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  • 1
    Publication Date: 2014-02-26
    Description: Zeitschriften und andere Medien werden in wachsendem Maße elektronisch publiziert. Hier entsteht für die Bibliotheken, welche diese Online-Publikationen ihren Lesern zur Verfügung stellen, ein neuer Bereich der Informationsvermittlung. Mit dem aufkommenden Standard der OpenURL ergeben sich neue Möglichkeiten, dem Benutzer weiterführende Links und Dienste anzubieten. Das Document-Linking-System SFX der Firma Ex Libris ist die erste und bekannteste Anwendung, die ein Managementsystem fr die Auswertung der OpenURL implementiert. Im Rahmen eines Projektes hat die Zentrale des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV) eine Evaluation von SFX durchgeführt. Als Ergebnis der Evaluation sollten Einsatzmöglichkeiten von SFX für die KOBV-Suchmaschine und in den lokalen Bibliothekssystemen und Informationsportalen aufgezeigt werden. Im Verlauf des Projektes hat sich das Produkt SFX als eine stabile Anwendung erwiesen, die dem Benutzer interessante zusätzliche Dienste bieten kann.
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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  • 2
    Publication Date: 2014-02-26
    Description: In this work we present an approach for the sensitivity analysis of linearly-implicit differential-algebraic equation systems. Solutions for both, states and sensitivities are obtained by applying an extrapolated linearly implicit Euler discretization scheme. This approach is compared to the widely used sensitivity extensions of multi-step BDF methods by means of case studies. Especially, we point out the benefit of this method in the context of dynamic optimization using the sequential approach.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 3
    Publication Date: 2014-09-30
    Description: Decomposition of the high dimensional conformational space of bio-molecules into metastable subsets is used for data reduction of long molecular trajectories in order to facilitate chemical analysis and to improve convergence of simulations within these subsets. The metastability is identified by the Perron-cluster cluster analysis of a Markov process that generates the thermodynamic distribution. A necessary prerequisite of this analysis is the discretization of the conformational space. A combinatorial approach via discretization of each degree of freedom will end in the so called ''curse of dimension''. In the following paper we analyze Hybrid Monte Carlo simulations of small, drug-like biomolecules and focus on the dihedral degrees of freedom as indicators of conformational changes. To avoid the ''curse of dimension'', the projection of the underlying Markov operator on each dihedral is analyzed according to its metastability. In each decomposition step of a recursive procedure, those significant dihedrals, which indicate high metastability, are used for further decomposition. The procedure is introduced as part of a hierarchical protocol of simulations at different temperatures. The convergence of simulations within metastable subsets is used as an ''a posteriori'' criterion for a successful identification of metastability. All results are presented with the visualization program AmiraMol.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 4
    Publication Date: 2019-05-10
    Description: The adaptive finite element code {\sc Kardos} solves nonlinear parabolic systems of partial differential equations. It is applied to a wide range of problems from physics, chemistry, and engineering in one, two, or three space dimensions. The implementation is based on the programming language C. Adaptive finite element techniques are employed to provide solvers of optimal complexity. This implies a posteriori error estimation, local mesh refinement, and preconditioning of linear systems. Linearely implicit time integrators of {\em Rosenbrock} type allow for controlling the time steps adaptively and for solving nonlinear problems without using {\em Newton's} iterations. The program has proved to be robust and reliable. The user's guide explains all details a user of {\sc Kardos} has to consider: the description of the partial differential equations with their boundary and initial conditions, the triangulation of the domain, and the setting of parameters controlling the numerical algorithm. A couple of examples makes familiar to problems which were treated with {\sc Kardos}. We are extending this guide continuously. The latest version is available by network: {\begin{rawhtml} 〈A href="http://www.zib.de/Numerik/software/kardos/"〉 〈i〉 Downloads.〈/i〉〈/a〉 \end{rawhtml}}
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 5
    Publication Date: 2016-06-09
    Description: This article studies the relation of the two scientific languages Chemistry and Mathematics via three selected comparisons: (a) QSSA versus dynamic ILDM in reaction kinetics, (b) lumping versus discrete Galerkin methods in polymer chemistry, and (c) geometrical conformations versus metastable conformations in drug design. The common clear message from these comparisons is that chemical intuition may pave the way for mathematical concepts just as chemical concepts may gain from mathematical precisioning. Along this line, significant improvements in chemical research and engineering have already been possible -- and can be further expected in the future from the dialogue between the two scientific languages.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 6
