62 research outputs found
Stochastic approach to DNA breathing dynamics
We propose a stochastic Gillespie scheme to describe the temporal
fluctuations of local denaturation zones in double-stranded DNA as a single
molecule time series. It is demonstrated that the model recovers the
equilibrium properties. We also study measurable dynamical quantities such as
the bubble size autocorrelation function. This efficient computational approach
will be useful to analyse in detail recent single molecule experiments on
clamped homopolymer breathing domains, to probe the parameter values of the
underlying Poland-Scheraga model, as well as to design experimental conditions
for similar setups.Comment: 7 pages, 6 figures, epl.cl
Information theoretical study of cross-talk mediated signal transduction in MAPK pathways
Biochemical networks related to similar functional pathways are often
correlated due to cross-talk among the homologous proteins in the different
networks. Using a stochastic framework, we address the functional significance
of the cross-talk between two pathways. Our theoretical analysis on generic
MAPK pathways reveals cross-talk is responsible for developing coordinated
fluctuations between the pathways. The extent of correlation evaluated in terms
of the information theoretic measure provides directionality to net information
propagation. Stochastic time series and scattered plot suggest that the
cross-talk generates synchronization within a cell as well as in a cellular
population. Depending on the number of input and output, we identify signal
integration and signal bifurcation motif that arise due to inter-pathway
connectivity in the composite network. Analysis using partial information
decomposition quantifies the net synergy in the information propagation through
these branched pathways.Comment: Revised version, 17 pages, 5 figure
ATLAS IBL Pixel Upgrade
The upgrade for ATLAS detector will undergo different phase towards
super-LHC. The first upgrade for the Pixel detector will consist of the
construction of a new pixel layer which will be installed during the first
shutdown of the LHC machine (LHC phase-I upgrade). The new detector, called
Insertable B-Layer (IBL), will be inserted between the existing pixel detector
and a new (smaller radius) beam-pipe at a radius of 3.3 cm. The IBL will
require the development of several new technologies to cope with increase of
radiation or pixel occupancy and also to improve the physics performance which
will be achieved by reducing the pixel size and of the material budget. Three
different promising sensor technologies (planar-Si, 3D-Si and diamond) are
currently under investigation for the pixel detector. An overview of the
project with particular emphasis on pixel module is presented in this paper.Comment: 3 pages, 3 figures, presented at the 12th Topical Seminar on
Innovative Particle and Radiation Detectors (IPRD10) 7 - 10 June 2010, Siena
(IT). Accepted by Nuclear Physics B (Proceedings Supplements) (2011
Role of relaxation time scale in noisy signal transduction
Intracellular fluctuations, mainly triggered by gene expression, are an
inevitable phenomenon observed in living cells. It influences generation of
phenotypic diversity in genetically identical cells. Such variation of cellular
components is beneficial in some contexts but detrimental in others. To
quantify the fluctuations in a gene product, we undertake an analytical scheme
for studying few naturally abundant linear as well as branched chain network
motifs. We solve the Langevin equations associated with each motif under the
purview of linear noise approximation and quantify Fano factor and mutual
information. Both quantifiable expressions exclusively depend on the relaxation
time (decay rate constant) and steady state population of the network
components. We investigate the effect of relaxation time constraints on Fano
factor and mutual information to indentify a time scale domain where a network
can recognize the fluctuations associated with the input signal more reliably.
We also show how input population affects both quantities. We extend our
calculation to long chain linear motif and show that with increasing chain
length, the Fano factor value increases but the mutual information processing
capability decreases. In this type of motif, the intermediate components are
shown to act as a noise filter that tune up input fluctuations and maintain
optimum fluctuations in the output. For branched chain motifs, both quantities
vary within a large scale due to their network architecture and facilitate
survival of living system in diverse environmental conditions.Comment: 14 pages, 6 figure
Adiabatic noise-induced escape rate for nonequilibrium open systems
We consider the motion of an overdamped particle in a force field in presence
of an external, adiabatic noise, without the restriction that the noise process
is Gaussian or the stochastic process is Markovian. We examine the condition
for attainment of steady state for this nonequilibrium open system and
calculate the adiabatic noise-induced rate of escape of the particle over a
barrier.Comment: 6 pages, 3 figure
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