@unpublished{Dandekar2007, author = {Dandekar, Thomas}, title = {Some general system properties of a living observer and the environment he explores}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33537}, year = {2007}, abstract = {In a nice assay published in Nature in 1993 the physicist Richard God III started from a human observer and made a number of witty conclusions about our future prospects giving estimates for the existence of the Berlin Wall, the human race and all the rest of the universe. In the same spirit, we derive implications for "the meaning of life, the universe and all the rest" from few principles. Adams´ absurd answer "42" tells the lesson "garbage in / garbage out" - or suggests that the question is non calculable. We show that experience of "meaning" and to decide fundamental questions which can not be decided by formal systems imply central properties of life: Ever higher levels of internal representation of the world and an escalating tendency to become more complex. An observer, "collecting observations" and three measures for complexity are examined. A theory on living systems is derived focussing on their internal representation of information. Living systems are more complex than Kolmogorov complexity ("life is NOT simple") and overcome decision limits (G{\"o}del theorem) for formal systems as illustrated for cell cycle. Only a world with very fine tuned environments allows life. Such a world is itself rather complex and hence excessive large in its space of different states - a living observer has thus a high probability to reside in a complex and fine tuned universe.}, subject = {Komplex }, language = {en} } @unpublished{Dandekar2008, author = {Dandekar, Thomas}, title = {Why are nature´s constants so fine-tuned? The case for an escalating complex universe}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-34488}, year = {2008}, abstract = {Why is our universe so fine-tuned? In this preprint we discuss that this is not a strange accident but that fine-tuned universes can be considered to be exceedingly large if one counts the number of observable different states (i.e. one aspect of the more general preprint http://www.opus-bayern.de/uni-wuerzburg/volltexte/2009/3353/). Looking at parameter variation for the same set of physical laws simple and complex processes (including life) and worlds in a multiverse are compared in simple examples. Next the anthropocentric principle is extended as many conditions which are generally interpreted anthropocentric only ensure a large space of different system states. In particular, the observed over-tuning beyond the level for our existence is explainable by these system considerations. More formally, the state space for different systems becomes measurable and comparable looking at their output behaviour. We show that highly interacting processes are more complex then Chaitin complexity, the latter denotes processes not compressible by shorter descriptions (Kolomogorov complexity). The complexity considerations help to better study and compare different processes (programs, living cells, environments and worlds) including dynamic behaviour and can be used for model selection in theoretical physics. Moreover, the large size (in terms of different states) of a world allowing complex processes including life can in a model calculation be determined applying discrete histories from quantum spin-loop theory. Nevertheless there remains a lot to be done - hopefully the preprint stimulates further efforts in this area.}, subject = {Natur}, language = {en} } @phdthesis{Fleszar2018, author = {Fleszar, Krzysztof}, title = {Network-Design Problems in Graphs and on the Plane}, edition = {1. Auflage}, publisher = {W{\"u}rzburg University Press}, address = {W{\"u}rzburg}, isbn = {978-3-95826-076-4 (Print)}, doi = {10.25972/WUP-978-3-95826-077-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154904}, school = {W{\"u}rzburg University Press}, pages = {xi, 204}, year = {2018}, abstract = {A network design problem defines an infinite set whose elements, called instances, describe relationships and network constraints. It asks for an algorithm that, given an instance of this set, designs a network that respects the given constraints and at the same time optimizes some given criterion. In my thesis, I develop algorithms whose solutions are optimum or close to an optimum value within some guaranteed bound. I also examine the computational complexity of these problems. Problems from two vast areas are considered: graphs and the Euclidean plane. In the Maximum Edge Disjoint Paths problem, we are given a graph and a subset of vertex pairs that are called terminal pairs. We are asked for a set of paths where the endpoints of each path form a terminal pair. The constraint is that any two paths share at most one inner vertex. The optimization criterion is to maximize the cardinality of the set. In the hard-capacitated k-Facility Location problem, we are given an integer k and a complete graph where the distances obey a given metric and where each node has two numerical values: a capacity and