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## Computation of population and physiological risk parameters from cancer data

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 107 p.; 723665 bytes; 723422 bytes; application/pdf; application/pdf

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by David Hensle.; Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.; Includes bibliographical references (p. 106-107).; This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.

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## Multiresolution computation of visible-surface representations

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 281 leaves; 28105944 bytes; 28105700 bytes; application/pdf; application/pdf

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by Demetri Terzopoulos.; Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1984.; MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING.; Bibliography: leaves 267-281.

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## Problems in decentralized decision making and computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: [6], 264 leaves; 14142694 bytes; 14142453 bytes; application/pdf; application/pdf

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by John Nikolas Tsitsiklis.; Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1985.; Bibliography: leaves 256-264.

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## Communication complexity of some problems in distributed computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 5, 158 leaves; 12062591 bytes; 12062346 bytes; application/pdf; application/pdf

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by Zhi-Quan Luo.; Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1989.; Includes bibliographical references (leaves 153-158).

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## Pulse computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 214 leaves; 12789114 bytes; 12788866 bytes; application/pdf; application/pdf

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by Gill Andrews Pratt.; Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1990.; Includes bibliographical references (leaves 134-135).

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## Cellular computation and communications using engineered genetic regulatory networks

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 138 p.; 10811566 bytes; 10811322 bytes; application/pdf; application/pdf

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In this thesis, I present an engineering discipline for obtaining complex, predictable, and reliable cell behaviors by embedding biochemical logic circuits and programmed intercellular communications into cells. To accomplish this goal, I provide a well-characterized component library, a biocircuit design methodology, and software design tools. I have built and characterized an initial cellular gate library with biochemical gates that implement the NOT, IMPLIES, and AND logic functions in E. coli cells. The logic gates perform computation using DNA-binding proteins, small molecules that interact with these proteins, and segments of DNA that regulate the expression of the proteins. I introduce genetic process engineering, a methodology for modifying the DNA encoding of existing genetic elements to achieve the desired input/output behavior for constructing reliable circuits of significant complexity. I demonstrate the feasibility of digital computation in cells by building several operational in-vivo digital logic circuits, each composed of three gates that have been optimized by genetic process engineering.; (cont.) I also demonstrate engineered intercellular communications with programmed enzymatic activity and chemical diffusions to carry messages...

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## Self-distributing computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 55 leaves; 3623458 bytes; 3623219 bytes; application/pdf; application/pdf

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by Thomas R. Woodfin.; Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.; Includes bibliographical references (leaves 54-55).

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## Avalanche : a framework for parallel and distributed computation; Framework for parallel and distributed computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 45 p.; 1891782 bytes; 1891542 bytes; application/pdf; application/pdf

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by Uriel Schafer.; Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.; Includes bibliographical references (p. 45).

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## A formal model of non-determinate dataflow computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 79 leaves; 3940304 bytes; 3948689 bytes; application/pdf; application/pdf

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by Jarvis Dean Brock.; Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1983.; MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING; Vita.; Bibliography: leaves 75-78.

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## Synthesis and evaluation of fault-tolerant quantum computer architectures

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 247 p.; 13338513 bytes; 13370932 bytes; application/pdf; application/pdf

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Fault-tolerance is the cornerstone of practical, large-scale quantum computing, pushed into its prominent position with heroic theoretical efforts. The fault-tolerance threshold, which is the component failure probability below which arbitrarily reliable quantum computation becomes possible, is one standard quality measure of fault-tolerant designs based on recursive simulation. However, there is a gulf between theoretical achievements and the physical reality and complexity of envisioned quantum computing systems. This thesis takes a step toward bridging that gap. We develop a new experimental method for estimating fault-tolerance thresholds that applies to realistic models of quantum computer architectures, and demonstrate this technique numerically. We clarify a central problem for experimental approaches to fault-tolerance evaluation--namely, distinguishing between potentially optimistic pseudo-thresholds and actual thresholds that determine scalability. Next, we create a system architecture model for the trapped-ion quantum computer, discuss potential layouts, and numerically estimate the fault-tolerance threshold for this system when it is constrained to a local layout. Finally, we place the problem of evaluation and synthesis of fault-tolerant quantum computers into a broader framework by considering a software architecture for quantum computer design.; by Andrew W. Cross.; Thesis (S.M.)--Massachusetts Institute of Technology...

