Related papers: Regulated Multiset Rewriting Systems
Purpose of Review: To effectively synthesise and analyse multi-robot behaviour, we require formal task-level models which accurately capture multi-robot execution. In this paper, we review modelling formalisms for multi-robot systems under…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
We study special systems with infinitely many degrees of freedom with regard to dynamical evolution and fulfillment of constraint conditions. Attention is focused on establishing a meaningful functional framework, and for that purpose,…
We show how a bi-directional grammar can be used to specify and verbalise answer set programs in controlled natural language. We start from a program specification in controlled natural language and translate this specification…
The aim of this work is to address issues where formal specifications cannot be realized on a given dynamical system subjected to a changing environment. Such failures occur whenever the dynamics of the system restrict the robot in such a…
A novel information-theoretic method for reconstruction of interaction networks is introduced. We prove that the method is exact for some class of networks. Performance tests on large synthetic transcriptional regulatory networks produce…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
In synchronous rewriting, the productions of two rewriting systems are paired and applied synchronously in the derivation of a pair of strings. We present a new synchronous rewriting system and argue that it can handle certain phenomena…
Humans and animals exhibit a range of interesting behaviors in dynamic environments, and it is unclear how our brains actively reformat this dense sensory information to enable these behaviors. Experimental neuroscience is undergoing a…
Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central…
Several types of term rewriting systems can be distinguished by the way their rules overlap. In particular, we define the classes of prefix, suffix, bottom-up and top-down systems, which generalize similar classes on words. Our aim is to…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…
One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of…
Reactive systems \`a la Leifer and Milner, an abstract categorical framework for rewriting, provide a suitable framework for deriving bisimulation congruences. This is done by synthesizing interactions with the environment in order to…
All current investigations to analyze the derivational complexity of term rewrite systems are based on a single termination method, possibly preceded by transformations. However, the exclusive use of direct criteria is problematic due to…
The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
What makes living systems flexible so that they can react quickly and adapt easily to changing environments? This question has not only engaged biologists for decades but is also of great interest to computer scientists and engineers who…