VictorJuiz/thesis huggingface dataset:
Detailed Modeling of Soot Formation/Oxidation in Laminar Coflow Diffusion Flames

The first goal of this thesis is to develop and validate a modeling tool into which fundamental combustion chemistry and aerosol dynamics theory are implemented for investigating soot formation/oxidation in multi-dimensional laminar coflow diffusion flames taking into account soot polydispersity and fractal-like aggregate structure. The second goal is to use the tool to study soot aggregate formation/oxidation in experimentally studied laminar coflow diffusion flames to advance the understanding of soot aggregate formation/oxidation mechanism. The first part of the thesis deals with the large CPU time problem when detailed models are coupled together. Using the domain decomposition method, a high performance parallel flame code is successfully developed. An advanced sectional aerosol dynamics model which can model fractal-like aggregate structure is successfully implemented into the parallel flame code. The performance of the parallel code is demonstrated through its application to the modeling of soot formation/oxidation in a laminar coflow CH4/air diffusion flame. The parallel efficiency reaches as high as 83%. The second part of the thesis numerically explores soot aggregate formation in a laminar coflow C2H4/air diffusion flame using detailed PAH-based combustion chemistry and a PAH-based soot formation/oxidation model. Compared to the measured data, flame temperature, axial velocity, C2H2 and OH concentrations, soot volume fraction, the average diameter and the number density of primary particles are reasonably well predicted. However, it is very challenging to predict effectively the average degree of particle aggregation. To do so, particle-particle and fluid-particle interactions that may cause non-unitary soot coagulation efficiency need to be considered. The original coagulation model is enhanced in this thesis to accommodate soot coagulation efficiency. Different types of soot coagulation efficiency are numerically investigated. It is found that a simple adjustment of soot coagulation efficiency from 100% to 20% provides good predictions on soot aggregate structure as well as flame properties. In the third part of the thesis, the effects of oxidation-driven soot aggregate fragmentation on aggregate structure and soot oxidation rate are studied. Three fragmentation models with different fragmentation patterns are developed and implemented into the sectional aerosol dynamics model. The implementation of oxidation-driven aggregate fragmentation significantly improves the prediction of soot aggregate structure in the soot oxidation region.

Keywords: Soot Formation
Numerical Simulation
Aggregate Fragmentation
Parallel Computing
Laminar Coflow Diffusion Flame
Advisor: Thomson, Murray J.
Linker-based Lecithin Microemulsions as Transdermal Drug Delivery Systems

The interest in microemulsions as transdermal delivery systems have been motivated by their large surface area for mass transfer, their high solubilization capacity of hydrophobic actives, and their ability to improve skin penetration. Lecithins (mixtures of phospholipids similar to those find in the skin) have been proposed as ideal surfactants in microemulsions due to their skin compatibility. Unfortunately, their incorporation into microemulsions used to require toxic medium-chain alcohols or viscous polymeric co-surfactants. Recently, microemulsion-base “green solvents” were formulated with lecithin and linker molecules. The main objective of this dissertation was to test this concept of linker-based lecithin microemulsions in transdermal delivery. In the first part of this study, linker-based lecithin formulations were developed using soybean lecithin as main surfactant, sorbitol monooleate as lipophilic linker, and caprylic acid/sodium caprylate as hydrophilic linkers. These additives, at the suggested concentration, are safe for cosmetic and pharmaceutical applications. The low toxicity of these formulations was confirmed in cultured human skin tissues. The solubilization and permeation of a common anaesthetic, lidocaine, was evaluated. The concept of “skin” permeability was introduced to account for the differences in solvent-skin partition when comparing different delivery systems. The linker-based lecithin microemulsion produced a substantial absorption of lidocaine into the skin, when compared to a conventional pentanol-lecithin microemulsion. The second part of this study takes advantage of the lidocaine adsorbed in the skin with the linker-based lecithin microemulsion as reservoir for in situ skin patches. The in situ patches were able to release 90% of the lidocaine over 24 hours, which is comparable to the release profile obtained from conventional polymer or gel-based patches. In the third part of this work, the role of surfactant droplets on the transport of lidocaine was studied. A mass balance model that accounted for mass transfer and partition coefficients was introduced. The parameters generated from the model confirm that in most cases the transport through the skin limits the overall penetration of lidocaine. Besides the conventional diffusion mechanism, the results suggest that surfactant droplets, carrying lidocaine, also penetrate into the skin and contribute to the accumulation of the lidocaine in the skin.

