Related papers: Processive and Distributive Non-Equilibrium Networ…

Many biochemical processes can successfully be described by dynamical systems allowing some form of switching when, depending on their initial conditions, solutions of the dynamical system end up in different regions of state space…

Computing equilibrium states in condensed-matter many-body systems, such as solvated proteins, is a long-standing challenge. Lacking methods for generating statistically independent equilibrium samples in "one shot", vast computational…

Demonstrating a quantum computational advantage will require high-fidelity control and readout of multi-qubit systems. As system size increases, multiplexed qubit readout becomes a practical necessity to limit the growth of resource…

Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…

Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…

We study financial networks where banks are connected through bilateral liabilities and may default when resources are insufficient to meet obligations. We consider both the standard proportional clearing model and a priority-proportional…

Several mechanisms have been proposed to explain the spontaneous generation of self-organized patterns, hypothesised to play a role in the formation of many of the magnificent patterns observed in Nature. In several cases of interest, the…

Real-time hierarchical energy-sharing markets are promising to coordinate large numbers of prosumers. Still, most existing clearing methods rely on linearized or DC power-flow models and do not explicitly handle reactive power or…

Disordered many-body systems exhibit a wide range of emergent phenomena across different scales. These complex behaviors can be utilized for various information processing tasks such as error correction, learning, and optimization. Despite…

In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory…

Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…

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…

The impossibility of attaining equilibrium for cyclic chemical reaction networks with irreversible steps is apparently due to a divergent entropy production rate. A deeper reason seems to be the violation of the detailed balance condition.…

While machine-learning models are flourishing and transforming many aspects of everyday life, the inability of humans to understand complex models poses difficulties for these models to be fully trusted and embraced. Thus, interpretability…

We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…

We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are…

Deep learning has redefined the field of artificial intelligence (AI) thanks to the rise of artificial neural networks, which are architectures inspired by their neurological counterpart in the brain. Through the years, this dualism between…

Designing reaction pathways that maximize the production of a target compound in a given metabolic network is a fundamental problem in systems biology. In this study, we systematically explore the non-oxidative glycolysis metabolic network,…

A Topological examination of phospholipid dynamics in the Far from Equilibrium state has demonstrated that metabolically active cells use waste heat to generate spatially patterned membrane flows by forced convection and shear. This paper…

Across all scales of the physical world, dynamical systems can often be usefully represented as abstract networks that encode the system's units and inter-unit interactions. Understanding how physical rules shape the topological structure…