In this thesis we present two novel algorithms that make use of DNA sequencing data in a principled yet practical way. The fi rst method estimates the history of eff ective population sizes of a species using a coalescent hidden Markov model (HMM). Previous coalescent HMMs could only handle a few sequences, since the set of coalescent trees makes the statespace prohibitively large. Our algorithm uses a modifi ed state-space to make inference computationally feasible while still retaining the essential genealogical features of a sample. We apply this algorithm, called diCal, to human data to learn more about major events in human history, such as the out-of-Africa migration. We also provide several extensions to diCal that make the computation faster, more automated, and applicable in a wider variety of scenarios.

关键词：DNA测序；人口基因组；可伸缩算法

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With the use of Big Data gathered from over 50 buildings on the campus of University of California, Berkeley, and the SAP data analytics tool - HANA, our team has designed two solutions that seek to optimize energy and water usage. This document presents the problem we set out to solve, the results of an industry analysis carried out to determine the marketability of our solutions, our intellectual property strategy, our individual contributions to the technical aspects of the project, and our individual concluding reflections.

关键词：大数据；数据分析；知识产权战略

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In this dissertation, we present several techniques used to automatically generate virtual models of indoor building environments. The interior environment of a building is scanned by a custom hardware system, which provides raw laser and camera sensor readings used to develop these models. Our modeling techniques can be separated into three categories: 2D  floor plan models, simpli ed 2.5D extruded models, and fully complex and detailed 3D models. All models are produced automatically from the output data of a backpack-mounted ambulatory scanning system, which can scan multiple  floors of a building efficiently. We can capture the entirety of a large building in only a few hours, including staircases and other hard to reach locations, which improves upon the state-of-the-art static scanning by several orders of magnitude. Our algorithms are capable of producing many kinds of 3D virtual building models while traversing through a GPS-denied environment, including point clouds, 2D  floor plans, and 3D building models.

关键词：室内建筑环境；虚拟模型；传感器

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Embedded software is typically developed using traditional programming languages like C and C++. However, these traditional types of programming languages are not well suited for embedded systems development. The model-based embedded software project extends the code-generating capabilities of Ptolemy II to help users develop software using model-based design techniques for ARM mbed devices. In particular, this project primarily focuses on automatically generating C/C++ code in Ptolemy II for Synchronous Data Flow (SDF) and Finite State Machine (FSM) models. This makes it easier to design and debug, leading to faster and more robust software development.

关键词：嵌入式软件；FSM；C ++；数据流

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The field of lab-on-a-chip offers exciting new capabilities for chemical and biological assays, including increased automation, higher throughput, heightened sensitivity of detection, and reduced sample and reagent usage. This area of study has seen remarkable progress in the last decade, with applications ranging from drug development to point-of-care diagnostics. The research presented herein focuses on the development of semiconductor-based optoelectrowetting (OEW) and optoelectronic tweezers (OET) platforms, which can respectively perform operations on droplets and cells/particles. This thesis discusses progress achieved on both OEW and OET platforms. For OEW, a novel optimization model has been developed to accurately predict the interaction of droplets, semiconductor layers, and a programmable DLPbased optical source.

关键词：生物测定；细胞/粒子；光流体设备；细胞操纵

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The exploration and understanding of electronic material properties and how they can be implemented into a usable form for electronics is the driving force behind developing new types of devices and electronic systems. Within these new types of electronic systems, transparent and flexible electronics represent two emerging fields that have gathered much attention.

关键词：电子材料；子系统；氧化物薄膜；晶体管

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The goal of our capstone is to develop a new interactive device by following the product development cycle from user research through to a final, user-tested prototype. After a brainstorming process and consulting with potential users, we uncovered the common problem of forgetting items such as keys or wallets. These are items that are generally needed every day, but are easy to accidentally leave behind. There is also usually a cost associated with forgetting these items, such as being late to work or paying for a locksmith. We determined that an Internet of Things, connected device solution was appropriate for solving this common problem.

关键词：用户测试；互动装置；Kinoma

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In this dissertation, we address the burgeoning fields of diffractive optics, metals-optics and plasmonics, and computational inverse problems in the engineering design of electromagnetic structures. We focus on the application of the optical nano-focusing system that will enable Heat-Assisted Magnetic Recording (HAMR), a higher density magnetic recording technology that will fulfill the exploding worldwide demand of digital data storage. The heart of HAMR is a system that focuses light to a nano- sub-diffraction-limit spot with an extremely high power density via an optical antenna. We approach this engineering problem by first discussing the fundamental limits of nano-focusing and the material limits for metal-optics and plasmonics. Then, we use efficient gradient-based optimization algorithms to computationally design shapes of 3D nanostructures that outperform human designs on the basis of mass-market product requirements.

关键词：衍射光学元件；金属光学；等离子体；电磁设计

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Low power wireless medical devices are currently in the spotlight due to the development of remote medical diagnosis systems and longterm treatment assistances. In general, biosignals detected by sensors are extremely weak for further processing. The quality of a lownoise amplifier (LNA) determines the accuracy of the original signals later on. Our main goal is to design an LNA that is suitable for biosignal acquisition systems. We primarily focus on the implantable medical system recording an electrical signal of a person’s heart. The LNA provides enough voltage gain to amplify the signals while reducing the noise contamination significantly. In addition, its power consumption is minimized to enhance the lifespan of the whole system.

关键词：无线医疗；LNA；生物信号；降低噪音

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Described in the following report are a series of design decisions and experiments towards demonstrating a prototype bilayer InAs Tunneling Field E ect Transistor (TFET), a new type of transistor which could exhibit a steeper sub-threshold slope and could enable lower- power electronics. In the process of designing and fabricating this device, n-channel InAs on insulator MOSFETs were fabricated and characterized to better inform the TFET design and fabrication. While in this work, a TFET with the desired characteristics was never realized, others were able to demonstrate similar tunneling devices with poor subthreshold slopes. A simple model is presented which explains the sensitivity of the performance of the TFET to interface traps.

关键词：晶体管；绝缘体；InAs；TFET

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