Keywords: lecithin microemulsions
transdermal drug delivery
Advisor: Acosta, Edgar
Development of a Flat Panel Detector with Avalanche Gain for Interventional Radiology

A number of interventional procedures such as cardiac catheterization, angiography and the deployment of endovascular devices are routinely performed using x-ray fluoroscopy. To minimize the patient’s exposure to ionizing radiation, each fluoroscopic image is acquired using a very low x-ray exposure (~ 1 uR at the detector). At such an exposure, most semiconductor-based digital flat panel detectors (FPD) are not x-ray quantum noise limited (QNL) due to the presence of electronic noise which substantially degrades their imaging performance. The goal of this thesis was to investigate how a FPD based on amorphous selenium (a-Se) with internal avalanche multiplication gain could be used for QNL fluoroscopic imaging at the lowest clinical exposures while satisfying all of the requirements of a FPD for interventional radiology. Towards this end, it was first determined whether a-Se can reliably provide avalanche multiplication gain in the solid-state. An experimental method was developed which enabled the application of sufficiently large electric field strengths across the a-Se. This method resulted in avalanche gains as high as 10000 at an applied field of 105 V/um using optical excitation. This was the first time such high avalanche gains have been reported in a solid-state detector based on an amorphous material. Secondly, it was investigated how the solid-state a-Se avalanche detector could be used to image X-rays at diagnostic radiographic energies (~ 75 kVp). A dual-layered direct-conversion FPD architecture was proposed. It consisted of an x-ray drift region and a charge avalanche multiplication region and was found to eliminate depth-dependent gain fluctuation noise. It was shown that electric field strength non-uniformities in the a-Se do not degrade the detective quantum efficiency (DQE). Lastly, it was determined whether the solid-state a-Se avalanche detector satisfies all of the requirements of interventional radiology. Experimental results have shown that the total noise produced by the detector is negligible and that QNL operation at the lowest fluoroscopic exposures is indeed possible without any adverse effects occurring at much larger radiographic exposures. In conclusion, no fundamental obstacles were found preventing the use of avalanche a-Se in next-generation solid-state QNL FPDs for use in interventional radiology.

Keywords: interventional radiology
flat panel detector
flat panel imager
avalanche multiplication
amorphous selenium
fluoroscopy
Advisor: Rowlands, John A.
Music as The Between: The Idea of Meeting in Existence, Music and Education

As a violinist, teacher, and thinker, I am concerned to articulate the relevance of music to the lives of my audience, my students and myself. But my concern is not merely to describe the meanings that people experience when they engage music. Rather, I am interested in constituting the musical relevance that each of us must actualize as we work to make our lives vital and meaningful. Accordingly, in my study I articulate in philosophical, yet practical, terms, a particular attitude of musical engagement that I call meeting. Grounded in Martin Buber’s idea of human existence as I-Thou, my conception of meeting has a specific character. Each side of the meeting must meet itself in its work to constitute the adequacy of its engagement with the other as it must meet with the other in its work to constitute the adequacy of its engagement with itself. It follows that the essence of human meeting is not merely the “reality” – physical, cultural, intellectual – of people who come together. Rather, the essence is their self-critical thought that is created as they share their lives with each other. The focus, then, is not the meeting’s outcome but rather the meeting itself insofar as it constitutes mutual understanding, communication and love. Thus, at the heart of my study, I constitute music in the same way, not as a physical or cultural “reality,” but rather as the meeting between music and musical participant that demands that each – music and participant – attend to self and other. The idea that music’s whole being is meeting has profound implications for how we conceive of music education. Accordingly, the ultimate purpose of my study is to bring my ideas of musical meeting to bear upon how we teach and learn music in the classroom.

Keywords: music
meeting
existence
education
aesthetics
philosophy
meaning
Advisor: Shand, Patricia
A Reasoning Module for Long-lived Cognitive Agents

In this thesis we study a reasoning module for agents that have cognitive abilities, such as memory, perception, action, and are expected to function autonomously for long periods of time. The module provides the ability to reason about action and change using the language of the situation calculus and variants of the basic action theories. The main focus of this thesis is on the logical problem of progressing an action theory. First, we investigate the conjecture by Lin and Reiter that a practical first-order definition of progression is not appropriate for the general case. We show that Lin and Reiter were indeed correct in their intuitions by providing a proof for the conjecture, thus resolving the open question about the first-order definability of progression and justifying the need for a second-order definition. Then we proceed to identify three cases where it is possible to obtain a first-order progression with the desired properties: i) we extend earlier work by Lin and Reiter and present a case where we restrict our attention to a practical class of queries that may only quantify over situations in a limited way; ii) we revisit the local-effect assumption of Liu and Levesque that requires that the effects of an action are fixed by the arguments of the action and show that in this case a first-order progression is suitable; iii) we investigate a way that the local-effect assumption can be relaxed and show that when the initial knowledge base is a database of possible closures and the effects of the actions are range-restricted then a first-order progression is also suitable under a just-in-time assumption. Finally, we examine a special case of the action theories with range-restricted effects and present an algorithm for computing a finite progression. We prove the correctness and the complexity of the algorithm, and show its application in a simple example that is inspired by video games.

