VictorJuiz/thesis huggingface dataset:
Electric field response in molecules and materials [electronic resource] : computational studies of extreme conditions and strong fields
Keywords: Materials Science and Engineering.

With advances in hardware and theory continually expanding the domain of numerical methods, many engineering problems are finding answers with the help of first principles computations. A growing body of research successfully employs electronic structure methods to study complex phenomena from nanometer-scale devices to single molecules. In particular, the scalability and simplicity of density-functional theory (DFT) based methods has led to their widespread application in studying materials and molecules. Time-dependent DFT (TD-DFT) is the extension of DFT to time-dependent systems, employed for studying dynamical processes like electric field response while retaining the favorable scaling of DFT methods. The electric field response of a system bears information about electronic properties, linear and nonlinear optical spectra, electron and ion dynamics, and electron-electron interaction. By applying simulated electric fields with a combination of DFT, molecular dynamics (MD) and time-dependent DFT (TD-DFT), we present studies of optical signatures in condensed matter at extreme conditions and strong field ionic response in molecules. We first present a method for identifying optical/UV signatures of chemical intermediates in reacting systems, and its application to shock-induced chemistry in the energetic material nitromethane. We find a connection between transient reaction byproducts and enhanced optical response across the entire visible spectrum, with the inclusion of a TD-DFT kernel affecting the amplitudes of the computed spectra by up to 30%. We then explore the pyrolysis of a phenolic resin similar to that used in atmospheric entry heat shields (famous for landing NASA's Mars Science Laboratory) and test the robustness of linear regression-based models for predicting features of composition from computed vibrational and electronic spectra. Lastly, by turning up the field amplitude well beyond the linear response regime, we present studies of the coupled electronic and ionic response of a molecule to a strong terahertz (THz) pulse. A lofty engineer's dream is to coherently rearrange atoms and chemical bonds at will using an electric field, but a back-of-the-envelope estimate suggests that a field strong enough to coherently rearrange bonds would push electrons through diamond, and attempts to coherently control bonds are known to suffer from intramolecular vibrational redistribution (IVR). Motivated by recent advances in strong terahertz (THz) pulse generation, we have investigated the potential of THz pulses to circumvent these obstacles. Employing TDDFT-Ehrenfest simulations, I discover that strong THz pulses can drive isomerization of the LiNC molecule over barriers greater than 0.2 eV with very low ionization rates and, in the best case, less than 10 meV of residual excess energy. This work points to new possibilities in predictively manipulating chemical bonds in molecules and materials.
Electrical, mechanical, and optical characterization of two-dimensional materials with molecular overlayers [electronic resource]
Keywords: Physics.

A two-dimensional object is entirely surface, with no interior. Its immediate surroundings will accordingly influence its response to electrical, mechanical, and optical stimuli. This thesis explores two different two-dimensional electron systems with molecular overlayers: the surface electron liquid in strontium titanate induced by electrolyte gating, and graphene decorated by ordered adsorbates. Strontium titanate is a band insulator that goes superconducting when doped with remarkably few electrons. By accumulating positive ions at a strontium titanate surface, the electrolyte gating technique can create a two-dimensional electron system with gate-tunable superconductivity. I combine an electrolyte gate with nanopatterned metal-oxide gates to realize the first gate-tunable superconducting weak link in this promising correlated electron system. With the same technique I create a ballistic one-dimensional channel in strontium titanate, and use this channel to perform in-plane tunneling spectroscopy of the superconducting state. Finally, using strontium titanate as a test case, I describe a method to improve mobility of generic electrolyte-gated surface systems by protecting the channel with a thin layer of hexagonal boron nitride. In the second part of this thesis, I use high-resolution atomic force microscopy to reveal a nanotexture that unexpectedly forms on flakes of graphene (and boron nitride) prepared in laboratory air: a "superlattice" of topographic stripes whose period is 4 nm. I argue that these stripes are self-assembled environmental adsorbates, and show that they are responsible for graphene's strongly anisotropic friction--a property previously believed to result from periodic rippling of the graphene sheet itself. In agreement with this self-assembly picture, I demonstrate that the local axis of high friction can be patterned with submicron precision by appropriate mechanical contact. I further show that the stripes produce anisotropic optical response, and I discuss the potential influence of the stripe-superlattice on graphene's electronic properties.
Electromagnetic actuation for ferrofluid-based droplet microfluidics [electronic resource]
Keywords: Electrical Engineering.

