相关论文: The Number of Multistate Nested Canalyzing Functio…

Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…

Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…

Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…

Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…

Traditional mathematical approaches to studying analytically the dynamics of neural networks rely on the mean-field approximation, which is rigorously applicable only to networks of infinite size. However, all existing real biological…

Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…

The ability to reroute and control flow is vital to the function of venation networks across a wide range of organisms. By modifying individual edges in these networks, either by adjusting edge conductances or creating and destroying edges,…

Polynomial dynamical systems are widely used to model and study real phenomena. In biochemistry, they are the preferred choice for modelling the concentration of chemical species in reaction networks with mass-action kinetics. These systems…

In this paper we consider the problem of controlling a limited number of target nodes of a network. Equivalently, we can see this problem as controlling the target variables of a structured system, where the state variables of the system…

Nested canalization (NC) is a property of Boolean functions which has been recently extended to multivalued functions. We study the effect of the Van Ham mapping (from multivalued to Boolean functions) on this property. We introduce the…

In this note we describe the theory of functional asynchronous networks and one of the main results, the Modularization of Dynamics Theorem, which for a large class of functional asynchronous networks gives a factorization of dynamics in…

A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…

The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…

Identifying and explaining the structure of complex networks at different scales has become an important problem across disciplines. At the mesoscale, modular architecture has attracted most of the attention. At the macroscale, other…

Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…

Counting the number of isomers of a chemical molecule is one of the formative problems of graph theory. However, recent progress has been slow, and the problem has largely been ignored in modern network science. Here we provide an…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

Wider adoption of neural networks in many critical domains such as finance and healthcare is being hindered by the need to explain their predictions and to impose additional constraints on them. Monotonicity constraint is one of the most…

We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with…

Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive…