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2015

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Modeling Platelets On Parallel Computers, Seetha Malavika Pothapragada Dec 2015

Modeling Platelets On Parallel Computers, Seetha Malavika Pothapragada

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Mechanical Heart Valves (MHV) provides life-saving solutions to patients suffering from cardiovascular diseases. But these devices are often plagued by non-physiological flow patterns resulting in increased shear stress conditions. This leads to platelet damage, a precursor of thromboembolism, thus impeding the device usability and demanding lifelong anticoagulation treatments. While the flow and stresses are in the micron level, the platelet behavior is at the nm level, thus presenting a major computational challenge for simulating this multiscale multi-physics modeling problem. This dissertation focuses on using parallel computers to develop a computational framework based on n-particle simulations, defined by Coarse Grained Molecular …

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Breath Biomarkers Detection By Chemical Sensors, Yan Li Dec 2015

Breath Biomarkers Detection By Chemical Sensors, Yan Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Our breath is a very complex mixture of chemical compositions. Usually, the majority of our exhaled breath consists of nitrogen, oxygen, carbon dioxides, water and inert gases. The remaining small fraction of breath contains thousands of components in trace amount, including inorganic gas molecules like nitric monoxide and diverse kinds of volatile organic compounds (VOCs). The concentrations of our exhaled gases are at a relatively stable level, though minor fluctuations may occur at different time of the day and they are also linked to the body status. Sometimes, if a specific breath gas of some appears to have an abnormal …

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Regularized Geometry Of The Loop Space, Cheng Hao Dec 2015

Regularized Geometry Of The Loop Space, Cheng Hao

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Interest in nonlinear sigma models with target space a symmetric space of positive curvature comes from both mathematics and physics. In this dissertation we focus on the two-dimensional nonlinear sigma model with target space the k-dimensional projective space P^k. We study the properties of a finite-dimensional approximation, which we denote by L_N(P^k), to the loop space L(P^k), and construct resolutions of singularities for these truncated loop spaces. We also look into the geometries of such spaces and propose a conjecture about the mass gap of the Schrodinger operator H on L_N(P^k) with analytic formula. | 55 pages

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$E_\Infty$-Comodules And Topological Manifolds, Anibal Medina Dec 2015

$E_\Infty$-Comodules And Topological Manifolds, Anibal Medina

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The first story begins with a question of Steenrod. He asked if the product in the cohomology of a triangulated space, which is associative and graded commutative, can be induced from a cochain level product satisfying the same two properties. He answered it in the negative after identifying homological obstructions among a collection of chain maps he constructed. Using later language, his construction could be said to endow the simplicial chains with an $E_\infty$-coalgebra structure. The second story also begins with a question: when is a space homotopy equivalent to a topological manifold? For dimensions greater than 4, an answer …

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Tritangents To Spherical Curves, Yury Arkady Sobolev Dec 2015

Tritangents To Spherical Curves, Yury Arkady Sobolev

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

A generic smooth immersed closed curve in the 2-sphere has a finite number of circles tangent to it in three points. We present a classification of these tritangent circles and study how each class changes during deformations of the curve. We relate these classes to finite type invariants of the curve and derive a relation among the numbers of tritangent circles in the classes and finite type invariants of the curve. | 39 pages

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Conical Kahler-Einstein Metrics And Its Applications, Chengjian Yao Dec 2015

Conical Kahler-Einstein Metrics And Its Applications, Chengjian Yao

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this dissertation we prove certain deformation behaviors of Kahler-Einstein metrics with singularities. Based on smooth approximation and a priori estimates, we first give a new proof to Donaldson's Openness Theorem of deforming the cone angle of conical Kahler-Einstein metric on smooth Fano manifold, and prove a direct generalization to conical Kahler-Einstein metrics along simple normal crossing pluri-anti-canonical divisors on smooth Fano manifold. Then we use continuity method to study the deformation of weak conical Kahler-Einstein metric on Q-Fano variety. The idea of our new proof above is generalized to prove the openness part of the continuity method argument, while …

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Multi-Model Validation Assessment Of Groundwater Flow Simulation Models Using Area Metric Approach, Omkar Aphale Dec 2015

Multi-Model Validation Assessment Of Groundwater Flow Simulation Models Using Area Metric Approach, Omkar Aphale

