Noise-induced dynamics in bistable systems with delay

Noise-induced dynamics of a prototypical bistable system with delayed feedback is studied theoretically and numerically. For small noise and magnitude of the feedback, the problem is reduced to the analysis of the two-state model with transition rates depending on the earlier state of the system. In this two-state approximation, we found analytical formulae for the autocorrelation function, the power spectrum, and the linear response to a periodic perturbation. They show very good agreement with direct numerical simulations of the original Langevin equation. The power spectrum has a pronounced peak at the frequency corresponding to the inverse delay time, whose amplitude has a maximum at a certain noise level, thus demonstrating coherence resonance. The linear response to the external periodic force also has maxima at the frequencies corresponding to the inverse delay time and its harmonics.Comment: 4 pages, 4 figures, submitted to Physical Review Letter

Deterministic and stochastic descriptions of gene expression dynamics

A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or implicitly etc. Here we consider simple systems of unregulated (constitutive) gene expression and compare different mathematical descriptions systematically to obtain insight into the errors that are introduced by various common approximations such as describing cell growth and division by an effective protein degradation term. In particular, we show that the population average of protein content of a cell exhibits a subtle dependence on the dynamics of growth and division, the specific model for volume growth and the age structure of the population. Nevertheless, the error made by models with implicit cell growth and division is quite small. Furthermore, we compare various models that are partially stochastic to investigate the impact of different sources of (intrinsic) noise. This comparison indicates that different sources of noise (protein synthesis, partitioning in cell division) contribute comparable amounts of noise if protein synthesis is not or only weakly bursty. If protein synthesis is very bursty, the burstiness is the dominant noise source, independent of other details of the model. Finally, we discuss two sources of extrinsic noise: cell-to-cell variations in protein content due to cells being at different stages in the division cycles, which we show to be small (for the protein concentration and, surprisingly, also for the protein copy number per cell) and fluctuations in the growth rate, which can have a significant impact.Comment: 23 pages, 5 figures; Journal of Statistical physics (2012

Comments on Non-Commutative Phenomenology

It is natural to ask whether non-commutative geometry plays a role in four dimensional physics. By performing explicit computations in various toy models, we show that quantum effects lead to violations of Lorentz invariance at the level of operators of dimension three or four. The resulting constraints are very stringent.Comment: Correction of an error in the U(1) and U(N) calculation leads to stronger limits than those given previously Clarifying comments and reference adde

Missouri 2011 Soft Red Winter Wheat Performance Tests

This report is published by the MU Variety Testing Program, Division of Plant Sciences, University of Missouri. The work was supported by fees from companies and organizations submitting varieties for evaluation. The large number of varieties available makes selection of a superior variety difficult. To select intelligently, producers need a reliable, unbiased, up-to-date source of information that will permit valid comparisons among available varieties. The objective of the MU Variety Testing Program is to provide this information. Tests are conducted under as close to uniform conditions as possible. Small plots are used to reduce the chance of soil and other variations occurring among variety plots. Results obtained should aid individual growers in judging the relative merits of many of the commercial wheat varieties available in Missouri

Monomeric Bistability and the Role of Autoloops in Gene Regulation

Genetic toggle switches are widespread in gene regulatory networks (GRN). Bistability, namely the ability to choose among two different stable states, is an essential feature of switching and memory devices. Cells have many regulatory circuits able to provide bistability that endow a cell with efficient and reliable switching between different physiological modes of operation. It is often assumed that negative feedbacks with cooperative binding (i.e. the formation of dimers or multimers) are a prerequisite for bistability. Here we analyze the relation between bistability in GRN under monomeric regulation and the role of autoloops under a deterministic setting. Using a simple geometric argument, we show analytically that bistability can also emerge without multimeric regulation, provided that at least one regulatory autoloop is present

Dynamically Driven Renormalization Group Applied to Sandpile Models

The general framework for the renormalization group analysis of self-organized critical sandpile models is formulated. The usual real space renormalization scheme for lattice models when applied to nonequilibrium dynamical models must be supplemented by feedback relations coming from the stationarity conditions. On the basis of these ideas the Dynamically Driven Renormalization Group is applied to describe the boundary and bulk critical behavior of sandpile models. A detailed description of the branching nature of sandpile avalanches is given in terms of the generating functions of the underlying branching process.Comment: 18 RevTeX pages, 5 figure

Anapole Moment and Other Constraints on the Strangeness Conserving Hadronic Weak Interaction

Standard analyses of low-energy NN and nuclear parity-violating observables have been based on a pi-, rho-, and omega-exchange model capable of describing all five independent s-p partial waves. Here a parallel analysis is performed for the one-body, exchange-current, and nuclear polarization contributions to the anapole moments of 133Cs and 205Tl. The resulting constraints are not consistent, though there remains some degree of uncertainty in the nuclear structure analysis of the atomic moments.Comment: Revtex, 10 pages, 1 figur

High Preservation of CpG Cytosine Methylation Patterns at Imprinted Gene Loci in Liver and Brain of Aged Mice

A gradual loss of the correct patterning of 5-methyl cytosine marks in gene promoter regions has been implicated in aging and age-related diseases, most notably cancer. While a number of studies have examined DNA methylation in aging, there is no consensus on the magnitude of the effects, particularly at imprinted loci. Imprinted genes are likely candidate to undergo age-related changes because of their demonstrated plasticity in utero, for example, in response to environmental cues. Here we quantitatively analyzed a total of 100 individual CpG sites in promoter regions of 11 imprinted and non-imprinted genes in liver and cerebral cortex of young and old mice using mass spectrometry. The results indicate a remarkably high preservation of methylation marks during the aging process in both organs. To test if increased genotoxic stress associated with premature aging would destabilize DNA methylation we analyzed two DNA repair defective mouse models showing a host of premature aging symptoms in liver and brain. However, also in these animals, at the end of their life span, we found a similarly high preservation of DNA methylation marks. We conclude that patterns of DNA methylation in gene promoters of imprinted genes are surprisingly stable over time in normal, postmitotic tissues and that the

An examination of the effects of self-regulatory focus on the perception of the media richness: the case of email

Communication is a key element in organizations’ business success. The media richness theory and the channel expansion theory are two of the most influential theories regarding the selection and use of communication media in organizations; however, literature has focused little on the effects of self-regulation by managers and employees in these theories. To analyze these topics, this study develops an empirical investigation by gathering data from 600 managers and employees using a questionnaire. The results suggest that the perception of media richness is positively affected when the individual shows a promotion focus or strategy.Peer ReviewedPostprint (author’s final draft

3D Position Sensitive XeTPC for Dark Matter Search

The technique to realize 3D position sensitivity in a two-phase xenon time projection chamber (XeTPC) for dark matter search is described. Results from a prototype detector (XENON3) are presented.Comment: Presented at the 7th UCLA Symposium on "Sources and Detection of Dark Matter and Dark Energy in the Universe