Keywords: situation calculus
computer science
artificial intelligence
mathematical logic
agent
knowledge representation
reasoning
reasoning about action
intelligent agent
Advisor: Levesque, Hector J.
First Passage Times: Integral Equations, Randomization and Analytical Approximations

The first passage time (FPT) problem for Brownian motion has been extensively studied in the literature. In particular, many incarnations of integral equations which link the density of the hitting time to the equation for the boundary itself have appeared. Most interestingly, Peskir (2002b) demonstrates that a master integral equation can be used to generate a countable number of new integrals via its differentiation or integration. In this thesis, we generalize Peskir's results and provide a more powerful unifying framework for generating integral equations through a new class of martingales. We obtain a continuum of new Volterra type equations and prove uniqueness for a subclass. The uniqueness result is then employed to demonstrate how certain functional transforms of the boundary affect the density function. Furthermore, we generalize a class of Fredholm integral equations and show its fundamental connection to the new class of Volterra equations. The Fredholm equations are then shown to provide a unified approach for computing the FPT distribution for linear, square root and quadratic boundaries. In addition, through the Fredholm equations, we analyze a polynomial expansion of the FPT density and employ a regularization method to solve for the coefficients. Moreover, the Volterra and Fredholm equations help us to examine a modification of the classical FPT under which we randomize, independently, the starting point of the Brownian motion. This randomized problem seeks the distribution of the starting point and takes the boundary and the (unconditional) FPT distribution as inputs. We show the existence and uniqueness of this random variable and solve the problem analytically for the linear boundary. The randomization technique is then drawn on to provide a structural framework for modeling mortality. We motivate the model and its natural inducement of 'risk-neutral' measures to price mortality linked financial products. Finally, we address the inverse FPT problem and show that in the case of the scale family of distributions, it is reducible to nding a single, base boundary. This result was applied to the exponential and uniform distributions to obtain analytical approximations of their corresponding base boundaries and, through the scaling property, for a general boundary.

Keywords: first passage time
Brownian motion
integral equations
hitting time
boundary function
martingales
Advisor: Jaimungal, Sebastian
Alexander, Kreinin
Intracellular Signaling Pathways Regulating Hepatic Apolipoprotein B100 Production: Roles of Mitogen-activated Protein Kinases (MAPKs) and Inhibitor of NFkappaB Kinase (IKK)-NFkappaB

Apolipoprotein B100 (apoB), the structural protein component of triglyceride-rich very low density lipoprotein (VLDL) and atherogenic low density lipoprotein, is considered an important risk indicator of atherosclerosis. In insulin resistant states, hepatic overproduction of apoB leads to metabolic dyslipidemia, characterized by high circulating VLDL and hypertriglyceridemia. Since the mitogen-activated protein kinases (MAPKs) and the inhibitor of NFkappaB kinase (IKK)-NFkappaB cascades are perturbed in insulin resistance, we hypothesized that the MAPKs (ERK, p38 and JNK) and the IKK-NFkappaB pathways regulate hepatic apoB output. We modulated these pathways in HepG2, a human hepatoma cell line, and primary hamster hepatocytes using chemical inhibitors and protein overexpression. ApoB synthesis and secretion were examined by metabolic pulse labeling. HepG2 is typically defective in secreting apoB as large VLDL particles and secretes smaller triglyceride-poor apoB-particles. Under continuous pulse labeling, ERK inhibition not only increased apoB secretion, it enabled HepG2 to secrete VLDL-sized particles in the presence of exogenous fatty acid (oleate). Concomitant with the increased apoB-particle size, ERK inhibition raised intracellular triglyceride level and diacylglycerol acyltransferase (DGAT) 1 and DGAT2 mRNA levels. Conversely, ERK activation decreased VLDL-apoB secretion from primary hepatocytes. In contrast to ERK, p38 or JNK inhibition decreased apoB secretion without affecting apoB-particle size from oleate-treated HepG2 cells. JNK inhibition also modulated apoB levels in primary hamster hepatocytes. Interestingly, the development of diet-induced hepatic insulin resistance was associated with decreased ERK, and enhanced p38 and NFkappaB activities. Thus we investigated the role of the NFkappaB pathway in regulating hepatic apoB production. IKK inhibition decreased and IKK overexpression increased apoB levels by modulating apoB mRNA translation and protein stability. IKK inhibition also suppressed hepatic apoB overproduction in an insulin resistance model, the fructose-fed hamster. Altogether, our results suggest that among the MAPK cascades, the MEK-ERK pathway is crucial in regulating apoB-lipoprotein assembly, possibly by modulating lipid availability to newly-synthesized apoB. The inflammatory IKK-NFkappaB cascade is also involved in regulating apoB synthesis and secretion. We postulate that dysregulation in the MAPK or NFkappaB cascades in insulin resistant and inflammatory states may contribute to hepatic apoB overproduction, and the common phenotype of hypertriglyceridemia and dyslipidemia.

