Related papers: Size limits sensitivity in all kinetic schemes
Collective behaviour in biological systems is often accompanied by strong correlations. The question has therefore arisen of whether correlation is amplified by the vicinity to some critical point in the parameters space. Biological…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
Can the properties of the thermodynamic limit of a many-body quantum system be extrapolated by analysing a sequence of finite-size cases? We present a model for which such an approach gives completely misleading results: a translationally…
The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and…
Random exchange kinetic models are widely employed to describe the conservative dynamics of large interacting systems. Due to their simplicity and generality, they are quite popular in several fields, from statistical mechanics to…
We study the equilibrium and near-equilibrium properties of a holographic five-dimensional model consisting of Einstein gravity coupled to a scalar field with a non-trivial potential. The dual four-dimensional gauge theory is not conformal…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
Adaptation is used by biological sensory systems to respond to a wide range of environmental signals, by adapting their response properties to the statistics of the stimulus in order to maximize information transmission. We derive rules of…
We consider an evolutionary PDE system coupling the Cahn-Hilliard equation with singular potential, mass source and transport effects, to a Brinkman-type relation for the macroscopic velocity field and to a further equation describing the…
The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing…
Sensors often serve at least two purposes: predicting their input and minimizing dissipated heat. However, determining whether or not a particular sensor is evolved or designed to be accurate and efficient is difficult. This arises partly…
The standard quantum limit bounds the precision of measurements that can be achieved by ensembles of uncorrelated particles. Fundamentally, this limit arises from the non-commuting nature of quantum mechanics, leading to the presence of…
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological…
A mechanical system consisting of an elastic beam under harmonic excitation and an attached sliding body is investigated. Recent experimental observations suggest that the system passively (self-)adapts the axial location of the slider to…
A polymer-chain network is a collection of interconnected polymer-chains, made themselves of the repetition of a single pattern called a monomer. Our first main result establishes that, for a class of models for polymer-chain networks, the…
We study in this paper certain properties of the responses of dynamical systems to external inputs. The motivation arises from molecular systems biology. and, in particular, the recent discovery of an important transient property, related…
We review the standard lock and key (LK) model for binding small ligands to larger adsorbent molecule. We discuss three levels of the traditional LK model for binding. Within this model the binding constant or the Gibbs energy of the…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…