A Framework for Creativity Enhancement of Painterly Rendering

東京電機大学201

Modeling and simulations of single stranded rna viruses

The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models simplify complex structures such as viruses and let us study general behavior of the complex biological systems that otherwise cannot be studied with all-atom details. Second, we modeled the first all-atom T=3, icosahedral, single stranded RNA virus, Pariacoto virus (PaV). The x-ray structure of PaV shows only 35% of the total RNA genome and 88% of the capsid. We modeled both missing portions of RNA and protein. The final model of the PaV demonstrated that the positively charged protein N- terminus was located deep inside the RNA. We propose that the positively charged N- terminal tails make contact with the RNA genome and neutralize the negative charges in RNA and subsequently collapse the RNA/protein complex into an icosahedral virus. Third, we simulated T=1 empty capsids using a coarse-grained model of three capsid proteins as a wedge-shaped triangular capsid unit. We varied the edge angle and the potentials of the capsid units to perform empty capsid assembly simulations. The final model and the potential are further improved for the whole virus assembly simulations. Finally, we performed stability and assembly simulations of the whole virus using coarse-grained models. We tested various strengths of RNA-protein tail and capsid protein-capsid protein attractions in our stability simulations and narrowed our search for optimal potentials for assembly. The assembly simulations were carried out with two different protocols: co-transcriptional and post-transcriptional. The co-transcriptional assembly protocol mimics the assembly occurring during the replication of the new RNA. Proteins bind the partly transcribed RNA in this protocol. The post-transcriptional assembly protocol assumes that the RNA is completely transcribed in the absence of proteins. Proteins later bind to the fully transcribed RNA. We found that both protocols can assemble viruses, when the RNA structure is compact enough to yield a successful virus particle. The post-transcriptional protocol depends more on the compactness of the RNA structure compared to the co-transcriptional assembly protocol. Viruses can exploit both assembly protocols based on the location of RNA replication and the compactness of the final structure of the RNA.PhDCommittee Chair: Stephen C. Harvey; Committee Member: Adegboyega Oyelere; Committee Member: Loren Williams; Committee Member: Rigoberto Hernandez; Committee Member: Roger Wartel

Breaking Barriers: Diversity and Equity in Chemistry

This book is being made available in both PDF and ePub formats for the convenience of the reader.The field of chemistry has long been associated with the pursuit of objective facts and the uncovering of the building blocks of our universe. However, this view can often exclude the important role that diversity, equity, and inclusion (DEI) play in the advancement of scientific knowledge. By highlighting the contributions of minority chemists and integrating DEI principles into chemistry education, we can promote a more inclusive environment and foster greater understanding of the complex connections between chemistry and society. In the first section, we provide a biography of each chemist, discussing their personal and professional lives and how their minority identity has interacted with their careers. The second section summarizes their research and accomplishments in the field of chemistry, emphasizing the importance of their work and the implications it has had on the broader scientific community. Finally, the third section explores how their research is related to the topics and contents taught in general chemistry, creating a connection between the material students learn in the classroom and the real-world applications of chemistry. In recent years, there has been a growing recognition of the need to incorporate DEI into STEM education, and chemistry is no exception. Despite this, there remains a scarcity of learning materials that directly introduce diversity and equality in chemistry education. As a result, students may view chemistry as an isolated discipline that is removed from the broader community. This book aims to challenge that perception by introducing readers to minority chemists, their research, and the ways in which their work is related to topics taught in general chemistry courses. By exploring the lives and research of chemists who come from diverse backgrounds, we hope to showcase the importance of diverse perspectives in the advancement of the field and inspire a new generation of scientists who embrace and promote DEI in their own work. Each chapter of this book is divided into three main sections, highlighting the personal and professional lives of these extraordinary individuals and demonstrating the impact their work has had on the field

Immersion Into Noise

Joseph Nechvatal's Immersion Into Noise investigates multiple aspects of cultural noise by applying our audio understanding of noise to the visual, architectual and cognative domains. The author takes the reader through phenomenal aspects of the art of noise into algorithmic and network contexts, beginning in the Abside of the Grotte de Lascaux

