Charge Transfer in Deoxyribonucleic Acid (DNA): Static Disorder, Dynamic Fluctuations and Complex Kinetic.

The fact that loosely bonded DNA bases could tolerate large structural fluctuations, form a dissipative environment for a charge traveling through the DNA. Nonlinear stochastic nature of structural fluctuations facilitates rich charge dynamics in DNA. We study the complex charge dynamics by solving a nonlinear, stochastic, coupled system of differential equations. Charge transfer between donor and acceptor in DNA occurs via different mechanisms depending on the distance between donor and acceptor. It changes from tunneling regime to a polaron assisted hopping regime depending on the donor-acceptor separation. Also we found that charge transport strongly depends on the feasibility of polaron formation. Hence it has complex dependence on temperature and charge-vibrations coupling strength. Mismatched base pairs, such as different conformations of the G・A mispair, cause only minor structural changes in the host DNA molecule, thereby making mispair recognition an arduous task. Electron transport in DNA that depends strongly on the hopping transfer integrals between the nearest base pairs, which in turn are affected by the presence of a mispair, might be an attractive approach in this regard. I report here on our investigations, via the I –V characteristics, of the effect of a mispair on the electrical properties of homogeneous and generic DNA molecules. The I –V characteristics of DNA were studied numerically within the double-stranded tight-binding model. The parameters of the tight-binding model, such as the transfer integrals and on-site energies, are determined from first-principles calculations. The changes in electrical current through the DNA chain due to the presence of a mispair depend on the conformation of the G・A mispair and are appreciable for DNA consisting of up to 90 base pairs. For homogeneous DNA sequences the current through DNA is suppressed and the strongest suppression is realized for the G(anti)・A(syn) conformation of the G・A mispair. For inhomogeneous (generic) DNA molecules, the mispair result can be either suppression or an enhancement of the current, depending on the type of mispairs and actual DNA sequence

Advances in Evolutionary Algorithms

With the recent trends towards massive data sets and significant computational power, combined with evolutionary algorithmic advances evolutionary computation is becoming much more relevant to practice. Aim of the book is to present recent improvements, innovative ideas and concepts in a part of a huge EA field

Plasmonic Nanoplatforms for Biochemical Sensing and Medical Applications

Plasmonics, the science of the excitation of surface plasmon polaritons (SPP) at the metal-dielectric interface under intense beam radiation, has been studied for its immense potential for developing numerous nanophotonic devices, optical circuits and lab-on-a-chip devices. The key feature, which makes the plasmonic structures promising is the ability to support strong resonances with different behaviors and tunable localized hotspots, excitable in a wide spectral range. Therefore, the fundamental understanding of light-matter interactions at subwavelength nanostructures and use of this understanding to tailor plasmonic nanostructures with the ability to sustain high-quality tunable resonant modes are essential toward the realization of highly functional devices with a wide range of applications from sensing to switching. We investigated the excitation of various plasmonic resonance modes (i.e. Fano resonances, and toroidal moments) using both optical and terahertz (THz) plasmonic metamolecules. By designing and fabricating various nanostructures, we successfully predicted, demonstrated and analyzed the excitation of plasmonic resonances, numerically and experimentally. A simple comparison between the sensitivity and lineshape quality of various optically driven resonances reveals that nonradiative toroidal moments are exotic plasmonic modes with strong sensitivity to environmental perturbations. Employing toroidal plasmonic metasurfaces, we demonstrated ultrafast plasmonic switches and highly sensitive sensors. Focusing on the biomedical applications of toroidal moments, we developed plasmonic metamaterials for fast and cost-effective infection diagnosis using the THz range of the spectrum. We used the exotic behavior of toroidal moments for the identification of Zika-virus (ZIKV) envelope proteins as the infectious nano-agents through two protocols: 1) direct biding of targeted biomarkers to the plasmonic metasurfaces, and 2) attaching gold nanoparticles to the plasmonic metasurfaces and binding the proteins to the particles to enhance the sensitivity. This led to developing ultrasensitive THz plasmonic metasensors for detection of nanoscale and low-molecular-weight biomarkers at the picomolar range of concentration. In summary, by using high-quality and pronounced toroidal moments as sensitive resonances, we have successfully designed, fabricated and characterized novel plasmonic toroidal metamaterials for the detection of infectious biomarkers using different methods. The proposed approach allowed us to compare and analyze the binding properties, sensitivity, repeatability, and limit of detection of the metasensing device

