Related papers: Quantifying fluctuations in reversible enzymatic c…
In spatially distributed cellular systems, it is often convenient to represent complicated auxiliary pathways and spatial transport by time-delayed reaction rates. Furthermore, many of the reactants appear in low numbers necessitating a…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
We investigate the probability distribution of the quantum fluctuations of thermodynamic functions of finite, ballistic, phase-coherent Fermi gases. Depending on the chaotic or integrable nature of the underlying classical dynamics, on the…
A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature…
We examine the question of whether the formal expressions of equilibrium statistical mechanics can be applied to time independent non-dissipative systems that are not in true thermodynamic equilibrium and are nonergodic. By assuming the…
We obtain lower and upper bounds on the skewness and kurtosis associated with the cycle completion time of unicyclic enzymatic reaction schemes. Analogous to a well known lower bound on the randomness parameter, the lower bounds on skewness…
Diverse physical systems are characterized by their response to small perturbations. Near thermodynamic equilibrium, the fluctuation-dissipation theorem provides a powerful theoretical and experimental tool to determine the nature of…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
This study proposes a novel approach to quantifying uncertainties of constitutive relations inferred from noisy experimental data using inverse modelling. We focus on electrochemical systems in which charged species (e.g., Lithium ions) are…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Fluctuation Theorems are central in stochastic thermodynamics, as they allow for quantifying the irreversibility of single trajectories. Although they have been experimentally checked in the classical regime, a practical demonstration in…
We investigate the model of "reversible ratchet" with interacting particles, introduced by us earlier [Europhys. Lett. 84, 50009 (2008)]. We further clarify the effect of efficiency enhancement due to interaction and show that it is of…
Intracellular transmission of information via chemical and transcriptional networks is thwarted by a physical limitation: the finite copy number of the constituent chemical species introduces unavoidable intrinsic noise. Here we provide a…
Fluctuation theorems are relations constraining the out-of-equilibrium fluctuations of thermodynamic quantities like the entropy production that were initially introduced for classical or quantum systems in contact with a thermal bath. Here…
Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…
A short review is presented of a recently developed computational approach which allows the study of the resistance noise over the full range of bias values, from the linear regime up to electrical breakdown. Resistance noise is described…
"\textit{The noise is the signal}"[R. Landauer, Nature \textbf{392}, 658 (1998)] emphasizes the rich information content encoded in fluctuations. This paper assesses the dynamical role of fluctuations of a quantum system driven far from…
The effect of a change of noise amplitudes in overdamped diffusive systems is linked to their unperturbed behavior by means of a nonequilibrium fluctuation-response relation. This formula holds also for systems with state-independent…
We introduce a framework to identify Fluctuation Relations for vector-valued observables in physical systems evolving through a stochastic dynamics. These relations arise from the particular structure of a suitable entropic functional and…
In this note we discuss a paradigmatic example of interacting particles subject to non conservative external forces and to the action of thermostats consisting of external (finite) reservoirs of particles. We then consider a model of…