VictorJuiz/thesis huggingface dataset:
Predicting Phonon Transport in Semiconductor Nanostructures using Atomistic Calculations and the Boltzmann Transport Equation

The mechanisms of thermal transport in defect-free silicon nanostructures are examined using a combination of lattice dynamics (LD) calculations and the Boltzmann transport equation (BTE). To begin, the thermal conductivity reduction in thin films is examined using a hierarchical method that first predicts phonon transport properties using LD calculations, and then solves the phonon BTE using the lattice Boltzmann method. This approach, which considers all of the phonons in the first Brillouin-zone, is used to assess the suitability of common assumptions used to reduce the computational effort. Specifically, we assess the validity of: (i) neglecting the contributions of optical modes, (ii) the isotropic approximation, (iii) assuming an averaged bulk mean-free path (i.e., the Gray approximation), and (iv) using the Matthiessen rule to combine the effect of different scattering mechanisms. Because the frequency-dependent contributions to thermal conductivity change as the film thickness is reduced, assumptions that are valid for bulk are not necessarily valid for thin films. Using knowledge gained from this study, an analytical model for the length-dependence of thin film thermal conductivity is presented and compared to the predictions of the LD-based calculations. The model contains no fitting parameters and only requires the bulk lattice constant, bulk thermal conductivity, and an acoustic phonon speed as inputs. By including the mode-dependence of the phonon lifetimes resulting from phonon-phonon and phonon-boundary scattering, the model predictions capture the approach to the bulk thermal conductivity better than predictions made using Gray models based on a single lifetime. Both the model and the LD-based method are used to assess a procedure commonly used to extract bulk thermal conductivities from length-dependent molecular dynamics simulation data. Because the mode-dependence of thermal conductivity is not included in the derivation of this extrapolation procedure, using it can result in significant error. Finally, phonon transport across a silicon/vacuum-gap/silicon structure is modelled using lattice dynamics and Landauer theory. The phonons transmit thermal energy across the vacuum gap via atomic interactions between the leads. Because the incident phonons do not encounter a classically impenetrable potential barrier, this mechanism is not a tunneling phenomenon. The heat flux due to phonon transport can be 4 orders of magnitude larger than that due to photon transport predicted from near-field radiation theory.

Keywords: nanoscale heat transfer
solid state physics
phonon Boltzmann transport equation
molecular dynamics simulation
lattice dynamics calculations
thin film
Advisor: Amon, Cristina
Modeling of Kraft Mill Chemical Balance

The reduction of mill effluent discharge as a result of stringent environmental legislations can have a significant impact on sodium (Na) and sulfur (S) balances in the kraft pulping process. In order to maintain a proper balance of Na and S, kraft mills may need to adopt different makeup strategies. For this purpose, a dynamic model was developed to predict the Na and S balance in the kraft recovery cycle, as well as the accumulation of undesirable non-process elements such as chlorine (Cl) and potassium (K). The model was developed using the CADSIM software and was validated using data obtained from a Brazilian bleached kraft pulp mill. The calculated data from the model showed good agreement with mill data with respect to all parts of the mill simulated. Dynamic tests designed to calculate the white liquor sulfidity over specific periods of time also presented good agreement. The result indicates that the model is able to describe the balance of chlorine, potassium, sodium and sulfur in the kraft process. A study conducted to evaluate the Cl and K accumulation agrees with the expected behaviour observed in mill data. The presence of ash treatment systems allow to reduce Cl and K contents in recovery boiler precipitator ash from 4.2 mol% Cl(Na+K) to 1.25 mol % and from 2.25 mol % K/(Na+K) to 0.8 mol% for 100% ash treated. The tests performed for Na and S balances focused in the makeup requirement for two situations: ash purging and ash treatment to control Cl and K levels. The use of ash treatment systems reduced Na and S makeup requirement from 5 to 50% depending on the amount of ash treated. A simple mathematical model was then used to estimate the Cl balances around the recovery cycle. Given that the proper simplifications are applied, the CADSIM model and the CSTR model presented good agreement in estimating the Cl balances. This result provided not only another method for the CADSIM model to be validated but also a way to calculate a rough estimate for Cl balance.

