47 research outputs found
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
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
Diagonalization of a real-symmetric Hamiltonian by genetic algorithm: a recipe based on minimization of Rayleigh quotient
A genetic algorithm-based recipe involving minimization of the Rayleigh quotient is proposed for the sequential extraction of eigenvalues and eigenvectors of a real symmetric matrix with and without basis optimization. Important features of the method are analysed, and possible directions of development suggested
Lyoluminescence:a theoretical approach
When strongly energized halide or organic crystals are dissolved in a liquid solvent (like water), light is emitted as a result of a recombination process. This phenomenon is called lyoluminescence. The emitted light intensity, called the lyoluminescent intensity, depends on a class of factors like radiation dose, probability of radiative recombination, rate of dissolution in the solvent, etc. Combining some of these numerous effects we develop a nonlinear differential equation and analyze it by a dynamical system analysis as well as by exact numerical integration. The corresponding plot of the theoretical lyoluminescent intensity versus time graph, called the glow curve (Fig. (1)), matches very well with the shape of the experimental curve (Fig. (2)) for a vast range of characteristic values of the controlling parameters. ©2000 The American Physical Society
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
Interplay of degeneracy and non-degeneracy in fluctuations propagation in coherent feed-forward loop motif
We present a stochastic framework to decipher fluctuations propagation in
classes of coherent feed-forward loops. The systematic contribution of the
direct (one-step) and indirect (two-step) pathways is considered to quantify
fluctuations of the output node. We also consider both additive and
multiplicative integration mechanisms of the two parallel pathways (one-step
and two-step). Analytical expression of the output node's coefficient of
variation shows contributions of intrinsic, one-step, two-step, and
cross-interaction in closed form. We observe a diverse range of degeneracy and
non-degeneracy in each of the decomposed fluctuations term and their
contribution to the overall output fluctuations of each coherent feed-forward
loop motif. Analysis of output fluctuations reveals a maximal level of
fluctuations of the coherent feed-forward loop motif of type 1.Comment: 20 pages, 4 figure