Related papers: Regulated Multiset Rewriting Systems
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
A novel method for control of dynamical systems, proposed in the paper, ensures an output signal belonging to the given set at any time. The method is based on a special change of coordinates such that the initial problem with given…
Membrane systems are a biologically-inspired computational model based on the structure of biological cells and the way chemicals interact and traverse their membranes. Although their dynamics are described by rules, encoding membrane…
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
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…
The goal of the paper is to automatize the selection of mechanisms which are able to describe a set of measurements. In order to do so first we construct a set of possible mechanism fulfilling chemically reasonable requirements with a given…
We present an approach to the verification of systems for whose description some elements - constants or functions - are underspecified and can be regarded as parameters, and, in particular, describe a method for automatically generating…
Logical rules are a popular knowledge representation language in many domains, representing background knowledge and encoding information that can be derived from given facts in a compact form. However, rule formulation is a complex process…
We propose a formalism to model and reason about reconfigurable multi-agent systems. In our formalism, agents interact and communicate in different modes so that they can pursue joint tasks; agents may dynamically synchronize, exchange…
Logically constrained term rewriting systems (LCTRSs) are a program analyzing formalism with native support for data types which are not (co)inductively defined. As a first-order formalism, LCTRSs have accommodated only analysis of…
We introduce an algebraic analogue of dynamical systems, based on term rewriting. We show that a recursive function applied to the output of an iterated rewriting system defines a formal class of models into which all the main architectures…
We consider the basic features of complex dynamic and control systems, including systems having hierarchical structure. Special attention is paid to the problems of design and synthesis of complex systems and control models, and to the…
This paper describes some biologically-inspired processes that could be used to build the sort of networks that we associate with the human brain. New to this paper, a 'refined' neuron will be proposed. This is a group of neurons that by…
We develop a novel method to analyze the dynamics of stochastic rewriting systems evolving over finitary adhesive, extensive categories. Our formalism is based on the so-called rule algebra framework and exhibits an intimate relationship…
In this paper we show how string rewriting methods can be applied to give a new method of computing double cosets. Previous methods for double cosets were enumerative and thus restricted to finite examples. Our rewriting methods do not…
Multisets are sets that allow repetition of elements. As such, multisets pave the way to a number of interesting possibilities of theoretical and applied nature. In the present work, after revising the main aspects of traditional sets, we…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
Biological systems often consist of a small number of constituents and are therefore inherently noisy. To function effectively, these systems must employ mechanisms to constrain the accumulation of noise. Such mechanisms have been…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…