Realistic and verifiable coherent control of excitonic states in a light harvesting complex

We explore the feasibility of coherent control of excitonic dynamics in light harvesting complexes, analyzing the limits imposed by the open nature of these quantum systems. We establish feasible targets for phase and phase/amplitude control of the electronically excited state populations in the Fenna-Mathews-Olson (FMO) complex and analyze the robustness of this control with respect to orientational and energetic disorder, as well as decoherence arising from coupling to the protein environment. We further present two possible routes to verification of the control target, with simulations for the FMO complex showing that steering of the excited state is experimentally verifiable either by extending excitonic coherence or by producing novel states in a pump-probe setup. Our results provide a first step toward coherent control of these complex biological quantum systems in an ultrafast spectroscopy setup.Comment: 12 pages, 8 figure

Evolving Non-Dominated Parameter Sets for Computational Models from Multiple Experiments

© Peter C. R. Lane, Fernand Gobet. This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY-NC 3.0)Creating robust, reproducible and optimal computational models is a key challenge for theorists in many sciences. Psychology and cognitive science face particular challenges as large amounts of data are collected and many models are not amenable to analytical techniques for calculating parameter sets. Particular problems are to locate the full range of acceptable model parameters for a given dataset, and to confirm the consistency of model parameters across different datasets. Resolving these problems will provide a better understanding of the behaviour of computational models, and so support the development of general and robust models. In this article, we address these problems using evolutionary algorithms to develop parameters for computational models against multiple sets of experimental data; in particular, we propose the ‘speciated non-dominated sorting genetic algorithm’ for evolving models in several theories. We discuss the problem of developing a model of categorisation using twenty-nine sets of data and models drawn from four different theories. We find that the evolutionary algorithms generate high quality models, adapted to provide a good fit to all available data.Peer reviewedFinal Published versio

Free Search Towards Multidimensional Optimisation Problems

The article presents experimental results achieved from a novel heuristic algorithm for real-value search and optimisation called Free Search (FS). The aim is to clarify the abilities of this method to return optimal solutions from multidimensional search spaces currently resistant to other search techniques

Partnering Strategies for Fitness Evaluation in a Pyramidal Evolutionary Algorithm

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes for (sub-)fitness evaluation purposes are examined for two multiple-choice optimisation problems. It is shown that random partnering strategies perform best by providing better sampling and more diversity

Towards a Theory-Guided Benchmarking Suite for Discrete Black-Box Optimization Heuristics: Profiling (1+λ)(1+\lambda) EA Variants on OneMax and LeadingOnes

Theoretical and empirical research on evolutionary computation methods complement each other by providing two fundamentally different approaches towards a better understanding of black-box optimization heuristics. In discrete optimization, both streams developed rather independently of each other, but we observe today an increasing interest in reconciling these two sub-branches. In continuous optimization, the COCO (COmparing Continuous Optimisers) benchmarking suite has established itself as an important platform that theoreticians and practitioners use to exchange research ideas and questions. No widely accepted equivalent exists in the research domain of discrete black-box optimization. Marking an important step towards filling this gap, we adjust the COCO software to pseudo-Boolean optimization problems, and obtain from this a benchmarking environment that allows a fine-grained empirical analysis of discrete black-box heuristics. In this documentation we demonstrate how this test bed can be used to profile the performance of evolutionary algorithms. More concretely, we study the optimization behavior of several $(1+\lambda)$ EA variants on the two benchmark problems OneMax and LeadingOnes. This comparison motivates a refined analysis for the optimization time of the $(1+\lambda)$ EA on LeadingOnes

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa

GreMuTRRR: A Novel Genetic Algorithm to Solve Distance Geometry Problem for Protein Structures

Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the protein structure one has to solve the Euclidean distance geometry problem given the incomplete interval distance data produced by NMR machines. In this paper, we propose a new genetic algorithm for solving the Euclidean distance geometry problem for protein structure prediction given sparse NMR data. Our genetic algorithm uses a greedy mutation operator to intensify the search, a twin removal technique for diversification in the population and a random restart method to recover stagnation. On a standard set of benchmark dataset, our algorithm significantly outperforms standard genetic algorithms.Comment: Accepted for publication in the 8th International Conference on Electrical and Computer Engineering (ICECE 2014