No description available.

Lipid bilayers are key components of biomembranes; they are self-assembled two-dimensional structures, primarily serving as barriers to the leakage of cell's contents. Lipid bilayers are typically charged in aqueous solution and may electrostatically interact with each other and with their environment. In this work, we investigate electrostatics of charged lipid bilayers with the main focus on the binding and bending of the bilayers. We first present a theoretical approach to charge-correlation attractions between like-charged lipid bilayers with neutralizing counterions assumed to be localized to the bilayer surface. In particular, we study the effect of nonzero ionic sizes on the attraction by treating the bilayer charges (both backbone charges and localized counterions) as forming a two-dimensional ionic fluid of hard spheres of the same diameter <i>D</i>. Using a two-dimensional Debye-H??ckel approach to this system, we examine how ion sizes influence the attraction. We find that the attraction gets stronger as surface charge densities or counterion valency increase, consistent with long-standing observations. Our results also indicate non-trivial dependence of the attraction on separations <i>h</i>: The attraction is enhanced by ion sizes for <i>h</i> ranges of physical interest, while it crosses over to the known <i>D</i>-independent universal behavior as <i>h</i> &rarr; &infin;; it remains finite as <i>h</i> &rarr; 0, as expected for a system of finite-sized ions. We also study the preferred curvature of an asymmetrically charged bilayer, in which the inner leaflet is negatively charged, while the outer one is neutral. In particular, we calculate the relaxed area difference &Delta; <i>A</i>₀ and the spontaneous curvature <i>C</i>₀ of the bilayer. We find &Delta; <i>A</i>₀ and <i>C</i>₀ are determined by the balance of a few distinct contributions: net charge repulsions, charge correlations, and the entropy associated with counterion release from the bilayer. The entropic effect is dominant for weakly charged surfaces in the presence of monovalent counterions only and tends to expand the inner leaflet, leading to negative &Delta; <i>A</i>₀ and <i>C</i>₀. In the presence of even a small concentration of divalent counterions, however, charge correlations counterbalance the entropic effect and shrink the inner leaflet, leading to positive &Delta; <i>A</i>₀ and <i>C</i>₀. We outline biological implications of our results.

• Argonaute proteins are important effectors in RNA silencing pathways, but they must interact with other machinery to trigger silencing. Ago hooks have emerged as a conserved motif responsible for interaction with Argonaute proteins, but little is know about the sequence surrounding Ago hooks that must restrict or enable interaction with specific Argonautes. • Here we investigated the evolutionary dynamics of an Argonaute-binding platform in NRPE1, the largest subunit of RNA Polymerase V. We compared NRPE1 sequences from more than 50 species, including dense sampling of two plant lineages. • This study demonstrates that the Argonaute-binding platform of NRPE1 retains Ago-hooks, intrinsic disorder, and repetitive character while being highly labile at the sequence level. We reveal that loss of sequence conservation is due to relaxed selection and frequent expansions and contractions of tandem repeat arrays. These factors allow a complete restructuring of the Ago-binding platform over 50-60 million years. This evolutionary pattern is also detected in a second Ago-binding platform, suggesting it is a general mechanism. • The presence of labile repeat arrays in all analyzed NRPE1 Ago-binding platforms indicates that selection maintains repetitive character, potentially to retain the ability to rapidly restructure the Ago-binding platform.