    Publication Date: 2014-11-10
    Description: Several sets of reductions rules are known for preprocessing a graph when computing its treewidth. In this paper, we give reduction rules for a weighted variant of treewidth, motivated by the analysis of algorithms for probabilistic networks. We present two general reduction rules that are safe for weighted treewidth. They generalise many of the existing reduction rules for treewidth. Experimental results show that these reduction rules can significantly reduce the problem size for several instances of real-life probabilistic networks.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 7
    Publication Date: 2014-02-26
    Description: Signaling is crucial to the operation of modern telecommunication networks. A breakdown in the signaling infrastructure typically causes customer service failures, incurs revenue losses, and hampers the company image. Therefore, the signaling network has to be highest reliability and survivability. This in particular holds for the routers in such a network, called \textit{signaling transfer points\/} (STPs). The robustness of an STP can be improved by equally distributing the load over the internal processing units. Several constraints have to be taken into account. The load of the links connected to a processing unit changes over time introducing an imbalance of the load. In this paper, we show how integer linear programming can be applied to reduce the imbalance within an STP, while keeping the number of changes small. Two alternative models are presented. Computational experiments validate the integer programming approach in practice. The GSM network operator E-Plus saves substantial amounts of time and money by employing the proposed approach.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 8
    facet.materialart.
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    Publication Date: 2019-10-24
    Keywords: ddc:000
    Language: German
    Type: annualzib , doc-type:report
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  • 9
    Publication Date: 2020-11-13
    Description: In the problem of \emph{Online Call Admission in Optical Networks}, briefly called \textsc{oca}, we are given a graph $G=(V,E)$ together with a set of wavelengths~$W$ and a finite sequence $\sigma=r_1,r_2,\dots$ of calls which arrive in an online fashion. Each call~$r_j$ specifies a pair of nodes to be connected and an integral demand indicating the number of required lightpaths. A lightpath is a path in~$G$ together with a wavelength~$\lambda \in W$. Upon arrival of a call, an online algorithm must decide immediately and irrevocably whether to accept or to reject the call without any knowledge of calls which appear later in the sequence. If the call is accepted, the algorithm must provide the requested number of lightpaths to connect the specified nodes. The essential restriction is the wavelength conflict constraint: each wavelength is available only once per edge, which implies that two lightpaths sharing an edge must have different wavelengths. Each accepted call contributes a benefit equal to its demand to the overall profit. The objective in \textsc{oca} is to maximize the overall profit. Competitive algorithms for \textsc{oca} have been known for the special case where every call requests just a single lightpath. In this paper we present the first competitive online algorithms for the general case of larger demands.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 10
    Publication Date: 2020-11-13
    Description: Traditional optimization techniques assume, in general, knowledge of all data of a problem instance. There are many cases in practice, however, where decisions have to be made before complete information about the data is available. In fact, it may be necessary to produce a part of the problem solution as soon as a new piece of information becomes known. This is called an \emph{online situation}, and an algorithm is termed \emph{online}, if it makes a decision (computes a partial solution) whenever a new piece of data requests an action. \emph{Competitive analysis} has become a standard yardstick to measure the quality of online algorithms. One compares the solution produced by an online algorithm to that of an optimal (clairvoyant) offline algorithm. An online algorithm is called $c$-competitive if on every input the solution it produces has cost'' at most $c$~times that of the optimal offline algorithm. This situation can be imagined as a game between an online player and a malicious adversary. Although competitive analysis is a worst-case analysis and henceforth pessimistic, it often allows important insights into the problem structure. One can obtain an idea about what kind of strategies are promising for real-world systems and why. On the other hand there are also cases where the offline adversary is simply too powerful and allows only trivial competitiveness results. This phenomenon is called hitting the triviality barrier''. We investigate several online problems by means of competitive analysis. We also introduce new concepts to overcome the weaknesses of the standard approach and to go beyond the triviality barrier.
