Model fluid in a porous medium: results for a Bethe lattice

We consider a lattice gas with quenched impurities or `quenched-annealed binary mixture' on the Bethe lattice. The quenched part represents a porous matrix in which the (annealed) lattice gas resides. This model features the 3 main factors of fluids in random porous media: wetting, randomness and confinement. The recursive character of the Bethe lattice enables an exact treatment, whose key ingredient is an integral equation yielding the one-particle effective field distribution. Our analysis shows that this distribution consists of two essentially different parts. The first one is a continuous spectrum and corresponds to the macroscopic volume accessible to the fluid, the second is discrete and comes from finite closed cavities in the porous medium. Those closed cavities are in equilibrium with the bulk fluid within the grand canonical ensemble we use, but are inaccessible in real experimental situations. Fortunately, we are able to isolate their contributions. Separation of the discrete spectrum facilitates also the numerical solution of the main equation. The numerical calculations show that the continuous spectrum becomes more and more rough as the temperature decreases, and this limits the accuracy of the solution at low temperatures.Comment: 13 pages, 12 figure

New combined PIC-MCC approach for fast simulation of a radio frequency discharge at low gas pressure

A new combined PIC-MCC approach is developed for accurate and fast simulation of a radio frequency discharge at low gas pressure and high density of plasma. Test calculations of transition between different modes of electron heating in a ccrf discharge in helium and argon show a good agreement with experimental data. We demonstrate high efficiency of the combined PIC-MCC algorithm, especially for the collisionless regime of electron heating.Comment: 6 paged, 8 figure

The effect of discharge chamber geometry on the ignition of low-pressure rf capacitive discharges

This paper reports measured and calculated breakdown curves in several gases of rf capacitive discharges excited at 13.56 MHz in chambers of three different geometries: parallel plates surrounded by a dielectric cylinder (“symmetric parallel plate”), parallel plates surrounded by a grounded metallic cylinder (“asymmetric parallel plate”), and parallel plates inside a much larger grounded metallic chamber (“large chamber”). The breakdown curves for the symmetric chamber have a multivalued section at low pressure. For the asymmetric chamber the breakdown curves are shifted to lower pressures and rf voltages, but the multivalued feature is still present. At higher pressures the breakdown voltages are much lower than for the symmetric geometry. For the large chamber geometry the multivalued behavior is not observed. The breakdown curves were also calculated using a numerical model based on fluid equations, giving results that are in satisfactory agreement with the measurements

Modes and the alpha-gamma transition in rf capacitive discharges in N2O at different rf frequencies

This paper reports current-voltage characteristics and pressure-voltage transition curves from the weak-current a-mode to the strong-current g-mode for rf capacitive discharges in N2O at frequencies of 2 MHz, 13.56 MHz, and 27.12 MHz. At 2 MHz the rf discharge is mostly resistive whereas at 13.56 MHz and 27.12 MHz it is mostly capacitive. The weak-current a-mode was found to exist only above a certain minimum gas pressure for all frequencies studied [N. Yatsenko Sov. Phys. Tech. Phys. 26, 678 (19810] previously proposed that the a−g transition corresponds to breakdown of the sheaths. However, we show that this is the case only for sufficiently high gas pressures. At lower pressure there is a smooth transition from the weak-current a-mode to a strong-current g-mode, in which the sheaths produce fast electrons but the sheath has not undergone breakdown

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions

<p>Abstract</p> <p>Background</p> <p>Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered.</p> <p>Results</p> <p>To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-κB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies.</p> <p>To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD). The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA.</p> <p>Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced false positives at least at higher stringencies.</p> <p>Conclusion</p> <p>Based on this analysis, SiteGA adds substantial specificity even to optimized PWMs and may be considered for large-scale genome analysis. It adds to the range of techniques available for TFBS prediction, and EPD analysis has led to a list of genes which appear to be regulated by the above TFs.</p