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

A model's validity, or its goodness-of-fit to the real world system, is commonly assessed by quantifying the level of agreement between the observed data and their corresponding model-simulated outputs. However, the observed data could be uncertain given inaccuracies in the observational tools and techniques while the model-simulated outputs may be incomparable since models are simplified versions, and not exact replicas, of the real world system. This limits the abilities of the traditional validation approaches. Here, an alternative approach called the area metric (Ferson et al. 2008) was adopted for multi-model validation assessment. This approach quantifies the level of agreement between …

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Essays On The Macroeconomic Consequences Of Market Frictions, Xin Tang Dec 2015

Essays On The Macroeconomic Consequences Of Market Frictions, Xin Tang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This thesis studies the implications of firms' and households' decisions on macro and environmental aggregates in economies with market frictions using quantitative macroeconomic methods. The thesis consists three chapters. In each chapter, I study respectively the effects of product market frictions on firms' emission decisions, the effects of financial frictions on firms' hiring decisions, and those on households' consumption-saving choices. In Chapter 2, I study the effects of product market frictions on firm size distribution and its subsequent impact on aggregate output and industrial pollution in China. Using a unique micro-level manufacturing census, I find that larger firms generate and …

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Harnessing Multicore Parallelism For High Performance Data Replication, Tan Li Dec 2015

Harnessing Multicore Parallelism For High Performance Data Replication, Tan Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

High speed data replication is vital to the data intensive scientific computing that often requires transferring large volumes of observation and simulation data efficiently among geographically dispersed facilities. Enterprise cloud services also depend on effective data replication to scale out of their own data centers, and to optimize work completed per dollar invested. In addition, end consumers are also extremely sensitive to the latency and responsiveness to share data within the network of friends, web-based services and their personal mobile devices. Recent hardware advances offer the opportunity to enable ultra high-speed data replication by aggressively adding more CPU cores, higher …

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Improvements In Lesion Detection In X-Ray Breast Tomosynthesis And In Emission Tomography, Yihuan Lu Dec 2015

Improvements In Lesion Detection In X-Ray Breast Tomosynthesis And In Emission Tomography, Yihuan Lu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Cancerous lesions can be viewed using several medical imaging modalities. I address breast cancer as seen in contrast-enhanced dual-energy digital breast tomosynthesis (CE-DE-DBT) and liver imaging of liver neuroendocrine metastases as seen by SPECT (Single Photon Emission Computed Tomography). The overall goal is to enhance the ability to detect such lesions by improvements in image acquisition and data processing methods. In CE-DE-DBT the presence of scattered photons can yield image artifacts that mask the breast lesion. I present a scatter correction method based on interpolating scatter tails at the image periphery. I validate the method using a pinhole array technique …

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Problems And Solutions For Backscatter-Based Tag-To-Tag Communication In The Internet Of Things, Zhe Shen Dec 2015

Problems And Solutions For Backscatter-Based Tag-To-Tag Communication In The Internet Of Things, Zhe Shen

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The Internet of Things (IoT) has been developing for decades and has been considered as the future of the Internet. The basic idea of the IoT is to enable a wide range of objects (things) around us to interact and cooperate with each other so that certain goals are reached. An important technology that will be part of the IoT is Radio Frequency IDentification (RFID). RFID is based on the concept of backscatter-based communication and the use of inexpensive RFID tags. A very exciting direction of work in the last few years has been the research on backscatter-based tag-to-tag (BBTT) …

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Convergent Lagrangian Particle Algorithms For Compressible Fluid Dynamics, Hsin-Chiang Chen Dec 2015

Convergent Lagrangian Particle Algorithms For Compressible Fluid Dynamics, Hsin-Chiang Chen

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The goal of this thesis is the study of Lagrangian particle methods for complex multiscale hydrodynamic problems. This research has been motivated by difficulties arising in traditional mesh-based methods for the simulation of certain classes of highly non-uniform, complex free surface or multiphase problems. For such problems, Eulerian meshes enhanced with special algorithms for resolving interfaces such as volume-of-fluid, the level set method, arbitrary Lagrangian Eulerian methods, or the method of front tracking which is a hybrid method involving a moving Lagrangian mesh over a fixed Eulerian mesh, are often used. In addition, they require adaptive mesh refinement (AMR). All …

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Statistical Methods For Optimizing Task Performance In Nuclear Medicine Imaging And In X-Ray Breast Imaging, Lin Chen Dec 2015