Keywords: Chemical Balance
Kraft Process
Simulation
CADSIM Plus
Cl and K
Na and S
Advisor: Tran, Honghi
Exceptional Security Practices, Human Rights Abuses, and the Politics of Legal Legitimation in the American “Global War on Terror”

Given the contradictory reality of a well-developed human rights and humanitarian regime alongside extensive human rights abuses committed in the “Global War on Terror,” the dissertation asks how and why law has shaped contemporary security policy. Focusing on the American case over time, I examine this problem empirically by tracing the changing impact of both international and domestic legal and normative constraints on torture and interrogation, detention and trial, and surveillance practices, culminating in post-9/11 counterterrorism doctrine. I find that policy makers have increasingly violated rules with the adoption of controversial security and intelligence policies, but have simultaneously employed legalistic arguments to evade responsibility for human rights abuses. Using contrasting realist, decisionist, liberal, and constructivist accounts of the nature of state compliance with norms and law found in International Relations and legal scholarship, the dissertation theoretically explains this outcome and with it, law’s ability to moderate national security practice. In so doing, I propose an original reading of law as a permissive constraint, which challenges us to rethink paradigmatic assumptions in a way that accommodates both strategic and normative factors and recognizes the role of practice in giving content to rules.

Keywords: International Relations
International Law
American Foreign Policy
Human Rights
War on Terror
Torture
Detention
Surveillance
Advisor: Welch, David A.
A Study on Vibration-induced Particle Motion under Microgravity

Production of protein and semi-conductor crystals with advanced quality and properties is considered to be possible under microgravity conditions due to the absence of natural convection effects. Such materials have several beneficial properties that can improve the human life. An example is the synthesis of protein crystals with improved structure that can be determined for the production of advanced drugs. In the past experiments conducted aboard several space platforms, however, g-jitter induced convective flow may have resulted in certain effects that reduced the quality of the produced crystals. To investigate the effects of g-jitter on the motion of small particles, experiments were conducted under normal gravity by suspending spherical stainless steel particles of different sizes with a thin wire or synthetic silk thread in a rectangular fluid cell. The fluid viscosities were 350 and 1,000 times higher than water. To produce the g-jitter induced motion in the fluid, the cell was subjected to horizontal sinusoidal vibrations with different frequencies and amplitudes. The focus of the experiments so far has been on vibration-induced force on the particle vibrating parallel to a near wall. Relatively low viscosity fluids such as water have been previously determined to produce a force on the particle which attracts the particle to the nearest fluid cell wall. The present experiments with a more viscous fluid have revealed an interesting change in the force from attraction in low viscosity fluids to repulsion in high viscosity liquids. Moreover, the repulsion force has been observed to increase with an increase in the fluid viscosity and the fluid cell amplitude. A numerical code, Partflow3d, has also been used to predict the vibration effects on the particle. Although, based on the objectives of this study, the numerical simulations were conducted only for a wire-free particle under microgravity, their results were qualitatively in agreement with the experimental results. The numerical simulations also revealed that the physical mechanism of the hydrodynamic attraction-repulsion force on the particle is related to Bernoulli’s principle of reduced pressure in high velocity zones in the fluid surrounding the particle. The results so far have shown new aspects of the g-jitter induced motion of the particle near a fluid cell wall. Better understanding of the forces affecting the particles in a fluid cell subjected to small vibrations, can reveal novel ways to produce new advanced materials and also improve material processing both in microgravity and normal gravity conditions.

Keywords: Microgravity
Particle
Advisor: Kawaji, Masahiro
The Investigation of Peptide and Protein-glycosaminoglycan Binding Interactions using Fluorescent Probes

The structural complexity of glycosaminoglycans (GAGs) such as heparin and heparan sulfate (HS) and their numerous biological roles, brings forth the need to develop new methods, capable of studying GAGs and their interactions with peptides and proteins under native settings. This thesis explores the development of chemical tools to study heparin/HS binding interactions under physiologically relevant conditions using fluorescence. In chapter 2, we designed peptide-based quinolinium probes to study the structural requirements of cationic peptides required for high affinity peptide-heparin interactions. These fluorescent probes enabled the study of peptide-heparin interactions at nM concentrations allowing the calculation of peptide-heparin binding constants. It was observed that peptides with positive charge displayed on one face of an α-helix in a continuous arrangement bound to heparin with the highest affinity and that heparin likely prefers to bind to these peptides while remaining in an extended conformation. In chapter 3, we set out to study an important biological role of HS which involves the binding and sequestering of proteins at the cell surface, facilitating endocytosis. HS has been implicated in the mechanism of cell penetrating peptide (CPP) cell uptake, with different CPPs showing different degrees of HS dependence on uptake as well as different mechanisms of entry. The role of HS in the mechanism of CPP uptake was investigated in chapter 3 using fluorescent peptide-based probes incorporating fluorophore/quencher pairs. These were used to identify and characterize the ability of heparin/HS to bind and cluster with CPPs to form colloidally stable aggregates. It was shown that the CPP Antp formed much more stable clusters with heparin than the TAT peptide despite both peptides having similar binding affinity for a single heparin chain. These findings were used to explain the cell surface HS dependence of Antp on cell uptake via endocytosis in contrast to the low dependance of TAT on HS and its uptake via translocation. A general model relating the ability of a CPP to cluster surface HS to its preferred mechanism of cell entry was proposed. In chapter 4, a strategy to selectively, and site specifically acylate carbohydrate binding proteins was developed using thioester-based affinity conjugates. It was possible to label maltose binding protein, a periplasmic protein, with high yield and selectivity at a single lysine residue proximal to the maltose binding site. Selective protein labeling could be carried out in bacterial cell extracts and in live bacterial cells. This strategy can potentially be applied to develop protein-based carbohydrate biosensors as well as profile carbohydrate binding proteins in biological samples.

