Edges and switches, tunnels and bridges

Abstract. Edge casing is a well-known method to improve the readability of drawings of non-planar graphs. A cased drawing orders the edges of each edge crossing and interrupts the lower edge in an appropriate neighborhood of the crossing. Certain orders will lead to a more readable drawing than others. We formulate several optimization criteria that try to capture the concept of a "good" cased drawing. Further, we address the algorithmic question of how to turn a given drawing into an optimal cased drawing. For many of the resulting optimization problems, we either find polynomial time algorithms or NP-hardness results

Drawing graphs for cartographic applications

Graph Drawing is a relatively young area that combines elements of graph theory, algorithms, (computational) geometry and (computational) topology. Research in this field concentrates on developing algorithms for drawing graphs while satisfying certain aesthetic criteria. These criteria are often expressed in properties like edge complexity, number of edge crossings, angular resolutions, shapes of faces or graph symmetries and in general aim at creating a drawing of a graph that conveys the information to the reader in the best possible way. Graph drawing has applications in a wide variety of areas which include cartography, VLSI design and information visualization. In this thesis we consider several graph drawing problems. The first problem we address is rectilinear cartogram construction. A cartogram, also known as value-by-area map, is a technique used by cartographers to visualize statistical data over a set of geographical regions like countries, states or counties. The regions of a cartogram are deformed such that the area of a region corresponds to a particular geographic variable. The shapes of the regions depend on the type of cartogram. We consider rectilinear cartograms of constant complexity, that is cartograms where each region is a rectilinear polygon with a constant number of vertices. Whether a cartogram is good is determined by how closely the cartogram resembles the original map and how precisely the area of its regions describe the associated values. The cartographic error is defined for each region as jAc¡Asj=As, where Ac is the area of the region in the cartogram and As is the specified area of that region, given by the geographic variable to be shown. In this thesis we consider the construction of rectilinear cartograms that have correct adjacencies of the regions and zero cartographic error. We show that any plane triangulated graph admits a rectilinear cartogram where every region has at most 40 vertices which can be constructed in O(nlogn) time. We also present experimental results that show that in practice the algorithm works significantly better than suggested by the complexity bounds. In our experiments on real-world data we were always able to construct a cartogram where the average number of vertices per region does not exceed five. Since a rectangle has four vertices, this means that most of the regions of our rectilinear car tograms are in fact rectangles. Moreover, the maximum number vertices of each region in these cartograms never exceeded ten. The second problem we address in this thesis concerns cased drawings of graphs. The vertices of a drawing are commonly marked with a disk, but differentiating between vertices and edge crossings in a dense graph can still be difficult. Edge casing is a wellknown method—used, for example, in electrical drawings, when depicting knots, and, more generally, in information visualization—to alleviate this problem and to improve the readability of a drawing. A cased drawing orders the edges of each crossing and interrupts the lower edge in an appropriate neighborhood of the crossing. One can also envision that every edge is encased in a strip of the background color and that the casing of the upper edge covers the lower edge at the crossing. If there are no application-specific restrictions that dictate the order of the edges at each crossing, then we can in principle choose freely how to arrange them. However, certain orders will lead to a more readable drawing than others. In this thesis we formulate aesthetic criteria for a cased drawing as optimization problems and solve these problems. For most of the problems we present either a polynomial time algorithm or demonstrate that the problem is NP-hard. Finally we consider a combinatorial question in computational topology concerning three types of objects: closed curves in the plane, surfaces immersed in the plane, and surfaces embedded in space. In particular, we study casings of closed curves in the plane to decide whether these curves can be embedded as the boundaries of certain special surfaces. We show that it is NP-complete to determine whether an immersed disk is the projection of a surface embedded in space, or whether a curve is the boundary of an immersed surface in the plane that is not constrained to be a disk. However, when a casing is supplied with a self-intersecting curve, describing which component of the curve lies above and which below at each crossing, we can determine in time linear in the number of crossings whether the cased curve forms the projected boundary of a surface in space. As a related result, we show that an immersed surface with a single boundary curve that crosses itself n times has at most 2n=2 combinatorially distinct spatial embeddings and we discuss the existence of fixed-parameter tractable algorithms for related problems