Statistical Methods For Optimizing Task Performance In Nuclear Medicine Imaging And In X-Ray Breast Imaging, Lin Chen

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In many medical imaging systems used in radiology, the hardware delivers raw data to a sensor and a computer is used to convert the sensor data to a viewable image by implementing tomographic reconstruction algorithms. The radiologist views the image and performs a task, such as detecting a lesion. Engineers and applied mathematicians seek to improve medical imaging systems by making hardware changes and changes in the reconstruction algorithm. Improvement in this thesis is measured by scalar figures of merit, FOM, for task performance. We consider two modalities: SPECT (Single Photon Emission Computed Tomography) and Contrast-Enhanced DBT (Digital Breast Tomosynthesis). …

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Motivating Students With Learning Disabilities To Achieve Through The Use Of Authentic Projects And Technology, Meagan King Dec 2015

Motivating Students With Learning Disabilities To Achieve Through The Use Of Authentic Projects And Technology, Meagan King

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The purpose of this thesis is to evaluate effective methods that help students with learning disabilities achieve better quality writing. The types of methods that were reviewed were authentic writing projects, process writing, and peer work through the analysis of scholarly and personal research. Using technology to enhance understanding was also evaluated in relation to these methods. The study concluded that these effective methods increase student motivation because of their applicability to the real world. The study also concluded that as a result of the motivation produced by authentic writing projects, students develop more confidence in themselves as writers and …

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An Empirical Study On Concentration-Qtc Model, Tian Feng Dec 2015

An Empirical Study On Concentration-Qtc Model, Tian Feng

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

QT interval is a measure of the time from the beginning of the Q wave to the end of the T wave in the heart's electrical cycle, it is often corrected to lessen its dependence to heart rate, and the corrected value is known as the QTc interval. Prolongation of the QTc interval is a primary biomarker for assessing proarrhythmic risk of drugs, thus it is routinely evaluated in new drug development. Concentration-QTc model with data from early phase single ascending dose (SAD) study is widely used to evaluate the drug-induced QTc prolongation, and the mixed effects model (MEM) is …

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Turbulent Combustion Study Of Scramjet Problem, Xiaoxue Gong Dec 2015

Turbulent Combustion Study Of Scramjet Problem, Xiaoxue Gong

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this thesis we study the turbulent mixing and turbulent combustion in a model scramjet combustor with a Large Eddy Simulation (LES) strategy. LES resolves the large and energetic motions while the small subscale motions are modeled. Here the filtered Navier-Stokes equations are solved by a fifth- order finite difference Weighted-Essentially Non-Oscillatory (WENO) scheme dimension by dimension. Subgrid terms are closed by the dynamic Smagorin- sky model. Chemical source terms are calculated directly using a finite rate chemistry model with a reduced chemistry mechanism. The equilibrium tur- bulent boundary layer model of J. Larsson is used to calculate the shear …

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Statistical Methods For Association Analysis Of Biological Data, Erya Huang Dec 2015

Statistical Methods For Association Analysis Of Biological Data, Erya Huang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Genome-wide association studies (GWA studies) are an important tool for identifying disease susceptibility variants for common and complex diseases. Traditional approaches to data analysis in GWA studies suffer with the multiple testing problem and also ignore any potential relationships between gene variants. We introduced here a novel two-stage framework with the combination of partial correlation network analysis (PCNA) and data mining techniques. This network-based technique, focusing on SNPs in joint modeling and their partial associations, alleviated the multiple testing problem and consequently increased the power to detect biologically relevant variants and their associations. Variable selection was achieved through penalized logistic …

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Analysis Of Three Geometric Optimization Problems: Local Greedy Routing In Triangulations, Touring Sequences Of Polygons, And Hitting Sets Of Segments, Kan Huang Dec 2015

Analysis Of Three Geometric Optimization Problems: Local Greedy Routing In Triangulations, Touring Sequences Of Polygons, And Hitting Sets Of Segments, Kan Huang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Finding short paths to visit places and finding small sets to hit objects are two core problems in Computational Geometry. We consider these problems in various geometric settings. The first one is greedy routing in a triangulation, which has applications in sensor networks and robotic swarm exploration. The second problem we consider is finding the shortest path to tour a sequence of polygons (TPP). We prove the problem is NP-hard if the polygons are non-convex even they are disjoint. We also obtain results on TPP with time constraints, which means the visitor is required to stay in a polygon for …

