Transient Pulse Formation in Jasmonate Signaling Pathway

The jasmonate (JA) signaling pathway in plants is activated as defense response to a number of stresses like attacks by pests or pathogens and wounding by animals. Some recent experiments provide significant new knowledge on the molecular detail and connectivity of the pathway. The pathway has two major components in the form of feedback loops, one negative and the other positive. We construct a minimal mathematical model, incorporating the feedback loops, to study the dynamics of the JA signaling pathway. The model exhibits transient gene expression activity in the form of JA pulses in agreement with experimental observations. The dependence of the pulse amplitude, duration and peak time on the key parameters of the model is determined computationally. The deterministic and stochastic aspects of the pathway dynamics are investigated using both the full mathematical model as well as a reduced version of it. We also compare the mechanism of pulse formation with the known mechanisms of pulse generation in some bacterial and viral systems

Modulus stabilization in a non-flat warped braneworld scenario

The stability of the modular field in a warped brane world scenario has been a subject of interest for a long time. Goldberger \& Wise ( GW ) proposed a mechanism to achieve this by invoking a massive scalar field in the bulk space-time neglecting the back-reaction. In this work, we examine the possibility of stabilizing the modulus without bringing in any external scalar field. We show that instead of flat 3-branes as considered in Randall-Sundrum ( RS ) warped braneworld model, if one considers a more generalized version of warped geometry with de-Sitter 3-brane, then the brane vacuum energy automatically leads to a modulus potential with a metastable minimum. Our result further reveals that in this scenario the gauge hierarchy problem can also be resolved for appropriate choice of brane cosmological constant.Comment: 8 pages, 4 figure

Nucleosynthesis in the outflows associated with accretion disks of Type II collapsars

We investigate nucleosynthesis inside the outflows from gamma-ray burst (GRB) accretion disks formed by the Type II collapsars. In these collapsars, massive stars undergo core collapse to form a proto-neutron star initially and a mild supernova explosion is driven. The supernova ejecta lack momentum and subsequently this newly formed neutron star gets transformed to a stellar mass black hole via massive fallback. The hydrodynamics and the nucleosynthesis in these accretion disks has been studied extensively in the past. Several heavy elements are synthesized in the disk and much of these heavy elements are ejected from the disk via winds and outflows. We study nucleosynthesis in the outflows launched from these disks by using an adiabatic, spherically expanding outflow model, to understand which of these elements thus synthesized in the disk survive in the outflow. While studying this we find that many new elements like isotopes of titanium, copper, zinc etc. are present in the outflows. 56Ni is abundantly synthesized in most of the cases in the outflow which implies that the outflows from these disks in a majority of cases will lead to an observable supernova explosion. It is mainly present when outflow is considered from the He-rich, 56Ni/54Fe rich zones of the disks. However, outflow from the Si-rich zone of the disk remains rich in silicon. Although, emission lines of many of these heavy elements have been observed in the X-ray afterglows of several GRBs by Chandra, BeppoSAX, XMM-Newton etc., Swift seems to have not detected these lines yet.Comment: 15 pages including 8 figures; accepted for publication in The Astrophysical Journa

Functional characteristics of a double positive feedback loop coupled with autorepression

We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of pancreatic $\beta$-cells. The model exhibits bistability and hysteresis in appropriate parameter regions. The two stable steady states correspond to low (OFF state) and high (ON state) protein levels respectively. Using a deterministic approach, we show that the region of bistability increases in extent when the copy number of one of the genes is reduced from two to one. The negative feedback loop has the effect of reducing the size of the bistable region. Loss of a gene copy, brought about by mutations, hampers the normal functioning of the $\beta$-cells giving rise to the genetic disorder, maturity-onset diabetes of the young (MODY). The diabetic phenotype makes its appearance when a sizable fraction of the $\beta$-cells is in the OFF state. Using stochastic simulation techniques, we show that, on reduction of the gene copy number, there is a transition from the monostable ON to the ON state in the bistable region of the parameter space. Fluctuations in the protein levels, arising due to the stochastic nature of gene expression, can give rise to transitions between the ON and OFF states. We show that as the strength of autorepression increases, the ON$\to$OFF state transitions become less probable whereas the reverse transitions are more probable. The implications of the results in the context of the occurrence of MODY are pointed out..Comment: 9 pages 14 figure

Establishing a relation between mass and spin of stellar mass black holes

Stellar mass black holes (SMBHs), forming by the core collapse of very massive, rapidly rotating stars, are expected to exhibit a high density accretion disk around them developed from the spinning mantle of the collapsing star. A wide class of such disks, due to their high density and temperature, are effective emitters of neutrinos and hence called neutrino cooled disks. Tracking the physics relating the observed (neutrino) luminosity to the mass, spin of black holes (BHs) and the accretion rate (M_dot) of such disks, here we establish a correlation between the spin and mass of SMBHs at their formation stage. Our work shows that spinning BHs are more massive than non-spinning BHs for a given M_dot. However, slowly spinning BHs can turn out to be more massive than spinning BHs if M_dot at their formation stage was higher compared to faster spinning BHs.Comment: 7 pages including 3 figures and supplementary information; accepted for publication in Physical Review Letter

Emergent Bistability : Effects of Additive and Multiplicative Noise

Positive feedback and cooperativity in the regulation of gene expression are generally considered to be necessary for obtaining bistable expression states. Recently, a novel mechanism of bistability termed emergent bistability has been proposed which involves only positive feedback and no cooperativity in the regulation. An additional positive feedback loop is effectively generated due to the inhibition of cellular growth by the synthesized proteins. The mechanism, demonstrated for a synthetic circuit, may be prevalent in natural systems also as some recent experimental results appear to suggest. In this paper, we study the effects of additive and multiplicative noise on the dynamics governing emergent bistability. The calculational scheme employed is based on the Langevin and Fokker-Planck formalisms. The steady state probability distributions of protein levels and the mean first passage times are computed for different noise strengths and system parameters. In the region of bistability, the bimodal probability distribution is shown to be a linear combination of a lognormal and a Gaussian distribution. The variances of the individual distributions and the relative weights of the distributions are further calculated for varying noise strengths and system parameters. The experimental relevance of the model results is also pointed out.Comment: 16 pages, 11 figures, version accepted for publication in Eur. Phys. J.