Hybrid IP/SDN networking: open implementation and experiment management tools

The introduction of SDN in large-scale IP provider networks is still an open issue and different solutions have been suggested so far. In this paper we propose a hybrid approach that allows the coexistence of traditional IP routing with SDN based forwarding within the same provider domain. The solution is called OSHI - Open Source Hybrid IP/SDN networking as we have fully implemented it combining and extending Open Source software. We discuss the OSHI system architecture and the design and implementation of advanced services like Pseudo Wires and Virtual Switches. In addition, we describe a set of Open Source management tools for the emulation of the proposed solution using either the Mininet emulator or distributed physical testbeds. We refer to this suite of tools as Mantoo (Management tools). Mantoo includes an extensible web-based graphical topology designer, which provides different layered network "views" (e.g. from physical links to service relationships among nodes). The suite can validate an input topology, automatically deploy it over a Mininet emulator or a distributed SDN testbed and allows access to emulated nodes by opening consoles in the web GUI. Mantoo provides also tools to evaluate the performance of the deployed nodes.Comment: Accepted for publication in IEEE Transaction of Network and Service Management - December 2015 http://dx.doi.org/10.1109/TNSM.2015.250762

Deliverable DJRA1.2. Solutions and protocols proposal for the network control, management and monitoring in a virtualized network context

This deliverable presents several research proposals for the FEDERICA network, in different subjects, such as monitoring, routing, signalling, resource discovery, and isolation. For each topic one or more possible solutions are elaborated, explaining the background, functioning and the implications of the proposed solutions.This deliverable goes further on the research aspects within FEDERICA. First of all the architecture of the control plane for the FEDERICA infrastructure will be defined. Several possibilities could be implemented, using the basic FEDERICA infrastructure as a starting point. The focus on this document is the intra-domain aspects of the control plane and their properties. Also some inter-domain aspects are addressed. The main objective of this deliverable is to lay great stress on creating and implementing the prototype/tool for the FEDERICA slice-oriented control system using the appropriate framework. This deliverable goes deeply into the definition of the containers between entities and their syntax, preparing this tool for the future implementation of any kind of algorithm related to the control plane, for both to apply UPB policies or to configure it by hand. We opt for an open solution despite the real time limitations that we could have (for instance, opening web services connexions or applying fast recovering mechanisms). The application being developed is the central element in the control plane, and additional features must be added to this application. This control plane, from the functionality point of view, is composed by several procedures that provide a reliable application and that include some mechanisms or algorithms to be able to discover and assign resources to the user. To achieve this, several topics must be researched in order to propose new protocols for the virtual infrastructure. The topics and necessary features covered in this document include resource discovery, resource allocation, signalling, routing, isolation and monitoring. All these topics must be researched in order to find a good solution for the FEDERICA network. Some of these algorithms have started to be analyzed and will be expanded in the next deliverable. Current standardization and existing solutions have been investigated in order to find a good solution for FEDERICA. Resource discovery is an important issue within the FEDERICA network, as manual resource discovery is no option, due to scalability requirement. Furthermore, no standardization exists, so knowledge must be obtained from related work. Ideally, the proposed solutions for these topics should not only be adequate specifically for this infrastructure, but could also be applied to other virtualized networks.Postprint (published version

Computational study of RTI - 371, a positive allosteric modulator of the cannabinoid CB1 receptor

