相关论文: Exponential equilibration of genetic circuits usin…
We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…
We present a study of the equilibration process of nonequilibrium systems by means of molecular dynamics simulation technique. The nonequilibrium conditions are achieved in systems by defining velocity components of the constituent atoms…
Sensitive detection of low-abundance molecular targets is widely assumed to require enzymatic amplification, such as PCR, to achieve low detection limits. In amplification-free platforms, sensitivity is traditionally constrained by…
The time evolution of the entanglement entropy in non-equilibrium quantum systems provides crucial information about the structure of the time-dependent state. For quantum quench protocols, by combining a quasiparticle picture for the…
We consider the linear growth-fragmentation equation arising in the modelling of cell division or polymerisation processes. For constant coefficients, we prove that the dynamics converges to the steady state with an exponential rate. The…
We study the convergence to equilibrium of a class of nonlinear recombination models. In analogy with Boltzmann's H theorem from kinetic theory, and in contrast with previous analysis of these models, convergence is measured in terms of…
We review the conformal field theory approach to entanglement entropy. We show how to apply these methods to the calculation of the entanglement entropy of a single interval, and the generalization to different situations such as finite…
The aim of this study is to generalise recent results of the two last authors on en-tropy methods for measure solutions of the renewal equation to other classes of structured population problems. Specifically, we develop a generalised…
We establish sharp long time asymptotic behaviour for a family of entropies to defective Fokker-Planck equations and show that, much like defective finite dimensional ODEs, their decay rate is an exponential multiplied by a polynomial in…
This paper presents a thermodynamically consistent model for multicomponent electrolyte solutions. The first part of this paper derives the general governing equations for nonequilibrium systems within the theory of nonequilibrium…
A mathematical model for a two-gene regulatory network is derived and several of their properties analyzed. Due to the presence of mixed continuous/discrete dynamics and hysteresis, we employ a hybrid systems model to capture the dynamics…
The thermodynamic definition of entropy can be extended to nonequilibrium systems based on its relation to information. To apply this definition in practice requires access to the physical system's microstates, which may be prohibitively…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
Bayesian optimal experimental design provides a principled framework for selecting experimental settings that maximize obtained information. In this work, we focus on estimating the expected information gain in the setting where the…
We report on the dynamical formation of exceptional degeneracies in basic correlation functions of non-integrable one- and two-dimensional systems quenched to the vicinity of a critical point. Remarkably, fine-tuned semi-metallic points in…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
Most natural systems operate far from equilibrium, displaying time-asymmetric, irreversible dynamics characterized by a positive entropy production while exchanging energy and matter with the environment. Although stochastic thermodynamics…
In this paper, we study the equilibrium behavior of Eigen's quasispecies equations for an arbitrary gene network. We consider a genome consisting of $ N $ genes, so that each gene sequence $ \sigma $ may be written as $ \sigma = \sigma_1…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
It is shown how the phase-damping master equation, either in Markovian and nonMarkovian regimes, can be obtained as an averaged random unitary evolution. This, apart from offering a common mathematical setup for both regimes, enables us to…