Structural optimization of self-supported dome roof frames under gust wind loads

PhD ThesisDome roofs are large structures often subject to variable wind, snow and other loading conditions, in addition to their own weight. A wide variety of structural designs are used in practice, and finding the optimal arrangement of trusses or girders, along with suitable section properties, is a common subject for structural optimization studies. This thesis focuses on self-supported dome roofs for fuel storage tanks, and a variety of optimization techniques are adapted, developed and compared. Various load conditions have been compared using detailed fluid and stress analysis in ANSYS. From results for full and empty storage tanks, with wind and/or snow external loads, the worst cases are for wind loading alone, i.e., snow loading counters the lift force from the wind. Consequently, the case of an empty fuel storage tank subject to wind loading is used as the basis for the structural optimization. To speed up the optimization, a simplified frame analysis was developed in Matlab and integrated with the optimization code. In addition, the wind loads were modelled in ANSYS for a range of dome radii and imported into the Matlab, and a number of different dome designs were used as case studies: these were ribbed, Schwedler, Lamella and geodesic. The principal method used to optimize the frame is Morphing Evolutionary Structural Optimization (MESO), in which an initial overdesigned frame is iteratively analysed and reduced in overall weight by reducing the sections of key frame members. The frame is progressively weakened, but without compromising the structural integrity, until it is no longer possible to reduce the weight. However, there are additional parameters that MESO is not suited to, such as dome radius and those affecting the overall structure of the dome frame (numbers and placements of rings, etc.), and a variety of metaheuristic optimization techniques have been studied: Artificial Bee Colony (ABC), Bees Algorithm (BA), Differential Evolution (DE), Particle Swarm Optimization (PSO) and Simulated Annealing (SA). These can be used instead of MESO, or in a hybrid form where MESO optimizes the frame member sections. Although the focus in this thesis is on minimizing the total structural weight, the importance of other characteristics of the design, especially structural stiffness, is considered and also integrated with the MESO process. The hybrid methods MESO-ABC and MESO-DE performed best overall.Higher Committee for Education Development (HCED), IRA

Particle Swarm Optimization of Low-Thrust, Geocentric-to-Halo-Orbit Transfers

Missions to Lagrange points are becoming increasingly popular amongst spacecraft mission planners. Lagrange points are locations in space where the gravity force from two bodies, and the centrifugal force acting on a third body, cancel. To date, all spacecraft that have visited a Lagrange point have done so using high-thrust, chemical propulsion. Due to the increasing availability of low-thrust (high efficiency) propulsive devices, and their increasing capability in terms of fuel efficiency and instantaneous thrust, it has now become possible for a spacecraft to reach a Lagrange point orbit without the aid of chemical propellant. While at any given time there are many paths for a low-thrust trajectory to take, only one is optimal. The traditional approach to spacecraft trajectory optimization utilizes some form of gradient-based algorithm. While these algorithms offer numerous advantages, they also have a few significant shortcomings. The three most significant shortcomings are: (1) the fact that an initial guess solution is required to initialize the algorithm, (2) the radius of convergence can be quite small and can allow the algorithm to become trapped in local minima, and (3) gradient information is not always assessable nor always trustworthy for a given problem. To avoid these problems, this dissertation is focused on optimizing a low-thrust transfer trajectory from a geocentric orbit to an Earth-Moon, L1, Lagrange point orbit using the method of Particle Swarm Optimization (PSO). The PSO method is an evolutionary heuristic that was originally written to model birds swarming to locate hidden food sources. This PSO method will enable the exploration of the invariant stable manifold of the target Lagrange point orbit in an effort to optimize the spacecraft\u27s low-thrust trajectory. Examples of these optimized trajectories are presented and contrasted with those found using traditional, gradient-based approaches. In summary, the results of this dissertation find that the PSO method does, indeed, successfully optimize the low-thrust trajectory transfer problem without the need for initial guessing. Furthermore, a two-degree-of-freedom PSO problem formulation significantly outperformed a one-degree-of-freedom formulation by at least an order of magnitude, in terms of CPU time. Finally, the PSO method is also used to solve a traditional, two-burn, impulsive transfer to a Lagrange point orbit using a hybrid optimization algorithm that incorporates a gradient-based shooting algorithm as a pre-optimizer. Surprisingly, the results of this study show that fast transfers outperform slow transfers in terms of both delta-V and time of flight

Applied Metaheuristic Computing

For decades, Applied Metaheuristic Computing (AMC) has been a prevailing optimization technique for tackling perplexing engineering and business problems, such as scheduling, routing, ordering, bin packing, assignment, facility layout planning, among others. This is partly because the classic exact methods are constrained with prior assumptions, and partly due to the heuristics being problem-dependent and lacking generalization. AMC, on the contrary, guides the course of low-level heuristics to search beyond the local optimality, which impairs the capability of traditional computation methods. This topic series has collected quality papers proposing cutting-edge methodology and innovative applications which drive the advances of AMC

Multi-Objective and Multi-Attribute Optimisation for Sustainable Development Decision Aiding

Optimization is considered as a decision-making process for getting the most out of available resources for the best attainable results. Many real-world problems are multi-objective or multi-attribute problems that naturally involve several competing objectives that need to be optimized simultaneously, while respecting some constraints or involving selection among feasible discrete alternatives. In this Reprint of the Special Issue, 19 research papers co-authored by 88 researchers from 14 different countries explore aspects of multi-objective or multi-attribute modeling and optimization in crisp or uncertain environments by suggesting multiple-attribute decision-making (MADM) and multi-objective decision-making (MODM) approaches. The papers elaborate upon the approaches of state-of-the-art case studies in selected areas of applications related to sustainable development decision aiding in engineering and management, including construction, transportation, infrastructure development, production, and organization management

Particle Swarm Optimization

Particle swarm optimization (PSO) is a population based stochastic optimization technique influenced by the social behavior of bird flocking or fish schooling.PSO shares many similarities with evolutionary computation techniques such as Genetic Algorithms (GA). The system is initialized with a population of random solutions and searches for optima by updating generations. However, unlike GA, PSO has no evolution operators such as crossover and mutation. In PSO, the potential solutions, called particles, fly through the problem space by following the current optimum particles. This book represents the contributions of the top researchers in this field and will serve as a valuable tool for professionals in this interdisciplinary field