Related papers: Fundamental Limits and Tradeoffs in Autocatalytic …
The speed limits on entanglement are defined as the maximal rate at which entanglement can be generated or degraded in a physical process. We derive the speed limits on entanglement, using the relative entropy of entanglement and…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
In areas such as computer software and hardware, manufacturing systems, and transportation, engineers encounter networks with arbitrarily large numbers of isomorphic subprocesses. Parameterized systems provide a framework for modeling such…
In a traffic network, vehicles normally select their routes selfishly. Consequently, traffic networks normally operate at an equilibrium characterized by Wardrop conditions. However, it is well known that equilibria are inefficient in…
Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive equilibria, we identify structural network conditions that…
Connectivity is a fundamental structural feature of a network that determines the outcome of any dynamics that happens on top of it. However, an analytical approach to obtain connection probabilities between nodes associated to paths of…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…
The identification of the limiting factors in the dynamical behavior of complex systems is an important interdisciplinary problem which often can be traced to the spectral properties of an underlying network. By deriving a general relation…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
A semiclassical method of complex trajectories for the calculation of the tunneling exponent in systems with many degrees of freedom is further developed. It is supplemented with an easily implementable technique, which enables one to…
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly…
A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life such as sugars, nucleotides, amino acids, and lipids to "molecular food sources" that have likely…
Qualitative attributes of the region between order and disorder are examined to explore models of genetic and protein networks. Results show how the connectivity of vertices and the strength of their connections are related and how their…
Active materials form a class of far-from-equilibrium systems that are driven internally and exhibit self-organization which can be harnessed to perform mechanical work. Inspired by experiments on synthetic active networks we examine limits…
Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…
A Markov chain model for spatially distributed autocatalytic systems with a quadratic reaction rate is considered. An approximate solution for the local probability distribution is obtained in the form of a perturbation expansion for the…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
In resource limited computing systems, sequence prediction models must operate under tight constraints. Various models are available that cater to prediction under these conditions that in some way focus on reducing the cost of…
Speed limit for classical stochastic Markov processes with discrete states is studied. We find that a trade-off inequality exists between the speed of the state transformation and the entropy production. The dynamical activity determines…