A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by Quantum mechanics/Molecular mechanics studies

The Ran GTPase protein is a guanine nucleotide-binding protein (GNBP) with an acknowledged profile in cancer onset, progression and metastases. The complex mechanism adopted by GNBPs in exchanging GDP for GTP is an intriguing process and crucial for Ran viability. The successful completion of the process is a fundamental aspect of propagating downstream signalling events. QM/MM molecular dynamics simulations were employed in this study to provide a deeper mechanistic understanding of the initiation of nucleotide exchange in Ran. Results indicate significant disruption of the metal-binding site upon interaction with RCC1 (the Ran guanine nucleotide exchange factor), overall culminating in the prominent shift of the divalent magnesium ion. The observed ion drifting is reasoned to occur as a consequence of the complex formation between Ran and RCC1 and is postulated to be a critical factor in the exchange process adopted by Ran. This is the first report to observe and detail such intricate dynamics for a protein in Ras superfamily.

Positive Encounters: An Investigative Study on the Effects of Interactions between Cations and Quantum Dots

Thesis (Ph.D.)--University of Washington, 2016-06

Memory effects and geometrical considerations in open quantum systems

This thesis discusses memory effects in open quantum systems with an emphasis on the Breuer, Laine, Piilo (BLP) measure of non-Markovianity. It is shown how the calculation of the measure can be simplifed and how quantum information protocols can bene t from memory e ects. The superdense coding protocol is used as an example of this. The quantum Zeno effect will also be studied from the point of view of memory e ects. Finally the geometric ideas used in simplifying the calculation of the BLP measure are applied in studying the amount of resources needed for detecting bipartite quantum correlations. It is shown that to decide without prior information if an unknown quantum state is entangled or not, an informationally complete measurement is required. The first part of the thesis contains an introduction to the theoretical ideas such as quantum states, closed and open quantum systems and necessary mathematical tools. The theory is then applied in the second part of the thesis as the results obtained in the original publications I-VI are presented and discussed.

EXCITON ENGINEERING THROUGH TUNALBLE FLUORESCENT QUANTUM DEFECTS

This thesis demonstrates exciton engineering in semiconducting single-walled carbon nanotubes through tunable fluorescent quantum defects. By introducing different functional moieties on the sp2 lattice of carbon nanotubes, the nanotube photoluminescence is systematically tuned over 68 meV in the second near-infrared window. This new class of quantum emitters is enabled by a new chemistry that allows covalent attachment of alkyl/aryl functional groups from their iodide precursors in aqueous solution. Using aminoaryl quantum defects, we show that the pH and temperature of complex fluids can be optically measured through defect photoluminescence that encodes the local environment information. Furthermore, defect-bound trions, which are electron-hole-electron tri-carrier quasi-particles, are observed in alkylated single-walled carbon nanotubes at room temperature with surprisingly high photoluminescence brightness. Collectively, the emission from defect-bound excitons and trions in (6,5)-single walled carbon nanotubes is 18-fold brighter than that of the native exciton. These findings pave the way to chemical tailoring of the electronic and optical properties of carbon nanostructures with fluorescent quantum defects and may find applications in optoelectronics and bioimaging.

Functional surface chemistry of carbon-based nanostructures

The recently discovered abilities to synthesize single-walled carbon nanotubes and prepare single layer graphene have spurred interest in these sp2-bonded carbon nanostructures. In particular, studies of their potential use in electronic devices are many as silicon integrated circuits are encountering processing limitations, quantum effects, and thermal management issues due to rapid device scaling. Nanotube and graphene implementation in devices does come with significant hurdles itself. Among these issues are the ability to dope these materials and understanding what influences defects have on expected properties. Because these nanostructures are entirely all-surface, with every atom exposed to ambient, introduction of defects and doping by chemical means is expected to be an effective route for addressing these issues. Raman spectroscopy has been a proven characterization method for understanding vibrational and even electronic structure of graphene, nanotubes, and graphite, especially when combined with electrical measurements, due to a wealth of information contained in each spectrum. In Chapter 1, a discussion of the electronic structure of graphene is presented. This outlines the foundation for all sp2-bonded carbon electronic properties and is easily extended to carbon nanotubes. Motivation for why these materials are of interest is readily gained. Chapter 2 presents various synthesis/preparation methods for both nanotubes and graphene, discusses fabrication techniques for making devices, and describes characterization methods such as electrical measurements as well as static and time-resolved Raman spectroscopy. Chapter 3 outlines changes in the Raman spectra of individual metallic single-walled carbon nantoubes (SWNTs) upon sidewall covalent bond formation. It is observed that the initial degree of disorder has a strong influence on covalent sidewall functionalization which has implications on developing electronically selective covalent chemistries and assessing their selectivity in separating metallic and semiconducting SWNTs. Chapter 4 describes how optical phonon population extinction lifetime is affected by covalent functionalization and doping and includes discussions on static Raman linewidths. Increasing defect concentration is shown to decrease G-band phonon population lifetime and increase G-band linewidth. Doping only increases G-band linewidth, leaving non-equilibrium population decay rate unaffected. Phonon mediated electron scattering is especially strong in nanotubes making optical phonon decay of interest for device applications. Optical phonon decay also has implications on device thermal management. Chapter 5 treats doping of graphene showing ambient air can lead to inadvertent Fermi level shifts which exemplifies the sensitivity that sp2-bonded carbon nanostructures have to chemical doping through sidewall adsorption. Removal of this doping allows for an investigation of electron-phonon coupling dependence on temperature, also of interest for devices operating above room temperature. Finally, in Chapter 6, utilizing the information obtained in previous chapters, single carbon nanotube diodes are fabricated and characterized. Electrical performance shows these diodes are nearly ideal and photovoltaic response yields 1.4 nA and 205 mV of short circuit current and open circuit voltage from a single nanotube device. A summary and discussion of future directions in Chapter 7 concludes my work.