Magnetic actuation is an attractive method for microfluidic manipulations, given that strong magnetic fields can be applied on biological materials or fluids with negligible physiological impact. Despite its common use in passive microfluidic systems, there's been limited development for active microfluidic systems, mainly due to the limitations of conventional magnetic sources. Permanent magnets, although magnetically strong, lack switching capability. Strong electromagnets are too large to be integrated in microfluidic systems and small electromagnets generate weak forces. This dissertation demonstrates the use of miniature electropermanent magnets (EPMs) for the first time in microfluidic systems. EPMs combine the switching capability of electromagnets with the strength of permanent magnets into a compact package. In this work, EPMs are integrated with PDMS microfluidic chips and used to manipulate aqueous droplets in an oil-based ferrofluid. A PDMS compatible ferrofluid is presented and used as the continuous phase for the droplet microfluidic system. Using fast EPM switching (under 100 microseconds), magnetic fields of up to 300 mT are generated in close proximity (under 200 micrometers) to the microchannels. On-demand droplet displacement is demonstrated and used for sorting. Displacement velocities up to 300 micrometers/s are demonstrated for 50 micrometer droplets. EPM-driven droplet size modulation is demonstrated and used to control the sizes of droplets during generation. Droplet size increases of up to 44% are demonstrated for a continuous stream and for a single droplet. In addition, cell viability is tested in the ferrofluid-based droplet microfluidic system. Cells are encapsulated in serum-free media droplets, surrounded by the ferrofluid continuous phase, and their viability is tracked over several hours. Results show that cell viability is not significantly affected by encapsulating them in droplets surrounded with ferrofluids with 4.5% concentration of passivated iron oxide nanoparticles. The work presented in this dissertation demonstrates that EPMs are a viable magnetic source for active microfluidic systems. Coupled with ferrofluids, EPM-driven microfluidics could present an attractive new direction for the field and enable new applications.
Electron transport engineering in photon-enhanced thermionic energy converters [electronic resource]
Keywords: Materials Science and Engineering.

A new physical mechanism for direct conversion of solar energy to electricity, called photon-enhanced thermionic emission (PETE), has attracted significant attention as a technology with the promise of very high power conversion efficiencies. The PETE mechanism involves thermionic emission of photoexcited electrons from a high temperature semiconductor cathode, followed by collection at a lower temperature, low work function anode. Due to its combination of photovoltaic and thermal processes, PETE has the potential to achieve efficiencies far above the fundamental limits for single-junction photovoltaics. In this work, two approaches to engineering electron transport in PETE energy converters are presented. A triode device with an electron-transparent gate electrode can be used to overcome space charge limitations that may reduce PETE converter efficiency. Graphene is considered as a candidate gate material, and SEM-based experimental measurements of its transparency to low energy (down to ~5 eV) electrons are reported. Even with an effective gate, the PETE process requires emission of electrons into vacuum, posing significant challenges to realizing efficient converters. To overcome this challenge, a solid-state PETE device structure is proposed, in which the vacuum gap is replaced by semiconductor nanowires that bridge the electrodes. These nanowires provide a path for electron transport while minimizing thermal conduction between the electrodes. Theoretical efficiencies for this device architecture are reported, and the implications of these results for realizing solid-state PETE converters are discussed.
Electronic readout strategies for silicon photomultiplier-based positron emission tomography detectors [electronic resource]
Keywords: Electrical Engineering.

The new generation of positron emission tomography (PET) scanners based on silicon photo-multiplier (SiPM) technology require thousands of readout channels. Due to the complexity of such systems, potential advances in PET such as 3D position sensitive detectors, depth of interaction (DOI) and optimized time of flight (TOF) design have not been fully implemented in commercial scanners. This thesis proposes and tests readout strategies that greatly simplify the readout of advanced PET detectors. A pulse width modulation (PWM) readout strategy that allows for multiplexing without signal degradation is demonstrated on an ultra-high resolution 3D position- ing PET detector. The readout successfully resolves 0.5 mm x 0.5 mm x 1.0 mm LYSO crystals. The effects of multiplexing readout channels of state-of-the-art SiPM arrays on timing resolution are also thoroughly investigated. A TOF DOI detector with sub 300 ps full width half maximum (FWHM) coincidence time resolution is demonstrated with a 32:1 crystal to timing channel multiplexing ratio, and a passive binary positioning scheme. This module is then tested using analog and digital electro-optical readout to enable MR compatibility for a simultaneous PET/MR design. Finally, 3D printed phantoms to test the effects of these novel PET detectors on image quality are introduced. The strategies presented in this thesis significantly simplify PET readout, while increasing its imaging capabilities.
Electrons in quantum confined nanoparticle assemblies [electronic resource]
Keywords: Mechanical Engineering.

