A stochastic SICA epidemic model for HIV transmission

We propose a stochastic SICA epidemic model for HIV transmission, described by stochastic ordinary differential equations, and discuss its perturbation by environmental white noise. Existence and uniqueness of the global positive solution to the stochastic HIV system is proven, and conditions under which extinction and persistence in mean hold, are given. The theoretical results are illustrated via numerical simulations.Comment: This is a preprint of a paper whose final and definite form is with 'Applied Mathematics Letters', ISSN 0893-9659. Submitted 22/Jan/2018; Revised 03/May/2018; Accepted for publication 03/May/201

Heavy Quark Radiative Energy Loss - Applications to RHIC

Heavy quark energy loss in a hot QCD plasma is computed taking into account the competing effects due to suppression of zeroth order gluon radiation bellow the plasma frequency and the enhancement of gluon radiation due to transition energy loss and medium induced Bremsstrahlung. Heavy quark medium induced radiative energy loss is derived to all orders in opacity, $(L/\lambda_g)^n$. Numerical evaluation of the energy loss suggest small suppression of high $p_\perp$ charm quarks, and therefore provide a possible explanation for the null effects observed by PHENIX in the prompt electron spectrum in $Au+Au$ as $\sqrt{s}=130$ and 200 AGeV.Comment: 4 pages, 4 figures, Contributed to 17th International Conference on Ultra Relativistic Nucleus-Nucleus Collisions (Quark Matter 2004), Oakland, California, 11-17 Jan 200

Quantitative modeling and data analysis of SELEX experiments

SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an experimental procedure that allows extracting, from an initially random pool of DNA, those oligomers with high affinity for a given DNA-binding protein. We address what is a suitable experimental and computational procedure to infer parameters of transcription factor-DNA interaction from SELEX experiments. To answer this, we use a biophysical model of transcription factor-DNA interactions to quantitatively model SELEX. We show that a standard procedure is unsuitable for obtaining accurate interaction parameters. However, we theoretically show that a modified experiment in which chemical potential is fixed through different rounds of the experiment allows robust generation of an appropriate data set. Based on our quantitative model, we propose a novel bioinformatic method of data analysis for such modified experiment and apply it to extract the interaction parameters for a mammalian transcription factor CTF/NFI. From a practical point of view, our method results in a significantly improved false positive/false negative trade-off, as compared to both the standard information theory based method and a widely used empirically formulated procedure.Comment: 29 pages, 8 figures, to appear in Physical Biolog

Computer simulation of low-energy excitations in amorphous silicon with voids

We use empirical molecular dynamics technique to study the low-energy vibrations in a large 4096 atom model for pure amorphous silicon and a set of models with voids of different size based on it. Numerical vibrational eigenvalues and eigenvectors for our models are obtained by exact diagonalization of their dynamical matrices. Our calculations show that localized low-energy vibrational excitations of rather complex structure are present in amorphous silicon models with voids. According to their spatial localization patterns we make an attempt to classify these excitations as modes associated with the void and "mixed" modes associated with the interaction of the void with strained regions of silicon network.Comment: Was presented at ICAMS18 conference, Snowbird UT, August 1999. Submitted to J. of Non-Cryst. Solid

Diagnosing Energy Loss: PHENIX Results on High-pT Hadron Spectra

Measurements of inclusive spectra of hadrons at large transverse momentum over a broad range of energy in different collision systems have been performed with the PHENIX experiment at RHIC. The data allow to study the energy and system size dependence of the suppression observed in RAA of high-pT hadrons at sqrt(s_NN)= 200 GeV. Due to the large energy range from sqrt(s_NN)= 22 GeV to 200 GeV, the results can be compared to results from CERN SPS at a similar energy. The large Au+Au dataset from the 2004 run of RHIC also allows to constrain theoretical models that describe the hot and dense matter produced in such collisions. Investigation of particle ratios such as eta/pi0 helps understanding the mechanisms of energy loss.Comment: 4 pages, 6 figures. To appear in the proceedings of the 19th International Conference on Ultra-Relativistic Nucleus-Nucleus Collisions (Quark Matter 2006), Shanghai, China, November 14-20, 200

