VictorJuiz/thesis huggingface dataset:
Quantum-Classical Master Equation Dynamics: An Analysis of Decoherence and Surface-hopping Techniques
Keywords: Quantum-classical molecular dynamics
decoherence
surface-hopping schemes
nonadiabatic dynamics

In this thesis quantum-classical dynamics is applied to the study of quantum condensed phase processes. This approach is based on the quantum-classical Liouville equation where the dynamics of a small subset of the degrees of freedom are treated quantum mechanically while the remaining degrees of freedom are treated by classical mechanics to a good approximation. We use this approach as it is computationally tractable, and the resulting equation of motion accurately accounts for the quantum and classical dynamics, as well as the coupling between these two components of the system. By recasting the quantum-classical Liouville equation into the form of a generalized master equation we investigate connections to surface-hopping. The link between these approaches is decoherence arising from interaction of the subsystem with the environment. We derive an evolution equation for the subsystem which contains terms accounting for the effects of the environment. One of these terms involves a memory kernel that accounts for the coherent dynamics. If this term decays rapidly, a Markovian approximation can be made. By lifting the resulting subsystem master equation into the full phase space, we obtain a Markovian master equation that prescribes surface-hopping-like dynamics. Our analysis outlines the conditions under which such a description is valid. Next, we consider the calculation of the rate constant for a quantum mechanical barrier crossing process. Starting from the reactive-flux autocorrelation function, we derive a quantum-classical expression for the rate kernel. This expression involves quantum-classical evolution of a species operator averaged over the initial quantum equilibrium structure of the system making it possible to compute the rate constant via computer simulation. Using a simple model for a proton transfer reaction we compare the results of the rate calculation obtained by quantum-classical Liouville dynamics with that of master equation dynamics. The master equation provides a good approximation to the full quantum-classical Liouville calculation for our model and a more stable algorithm results due to the elimination of oscillating phase factors in the simulation. Finally, we make use of the theoretical framework established in this thesis to analyze some aspects of decoherence used in popular surface-hopping techniques.
Silicon Inverse Opal-based Materials as Electrodes for Lithium-ion Batteries: Synthesis, Characterisation and Electrochemical Performance
Keywords: batteries
lithium-ion batteries
Li-ion batteries
anode
negative electrode
silicon
inverse opal
inverse colloidal crystal
macroporous material

Three-dimensional macroporous structures (‘opals’ and ‘inverse opals’) can be produced by colloidal crystal templating, one of the most intensively studied areas in materials science today. There are several potential advantages of lithium-ion battery electrodes based on inverse opal structures. High electrode surface, easier electrolyte access to the bulk of electrode and reduced lithium diffusion lengths allow higher discharge rates. Highly open structures provide for better mechanical stability to volume swings during cycling. Silicon is one of the most promising anode materials for lithium-ion batteries. Its theoretical capacity exceeds capacities of all other materials besides metallic lithium. Silicon is abundant, cheap, and its use would allow for incorporation of microbattery production into the semiconductor manufacturing. Performance of silicon is restricted mainly by large volume changes during cycling. The objective of this work was to investigate how the inverse opal structures influence the performance of silicon electrodes. Several types of silicon-based inverse opal films were synthesised, and their electrochemical performance was studied. Amorphous silicon inverse opals were fabricated via chemical vapour deposition and characterised by various techniques. Galvanostatic cycling of these materials confirmed the feasibility of the approach taken, since the electrodes demonstrated high capacities and decent capacity retentions. The rate performance of amorphous silicon inverse opals was unsatisfactory due to low conductivity of silicon. The conductivity of silicon inverse opals was improved by crystallisation. Nanocrystalline silicon inverse opals demonstrated much better rate capabilities, but the capacities faded to zero after several cycles. Silicon-carbon composite inverse opal materials were synthesised by depositing a thin layer of carbon via pyrolysis of a sucrose-based precursor onto the silicon inverse opals in an attempt to further increase conductivity and achieve mechanical stabilisation of the structures. The amount of carbon deposited proved to be insufficient to stabilise the structures, and silicon-carbon composites demonstrated unsatisfactory electrochemical behaviour. Carbon inverse opals were coated with amorphous silicon producing another type of macroporous composites. These electrodes demonstrated significant improvement both in capacity retentions and in rate capabilities. The inner carbon matrix not only increased the material conductivity, but also resulted in lower silicon pulverisation during cycling.
Elastic Scattering Phenomena in Molecularly-linked Gold Nanoparticle Films
Keywords: electronic scattering
conductance
self-assembled nanoparticle film
quasilocalized hopping
weak localization
reflectionless tunneling

