Related papers: Stochastic approach to DNA breathing dynamics
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…
Stochastic processes offer a fundamentally different paradigm of dynamics than deterministic processes, the most prominent example of the latter being Newton's laws of motion. Here, we discuss in a pedagogical manner a simple and…
We consider the dynamics of a model introduced recently by Bialas, Burda and Johnston. At equilibrium the model exhibits a transition between a fluid and a condensed phase. For long evolution times the dynamics of condensation possesses a…
Sparse functional/longitudinal data have attracted widespread interest due to the prevalence of such data in social and life sciences. A prominent scenario where such data are routinely encountered are accelerated longitudinal studies,…
Single-point measurements of fluctuations in the scrape-off layer of magnetized plasmas are generally found to be dominated by large-amplitude bursts which are associated with radial motion of blob-like structures. A stochastic model for…
Spatio-temporal bifurcations and complex dynamics in globally coupled intrinsically bistable electrochemical systems with an S-shaped current-voltage characteristic under galvanostatic control are studied theoretically on a one-dimensional…
In this work we employ the split-step technique combined with a Legendre pseudospectral representation to solve various time-dependent Gross-Pitaevskii equations (GPE). Our findings based on the numerical accuracy of this approach applied…
We present an analitical study of the dynamical process of the approach to steady state for a driven diffusive system represented by the microemulsion phase of a ternary mixture. The external applied field is given by a plane Couette shear…
We investigate the dynamics of atomic and molecular bosons weakly coupled via Feshbach detuning in the presence of Gaussian white noise. The time-evolution of the population imbalance between the two species, as well as the coherence of the…
The discrete self-trapping equation (DST) represents an useful model for several properties of one-dimensional nonlinear molecular crystals. The modulational instability of DST equation is discussed from a statistical point of view,…
We present a Bayesian non-parametric way of inferring stochastic differential equations for both regression tasks and continuous-time dynamical modelling. The work has high emphasis on the stochastic part of the differential equation, also…
We deal with a small enough tumor section to consider it homogeneous, such that populations of lymphocytes and cancer cells are independent of spatial coordinates. A stochastic model based in one step processes is developed to take into…
Many of the existing stochastic models of gene expression contain the first-order decay reaction term that may describe active protein degradation or dilution. If the model variable is interpreted as the molecule number, and not…
We introduce a method for engineering discrete local dynamics in globally-driven dual-species neutral atom experiments, allowing us to study emergent digital models through uniform analog controls. Leveraging the new opportunities offered…
Motivated by the desire to understand complex transient behaviour in fluid flows, we study the dynamics of an air bubble driven by the steady motion of a suspending viscous fluid within a Hele-Shaw channel with a centred depth perturbation.…
Stochastic thermodynamics provides a framework for describing small systems like colloids or biomolecules driven out of equilibrium but still in contact with a heat bath. Both, a first-law like energy balance involving exchanged heat and…
We study the dynamics of strongly repulsive Bose gas in tilted or driven bichromatic optical lattices. Using the Bose-Fermi mapping and exact numerical method, we calculate the reduced single-particle density matrices, and study the…
We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski…
In this paper, we consider two stochastic models of gene expression in prokaryotic cells. In the first model, sixteen biochemical reactions involved in transcription, translation and transcriptional regulation in the presence of inducer…
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…