. As the IRES sequence is highly conserved throughout the HCV genotypes and the translation is the first obligatory step of the HCV life cycle, the IRE'S-mediated translation, or more specifically, the ribosome HCV RNA interaction is an attractive target to design effective antivirals. This article will focus on the mechanism of the HCV IRES translation and the various ways in which the interaction of ribosome and IRES has been targeted.

Quantum measurement of an electron in a disordered potential: Delocalization versus measurement voltages

Quantum point contact (QPC), one of the typical mesoscopic transport devices, has been suggested to be an efficient detector for quantum measurement. In the context of two-state charge qubit, our previous studies showed that the QPC's measurement back-action cannot be described by the conventional Lindblad quantum master equation. In this work, we study the measurement problem of a multistate system, say, an electron in disordered potential, subject to the quantum measurement of the mesoscopic detector QPC. The effect of measurement back-action and the detector's readout current are analyzed, where particular attention is focused on some new features and the underlying physics associated with the measurement-induced delocalization versus the measurement voltages.

High-field cyclotron resonance and electron-phonon interaction in modulation-doped multiple quantum well structures

A systematic study of electron cyclotron resonance (CR) in two sets of GaAs/Al0.3Ga0.7As modulation-doped quantum-well samples (well widths between 12 and 24 nm) has been carried out in magnetic fields up to 30 T. Polaron CR is the dominant transition in the region of GaAs optical phonons for the set of lightly doped samples, and the results are in good agreement with calculations that include the interaction with interface optical phonons. The results from the heavily doped set are markedly different. At low magnetic fields (below the GaAs reststrahlen region), all three samples exhibit almost identical CR which shows little effect of the polaron interaction due to screening and Pauli-principle effects. Above the GaAs LO-phonon region (B > similar to 23 T), the three samples behave very differently. For the most lightly doped sample (3 x 10(11) cm(-2)) only one transition minimum is observed, which can be explained as screened polaron CR. A sample of intermediate density (6 x 10(11) cm(-2)) shows two lines above 23 T; the higher frequency branch is indistinguishable from the positions of the single line of the low density sample. For the most heavily, doped sample (1.2 x 10(12) cm(-2)) there is no evidence of high frequency resonance, and the strong, single line observed is indistinguishable from the lower branch observed from sample with intermediate doping density. We suggest that the low frequency branch in our experiment is a magnetoplasmon resonance red-shifted by disorder, and the upper branch is single-particle-like screened polaron CR. (C) 1998 Elsevier Science B.V. All rights reserved.

High-field cyclotron resonance and electron-phonon interaction in modulation-doped multiple quantum well structures

A systematic study of electron cyclotron resonance (CR) in two sets of GaAs/Al0.3Ga0.7As modulation-doped quantum-well samples (well widths between 12 and 24 nm) has been carried out in magnetic fields up to 30 T. Polaron CR is the dominant transition in the region of GaAs optical phonons for the set of lightly doped samples, and the results are in good agreement with calculations that include the interaction with interface optical phonons. The results from the heavily doped set are markedly different. At low magnetic fields (below the GaAs reststrahlen region), all three samples exhibit almost identical CR which shows little effect of the polaron interaction due to screening and Pauli-principle effects. Above the GaAs LO-phonon region (B > similar to 23 T), the three samples behave very differently. For the most lightly doped sample (3 x 10(11) cm(-2)) only one transition minimum is observed, which can be explained as screened polaron CR. A sample of intermediate density (6 x 10(11) cm(-2)) shows two lines above 23 T; the higher frequency branch is indistinguishable from the positions of the single line of the low density sample. For the most heavily, doped sample (1.2 x 10(12) cm(-2)) there is no evidence of high frequency resonance, and the strong, single line observed is indistinguishable from the lower branch observed from sample with intermediate doping density. We suggest that the low frequency branch in our experiment is a magnetoplasmon resonance red-shifted by disorder, and the upper branch is single-particle-like screened polaron CR. (C) 1998 Elsevier Science B.V. All rights reserved.

Effect of Target Polarization in Electron-Ion Recombination

We present results of a study of the effect of target polarization on electron-ion recombination, and show that coherent radiation by the target electrons gives a large contribution to the recombination rate. It significantly modifies the nonresonant photorecombination background. A procedure has been devised whereby this contribution can be evaluated together with the conventional radiative recombination, independently of the dielectronic recombination component. Numerical results are presented for Zn2+, Cd2+, Sn4+, and Xe8+, showing up to an order-of-magnitude enhancement.