Thesis (Ed.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / The use of three-dimensional molecular models to elucidate many of the unobservable properties of atoms and molecules has constantly been recommended. This study compares two methods of teaching atomic structure and valency theory at the secondary school level in chemistry - one method using models, the other method not using models. Six suburban high schools consisting of 18 chemistry classes and 449 students were divided into two groups - control and experimental. Both groups were taught a five-week unit on atomic structure, valency, and bonding theory. All students used the same chemistry text book and each teacher followed the same outline and syllabus. The experimental schools used colored three-dimensional molecular models; whereas the control schools were restricted to the use of the blackboard as the only visual aid. The control and experimental groups were kept separate to minimize class carry-over and interchange. The otis Quick Scoring Test of Intelligence and the Sequential Test of Educational Progress in Science Form 2B were administered as pretests. Levels of significance were established among the means for the two tests. The scores failed to reveal any significant differences between the control and experimental groups. The author's instrument - an Atomic Structure and Valency Achievement Test - was administered to all students at the completion of the five-week unit. This instrument was shown to possess a reliability coefficient sufficiently high to warrant its use as a test for measuring achievement of the particular unit under study. The reliability coefficient was calculated to be 0.725 based on the difficulty and intercorrelation of the test items. The achievement test on atomic structure and valency theory consisted of eighty items. These eighty items were selected from a group of 120 items which had been correlated with the unit material. Ninety items were selected by a committee of chemistry teachers not involved in the study. Eighty of the best items were selected and were administered to 150 chemistry students in a pilot stuqy. Each item was then examined for content and wording. Needed corrections were made and a final test was constructed. A simple analysis of variance model and t-tests showed that there were statistically significant differences found in the experimental groups which have been exposed to the molecular models. These differences were based on the use of the author's instrument as the criterion. The use of the three-dimensional molecular models in the experimental group produced higher achievement as measured by the Atomic Structure and Chemical Bonding Achievement Test. The average mean difference between scores on this 80-item test between the control and experimental groups was almost 20 points. Thus students exposed to the models in this study were more prepared to comprehend some of the unobservable characteristics of atoms and molecules. / 2999-01-01

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (p. 105-116).

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 97-102).

To solve the programmability issue of membrane computing models, the automatic design of membrane systems is a newly initiated and promising research direction. In this paper, we propose an automatic design method, Permutation Penalty Genetic Algorithm (PPGA), for a deterministic and non-halting membrane system by tuning membrane structures, initial objects and evolution rules. The main ideas of PPGA are the introduction of the permutation encoding technique for a membrane system, a penalty function evaluation approach for a candidate membrane system and a genetic algorithm for evolving a population of membrane systems toward a successful one fulfilling a given computational task. Experimental results show that PPGA can successfully accomplish the automatic design of a cell-like membrane system for computing the square of n ( n >/= 1 is a natural number) and can find the minimal membrane systems with respect to their membrane structures, alphabet, initial objects, and evolution rules for fulfilling the given task. We also provide the guidelines on how to set the parameters of PPGA.

No description available.

While there have been many recently developed Elastic Network Models (ENM) to calculate the fluctuation dynamics of proteins, e.g., Gaussian Network Model (GNM), Anisotropic Network Model (ANM), Distance Network Model (DNM), the concept of loading these models to study the molecular mechanics and constitutive behavior of structural proteins has remained relatively untouched, until very recently. This work entails using the ANM as the framework for developing a finite element model of a 9–monomer strand of actin. Critical input parameters to the model, such as the cutoff radius, r[subscript c], and spring constant, k, are generated by matching the all-atom steered molecular dynamics (SMD) residue displacements to that of the ANM. The parameters yielding the best match between the SMD and structural ENM (SENM) simulations will then be input into the finite element model (FEM) for a more in depth analysis. The finite element model incorporates a 9–monomer strand of actin. The F–actin strand is subjected axial and torsional loads comparable to those seen in vivo. Key areas of interest in the protein are examined, such as the nucleotide binding pocket (NBP) and the DNase I binding loop, to demonstrate how loading affects the protein’s conformation. Local residue displacements are tracked in an effort to garner a better understanding of how various loads are transmitted through F–actin during key events. Insights and conclusions are discussed along with the implications of this work. / text

