The ARR4 gene from Saccharomyces cerevisiae was highly homological with E. coli arsA. The defective nucleotide-binding domain of ARR4[G30R] exhibited negative dominance from the growth curve experiment, showing that ARR4 protein might act as a dimer in vivo. On the nonreducing gel, the purified 40 kDa ARR4 presented as monomer, dimer and oligomer conformational states. Besides, the chemical cross-linking experiments confirmed the positional size of dimeric ARR4. The metal ions of Co2+, Sb3+, As3+ and As5+ have not effect on the ATPase activity and ARR4 oligomerization. ARR4 exhibit a low level of Mg2+-ATPase activity in the range of 50-70 and 100-120 nmol/min/mg respectively as estimated by phosphate released and NADH-coupled assay. The maximal activity was obtained at a ratio of ATP:Mg2+ of 2:1 and the ATPase activity of ARR4[G30R] was about 50% of that of the ARR4 from both ATPase assays. In the presence of ATP or Mg2+, ARR4 has similar ratios of dimer and monomer. When incubated with Mg2+-ATP, ARR4 tended to form more dimer than with ATP and Mg2+ individually. ARR4[G30R] exhibited less dimer formation. Mixing ARR4 and ARR4[G30R] at a constant total protein concentration with different molar ratios (1:1, 1:2 and 1:4), a near linear relationship of activity versus amount of the ARR4 protein was observed. This observation suggests that ATP hydrolysis takes places in one ATP binding site independent of the other site of NBD. The proportional ATPase activities were consistent with the ratios of ARR4-ARR4[G30R] dimerization on the nonreducing gels. In conclusion, the conformational changes induced by Mg2+-ATP is related to the dimerization of ARR4 and both its NBDs would hydrolyze ATP independently.

Starting from a classical mechanical model, a set of Langevin equations for the surface diffusion of adsorbed molecules is developed. In contrast to previous work, these Langevin equations take full account of the rotations and internal vibrations of the adsorbed molecule. These equations are then applied to a stiff dimer diffusing in one dimension, and the results compared with previous calculations for the same system. It is shown that the modifications in our new approach give significantly different results than this previous calculation, and therefore must be taken into account in future calculations for systems of this kind. Next a new approximation method is developed by assuming that the motion of the molecule is confined to the lowest energy path between adsorption sites. This method is applicable to an arbitrarily complex molecule, and is complimentary to the first method, in that it can account for deformation of the molecule by the surface but not the internal vibrations of the molecule (whereas the first method accounts for internal vibrations but not deformation). This approximation method is then applied to a flexible dimer in two dimensions (one dimension along the surface and one perpendicular). The results are discussed and compared with those of the stiff dimer in one dimension, explaining and clarifying the difference between our results and those of previous calculations.

Driven by exciting new research and applications, top-down and bottom-up fabrication techniques are producing ever more intricate, reproducible, plasmonic nano-architectures with gaps and junctions approaching the single nanometre and atomic scales. Such atomic-sized features promote the intersection of physics, chemistry and biology in plasmonics. Consequently, understanding light-matter interactions in such closely spaced, electromagnetically coupled, metallic nanosystems is of vital importance to a tremendous variety of current and future nanophotonic technologies. This thesis describes the first dynamically controlled, optically broadband, experimental investigations of light-driven plasmonic coupling between two metal nanostructures with sub-nanometre separation. A new experimental apparatus and nanosystem alignment technique was developed to enable the required sub-nanometre inter-nanoparticle geometry to be created and probed. Two conducting atomic force microscopy tips with nanoparticle functionalised apices are brought into nanoscale `tip-to-tip' axial alignment with dynamically-controlled spacing and ultra-wide optical access. Resonant electrical parametric mixing, created by oscillating the electromechanically coupled tips, is utilised to extract an electronic signal due to nanoscale changes in inter-tip position. Experimental results match theory confirming the viability of the technique. By functionalising the tip apices, this unique multi-functional observation platform allows the plasmonic response of nanoparticle dimers with sub-nanometre separations to be characterised. By simultaneously capturing both the electrical and optical properties of tip-mounted gold nanoparticles with controllable sub-nanometre separation, the first evidence for the quantum regime of optically driven tunnelling plasmonics is revealed in unprecedented detail. It is demonstrated that quantum mechanical effects are critically important at approximately the 0.3 nm scale where spatially non-local tunnelling plasmonics controls the optical response. All observed phenomena are in good agreement with a recently developed quantum-corrected model of plasmonic systems. The findings imply that tunnelling establishes a quantum limit for plasmonic field enhancement and confinement. Additionally, the work suggests the highly enhanced local density of photonic states in nanoscale cavities could enable coherent plasmon-exciton coupling. This thesis prompts new experimental and theoretical investigations into quantum-domain plasmonic systems, and impacts the future of nanoplasmonic device engineering, nanoscale photochemistry and plasmon-mediated electron tunnelling.