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A Novel Methodology For Stochastic Formulation Of Short Term Cloud Cover Forecasts, Ya-Ting Huang Dec 2015

A Novel Methodology For Stochastic Formulation Of Short Term Cloud Cover Forecasts, Ya-Ting Huang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Following the chaos theory proposed by Lorenz, probabilistic approaches have been widely used in numerical weather prediction research. This paper introduces an innate methodology to measure the uncertainty of stochastic cloud boundary forecast. A stochastic partial differential equation is inserted into a numerical weather prediction model, and backtested to validate the probabilistic results of the model. This methodology can be applied to a variety of topics in numerical weather prediction research. The proposed method is applied to the short term forecast of cloud cover. A two parameter model based on physical principles of wind velocity dispersion and surface evaporation rate …

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Structure-Based Drug Design Targeting Hivgp41, Lingling Jiang Dec 2015

Structure-Based Drug Design Targeting Hivgp41, Lingling Jiang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This dissertation presents method development and application of computational procedures for structure-based drug design, with a particular focus on the clinical relevant drug target HIVgp41. Chapter 1 introduces the main computational techniques used in this study, including atomic-level molecular dynamics simulations, free energy calculations, and molecular docking. The importance of targeting HIVgp41, a viral envelope protein involved in viral entry and membrane fusion, is also discussed. In particular, the only FDA approved gp41 inhibitor, a peptide called T20, suffers from side effects, expense, and is subject to drug resistance. Thus, improved understanding of the binding mechanisms of T20 is of …

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Regime Switching And Long Memory In High Frequency Financial Data, Xiao Zhang Dec 2015

Regime Switching And Long Memory In High Frequency Financial Data, Xiao Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This thesis is to incorporate Markov Regime Switching model with Fractionally Integrated process in order to capture abrupt change and regime persistence simultaneously in long memory dynamic volatility process. We adapt truncated ARCH\(\infty\) to estimation scheme of our model. We carry out standard back testing procedure to validate Regime Switching FIGARCH VaR based forecasts, on S\&P 500 and SHSZ 300 data in 1 minute and 5 minute frequencies. In the Chapter 1, Regime Switching model , and parameter estimation steps based on truncated ARCH infinite and Hamilton filter will be given. Topics like stationary conditions of RS-FIGARCH and standard Normal …

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Asset Pricing In Intraday Trading, Yuzhong Zhang Dec 2015

Asset Pricing In Intraday Trading, Yuzhong Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The dissertation consists of three parts. In first part, a general equilibrium for asset pricing is proposed which incorporates asymmetric information as the key element determining security prices. The concepts of completeness, arbitrage, state price deflator and equivalent martingale measure are extended. It is shown in the model that in a so-called quasi-complete market, agents with differential information can reach an agreement on a universal equilibrium price. And as a consequence, information asymmetry can lead to mispricing as well. Second part investigates the market intrinsic time, such as volume clock and transaction clock. The normality of asset returns are shown …

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Multiple Change-Points Estimation In Garch Models, Sichen Zhou Dec 2015

Multiple Change-Points Estimation In Garch Models, Sichen Zhou

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The generalized conditional heteroscedastic (GARCH) models are often used to estimate volatility in financial markets as they mimic the patterns in real world with volatility clustering as well as high excess kurtosis. However, in applications to asset return series, they usually possess undesired persistence in volatility, which can be explained by structure changes in parameters associated with significant economic events such as financial crises. From this motivation, we provide an estimation procedure for multiple parameter changes in GARCH models. By introducing the specified forward and backward filtration and combining them with Bayes' theorem, our estimation procedure has attractive statistical and …

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An In Vivo Assessment Of The Effects Of Using Different Implant Abutment Occluding Materials On Implant Microleakage And The Peri-Implant Microbiome, Caroline Rubino Dec 2015

An In Vivo Assessment Of The Effects Of Using Different Implant Abutment Occluding Materials On Implant Microleakage And The Peri-Implant Microbiome, Caroline Rubino

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Microleakage may be a factor in the progression of peri-implant pathology. Microleakage in implant dentistry refers to the passage of bacteria, fluids, molecules or ions between the abutment-implant interface to and from the surrounding periodontal tissues. This creates a zone of inflammation and reservoir of bacteria at the implant-abutment interface. Bone loss typically occurs within the first year of abutment connection and then stabilizes. It has not yet been definitively proven that the occurrence of microleakage cannot contribute to future bone loss or impede the treatment of peri-implant disease. Therefore, strategies to reduce or eliminate microleakage are sought out. Recent …

