Co-optimization: a generalization of coevolution

Many problems encountered in computer science are best stated in terms of interactions amongst individuals. For example, many problems are most naturally phrased in terms of finding a candidate solution which performs best against a set of test cases. In such situations, methods are needed to find candidate solutions which are expected to perform best over all test cases. Coevolution holds the promise of addressing such problems by employing principles from biological evolution, where populations of candidate solutions and test cases are evolved over time to produce higher quality solutions...This thesis presents a generalization of coevolution to co-optimization, where optimization techniques that do not rely on evolutionary principles may be used. Instead of introducing a new addition to coevolution in order to make it better suited for a particular class of problems, this thesis suggests removing the evolutionary model in favor of a technique better suited for that class of problems --Abstract, page iii

Damage Diagnosis of Structures Using Modal Data and Static Response

This paper is aimed at presenting three methods to detect and estimate damage using modal data and static response of a damaged structure. The proposed methods use modal data with and without noise or static displacement to formulate objective functions. Damage location and severity in structural elements are determined using optimization of the objective functions by the simulated annealing algorithm. These methods have been applied to three examples, namely a three-story plane frame, cantilever plate and benchmark problem provided by the IASC-ASCE Task Group on Structural Health Monitoring. Also, the effect of the discrepancy in mass and stiffness between the finite element model and the actual tested system has been investigated. The obtained results indicate that the proposed methods can be viewed as a powerful and reliable method for structural damage detection and estimation

Model of ionic currents through microtubule nanopores and the lumen

It has been suggested that microtubules and other cytoskeletal filaments may act as electrical transmission lines. An electrical circuit model of the microtubule is constructed incorporating features of its cylindrical structure with nanopores in its walls. This model is used to study how ionic conductance along the lumen is affected by flux through the nanopores when an external potential is applied across its two ends. Based on the results of Brownian dynamics simulations, the nanopores were found to have asymmetric inner and outer conductances, manifested as nonlinear IV curves. Our simulations indicate that a combination of this asymmetry and an internal voltage source arising from the motion of the C-terminal tails causes a net current to be pumped across the microtubule wall and propagate down the microtubule through the lumen. This effect is demonstrated to enhance and add directly to the longitudinal current through the lumen resulting from an external voltage source, and could be significant in amplifying low-intensity endogenous currents within the cellular environment or as a nano-bioelectronic device.Comment: 43 pages, 6 figures, revised versio

Collision-free path planning for robots using B-splines and simulated annealing

This thesis describes a technique to obtain an optimal collision-free path for an automated guided vehicle (AGV) and/or robot in two and three dimensions by synthesizing a B-spline curve under geometric and intrinsic constraints. The problem is formulated as a combinatorial optimization problem and solved by using simulated annealing. A two-link planar manipulator is included to show that the B-spline curve can also be synthesized by adding kinematic characteristics of the robot. A cost function, which includes obstacle proximity, excessive arc length, uneven parametric distribution and, possibly, link proximity costs, is developed for the simulated annealing algorithm. Three possible cases for the orientation of the moving object are explored: (a) fixed orientation, (b) orientation as another independent variable, and (c) orientation given by the slope of the curve. To demonstrate the robustness of the technique, several examples are presented. Objects are modeled as ellipsoid type shapes. The procedure to obtain the describing parameters of the ellipsoid is also presented

Relaxing Synchronization in Distributed Simulated Annealing

Simulated annealing is an attractive, but expensive, heuristic for approximating the solution to combinatorial optimization problems. Since simulated annealing is a general purpose method, it can be applied to the broad range of NP-complete problems such as the traveling salesman problem, graph theory, and cell placement with a careful control of the cooling schedule. Attempts to parallelize simulated annealing, particularly on distributed memory multicomputers, are hampered by the algorithm’s requirement of a globally consistent system state. In a multicomputer, maintaining the global state S involves explicit message traffic and is a critical performance bottleneck. One way to mitigate this bottleneck is to amortize the overhead of these state updates over as many parallel state changes as possible. By using this technique, errors in the actual cost C(S) of a particular state S will be introduced into the annealing process. This dissertation places analytically derived bounds on the cost error in order to assure convergence to the correct result. The resulting parallel Simulated Annealing algorithm dynamically changes the frequency of global updates as a function of the annealing control parameter, i.e. temperature. Implementation results on an Intel iPSC/2 are reported

