MSA for Optimal Reconfiguration and Capacitor Allocation in Radial/Ring Distribution Networks

This work presents a hybrid heuristic search algorithm called Moth Swarm Algorithm (MSA) in the context of power loss minimization of radial distribution networks (RDN) through optimal allocation and rating of shunt capacitors for enhancing the performance of distribution networks. With MSA, different optimization operators are used to mimic a set of behavioral patterns of moths in nature, which allows for flexible and powerful optimizer. Hence, a new dynamic selection strategy of crossover points is proposed based on population diversity to handle the difference vectors Lévy-mutation to force MSA jump out of stagnation and enhance its exploration ability. In addition, a spiral motion, adaptive Gaussian walks, and a novel associative learning mechanism with immediate memory are implemented to exploit the promising areas in the search space. In this article, the MSA is tested to adapt the objective function to reduce the system power losses, reduce total system cost and consequently increase the annual net saving with inequity constrains on capacitor size and voltage limits. The validation of the proposed algorithm has been tested and verified through small, medium and large scales of standard RDN of IEEE (33, 69, 85-bus) systems and also on ring main systems of 33 and 69-bus. In addition, the obtained results are compared with other algorithms to highlight the advantages of the proposed approach. Numerical results stated that the MSA can achieve optimal solutions for losses reduction and capacitor locations with finest performance compared with many existing algorithms

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.Comment: 29 page

Attraction and diffusion in nature-inspired optimization algorithms

Nature-inspired algorithms usually use some form of attraction and diffusion as a mechanism for exploitation and exploration. In this paper, we investigate the role of attraction and diffusion in algorithms and their ways in controlling the behaviour and performance of nature-inspired algorithms. We highlight different ways of the implementations of attraction in algorithms such as the firefly algorithm, charged system search, and the gravitational search algorithm. We also analyze diffusion mechanisms such as random walks for exploration in algorithms. It is clear that attraction can be an effective way for enhancing exploitation, while diffusion is a common way for exploration. Furthermore, we also discuss the role of parameter tuning and parameter control in modern metaheuristic algorithms, and then point out some key topics for further research

New directional bat algorithm for continuous optimization problems

Bat algorithm (BA) is a recent optimization algorithm based on swarm intelligence and inspiration from the echolocation behavior of bats. One of the issues in the standard bat algorithm is the premature convergence that can occur due to the low exploration ability of the algorithm under some conditions. To overcome this deficiency, directional echolocation is introduced to the standard bat algorithm to enhance its exploration and exploitation capabilities. In addition to such directional echolocation, three other improvements have been embedded into the standard bat algorithm to enhance its performance. The new proposed approach, namely the directional Bat Algorithm (dBA), has been then tested using several standard and non-standard benchmarks from the CEC’2005 benchmark suite. The performance of dBA has been compared with ten other algorithms and BA variants using non-parametric statistical tests. The statistical test results show the superiority of the directional bat algorithm

From RNA folding to inverse folding: a computational study: Folding and design of RNA molecules

Since the discovery of the structure of DNA in the early 1953s and its double-chained complement of information hinting at its means of replication, biologists have recognized the strong connection between molecular structure and function. In the past two decades, there has been a surge of research on an ever-growing class of RNA molecules that are non-coding but whose various folded structures allow a diverse array of vital functions. From the well-known splicing and modification of ribosomal RNA, non-coding RNAs (ncRNAs) are now known to be intimately involved in possibly every stage of DNA translation and protein transcription, as well as RNA signalling and gene regulation processes. Despite the rapid development and declining cost of modern molecular methods, they typically can only describe ncRNA's structural conformations in vitro, which differ from their in vivo counterparts. Moreover, it is estimated that only a tiny fraction of known ncRNAs has been documented experimentally, often at a high cost. There is thus a growing realization that computational methods must play a central role in the analysis of ncRNAs. Not only do computational approaches hold the promise of rapidly characterizing many ncRNAs yet to be described, but there is also the hope that by understanding the rules that determine their structure, we will gain better insight into their function and design. Many studies revealed that the ncRNA functions are performed by high-level structures that often depend on their low-level structures, such as the secondary structure. This thesis studies the computational folding mechanism and inverse folding of ncRNAs at the secondary level. In this thesis, we describe the development of two bioinformatic tools that have the potential to improve our understanding of RNA secondary structure. These tools are as follows: (1) RAFFT for efficient prediction of pseudoknot-free RNA folding pathways using the fast Fourier transform (FFT)}; (2) aRNAque, an evolutionary algorithm inspired by Lévy flights for RNA inverse folding with or without pseudoknot (A secondary structure that often poses difficulties for bio-computational detection). The first tool, RAFFT, implements a novel heuristic to predict RNA secondary structure formation pathways that has two components: (i) a folding algorithm and (ii) a kinetic ansatz. When considering the best prediction in the ensemble of 50 secondary structures predicted by RAFFT, its performance matches the recent deep-learning-based structure prediction methods. RAFFT also acts as a folding kinetic ansatz, which we tested on two RNAs: the CFSE and a classic bi-stable sequence. In both test cases, fewer structures were required to reproduce the full kinetics, whereas known methods (such as Treekin) required a sample of 20,000 structures and more. The second tool, aRNAque, implements an evolutionary algorithm (EA) inspired by the Lévy flight, allowing both local global search and which supports pseudoknotted target structures. The number of point mutations at every step of aRNAque's EA is drawn from a Zipf distribution. Therefore, our proposed method increases the diversity of designed RNA sequences and reduces the average number of evaluations of the evolutionary algorithm. The overall performance showed improved empirical results compared to existing tools through intensive benchmarks on both pseudoknotted and pseudoknot-free datasets. In conclusion, we highlight some promising extensions of the versatile RAFFT method to RNA-RNA interaction studies. We also provide an outlook on both tools' implications in studying evolutionary dynamics