A Multi-Dimensional Width-Bounded Geometric Separator and its Applications to Protein Folding

We used a divide-and-conquer algorithm to recursively solve the two-dimensional problem of protein folding of an HP sequence with the maximum number of H-H contacts. We derived both lower and upper bounds for the algorithmic complexity by using the newly introduced concept of multi-directional width-bounded geometric separator. We proved that for a grid graph G with n grid points P, there exists a balanced separator A subseteq P$ such that A has less than or equal to 1.02074 sqrt{n} points, and G-A has two disconnected subgraphs with less than or equal to {2over 3}n nodes on each subgraph. We also derive a 0.7555sqrt {n} lower bound for our balanced separator. Based on our multidirectional width-bounded geometric separator, we found that there is an O(n^{5.563sqrt{n}}) time algorithm for the 2D protein folding problem in the HP model. We also extended the upper bound results to rectangular and triangular lattices

On the Parameterized Complexity of Red-Blue Points Separation

We study the following geometric separation problem: Given a set R of red points and a set B of blue points in the plane, find a minimum-size set of lines that separate R from B. We show that, in its full generality, parameterized by the number of lines k in the solution, the problem is unlikely to be solvable significantly faster than the bruteforce nO(k) -time algorithm, where n is the total number of points. Indeed, we show that an algorithm running in time f(k)nᵒ(k/log k) , for any computable function f, would disprove ETH. Our reduction crucially relies on selecting lines from a set with a large number of different slopes (i.e., this number is not a function of k). Conjecturing that the problem variant where the lines are required to be axis-parallel is FPT in the number of lines, we show the following preliminary result. Separating R from B with a minimum-size set of axis-parallel lines is FPT in the size of either set, and can be solved in time O∗(9|B|) (assuming that B is the smaller set)

Polymer Processing: Modeling and Correlations Finalized to Tailoring the Plastic Part Morphology and Properties

The analysis of polymer processing operations is a wide and complex subject; during polymer processing, viscoelastic fluids are forced to deform into desired geometries using non-homogeneous velocity and temperature fields down to solidification. The objective of analysis is the identification of processing conditions, which are finalized in the optimization of product final properties, which, in turn, are determined by the final part morphology. Depending on the operating conditions, the properties of the final part can change more than one order of magnitude. Properties of interest include the mechanical, optical, barrier, permeability, and biodegradability, and any other property of practical relevance including the characteristics of the surfaces as its finishing and wettability, which are connected to one another. The scope of this Special Issue is to select progress in or reviews of the understanding/description of the phenomena involved along the chain of processing–morphology–properties. Along this virtual chain, modeling may be a useful approach, and within the objective of understanding fundamental aspects, it may also be relevant to compare selected characteristics of the process and the material with the characteristics of the resulting morphology and then with the properties of the final part. This approach suggests the title: “Polymer Processing: Modeling and Correlations Finalized to Tailoring the Plastic Part Morphology and Properties”

Exact rotamer optimization for computational protein design

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.Includes bibliographical references (leaves 235-244).The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* search (DEE/A*) have proven useful, but may not be strong enough as we attempt to solve protein design problems where a large number of similar rotamers is eligible and the network of interactions between residues is dense. In this thesis, we present an exact solution method, named BroMAP (branch-and-bound rotamer optimization using MAP estimation), for such protein design problems. The design goal of BroMAP is to be able to expand smaller search trees than conventional branch-and-bound methods while performing only a moderate amount of computation in each node, thereby reducing the total running time. To achieve that, BroMAP attempts reduction of the problem size within each node through DEE and elimination by energy lower bounds from approximate maximurn-a-posteriori (MAP) estimation. The lower bounds are also exploited in branching and subproblem selection for fast discovery of strong upper bounds. Our computational results show that BroMAP tends to be faster than DEE/A* for large protein design cases. BroMAP also solved cases that were not solvable by DEE/A* within the maximum allowed time, and did not incur significant disadvantage for cases where DEE/A* performed well. In the second part of the thesis, we explore several ways of improving the energy lower bounds by using Lagrangian relaxation. Through computational experiments, solving the dual problem derived from cyclic subgraphs, such as triplets, is shown to produce stronger lower bounds than using the tree-reweighted max-product algorithm.(cont.) In the second approach, the Lagrangian relaxation is tightened through addition of violated valid inequalities. Finally, we suggest a way of computing individual lower bounds using the dual method. The preliminary results from evaluating BroMAP employing the dual bounds suggest that the use of the strengthened bounds does not in general improve the running time of BroMAP due to the longer running time of the dual method.by Eun-Jong Hong.Ph.D