Lipid bilayers are key components of biomembranes; they are self-assembled two-dimensional structures, primarily serving as barriers to the leakage of cell's contents. Lipid bilayers are typically charged in aqueous solution and may electrostatically interact with each other and with their environment. In this work, we investigate electrostatics of charged lipid bilayers with the main focus on the binding and bending of the bilayers. We first present a theoretical approach to charge-correlation attractions between like-charged lipid bilayers with neutralizing counterions assumed to be localized to the bilayer surface. In particular, we study the effect of nonzero ionic sizes on the attraction by treating the bilayer charges (both backbone charges and localized counterions) as forming a two-dimensional ionic fluid of hard spheres of the same diameter <i>D</i>. Using a two-dimensional Debye-Hückel approach to this system, we examine how ion sizes influence the attraction. We find that the attraction gets stronger as surface charge densities or counterion valency increase, consistent with long-standing observations. Our results also indicate non-trivial dependence of the attraction on separations <i>h</i>: The attraction is enhanced by ion sizes for <i>h</i> ranges of physical interest, while it crosses over to the known <i>D</i>-independent universal behavior as <i>h</i> &rarr; &infin;; it remains finite as <i>h</i> &rarr; 0, as expected for a system of finite-sized ions. We also study the preferred curvature of an asymmetrically charged bilayer, in which the inner leaflet is negatively charged, while the outer one is neutral. In particular, we calculate the relaxed area difference &Delta; <i>A</i>₀ and the spontaneous curvature <i>C</i>₀ of the bilayer. We find &Delta; <i>A</i>₀ and <i>C</i>₀ are determined by the balance of a few distinct contributions: net charge repulsions, charge correlations, and the entropy associated with counterion release from the bilayer. The entropic effect is dominant for weakly charged surfaces in the presence of monovalent counterions only and tends to expand the inner leaflet, leading to negative &Delta; <i>A</i>₀ and <i>C</i>₀. In the presence of even a small concentration of divalent counterions, however, charge correlations counterbalance the entropic effect and shrink the inner leaflet, leading to positive &Delta; <i>A</i>₀ and <i>C</i>₀. We outline biological implications of our results.

In this paper we discuss iterative algorithms for solving the split feasibility problem (SFP). We study the CQ algorithm from two approaches: one is an optimization approach and the other is a fixed point approach. We prove its convergence first as the gradient-projection algorithm and secondly as a fixed point algorithm. We also study a relaxed CQ algorithm in the case where the sets C and Q are level sets of convex functions. In such case we present a convergence theorem and provide a different and much simpler proof compared with that of Yang [7].

In this thesis, we investigate graphs and hypergraphs that have (relaxed) product structures. In the class of graphs, we discuss in detail \\emph{RSP-relations}, a relaxation of relations fulfilling the square property and therefore of the product relation $\\sigma$, that identifies the copies of the prime factors of a graph w.r.t. the Cartesian product. For $K_{2,3}$-free graphs finest RSP-relations can be computed in polynomial-time. In general, however, they are not unique and their number may even grow exponentially. Explicit constructions of such relations in complete and complete bipartite graphs are given. Furthermore, we establish the close connection of (\\emph{well-behaved}) RSP-relations to \\mbox{(quasi-)covers} of graphs and equitable partitions. Thereby, we characterize the existence of non-trivial RSP-relations by means of the existence of spanning subgraphs that yield quasi-covers of the graph under investigation. We show, how equitable partitions on the vertex set of a graph $G$ arise in a natural way from well-behaved RSP-relations on $E(G)$. These partitions in turn give rise to quotient graphs that have rich product structure even if $G$ itself is prime. This product structure of the quotient graph is still retained even for RSP-relations that are not well-behaved. Furthermore, we will see that a (finest) RSP-relation of a product graph can be obtained easily from (finest) RSP-relations on the prime factors w.r.t. certain products and in what manner the quotient graphs of the product w.r.t. such an RSP-relation result from the quotient graphs of the factors and the respective product. In addition, we examine relations on the edge sets of \\emph{hyper}graphs that satisfy the grid property, the hypergraph analog of the square property. We introduce the \\emph{strong} and the \\emph{relaxed} grid property as variations of the grid property, the latter generalizing the relaxed square property. We thereby show, that many, although not all results for graphs and the (relaxed) square property can be transferred to hypergraphs. Similar to the graph case, any equivalence relation $R$ on the edge set of a hypergraph $H$ that satisfies the relaxed grid property induces a partition of the vertex set of $H$ which in turn determines quotient hypergraphs that have non-trivial product structures. Besides, we introduce the notion of \\emph{(Cartesian) hypergraph bundles}, the analog of (Cartesian) graph bundles and point out the connection between the grid property and hypergraph bundles. Finally, we show that every connected thin hypergraph $H$ has a unique prime factorization with respect to the normal and strong (hypergraph) product. Both products coincide with the usual strong \\emph{graph} product whenever $H$ is a graph. We introduce the notion of the Cartesian skeleton of hypergraphs as a natural generalization of the Cartesian skeleton of graphs and prove that it is uniquely defined for thin hypergraphs. Moreover, we show that the Cartesian skeleton of thin hypergraphs and its PFD w.r.t. the strong and the normal product can be computed in polynomial time.