an opening cost. We are asked for a subset of k nodes, called facilities, and an assignment of all the nodes, called clients, to the facilities. The constraint is that the number of clients assigned to a facility cannot exceed the facility's capacity value. The optimization criterion is to minimize the total cost which consists of the total opening cost of the facilities and the total distance between the clients and the facilities they are assigned to. In the Stabbing problem, we are given a set of axis-aligned rectangles in the plane. We are asked for a set of horizontal line segments such that, for every rectangle, there is a line segment crossing its left and right edge. The optimization criterion is to minimize the total length of the line segments. In the k-Colored Non-Crossing Euclidean Steiner Forest problem, we are given an integer k and a finite set of points in the plane where each point has one of k colors. For every color, we are asked for a drawing that connects all the points of the same color. The constraint is that drawings of different colors are not allowed to cross each other. The optimization criterion is to minimize the total length of the drawings. In the Minimum Rectilinear Polygon for Given Angle Sequence problem, we are given an angle sequence of left (+90°) turns and right (-90°) turns. We are asked for an axis-parallel simple polygon where the angles of the vertices yield the given sequence when walking around the polygon in counter-clockwise manner. The optimization criteria considered are to minimize the perimeter, the area, and the size of the axis-parallel bounding box of the polygon.}, subject = {Euklidische Ebene}, language = {en} } @phdthesis{Meister2006, author = {Meister, Daniel}, title = {The complexity of membership problems for finite recurrent systems and minimal triangulations}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-18837}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {The dissertation thesis studies the complexity of membership problems. Generally, membership problems consider the question whether a given object belongs to a set. Object and set are part of the input. The thesis studies the complexity of membership problems for two special kinds of sets. The first problem class asks whether a given natural number belongs to a set of natural numbers. The set of natural numbers is defined via finite recurrent systems: sets are built by iterative application of operations, like union, intersection, complementation and arithmetical operations, to already defined sets. This general problem implies further problems by restricting the set of used operations. The thesis contains completeness results for well-known complexity classes as well as undecidability results for these problems. The second problem class asks whether a given graph is a minimal triangulation of another graph. A graph is a triangulation of another graph, if it is a chordal spanning supergraph of the second graph. If no proper supergraph of the first graph is a triangulation of the second graph, the first graph is a minimal triangulation of the second graph. The complexity of the membership problem for minimal triangulations of several graph classes is investigated. Restricted variants are solved by linear-time algorithms. These algorithms rely on appropriate characterisations of minimal triangulations.}, subject = {Komplexit{\"a}t}, language = {en} } @article{TolayBuchberger2021, author = {Tolay, Nazife and Buchberger, Alexander}, title = {Comparative profiling of stress granule clearance reveals differential contributions of the ubiquitin system}, series = {Life Science Alliance}, volume = {4}, journal = {Life Science Alliance}, number = {5}, doi = {10.26508/lsa.202000927}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259810}, pages = {e202000927}, year = {2021}, abstract = {Stress granules (SGs) are cytoplasmic condensates containing untranslated mRNP complexes. They are induced by various proteotoxic conditions such as heat, oxidative, and osmotic stress. SGs are believed to protect mRNPs from degradation and to enable cells to rapidly resume translation when stress conditions subside. SG dynamics are controlled by various posttranslationalmodifications, but the role of the ubiquitin system has remained controversial. Here, we present a comparative analysis addressing the involvement of the ubiquitin system in SG clearance. Using high-resolution immuno-fluorescence microscopy, we found that ubiquitin associated to varying extent with SGs induced by heat, arsenite, H2O2, sorbitol, or combined puromycin and Hsp70 inhibitor treatment. SG-associated ubiquitin species included K48- and K63-linked conjugates, whereas free ubiquitin was not significantly enriched. Inhibition of the ubiquitin activating enzyme, deubiquitylating enzymes, the 26S proteasome and p97/VCP impaired the clearance of arsenite- and heat-induced SGs, whereas SGs induced by other stress conditions were little affected. Our data underline the differential involvement of the ubiquitin system in SG clearance, a process important to prevent the formation of disease-linked aberrant SGs.