相关论文: Critical lack of equilibrium in stochastic kinetic…
Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…
The aim of this article is to build on the use of tools from computational algebra initiated in Craciun, Dickenstein, Shiu, Sturmfels (JSC, 2009), for the study of general kinetic systems, which have a wide range of applications in…
Detailed balance of a chemical reaction network can be defined in several different ways. Here we investigate the relationship among four types of detailed balance conditions: deterministic, stochastic, local, and zero-order local detailed…
Living systems are typically characterized by irreversible processes. A condition equivalent to the reversibility is the detailed balance, whose absence is an obstacle for analytically solving ecological models. We revisit a promising model…
The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation,…
Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. In spite of their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to…
We study stochastic copying schemes in which discrimination between a right and a wrong match is achieved via different kinetic barriers or different binding energies of the two matches. We demonstrate that, in single-step reactions, the…
We develop a general framework for the discussion of detailed balance and analyse its microscopic background. We find that there should be two additions to the well-known $T$- or $PT$-invariance of the microscopic laws of motion: 1.…
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…
We present an overview of the effects of detailed-balance violating perturbations on the universal static and dynamic scaling behavior near a critical point. It is demonstrated that the standard critical dynamics universality classes are…
When modelling driven steady states of matter, it is common practice either to choose transition rates arbitrarily, or to assume that the principle of detailed balance remains valid away from equilibrium. Neither of those practices is…
In this paper we study a simple stochastic version of the Hopfield-Ninio kinetic proofreading model. The model is characterized by means of two parameters, the unbinding time, which depends on the binding energy between a ligand and a…
For a paradigmatic model of chemotaxis, we analyze the effect how a nonzero affinity driving receptors out of equilibrium affects sensitivity. This affinity arises whenever changes in receptor activity involve ATP hydrolysis. The…
Mass action type deterministic kinetic models of ion channels are usually constructed in such a way as to obey the principle of detailed balance (or, microscopic reversibility) for two reasons: first, the authors aspire to have models…
We further clarify the relation between detailed-balanced and complex-balanced equilibria of reversible chemical reaction networks. Our results hold for arbitrary kinetics and also for boundary equilibria. Detailed balance, complex balance,…