No description available.

According to the World Health Organization, urban air pollution is a high public health priority due its linkage to cardio-pulmonary disease and association with increased mortality and morbidity (1, 2). Additionally, air pollution impacts climate change, visibility, and ecosystem health. The development of effective strategies for improving air quality requires accurate estimates of air pollutant emissions. In response to the need for new approaches to measuring emissions, we have designed a mobile Flux Lab for the Atmospheric Measurement of Emissions (FLAME) that applies a proven, science-based method known as eddy covariance for the direct quantification of anthropogenic emissions to the atmosphere. The mobile flux lab is a tool with novel, multifaceted abilities to assess air quality and improve the fidelity of emission inventories. Measurements of air pollutant concentrations in multiple locations at the neighborhood scale can provide much greater spatial resolution for population exposure assessments. The lab's mobility allows it to target specific sources, and plumes from these can be analyzed to determine emission factors. Through eddy covariance, the lab provides the new ability to directly measure emissions of a suite of air pollutants. We have deployed the FLAME to three different settings: a rural Appalachian town where coal transport is the dominant industry; schools in the medium-sized city of Roanoke, Virginia; and the large urban areas around Norfolk, Virginia, to measure neighborhood-scale emissions of air pollution. These areas routinely experience high ozone and particulate matter concentrations and include a diverse array of residential neighborhoods and industries. The FLAME is able to capture emissions from all ground-based sources, such as motor vehicles, rail and barge traffic, refuse fires and refueling stations, for which no direct measurement method has been available previously. Experiments focus on carbon dioxide (CO₂), the principal greenhouse gas responsible for climate change; nitrogen oxides (NOx), a key ingredient in ground-level ozone and acid rain; volatile organic compounds (VOCs), a second key ingredient in ozone and many of which are air toxics; and fine particulate matter (PM2.5), a cause of mortality, decreased visibility, and climate change. This research provides some of the first measurements of neighborhood-scale anthropogenic emissions of CO₂, NOx, VOCs and PM2.5 and as a result, the first opportunity to validate official emission inventories directly. The results indicate that a mobile eddy covariance system can be used successfully to measure fluxes of multiple pollutants in a variety of urban settings. With certain pollutants in certain locations, flux measurements confirmed inventories, but in others, they disagreed by factors of up to five, suggesting that parts of the inventory may be severely over- or underestimated. Over the scale of a few kilometers within a city, emissions were highly heterogeneous in both space and time. FLAME-based measurements also confirmed published emission factors from coal barges and showed that idling vehicles are the dominant source of emissions of air toxics around seven schools in southwest Virginia. Measurements from this study corroborate existing emission inventories of CO₂ and NOx and suggest that inventories of PM2.5 may be overestimated. Despite the tremendous spatial and temporal variability in emissions found in dense urban areas, CO₂ fluxes on average are very similar across the areas in this study and other urban areas in the developed world. Nevertheless, the high level of variability in spatial and temporal patterns of emissions presents a challenge to air quality modelers. The finding that emissions from idling vehicles at schools are likely responsible for creating hot spots of air toxics adds to the urgency of implementing no-idling and other rules to reduce the exposure of children to such pollutants. Ultimately, the results of this study can be used in combination with knowledge from existing emission inventories to improve the science and policies surrounding air pollution. / Ph. D.

