Basic properties of epigenetic systems: lessons from the centromere

Chromatin-based epigenetic inheritance cooperates with cis-acting DNA sequence information to propagate gene expression states and chromosome architecture across cell division cycles. Histone proteins and their modifications are central components of epigenetic systems but how, and to what extent, they are propagated is a matter of continued debate. Centromeric nucleosomes, marked by the histone H3 variant CENP-A, are stable across mitotic divisions and are assembled in a locus specific and cell cycle controlled manner. The mechanism of inheritance of this unique chromatin domain has important implications for how general nucleosome transmission is controlled in space and time.

Breadth-first search and the Andrews-Curtis conjecture

Andrews and Curtis conjectured in 1965 that every balanced presentation of the trivial group can be transformed into a standard presentation by a finite sequence of elementary transformations. Recent computational work by Miasnikov and Myasnikov on this problem has been based on genetic algorithms. We show that a computational attack based on a breadth-first search of the tree of equivalent presentations is also viable, and seems to outperform that based on genetic algorithms. It allows us to extract shorter proofs (in some cases, provably shortest) and to consider the length thirteen case for two generators. We prove that, up to equivalence, there is a unique minimum potential counterexample.

A possible smoking susceptibility locus on chromosome 11p12: Evidence from sex-limitation linkage analyses in a sample of Australian twin families

Many twin studies have identified sex differences in the influence of genetic and environmental factors on smoking behaviors. We explore the evidence for sex differences for smoking initiation and cigarette consumption in a sample of Australian twin families, and extend these models to incorporate sex differences in linkage analyses for these traits. We further examine the impact of including or excluding non-smokers in genetic analyses of tobacco consumption. Accounting for sex differences improved linkage results in some instances. We identified one region suggestive of linkage on chromosome 11p12. This locus, as well as another region identified on chromosome 6p12, replicates regions identified in previous studies.

A general-purpose tunable landscape generator

The research literature on metalieuristic and evolutionary computation has proposed a large number of algorithms for the solution of challenging real-world optimization problems. It is often not possible to study theoretically the performance of these algorithms unless significant assumptions are made on either the algorithm itself or the problems to which it is applied, or both. As a consequence, metalieuristics are typically evaluated empirically using a set of test problems. Unfortunately, relatively little attention has been given to the development of methodologies and tools for the large-scale empirical evaluation and/or comparison of metaheuristics. In this paper, we propose a landscape (test-problem) generator that can be used to generate optimization problem instances for continuous, bound-constrained optimization problems. The landscape generator is parameterized by a small number of parameters, and the values of these parameters have a direct and intuitive interpretation in terms of the geometric features of the landscapes that they produce. An experimental space is defined over algorithms and problems, via a tuple of parameters for any specified algorithm and problem class (here determined by the landscape generator). An experiment is then clearly specified as a point in this space, in a way that is analogous to other areas of experimental algorithmics, and more generally in experimental design. Experimental results are presented, demonstrating the use of the landscape generator. In particular, we analyze some simple, continuous estimation of distribution algorithms, and gain new insights into the behavior of these algorithms using the landscape generator.

Optimization of PCB component placements for the collect-and-place machines

This paper presents two hybrid genetic algorithms (HGAs) to optimize the component placement operation for the collect-and-place machines in printed circuit board (PCB) assembly. The component placement problem is to optimize (i) the assignment of components to a movable revolver head or assembly tour, (ii) the sequence of component placements on a stationary PCB in each tour, and (iii) the arrangement of component types to stationary feeders simultaneously. The objective of the problem is to minimize the total traveling time spent by the revolver head for assembling all components on the PCB. The major difference between the HGAs is that the initial solutions are generated randomly in HGA1. The Clarke and Wright saving method, the nearest neighbor heuristic, and the neighborhood frequency heuristic are incorporated into HGA2 for the initialization procedure. A computational study is carried out to compare the algorithms with different population sizes. It is proved that the performance of HGA2 is superior to HGA1 in terms of the total assembly time.