It is now recognized that many G-protein-coupled receptors (GPCRs) contain allosteric binding sites for endogenous and/or synthetic ligands, which are topographically distinct from the agonist-binding site, which is known as the orthosteric site. In contrast to the direct effects on receptor function that are mediated by orthosteric ligands, allosteric drugs act by modulating receptor activity through conformational changes in the receptor that are transmitted from the allosteric to the orthosteric site and/or to effector coupling sites. 3â-(4-methylphenyl)-2â-[3-(4-chlorophenyl)isoxazol-5-yl]tropane (RTI-371) has been shown to be a positive allosteric modulator of human cannabinoid receptor type 1 (CB1). RTI-371 increases the affinity of traditional cannabinoid agonist, CP55,940 and boosts its efficacy. These effects suggest that this compound may cause a structural change in the CB1 receptor, such that the intrinsic activity of CP55,940 is enhanced, perhaps by stabilizing the active conformation of the receptor. RTI-371 has also been reported to be devoid of activity in the absence of agonist, making RTI-371 neither an agonist nor an antagonist at CB1 when applied alone. The goal of this thesis project was to understand the action of RTI - 371 at the molecular level. To this end, five specific aims were pursued. First, a complete Jaguar conformational analysis of RTI-371 was accomplished, establishing both the minimum energy conformations and the global minimum energy conformation of RTI-371. Second, to identify the binding site of RTI-371 at CB1, the forced-biased Metropolis Monte Carlo simulated annealing program (MMC) was employed. Third, because an increase in CP55,940 affinity could be achieved by receptor exit route blockade, the program CAVER was used to identify all exit routes and the most likely exit route for CP55,940 from CB1. Fourth, the results of MMC and CAVER were used to identify the most likely binding site region for RTI-371 at CB1. Fifth, binding sites for RTI-371 in this region of the receptor were explored using an automated docking program Glide. The most favorable binding site identified for RTI-371 at CB1 is consistent with the reported pharmacology of RTI-371, i.e., its ability to boost CP55,940 affinity and efficacy through stabilizing the active state of CB1 receptor

Jökulhlaups in Iceland : sources, release and drainage

Jökulhlaups in Iceland may originate from marginal or subglacial sources of water melted by atmospheric processes, permanent geothermal heat or volcanic eruptions. Glacier-volcano interactions produce meltwater that either drains toward the glacier margin or accumulates in subglacial lakes. Accumulated meltwater drains periodically in jökulhlaups from the subglacial lakes and occasionally during volcanic eruptions. During the 20th century 15 subglacial volcanic eruptions (10 major and 5 minor events) took place, about one-third of all eruptions in Iceland during that century. The release of meltwater from glacial lakes can take place as a result of two different conduit initiation mechanisms and the subsequent drainage from the lake occurs by two different modes. Drainage can begin at pressures lower than the ice overburden in conduits that expand slowly over days or weeks due to melting of the ice walls by frictional and sensible heat in the water. Alternatively, the lake level may rise until the glacier is lifted along the flowpath to make space for the water and water discharges rise linearly, peaking in a time interval of several hours to 1-2 days. In this case, discharge rises faster than can be accommodated by melting of the conduits. The rapidly-rising floods are often associated with large discharges and floods following rapid filling of subglacial lakes during subglacial eruptions or dumping of one marginal lake into another. Jökulhlaups during eruptions in steep ice and snow-covered stratovolcanoes are swift and dangerous and may become lahars and debris-laden floods. Normally jökulhlaups do not lead to glacier surges but eruptions in ice-capped stratovolcanoes have caused rapid and extensive glacier sliding. Jökulhlaups have significant landscaping potential: they erode large canyons and transport and deposit enormous quantities of sediment and icebergs over vast outwash plains and sandur deltas. Jökulhlaups from subglacial lakes may transport on the order of 107 tons of sediment per event but during violent volcanic eruptions the sediment load has been 108 tons. Pleistocene glacial river canyons may have been formed in such catastrophic floods from subglacial lakes. Jökulhlaups have threatened human populations, farms and hydroelectric power plants on glacier-fed rivers. They have damaged cultivated and vegetation areas, disrupted roads on the outwash plains and have even generated flood waves in coastal waters. Iceland is a unique and valuable study-site for glaciovolcanic interactions. This applies to the heat exchange between magma and the glacier, the dynamical response of the glacier to subglacial eruptions, the structure and growth sequence of hyaloclastite ridges and tuyas formed by subglacial eruptions, and jökulhlaups due to volcanic eruptions. The jökuhlaups can be seen as modern analogues of past megafloods on the Earth and their exploration may improve understanding of ice-volcano processes on other planets

Single-Electron Traps: A Quantitative Comparison of Theory and Experiment

We have carried out a coordinated experimental and theoretical study of single-electron traps based on submicron aluminum islands and aluminum oxide tunnel junctions. The results of geometrical modeling using a modified version of MIT's FastCap were used as input data for the general-purpose single-electron circuit simulator MOSES. The analysis indicates reasonable quantitative agreement between theory and experiment for those trap characteristics which are not affected by random offset charges. The observed differences between theory and experiment (ranging from a few to fifty percent) can be readily explained by the uncertainty in the exact geometry of the experimental nanostructures.Comment: 17 pages, 21 figures, RevTex, eps