Deformed-jellium model for the fission of multiply charged metal clusters

A deformed-jellium model is used to calculate the fission barrier height of positive doubly charged sodium clusters within an extended Thomas-Fermi approximation. The fissioning cluster is continuously deformed from the parent configuration until it splits into two fragments. Although the shape of the fission barrier obviously depends on the parametrization of the fission path, we have found that remarkably, the maximum of the barrier corresponds to a configuration in which the emerging fragments are already formed and rather well apart. The implication of this finding in the calculation of critical numbers for fission is illustrated in the case of multiply charged Na clusters.

Effective t-J model Hamiltonian parameters of monolayered cuprate superconductors from ab initio electronic structure calculations

The magnetic coupling constant of selected cuprate superconductor parent compounds has been determined by means of embedded cluster model and periodic calculations carried out at the same level of theory. The agreement between both approaches validates the cluster model. This model is subsequently employed in state-of-the-art configuration interaction calculations aimed to obtain accurate values of the magnetic coupling constant and hopping integral for a series of superconducting cuprates. Likewise, a systematic study of the performance of different ab initio explicitly correlated wave function methods and of several density functional approaches is presented. The accurate determination of the parameters of the t-J Hamiltonian has several consequences. First, it suggests that the appearance of high-Tc superconductivity in existing monolayered cuprates occurs with J/t in the 0.20¿0.35 regime. Second, J/t=0.20 is predicted to be the threshold for the existence of superconductivity and, third, a simple and accurate relationship between the critical temperatures at optimum doping and these parameters is found. However, this quantitative electronic structure versus Tc relationship is only found when both J and t are obtained at the most accurate level of theory.

Nuclear incompressibility in the quasilocal density functional theory

We explore the ability of the recently established quasilocal density functional theory for describing the isoscalar giant monopole resonance. Within this theory we use the scaling approach and perform constrained calculations for obtaining the cubic and inverse energy weighted moments (sum rules) of the RPA strength. The meaning of the sum rule approach in this case is discussed. Numerical calculations are carried out using Gogny forces and an excellent agreement is found with HF+RPA results previously reported in literature. The nuclear matter compression modulus predicted in our model lies in the range 210230 MeV which agrees with earlier findings. The information provided by the sum rule approach in the case of nuclei near the neutron drip line is also discussed.

Not the outside but the inside matters : functional analysis of Capricious and Tartan during Drosophila tracheal morphogenesis