Electrostatic capacitors have wide applications in energy storage and power quality management. Compared to electrochemical batteries, they offer higher power densities and superior cycling performances as neither chemical bond formation nor ion transport processes are involved in these devices. Nevertheless, their energy densities need to be improved. One possible way is to replace conventional metallic electrodes by nanoparticle electrodes with respectful electron conductivity and discrete energy levels in the conduction band. Electronic structures of individual quantum dots of the same material can be modified by their sizes. The degree of symmetry loss and surface/volume atom ratio affect the degree of differences in energy levels from those of their bulk form. Mediated by capping ligands, similar-sized colloidal quantum dots can self-assemble into superlattice films or solids. When quantum dots are assembled into monolayers at the water-air interface by Langmuir-Blodgett method, density of dislocations can be reduced by providing mechanical perturbations that facilitate thermal equilibrium. Electronic structures of quantum dot assemblies can be affected by interparticle spacing, sizes, and size variation. They change the degree of electronic coupling, which is in the form of electron wavefunction extension between quantum dots. Electron mobility can be estimated according to the electronic structures of the quantum dot assemblies, and high electron mobility are associated with monodisperse quantum dots with short ligands. Improved capacitance are obtained on capacitors where quantum dots are incorporated. It is possibly attributed to enlarged surface area of quantum dot arrays. Evidence on breakdown voltage improvement suggest potential of storing charges with higher energy density.
Elevated temperature photo-electrochemical water splitting [electronic resource]
Keywords: Materials Science and Engineering.

In order for solar energy to become a major contributor to utility-scale electricity production across the country, it is critical to tackle the inherently intermittent nature and geographically uneven distribution of solar energy. Due to the high energy densities and transportability, solar fuels, such as hydrogen and hydrocarbons, remain the most promising media to store and provide solar energy when and where it is needed. Photo-electrochemical (PEC) water splitting is a particular cost-effective and efficient approach to store solar energy into hydrogen. An overwhelming majority of the work has focused on ambient-temperature PEC cells, as it is believed that the efficiency of photovoltaic devices decreases with increasing temperature. While that the photovoltage generally decreases with temperature due to the rising intrinsic carrier concentration, electrocatalytic activity and minority/majority carrier transport properties in many materials actually improve with temperature. Therefore, it leaves an open question whether it is optimal to operate PEC cells at ambient temperatures. Motivated by that, I have carried out extensive investigation in elevated temperature photo-electrochemical water splitting. In this thesis, I will first discuss the non-trivial effect of temperature on PEC cells in aqueous solutions based on hematite (a-Fe2O3) thin film photoanode, grown by pulsed-laser deposition, as a model system. Building on top of that, I explicitly demonstrate that thermal energy significantly improves the saturation photocurrent in BiVO4 photoanode with only slight loss of the onset potential, the mechanism of which is rigorously attributed to the thermally activated minority carrier hopping. Furthermore, I extend the investigated temperature range even beyond 100 oC where the existing design of PEC cells in aqueous electrolyte are no longer applicable. This is achieved by an innovative design of liquid-free PEC cell with both theoretical analysis and experimental demonstration. Our observation confirms that increasing temperature could be an effective route to activing PEC cells, which contrasts with the prevailing understanding that the decreasing photovoltage dominates the temperature dependence of the energy conversion efficiency.
Elucidating in vitro activation of [FeFe] hydrogenase [electronic resource]
Keywords: Chemical Engineering.