Probing the interactions between ionic liquids and water: experimental and quantum chemical approach

For an adequate choice or design of ionic liquids, the knowledge of their interaction with other solutes and solvents is an essential feature for predicting the reactivity and selectivity of systems involving these compounds. In this work, the activity coefficient of water in several imidazolium-based ionic liquids with the common cation 1-butyl-3-methylimidazolium was measured at 298.2 K. To contribute to a deeper insight into the interaction between ionic liquids and water, COSMO-RS was used to predict the activity coefficient of water in the studied ionic liquids along with the excess enthalpies. The results showed good agreement between experimental and predicted activity coefficient of water in ionic liquids and that the interaction of water and ionic liquids was strongly influenced by the hydrogen bonding of the anion with water. Accordingly, the intensity of interaction of the anions with water can be ranked as the following: [CF3SO3](-) < [SCN](-) < [TFA](-) < Br(-) < [TOS](-) < Cl(-) < [CH3SO3](-) [DMP](-) < [Ac](-). In addition, fluorination and aromatization of anions are shown to reduce their interaction with water. The effect of temperature on the activity coefficient of water at infinite dilution was measured by inverse gas chromatography and predicted by COSMO-RS. Further analysis based on COSMO-RS provided information on the nature of hydrogen bonding between water and anion as well as the possibility of anion-water complex formation.

Ab Initio Quantum Chemical Studies on Neutral-Radical Reactions of Ethynyl (C2H) and Cyano (CN) with Unsaturated Hydrocarbons

An Ab Initio/RRKM study of the reaction mechanism and product branching ratios of neutral-radical ethynyl (C2H) and cyano (CN) radical species with unsaturated hydrocarbons is performed. The reactions studied apply to cold conditions such as planetary atmospheres including Titan, the Interstellar Medium (ISM), icy bodies and molecular clouds. The reactions of C2H and CN additions to gaseous unsaturated hydrocarbons are an active area of study. NASA’s Cassini/Huygens mission found a high concentration of C2H and CN from photolysis of ethyne (C2H2) and hydrogen cyanide (HCN), respectively, in the organic haze layers of the atmosphere of Titan. The reactions involved in the atmospheric chemistry of Titan lead to a vast array of larger, more complex intermediates and products and may also serve as a chemical model of Earth’s primordial atmospheric conditions. The C2H and CN additions are rapid and exothermic, and often occur barrierlessly to various carbon sites of unsaturated hydrocarbons. The reaction mechanism is proposed on the basis of the resulting potential energy surface (PES) that includes all the possible intermediates and transition states that can occur, and all the products that lie on the surface. The B3LYP/6-311g(d,p) level of theory is employed to determine optimized electronic structures, moments of inertia, vibrational frequencies, and zero-point energy. They are followed by single point higher-level CCSD(T)/cc-vtz calculations, including extrapolations to complete basis sets (CBS) of the reactants and products. A microcanonical RRKM study predicts single-collision (zero-pressure limit) rate constants of all reaction paths on the potential energy surface, which is then used to compute the branching ratios of the products that result. These theoretical calculations are conducted either jointly or in parallel to experimental work to elucidate the chemical composition of Titan’s atmosphere, the ISM, and cold celestial bodies.

The case for quantum key distribution

Quantum key distribution (QKD) promises secure key agreement by using quantum mechanical systems. We argue that QKD will be an important part of future cryptographic infrastructures. It can provide long-term confidentiality for encrypted information without reliance on computational assumptions. Although QKD still requires authentication to prevent man-in-the-middle attacks, it can make use of either information-theoretically secure symmetric key authentication or computationally secure public key authentication: even when using public key authentication, we argue that QKD still offers stronger security than classical key agreement.

Is there something quantum-like about the human mental lexicon?

Following an early claim by Nelson & McEvoy suggesting that word associations can display `spooky action at a distance behaviour', a serious investigation of the potentially quantum nature of such associations is currently underway. In this paper quantum theory is proposed as a framework suitable for modelling the mental lexicon, specifically the results obtained from both intralist and extralist word association experiments. Some initial models exploring this hypothesis are discussed, and they appear to be capable of substantial agreement with pre-existing experimental data. The paper concludes with a discussion of some experiments that will be performed in order to test these models.

