Homoclinic bifurcations in low-Prandtl-number Rayleigh-B\'{e}nard convection with uniform rotation

We present results of direct numerical simulations on homoclinic gluing and ungluing bifurcations in low-Prandtl-number ($0 \leq Pr \leq 0.025$) Rayleigh-B\'{e}nard system rotating slowly and uniformly about a vertical axis. We have performed simulations with \textit{stress-free} top and bottom boundaries for several values of Taylor number ($5 \leq Ta \leq 50$) near the instability onset. We observe a single homoclinic ungluing bifurcation, marked by the spontaneous breaking of a larger limit cycle into two limit cycles with the variation of the reduced Rayleigh number $r$ for smaller values of $Ta (< 25)$. A pair of homoclinic bifurcations, instead of one bifurcation, is observed with variation of $r$ for slightly higher values of $Ta$ ($25 \leq Ta \leq 50$) in the same fluid dynamical system. The variation of the bifurcation threshold with $Ta$ is also investigated. We have also constructed a low-dimensional model which qualitatively captures the dynamics of the system near the homoclinic bifurcations for low rotation rates. The model is used to study the unfolding of bifurcations and the variation of the homoclinic bifurcation threshold with $Pr$.Comment: 6 pages, 7 figures, 1 tabl

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

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

Dependence of acoustic surface gravity on disc thickness for accreting astrophysical black holes

For axially symmetric accretion maintained in hydrostatic equilibrium along the vertical direction, we investigate how the characteristic features of the embedded acoustic geometry depends on the background Kerr metric, and how such dependence is governed by three different expressions of the thickness of the matter flow. We first obtain the location of the sonic points and stationary shock between the sonic points. We then linearly perturb the flow to obtain the corresponding metric elements of the acoustic space-time. We thus construct the causal structure to establish that the sonic points and the shocks are actually the analogue black hole type and white hole type horizons, respectively. We finally compute the value of the acoustic surface gravity as a function of the spin angular momentum of the rotating black hole for three different flow thicknesses considered in the present work. We find that for some flow models, the intrinsic acoustic geometry, although in principle may be extended up to the outer gravitational horizon of the astrophysical black hole, cannot be constructed beyond a certain truncation radius as imposed by the expressions of the thickness function of the corresponding flow.Comment: 22 pages, 9 figure