Optimization of micropillar sequences for fluid flow sculpting

Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has successfully demonstrated manual design of pillar sequences to achieve desired transformations of the flow cross-section, with experimental validation. However, such a method is not ideal for seeking out complex sculpted shapes as the search space quickly becomes too large for efficient manual discovery. We explore fast, automated optimization methods to solve this problem. We formulate the inertial flow physics in microchannels with different micropillar configurations as a set of state transition matrix operations. These state transition matrices are constructed from experimentally validated streamtraces. This facilitates modeling the effect of a sequence of micropillars as nested matrix-matrix products, which have very efficient numerical implementations. With this new forward model, arbitrary micropillar sequences can be rapidly simulated with various inlet configurations, allowing optimization routines quick access to a large search space. We integrate this framework with the genetic algorithm and showcase its applicability by designing micropillar sequences for various useful transformations. We computationally discover micropillar sequences for complex transformations that are substantially shorter than manually designed sequences. We also determine sequences for novel transformations that were difficult to manually design. Finally, we experimentally validate these computational designs by fabricating devices and comparing predictions with the results from confocal microscopy

In Silico Sequence Optimization for the Reproducible Generation of DNA Structures

Biologically, deoxyribonucleic acid (DNA) molecules have been used for information storage for more than 3 billion years. Today, modern synthesis tools have made it possible to use synthetic DNA molecules as a material for engineering nanoscale structures. These self-assembling structures are capable of both resolutions as fine as 4 angstroms and executing programed dynamic behavior. Numerous approaches for creating structures from DNA have been proposed and validated, however it remains commonplace for engineered systems to exhibit unexpected behaviors such as low formation yields, poor performance, or total failure. It is plausible that at least some of these behaviors arise due to the formation of non-target structures, but how to quantify and avoid these interfering structures remains a critical question. To evaluate the impacts of non-target structures on system behavior, three co-dependent scientific developments were necessary. First, three new optimization criteria for quantifying system quality were proposed and studied. This led to the discovery that relatively small intramolecular structures lead to surprisingly large deviations in system behavior such as reaction kinetics. Second, a new heuristic algorithm for generating high quality systems was developed. This algorithm enabled the experimental characterization of newly generated systems, thus validating the optimization criteria and confirming the finding that almost all kinetic variation can be explained by non-target intramolecular structures. Finally, these studies necessitated the creation of two new software tools; one for analyzing existing DNA systems (the “Device Profiler” software) and another for generating fit DNA systems (the “Sequence Evolver” software). In order to enable these tools to handle the size and complexity of state-of-the-art systems, it was necessary to invent efficient software implementations of the metrics and algorithm. The performance of the software was benchmarked against several alternative tools in use by the DNA nanotechnology community, with the results indicating a marked improvement in system quality over current state-of-the-art methods. Ultimately, the new optimization criteria, heuristic algorithm, and software cooperatively enabled an improved method for generating DNA systems with kinetically uniform behaviors

Evolutionary algorithms and other metaheuristics in water resources: Current status, research challenges and future directions

Copyright © 2014 Elsevier. NOTICE: this is the author’s version of a work that was accepted for publication in Environmental Modelling and Software. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Environmental Modelling and Software Vol. 62 (2014), DOI: 10.1016/j.envsoft.2014.09.013The development and application of evolutionary algorithms (EAs) and other metaheuristics for the optimisation of water resources systems has been an active research field for over two decades. Research to date has emphasized algorithmic improvements and individual applications in specific areas (e.g. model calibration, water distribution systems, groundwater management, river-basin planning and management, etc.). However, there has been limited synthesis between shared problem traits, common EA challenges, and needed advances across major applications. This paper clarifies the current status and future research directions for better solving key water resources problems using EAs. Advances in understanding fitness landscape properties and their effects on algorithm performance are critical. Future EA-based applications to real-world problems require a fundamental shift of focus towards improving problem formulations, understanding general theoretic frameworks for problem decompositions, major advances in EA computational efficiency, and most importantly aiding real decision-making in complex, uncertain application contexts

PasMoQAP: A Parallel Asynchronous Memetic Algorithm for solving the Multi-Objective Quadratic Assignment Problem