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## Computation of the one-dimensional unwrapped phase

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 102 p.; 5467498 bytes; 5780699 bytes; application/pdf; application/pdf

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In this thesis, the computation of the unwrapped phase of the discrete-time Fourier transform (DTFT) of a one-dimensional finite-length signal is explored. The phase of the DTFT is not unique, and may contain integer multiple of 27r discontinuities. The unwrapped phase is the instance of the phase function chosen to ensure continuity. This thesis presents existing algorithms for computing the unwrapped phase, discussing their weaknesses and strengths. Then two composite algorithms are proposed that use the existing ones, combining their strengths while avoiding their weaknesses. The core of the proposed methods is based on recent advances in polynomial factoring. The proposed methods are implemented and compared to the existing ones.; by Zahi Nadim Karam.; Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.; Includes bibliographical references (p. 101-102). "Cepstrum bibliography" (p. 67-100).

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## Modelling morphogenesis as an amorphous computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 58 leaves

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This thesis presents a programming-language viewpoint for morphogenesis, the process of shape formation during embryological development. We model morphogenesis as a self-organizing, self-repairing amorphous computation and describe how we can program large-scale shape formation by giving local instructions to cell-like objects. Our goal is to simulate systems that display properties, like robustness, regeneration, and evolvability, that are present in biological systems but ordinarily not present in computer systems. Consistent with the theory of facilitated variation from evolutionary biology, we find that many of these properties can be introduced and conserved by a hierarchical organization of growth specification.; by Arnab Bhattacharyya.; Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.; Includes bibliographical references (leaves 57-58).

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## Robust network computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 98 p.

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In this thesis, we present various models of distributed computation and algorithms for these models. The underlying theme is to come up with fast algorithms that can tolerate faults in the underlying network. We begin with the classical message-passing model of computation, surveying many known results. We give a new, universally optimal, edge-biconnectivity algorithm for the classical model. We also give a near-optimal sub-linear algorithm for identifying bridges, when all nodes are activated simultaneously. After discussing some ways in which the classical model is unrealistic, we survey known techniques for adapting the classical model to the real world. We describe a new balancing model of computation. The intent is that algorithms in this model should be automatically fault-tolerant. Existing algorithms that can be expressed in this model are discussed, including ones for clustering, maximum flow, and synchronization. We discuss the use of agents in our model, and give new agent-based algorithms for census and biconnectivity. Inspired by the balancing model, we look at two problems in more depth.; (cont.) First, we give matching upper and lower bounds on the time complexity of the census algorithm, and we show how the census algorithm can be used to name nodes uniquely in a faulty network. Second...

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## Characterization and computation of equilibria in infinite games

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 82 p.

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Broadly, we study continuous games (those with continuous strategy spaces and utility functions) with a view towards computation of equilibria. We cover all of the game-theoretic background needed to understand these results in detail. Then we present new work, which can be divided into three parts. First, it is known that arbitrary continuous games may have arbitrarily complicated equilibria, so we investigate some properties of games with polynomial utility functions and a class of games with polynomial-like utility functions called separable games. We prove new bounds on the complexity of equilibria of separable games in terms of the complexity of the utility functions. In order to measure this complexity we propose a new definition for the rank of a continuous game; when applied to the case of finite games this improves on the results known in that setting. Furthermore, we prove a characterization theorem showing that several conditions which are necessary for a game to possess a finite-dimensional representation each define the class of separable games precisely, providing evidence that separable games are the natural class of continuous games in which to study computation. The characterization theorem also provides a natural connection between separability and the notion of the rank of a game. Second...

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## The study of entangled states in quantum computation and quantum information science

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 274 p.

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This thesis explores the use of entangled states in quantum computation and quantum information science. Entanglement, a quantum phenomenon with no classical counterpart, has been identified as an important and quantifiable resource in many areas of theoretical quantum information science, including quantum error correction, quantum cryptography, and quantum algorithms. We first investigate the equivalence classes of a particular class of entangled states (known as graph states due to their association with mathematical graphs) under local operations. We prove that for graph states corresponding to graphs with neither cycles of length 3 nor 4, the equivalence classes can be characterized in a very simple way. We also present software for analyzing and manipulating graph states. We then study quantum error-correcting codes whose codewords are highly entangled states. An important area of investigation concerning QECCs is to determine which resources are necessary in order to carry out any computation on the code to an arbitrary degree of accuracy, while simultaneously maintaining a high degree of resistance to noise. We prove that transversal gates, which are designed to prevent the propagation of errors through a system, are insufficient to achieve universal computation on almost all QECCs. Finally...

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## Design study of a novel computer instruction execution unit

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 141 p.

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The goal of the "Fresh Breeze Project" is to develop a multi-core chip architecture that supports a better programming model for parallel computing. This architecture combines simultaneous multithreading, a global shared address space, no memory update, and a cycle-free heap to provide a platform for robust, general-purpose, parallel computation. These design choices help simplify classically hard problems such as memory coherency, control flow, and synchronization. An HDL implementation of the core execution unit of a single processing core (many cores are on a single chip) forms the basis of further simulation and synthesis. The design must first be broken down into functional logic blocks and translated into hardware modules. The language Bluespec Verilog allows this description to be constructed in terms of higher-level "guarded atomic actions" triggered by a rule based system.; by Albert Chiou.; Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.; Includes bibliographical references (p. 32).