The tubular structures, which transport essential gases, liquids, or cells from one site to another, are shared among various divergent organisms. These highly organized tubular networks include lung, kidney, vasculature and mammary gland in mammals as well as trachea and salivary gland in Drosophila melanogaster. Many questions regarding the tubular morphogenesis cannot be addressed sufficiently by investigating the mammalian organs because their structures are extremely complex and therefore, systematic analyses of genetic and cellular programs guiding the development is not possible. In contrast, the Drosophila tracheal development provides an excellent model system since many molecular markers and powerful tools for genetic manipulations are available. Two mechanisms were shown to be important for the outgrowth of tracheal cells: the FGF signaling pathway and the interaction between the tracheal cells and the surrounding mesodermal cells. The Drosophila FGF ligand encoded by branchless (bnl) is localized in groups of cells near tracheal metameres. The tracheal cells expressing the FGF receptor breathless (btl) respond to these sources of FGF ligand and extend towards them. However, this FGF signaling pathway is not sufficient for the formation of continuous dorsal trunk, the only muticellular tube in tracheal system. Recently, it was found out that single mesodermal cells called bridge-cells are essential for the formation of continuous dorsal trunk as they direct the outgrowth of dorsal trunk cells towards the correct targets. The results in this PhD thesis demonstrate that a cell adhesion molecule Capricious (Caps), which is specifically localized on the surface of bridge-cells, plays an essential role in guiding the outgrowing dorsal trunk cells towards their correct targets. When caps is lacking, some bridge-cells cannot stretch properly towards the adjacent posterior tracheal metameres and thus fail to interconnect the juxtaposing dorsal trunk cells. Consequently, discontinuous dorsal trunks containing interruptions at several positions are formed. On the other hand, when caps is ectopically expressed in the mesodermal cells through a twi-GAL4 driver, these mesodermal cells acquire a guidance function through ectopic caps and misguide the outgrowing dorsal trunk cells in abnormal directions. As a result, disconnected dorsal trunks are formed. These loss- and gain-of-function studies suggest that Caps presumably establishes the cell-to-cell contact between the bridge-cells and the tracheal cells and thereby mediates directly the guidance function of bridge-cells. The most similar protein known to Caps is another cell adhesion molecule called Tartan (Trn). Interestingly, trn is expressed in the mesodermal cells but not in the bridge-cells. When trn is lacking, the outgrowth of not only the dorsal trunks but also the lateral trunks are disrupted. However, in contrast to the ectopic expression of caps, the misexpression of trn does not affect tracheal development. Whereas Trn requires only its extracellular domain to mediate the matrix function, Caps requires both its extracellular and intracellular domains to function as a guidance molecule in the bridge-cells. These observations suggest that Trn functions differently from Caps during tracheal morphogenesis. Presumably, Trn mediates a matrix function of mesodermal cells, which support the tracheal cells to extend efficiently through the surrounding mesodermal tissue. In order to determine which domains dictate the functional specificity of Caps, two hybrid proteins CapsEdTrnId, which contains the Caps extracellular domain and the Trn intracellular domain, and TrnEdCapsId, which consists of the Trn extracellular domain and the Caps intracellular domain, were constructed. Gain of function and rescue experiments with these hybrid proteins suggest on one hand that the extracellular domains of Caps and Trn are functionally redundant and on the other hand that the intracellular domain dictates the functional specificity of Caps. In order to identify putative interactors of Caps, yeast two-hybrid screening was performed. An in vivo interaction assay in yeast suggests that Ras64B interacts specifically with the Caps intracellular domain. In addition, an in vitro binding assay reveals a direct interaction between an inactive form of Ras64B and the Caps intracellular domain. ras64B, which encodes a small GTPase, is expressed in the mesodermal cells concurrently as caps. Finally, a gain-of-function study with the constitutively active Ras64B suggests that Ras64B presumably functions downstream of Caps. All these results suggest consistently that the small GTPase Ras64B binds specifically to the Caps intracellular domain and may thereby mediate the guidance function of Caps.

Development and applications of density matrix functional theory of generalized Hubbard Models