Multi-Objective Optimization Problems (MOPs) have attracted growing attention during the last decades. Multi-Objective Evolutionary Algorithms (MOEAs) have been extensively used to address MOPs because are able to approximate a set of non-dominated high-quality solutions. The Multi-Objective Quadratic Assignment Problem (mQAP) is a MOP. The mQAP is a generalization of the classical QAP which has been extensively studied, and used in several real-life applications. The mQAP is defined as having as input several flows between the facilities which generate multiple cost functions that must be optimized simultaneously. In this study, we propose PasMoQAP, a parallel asynchronous memetic algorithm to solve the Multi-Objective Quadratic Assignment Problem. PasMoQAP is based on an island model that structures the population by creating sub-populations. The memetic algorithm on each island individually evolve a reduced population of solutions, and they asynchronously cooperate by sending selected solutions to the neighboring islands. The experimental results show that our approach significatively outperforms all the island-based variants of the multi-objective evolutionary algorithm NSGA-II. We show that PasMoQAP is a suitable alternative to solve the Multi-Objective Quadratic Assignment Problem.Comment: 8 pages, 3 figures, 2 tables. Accepted at Conference on Evolutionary Computation 2017 (CEC 2017

A hybrid swarm-based algorithm for single-objective optimization problems involving high-cost analyses

In many technical fields, single-objective optimization procedures in continuous domains involve expensive numerical simulations. In this context, an improvement of the Artificial Bee Colony (ABC) algorithm, called the Artificial super-Bee enhanced Colony (AsBeC), is presented. AsBeC is designed to provide fast convergence speed, high solution accuracy and robust performance over a wide range of problems. It implements enhancements of the ABC structure and hybridizations with interpolation strategies. The latter are inspired by the quadratic trust region approach for local investigation and by an efficient global optimizer for separable problems. Each modification and their combined effects are studied with appropriate metrics on a numerical benchmark, which is also used for comparing AsBeC with some effective ABC variants and other derivative-free algorithms. In addition, the presented algorithm is validated on two recent benchmarks adopted for competitions in international conferences. Results show remarkable competitiveness and robustness for AsBeC.Comment: 19 pages, 4 figures, Springer Swarm Intelligenc

Multi-agent evolutionary systems for the generation of complex virtual worlds

Modern films, games and virtual reality applications are dependent on convincing computer graphics. Highly complex models are a requirement for the successful delivery of many scenes and environments. While workflows such as rendering, compositing and animation have been streamlined to accommodate increasing demands, modelling complex models is still a laborious task. This paper introduces the computational benefits of an Interactive Genetic Algorithm (IGA) to computer graphics modelling while compensating the effects of user fatigue, a common issue with Interactive Evolutionary Computation. An intelligent agent is used in conjunction with an IGA that offers the potential to reduce the effects of user fatigue by learning from the choices made by the human designer and directing the search accordingly. This workflow accelerates the layout and distribution of basic elements to form complex models. It captures the designer's intent through interaction, and encourages playful discovery

Bio-mimetic Spiking Neural Networks for unsupervised clustering of spatio-temporal data

Spiking neural networks aspire to mimic the brain more closely than traditional artificial neural networks. They are characterised by a spike-like activation function inspired by the shape of an action potential in biological neurons. Spiking networks remain a niche area of research, perform worse than the traditional artificial networks, and their real-world applications are limited. We hypothesised that neuroscience-inspired spiking neural networks with spike-timing-dependent plasticity demonstrate useful learning capabilities. Our objective was to identify features which play a vital role in information processing in the brain but are not commonly used in artificial networks, implement them in spiking networks without copying constraints that apply to living organisms, and to characterise their effect on data processing. The networks we created are not brain models; our approach can be labelled as artificial life. We performed a literature review and selected features such as local weight updates, neuronal sub-types, modularity, homeostasis and structural plasticity. We used the review as a guide for developing the consecutive iterations of the network, and eventually a whole evolutionary developmental system. We analysed the model’s performance on clustering of spatio-temporal data. Our results show that combining evolution and unsupervised learning leads to a faster convergence on the optimal solutions, better stability of fit solutions than each approach separately. The choice of fitness definition affects the network’s performance on fitness-related and unrelated tasks. We found that neuron type-specific weight homeostasis can be used to stabilise the networks, thus enabling longer training. We also demonstrated that networks with a rudimentary architecture can evolve developmental rules which improve their fitness. This interdisciplinary work provides contributions to three fields: it proposes novel artificial intelligence approaches, tests the possible role of the selected biological phenomena in information processing in the brain, and explores the evolution of learning in an artificial life system