7,626 research outputs found
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 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.
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