Related papers: Topologically protected modes in non-equilibrium s…
In this paper we report that notions of topological protection can be applied to stationary configurations that are driven far from equilibrium by active, dissipative processes. We show this for physically two disparate cases : stochastic…
Topological protection has emerged as an organizing principle for understanding and engineering robust collective behavior in electronic and material systems. Recent work suggests that topology may also play a role in organizing stochastic…
In an equilibrium chemical reaction mixture, the number of molecules present obeys a Poisson distribution. We ask when the same is true of the steady state of a nonequilibrium reaction network and obtain an essentially complete answer. In…
Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…
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…
Living systems are maintained out-of-equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due…
Many examples from quantum and classical physics are known where topological protection is responsible for the robustness of the dynamics. Less explored is the role of topological protection in the context of classical oscillatory systems.…
We study biochemical reaction networks capable of product discrimination inspired by biological proofreading mechanisms. At equilibrium, product discrimination, the selective formation of a "correct" product with respect to an "incorrect…
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…
Organisms often use cyclic changes in the concentrations of chemicals species to precisely time biological functions. Underlying these biochemical clocks are chemical reactions and transport processes, which are inherently stochastic.…
The topological features of quantum many-body wave functions are known to have profound consequences for the physics of ground-states and their low-energy excitations. We describe how topology influences the dynamics of many-body systems…
We analyze experimental data obtained from an electrical circuit having components at different temperatures, showing how to predict its response to temperature variations. This illustrates in detail how to utilize a recent linear response…
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…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
Nonlinear transport has emerged as a powerful approach to probe the quantum geometry of electronic wavefunctions, such as Berry curvature and quantum metric, in topological materials. While nonlinear responses governed by bulk quantum…
In this paper we investigate the applicability of non-equilibrium statistical mechanics to non-equilibrium damage phenomena. As an example, a fiber-bundle model with thermal noise and a fiber-bundle model with decay of fibers are…
Topological phases support edge states that can be robust to material deformations and other perturbations. While well-studied in quantum systems, topological phases have also been observed in stochastic and biochemical systems, yet it…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Limits on a system's response to external perturbations inform our understanding of how physical properties can be shaped by microscopic characteristics. Here, we derive constraints on the steady-state nonequilibrium response of physical…