L’utilisation systématique d’une théorie dite de Cauchy conduit souvent à des simplifications trop fortes de la réalité. En effet, certaines caractéristiques de la microstructure sont implicitement négligées dans ces approches. Des matériaux possèdent des microstructures à une échelle assez grande (micron, millimètre, centimètre), dont l’effet se répercute sur le comportement macroscopique. Le modèle de Cauchy est insuffisant pour décrire leur comportement global spécifique, lié par exemple à la concentration d’efforts ou de déformations, ou à des modes de déformations caractérisés par de forts gradients locaux induisant des comportements liés à ce qui se passe à des échelles plus petites. Un des domaines d’application les plus prometteurs des théories de milieux continus enrichis concerne les renforts tissés de composites. Cette classe de matériaux est constituée par le tissage de mèche, dont les rigidités sont très différentes en traction et en cisaillement : les mèches sont très raides en traction mais l’angle entre deux mèches peut varier très facilement. Ce contraste très marqué des propriétés mécaniques de la mesostructure du matériau permet de décrire ses propriétés homogénéisées dans le cadre d’une théorie de deuxième gradient. La manifestation macroscopique de la mesostructure peut en effet jouer un rôle majeur lors de la mise en forme des renforts de composites. Les modèles de Cauchy ne sont pas adaptés à la description de la réponse dynamique de certains matériaux microstructurés montrant des comportements dispersifs ou des band-gaps. Les théories de milieux continus enrichis sont de bonnes candidates pour modéliser les effets de la présence d’une microstructure. Elles peuvent également posséder des propriétés très particulières vis à vis de la propagation d’ondes, ce qui confère aux structures résultantes des solutions de choix comme écran ou absorbeur d’ondes qui peuvent innovantes dans le domaine du contrôle des vibrations ou dans le domaine de la furtivité. / The systematic use of a so-called Cauchy theory sometimes leads to an oversimplification of reality. Indeed, certain characteristics of the microstructure are implicitly neglected in these approaches. However, even if all the materials are heterogeneous on a sufficiently small scale and therefore possess a microstructure, this does not necessarily induce a specific behavior on a macroscopic scale. In this case, the Cauchy theory would be perfectly adapted to their description. On the other hand, other materials possess microstructures on a large-enough scale (micron, millimeter, centimeter), whose effects have repercussions on macroscopic behavior. The Cauchy model is then insufficient to describe their specific global behavior related to what occurs at smaller scales, e.g. concentration of forces or deformations, or strong local gradients. One of the most promising fields of application of enriched continuous theories concerns the study of the mechanical behavior of woven composite reinforcements. This class of materials, made up by weaving yarns (made up themselves of many thinner fibers), possess very different rigidities in tension and in shear: the yarns are very stiff in tension but the angle between two yarns can vary very easily. This very marked contrast of material mechanical properties makes it necessary to describe its homogenized properties within the framework of a second gradient theory (or a constrained micromorphic one). Cauchy models are also not well-suited for the description of the dynamic response of certain microstructured materials showing dispersive behaviors or band-gaps. Enriched continuous theories (and in particular the relaxed micromorphic model) can be good candidates for modeling these materials in a more precise and realistic way, since they can include the macroscopic manifestation of their microstructure. These microstructured materials may have original properties, to improve and optimize the responses of the structures that use them. Indeed, these structures are designed using such microstructured materials - also known as metamaterials - to exhibit improved strengths, shaping facilities, minimized weights, and much more. They can also possess innovative properties in the field of vibration control or in the field of stealth technology.

<p>This thesis concerns different aspects of dating divergence times in phylogenetic trees, using molecular data and multiple fossil age constraints.</p><p>Datings of phylogenetically basal eudicots, monocots and modern birds (Neoaves) are presented. Large phylograms and multiple fossil constraints were used in all these studies. Eudicots and monocots are suggested to be part of a rapid divergence of angiosperms in the Early Cretaceous, with most families present at the Cretaceous/Tertiary boundary. Stem lineages of Neoaves were present in the Late Cretaceous, but the main divergence of extant families took place around the Cre-taceous/Tertiary boundary.</p><p>A novel method and computer software for dating large phylogenetic trees, PATHd8, is presented. PATHd8 is a nonparametric smoothing method that smoothes one pair of sister groups at a time, by taking the mean of the added branch lengths from a terminal taxon to a node. Because of the local smoothing, the algorithm is simple, hence providing stable and very fast analyses, allowing for thousands of taxa and an arbitrary number of age constraints.</p><p>The importance of fossil constraints and their placement are discussed, and concluded to be the most important factor for obtaining reasonable age estimates.</p><p>Different dating methods are compared, and it is concluded that differences in age estimates are obtained from penalized likelihood, PATHd8, and the Bayesian autocorrelation method implemented in the multidivtime program. In the Bayesian method, prior assumptions about evolutionary rate at the root, rate variance and the level of rate smoothing between internal edges, are suggested to influence the results.</p>