1,329 research outputs found
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 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 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 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 resonance entails a reminiscence to
perturbative 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
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