Open Charm and Beauty at Ultrarelativistic Heavy Ion Colliders

Important goals of RHIC and LHC experiments with ion beams include the creation and study of new forms of matter, such as the Quark Gluon Plasma. Heavy quark production and attenuation will provide unique tomographic probes of that matter. We predict the suppression pattern of open charm and beauty in $Au+Au$ collisions at RHIC and LHC energies based on the DGLV formalism of radiative energy loss. A cancelation between effects due to the $\sqrt{s}$ energy dependence of the high $p_T$ slope and heavy quark energy loss is predicted to lead to surprising similarity of heavy quark suppression at RHIC and LHC.Comment: 4 pages, 6 *.eps files combined into 4 figure

Heavy-to-light ratios as a test of medium-induced energy loss at RHIC and the LHC

The ratio of nuclear modification factors of high-$p_T$ heavy-flavored mesons tolight-flavored hadrons (heavy-to-light ratio) is shown to be a sensitive tool to test medium-induced energy loss at RHIC and LHC energies. Heavy-to-light ratios of $D$ mesons at RHIC in the region $7<p_T<12$ GeV, and of $D$ and $B$ mesons at the LHC in the region $10<p_T<20$ GeV, are proposed for such a test. Finally, the different contributions to the nuclear modification factor for electrons at RHIC are analyzed. Preliminary PHENIX and STAR data are compatible with radiative energy loss provided the contribution of electrons from beauty decays is small compared to that from charm.Comment: 5 pages, latex, 4 eps figs included using graphicx; to appear in the proceedings of 18th International Conference on Ultrarelativistic Nucleus-Nucleus Collisions: Quark Matter 2005 (QM 2005), Budapest, Hungary, 4-9 Aug 200

Deletion of Integron-Associated Gene Cassettes Impact on the Surface Properties of Vibrio rotiferianus DAT722

Background: The integron is a genetic recombination system that catalyses the acquisition of genes on mobilisable elements called gene cassettes. In Vibrio species, multiple acquired gene cassettes form a cassette array that can comprise 1-3% of the bacterial genome. Since 75% of these gene cassettes contain genes encoding proteins of uncharacterised function, how the integron has driven adaptation and evolution in Vibrio species remains largely unknown. A feature of cassette arrays is the presence of large indels. Using Vibrio rotiferianus DAT722 as a model organism, the aim of this study was to determine how large cassette deletions affect vibrio physiology with a view to improving understanding into how cassette arrays influence bacterial host adaptation and evolution. Methodology/Principal Findings: Biological assays and proteomic techniques were utilised to determine how artificially engineered deletions in the cassette array of V. rotiferianus DAT722 affected cell physiology. Multiple phenotypes were identified including changes to growth and expression of outer membrane porins/proteins and metabolic proteins. Furthermore, the deletions altered cell surface polysaccharide with Proton Nuclear Magnetic Resonance on whole cell polysaccharide identifying changes in the carbohydrate ring proton region indicating that gene cassette products may decorate host cell polysaccharide via the addition or removal of functional groups. Conclusions/Significance: From this study, it was concluded that deletion of gene cassettes had a subtle effect on bacterial metabolism but altered host surface polysaccharide. Deletion (and most likely rearrangement and acquisition) of gene cassettes may provide the bacterium with a mechanism to alter its surface properties, thus impacting on phenotypes such as biofilm formation. Biofilm formation was shown to be altered in one of the deletion mutants used in this study. Reworking surface properties may provide an advantage to the bacterium's interactions with organisms such as bacteriophage, protozoan grazers or crustaceans. © 2013 Rapa et al

MIMO free-space optical communication employing subcarrier intensity modulation in atmospheric turbulence channels

In this paper, we analyse the error performance of transmitter/receiver array free-space optical (FSO) communication system employing binary phase shift keying (BPSK) subcarrier intensity modulation (SIM) in clear but turbulent atmospheric channel. Subcarrier modulation is employed to eliminate the need for adaptive threshold detector. Direct detection is employed at the receiver and each subcarrier is subsequently demodulated coherently. The effect of irradiance fading is mitigated with an array of lasers and photodetectors. The received signals are linearly combined using the optimal maximum ratio combining (MRC), the equal gain combining (EGC) and the selection combining (SelC). The bit error rate (BER) equations are derived considering additive white Gaussian noise and log normal intensity fluctuations. This work is part of the EU COST actions and EU projects