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The density of synaptic receptors in front of presynaptic release sites is stabilized in the presence of scaffold proteins, but the receptors and scaffold molecules have local exchanges with characteristic times shorter than that of the…
We investigate the stability of $N$-soliton molecules in dispersion-managed optical fibers with focus on the recently realized 2- and 3-soliton molecules. We calculate their binding energy using an averaged nonlinear Schr$\rm{\ddot…
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically…
We introduce a simple model of static networks, where nodes are located on a ring structure, and two accompanying dynamic rules of repeated averaging on periodic node states. We assume nodes can interact with neighbors, and will add…
Switch-like responses arising from bistability have been linked to cell signaling processes and memory. Revealing the shape and properties of the set of parameters that lead to bistability is necessary to understand the underlying…
The functions of many networked systems in physics, biology or engineering rely on a coordinated or synchronized dynamics of its constituents. In power grids for example, all generators must synchronize and run at the same frequency and…
We carry out a comprehensive linear stability analysis of active Brownian particle systems around a constant homogeneous state. These scalar models, being important prototypes for the continuous description of active matter, are…
Linear functions of the site frequency spectrum (SFS) play a major role for understanding and investigating genetic diversity. Estimators of the mutation rate (e.g. based on the total number of segregating sites or average of the pairwise…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
We study a multispecies $t$-PushTASEP system on a finite ring of $n$ sites with site-dependent rates $x_1,\dots,x_n$. Let $\lambda=(\lambda_1,\dots,\lambda_n)$ be a partition whose parts represent the species of the $n$ particles on the…
We consider cascades of enzymatic Goldbeter-Koshland loops with any number n of layers, for which there exist two layers involving the same phosphatase. Even if the number of variables and the number of conservation laws grow linearly with…
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…
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…
Multistable non-equilibrium systems are abundant outcomes of nonlinear dynamics with feedback but still relatively little is known about what determines the stability of the steady states and their switching rates in terms of entropy and…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
The equilibrium distribution function determines macroscopic observables in statistical physics. While conventional methods correct equilibrium distributions in weakly nonlinear or near-integrable systems, they fail in strongly nonlinear…
The random arrest of the diffusion of a single particle and its return to its origin has served as the paradigmatic example of a large variety of processes undergoing stochastic resetting. While the implications and applications of…
We present some new theoretical and computational results for the stationary points of bulk systems. First we demonstrate how the potential energy surface can be partitioned into catchment basins associated with every stationary point using…