In dieser Doktorarbeit wird eine akkurate Methode zur Bestimmung von Grundzustandseigenschaften stark korrelierter Elektronen im Rahmen von Gittermodellen entwickelt und angewandt. In der Dichtematrix-Funktional-Theorie (LDFT, vom englischen lattice density functional theory) ist die Ein-Teilchen-Dichtematrix γ die fundamentale Variable. Auf der Basis eines verallgemeinerten Hohenberg-Kohn-Theorems ergibt sich die Grundzustandsenergie Egs[γgs] = min° E[γ] durch die Minimierung des Energiefunktionals E[γ] bezüglich aller physikalischer bzw. repräsentativer γ. Das Energiefunktional kann in zwei Beiträge aufgeteilt werden: Das Funktional der kinetischen Energie T[γ], dessen lineare Abhängigkeit von γ genau bekannt ist, und das Funktional der Korrelationsenergie W[γ], dessen Abhängigkeit von γ nicht explizit bekannt ist. Das Auffinden präziser Näherungen für W[γ] stellt die tatsächliche Herausforderung dieser These dar. Einem Teil dieser Arbeit liegen vorausgegangene Studien zu Grunde, in denen eine Näherung des Funktionals W[γ] für das Hubbardmodell, basierend auf Skalierungshypothesen und exakten analytischen Ergebnissen für das Dimer, hergeleitet wird. Jedoch ist dieser Ansatz begrenzt auf spin-unabhängige und homogene Systeme. Um den Anwendungsbereich von LDFT zu erweitern, entwickeln wir drei verschiedene Ansätze zur Herleitung von W[γ], die das Studium von Systemen mit gebrochener Symmetrie ermöglichen. Zuerst wird das bisherige Skalierungsfunktional erweitert auf Systeme mit Ladungstransfer. Eine systematische Untersuchung der Abhängigkeit des Funktionals W[γ] von der Ladungsverteilung ergibt ähnliche Skalierungseigenschaften wie für den homogenen Fall. Daraufhin wird eine Erweiterung auf das Hubbardmodell auf bipartiten Gittern hergeleitet und an sowohl endlichen als auch unendlichen Systemen mit repulsiver und attraktiver Wechselwirkung angewandt. Die hohe Genauigkeit dieses Funktionals wird aufgezeigt. Es erweist sich jedoch als schwierig, diesen Ansatz auf komplexere Systeme zu übertragen, da bei der Berechnung von W[γ] das System als ganzes betrachtet wird. Um dieses Problem zu bewältigen, leiten wir eine weitere Näherung basierend auf lokalen Skalierungseigenschaften her. Dieses Funktional ist lokal bezüglich der Gitterplätze formuliert und ist daher anwendbar auf jede Art von geordneten oder ungeordneten Hamiltonoperatoren mit lokalen Wechselwirkungen. Als Anwendungen untersuchen wir den Metall-Isolator-Übergang sowohl im ionischen Hubbardmodell in einer und zwei Dimensionen als auch in eindimensionalen Hubbardketten mit nächsten und übernächsten Nachbarn. Schließlich entwickeln wir ein numerisches Verfahren zur Berechnung von W[γ], basierend auf exakten Diagonalisierungen eines effektiven Vielteilchen-Hamilton-Operators, welcher einen von einem effektiven Medium umgebenen Cluster beschreibt. Dieser effektive Hamiltonoperator hängt von der Dichtematrix γ ab und erlaubt die Herleitung von Näherungen an W[γ], dessen Qualität sich systematisch mit steigender Clustergröße verbessert. Die Formulierung ist spinabhängig und ermöglicht eine direkte Verallgemeinerung auf korrelierte Systeme mit mehreren Orbitalen, wie zum Beispiel auf den spd-Hamilton-Operator. Darüber hinaus berücksichtigt sie die Effekte kurzreichweitiger Ladungs- und Spinfluktuationen in dem Funktional. Für das Hubbardmodell wird die Genauigkeit der Methode durch Vergleich mit Bethe-Ansatz-Resultaten (1D) und Quanten-Monte-Carlo-Simulationen (2D) veranschaulicht. Zum Abschluss wird ein Ausblick auf relevante zukünftige Entwicklungen dieser Theorie gegeben.

Characterization of Lipid Droplets and Functional Analysis of Lipid Droplet-Associated Proteins in Dictyostelium discoideum