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Advances In Theory Of Coherent Electron Cooling, Andrey Elizarov Dec 2015

Advances In Theory Of Coherent Electron Cooling, Andrey Elizarov

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The coherent electron cooling is a novel hadron beam cooling technique that is being developed at Brookhaven National Laboratory. It is a realization of the stochastic cooling, in which an electron beam is used in the modulator, amplifier and kicker. In the modulator, hadrons create electron density perturbations. Then these perturbations are amplified in the free electron laser, while hadrons pass through dispersion section, where they are placed such that, in the kicker, amplified perturbations' electric fields accelerate or decelerate hadrons, depending on their velocities, cooling the beam. In the present dissertation, we describe ways to model the modulator section …

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5d Supersymmetry And Contact Geometry, Yiwen Pan Dec 2015

5d Supersymmetry And Contact Geometry, Yiwen Pan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Supersymmetry has been fruitful source of new Physics and Mathematics advancement. In particular, supersymmetric theories on curved manifolds often leads to very interesting connections between integrable geometry and supersymmetric physical quantities. In this dissertation, we summarize the author’s recent work on 5d N = 1 supersymmetric theories on curved 5d Riemannian manifolds and its relation to contact geometry, which is the odd- dimensional counterpart of symplectic geometry in even dimension. We will discuss the geometric implications of the Killing spinor equations derived from the rigid limit of 5d N = 1 supergravity. Combining with the dilatino equations, we see that …

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Resurgence And The Large N Expansion, Ricardo Vaz Dec 2015

Resurgence And The Large N Expansion, Ricardo Vaz

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this dissertation we focus on recent developments in the study of resurgence and the large N expansion. It is a well known fact that perturbative expansions, such as the large N expansion, are divergent asymptotic series. This is a signal that there are non- perturbative effects of the form exp(-N) that also need to be considered, and our original perturbative series should be upgraded to one including powers of both 1/N and exp(-N), which is called a transseries. The machinery needed to tackle transseries was developed in the 1980s under the formalism of so-called resurgence. Using its tools we …

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Formal Verification Of Nonlinear Biological Systems, Md Ariful Islam Dec 2015

Formal Verification Of Nonlinear Biological Systems, Md Ariful Islam

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Abstraction and composition have proved to be particularly useful in extending the reach of formal verification. Abstraction reduces the size of the system under investigation by neglecting details irrelevant to the properties of interest. Compositionality allows us to decompose large-scale system into smaller components and verify each component individually and reason about the verification of entire system from verified components. Together, these two techniques permit us to substitute a component with its equivalent abstraction such that the overall system retains the property of interest. In this thesis, we first show that in the context of the Iyer et al. (IMW) …

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Optimal Mass Transport And Its Applications, Zhengyu Su Dec 2015

Optimal Mass Transport And Its Applications, Zhengyu Su

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Optimal Mass Transport theory has deep roots in pure mathematics, combining complex analysis, Riemannian geometry and measure theory. Monge first raised the classical Optimal Mass Transport Problem that concerns determining the optimal way, with minimal transportation cost, to move a pile of soil from one place to another. Kantorovich has proven the existence and uniqueness of the optimal transport plan based on linear program. Monge-Kantorovich optimization has been used in numerous fields from physics, econometrics to computer science including computer vision, medical imaging and statistics. However, it has one fundamental disadvantage that the complexity is $O(k^2)$, which is unacceptable to …

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Synthetic Gene Design: Optimization And Analysis, Rukhsana Yeasmin Dec 2015

Synthetic Gene Design: Optimization And Analysis, Rukhsana Yeasmin

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

With the advance of synthetic biology has come increased interest in designing synthetic genes which optimize protein expression. We propose new algorithms for gene design under several different constraints. Our optimization criteria include finding minimum energy and maximum energy RNA structures for a given gene sequence, optimizing the amount of tRNA auto-correlation in genes and designing maximum and minimum auto-correlated sequences. We also develop methods to analyze and interpret tiled microarray genome expression data. Statistical analysis of the viral genome expression data enables us to discover unknown facts about its life cycle, its impact on the host cell shutoff mechanism. …

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