Robust Multi-Cellular Developmental Design

This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as well as the differentiation value of the cell in the phenotype, are controlled by a Neural Network (the genotype) that takes as inputs the chemicals produced by the neighboring cells at the previous time step. In the proposed model, the number of iterations of the growth process is not pre-determined, but emerges during evolution: only organisms for which the growth process stabilizes give a phenotype (the stable state), others are declared nonviable. The optimization of the controller is done using the NEAT algorithm, that optimizes both the topology and the weights of the Neural Networks. Though each cell only receives local information from its neighbors, the experimental results of the proposed approach on the 'flags' problems (the phenotype must match a given 2D pattern) are almost as good as those of a direct regression approach using the same model with global information. Moreover, the resulting multi-cellular organisms exhibit almost perfect self-healing characteristics

State-of-the-art in aerodynamic shape optimisation methods

Aerodynamic optimisation has become an indispensable component for any aerodynamic design over the past 60 years, with applications to aircraft, cars, trains, bridges, wind turbines, internal pipe flows, and cavities, among others, and is thus relevant in many facets of technology. With advancements in computational power, automated design optimisation procedures have become more competent, however, there is an ambiguity and bias throughout the literature with regards to relative performance of optimisation architectures and employed algorithms. This paper provides a well-balanced critical review of the dominant optimisation approaches that have been integrated with aerodynamic theory for the purpose of shape optimisation. A total of 229 papers, published in more than 120 journals and conference proceedings, have been classified into 6 different optimisation algorithm approaches. The material cited includes some of the most well-established authors and publications in the field of aerodynamic optimisation. This paper aims to eliminate bias toward certain algorithms by analysing the limitations, drawbacks, and the benefits of the most utilised optimisation approaches. This review provides comprehensive but straightforward insight for non-specialists and reference detailing the current state for specialist practitioners

Optimal signal processing in small stochastic biochemical networks

We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function performed by the network. Specifically, we study the maximum mutual information between the input (chemical) signal and the output (genetic) response attainable by the network in the context of an analytic model of particle number fluctuations. We perform this analysis for all biochemical circuits, including various feedback loops, that can be built out of 3 chemical species, each under the control of one regulator. We find that a generic network, constrained to low molecule numbers and reasonable response times, can transduce more information than a simple binary switch and, in fact, manages to achieve close to the optimal information transmission fidelity. These high-information solutions are robust to tenfold changes in most of the networks' biochemical parameters; moreover they are easier to achieve in networks containing cycles with an odd number of negative regulators (overall negative feedback) due to their decreased molecular noise (a result which we derive analytically). Finally, we demonstrate that a single circuit can support multiple high-information solutions. These findings suggest a potential resolution of the "cross-talk" dilemma as well as the previously unexplained observation that transcription factors which undergo proteolysis are more likely to be auto-repressive.Comment: 41 pages 7 figures, 5 table