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## Games, puzzles, and computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 153 leaves

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There is a fundamental connection between the notions of game and of computation. At its most basic level, this is implied by any game complexity result, but the connection is deeper than this. One example is the concept of alternating nondeterminism, which is intimately connected with two-player games. In the first half of this thesis, I develop the idea of game as computation to a greater degree than has been done previously. I present a general family of games, called Constraint Logic, which is both mathematically simple and ideally suited for reductions to many actual board games. A deterministic version of Constraint Logic corresponds to a novel kind of logic circuit which is monotone and reversible. At the other end of the spectrum, I show that a multiplayer version of Constraint Logic is undecidable. That there are undecidable games using finite physical resources is philosophically important, and raises issues related to the Church-Turing thesis. In the second half of this thesis, I apply the Constraint Logic formalism to many actual games and puzzles, providing new hardness proofs. These applications include sliding-block puzzles, sliding-coin puzzles, plank puzzles, hinged polygon dissections, Amazons, Kohane, Cross Purposes...

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## New tools to enable children to manipulate images through computer programming

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 55, [6] p.

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This thesis proposes a programmable toolkit for building image filters to make the concepts of basic image processing accessible and engaging to children. The toolkit was developed in the context of Scratch, a media-centric programming environment intended for children. For this thesis, I redesigned the image manipulation framework in Scratch to 'open the black box' of image processing. Through user testing done with children, it was shown that the new framework sufficiently exposed the image-processing concepts so that children were able to create their own compelling image-processing algorithms. Although this framework was not ideal for the Scratch programming environment, the concepts explored in this work can be used in classrooms that teach introductory computer programming through media computation, or in a separate programming environment for novices which focuses on basic image processing.; by Evelyn Eastmond.; Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.; Includes bibliographical references (p. 55).

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## Performance limits on chemical computation

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 174 p.; 6237476 bytes; 6237283 bytes; application/pdf; application/pdf

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A class of novel computers uses solute concentrations of distinct chemical species as logic signals and diffusion for signal transport. I establish a bound on the speed, density, and error rate of such computers from first principles. I let the chemical computer engineer choose a "design tuple" of independent parameters: number of chemical species, total solute concentration, signal molecule size, and a parameter called the "cell size". I establish a functional relation between the design tuple, and the "performance tuple": (operating frequency, signal density, error rate). I give a lower bound on the probability of a logic error in one computation step, and an upper bound on the frequency of operation, both as functions of the design tuple. I evaluate these bounds for ssDNA oligomers, and conclude that DNA computation has unacceptable error rates if the hybridization regions are less than eight nucleotides in length. I then argue that, given a suitable scalar-valued performance metric as a function over performance tuples, there is a globally optimal design tuple maximizing performance. I present two conjectures seeking to explain (a) why neurons use small molecules to transport information, and (b) why cells have the size they do. In part two I develop such a performance metric based on Toffoli's computation capacity and computation density...

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## Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science

Fonte: University of Cambridge; Faculty of Computer Science and Technology; Computer Laboratory
Publicador: University of Cambridge; Faculty of Computer Science and Technology; Computer Laboratory

Tipo: Thesis; doctoral; PhD

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#Research Subject Categories::TECHNOLOGY::Information technology::Computer science::Computer science#Research Subject Categories::NATURAL SCIENCES::Biology::Cell and molecular biology::Cell biology

To paraphrase Stan Ulam, a Polish mathematician who became a leading figure in the Manhattan Project, in this dissertation I focus not only on how computer science can help biologists, but also on how biology can inspire computer scientists. On one hand, computer science provides powerful abstraction tools for metabolic networks. Cell metabolism is the set of chemical reactions taking place in a cell, with the aim of maintaining the living state of the cell. Due to the intrinsic complexity of metabolic networks, predicting the phenotypic traits resulting from a given genotype and metabolic structure is a challenging task. To this end, mathematical models of metabolic networks, called genome-scale metabolic models, contain all known metabolic reactions in an organism and can be analyzed with computational methods. In this dissertation, I propose a set of methods to investigate models of metabolic networks. These include multi-objective optimization, sensitivity, robustness and identifiability analysis, and are applied to a set of genome-scale models. Then, I augment the framework to predict metabolic adaptation to a changing environment. The adaptation of a microorganism to new environmental conditions involves shifts in its biochemical network and in the gene expression level. However...

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