Immersion Into Noise

Joseph Nechvatal's Immersion Into Noise investigates multiple aspects of cultural noise by applying our audio understanding of noise to the visual, architectual and cognative domains. The author takes the reader through phenomenal aspects of the art of noise into algorithmic and network contexts, beginning in the Abside of the Grotte de Lascaux

CELLmicrocosmos - Integrative cell modeling at the molecular, mesoscopic and functional level

Sommer B. CELLmicrocosmos - Integrative cell modeling at the  molecular, mesoscopic and functional level. Bielefeld: Bielefeld University; 2012.The modeling of cells is an important application area of Systems Biology. In the context of this work, three cytological levels are defined: the mesoscopic, the molecular and the functional level. A number of related approaches which are quite diverse will be introduced during this work which can be categorized into these disciplines. But none of these approaches covers all areas. In this work, the combination of all three aforementioned cytological levels is presented, realized by the CELLmicrocosmos project, combining and extending different Bioinformatics-related methods. The mesoscopic level is covered by CellEditor which is a simple tool to generate eukaryotic or prokaryotic cell models. These are based on cell components represented by three-dimensional shapes. Different methods to generate these shapes are discussed by using partly external tools such as Amira, 3ds Max and/or Blender; abstract, interpretative, 3D-microscopy-based and molecular-structure-based cell component modeling. To communicate with these tools, CellEditor provides import as well as export capabilities based on the VRML97 format. In addition, different cytological coloring methods are discussed which can be applied to the cell models. MembraneEditor operates at the molecular level. This tool solves heterogeneous Membrane Packing Problems by distributing lipids on rectangular areas using collision detection. It provides fast and intuitive methods supporting a wide range of different application areas based on the PDB format. Moreover, a plugin interface enables the use of custom algorithms. In the context of this work, a high-density-generating lipid packing algorithm is evaluated; The Wanderer. The semi-automatic integration of proteins into the membrane is enabled by using data from the OPM and PDBTM database. Contrasting with the aforementioned structural levels, the third level covers the functional aspects of the cell. Here, protein-related networks or data sets can be imported and mapped into the previously generated cell models using the PathwayIntegration. For this purpose, data integration methods are applied, represented by the data warehouse DAWIS-M.D. which includes a number of established databases. This information is enriched by the text-mining data acquired from the ANDCell database. The localization of proteins is supported by different tools like the interactive Localization Table and the Localization Charts. The correlation of partly multi-layered cell components with protein-related networks is covered by the Network Mapping Problem. A special implementation of the ISOM layout is used for this purpose. Finally, a first approach to combine all these interrelated levels is represented; CellExplorer which integrates CellEditor as well as PathwayIntegration and imports structures generated with MembraneEditor. For this purpose, the shape-based cell components can be correlated with networks as well as molecular membrane structures using Membrane Mapping. It is shown that the tools discussed here can be applied to scientific as well as educational tasks: educational cell visualization, initial membrane modeling for molecular simulations, analysis of interrelated protein sets, cytological disease mapping. These are supported by the user-friendly combination of Java, Java 3D and Web Start technology. In the last part of this thesis the future of Integrative Cell Modeling is discussed. While the approaches discussed here represent basically three-dimensional snapshots of the cell, prospective approaches have to be extended into the fourth dimension; time

Rendering the reality: Development of a video mapping show on a mountain cliff face for a music festival