Probing effects of organic solvents on paracetamol crystallization using in silico and orthogonal in situ methods

This work entails efforts to understand effects of solvent choice on paracetamol crystallization. Various techniques have been developed and implemented to study aforementioned. A clear-cut, direct evidence of two-step nucleation mechanism is demonstrated using a bench top Raman spectrometer and a novel method named as OSANO.Polymorphismus ist die Eigenschaft vieler anorganischer und insbesondere organischer Moleküle, in mehr als einer Struktur zu kristallisieren. Es ist wichtig, die Faktoren zu verstehen, die den Polymorphismus beeinflussen, da er viele physikochemische Eigenschaften wie Stabilität und Löslichkeit beeinflusst. Nahezu 80 % der vermarkteten Medikamente weisen Polymorphismus auf. In dieser Arbeit wurde der Einfluss der Wahl des organischen Lösungsmittels auf den Polymorphismus von Paracetamol untersucht und verschiedene Methoden entwickelt und angewandt, um den Einfluss genauer zu verstehen. Es wurde festgestellt, dass Ethanol viel stärker auf Paracetamol-Kristallisation als Methanol wirkt. Nichtgleichgewichts-Molekulardynamiksimulationen mit periodischer, simulierter Abkühlung (Simulated Annealing) wurden verwendet, um Vorläufer der metastabilen Zwischenprodukte im Kristallisationsprozess zu untersuchen. Es wurde festgestellt, dass die Strukturen der Bausteine der Paracetamol-Kristalle durch geometrische Wechselwirkungen zwischen Lösungsmittel und Paracetamol bestimmt werden. Die statistisch häufigsten Bausteine in der Selbstassemblierung definieren die finale Kristallstruktur. Ein speziell angefertigter akustischer Levitator hat die Proben zuverlässig gehalten, wodurch die Untersuchung des Einflusses von Lösungsmitteln ermöglicht, heterogene Keimbildung abgeschwächt und andere Umgebungsfaktoren stabilisiert wurden. Die Kristallisation wurde in diesem Aufbau mit zeitaufgelöster In-situ-Raman-Spektroskopie verfolgt und mit einer neuen Zielfunktion basierenden Methode der nichtnegativen Matrixfaktorisierung (NMF) analysiert. Orthogonale Zeitrafferfotografie wurde in Verbindung mit NMF verwendet, um eindeutige und genaue Faktoren zu erhalten, die sich auf die Spektren und Konzentrationen verschiedener Anteile der Paracetamol-Kristallisation beziehen, die als latente Komponenten in den unbehandelten Daten vorhanden sind.Polymorphism is the property exhibited by many inorganic and organic molecules to crystallize in more than one crystal structure. There is a strong need for understanding the influencing factors on polymorphism, as it is responsible for differences in many physicochemical properties such as stability and solubility. Nearly 80 % of marketed drugs exhibit polymorphism. In this work, we took the model system of paracetamol to investigate the influence of solvent choice on its polymorphism. Different methods were developed and employed to understand the influence of small organic solvents on the crystallization of paracetamol. Non-equilibrium molecular dynamics simulations with periodic simulated annealing were used as a tool to probe the nature of precursors of the metastable intermediates occurring in the crystallization process. Using this method, it was found that the structures of the building blocks of crystals of paracetamol is governed by solvent-solute interactions. In situ Raman spectroscopy was used with a custom-made acoustic levitator to follow crystallization. This set-up is a reliable method for investigating solvent influence, attenuating heterogeneous nucleation and stabilizing other environmental factors. It was established that as a solvent, ethanol is much stronger than methanol in its effect of driving paracetamol solutions to their crystal form. The time-resolved Raman spectroscopy crystallization data was processed using a newly developed objective function based non-negative matrix factorization method (NMF). An orthogonal time-lapse photography was used in conjunction with NMF to get unique and accurate factors that pertain to the spectra and concentrations of different moieties of paracetamol crystallization existing as latent components in the untreated data