Central to this investigation are a pair of models for the phosphorelay, one of which is an Ordinary Differential Equations based model, and the other of which is a Chemical Master Equation based model. The ODE based model is used to rigorously demonstrate that a phosphorelay is monotone, and thus converges to some steady state. In turn, the steady state output is elucidated in terms of the parameters that determine the net influx and net efflux at each stage as well as the growth rate. This steady state output function provides an elaboration on a prior hypothesis which suggests that a long phosphorelay provides additional phosphoregulation targets. Specifically, we find that the output of a phosphorelay is proportional to the net influx rate divided by the sum of various products of efflux signals. In the large efflux signal limit, effluxes are effectively multiplied to generate the final output. In this way, the activity of phosphatases which act on multiple stages in the relay are multiplied, allowing the phosphorelay to act as an analog computation device for this specific function. Growth is shown to have an unexpectedly powerful effect on relay output. In the most extreme cases, the phosphorelay output is shown to obey a power law with respect to growth, with an exponent which can be as large as the length of the relay, and which is also mediated by other key architectural variations. Thus, the phosphorelay can be utilized as a device which allows an organism to select behavior by comparing its growth rate to a threshold, where the level and sharpness of this threshold can be controlled by architectural and parametric changes. These results also provide design laws for building phosphorelays which are robust to growth rate variation.

关键词：生物模块；模拟计算；射流；信息网络

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Sparse matrix-vector multiplication (SpMV) is an important kernel in scientific and engineering computing. Straightforward parallel implementations of SpMV often perform poorly, and with the increasing variety of architectural features in multicore processors, it is getting more difficult to determine the sparse matrix data structure and corresponding SpMV implementation that optimize performance. In this paper we present pOSKI, an autotuning system for SpMV that automatically searches over a large set of possible data structures and implementations to optimize SpMV performance on multicore platforms. pOSKI explores a design space that depends on both the nonzero pattern of the sparse matrix, typically not known until run-time, and the architecture, which is explored off-line as much as possible, in order to reduce tuning time. We demonstrate significant performance improvements compared to previous serial and parallel implementations, and compare performance to upper bounds based on architectural models.

关键词：工程计算；稀疏矩阵；向量乘法；多核处理器；数据结构

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This dissertation explores the application of computer science methodologies, techniques, and technologies to citizen science. Citizen science can be broadly de ned as scienti c research performed in part or in whole by volunteers who are not professional scientists. Such projects are increasingly making use of mobile and Internet technologies and social networking systems to collect or categorize data, and to coordinate efforts with other participants. The dissertation focuses on observations and experiences from the design, deployment, and testing of a citizen science project, CreekWatch. CreekWatch is a collaboration between an HCI research group and a government agency.

关键词：众包；互联网技术；社交网络

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We show that by storing only a fractional of the entire catalog everywhere, the system is able to fully support user demand at large scale. Second, we develop a Markov approximation technique to solve the problem of topology selection under node degree bound using a simple distributed algorithm. We prove that our algorithm achieves close-to-optimal solution, which we verify using extensive realworld trace simulations. On the system side, we show extensive results to test the algorithm's scalability and robustness to changes in user dynamics and demand patterns. We show that our solution achieves high utilization of cache nodes storage and bandwidth resources, and automatically learns and caches the video according to the demand patterns. We observe that there exists a complex interplay between disk space, network bandwidth and node degree bound. We also present guidelines to important practical design choices including caching update intervals, demand prediction and provisioning. We also demonstrate the feasibility and efficiency of our design choice by building and experimenting a prototype system at Berkeley.

关键词：拓扑选择；算法；用户动态需求；视频点播系统

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The construction of various of Klein bottles that belong to different regular homotopy classes, and which thus cannot be smoothly transformed into one another, is formally introduced. For all cases it is shown how these shapes can be partitioned into two Mobius bands and how the twistedness of these bands defines the homotopy type.

关键词：定期同伦类；不定向表面

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The increasing size of our datasets|and perhaps more importantly, the increasing complexity of the underlying distributions that we hope to understand|are exposing issues that seem to demand computational consideration. In this dissertation, we apply the computational perspective to three basic statistical questions which underlie and abstract several of the challenges encountered in the analysis of today's large datasets.

关键词：概率；统计数据；算法；大型数据集

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This is particularly true in urban environments where tall buildings block satellite view for GPS, and distortions in Earth’s magnetic field from power lines adversely affect compass readings.In this thesis, we describe an image based  localization  algorithm  for  estimating  the  pose  of  cell  phones  in  urban  environments.  This  is motivated by the fact that most of today’s cell phones are equipped with cameras whose imagery can be matched against an  image database for  localization purposes.

关键词：移动设备；手机；定位算法；GPS

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The National Research Council has highlighted the importance of the changeover to multicore architectures on software performance. They predict strong economic impacts for users in industry as a result of the change. This thesis is part of a larger research project that aims to quantify those effects. The main contribution of this thesis is to build a measure of how well firms can take advantage of multicore chips, which is a key ingredient in addressing this important problem. This measure is built up using unique data on firm software usage from the marketing firm Harte Hanks, and combining it with results from the Berkeley Software Parallelism Survey – a survey of parallelism experts run for this thesis. Alternative formulations for creating this parallelism measure are also discussed and evaluated, with the reasons for choosing the main formulation clearly expressed. Finally, this thesis highlights the limitations of this measure and discusses the other on-going initiatives that are underway to address them. This thesis also makes a supplemental contribution by highlighting a new case study detailing the impact of the changeover to multicore. It also reports additional results from the Berkeley Software Parallelism Survey that may be of interest to those assessing the presence of different types of parallelism or different computational motifs in mainstream software programs.

关键词：软件性能；转换多核；芯片；市场营销；并行度

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In my work I have theoretically explored the biophysical mechanisms and energy landscapes that give rise to the ratcheting phenomena and devised devices that operate off these principles. I demonstrate two generations of devices that produce mechanical force/deformation in response to a user specified ligand. The first generation devices, fabricatied using a combination nanoscale lithographic processes and bioconjugation techniques, were used to provide evidence that the proposed ratcheting phenomena can be exploited in synthetic architectures. Second generation devices fabricated using self-assembled DNA/hapten motifs were constructed to gain a precise understanding of ratcheting dynamics and design constraints. In addition, the self-assembled devices enabled fabrication en masse, which I feel will alleviate future experimental hurdles in analysis and facilitate its adaptation to technologies. The product of these efforts is an architecture that has the potential to enable numerous technologies in biosensing and drug delivery. For example, the coupling of molecule-specific actuation to the release of drugs or signaling molecules from nanocapsules or porous materials could be transformative. Such architectures could provide possible avenues to pressing issues in biology and medicine: drugs could eventually be triggered to release in the presence of molecular signals indicative of diseased states, early disease detection could be achieved by examining the cell microenvironment then releasing imaging agents and generalized control could exerted over the free molecule signaling networks of cells.

关键词：生物物理机制；棘轮现象；自动化微型机械；化学纳米机械

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Light trapping in solar cells allows for increased efficiency and reduced materials cost. It is well known that a 4n^2 factor of enhancement in absorption can be achieved by randomly texturing the surface of the solar cell, where n is the refractive index of the material. However, this limit only holds when the thickness of the solar cell is much greater than the wavelength of light. In the subwavelength regime, the fundamental question remains unanswered: what surface texture realizes the optimal absorption enhancement? We turn to computational inverse electromagnetic design in order to find nanoscale textures for light trapping, and observe spontaneous symmetry breaking in the creation of optimal design.

关键词：电磁逆设计；逆电磁；太阳能电池；纹理

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