Results are presented from a variety of molecular simulations of phase coexistence using the well established Gay-Berne (GB) liquid crystal model. Firstly, the simulation of bulk phase coexistence using the Gibbs ensemble Monte Carlo technique is presented, both for one and two-component GB systems. The one-component results, using a novel parameterisation of the GB, show a rich phase behaviour, displaying both isotropic and nematic-vapour coexistence, in good comparison with previous studies. A method for arriving at the two-component parameterisation is then discussed, followed by a novel application of the Gibbs ensemble to the isotropic-nematic transition in two-component systems. Results in broad agreement with theoretical predictions, subject to a large finite size effect, are obtained. Secondly, upon the basis of the one-component Gibbs results, results are presented from a series of molecular dynamics simulations of a free standing GB film in equilibrium with its own saturated vapour. The introduction of inhomogeneity is shown to induce a preferred molecular alignment in the nematic film perpendicular to the liquid-vapour interface. At slightly higher temperatures the nematic film is wet by the isotropic phase, displaying an intermediate ordering regime where the formation of short-lived nematic domains within the film is observed. This effect has been analysed using orientational correlation functions, and shown to result from a decoupling of the planar and perpendicular nematic ordering caused by the system inhomogeneity. A system-size analysis of this effect has also been undertaken, showing a definite increase in the range of decay of these orientational correlations with increasing system size.

o processo de inclusão social do aluno portador de deficiência visual é facilitado pela adoção de estratégias pedagógicas, e pela utilização de materiais didáticos adequados. Neste trabalho, com o objetivo de facilitar a compreensão de conceitos químicos básicos, desenvolvemos um material didático, constituído de bolas texturizadas, que representam elementos qUlmlcos freqüentemente citados em aulas de Química de nível introdutório. Este material permite que o aluno, por meio do toque, e com o uso de uma legenda escrita em Braille, reconheça os elementos químicos em uma Tabela Periódica, especialmente montada para tal fim. Utilizando este modelo texturizado, o aluno pode, também, estabelecer ligações entre átomos, montar moléculas e cadeias de compostos orgânicos. Desta forma, a tridimensionalidade molecular pode ser melhor compreendida. O material instrucional foi testado com alunos de classes variadas, pertencentes à oitava série do ensino fundamental ou a uma das séries do ensino médio, sendo demonstrada sua eficiência. Além disso, em paralelo, procurou-se conhecer as idéias de professores, diretamente envolvidos com a educação especial, com relação à inclusão social de alunos deficiente visuais . / Special educational strategies and specific instructional material are needed in order to promote School and Social inclusion of students with visual impairment. In this work, we present our results on the development and testing of a new instructional material , composed of a specially designed Periodic Table of elements in which the na me of each element is written according to the Braille system, and some elements are represented by texturized balls. The tactile recognition of elements and names were very helpful in developing basic concept on chemical bonding and chemical properties of elements and compounds. Using texturized ball and stick models, High School students with visual impairment were also able to construct physical representations of organic and inorganic molecules, as well as of some hydrocarbon molecular chains. These three dimension structural models allowed for a proper insight on the space orientation of simple molecules. Some teachers\' ideas on the process of Social inclusion of students with visual impairment are also presented and discussed.

o processo de inclusão social do aluno portador de deficiência visual é facilitado pela adoção de estratégias pedagógicas, e pela utilização de materiais didáticos adequados. Neste trabalho, com o objetivo de facilitar a compreensão de conceitos químicos básicos, desenvolvemos um material didático, constituído de bolas texturizadas, que representam elementos qUlmlcos freqüentemente citados em aulas de Química de nível introdutório. Este material permite que o aluno, por meio do toque, e com o uso de uma legenda escrita em Braille, reconheça os elementos químicos em uma Tabela Periódica, especialmente montada para tal fim. Utilizando este modelo texturizado, o aluno pode, também, estabelecer ligações entre átomos, montar moléculas e cadeias de compostos orgânicos. Desta forma, a tridimensionalidade molecular pode ser melhor compreendida. O material instrucional foi testado com alunos de classes variadas, pertencentes à oitava série do ensino fundamental ou a uma das séries do ensino médio, sendo demonstrada sua eficiência. Além disso, em paralelo, procurou-se conhecer as idéias de professores, diretamente envolvidos com a educação especial, com relação à inclusão social de alunos deficiente visuais . / Special educational strategies and specific instructional material are needed in order to promote School and Social inclusion of students with visual impairment. In this work, we present our results on the development and testing of a new instructional material , composed of a specially designed Periodic Table of elements in which the na me of each element is written according to the Braille system, and some elements are represented by texturized balls. The tactile recognition of elements and names were very helpful in developing basic concept on chemical bonding and chemical properties of elements and compounds. Using texturized ball and stick models, High School students with visual impairment were also able to construct physical representations of organic and inorganic molecules, as well as of some hydrocarbon molecular chains. These three dimension structural models allowed for a proper insight on the space orientation of simple molecules. Some teachers\' ideas on the process of Social inclusion of students with visual impairment are also presented and discussed.