We have investigated the conductance, g, of 1,4-butanedithiol linked Au nanoparticle films as a function of temperature, T, bias potential, V, and applied magnetic field, B. An interesting temperature dependence is observed for non-metallic films with thicknesses just below a critical film thickness: g ~ exp [-(T_0/T)^(1/2)] for 20 K < T < 300 K. We show that this temperature dependence is incompatible with an Efros-Shklovskii "variable range hopping" model, since "hopping distances" are too large to be consistent with tunneling processes, and tend to scale with size of super-clusters of molecularly-linked nanoparticles. We propose a "quasilocalized hopping" model based on competition between single-electron charging of super-clusters and electron backscattering within super-clusters to explain the observed temperature dependence. Various electron scattering time scales are extracted from magnetoconductance data using a modified "weak localization" model. Elastic scattering time scales are comparable to those required for an electron to traverse a nanoparticle, while inelastic and spin-orbit scattering time scales are consistent with those found in studies of conventionally-prepared granular Au films. At interfaces between metallic 1,4-butanedithiol-linked Au nanoparticle films and conventional superconductors, we find that g consistently exhibits peaks, as well as oscillations, that depend simultaneously on both V and B. Such peaks and correlated conductance oscillations are predicted by an enhanced Andreev reflection process due to disorder-driven elastic scattering and electron-hole interference in the nanoparticle film. While oscillations have been predicted by a so-called "reflectionless tunneling" model, they have not been observed at other normal-superconductor interfaces. We speculate that oscillations are observable in this system due to synthetically controlled uniformity of elastic scattering length (i.e., nanoparticle diameter) and a reduced number of current-carrying pathways, especially near the interface. Contrary to predictions of existing "reflectionless tunneling" models, we find that the periods of oscillation in B decrease as T increases. This suggests that the area of interfering pathways increases with T. We propose that this increasing area can be attributed to magnetic field penetration into the superconductor. Conductance data agrees remarkably well with known temperature dependence of penetration depth predicted by BCS theory. Our study shows that this additional region of flux must be considered in experimental and theoretical studies of "reflectionless tunneling", and underscores the utility of molecularly-linked nano\-particle films as a platform for studying charge transport.
NMR Studies of SH3 Domain Structure and Function
Keywords: SH3 domain
NMR
drk
fyn
CIN85
ubiquitination
protein folding

SH3 domains are excellent models for probing folding and protein interactions. This thesis describes NMR studies of several SH3 domains, including the N-terminal SH3 domain of the Drosophila adaptor protein Drk (drkN SH3 domain), the SH3 domain of the proto-oncogene tyrosine-kinase Fyn, and the SH3 domains of the human adaptor protein CIN85, involved in Cbl-mediated downregulation of epidermal growth factor receptor (EGFR) and other receptor tyrosine kinases (RTKs). The drkN SH3 domain is an ideal system for studying disordered states. The unique quality of this isolated domain is that it exists in an approximately 50/50 equilibrium between its folded and unfolded states under non-denaturating buffer conditions. Interestingly, the single T22G mutation dramatically stabilizes the domain. Here the NMR structures of the drkN SH3 domain and its T22G mutant are determined and compared in order to illuminate the causes of the marginal stability of the domain. Solvent exposure of the folded and the unfolded drkN SH3 domains are probed and compared with a novel NMR technique using molecular oxygen dissolved in solution as a paramagnetic probe. The changes in partial molar volume along the folding trajectories of the drkN SH3 and Fyn SH3 domains are also studied and analyzed here in terms of changes in protein hydration and packing accompanying folding. Finally, the interactions between the SH3 domains of CIN85 and ubiquitin are discussed. All three are shown to bind ubiquitin. The structure of the SH3-C domain in complex with ubiquitin is presented and the effect of disruption of ubiquitin binding on ubiquitination of CIN85 and EGFR in vivo is discussed. SH3 domains are easily amendable to a wide range of NMR approaches and provide a good system for development and testing of novel methods. Through the use of these approaches significant insights into details of SH3 domain structure, stability, mechanisms of folding and cellular function have been gained.
A Study of the Composition of Carryover Particles in Kraft Recovery Boilers
Keywords: Carryover
Composition
Black Liquor
Recovery Boiler

