Enhancement of the stability of genetic switches by overlapping upstream regulatory domains

We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterised by a well defined lifetime which grows sub-exponentially with the number of copies of the most-expressed transcription factor, in the regime accessible by our numerical simulations. The stability can be markedly enhanced by a suitable choice of overlap between the upstream regulatory domains. Our results suggest that robustness against biochemical noise can provide a selection pressure that drives operons, that regulate each other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX

Stability Properties of Nonhyperbolic Chaotic Attractors under Noise

We study local and global stability of nonhyperbolic chaotic attractors contaminated by noise. The former is given by the maximum distance of a noisy trajectory from the noisefree attractor, while the latter is provided by the minimal escape energy necessary to leave the basin of attraction, calculated with the Hamiltonian theory of large fluctuations. We establish the important and counterintuitive result that both concepts may be opposed to each other. Even when one attractor is globally more stable than another one, it can be locally less stable. Our results are exemplified with the Holmes map, for two different sets of parameter, and with a juxtaposition of the Holmes and the Ikeda maps. Finally, the experimental relevance of these findings is pointed out.Comment: Phys.Rev. Lett., to be publishe

Robust Trapped-Ion Quantum Logic Gates by Continuous Dynamical Decoupling

We introduce a novel scheme that combines phonon-mediated quantum logic gates in trapped ions with the benefits of continuous dynamical decoupling. We demonstrate theoretically that a strong driving of the qubit decouples it from external magnetic-field noise, enhancing the fidelity of two-qubit quantum gates. Moreover, the scheme does not require ground-state cooling, and is inherently robust to undesired ac-Stark shifts. The underlying mechanism can be extended to a variety of other systems where a strong driving protects the quantum coherence of the qubits without compromising the two-qubit couplings.Comment: Slightly longer than the published versio

Hyperon production in near threshold nucleon-nucleon collisions

We study the mechanism of the associated Lambda-kaon and Sigma-kaon production in nucleon-nucleon collisions over an extended range of near threshold beam energies within an effective Lagrangian model, to understand of the new data on pp --> p Lambda K+ and pp --> p Sigma0 K+ reactions published recently by the COSY-11 collaboration. In this theory, the hyperon production proceeds via the excitation of N*(1650), N*(1710), and N*(1720) baryonic resonances. Interplay of the relative contributions of various resonances to the cross sections, is discussed as a function of the beam energy over a larger near threshold energy domain. Predictions of our model are given for the total cross sections of pp --> p Sigma+K0, pp --> n Sigma+K+, and pn --> n Lambda K+ reactions.Comment: 16 pages, 4 figures, one new table added and dicussions are updated, version accepted for publication by Physical Review

Mechanical quality factor of a sapphire fiber at cryogenic temperatures

A mechanical quality factor of $1.1 \times 10^{7}$ was obtained for the 199 Hz bending vibrational mode in a monocrystalline sapphire fiber at 6 K. Consequently, we confirm that pendulum thermal noise of cryogenic mirrors used for gravitational wave detectors can be reduced by the sapphire fiber suspension.Comment: To be published to Physiscs Letters A. Number of pages: 10 Number of figures: 5 Number of tables:

Sampling rare switching events in biochemical networks

Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because switching events are rapid, yet infrequent. We present a simulation technique that makes it possible to predict the rate and mechanism of flipping of biochemical switches. The method uses a series of interfaces in phase space between the two stable steady states of the switch to generate transition trajectories in a ratchet-like manner. We demonstrate its use by calculating the spontaneous flipping rate of a symmetric model of a genetic switch consisting of two mutually repressing genes. The rate constant can be obtained orders of magnitude more efficiently than using brute-force simulations. For this model switch, we show that the switching mechanism, and consequently the switching rate, depends crucially on whether the binding of one regulatory protein to the DNA excludes the binding of the other one. Our technique could also be used to study rare events and non-equilibrium processes in soft condensed matter systems.Comment: 9 pages, 6 figures, last page contains supplementary informatio

Escaping from nonhyperbolic chaotic attractors

We study the noise-induced escape process from chaotic attractors in nonhyperbolic systems. We provide a general mechanism of escape in the low noise limit, employing the theory of large fluctuations. Specifically, this is achieved by solving the variational equations of the auxiliary Hamiltonian system and by incorporating the initial conditions on the chaotic attractor unambiguously. Our results are exemplified with the H{\'e}non and the Ikeda map and can be implemented straightforwardly to experimental data.Comment: replaced with published versio

Oscillating epidemics in a dynamic network model: stochastic and mean-field analysis

An adaptive network model using SIS epidemic propagation with link-type-dependent link activation and deletion is considered. Bifurcation analysis of the pairwise ODE approximation and the network-based stochastic simulation is carried out, showing that three typical behaviours may occur; namely, oscillations can be observed besides disease-free or endemic steady states. The oscillatory behaviour in the stochastic simulations is studied using Fourier analysis, as well as through analysing the exact master equations of the stochastic model. By going beyond simply comparing simulation results to mean-field models, our approach yields deeper insights into the observed phenomena and help better understand and map out the limitations of mean-field models

Analytical study of non Gaussian fluctuations in a stochastic scheme of autocatalytic reactions

A stochastic model of autocatalytic chemical reactions is studied both numerically and analytically. The van Kampen perturbative scheme is implemented, beyond the second order approximation, so to capture the non Gaussianity traits as displayed by the simulations. The method is targeted to the characterization of the third moments of the distribution of fluctuations, originating from a system of four populations in mutual interaction. The theory predictions agree well with the simulations, pointing to the validity of the van Kampen expansion beyond the conventional Gaussian solution.Comment: 15 pages, 8 figures, submitted to Phys. Rev.