Calculation of habitable dwelling surfaces : an empirical analysis for the agglomerations of Munich and Sydney

In many countries the calculation of habitable dwelling surface is characterised by a chaotic variety of calculation variants hardly comprehensible for the end user - sometimes not even reproducible for the expert. Therefore dossiers were analysed on the basis of a random choice in order to determine the method according to which the habitable dwelling surface was measured and to find out wether customers can scrutinize the calculations. The paper compares Sydney and Munich, where in both cases property prices are situated at the high end of the market

Theoretical and numerical investigation of plasmon nanofocusing in metallic tapered rods and grooves

Effective focusing of electromagnetic (EM) energy to nanoscale regions is one of the major challenges in nano-photonics and plasmonics. The strong localization of the optical energy into regions much smaller than allowed by the diffraction limit, also called nanofocusing, offers promising applications in nano-sensor technology, nanofabrication, near-field optics or spectroscopy. One of the most promising solutions to the problem of efficient nanofocusing is related to surface plasmon propagation in metallic structures. Metallic tapered rods, commonly used as probes in near field microscopy and spectroscopy, are of a particular interest. They can provide very strong EM field enhancement at the tip due to surface plasmons (SP’s) propagating towards the tip of the tapered metal rod. A large number of studies have been devoted to the manufacturing process of tapered rods or tapered fibers coated by a metal film. On the other hand, structures such as metallic V-grooves or metal wedges can also provide strong electric field enhancements but manufacturing of these structures is still a challenge. It has been shown, however, that the attainable electric field enhancement at the apex in the V-groove is higher than at the tip of a metal tapered rod when the dissipation level in the metal is strong. Metallic V-grooves also have very promising characteristics as plasmonic waveguides. This thesis will present a thorough theoretical and numerical investigation of nanofocusing during plasmon propagation along a metal tapered rod and into a metallic V-groove. Optimal structural parameters including optimal taper angle, taper length and shape of the taper are determined in order to achieve maximum field enhancement factors at the tip of the nanofocusing structure. An analytical investigation of plasmon nanofocusing by metal tapered rods is carried out by means of the geometric optics approximation (GOA), which is also called adiabatic nanofocusing. However, GOA is applicable only for analysing tapered structures with small taper angles and without considering a terminating tip structure in order to neglect reflections. Rigorous numerical methods are employed for analysing non-adiabatic nanofocusing, by tapered rod and V-grooves with larger taper angles and with a rounded tip. These structures cannot be studied by analytical methods due to the presence of reflected waves from the taper section, the tip and also from (artificial) computational boundaries. A new method is introduced to combine the advantages of GOA and rigorous numerical methods in order to reduce significantly the use of computational resources and yet achieve accurate results for the analysis of large tapered structures, within reasonable calculation time. Detailed comparison between GOA and rigorous numerical methods will be carried out in order to find the critical taper angle of the tapered structures at which GOA is still applicable. It will be demonstrated that optimal taper angles, at which maximum field enhancements occur, coincide with the critical angles, at which GOA is still applicable. It will be shown that the applicability of GOA can be substantially expanded to include structures which could be analysed previously by numerical methods only. The influence of the rounded tip, the taper angle and the role of dissipation onto the plasmon field distribution along the tapered rod and near the tip will be analysed analytically and numerically in detail. It will be demonstrated that electric field enhancement factors of up to ~ 2500 within nanoscale regions are predicted. These are sufficient, for instance, to detect single molecules using surface enhanced Raman spectroscopy (SERS) with the tip of a tapered rod, an approach also known as tip enhanced Raman spectroscopy or TERS. The results obtained in this project will be important for applications for which strong local field enhancement factors are crucial for the performance of devices such as near field microscopes or spectroscopy. The optimal design of nanofocusing structures, at which the delivery of electromagnetic energy to the nanometer region is most efficient, will lead to new applications in near field sensors, near field measuring technology, or generation of nanometer sized energy sources. This includes: applications in tip enhanced Raman spectroscopy (TERS); manipulation of nanoparticles and molecules; efficient coupling of optical energy into and out of plasmonic circuits; second harmonic generation in non-linear optics; or delivery of energy to quantum dots, for instance, for quantum computations.

Context-based chemistry : creating opportunities for fluid transitions between concepts and context

Nationally and internationally, context-based programs have been implemented in an attempt to engage students in chemistry through connecting the canonical science with the real-world. In Queensland, a context-based approach to chemistry was trialled in selected schools from 2002 but there is little research that investigates how students learn in a context-based setting. This paper presents one significant finding from an ethnographic study that explored the learning that occurred in an 11th grade context-based chemistry classroom in Queensland. The study found that by providing students with the opportunity to write, fluid transitions (or to-ing and fro-ing) between concepts and context were an outcome of context-based learning.