Related papers: Simulating and model checking membrane systems usi…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
Previous work has presented our ongoing e orts to define a "reference semantics" for the UML, that is, a mathematically defined system model that is envisaged to cover all of the UML eventually, and that also carefully avoids the…
Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
Bounded model finding is a key technique for validating software designs, usually obtained by translating high-level specifications into SAT/SMT problems. Although effective, such translations introduce a semantic gap and a dependency on…
Mathematical models simulate various events under different conditions, enabling an early overview of the system to be implemented in practice, reducing the waste of resources and in less time. In project optimization, these models play a…
This paper addresses the issue of specifying, simulating, and verifying reactive systems in rewriting logic. It presents an executable semantics for probabilistic, timed, and spatial concurrent constraint programming -- here called…
Membrane system computations proceed in a synchronous fashion: at each step all the applicable rules are actually applied. Hence each step depends on the previous one. This coarse view can be refined by looking at the dependencies among…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To…
Concurrent functional languages that are endowed with symbolic reasoning capabilities such as Maude offer a high-level, elegant, and efficient approach to programming and analyzing complex, highly nondeterministic software systems. Maude's…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…
Traditional approaches to training agents have generally involved a single, deterministic environment of minimal complexity to solve various tasks such as robot locomotion or computer vision. However, agents trained in static environments…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…
Rewriting is a formalism widely used in computer science and mathematical logic. The classical formalism has been extended, in the context of functional languages, with an order over the rules and, in the context of rewrite based languages,…
Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial…
The immune system can be thought as a complex network of different interacting elements. A cellular automaton, defined in shape-space, was recently shown to exhibit self-regulation and complex behavior and is, therefore, a good candidate to…
Model-based mutation testing uses altered test models to derive test cases that are able to reveal whether a modelled fault has been implemented. This requires conformance checking between the original and the mutated model. This paper…