Keywords: metabolism
lipids
signalling
lipoproteins
insulin resistance
inflammation
Advisor: Adeli, Khosrow
Composable, Distributed-state Models for High-dimensional Time Series

In this thesis we develop a class of nonlinear generative models for high-dimensional time series. The first key property of these models is their distributed, or "componential" latent state, which is characterized by binary stochastic variables which interact to explain the data. The second key property is the use of an undirected graphical model to represent the relationship between latent state (features) and observations. The final key property is composability: the proposed class of models can form the building blocks of deep networks by successively training each model on the features extracted by the previous one. We first propose a model based on the Restricted Boltzmann Machine (RBM) that uses an undirected model with binary latent variables and real-valued "visible" variables. The latent and visible variables at each time step receive directed connections from the visible variables at the last few time-steps. This "conditional" RBM (CRBM) makes on-line inference efficient and allows us to use a simple approximate learning procedure. We demonstrate the power of our approach by synthesizing various motion sequences and by performing on-line filling in of data lost during motion capture. We also explore CRBMs as priors in the context of Bayesian filtering applied to multi-view and monocular 3D person tracking. We extend the CRBM in a way that preserves its most important computational properties and introduces multiplicative three-way interactions that allow the effective interaction weight between two variables to be modulated by the dynamic state of a third variable. We introduce a factoring of the implied three-way weight tensor to permit a more compact parameterization. The resulting model can capture diverse styles of motion with a single set of parameters, and the three-way interactions greatly improve its ability to blend motion styles or to transition smoothly among them. In separate but related work, we revisit Products of Hidden Markov Models (PoHMMs). We show how the partition function can be estimated reliably via Annealed Importance Sampling. This enables us to demonstrate that PoHMMs outperform various flavours of HMMs on a variety of tasks and metrics, including log likelihood.

Keywords: machine learning
time series
neural networks
unsupervised learning
restricted Boltzmann machines
hidden Markov models
graphical models
motion capture
dynamical models
generative models
computer vision
tracking
Advisor: Hinton, Geoffrey
Roweis, Sam
Towards a Poetics of Freedom: An Interpretive Analysis of Ricoeur and Dante

This thesis’ task is to reinterpret Paul Ricoeur’s philosophy of the will, hermeneutics, and study of metaphor from a perspective that speaks to what his early work conceptualized as a poetics of freedom. Poetics, for Ricoeur, becomes a mode of expression capable of representing and illuminating what he considers the essential paradox of our human condition: a will that is both free and bound, “set free as freedom and responsible in its very deliverance.” A poetics of freedom, Ricoeur conceptualized in the beginning of his career, would be a mediation through which we perceive a tensional reconciliation of our conflicted natures, “a linguistic register suitable for speaking of liberated freedom and liberated man in his existential concreteness and totality.” Ricoeur, however, never developed the poetics of freedom beyond its original conceptualization. Through an interpretive analysis of Ricoeur's work, I reorient his later works on metaphor and hermeneutics towards the concerns that dominated the philosophy of the will and the existential philosophy to which it belongs. This study of Ricoeur’s philosophy of being occurs in discourse with a poetic text, Dante’s Commedia. The Commedia, I argue, is a text whose poetry explicitly and implicitly discloses the importance of hermeneutics and poetics in the arrival at self-understanding. The correlations that arise between its aesthetic discourse and Ricoeur’s contemporary perspective illuminate what I consider to be at the core of the philosophy of being: a primordial tension of selfhood conceptualized in terms of the dialectical relations that arise between freedom and nature, between objectivity and subjectivity, and between perspective and meaning; or in Dante’s terms, between my life and la nostra vita (our life).

Keywords: hermeneutics
Dante
Paul Ricoeur
Divine Commedy
Advisor: Valdes, Mario
Pietropaolo, Domenico