    Keywords: ddc:000
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 11
    Publication Date: 2014-02-26
    Description: The paper deals with the two-class priority M/M/1 system, where the prioritized class-1 customers are served under FCFS preemptive resume discipline and may become impatient during their waiting for service with generally distributed maximal waiting times but finite expectation. The class-2 customers have no impatience. The required mean service times may depend on the class of the customer. As the dynamics of class-1 customers are related to the well analyzed M/M/1+GI system, our aim is to derive characteristics for class-2 customers and for the whole system. The solution of the balance equations for the partial probability generating functions of the detailed system state process is given in terms of the weak solution of a family of boundary value problems for ordinary differential equations. By means of this solution formulae for the joint occupancy distribution and for the sojourn and waiting times of class-2 customers are derived generalizing results recently obtained by Choi et al. in case of deterministic maximal waiting times. For deterministic maximal waiting times partially new explicit formulae are given.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 12
    Publication Date: 2016-06-09
    Description: The bio-heat transfer equation is a macroscopic model for describing the heat transfer in microvascular tissue. So far the deduction of the Helmholtz term in the bio-heat transfer equation is not co role. In view of a future numerical application of this new mathematical model to treatment planning in hyperthermia we derive asymptotic estimates for first and second order correctors.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 13
    Publication Date: 2021-08-05
    Description: Mixed integer programs ($MIPs$) are commonly solved with branch and bound algorithms based on linear programming. The success and the speed of the algorithm strongly depends on the strategy used to select the branching variables. Today's state-of-the-art strategy is called \emph{pseudocost branching} and uses information of previous branchings to determine the current branching. We propose a modification of \emph{pseudocost branching} which we call \emph{history branching}. This strategy has been implemented in $SIP$, a state-of-the-art $MIP$ solver. We give computational results that show the superiority of the new strategy.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 14
    Publication Date: 2020-11-13
    Description: We consider the design of transparent optical networks from a practical perspective. Network operators aim at satisfying the communication demands at minimum cost. Such an optimization involves three interdependent planning issues: the dimensioning of the physical topology, the routing of lightpaths, and the wavelength assignment. Further topics include the reliability of the configuration and sparse wavelength conversion for efficient use of the capacities. In this paper, we investigate this extensive optical network design task. Using a flexible device-based model, we present an integer programming formulation that supports greenfield planning as well as expansion planning on top of an existing network. As solution method, we propose a suitable decomposition approach that separates the wavelength assignment from the dimensioning and routing. Our method in particular provides a lower bound on the total cost which allows to rate the solution quality. Computational experiments on realistic networks approve the solution approach to be appropriate.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 15
    Publication Date: 2020-11-13
    Description: Today's telecommunication networks are configured statically. Whenever a connection is established, the customer has permanent access to it. However, it is observed that usually the connection is not used continuously. At this point, dynamic provisioning could increase the utilization of network resources. WDM based Optical Transport Networks (OTNs) will shortly allow for fast dynamic network reconfiguration. This enables optical broadband leased line services on demand. Since service requests competing for network resources may lead to service blocking, it is vital to use appropriate strategies for routing and wavelength assignment in transparent optical networks. We simulate the service blocking probabilities of various dynamic algorithms for this problem using a well-founded traffic model for two realistic networks. One of the algorithms using shortest path routings performs best on all instances. Surprisingly, the tie-breaking rule between equally short paths in different wavelengths decides between success or failure.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 16
    Publication Date: 2020-11-13
    Description: Nachdem mit der KOBV-Suchmaschine die Online-Recherche in den wichtigsten Berliner und Brandenburgischen Bibliotheken realisiert ist, gehört der Aufbau der Online-Fernleihe als einer neuen, nutzerfreundlichen Dienstleistung zu den drängendsten Desideraten des KOBV. Dem Nutzer soll ein komfortabler Service geboten werden, der ihm im Anschluss an eine erfolgreiche Recherche die nahtlose - per Knopfdruck ausgelöste - Fernleih-Bestellung auf das gewünschte Medium erlaubt. Gleichzeitig trägt die Ablösung des traditionellen, per Post und Bücherauto versandten Roten Fernleihscheines durch eine sekundenschnelle Online-Kommunikation zu einer erheblichen Beschleunigung des Fernleih-Verfahrens bei. Der KOBV beteiligt sich an der Initiative der deutschen Bibliotheksverbünde zur Automatisierung und Beschleunigung der Fernleihe. Die Realisierung soll im KOBV in einem zweistufigen Verfahren erfolgen: (1) verbundinterne Fernleihe im KOBV und (2) verbundübergreifende Fernleihe in der Zusammenarbeit mit den anderen Verbünden. Eine Verbund-Fernleih-Software für den KOBV muss insbesondere den KOBV-spezifischen Gegebenheiten genügen, die in dieser Form in den anderen deutschen Verbünden nicht anzutreffen sind. Im Jahre 2001 hat eine KOBV-Arbeitsgruppe Spezifikationen für eine Verbund-Fernleih-Software erarbeitet, in der die Besonderheiten des KOBV mit berücksichtigt sind. Beim Aufbau der automatisierten Fernleihe als einer regulären KOBV-Dienstleistung geht es nicht allein darum, einen schnellen, komfortablen Service für Nutzer einzurichten, sondern darüber hinaus um eine weitreichende Rationalisierung innerhalb der Bibliotheken. Das vorliegende Spezifikationspapier zielt auf beide Faktoren ab, indem es die Fernleihe als integrierten Dienst entwirft, der von der Bestellung bis zur Bereitstellung des Mediums in der gebenden Bibliothek automatisiert - ohne manuelles Eingreifen der Fernleihstelle - abläuft: die jetzige manuell durchgeführte Fernleihe wird durch die automatisierte Fernleihe abgelöst.
