Design of plasma shutters for improved heavy ion acceleration by ultra-intense laser pulses

In this work, we investigate the application of the plasma shutters for heavy ion acceleration driven by a high-intensity laser pulse. We use particle-in-cell (PIC) and hydrodynamic simulations. The laser pulse, transmitted through the opaque shutter, gains a steep-rising front and its peak intensity is locally increased at the cost of losing part of its energy. These effects have a direct influence on subsequent ion acceleration from the ultrathin target behind the shutter. In our 3D simulations of silicon nitride plasma shutter and a silver target, the maximal energy of high-Z ions increases significantly when the shutter is included for both linearly and circularly polarized laser pulses. Moreover, application of the plasma shutter for linearly polarized pulse results in focusing of ions towards the laser axis in the plane perpendicular to the laser polarization. The generated high energy ion beam has significantly lower divergence compared to the broad ion cloud, generated without the shutter. The effects of prepulses are also investigated assuming a double plasma shutter. The first shutter can withstand the assumed sub-ns prepulse (treatment of ns and ps prepulses by other techniques is assumed) and the pulse shaping occursvia interaction with the second shutter. On the basis of our theoretical findings, we formulated an approach towards designing a double plasma shutter for high-intensity and high-power laser pulses and built a prototype.Comment: 30 pages 13 figure

СОСТАВ И СВОЙСТВА ПОВЕРХНОСТНЫХ СЛОЕВ, ФОРМИРУЕМЫХ ИОННО-АССИСТИРУЕМЫМ ОСАЖДЕНИЕМ КАТАЛИТИЧЕСКИХ МЕТАЛЛОВ ИЗ ПЛАЗМЫ ВАКУУМНОГО ДУГОВОГО РАЗРЯДА НА УГЛЕРОДНЫЕ ПОДЛОЖКИ

Surface layers were prepared by ion beam-assisted deposition (IBAD) of platinum and rare earth metals (Ce, Yb) on the carbon-based Toray Carbon Fiber Paper TGP-H-060 T catalyst support in effort to produce electrocatalysts for direct methanol and ethanol oxidation fuel cells (DMFC, DEFC) with polymer electrolyte membrane. The layer formation in the IBAD mode, by means of the metal deposition and the mixing of a precipitating layer with the substrate by accelerated (U = 10 kV) ions of the same metal, was carried out. In this process, a neutral fraction of metal vapor and ionized plasma of vacuum pulsed electric arc was used. The study of morphology and composition of the layers was performed by scanning electron microscopy and electron probe microanalysis, X-ray fluorescence analysis and Rutherford backscattering spectrometry. Properties of the prepared electrocatalysts were investigated by cyclic voltammetry. It was established that the prepared electrocatalysts show their activity in the processes of electrochemical methanol and ethanol oxidation. Поверхностные слои сформированы ионноассистируемым осаждением (IBAD) платины и редкоземельных металлов (Ce, Yb) на носитель Toray Carbon Fiber Paper TGP-H-060 Т с целью получения электрокатализаторов для топливных элементов прямого окисления метанола и этанола с полимерным мембранным электролитом. Формирование слоев проведено в режиме IBAD, при котором осаждение металла и перемешивание осаждаемого слоя с атомами поверхности подложки ускоренными (U = 10 кВ) ионами того же металла осуществляются соответственно из нейтральной фракции пара и плазмы вакуумного дугового разряда импульсного электродугового ионного источника. Исследование морфологии и состава слоев проведено методами сканирующей электронной микроскопии и электронно-зондового микроанализа, рентгеновского флуоресцентного анализа и спектрометрии резерфордовского обратного рассеяния. Свойства электрокатализаторов исследовались методом циклической вольтамперометрии. Получаемые электрокатализаторы проявляют активность в процессах окисления метанола и этанола.

Analysis of computational approaches for motif discovery

Recently, we performed an assessment of 13 popular computational tools for discovery of transcription factor binding sites (M. Tompa, N. Li, et al., "Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites", Nature Biotechnology, Jan. 2005). This paper contains follow-up analysis of the assessment results, and raises and discusses some important issues concerning the state of the art in motif discovery methods: 1. We categorize the objective functions used by existing tools, and design experiments to evaluate whether any of these objective functions is the right one to optimize. 2. We examine various features of the data sets that were used in the assessment, such as sequence length and motif degeneracy, and identify which features make data sets hard for current motif discovery tools. 3. We identify an important feature that has not yet been used by existing tools and propose a new objective function that incorporates this feature

TRANSFAC(®) and its module TRANSCompel(®): transcriptional gene regulation in eukaryotes

The TRANSFAC(®) database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel(®) on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match™ and Patch™ provides increased functionality for TRANSFAC(®). The list of databases which are linked to the common GENE table of TRANSFAC(®) and TRANSCompel(®) has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD™ and TRANSPRO™. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel(®) contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC(®), in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC(®) 7.0 and TRANSCompel(®) 7.0, are accessible under