Rendering the Reality, como conceito, quer difundir a ideia de que aquilo que as pessoas experimentam não é apenas a representação objetiva da realidade, mas a sua interpretação subjetiva. Todos podem perceber algo diferente dos outros e este aspeto é analisado neste trabalho através de uma imersão total no mundo das projeções. O principal objetivo desta tese de projeto, de facto, é desenvolver um espetáculo de video mapping sobre uma superfície irregular dentro de um festival de música. Para tal, inicialmente, foram analisados os antecedentes históricos e o estado da arte. Foi levado em consideração três tópicos principais: história do cinema, história do som no cinema, e história do video mapping. Relativamente a este último, no qual o desenvolvimento é mais recente, foi também discutida uma análise adicional e notícias relacionadas ao assunto. Posteriormente, foram apresentados e investigados alguns projetos inspiradores. Estes são instalações ou espetáculos que levam à concretização da tarefa principal. A parte central é o desenvolvimento do projeto. Primeiro, foi apresentado o conceito do festival e detalhes relacionados. Fundamental nesta secção é a análise do local, uma vez que o mapeamento da projeção teve de ser assentado numa falésia de uma montanha. Uma vez analisado o espaço, foram feitas muitas inspeções ao local a fim de produzir uma maquete. Esta última foi feita utilizando fotogrametria e impressão 3D. O protótipo 3D foi então mapeado e o conteúdo de vídeo foi projetado sobre ele. Os conteúdos para o video mapping foram devidamente registados, editados e distorcidos para se obter uma proposta do programa no protótipo. O resultado final é um video mapping de 3 minutos ao vivo feito de conteúdos visuais mistos e uma faixa musical criada para o efeito. Este resultado é a soma de todo o processo e dos obstáculos encontrados ao longo do percurso. Em conclusão, a relação que o público pode estabelecer com este espetáculo de video mapping não pode ser esclarecida, já que o festival não se realizou. Mas é evidente que o artista que desenvolveu o espetáculo tentou dar uma interpretação do festival e da sua localização através do conteúdo audiovisual, ou seja, tentando renderizar a realidade.Rendering the Reality, as a concept, wants to spread the idea that what people experience is not only the objective representation of reality but the subjective interpretation of it. Everyone can perceive something different from others and this aspect is analyzed in this work through full immersion in the world of projections. The main goal of this project thesis, indeed, is to develop a video mapping show on an irregular surface within a music festival. To do so, initially, the historical background and state of the art were analyzed. Three main topics were taken into consideration: History of filmmaking, History of sound in movies, and History of projection mapping. Concerning this latter, whose development is most recent, additional analysis and related news were discussed, too. Subsequently, some inspiring projects were presented and investigated. Those are installations or shows that lead to the concretization of the main task. The central part is the development of the project. First, the festival concept and related details were presented. Fundamental in this section is the analysis of the location since the projection mapping had to be settled on a cliff face of a mountain. Once analyzed the space, lots of site inspections were made in order to produce a maquette. This latter was made using photogrammetry and 3D printing. The 3D prototype, then, was mapped and video contents were projected on it. Contents for video mapping were appositely recorded, edited, and distorted to obtain a proposal of the show on the prototype. The final result is a 3-minute video mapping live made of mixed visual contents and a music track created for the purpose. This outcome is the sum of the entire process and obstacles encountered along the way. In conclusion, the relationship the audience can establish with this video mapping show cannot be clarified, as the festival did not take place. But it is clear that the artist who developed the show tried to give an interpretation of the festival and its location through the audiovisual content, that is, trying to render the reality

Rockscapes:A Study of Forms in the Natural Formations of Hyderabad

Rock formations in the Deccan Plateau are very old; some of them are older than 2.5 million years. Geologically, rocks constitute of various mineral compositions within the core and these decide how they are shaped due to weathering over many years. These beautifully weathered landscapes are affected by the recent rapid urbanization. Thus by photographically studying the forms and divulging the inner souls, this project attempts to sensitize a viewer towards these rockscapes. Photographs are presented in square format to highlight the form and texture. As per the psychology of shapes, square is quite balanced and that encourages the viewer to move around within the frame. It provides a clutter free and simple composition. In addition, the images are printed in monochrome to eliminate the visual dominance of color, to emphasize form and texture, to feel the timelessness and to amplify the use of negative space. By grouping the images, the subject matter is presented to the viewer with intended emphasis – singles, sky, plants, shadow and radials

非写実的画像生成のためのサンプリング法とカラーモデルの研究

東京電機大学201