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Bayesian Inference Frameworks for Fluorescence Microscopy Data Analysis

Description
In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different…

In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different illumination intensities or different local environments); and (3) inferring the camera gain. My general theoretical framework utilizes the Bayesian nonparametric Gaussian and beta-Bernoulli processes with a Markov chain Monte Carlo sampling scheme, which I further specify and implement for Total Internal Reflection Fluorescence (TIRF) microscopy data, benchmarking the method on synthetic data. These three frameworks are self-contained, and can be used concurrently so that the fluorescence profile and emitter locations are both considered unknown and, under some conditions, learned simultaneously. The framework I present is flexible and may be adapted to accommodate the inference of other parameters, such as emission photophysical kinetics and the trajectories of moving molecules. My TIRF-specific implementation may find use in the study of structures on cell membranes, or in studying local sample properties that affect fluorescent molecule photon emission rates.
ContributorsWallgren, Ross (Author) / Presse, Steve (Thesis advisor) / Armbruster, Hans (Thesis advisor) / McCulloch, Robert (Committee member) / Arizona State University (Publisher)
Created2019
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An improved mathematical formulation for the carbon capture and storage (CCS) problem

Description
Carbon Capture and Storage (CCS) is a climate stabilization strategy that prevents CO2 emissions from entering the atmosphere. Despite its benefits, impactful CCS projects require large investments in infrastructure, which could deter governments from implementing this strategy. In this sense, the development of innovative tools to support large-scale cost-efficient CCS…

Carbon Capture and Storage (CCS) is a climate stabilization strategy that prevents CO2 emissions from entering the atmosphere. Despite its benefits, impactful CCS projects require large investments in infrastructure, which could deter governments from implementing this strategy. In this sense, the development of innovative tools to support large-scale cost-efficient CCS deployment decisions is critical for climate change mitigation. This thesis proposes an improved mathematical formulation for the scalable infrastructure model for CCS (SimCCS), whose main objective is to design a minimum-cost pipe network to capture, transport, and store a target amount of CO2. Model decisions include source, reservoir, and pipe selection, as well as CO2 amounts to capture, store, and transport. By studying the SimCCS optimal solution and the subjacent network topology, new valid inequalities (VI) are proposed to strengthen the existing mathematical formulation. These constraints seek to improve the quality of the linear relaxation solutions in the branch and bound algorithm used to solve SimCCS. Each VI is explained with its intuitive description, mathematical structure and examples of resulting improvements. Further, all VIs are validated by assessing the impact of their elimination from the new formulation. The validated new formulation solves the 72-nodes Alberta problem up to 7 times faster than the original model. The upgraded model reduces the computation time required to solve SimCCS in 72% of randomly generated test instances, solving SimCCS up to 200 times faster. These formulations can be tested and then applied to enhance variants of the SimCCS and general fixed-charge network flow problems. Finally, an experience from testing a Benders decomposition approach for SimCCS is discussed and future scope of probable efficient solution-methods is outlined.
ContributorsLobo, Loy Joseph (Author) / Sefair, Jorge A (Thesis advisor) / Escobedo, Adolfo (Committee member) / Kuby, Michael (Committee member) / Middleton, Richard (Committee member) / Arizona State University (Publisher)
Created2017