Rectification of spatial disorder

We demonstrate that a large ensemble of noiseless globally coupled-pinned oscillators is capable of rectifying spatial disorder with spontaneous current activated through a dynamical phase transition mechanism, either of first or second order, depending on the profile of the pinning potential. In the presence of an external weak drive, the same collective mechanism can result in an absolute negative mobility, which, though not immediately related to symmetry breaking, is most prominent at the phase transition

Phase synchronization and noise-induced resonance in systems of coupled oscillators

We study synchronization and noise-induced resonance phenomena in systems of globally coupled oscillators, each possessing finite inertia. The behavior of the order parameter, which measures collective synchronization of the system, is investigated as the noise level and the coupling strength are varied, and hysteretic behavior is manifested. The power spectrum of the phase velocity is also examined and the quality factor as well as the response function is obtained to reveal noise-induced resonance behavior.Comment: to be published in Phys. Rev.

Resonant effects in a voltage-activated channel gating

The non-selective voltage activated cation channel from the human red cells, which is activated at depolarizing potentials, has been shown to exhibit counter-clockwise gating hysteresis. We have analyzed the phenomenon with the simplest possible phenomenological models by assuming $2\times 2$ discrete states, i.e. two normal open/closed states with two different states of ``gate tension.'' Rates of transitions between the two branches of the hysteresis curve have been modeled with single-barrier kinetics by introducing a real-valued ``reaction coordinate'' parameterizing the protein's conformational change. When described in terms of the effective potential with cyclic variations of the control parameter (an activating voltage), this model exhibits typical ``resonant effects'': synchronization, resonant activation and stochastic resonance. Occurrence of the phenomena is investigated by running the stochastic dynamics of the model and analyzing statistical properties of gating trajectories.Comment: 12 pages, 9 figure

Scale-free networks in complex systems

In the past few years, several studies have explored the topology of interactions in different complex systems. Areas of investigation span from biology to engineering, physics and the social sciences. Although having different microscopic dynamics, the results demonstrate that most systems under consideration tend to self-organize into structures that share common features. In particular, the networks of interaction are characterized by a power law distribution, $P(k)\sim k^{-\alpha}$, in the number of connections per node, $k$, over several orders of magnitude. Networks that fulfill this propriety of scale-invariance are referred to as ``scale-free''. In the present work we explore the implication of scale-free topologies in the antiferromagnetic (AF) Ising model and in a stochastic model of opinion formation. In the first case we show that the implicit disorder and frustration lead to a spin-glass phase transition not observed for the AF Ising model on standard lattices. We further illustrate that the opinion formation model produces a coherent, turbulent-like dynamics for a certain range of parameters. The influence, of random or targeted exclusion of nodes is studied.Comment: 9 pages, 4 figures. Proceeding to "SPIE International Symposium Microelectronics, MEMS, and Nanotechnology", 11-15 December 2005, Brisbane, Australi

Stochastic Resonance in Underdamped, Bistable Systems

We carry out a detailed numerical investigation of stochastic resonance in underdamped systems in the non-perturbative regime. We point out that an important distinction between stochastic resonance in overdamped and underdamped systems lies in the lack of dependence of the amplitude of the noise-averaged trajectory on the noise strength, in the latter case. We provide qualitative explanations for the observed behavior and show that signatures such as the initial decay and long-time oscillatory behaviour of the temporal correlation function and peaks in the noise and phase averaged power spectral density, clearly indicate the manifestation of resonant behaviour in noisy, underdamped bistable systems in the weak to moderate noise regime.Comment: Revtex; (10+8)pp including 8 figure

Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay

The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation. Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to environmental conditions. We developed a computational technique based on stochastic modeling, to infer condition-specific individual mRNA half-lives directly from gene expression time-courses. Predictions from our method were validated by experimentally measured mRNA decay rates during the intraerythrocytic developmental cycle of Plasmodium falciparum. We then applied our methodology to publicly available data on the reproductive and metabolic cycle of budding yeast. Strikingly, our analysis revealed, in all cases, the presence of periodic changes in decay rates of sequentially induced genes and co-ordination strategies between transcription and degradation, thus suggesting a general principle for the proper coordination of transcription and degradation machinery in response to internal and/or external stimuli. Citation: Cacace F, Paci P, Cusimano V, Germani A, Farina L (2012) Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay. PLoS Comput Biol 8(11): e1002772. doi:10.1371/journal.pcbi.100277