An integrated scheduling problem of PCB components on sequential pick-and-place machines:mathematical models and heuristic solutions

This paper formulates several mathematical models for determining the optimal sequence of component placements and assignment of component types to feeders simultaneously or the integrated scheduling problem for a type of surface mount technology placement machines, called the sequential pick-andplace (PAP) machine. A PAP machine has multiple stationary feeders storing components, a stationary working table holding a printed circuit board (PCB), and a movable placement head to pick up components from feeders and place them to a board. The objective of integrated problem is to minimize the total distance traveled by the placement head. Two integer nonlinear programming models are formulated first. Then, each of them is equivalently converted into an integer linear type. The models for the integrated problem are verified by two commercial packages. In addition, a hybrid genetic algorithm previously developed by the authors is adopted to solve the models. The algorithm not only generates the optimal solutions quickly for small-sized problems, but also outperforms the genetic algorithms developed by other researchers in terms of total traveling distance.

Integrated component scheduling models for chip shooter machines

This paper focuses on minimizing printed circuit board (PCB) assembly time for a chipshootermachine, which has a movable feeder carrier holding components, a movable X–Y table carrying a PCB, and a rotary turret with multiple assembly heads. The assembly time of the machine depends on two inter-related optimization problems: the component sequencing problem and the feeder arrangement problem. Nevertheless, they were often regarded as two individual problems and solved separately. This paper proposes two complete mathematical models for the integrated problem of the machine. The models are verified by two commercial packages. Finally, a hybrid genetic algorithm previously developed by the authors is presented to solve the model. The algorithm not only generates the optimal solutions quickly for small-sized problems, but also outperforms the genetic algorithms developed by other researchers in terms of total assembly time.

Evolutionary neural networks : models and applications

The scaling problems which afflict attempts to optimise neural networks (NNs) with genetic algorithms (GAs) are disclosed. A novel GA-NN hybrid is introduced, based on the bumptree, a little-used connectionist model. As well as being computationally efficient, the bumptree is shown to be more amenable to genetic coding lthan other NN models. A hierarchical genetic coding scheme is developed for the bumptree and shown to have low redundancy, as well as being complete and closed with respect to the search space. When applied to optimising bumptree architectures for classification problems the GA discovers bumptrees which significantly out-perform those constructed using a standard algorithm. The fields of artificial life, control and robotics are identified as likely application areas for the evolutionary optimisation of NNs. An artificial life case-study is presented and discussed. Experiments are reported which show that the GA-bumptree is able to learn simulated pole balancing and car parking tasks using only limited environmental feedback. A simple modification of the fitness function allows the GA-bumptree to learn mappings which are multi-modal, such as robot arm inverse kinematics. The dynamics of the 'geographic speciation' selection model used by the GA-bumptree are investigated empirically and the convergence profile is introduced as an analytical tool. The relationships between the rate of genetic convergence and the phenomena of speciation, genetic drift and punctuated equilibrium arc discussed. The importance of genetic linkage to GA design is discussed and two new recombination operators arc introduced. The first, linkage mapped crossover (LMX) is shown to be a generalisation of existing crossover operators. LMX provides a new framework for incorporating prior knowledge into GAs.Its adaptive form, ALMX, is shown to be able to infer linkage relationships automatically during genetic search.

Simulating Membrane Systems in Digital Computers

* Work partially supported by contribution of EU commission Under The Fifth Framework Programme, project “MolCoNet” IST-2001-32008.

Intelligent System for Computer Aided Assembly Process Planning

This paper presents the concepts of the intelligent system for aiding of the module assembly technology. The first part of this paper presents a project of intelligent support system for computer aided assembly process planning. The second part includes a coincidence description of the chosen aspects of implementation of this intelligent system using technologies of artificial intelligence (artificial neural networks, fuzzy logic, expert systems and genetic algorithms).