Carryover particles are partially/completely burned black liquor particles entrained in the flue gas in kraft recovery boilers. Understanding how carryover particles form and deposit on heat transfer tube surfaces is critically important in the design and operation of a recovery boiler. The tendency for a carryover particle to deposit on a tube surface depends on the particle temperature and composition at the moment of impact. This study was the first to examine systematically how carryover particle composition changes with the black liquor chemistry and burning conditions. The effect of black liquor composition and particle size, gas composition (O2 and SO2 concentrations) and temperature on the composition of carryover particles were studied using an Entrained Flow Reactor (EFR). Field studies were conducted on three operating boilers, where an air-cooled probe was used to collect carryover samples at the superheater entrance. The results show that the chloride (Cl) and potassium (K) contents in carryover particles were linearly proportional to their contents in black liquor. Cl and K were depleted during black liquor combustion due mainly to the vaporization of NaCl and KCl. The depletion of Cl is about three times greater than that of K. The significant depletion of Cl implies that carryover particles contain much less Cl, and hence, are less sticky than previously expected from black liquor composition. A dynamic model was also developed to predict the composition of carryover particles as a function of black liquor composition and burning conditions. Based on the data obtained experimentally in this study, the kinetic equations for the oxidation of sulphide available in the literature were modified and incorporated into the model to improve its sulphide and sulphate predictions. The model predicts the main components of carryover particles formed in both the EFR and three operating recovery boilers reasonably well, except for the K content, which is slightly over-predicted at high O2 concentrations (or high particle temperatures). Based on the predicted composition, it is possible to determine the thermal properties of carryover and to assess its fouling propensity in the boiler. The information helps boiler manufacturers and operators to identify locations in the boiler where massive carryover deposition may occur and to devise appropriate control strategies to minimize fouling and to improve boiler thermal efficiency.
Integration of Micro and Nanotechnologies for Multiplexed High-Throughput Infectious Disease Detection
Keywords: Nanotechnology
Infectious Disease Diagnostics
Microfluidics
Multiplexed Detection

This thesis presents the development and optimization of a high-throughput fluorescence microbead based approach for multiplexed, large scale medical diagnostics of biological fluids. Specifically, different sizes of semiconductor nanocrystals, called quantum dots, are infused into polystyrene microspheres, yielding a set of spectrally unique optical barcodes. The surface of these barcodes are then used for sandwich assays with target molecules and fluorophore-conjugated detection antibodies, changing the optical spectra of beads that have associated with (or captured) biomolecular targets. These assayed microbeads are analyzed at a single bead level in a high-throughput manner using an electrokinetic microfluidic system and laser induced fluorescence. Optical signals collected by solid state photodetectors are then processed using novel signal processing algorithms. This document will discuss developments made in each area of the platform as well as optimization of the platform for improved future performance.
Design and Characterization of Novel Nanomaterials for Cancer Imaging and Therapy
Keywords: Biomedical Engineering
Bionanotechnology

The emergence of bionanotechnology has allowed the design of novel technological tools for a variety of biomedical applications. Despite the incompatibility of native semiconductor quantum dots with biological environment, this class of nanocrystals was among the first nanomaterials to demonstrate their use in biological labeling and imaging applications. In this thesis, new surface modification chemistry and synthetic strategies were developed to produce high quality biocompatible and bioconjugatable near-infrared emitting quantum dots for deep tissue in vivo imaging and detection applications. By carefully selecting a specific mixture of semiconductor elements to obtain a desired bandgap energy and optimizing the procedure for surface coating, successful synthesis of high quality, watersoluble, near-infrared emitting quantum dots were demonstrated. These developments allows for the use of quantum dots as alternative contrast agents for sophisticated biological imaging applications that are currently unachievable using conventional uorophores. In addition, using metallic nanoparticles, it was found that cells possess the ability to differentiate nanoparticles of various sizes upon their binding with specific membrane receptors. These receptors undergo rapid cellular internalization which altered their trafficking dynamics and down-stream signaling processes. The amplitude of such alteration was highly dependent on the size of the nanoparticle with most efficient internalization occurring at 40 nm - 50 nm size range. These observations raise important questions regarding the mechanisms governing similar processes and cell behaviours documented during viral infections. Whether such biological phenomenon are evolutionarily conserved as natural defense mechanisms to counter foreign invasion, or whether many of the known viruses are naturally selected to breach the primary defense of cells - the plasma membrane, remains to be elucidated. In summary, nanotechnology offers great promises for biological research and medicine. This thesis demonstrates the use of semiconductor and metallic nanostructures for imaging, detecting and administrating therapeutics in cancerous cells, tissues and animal models. Although the results presented in this thesis are preliminary, and the technologies demonstrated are still years away from practical use, these studies nevertheless, pave the way for future experimental researches within the field of nanomedicine, and provide insights into the understanding of the most fundamental yet highly complex processes in cell biology.
Constitutive versus Regulated Traffic of GLUT4
Keywords: Type 2 Diabetes Mellitus
GLUT4 Glucose Transporter Traffic in Muscle