The sustainable production of hydrogen for use as a renewable energy source is a promising alternative to current fossil fuel-based technologies. We seek to exploit nature's prolific biological catalysts, hydrogenases, to replace fossil fuel-based hydrogen production with a carbon-neutral process. [FeFe] hydrogenases are specific and productive enzymes for hydrogen evolution, but the application of these complex proteins is limited by inefficient production methods. Here, we present progress towards a fully defined in vitro hydrogenase maturation system by elucidating the assembly requirements for producing fully active [FeFe] hydrogenase. The in vitro [FeFe] hydrogenase maturation system activates purified Clostridium pasteurianum CpI apoprotein using recombinant Shewanella oneidensis HydE, HydF, and HydG maturases, and exogenous small molecules. However, activation can only be achieved in the presence of a crude and undefined E. coli cell extract. In order to identify the protein(s) in the crude cell extract responsible for maturing the hydrogenase, various fractionation and protein separation techniques were implemented, and candidate proteins were evaluated for apo hydrogenase activation. For instance, prokaryotic frataxin, CyaY, interacts with iron sulfur cluster (isc) proteins and, when complexed with ferric iron fully enables activation of the hydrogenase while reducing the required amount of crude extract from 20% to 2% (v/v). Protease treatments were pursued to further separate protein fractions that retained hydrogenase-activating functionality. A 1hr, 60°C papain treatment was effective in significantly reducing proteomic content while maintaining the protein(s) responsible for activating the hydrogenase. After combining papain treatment with chromatography and LC-MS/MS analysis, the identified proteins suggested that oxidoreductases to play an essential role in donating electrons to the maturases. We present a thioredoxin based electron delivery system to active the first fully defined hydrogenase maturation system, requiring super-physiological thioredoxin concentrations. Finally, Ferrous transporter protein A, FeoA, was determined to be a promising candidate for fully maturing the hydrogenase by providing an electron delivery mechanism for H-cluster assembly and installation at physiological FeoA concentrations. In addition to its putative role as a ferrous iron trafficking protein, we propose a new functionality as an electron donor to satisfy the reduction requirements for the [FeFe] hydrogenase active site. These findings provide a deeper understanding of the mechanism for [FeFe] hydrogenase maturation. Further, this knowledge now enables genetic engineering of E. coli and photosynthetic organisms for the biological production of hydrogen as a clean and renewable alternative fuel.
"Elucidating the role of Casein Kinase 2 in regulating Glioblastoma Metastatic Potential"
Keywords:  Department of Biology
biology
cancer
glioblastoma
CK2
Thesis

Glioblastoma (GBM) is the most common malignant primary brain tumor comprising 40-50% of all adult cases. Despite standard treatment of care involving surgical resection followed by radiotherapy with chemotherapy, the median overall survival rate remains dismal at 14-15 months. The major barrier to effective treatment is GBM tumor metastasis, which enables tumors cells to have enhanced migratory and invasive potential. Recent work has demonstrated a link between Casein Kinase 2 and GBM tumorigenesis, indicating that CK2 modulation could be a promising therapeutic target for GBM. However, no one has studied the role of CK2 in GBM tumor metastatic potential, or the molecular mechanisms underlying tumor cell invasion and migration characteristic of the epithelial to mesenchymal transition (EMT). Here, we investigate the role of CK2 in GBM migration and invasion by using the wound-healing assay, trans well assay, and western blot analysis. We show that CK2 inhibition via CX-4945, a CK2 specific kinase inhibitor, decreases cell invasive potential, and this finding is recapitulated in two immortalized GBM cell lines. Additionally, we show that CK2 upregulation increases expression of mesenchymal markers, suggesting a potential role between CK2 expression, GBM invasiveness, and the EMT pathway. Furthermore, the data represent a major step in elucidating the molecular mechanisms of tumor metastasis, and help identify CK2 as a promising therapeutic target to more effectively treat GBM tumor recurrence.
Embedded entropy concept for fluid dynamic simulations with discontinuous Galerkin scheme [electronic resource]
Keywords: Mechanical Engineering.

The Discontinuous Galerkin (DG) method represents an attractive simulation technique for computational fluid dynamics. Compared to conventional finite-difference and finite-volume methods, the DG method enables the high-order discretization on unstructured meshes, utilizes a compact discretization, and is well suited for advanced refinement strategies. However, it has been recognized that high-order DG approximations suffer robustness when applied to solving nonlinear conservation laws. These nonlinear numerical instabilities arise at physical discontinuities and numerically under-resolved flow-field features. By addressing these issues, this thesis work is concerned with the development of a realizable and stable high-order DG method for application to complex flows, involving discontinuities, shocks, and chemical reaction. An entropy-bounded discontinuous Galerkin (EBDG) scheme is developed, and the scheme is proven to preserve physical realizability of flow variables, such as the positivity of pressure and density, the boundedness of transported scalars and the boundedness of minimum entropy. In numerical tests, the EBDG scheme shows superb numerical stability and capability of capturing strong shock waves, as well as preservation of high-order accuracy for smooth solutions. The EBDG scheme is further augmented with a shock indicator and an artificial viscosity method to eliminate the Gibbs phenomenon triggered around shock discontinuities. The numerical framework developed based on the EBDG scheme is applied to study detonation initiation by shock-wall interaction. Specific focus of this study is on characterizing the role of Mach shock reflection on ignition and initiation processes. Furthermore, the accuracy and computational cost of the DG solver is assessed against a state-of-the-art finite volume solver in the applications to direct numerical simulations and large-eddy simulations of decaying turbulence. The comparison shows that on regular hexahedral meshes the finite volume scheme only requires one third of flops needed for the DG scheme at the same level of accuracy, while on tetrahedral meshes the DG scheme outperforms the finite volume scheme due to its capability of preserving the higher-order accuracy on unstructured and irregular meshes.