Related papers: Fundamental Limits and Tradeoffs in Autocatalytic …
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
Autocatalysis lies at the heart of many (bio)chemical processes and is key to processes leading up to the origin of life. Two seemingly very different formalisms have emerged that define autocatalysis. Kauffman introduced collective…
In machine learning, there is a fundamental trade-off between ease of optimization and expressive power. Neural Networks, in particular, have enormous expressive power and yet are notoriously challenging to train. The nature of that…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
This paper analyzes stochastic networks consisting of a set of finite capacity sites where different classes of individuals move according to some routing policy. The associated Markov jump processes are analyzed under a thermodynamic limit…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
A plausible mechanism of self-regulation in technological chains of the kind wherein input resources are converted into common final product through sequences of processing links having uniform kinetic properties is discussed. A bottleneck…
The concept of limiting step gives the limit simplification: the whole network behaves as a single step. However, in its simplest form this idea is applicable only to the simplest linear cycles in steady states. For such the simplest cycles…
We study the dynamics of a system made up of particles of two different species undergoing irreversible quadratic autocatalytic reactions: $A + B \to 2A$. We especially focus on the reaction velocity and on the average time at which the…
We analyse the autocatalytic structure of technological networks and evaluate its significance for the dynamics of innovation patenting. To this aim, we define a directed network of technological fields based on the International Patents…
The approach of shortcuts to adiabaticity enables the effective execution of adiabatic dynamics in quantum information processing with enhanced speed. Owing to the inherent trade-off between dynamical speed and the cost associated with the…
Motivated by the possibility of electrochemical control of phase separation, a variational theory of thermodynamic stability is developed for driven reactive mixtures, based on a nonlinear generalization of the Cahn-Hilliard and Allen-Cahn…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We…
We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a…
We introduce economic models based on Boolean Delay Equations: this formalism makes easier to take into account the complexity of the interactions between firms and is particularly appropriate for studying the propagation of an initial…
Time-discrete dynamical systems on a finite state space have been used with great success to model natural and engineered systems such as biological networks, social networks, and engineered control systems. They have the advantage of being…
We study dynamical transportation networks in a framework that includes extensions of the classical Cell Transmission Model to arbitrary network topologies. The dynamics are modeled as systems of ordinary differential equations describing…
In small systems, quantitative discrepancies between stochastic and deterministic descriptions of chemical kinetics can be significant, with their magnitude depending on the specific reaction network. Here, we study the Finke-Watzky…
We explore the limit of stochastic differential equations driven by some random processes satisfying singularly perturbed second order stochastic differential equations. The main tool we employ is the universal limit theorem in rough path…