Glucose transporter GLUT4 allows glucose uptake into muscle and adipose cells. Insulin promotes recruitment and plasma membrane insertion of GLUT4 vesicles that can recycle constitutively. Obesity and type 2 diabetes mellitus are associated with defects in insulin-induced GLUT4 recruitment. Knowledge of alternative modes and steps of GLUT4 traffic in L6-GLUT4myc muscle cells may reveal possible targets for therapeutic intervention in insulin-resistant patients. Hypertonicity and Platelet Derived Growth Factor also increase surface GLUT4 levels but it was unknown if they tap on the same intracellular GLUT4 depots as insulin. We explored whether GLUT4 vesicles recycle using different compartments and mechanisms for the surface gain elicited by each stimulus. We hypothesized that all vesicle fusion steps require NSF but depend on individual v-SNAREs. Specifically, we tested effects of ATPase-deficient NSF or VAMP7 siRNA transfections, and endosomal ablation on GLUT4 traffic. We show that VAMP7 was required for basal and hypertonic recycling, while VAMP2 is exclusively used in response to insulin. As insulin action bifurcates downstream of phosphatidylinositol 3-kinase, we also hypothesized that the Rac-to-actin and Akt-to-AS160 branches regulate distinct GLUT4 traffic steps. For this we determined GLUT4myc localization in rounded myoblasts relative to a surface marker. Interfering with Rac, actin dynamics or actin-binding α-actinin4 maintained GLUT4 in a perinuclear region even under insulin-stimulation. Interfering with AS160 allowed significant GLUT4 accumulation beneath the membrane, but not fusion. We propose that actin dynamics and α-actinin4 are required for cortical GLUT4 tethering mechanisms, and AS160 contributes to GLUT4 docking/fusion. We confirmed that VAMP2 facilitates GLUT4 fusion, as tetanus toxin-based cleavage did not inhibit peripheral GLUT4 recruitment. Finally, AS160 targets Rab8A and Rab14 in muscle respectively affected GLUT4 availability for membrane fusion, and basal GLUT4 retention. This work will lead to future testing of strategies to selectively enhance vesicle availability, tethering, or surface fusion, for bypassing insulin resistance.
Translational Regulation in the Early Drosophila Embryo
Keywords: Drosophila
Translational regulation
RNA

Translational regulation is an important mechanism for regulating gene expression. Regulation of specific transcripts is often mediated by elements present in the 3′ untranslated region (UTR) of the mRNA. In the Drosophila embryo, translational repression of nanos mRNA is mediated by Smaug protein bound to specific sequences present in the 3′ UTR of the mRNA. Here I show that Smaug recruits Cup protein to the mRNA and that Cup in turn binds to the translation initiation factor eIF4E that is present at the 5′. The interaction between Cup and eIF4E prevents formation of a productive translation initiation complex on the mRNA. Therefore, Smaug-dependent translational repression functions at the initiation step via the indirect interaction of Smaug with eIF4E, which is mediated by Cup. In the second example of translational regulation presented here, I show that an element present in the 3′ untranslated region of the Hsp83 mRNA mediates translational enhancement in the Drosophila embryo. I have identified three proteins, Hrp48, DDP1 and PABP that interact with this element and have demonstrated that Hrp48 and DDP1 function in translational enhancement.
Regulation of GLUT4 Intrinsic Activity and Internalization in L6 Muscle Cells
Keywords: insulin
GLUT4
muscle contraction
glucose
muscle
diabetes
membrane traffic
endocytosis

GLUT4 is the principal insulin-responsive glucose transporter in skeletal muscle. Insulin stimulation leads to exocytosis of intracellular GLUT4-containing vesicles to the cell surface, thereby increasing glucose uptake. Muscle contraction also elevates cell surface GLUT4 by a less understood mechanism. Once at the cell surface, GLUT4 may be subject to additional regulation, such as by modulation of its internalization rate or its intrinsic activity. The objective of this thesis was to identify the mechanism of GLUT4 internalization in muscle cells and to determine whether it is regulated by insulin treatment or by the signals elicited by muscle contraction. Skeletal muscle cells in culture stably expressing myc-tagged GLUT4 were used. We found that GLUT4 internalizes simultaneously through a clathrin-dependent and a clathrin- and caveolae-independent and cholesterol- and dynamin-dependent pathway. Insulin did not regulate GLUT4 internalization. In contrast, mitochondrial uncoupling, which may mimic the heightened energy demand that occurs during muscle contraction, retarded GLUT4 internalization by inhibiting the clathrin-independent route. Activation of both AMP-dependent kinase (AMPK) and protein kinase C (PKC) was necessary and sufficient for this response. We further hypothesized that the intrinsic activity of GLUT4 may be regulated under some conditions, based on a discrepancy between the amount of cell surface transporters and the rate of glucose uptake. In particular, inhibitors of p38 mitogen-activated protein kinase (p38MAPK) lowered insulin-dependent glucose uptake without reducing the number of GLUT4 units at the surface. We found that p38MAPK is activated by insulin through TAB1-dependent autophosphorylation, yet p38MAPK was dispensable for insulin-stimulated glucose uptake. Mechanisms other than p38MAPK must be involved in the regulation of GLUT4 intrinsic activity. In conclusion, in addition to its exocytosis, the activity and endocytosis of GLUT4 are regulated by stimuli that increase the rate of glucose uptake into muscle.