Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach

We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic Gillespie scheme with the denaturation zones in double stranded DNA studied as a single molecule time series. Simulated Annealing is used to find the optimum value of the activation energy for which the equilibrium bubble size distribution matches with a given value. It is demonstrated that the method overcomes even large noise in the input surrogate data.Comment: 9 pages, 4 figures, iop article package include

Melting of antikaon condensate in protoneutron stars

We study the melting of a $K^-$ condensate in hot and neutrino-trapped protoneutron stars. In this connection, we adopt relativistic field theoretical models to describe the hadronic and condensed phases. It is observed that the critical temperature of antikaon condensation is enhanced as baryon density increases. For a fixed baryon density, the critical temperature of antikaon condensation in a protoneutron star is smaller than that of a neutron star. We also exhibit the phase diagram of a protoneutron star with a $K^-$ condensate.Comment: 17 pages including 7 figure

Low-Mass Dileptons at the CERN-SpS: Evidence for Chiral Restoration?

Using a rather complete description of the in-medium $\rho$ spectral function - being constrained by various independent experimental information - we calculate pertinent dilepton production rates from hot and dense hadronic matter. The strong broadening of the $\rho$ resonance entails a reminiscence to perturbative $q\bar q$ annihilation rates in the vicinity of the phase boundary. The application to dilepton observables in Pb(158AGeV)+Au collisions - incorporating recent information on the hadro-chemical composition at CERN-SpS energies - essentially supports the broadening scenario. Possible implications for the nature of chiral symmetry restoration are outlined.Comment: 6 pages ReVTeX including 5 eps-figure

Local simulation of singlet statistics for restricted set of measurement

The essence of Bell's theorem is that, in general, quantum statistics cannot be reproduced by local hidden variable (LHV) model. This impossibility is strongly manifested while analyzing the singlet state statistics for Bell-CHSH violations. In this work, we provide various subsets of two outcome POVMs for which a local hidden variable model can be constructed for singlet state.Comment: 2 column, 5 pages, 4 figures, new references, abstract modified, accepted in JP

FlipDyn with Control: Resource Takeover Games with Dynamics

We present the FlipDyn, a dynamic game in which two opponents (a defender and an adversary) choose strategies to optimally takeover a resource that involves a dynamical system. At any time instant, each player can take over the resource and thereby control the dynamical system after incurring a state-dependent and a control-dependent costs. The resulting model becomes a hybrid dynamical system where the discrete state (FlipDyn state) determines which player is in control of the resource. Our objective is to compute the Nash equilibria of this dynamic zero-sum game. Our contributions are four-fold. First, for any non-negative costs, we present analytical expressions for the saddle-point value of the FlipDyn game, along with the corresponding Nash equilibrium (NE) takeover strategies. Second, for continuous state, linear dynamical systems with quadratic costs, we establish sufficient conditions under which the game admits a NE in the space of linear state-feedback policies. Third, for scalar dynamical systems with quadratic costs, we derive the NE takeover strategies and saddle-point values independent of the continuous state of the dynamical system. Fourth and finally, for higher dimensional linear dynamical systems with quadratic costs, we derive approximate NE takeover strategies and control policies which enable the computation of bounds on the value functions of the game in each takeover state. We illustrate our findings through a numerical study involving the control of a linear dynamical system in the presence of an adversary.Comment: 17 Pages, 2 figures. Under review at IEEE TA

A microscopic description and ultrastructural characterisation of Dientamoeba fragilis: An emerging cause of human enteric disease

Dientamoeba fragilis is a pathogenic trichomonad found in the gastrointestinal tract of humans and is implicated as a cause of diarrhoea. Despite its discovery over a century ago, there has been no recent thorough description of this parasite by microscopy. Scanning electron microscopy, transmission electron microscopy, confocal and light microscopy were therefore used to characterise D. fragilis populations growing in xenic culture. Two different populations - smooth and ruffled cells - were identifiable by scanning electron microscopy. No flagella, pelta structures, undulating membrane or pseudocyst-like forms were present. The organelles in D. fragilis were analysed by transmission electron microscopy; like Trichomonas and Histomonas, D. fragilis contains hydrogenosomes that presumably represent the site of anaerobic respiration. The nuclear morphology of D. fragilis trophozoites grown in vitro and trophozoites from clinical isolates were also compared by confocal microscopy and light microscopy. The majority of cells grown in culture were mononucleate while most cells in permanent stained faecal smears were binucleate. The two nuclei of D. fragilis are morphologically indistinguishable and contain equivalent amounts of DNA as determined by DAPI staining. The approximate cell and nuclear volume of four isolates of D. fragilis were measured and shown to be comparable to other trichomonads. In addition, the discovery of a virus-like particle is reported, to our knowledge for the first time in D. fragilis. This study therefore provides extensive and novel details of the ultrastructure of a neglected protozoan parasite that is an emerging cause of human disease. © 2011 Australian Society for Parasitology Inc

Sequence sensitivity of breathing dynamics in heteropolymer DNA

We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy (FCS) is demonstrated.Comment: 4 pages, 5 figures, to appear in Physical Review Letter