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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  • 17
    Publication Date: 2020-12-14
    Description: In the online traveling salesman problem $OLTSP$ requests for visits to cities arrive online while the salesman is traveling. We study the $F{\_max}-OLTSP$ where the objective is to minimize the maximum flow time. This objective is particularly interesting for applications. Unfortunately, there can be no competitive algorithm, neither deterministic nor randomized. Hence, competitive analysis fails to distinguish online algorithms. Not even resource augmentation which is helpful in scheduling works as a remedy. This unsatisfactory situation motivates the search for alternative analysis methods. We introduce a natural restriction on the adversary for the $F{\_max}-OLTSP$ on the real line. A \emph{non-abusive adversary} may only move in a direction if there are yet unserved requests on this side. Our main result is an algorithm which achieves a constant competitive ratio against the non-abusive adversary.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 18
    Publication Date: 2016-06-30
    Description: While attribute-value pairs are a popular method to name objects, information retrieval from those attribute-based namespaces is not an easy task. The user has to recall correct attribute names and values and master the syntax and semantics of query formulation. This paper describes hierarchical structures in attribute-based namespaces, shows how to extract them efficiently and evaluates the quality of these structures in an user experiment. It proposes an user interface for browsing attribute-named object sets which makes this task resemble todays file-system browsers and compares the usability of this interface to normal form-based methods in an user study.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 19
    Publication Date: 2014-02-26
    Description: In this paper, we quantify and discuss the physical and surface chemical processes leading to the formation, temporal evolution and sedimentation of dust grains in brown dwarf and giant gas planet atmospheres: nucleation, growth, evaporation and gravitational settling. Considering dust particles of arbitrary sizes in the different hydrodynamical regimes (free molecular flow, laminar flow, turbulent flow), we evaluate the equilibrium drift velocities (final fall speeds) and the growth rates of the particles due to accretion of molecules. We show that a depth-dependent maximum size of the order of $a_{\rm max}\!\approx\!1\,\mu{\rm m\,(upper\ regions)} \ldots 100\,\mu{\rm m\,(lower\ regions)}$ exists, which depends on the condensate and the stellar parameters, beyond which gravitational settling is faster than growth. Larger particles can probably not be formed and sustained in brown dwarf atmospheres. We furthermore argue that the acceleration towards equilibrium drift is always very fast and that the temperature increase of the grains due to the release of latent heat during the growth process is negligible. Based on these findings, we formulate the problem of dust formation coupled to the local element depletion/enrichment of the gas in brown dwarf atmospheres by means of a system of partial differential equations. These equations state an extension of the moment method developed by Gail\plus Sedlmayr\,(1988) with an additional advective term to account for the effect of size-dependent drift velocities of the grains. A dimensionless analysis of the new equations reveals a hierarchy of nucleation $\to$ growth $\to$ drift $\to$ evaporation, which characterises the life cycle of dust grains in brown dwarf atmospheres. The developed moment equations can be included into hydrodynamics or classical stellar atmosphere models. Applications of this description will be presented in a forthcoming paper of this series.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 20
    Publication Date: 2021-01-21
    Description: Global grid environments do not only provide massive aggregated computing power but also an unprecedented amount of distributed storage space. Unfortunately, dynamic changes caused by component failures, local decisions, and irregular data updates make it difficult to efficiently use this capacity. In this paper, we address the problem of improving data availability in the presence of unreliable components. We present an analytical model for determining an optimal combination of distributed replica catalogs, catalog sizes, and replica servers. Empirical simulation results confirm the accuracy of our theoretical analysis. Our model captures the characteristics of highly dynamic environments like peer-to-peer networks, but it can also be applied to more centralized, less dynamic grid environments like the European {\em DataGrid}.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 21