Keywords: Fluorescent probes
Glycosaminoglycans
Advisor: Nitz, Mark
Quantitative Evaluation of Semiconductor Nanocrystals as Contrast Agents for Fluorescence Molecular Imaging

Fluorescence molecular imaging has been triggering interest in the scientific community for the last decade due to its great potential for improved early cancer detection and image-guided treatment. Semiconductor nanoparticles, also known as quantum dots, have been identified as potential contrast agents for molecular imaging, but there is a lack of quantitative contrast optimization studies that would enable precise and robust dosimetry calculations. These calculations are crucial to determine the feasibility, risk and cost of any contrast-enhanced clinical imaging procedure. This thesis presents a first attempt at developing a quantitative dosimetry framework for quantum dot-based contrast-enhanced fluorescence molecular imaging, by combining novel experimental methods and validated mathematical models. Three studies were completed to develop the dosimetry framework. In the first study, we design a novel homogenized optical tissue phantom approach to investigate with precision the effects of various photophysical parameters, such as the excitation and emission wavelengths, tissue absorption and scattering coefficient spectra, tissue autofluorescence spectra, target fluorescence spectra and target depth, on the detected contrast. In the second study, we use the approach to investigate the influence of tissue optical absorption and scattering on contrast behavior for various ex vivo tissue samples, and develop performance metrics to quantify the optimization results. In the third study, we perform vascular fluorescence contrast-enhanced imaging in the dorsal skinfold window chamber mouse model to investigate the effects of pharmacokinetics, blood absorption, vessel diameter and injected dose on the detected contrast. We also describe the relationship between the injected volume and vascular contrast, and transfer the performance metrics developed previously to estimate the minimum injection dose under various conditions. These studies are expected to serve as a stepping stone to further develop contrast optimization and dosimetry models for the emerging field of fluorescence molecular imaging.

Keywords: Fluorescence
Quantum Dots
Optimization
Dosimetry
Endoscopy
Biophotonics
Contrast
Nanotechnology
Advisor: Wilson, Brian Campbell
Concerto for Marimba Quartet and Orchestra

My Concerto for Marimba Quartet and Orchestra is designed to be a showcase for marimba ensemble, within the context of a traditional orchestral concerto. It is comprised of three movements. The language of the concerto is at times pluralistic, and at other times homogeneous. The music plays with repetition, simplicity, variability and persistence. The three movements that comprise this concerto are each designed to capitalize on the unique sound of the marimbas in combination with other instruments. In the first movement a small three-note motive (carefully selected to be easy to play rapidly with mallets) is translated from the marimbas to the ensemble to create homogenous textures that develop harmonically using pattern and repetition. The second movement is an exploration of the elasticity of rhythm. It sets the marimbas against still chords in the orchestra. It also employs a heightened level of chromaticism in passages that contrast with diatonic chords that are built from the three- note motive of the first movement. The final movement is an exploration of ensemble virtuosity. Rhythms and harmonic material are passed throughout the soloists and orchestra. This movement is designed to play with repetition and the expectations of a rondo form. Material from the two previous movements is recapped at the end.

Keywords: concerto
marimba
Quartet
Orchestra
Advisor: Kulesha, Gary
Poly (squaramides): Synthesis, Anion Sensing, and Self-assembly

