Bistability: Requirements on Cell-Volume, Protein Diffusion, and Thermodynamics

Bistability is considered wide-spread among bacteria and eukaryotic cells, useful e.g. for enzyme induction, bet hedging, and epigenetic switching. However, this phenomenon has mostly been described with deterministic dynamic or well-mixed stochastic models. Here, we map known biological bistable systems onto the well-characterized biochemical Schloegl model, using analytical calculations and stochastic spatio-temporal simulations. In addition to network architecture and strong thermodynamic driving away from equilibrium, we show that bistability requires fine-tuning towards small cell volumes (or compartments) and fast protein diffusion (well mixing). Bistability is thus fragile and hence may be restricted to small bacteria and eukaryotic nuclei, with switching triggered by volume changes during the cell cycle. For large volumes, single cells generally loose their ability for bistable switching and instead undergo a first-order phase transition.Comment: 23 pages, 8 figure

Dimension reduction for systems with slow relaxation

We develop reduced, stochastic models for high dimensional, dissipative dynamical systems that relax very slowly to equilibrium and can encode long term memory. We present a variety of empirical and first principles approaches for model reduction, and build a mathematical framework for analyzing the reduced models. We introduce the notions of universal and asymptotic filters to characterize `optimal' model reductions for sloppy linear models. We illustrate our methods by applying them to the practically important problem of modeling evaporation in oil spills.Comment: 48 Pages, 13 figures. Paper dedicated to the memory of Leo Kadanof

Particle abundance in a thermal plasma: quantum kinetics vs. Boltzmann equation

We study the abundance of a particle species in a thermalized plasma by introducing a quantum kinetic description based on the non-equilibrium effective action. A stochastic interpretation of quantum kinetics in terms of a Langevin equation emerges naturally. We consider a particle species that is stable in the vacuum and interacts with \emph{heavier} particles that constitute a thermal bath in equilibrium and define of a fully renormalized single particle distribution function. The distribution function thermalizes on a time scale determined by the \emph{quasiparticle} relaxation rate. The equilibrium distribution function depends on the full spectral density and features off-shell contributions to the particle abundance. A model of a bosonic field $\Phi$ in interaction with two \emph{heavier} bosonic fields is studied. We find substantial departures from the Bose-Einstein result both in the high temperature and the low temperature but high momentum region. In the latter the abundance is exponentially suppressed but larger than the Bose-Einstein result. We obtain the Boltzmann equation in renormalized perturbation theory and highlight the origin of the differences. We argue that the corrections to the abundance of cold dark matter candidates are observationally negligible and that recombination erases any possible spectral distortions of the CMB. However we expect that the enhancement at high temperature may be important for baryogenesis.Comment: 39 pages, 11 figures. Clarifying remarks. To appear in Physical Review

Nonlinear effects of dark energy clustering beyond the acoustic scales

We extend the resummation method of Anselmi & Pietroni (2012) to compute the total density power spectrum in models of quintessence characterized by a vanishing speed of sound. For standard $\Lambda$CDM cosmologies, this resummation scheme allows predictions with an accuracy at the few percent level beyond the range of scales where acoustic oscillations are present, therefore comparable to other, common numerical tools. In addition, our theoretical approach indicates an approximate but valuable and simple relation between the power spectra for standard quintessence models and models where scalar field perturbations appear at all scales. This, in turn, provides an educated guess for the prediction of nonlinear growth in models with generic speed of sound, particularly valuable since no numerical results are yet available.Comment: 28 pages, 12 figure

Non-linear Evolution of Baryon Acoustic Oscillations from Improved Perturbation Theory in Real and Redshift Spaces

We study the non-linear evolution of baryon acoustic oscillations in the matter power spectrum and correlation function from the improved perturbation theory (PT). Based on the framework of renormalized PT, we apply the {\it closure approximation} that truncates the infinite series of loop contributions at one-loop order, and obtain a closed set of integral equations for power spectrum and non-linear propagator. The resultant integral expressions keep important non-perturbative properties which can dramatically improve the prediction of non-linear power spectrum. Employing the Born approximation, we then derive the analytic expressions for non-linear power spectrum and the predictions are made for non-linear evolution of baryon acoustic oscillations in power spectrum and correlation function. A detailed comparison between improved PT results and N-body simulations shows that a percent-level agreement is achieved in a certain range in power spectrum and in a rather wider range in correlation function. Combining a model of non-linear redshift-space distortion, we also evaluate the power spectrum and correlation function in correlation function. In contrast to the results in real space, the agreement between N-body simulations and improved PT predictions tends to be worse, and a more elaborate modeling for redshift-space distortion needs to be developed. Nevertheless, with currently existing model, we find that the prediction of correlation function has a sufficient accuracy compared with the cosmic-variance errors for future galaxy surveys with volume of a few (Gpc/h)^3 at z>=0.5.Comment: 25 pages, 15 figures, accepted for publication in Phys.Rev.