    Publication Date: 2021-01-22
    Description: Das Management von großen Datenmengen spielt eine immer wichtigere Rolle, wie aktuelle Entwicklungen in der Hochenergiephysik [2] zeigen. Für das DataGrid-Projekt zum Beispiel ist es notwendig, große Datenmengen auf mehrere Rechenzentren in Europa zu verteilen und die Daten untereinander zu synchronisieren. Auch innerhalb von Clustern gewinnen mit zunehmender Anzahl der Knoten Werkzeuge zur effizienten Synchronisation und Verteilung von Daten an Bedeutung. Im Rahmen dieser Arbeit wurde ein effizientes Verfahren zur Synchronisation von verteilten Verzeichnisstrukturen entwickelt und implementiert. Mit diesem Verfahren ist es möglich, unabhängige Änderungen an beliebigen Repositories gleichzeitig durchzuführen. Das Verfahren benötigt keine zentrale Instanz, wodurch eine gegenüber vielen existierenden Verfahren verbesserte Skalierbarkeit erreicht werden konnte. Dabei wurden Erkenntnisse aus der Graphentheorie eingesetzt und weiterentwickelt, um die Netzwerktopolo-gie und -handbreiten zwischen den Rechnern zu berücksichtigen. Durch die Verwendung einer Offline-Synchronisation werden Änderungen erst dann an andere Rechner propagiert, wenn der Nutzer dies anstößt. Das kann zum Beispiel nach einer abgeschlossenen Transaktion, die Änderungen an mehreren Dateien beinhaltet, angemessen sein.
    Description: Current developments in high energy physics [2] show that the management of large datasets plays an important role. For the DataGrid project it is necessary to distribute large datasets over several computing centers all over Europe and to synchronize these datasets. Within clusters tools for efficient synchronization and distribution of data become more important, too. In this thesis, a method to synchronize distributed directory structures was developed and implemented which makes it possible to perform independent changes to arbitrary repositories simultaneously. This method needs no central instance and therefore the presented system achieves a better scalability than many existing systems. Knowledge from graph theory was used and improved to take the network topology and the network bandwidth between the computers into account. By using offline synchronization, changes will only be propagated when the user initiates it. This can be reasonable after a completed transaction which consists of changes on several files.
    Keywords: ddc:000
    Language: German
    Type: masterthesis , doc-type:masterThesis
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  • 22
    Publication Date: 2020-11-17
    Description: An instance of the \emph{maximum coverage} problem is given by a set of weighted ground elements and a cost weighted family of subsets of the ground element set. The goal is to select a subfamily of total cost of at most that of a given budget maximizing the weight of the covered elements. We formulate the problem on graphs: In this situation the set of ground elements is specified by the nodes of a graph, while the family of covering sets is restricted to connected subgraphs. We show that on general graphs the problem is polynomial time solvable if restricted to sets of size at most~$2$, but becomes NP-hard if sets of size~$3$ are permitted. On trees, we prove polynomial time solvability if each node appears in a fixed number of sets. In contrast, if vertices are allowed to appear an unbounded number of times, the problem is NP-hard even on stars. We finally give polynomial time algorithms for special cases where the subgraphs form paths and the host graph is a line, a cycle or a star.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 23
    facet.materialart.
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    Publication Date: 2014-02-26
    Description: Hinter der für den Uneingeweihten etwas kryptischen Frage "P = NP?" verbirgt sich das derzeit wichtigste Problem der Komplexitätstheorie. Dieser Artikel erläutert einige Aspekte der Theorie und erklärt informell, was "P = NP?" bedeutet. Es geht nicht nur um komplizierte algorithmische Mathematik und Informatik, sondern um grundsätzliche Fragen unserer Lebensumwelt. Kann man vielleicht beweisen, dass es für viele Probleme unseres Alltags keine effizienten Lösungsmethoden gibt?