The focus of the research presented in this thesis is the design, synthesis, and anion recognition properties of a structurally novel class of poly(amides) that incorporates the diaminocyclobutenedione (squaramide) group into the polymer backbone. In Chapter 1, a brief overview of different anion-responsive synthetic macromolecules is presented. Emphasis is placed on the wide structural diversity of the polymers, the mechanisms of their anion-induced responses, and features such as signal amplification, multivalency, and cooperative behavior that can be exploited productively in the context of anion recognition and sensing. Chapter 2 describes a new method for the regioselective preparation of squaramides, using Lewis acid-catalyzed condensations of diethyl squarate and different anilines. Zinc trifluoromethanesulfonate promotes efficient condensations of anilines with squarate esters, providing access to symmetrical and unsymmetrical squaramides in high yields from readily available starting materials. Colorimetric anion-sensing behavior and computational studies illustrating the enhanced hydrogen bond donor ability and acidity of squaramides in comparison to ureas are presented. In Chapter 3, the application of the synthetic method described above to the selective preparation of polysquaramides composed of 1,2-isomeric repeat units is described. The optical, thermal and aggregation properties of these materials are also discussed. Finally, Chapter 4 describes self-assembly properties as well as applications of these materials in the area of anion recognition and sensing. Incorporating an anion-binding squaramide group into a polymeric architecture results in drastic alterations in the selectivity and magnitude of its anion-induced response, resulting in a sensitive and discriminating turn-on fluorescence sensor for dihydrogenphosphate ions. This unusual behavior is the result of a cooperative, anion-triggered aggregation process that was further probed by dynamic light scattering (DLS), transmission electron microscopy (TEM) and laser confocal microscopy.

Keywords: Anion Recognition and Sensing
Polymers
Supramolecular Chemistry
Self-Assembly
Advisor: Taylor, Mark S.
Aspects of Persian Phonology and Morpho-phonology

This thesis deals with aspects of Persian phonology and morpho-phonology which are less studied or controversial, and has two specific goals: (i) to examine the structure of the Persian vowel system with the goal of understanding the asymmetries in patterning of different vowels in the system; (ii) to examine some suffixation processes in Persian with the goal of understanding the seeming irregularities in morphophonemics. The more generals goals of this work are to contribute to the discussions of: (i) determining dimensions of contrast in a vowel system; (ii) interactions of vowels and consonants at a morpheme boundary. Although the main focus of this work is on the synchronic status of these issues in Persian from a theoretical viewpoint, many discussions in the thesis benefit from an historical and/or an experimental investigation. As such, the thesis contributes both to the field of theoretical and experimental phonology, and offers both synchronic and historical perspectives on many issues at hand.

Keywords: Phonology, Morpho-phonology, Vowels, Suffixation, Persian
Advisor: Rice, Keren
Biomarkers of Optic Nerve Head Glial Cell Activation Following Biomechanical Insult

Glaucoma is a leading cause of irreversible blindness worldwide. Primary Open Angle Glaucoma is the most common form of the disease and can be characterized by the slow and irreversible apoptotic death of retinal ganglion cells, a unique optic nerve neuropathy resulting in loss of vision. Increased intra-ocular pressure is known to be a leading risk-factor for glaucoma, and lowering IOP is currently the only evidence based method for the clinical management of the disease. However the exact mechanism by which an elevated IOP leads to the death of the retinal ganglion cells is still poorly understood. By using previous finite element models of glaucoma to quantify the biomechanical environment within the optic nerve head we have built human primary cell culture models in an attempt to replicate aspects of early glaucomatous optic neuropathy. In these models we mimic the in vivo biomechanical environment in the lamina cribrosa by growing human optic nerve head astrocytes and lamina cribrosa cells on compliant substrates and subjecting the cells to deformation. Specifically, a global protein scan using isobaric tags for relative and absolute quantitation (iTRAQ) was performed on all the experiments to identify potential biomarkers for glaucoma. A secondary analysis using enzyme-linked immunosorbent assay (ELISA) identified extracellular proteins of interest. Over 520 proteins were identified in response to biomechnical strain from both cell types. Many of these proteins centred on TGF-, p53 and TNF, which have previously been shown to play a role in the pathogenesis of glaucoma. Proteins found in astrocytes were astrocytic phosphoprotein (PEA15), UDP-glucose dehydrogenase (UGDH), and annexin A4 (ANXA4). LC proteins were bcl-2-associated athanogene 5 (BAG5), nucleolar protein 66 (NO66) and Eukaryotic translation initiation factor 5A (eIF-5A). These proteomic results will enable a series of functional studies looking into the role select markers play in ONH glial cell activation, a process still not well understood. Candidates for this work will be prioritized based on novelty and relevance to mechanisms of cellular stress and death. We hypothesize that study of these molecular pathways will provide insight into this process, as well as improve our understanding of how glial activation contributes to the development of glaucomatous optic neuropathy.

Keywords: Biomarker
Glial Cells
Astrocyte
Lamina Cribrosa Cells
Optic Nerve Head
Glaucoma
Proteomics
iTRAQ
Advisor: Flanagan, John G.