Lipid droplets (LDs) are the universal storage form of fat as a reservoir of metabolic energy in animals, plants, bacteria and single celled eukaryotes. Dictyostelium LD formation was investigated in response to the addition of different nutrients to the growth medium. LDs were induced by adding exogenous cholesterol, palmitic acid (PA) as well as growth in bacterial suspension, while glucose addition fails to form LDs. Among these nutrients, PA addition is most effective to stimulate LD formation, and depletion of PA from the medium caused LD degradation. The neutral lipids incorporated into the LD-core are composed of triacylglycerol (TAG), steryl esters, and an unknown neutral lipid (UKL) species when the cells were loaded simultaneously with cholesterol and PA. In order to avoid the contamination with other cellular organelles, the LD-purification method was modified. The isolated LD fraction was analysed by mass spectrometry and 100 proteins were identified. Nineteen of these appear to be directly involved in lipid metabolism or function in regulating LD morphology. Together with a previous study, a total of 13 proteins from the LD-proteome were confirmed to localize to LDs after the induction with PA. Among the identified LD-proteins, the localization of Ldp (lipid droplet membrane protein), GPAT3 (glycerol-3-phosphate acyltransferase 3) and AGPAT3 (1-acylglycerol-3-phosphate-acyltransferase 3) were further verified by GFP-tagging at the N-termini or C-termini of the respective proteins. Fluorescence microscopy demonstrated that PA-treatment stimulated the translocation of the three proteins from the ER to LDs. In order to clarify DGAT (diacylglycerol acyltransferase) function in Dictyostelium, the localization of DGAT1, that is not present in LD-proteome, was also investigated. GFP-tagged DGAT1 localized to the ER both, in the presence and absence of PA, which is different from the previously observed localization of GFP-tagged DGAT2, which almost exclusively binds to LDs. The investigation of the cellular neutral lipid level helps to elucidate the mechanism responsible for LD-formation in Dictyostelium cells. Ldp and two short-chain dehydrogenases, ADH (alcohol dehydrogenase) and Ali (ADH-like protein), are not involved in neutral lipid biosynthesis. GPAT, AGPAT and DGAT are three transferases responsible for the three acylation steps of de novo TAG synthesis. Knock-out (KO) of AGPAT3 and DGAT2 did not affect storage-fat formation significantly, whereas cells lacking GPAT3 or DGAT1 decreased TAG and LD accumulation dramatically. Furthermore, DGAT1 is responsible for the accumulation of the unknown lipid UKL. Overexpression of DGAT2 can rescue the reduced TAG content of the DGAT1-KO mutant, but fails to restore UKL content in these cells, indicating that of DGAT1 and DGAT2 have overlapping functions in TAG synthesis, but the role in UKL formation is unique to DGAT1. Both GPAT3 and DGAT1 affect phagocytic activity. Mutation of GPAT3 increases it but a DGAT1-KO decreases phagocytosis. The double knockout of DGAT1 and 2 also impairs the ability to grow on a bacterial lawn, which again can be rescued by overexpression of DGAT2. These and other results are incorporated into a new model, which proposes that up-regulation of phagocytosis serves to replenish precursor molecules of membrane lipid synthesis, whereas phagocytosis is down-regulated when excess fatty acids are used for storage-fat formation.  

ACTORS: A Model of Concurrent Computation in Distributed Systems

A foundational model of concurrency is developed in this thesis. We examine issues in the design of parallel systems and show why the actor model is suitable for exploiting large-scale parallelism. Concurrency in actors is constrained only by the availability of hardware resources and by the logical dependence inherent in the computation. Unlike dataflow and functional programming, however, actors are dynamically reconfigurable and can model shared resources with changing local state. Concurrency is spawned in actors using asynchronous message-passing, pipelining, and the dynamic creation of actors. This thesis deals with some central issues in distributed computing. Specifically, problems of divergence and deadlock are addressed. For example, actors permit dynamic deadlock detection and removal. The problem of divergence is contained because independent transactions can execute concurrently and potentially infinite processes are nevertheless available for interaction.

"Functional Upregulation of Ca2+ -Activated K+ Channels in the Development of Substantia Nigra Dopamine Neurons"

Many connections in the basal ganglia are made around birth when animals are exposed to a host of new affective, cognitive, and sensori-motor stimuli. It is thought that dopamine modulates cortico-striatal synapses that result in the strengthening of those connections that lead to desired outcomes. We propose that there must be a time before which stimuli cannot be processed into functional connections, otherwise it would imply an effective link between stimulus, response, and reward in uterus. Consistent with these ideas, we present evidence that early in development dopamine neurons are electrically immature and do not produce high-frequency firing in response to salient stimuli. We ask first, what makes dopamine neurons immature? and second, what are the implications of this immaturity for the basal ganglia? As an answer to the first question, we find that at birth the outward current is small (3nS-V), insensitive to Ca2z, TEA, BK, and SK blockers. Rapidly after birth, the outward current increases to 15nS-V and becomes sensitive to Ca2z, TEA, BK, and SK blockers. We make a detailed analysis of the kinetics of the components of the outward currents and produce a model for BK and SK channels that we use to reproduce the outward current, and to infer the geometrical arrangement of BK and Ca2z channels in clusters. In the first cluster, T-type Ca2z and BK channels are coupled within distances of *20 nm (200 A˚). The second cluster consists of L-type Ca2z and BK channels that are spread over distances of at least 60 nm. As for the second question, we propose that early in development, the mechanism of action selection is in a ‘‘locked-in’’ state that would prevent dopamine neurons from reinforcing cortico-striatal synapses that do not have a functional experiential- based value.