A Metaheuristic Approach to Solving the Generalized Vertex Cover Problem

AMS Subj. Classification: 90C27, 05C85, 90C59

Multiobjective design optimization of IGBT power modules considering power cycling and thermal cycling

Insulated-gate bipolar transistor (IGBT) power modules find widespread use in numerous power conversion applications where their reliability is of significant concern. Standard IGBT modules are fabricated for general-purpose applications while little has been designed for bespoke applications. However, conventional design of IGBTs can be improved by the multiobjective optimization technique. This paper proposes a novel design method to consider die-attachment solder failures induced by short power cycling and baseplate solder fatigue induced by the thermal cycling which are among major failure mechanisms of IGBTs. Thermal resistance is calculated analytically and the plastic work design is obtained with a high-fidelity finite-element model, which has been validated experimentally. The objective of minimizing the plastic work and constrain functions is formulated by the surrogate model. The nondominated sorting genetic algorithm-II is used to search for the Pareto-optimal solutions and the best design. The result of this combination generates an effective approach to optimize the physical structure of power electronic modules, taking account of historical environmental and operational conditions in the field.

Parameter optimization for noise and vibration reduction associated with position and speed sensorless control of permanent magnet machines at low speed

With the advantages and popularity of Permanent Magnet (PM) motors due to their high power density, there is an increasing incentive to use them in variety of applications including electric actuation. These applications have strict noise emission standards. The generation of audible noise and associated vibration modes are characteristics of all electric motors, it is especially problematic in low speed sensorless control rotary actuation applications using high frequency voltage injection technique. This dissertation is aimed at solving the problem of optimizing the sensorless control algorithm for low noise and vibration while achieving at least 12 bit absolute accuracy for speed and position control. The low speed sensorless algorithm is simulated using an improved Phase Variable Model, developed and implemented in a hardware-in-the-loop prototyping environment. Two experimental testbeds were developed and built to test and verify the algorithm in real time.^ A neural network based modeling approach was used to predict the audible noise due to the high frequency injected carrier signal. This model was created based on noise measurements in an especially built chamber. The developed noise model is then integrated into the high frequency based sensorless control scheme so that appropriate tradeoffs and mitigation techniques can be devised. This will improve the position estimation and control performance while keeping the noise below a certain level. Genetic algorithms were used for including the noise optimization parameters into the developed control algorithm.^ A novel wavelet based filtering approach was proposed in this dissertation for the sensorless control algorithm at low speed. This novel filter was capable of extracting the position information at low values of injection voltage where conventional filters fail. This filtering approach can be used in practice to reduce the injected voltage in sensorless control algorithm resulting in significant reduction of noise and vibration.^ Online optimization of sensorless position estimation algorithm was performed to reduce vibration and to improve the position estimation performance. The results obtained are important and represent original contributions that can be helpful in choosing optimal parameters for sensorless control algorithm in many practical applications.^

Optimization of transit transfer times: A system-wide approach

This dissertation presents a system-wide approach, based on genetic algorithms, for the optimization of transfer times for an entire bus transit system. Optimization of transfer times in a transit system is a complicated problem because of the large set of binary and discrete values involved. The combinatorial nature of the problem imposes a computational burden and makes it difficult to solve by classical mathematical programming methods. ^ The genetic algorithm proposed in this research attempts to find an optimal solution for the transfer time optimization problem by searching for a combination of adjustments to the timetable for all the routes in the system. It makes use of existing scheduled timetables, ridership demand at all transfer locations, and takes into consideration the randomness of bus arrivals. ^ Data from Broward County Transit are used to compute total transfer times. The proposed genetic algorithm-based approach proves to be capable of producing substantial time savings compared to the existing transfer times in a reasonable amount of time. ^ The dissertation also addresses the issues related to spatial and temporal modeling, variability in bus arrival and departure times, walking time, as well as the integration of scheduling and ridership data. ^

Tool cutting force modeling and wear estimation of micro -end-milling operations

The applications of micro-end-milling operations have increased recently. A Micro-End-Milling Operation Guide and Research Tool (MOGART) package has been developed for the study and monitoring of micro-end-milling operations. It includes an analytical cutting force model, neural network based data mapping and forecasting processes, and genetic algorithms based optimization routines. MOGART uses neural networks to estimate tool machinability and forecast tool wear from the experimental cutting force data, and genetic algorithms with the analytical model to monitor tool wear, breakage, run-out, cutting conditions from the cutting force profiles. ^ The performance of MOGART has been tested on the experimental data of over 800 experimental cases and very good agreement has been observed between the theoretical and experimental results. The MOGART package has been applied to the micro-end-milling operation study of Engineering Prototype Center of Radio Technology Division of Motorola Inc. ^