Les modèles physiques moléculaires sont depuis longtemps utilisés dans le domaine de la biologie structurale et de la chimie. Malgré l’apparition de représentations numériques qui offrent une grande variété de visualisations moléculaires dynamiques et permettent notamment d’analyser visuellement les résultats de simulations, les modèles physiques moléculaires sont encore fréquemment utilisés. En effet, la manipulation directe et la construction manuelle de modèles physiques moléculaires facilitent l’élaboration et la mémorisation d’une représentation mentale des structures moléculaires 3D. Les techniques d’interaction avec des objets 3D n’atteignent pas encore la finesse et la richesse de perception et de manipulation des modèles physiques. Par ailleurs, l’interaction avec des représentations moléculaires virtuelles est rendue particulièrement difficile car les structures moléculaires sont très complexes du fait de leur taille, de leur caractère tridimensionnel et de leur flexibilité, auquel s'ajoutent la quantité et la variété des informations qui les caractérisent. Pour aborder la problématique de l'interaction avec ces structures moléculaires, nous proposons dans cette thèse de concevoir une interface tangible moléculaire combinant les avantages des représentations physiques et virtuelles. Pour réaliser une interface tangible flexible et modulaire, à l’image des biomolécules à manipuler, ce travail de thèse a dû relever plusieurs défis scientifiques avec pour contrainte majeure le fait de proposer une approche se passant de marqueurs et dispositif de capture 3D complexe. La première étape fut de choisir, concevoir et fabriquer un modèle physique permettant la manipulation de molécules avec de nombreux degrés de libertés. La seconde étape consistait à créer un modèle numérique permettant de reproduire le comportement mécanique du modèle physique. Enfin, il a fallu concevoir des méthodes de recalage utilisant des techniques de traitement d'image en temps réel pour que le modèle physique puisse contrôler, par couplage, son avatar virtuel. En terme de traitement d’image, de nouvelles méthodes ont été conçues implémentées et évaluées afin d'une part, d’identifier et de suivre les atomes dans l’espace image et d'autre part, d'alimenter la méthode de reconstruction 3D avec un faible nombre de points. L'une de nos contributions a été d'adapter la méthode de Structure from Motion en incluant des connaissances biochimiques pour guider la reconstruction. Par ailleurs, la visualisation conjointe de modèles physiques de molécules et de leur avatar virtuel dynamique, parfois co-localisé dans un contexte de réalité augmentée, a été abordée. Pour cela, des méthodes de visualisation haute performance adaptées à ce contexte ont été conçues afin d’améliorer la perception des formes et cavités, caractéristiques importantes des molécules biologiques. Par exemple, l’occultation ambiante ou le raycasting de sphères avec des ombres portées dynamiques permettent d’augmenter un modèle physique en tenant compte de l’illumination réelle pour une meilleure intégration en réalité augmentée. Les retombées de ce travail en terme d’usage sont nombreuses dans le domaine de la recherche et de la pédagogie en biologie moléculaire, comme dans le domaine de la conception de médicaments et plus particulièrement du Rational Drug Design. L'expert doit être au centre de la tâche de conception de médicament pour la rendre plus efficace et rationnelle, à l’image du succès du jeu sérieux Fold’It, auquel s’ajoute le bénéfice de l’utilisation d’interface tangible capable de manipuler les nombreux degrés de liberté intrinsèques des biomolécules. / Physical molecular models have long been used in the structural biology and chemistry fields. Despite the emergence of numerical representations offering various and dynamic molecular visualizations to analyze the simulation results, molecular physical models are still being used. Direct manipulation and assembly of physical models ease to create and memorize a mental representation of 3D molecular structures. Interaction techniques to manipulate virtual 3D objects are not reaching the fineness and the benefits of the perceptual cues and manipulation skills of physical models. Moreover, interacting with virtual molecular representations remains a hard task because of the complexity of molecular structures, their size, their flexibility and the various data that define them. In this thesis, we address this issue by designing a molecular tangible interface combining the perks of physical and virtual representations. To match the flexibility and modularity of biomolecules to manipulate, this work met challenges in different scientific fields with the constraint to not use a tracker based system. The first step was to choose, conceive and build a physical model to handle the manifold degrees of freedom of molecules. The second step consisted in creating a numerical representation of mechanical properties of the physical model. Lastly, we needed to develop tracking methods using real-time image processing algorithms in order to control the virtual representation by coupling it to the physical one. New image processing methods have been implemented and evaluated to identify and track atoms in the image space. A Structure from Motion method was designed and adapted to reconstruct in 3D the atom positions by using a small amount of points and by including biochemical knowledge to guide the reconstruction. At last, we address the visualization of physical and dynamic virtual representations, sometimes co-localized in an Augmented Reality context. High performance visualization methods adapted to this context have been developed to enhance shape and cavity perception, two major specifics of biological molecules. For instance, ambient occlusion or sphere raycasting with dynamic shadows can augment a physical object taking the real illumination of the scene for a better insertion in an Augmented Reality context. The impact of this work targets both the education in molecular biology and the research field: the rational drug design field could benefit from the expertise of the user to optimize the design of drugs by manipulating biomolecule's numerous degrees of freedom using a tangible interface. Just like Fold'It is contributing to solve the folding problem, a similar approach could be used to solve the molecular docking problem using advanced manipulation interfaces.