Low genetic diversity and functional constraint in loci encoding Plasmodium vivax P12 and P38 proteins in the Colombian population

Background Plasmodium vivax is one of the five species causing malaria in human beings, affecting around 391 million people annually. The development of an anti-malarial vaccine has been proposed as an alternative for controlling this disease. However, its development has been hampered by allele-specific responses produced by the high genetic diversity shown by some parasite antigens. Evaluating these antigens’ genetic diversity is thus essential when designing a completely effective vaccine. Methods The gene sequences of Plasmodium vivax p12 (pv12) and p38 (pv38), obtained from field isolates in Colombia, were used for evaluating haplotype polymorphism and distribution by population genetics analysis. The evolutionary forces generating the variation pattern so observed were also determined. Results Both pv12 and pv38 were shown to have low genetic diversity. The neutral model for pv12 could not be discarded, whilst polymorphism in pv38 was maintained by balanced selection restricted to the gene’s 5′ region. Both encoded proteins seemed to have functional/structural constraints due to the presence of s48/45 domains, which were seen to be highly conserved.

Functional Upregulation of Ca2+ -Activated K+ Channels in the Development of Substantia Nigra Dopamine Neurons

Many connections in the basal ganglia are made around birth when animals are exposed to a host of new affective, cognitive, and sensori-motor stimuli. It is thought that dopamine modulates cortico-striatal synapses that result in the strengthening of those connections that lead to desired outcomes. We propose that there must be a time before which stimuli cannot be processed into functional connections, otherwise it would imply an effective link between stimulus, response, and reward in uterus. Consistent with these ideas, we present evidence that early in development dopamine neurons are electrically immature and do not produce high-frequency firing in response to salient stimuli. We ask first, what makes dopamine neurons immature? and second, what are the implications of this immaturity for the basal ganglia? As an answer to the first question, we find that at birth the outward current is small (3nS-V), insensitive to Ca2+, TEA, BK, and SK blockers. Rapidly after birth, the outward current increases to 15nS-V and becomes sensitive to Ca2+, TEA, BK, and SK blockers. We make a detailed analysis of the kinetics of the components of the outward currents and produce a model for BK and SK channels that we use to reproduce the outward current, and to infer the geometrical arrangement of BK and Ca2+ channels in clusters. In the first cluster, T-type Ca2+ and BK channels are coupled within distances of similar to 20 nm (200 parallel to). The second cluster consists of L-type Ca2+ and BK channels that are spread over distances of at least 60 nm. As for the second question, we propose that early in development, the mechanism of action selection is in a "locked-in" state that would prevent dopamine neurons from reinforcing cortico-striatal synapses that do not have a functional experiential-based value.

Exploring chromium (VI) dioxodihalides chemistry: is density functional theory the most suitable tool?

A comparative systematic study of the CrO2F2 compound has been performed using different conventional ab initio methodologies and density functional procedures. Two points have been analyzed: first, the accuracy of results yielded by each method under study, and second, the computational cost required to reach such results. Weighing up both aspects, density functional theory has been found to be more appropriate than the Hartree-Fock (HF) and the analyzed post-HF methods. Hence, the structural characterization and spectroscopic elucidation of the full CrO2X2 series (X=F,Cl,Br,I) has been done at this level of theory. Emphasis has been given to the unknown CrO2I2 species, and specially to the UV/visible spectra of all four compounds. Furthermore, a topological analysis in terms of charge density distributions has revealed why the valence shell electron pair repulsion model fails in predicting the molecular shape of such CrO2X2 complexes

Calibration and sensitivity analysis of a river water quality model under unsteady flow conditions

Water quality models generally require a relatively large number of parameters to define their functional relationships, and since prior information on parameter values is limited, these are commonly defined by fitting the model to observed data. In this paper, the identifiability of water quality parameters and the associated uncertainty in model simulations are investigated. A modification to the water quality model `Quality Simulation Along River Systems' is presented in which an improved flow component is used within the existing water quality model framework. The performance of the model is evaluated in an application to the Bedford Ouse river, UK, using a Monte-Carlo analysis toolbox. The essential framework of the model proved to be sound, and calibration and validation performance was generally good. However some supposedly important water quality parameters associated with algal activity were found to be completely insensitive, and hence non-identifiable, within the model structure, while others (nitrification and sedimentation) had optimum values at or close to zero, indicating that those processes were not detectable from the data set examined. (C) 2003 Elsevier Science B.V. All rights reserved.