Bacterial cell division relies on the cell division septum to form at the mid-cell position. In gram negative bacteria, this is mediated by three proteins, MinC, MinD and MinE. Together these proteins interact with each other and the membrane in a dynamic, oscillating process which prevents cell division septum formation at the cell poles. The early phase of this process involves MinD binding to the membrane, which is triggered upon binding of ATP. Subsequent interactions with MinE result in stimulation of the ATPase activity of MinD. After hydrolysis, MinD is released from the membrane and diffuses to a new binding site. Many in silico models have been constructed of the Min system in an attempt to describe its self-organizing behaviour. A limitation of these models is that, in order to prevent rapid re-binding of MinD to the membrane after hydrolysis of ATP, the exchange of bound ADP for ATP is assumed to be a slow process, on the order of 1/s . In order to provide experimental evidence of the rate of nucleotide binding, we performed a series of triple-resonance NMR experiments to complete a partial assignment of backbone atom resonances, which required the application of deuterium labelling and amino acid-specific selective unlabelling. After the introduction of ATP, it was discovered that no dimerization had been induced, in contrast with existing literature. It was proposed that MinD from N. gonorrhoeae only forms a dimer in the presence of a membrane, while literature with MinD from E. coli shows it does not have this requirement. Interestingly while dimerization had not been induced, there was a persistent population of dimeric species even in the absence of nucleotide. This was discovered to be the result of disulfide formation, likely an artifact of established purification protocols. Binding of both ADP and ATP to MinD were studied by titration using NMR, with the relative affinity of both nucleotides to MinD being indistinguishable. By analyzing peak coalescence in the half-bound condition, a maximum rate was determined for nucleotide binding, with the lifetime being on the order of 170ms. Results from this experiment support models requiring a slow nucleotide binding step, and help enhance understanding of how Min proteins sustain oscillations required for normal cell division.

Many who study complex systems believe that the complexity we observe in the world around us is frequently the product of a large number of interactions between components following a simple rule. However, the task of discerning the rule governing the evolution of any given system is often quite difficult, requiring intuition, guesswork, and a great deal of expertise in that domain. To circumvent this issue, researchers have considered the inverse problem where one searches among many candidate rules to reveal those producing interesting behavior. This approach has its own challenges because the search space grows exponentially and interesting behavior is rare and difficult to rigorously define. Therefore, the contribution of this work includes tools and techniques for searching for dimer automaton rules that exhibit self-organization (the transformation of disorder into structure in the absence of centralized control). Dimer automata are simple, discrete, asynchronous rewriting systems that operate over the edges of an arbitrary graph. Specifically, these contributions include a number of novel, surprising, and useful applications of dimer automata, practical methods for measuring self-organization, advanced techniques for searching for dimer automaton rules, and two efficient GPU parallelizations of dimer automata to make searching and simulation more tractable. / Ph. D.

No description available.

This dissertation consists of three major studies. The first study, described in Chapter 3, focuses on the experimental work we carried out; experimental study of the electronic transition dipole moment matrix elements (TDMM) for the and electronic transitions of the sodium dimer molecule. Here we obtained the electronic transition dipole moments through Autler-Townes and resolved fluorescence spectroscopy and compared them to the theory. The second study, described in Chapter 4, is on sodium dimer ion-pair states. In this work, we calculated the radiative lifetimes and electronic transition dipole moments between Na2 ion-pair states ( , , , ) and state. This study was published in 2015. The last study, described in Chapter 5, is the total lifetime (bound-bound plus bound-free) and transition dipole moment calculations of the ion-pair electronic states, , of the lithium dimer molecule. / Physics

No description available.