Защитные свойства Zr-содержащих конверсионных покрытий на цинке

The aim of the study is to develop an environmentally friendly chromium-free passivation technology for galvanized steel. Passivation of zinc coatings was carried out by deposition of conversion coatings from solutions containing ZrO(NO3)2, Na2SiF6 and oxidizer H2O2 or K2S2O8. The effect of the solution pH, the concentration of Na2SiF6 and the type of oxidizer on the protective properties of coatings was studied by the drop method and electrochemical method of linear voltammetry in 3 % NaCl using the full factor experiment 23 . The main effects and effects of the interaction of the studied factors for the darkening time of the droplet and the dissolution potential of zinc are calculated. The solution pH in the presence of the oxidizing agent K2S2O8 influences the both parameters in the most extent. Concentration of Na2SiF6 has a significant effect on the dissolution potential of zinc and the least effect on the darkening time of the droplet. An increase in the solution pH and the concentration of Na2SiF6 increases the protective properties of the coatings. Measurements of the mass loss and open circuit potential during the resource testing of conversion coatings in 3% NaCl showed an increase in the corrosion rate over time.Цель исследования − разработка экологически безопасной бесхромовой технологии пассивации гальванически оцинкованной стали. Пассивация гальванических цинковых покрытий проводилась осаждением на них конверсионных покрытий из растворов, содержащих ZrO(NO3)2, Na2SiF6 и окислитель H2O2 или K2S2O8. Изучалось влияние pH раствора, концентрации Na2SiF6 и типа окислителя на показатели защитных свойств покрытий методом капли и электрохимическим методом линейной вольтамперометрии в 3 %-ном NaCl с использованием полного факторного эксперимента 23 . Рассчитаны главные эффекты и эффекты взаимодействия исследованных факторов для времени потемнения капли и потенциала растворения цинка. Наибольшее влияние на оба показателя оказывает pH раствора в присутствии окислителя K2S2O8. Концентрация Na2SiF6 оказывает значительное влияние на потенциал растворения цинка и наименьшее влияние на время потемнения капли. Увеличение pH раствора и концентрации Na2SiF6 увеличивает показатели защитных свойств покрытий. Измерения потери массы и потенциала разомкнутой цепи в процессе ресурсных испытаний конверсионных покрытий в 3 %-ном NaCl показали возрастание скорости коррозии со временем

Design of a combinatorial DNA microarray for protein-DNA interaction studies

BACKGROUND: Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding microarrays were developed as a potentially scalable approach to tackle transcription factor binding site identification. RESULTS: Here we present an algorithmic approach to experimental design of a microarray that allows for testing full specificity of a transcription factor binding to all possible DNA binding sites of a given length, with optimally efficient use of the array. This design is universal, works for any factor that binds a sequence motif and is not species-specific. Furthermore, simulation results show that data produced with the designed arrays is easier to analyze and would result in more precise identification of binding sites. CONCLUSION: In this study, we present a design of a double stranded DNA microarray for protein-DNA interaction studies and show that our algorithm allows optimally efficient use of the arrays for this purpose. We believe such a design will prove useful for transcription factor binding site identification and other biological problems

A Bayesian Search for Transcriptional Motifs

Identifying transcription factor (TF) binding sites (TFBSs) is an important step towards understanding transcriptional regulation. A common approach is to use gaplessly aligned, experimentally supported TFBSs for a particular TF, and algorithmically search for more occurrences of the same TFBSs. The largest publicly available databases of TF binding specificities contain models which are represented as position weight matrices (PWM). There are other methods using more sophisticated representations, but these have more limited databases, or aren't publicly available. Therefore, this paper focuses on methods that search using one PWM per TF. An algorithm, MATCHTM, for identifying TFBSs corresponding to a particular PWM is available, but is not based on a rigorous statistical model of TF binding, making it difficult to interpret or adjust the parameters and output of the algorithm. Furthermore, there is no public description of the algorithm sufficient to exactly reproduce it. Another algorithm, MAST, computes a p-value for the presence of a TFBS using true probabilities of finding each base at each offset from that position. We developed a statistical model, BaSeTraM, for the binding of TFs to TFBSs, taking into account random variation in the base present at each position within a TFBS. Treating the counts in the matrices and the sequences of sites as random variables, we combine this TFBS composition model with a background model to obtain a Bayesian classifier. We implemented our classifier in a package (SBaSeTraM). We tested SBaSeTraM against a MATCHTM implementation by searching all probes used in an experimental Saccharomyces cerevisiae TF binding dataset, and comparing our predictions to the data. We found no statistically significant differences in sensitivity between the algorithms (at fixed selectivity), indicating that SBaSeTraM's performance is at least comparable to the leading currently available algorithm. Our software is freely available at: http://wiki.github.com/A1kmm/sbasetram/building-the-tools

Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach

A computational approach for identifying functionally relevant SNPs in gene LIG1 has been proposed. LIG1 is a crucial gene which is involved in excision repair pathways and mutations in this gene may lead to increase sensitivity towards DNA damaging agents. A total of 792 SNPs were reported to be associated with gene LIG1 in dbSNP. Different web server namely SIFT, PolyPhen, CUPSAT, FASTSNP, MAPPER and dbSMR were used to identify potentially functional SNPs in gene LIG1. SIFT, PolyPhen and CUPSAT servers predicted eleven nsSNPs to be intolerant, thirteen nsSNP to be damaging and two nsSNPs have the potential to destabilize protein structure. The nsSNP rs11666150 was predicted to be damaging by all three servers and its mutant structure showed significant increase in overall energy. FASTSNP predicted twenty SNPs to be present in splicing modifier binding sites while rSNP module from MAPPER server predicted nine SNPs to influence the binding of transcription factors. The results from the study may provide vital clues in establishing affect of polymorphism on phenotype and in elucidating drug response