Modeling chemotaxis reveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase

Understanding how multiple signals are integrated in living cells to produce a balanced response is a major challenge in biology. Two-component signal transduction pathways, such as bacterial chemotaxis, comprise histidine protein kinases (HPKs) and response regulators (RRs). These are used to sense and respond to changes in the environment. Rhodobacter sphaeroides has a complex chemosensory network with two signaling clusters, each containing a HPK, CheA. Here we demonstrate, using a mathematical model, how the outputs of the two signaling clusters may be integrated. We use our mathematical model supported by experimental data to predict that: (1) the main RR controlling flagellar rotation, CheY6, aided by its specific phosphatase, the bifunctional kinase CheA3, acts as a phosphate sink for the other RRs; and (2) a phosphorelay pathway involving CheB2 connects the cytoplasmic cluster kinase CheA3 with the polar localised kinase CheA2, and allows CheA3-P to phosphorylate non-cognate chemotaxis RRs. These two mechanisms enable the bifunctional kinase/phosphatase activity of CheA3 to integrate and tune the sensory output of each signaling cluster to produce a balanced response. The signal integration mechanisms identified here may be widely used by other bacteria, since like R. sphaeroides, over 50% of chemotactic bacteria have multiple cheA homologues and need to integrate signals from different sources.

Searching efficiency and the functional response of a pause-travel forager

1. The feeding rates of many predators and parasitoids exhibit type II functional responses, with a decelerating rate of increase to reach an asymptotic value as the density of their prey or hosts increases. Holling's disc equation describes such relationships and predicts that the asymptotic feeding rate at high prey densities is set by handling time, while the rate at which feeding rate increases with increased prey density is determined by searching efficiency. Searching efficiency and handling time are also parameters in other models which describe the functional response. Models which incorporate functional responses in order to make predictions of the effects of food shortage thus rely upon a clear understanding and accurate quantification of searching efficiency and handling time. 2. Blackbird Turdus merula exhibit a type II functional response and use pause-travel foraging, a foraging technique in which animals search for prey while stationary and then move to capture prey. Pause-travel foraging allows accurate direct measurement of feeding rate and both searching efficiency and handling time. We use Blackbirds as a model species to: (i) compare observed measures of both searching efficiency and handling time with those estimated by statistically fitting the disc equation to the observed functional response; and (ii) investigate alternative measures of searching efficiency derived by the established method where search area is assumed to be circular and a new method that we propose where it is not. 3. We find that the disc equation can adequately explain the functional response of blackbirds feeding on artificial prey. However, this depends critically upon how searching efficiency is measured. Two variations on the previous method of measuring search area (a component of searching efficiency) overestimated searching efficiency, and hence predicted feeding rates higher than those observed. Two variations of our alternative approach produced lower estimates of searching efficiency, closer to that estimated by fitting the disc equation, and hence more accurately predicted feeding rate. Our study shows the limitations of the previous method of measuring searching efficiency, and describes a new method for measuring searching efficiency more accurately.

Mixed Logit Model Performance and Distributional Assumptions: Preferences and GM foods

Using mixed logit models to analyse choice data is common but requires ex ante specification of the functional forms of preference distributions. We make the case for greater use of bounded functional forms and propose the use of the Marginal Likelihood, calculated using Bayesian techniques, as a single measure of model performance across non nested mixed logit specifications. Using this measure leads to very different rankings of model specifications compared to alternative rule of thumb measures. The approach is illustrated using data from a choice experiment regarding GM food types which provides insights regarding the recent WTO dispute between the EU and the US, Canada and Argentina and whether labelling and trade regimes should be based on the production process or product composition.