Related papers: The many roads to the simulation of reaction syste…
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…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of…
We present a parallel implementation of cellular automata to simulate chemical reactions on surfaces. The scaling of the computer time with the number of processors for this parallel implementation is quite close to the ideal T/P, where T…
This paper presents RDCSim, an interactive simulator for reaction--diffusion chemistry (RDC) research, being developed as part of an ongoing project studying how humans interact with unconventional computing systems. While much research…
We study the opportunities for parallelism for the simulation of surface reactions. We introduce the concept of a partition and we give new simulation methods based on Cellular Automaton using partitions. We elaborate on the advantages and…
Simulation especially real-time simulation have been widely used for the design and testing of real-time systems. The advancement of simulation tools has largely attributed to the evolution of computing technologies. With the reduced cost…
Reaction systems, introduced by Ehrenfeucht and Rozenberg, are elementary computational models based on biochemical reactions transpiring within the living cells. Numerous studies focus on mathematical aspects of minimal reaction systems…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
When designing systems that are complex, dynamic and stochastic in nature, simulation is generally recognised as one of the best design support technologies, and a valuable aid in the strategic and tactical decision making process. A…
Simulators are a critical component of modern robotics research. Strategies for both perception and decision making can be studied in simulation first before deployed to real world systems, saving on time and costs. Despite significant…
We created an efficient algorithm suitable for graphics processing units (GPUs) to perform Monte Carlo simulations of a subset of reaction-diffusion models. The algorithm uses techniques that are specific to GPU programming, and combines…
Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein/protein interactions and post-transcriptional modifications. The response to death receptor stimulation varies significantly from one cell line…
We show how a quantum computer can be employed to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…