Technical Institute, Kevin Street: Prospectus 1938-39

Courses and timetables for Dublin Institute of Technology, Kevin Street

Polyimides for piezoelectric materials, magnetoelectric nanocomposites and battery separators: synthesis and characterization

329 p.Se ha sintetizado una serie de poliimidas y copoliimidas que contienen grupos nitrilo en su estructura, y posteriormente han sido polarizadas por corona con objeto de dotarlas de comportamiento piezoeléctrico. Las condiciones de la polarización por corona han sido optimizadas para las muestras estudiadas, mostrando los coeficientes una buena estabilidad térmica y a lo largo del tiempo. Además, se ha estudiado la influencia en la piezoelectricidad de la unidad repetitiva con dos grupos nitrilo, observando que un incremento progresivo del contenido en el componente con dos grupos nitrilo (2CN) aumenta la respuesta piezoeléctrica. Los films poliméricos han demostrado alta estabilidad térmica mediante DSC y TGA, demostrando su uso a temperaturas superiores a 100ºC.Las propiedades dieléctricas de las muestras han sido determinadas mediante espectroscopia dieléctrica para comprender el comportamiento dieléctrico de los films de poliimida. Se ha analizado la contribución de los grupos nitrilo en las relajaciones dieléctricas y en los tipos de polarización que se ven implicados.El uso de poliimidas en nanocomposites magnetoeléctricos (ME) ha sido demostrado. Se ha medido el coeficiente magnetoeléctrico en un film de nanocomposite, preparado mediante un método de polimerización in-situ, usando nanopartículas esféricas de ferrita de cobalto como inclusión y una copoliimida amorfa, como matriz. Se han preparado diferentes fibras de poliimida mediante electrospinning (electrohilado), han sido caracterizadas y testadas como separadores para baterías de ion Litio

Proceedings of the Scientific-Practical Conference "Research and Development - 2016"

talent management; sensor arrays; automatic speech recognition; dry separation technology; oil production; oil waste; laser technolog

Beta-cyclodextrin Conjugated Magnetic Nanoparticles for Bio-and Environmental Applications

Ph.DDOCTOR OF PHILOSOPH

MEMS micro-contact printing engines

This thesis investigates micro-contact printing (µCP) engines using micro-electro-mechanical systems (MEMS). Such engines are self-contained and do not require further optical alignment and precision manipulation equipment. Hence they provide a low-cost and accessible method of multilevel surface patterning with sub-micron resolution. Applications include the field of biotechnology where the placement of biological ligands at well controlled locations on substrates is often required for biological assays, cell studies and manipulation, or for the fabrication of biosensors. A miniaturised silicon µCP engine is designed and fabricated using a wafer-scale MEMS fabrication process and single level and bi-level µCP are successfully demonstrated. The performance of the engine is fully characterised and two actuation modes, mechanical and electrostatic, are investigated. In addition, a novel method of integrating the stamp material into the MEMS process flow by spray coating is reported. A second µCP engine formed by wafer-scale replica moulding of a polymer is developed to further drive down cost and complexity. This system carries six complementary patterns and allows six-level µCP with a layer-to-layer accuracy of 10 µm over a 5 mm x 5 mm area without the use of external aligning equipment. This is the first such report of aligned multilevel µCP. Lastly, the integration of the replica moulded engine with a hydraulic drive for controlled actuation is investigated. This approach is promising and proof of concept has been provided for single-level patterning

47th Rocky Mountain Conference on Analytical Chemistry

Final program, abstracts, and information about the 47th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Denver, Colorado, July 31 - August 4, 2005