Related papers: Regulated Multiset Rewriting Systems
This article focuses on the optimization of a complex system which is composed of several subsystems. On the one hand, these subsystems are subject to multiple objectives, local constraints as well as local variables, and they are…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
We discuss various formalisms to describe string-to-string transformations. Many are based on automata and can be seen as operational descriptions, allowing direct implementations when the input scanner is deterministic. Alternatively, one…
Sufficient conditions for the controllability of a conservative reduced system are given. Several examples illustrating the theory are also presented.
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
This is a short note with some (very elementary) remarks concerning realization theory and the choice of inputs for identifying systems. Its goal is to bring some of these facts to the attention of the systems biology community.
Influence systems form a large class of multiagent systems designed to model how influence, broadly defined, spreads across a dynamic network. We build a general analytical framework which we then use to prove that, while sometimes chaotic,…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
New measures for the quantization of systems with constraints are discussed and applied to several examples, in particular, examples of alternative but equivalent formulations of given first-class constraints, as well as a comparison of…
In this paper, we present a model based on relations for bigraphical reactive systems [Milner09]. Its defining characteristics are that validity and reaction relations are captured as traces in a multi-set rewriting system. The relational…
Controlling a dynamical system is the ability of changing its configuration arbitrarily through a suitable choice of inputs. It is a very well studied concept in control theory, with wide ranging applications in medicine, biology, social…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
In this paper I present some of the most representative biological models applied to robotics. In particular, this work represents a survey of some models inspired, or making use of concepts, by gene regulatory networks (GRNs): these…
Considerable interest has recently been focused on studying multiple phenotypes simultaneously in both epidemiological and genomic studies, either to capture the multidimensionality of complex disorders or to understand shared etiology of…
With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the…
Living organisms exhibit remarkable adaptations across all scales, from molecules to ecosystems. We believe that many of these adaptations correspond to optimal solutions driven by evolution, training, and underlying physical and chemical…
Model selection methods are used in different scientific contexts to represent a characteristic data set in terms of a reduced number of parameters. Apparently, these methods have not found their way into the literature on multibody systems…
In this article we propose a set of simple principles to guide empirical practice in synthetic control studies. The proposed principles follow from formal properties of synthetic control estimators, and pertain to the nature, implications,…
Resetting, as a protocol that restarts the evolution of a system, can significantly influence stochastic dynamics. One notable effect is the emergence of stationary states in unbounded potentials, where such states would otherwise be absent…