}, language = {en} } @article{WehnerRoehrStepanenkoetal.2020, author = {Wehner, Marius and R{\"o}hr, Merle Insa Silja and Stepanenko, Vladimir and W{\"u}rthner, Frank}, title = {Control of self-assembly pathways toward conglomerate and racemic supramolecular polymers}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, doi = {10.1038/s41467-020-19189-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230580}, year = {2020}, abstract = {Homo- and heterochiral aggregation during crystallization of organic molecules has significance both for fundamental questions related to the origin of life as well as for the separation of homochiral compounds from their racemates in industrial processes. Herein, we analyse these phenomena at the lowest level of hierarchy - that is the self-assembly of a racemic mixture of (R,R)- and (S,S)-PBI into 1D supramolecular polymers. By a combination of UV/vis and NMR spectroscopy as well as atomic force microscopy, we demonstrate that homochiral aggregation of the racemic mixture leads to the formation of two types of supramolecular conglomerates under kinetic control, while under thermodynamic control heterochiral aggregation is preferred, affording a racemic supramolecular polymer. FT-IR spectroscopy and quantum-chemical calculations reveal unique packing arrangements and hydrogen-bonding patterns within these supramolecular polymers. Time-, concentration- and temperature-dependent UV/vis experiments provide further insights into the kinetic and thermodynamic control of the conglomerate and racemic supramolecular polymer formation. Homo- and heterochiral aggregation is a process of interest to prebiotic and chiral separation chemistry. Here, the authors analyze the self-assembly of a racemic mixture into 1D supramolecular polymers and find homochiral aggregation into conglomerates under kinetic control, while under thermodynamic control a racemic polymer is formed.}, language = {en} } @phdthesis{Zink2024, author = {Zink, Johannes}, title = {Algorithms for Drawing Graphs and Polylines with Straight-Line Segments}, doi = {10.25972/OPUS-35475}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-354756}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {Graphs provide a key means to model relationships between entities. They consist of vertices representing the entities, and edges representing relationships between pairs of entities. To make people conceive the structure of a graph, it is almost inevitable to visualize the graph. We call such a visualization a graph drawing. Moreover, we have a straight-line graph drawing if each vertex is represented as a point (or a small geometric object, e.g., a rectangle) and each edge is represented as a line segment between its two vertices. A polyline is a very simple straight-line graph drawing, where the vertices form a sequence according to which the vertices are connected by edges. An example of a polyline in practice is a GPS trajectory. The underlying road network, in turn, can be modeled as a graph. This book addresses problems that arise when working with straight-line graph drawings and polylines. In particular, we study algorithms for recognizing certain graphs representable with line segments, for generating straight-line graph drawings, and for abstracting polylines. In the first part, we first examine, how and in which time we can decide whether a given graph is a stick graph, that is, whether its vertices can be represented as vertical and horizontal line segments on a diagonal line, which intersect if and only if there is an edge between them. We then consider the visual complexity of graphs. Specifically, we investigate, for certain classes of graphs, how many line segments are necessary for any straight-line graph drawing, and whether three (or more) different slopes of the line segments are sufficient to draw all edges. Last, we study the question, how to assign (ordered) colors to the vertices of a graph with both directed and undirected edges such that no neighboring vertices get the same color and colors are ascending along directed edges. Here, the special property of the considered graph is that the vertices can be represented as intervals that overlap if and only if there is an edge between them. The latter problem is motivated by an application in automated drawing of cable plans with vertical and horizontal line segments, which we cover in the second part. We describe an algorithm that gets the abstract description of a cable plan as input, and generates a drawing that takes into account the special properties of these cable plans, like plugs and groups of wires. We then experimentally evaluate the quality of the resulting drawings. In the third part, we study the problem of abstracting (or simplifying) a single polyline and a bundle of polylines. In this problem, the objective is to remove as many vertices as possible from the given polyline(s) while keeping each resulting polyline sufficiently similar to its original course (according to a given similarity measure).}, subject = {Graphenzeichnen}, language = {en} }