A água, conhecida como solvente universal, participa da maioria das reações químicas e composições biológicas, tem importância vital em nosso planeta, tornando a vida como conhecemos inconcebível sem a sua presença. Tais propriedades advêm da forma como as moléculas interagem entre si, e a principal ligação química existente é a ligação de hidrogênio. Portanto, compreender como ela acontece e ser capaz de manipulá-la pode ser considerada uma importante técnica na busca de novos comportamentos. Esta dissertação visa compreender como o campo elétrico nas suas variantes: direção, sentido e intensidade podem afetar a água. Sendo tal estudo realizado através de cálculos utilizando métodos de química quântica: Teoria do Funcional da Densidade e a Teoria de Perturbação Moller-Plesset de segunda ordem. Como resultado obteve-se que quando o campo elétrico é aplicado em uma direção e sentido fora do plano da ligação de hidrogênio, a estrutura inicial tende a se rearranjar produzindo uma estrutura mais fracamente ligada do que a ordinária. Quando aplicamos o campo no plano da ligação de hidrogênio, temos resultados mais pronunciados, sendo que, se o sentido for : Doador -> Receptor a estrutura resultante estará mais fracamente ligada e se o sentido for Receptor -> Doador a estrutura produzida estará mais fortemente ligada. Os resultados obtidos mostram também que tais mudanças acontecem principalmente devido a alterações eletrostáticas, como mudança na densidade de carga da ligação de hidrogênio. Também confirmou-se um ponto crítico no campo 0,15 V/Å, como sugerido na literatura. Esta singularidade foi atribuída neste trabalho à uma transição estrutural. O campo também modificou a importância das interações secundárias, principalmente entre os átomos de oxigênio, e ao desligá-lo, o sistema tende a voltar ao estado inicial. / The water is know as the universal solvent, part of most chemical reactions and biological compositions, it is vitally important to our planet, making life as we know it inconceivable without its presence. These properties arise from how the molecules interact, and the main existing chemical link is the hydrogen bond. Therefore, to understand how this happens and be able to manipulate it can be considered an important technique in the search for new behaviors. Thus, this paper aims to understand how the electric field in its variants: direction, sense and intensity can affect the water. This study is undertaken through calculations using quantum chemistry methods: Density Functional Theory and Moller-Plesset Perturbation Theory to Second Order. As a result was found that when the electric field is applied in direction and sense out of the plane of the hydrogen bond, the initial structure tends to rearrange itself to produce a more loosely bound than the ordinary. When the electric field is applied in the hydrogen bond plane, the have results obtained are more pronounced. Sense is: Donor -> Receiver initial structure will be more loosely connected and that when the sense is Receiver -> Donor initial structure will be tightly linked. Our results also show that such changes occur mainly due to electrostatic changes, mainly in the change in the charge density of hydrogen bond. It was also confirmed a critical point in the field 0, 15 V / Å, as suggested by Vegiri. This was attributed to a structural transition. The field also changed the importance of secondary interactions, especially between the oxygen atoms. And when the field is shutdown the system tends back to its to initial structure.

The aim of this thesis is to generalise Reid's recipe as first defined by Reid for $G-\Hilb(\mathbb{C}^3)$ ($G$ a finite abelian subgroup of $\SL(3, \mathbb{C})$) to the setting of consistent dimer models. We study the $\theta$-stable representations of a quiver $Q$ with relations $\mathcal{R}$ dual to a consistent dimer model $\Gamma$ in order to introduce a well-defined recipe that marks interior lattice points and interior line segments of a cross-section of the toric fan $\Sigma$ of the moduli space $\mathcal{M}_A(\theta)$ with vertices of $Q$, where $A=\mathbb{C}Q/\langle \mathcal{R}\rangle$. After analysing the behaviour of 'meandering walks' on a consistent dimer model $\Gamma$ and assuming two technical conjectures, we introduce an algorithm - the arrow contraction algorithm - that allows us to produce new consistent dimer models from old. This algorithm could be used in the future to show that in doing combinatorial Reid's recipe, every vertex of $Q$ appears 'once' and that combinatorial Reid's recipe encodes the relations of the tautological line bundles of $\mathcal{M}_A(\theta)$ in $\Pic(\mathcal{M}_A(\theta))$.