Related papers: Designing biological circuits: from principles to …
Global routing has been a historically challenging problem in electronic circuit design, where the challenge is to connect a large and arbitrary number of circuit components with wires without violating the design rules for the printed…
Bio-inspired control of motion is an active field of research with many applications in real world tasks. In the case of robotic systems that need to exhibit oscillatory behaviour (i.e. locomotion of snake-type or legged robots), Central…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Despite the advent of several novel, synthetic gene drive mechanisms and their potential to one-day control a number of devastating diseases, among other applications, practical use of these systems remains contentious and risky. In…
The computational modeling of genetic regulatory networks is now common place, either by fitting a system to experimental data or by exploring the behaviour of abstract systems with the aim of identifying underlying principles. This paper…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Advances in science and engineering often reveal the limitations of classical approaches initially used to understand, predict, and control phenomena. With progress, conceptual categories must often be re-evaluated to better track recently…
Lots of bio-inspired research works have been conducted in self-adaptive software. They have focused on the external behavior of biological entities without their genetic material that causes this behavior and constitutes the challenge this…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
This paper proposes a methodology of integrating the Linear Graph (LG) approach with Genetic Programming (GP) for generating an automated multi-domain engineering design approach by using the in-house developed LG MATLAB toolbox and the GP…
The field of computational modeling of the brain is advancing so rapidly that now it is possible to model large scale networks representing different brain regions with a high level of biological detail in terms of numbers and synapses. For…
One of the central tasks in many-body physics is the determination of phase diagrams. However, mapping out a phase diagram generally requires a great deal of human intuition and understanding. To automate this process, one can frame it as a…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
We describe an approach to model genetic regulatory networks at the level of promotion-inhibition circuitry through a class of stochastic spin models that includes spatial and temporal density fluctuations in a natural way. The formalism…
The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the unbinding of a repressor (negative control).…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…