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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  • 24
    Publication Date: 2020-03-11
    Description: The Cooperative Library Network Berlin-Brandenburg (KOBV) has set the development of a genuine library information portal for the two German Lander (federal states) Berlin and Brandenburg as its main task for the next years. This joined effort is driven by the vision of an user friendly Internet information portal which is accessible anytime, from anywhere in the world. The idea of a regional information portal can be understood as the logically consistent development of the basic ideas of the KOBV. Starting in 1997, the consortia has set the implementation of a virtual OPAC instead of a physical union catalogue as its goal. The result was the KOBV-Search Engine which already has some qualities of a portal itself. The paper begins with initial remarks about the German library world, which do form the background for the project and its initiator - the KOBV consortia. After this preliminary part, different types of portals are introduced. The basic features of the KOBV-Search Engine as one of the cornerstones of the future portal are discussed in the following. The information portal will be much richer in content and services for the end-user. Two aspects are focused on in more detail: the presentation of resources, which becomes a compelling requirement because of the broader range of content and the personalization of services, as one important feature to suit user's individual needs.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 25
    Publication Date: 2019-01-29
    Description: The paper presents a particle method framework for resolving molecular dynamics. Error estimators for both the temporal and spatial discretization are advocated and facilitate a fully adaptive propagation. For time integration, the implicit trapezoidal rule is employed, where an explicit predictor enables large time steps. The framework is developed and exemplified in the context of the classical Liouville equation, where Gaussian phase-space packets are used as particles. Simplified variants are discussed shortly, which should prove to be easily implementable in common molecular dynamics codes. A concept is illustrated by numerical examples for one-dimensional dynamics in double well potential.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 26
    Publication Date: 2019-01-29
    Description: The paper deals with three different Newton algorithms that have recently been worked out in the general frame of affine invariance. Of particular interest is their performance in the numerical solution of discretized boundary value problems (BVPs) for nonlinear partial differential equations (PDEs). Exact Newton methods, where the arising linear systems are solved by direct elimination, and inexact Newton methods, where an inner iteration is used instead, are synoptically presented, both in affine invariant convergence theory and in numerical experiments. The three types of algorithms are: (a) affine covariant (formerly just called affine invariant) Newton algorithms, oriented toward the iterative errors, (b) affine contravariant Newton algorithms, based on iterative residual norms, and (c) affine conjugate Newton algorithms for convex optimization problems and discrete nonlinear elliptic PDEs.
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  • 27
    Publication Date: 2014-02-26
    Description: In Analogie zu den Elektrizitätsnetzen electricity grid), von denen die technische Revolution ausging, wurde der Begriff Computational Grid (kurz Grid) geprägt. Ein wichtiger Bestandteil des Systems liegt im benutzerfreundlichen Zugang und der koordinierten Nutzung der weltweit verteilten Speicherressourcen und Rechnerkapazitäten. Bei der Entwicklung dazu notwendiger Technologien und Software (Middleware) profitiert man von Kenntnissen und Erfahrungen bei der Entwicklung verteilter Algorithmen, dem Software-Engineering und dem Supercomputing.
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    Language: German
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  • 28
    Publication Date: 2020-02-11
    Description: In this article we study the problem of designing a nation-wide communication network. Such networks usually consist of an access layer, a backbone layer, and maybe several intermediate layers. The nodes of each layer must be connected to those of the next layer in a tree-like fashion. The backbone layer has to satisfy certain survivability and routing constraints. Given the node locations, the demands between them, the possible connections and hardware configurations, and various other technical and administrational constraints, the goal is to decide, which node is assigned to which network level, how the nodes are connected, what hardware must be installed, and how traffic is routed in the backbone. Mixed integer linear programming models and solution methods are presented for both the access and the backbone network design problem. The focus is on the design of IP-over-SDH networks, but the access network design model and large parts of the backbone network design models are general and also applicable for other types of communication networks. Results obtained with these methods in the planning of the German research network are presented.
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  • 29
    Publication Date: 2021-02-19
    Description: We present an online algorithm for a real-world vehicle dispatching problem at ADAC, the German Automobile Association.
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  • 30
    Publication Date: 2020-03-11
    Description: Eine fremddatengestützte Katalogisierung bedeutet für die einzelne Bibliothek unbestritten eine Zeit- und Kostenersparnis. Dieser Report beleuchtet die unterschiedlichen Faktoren technischer und organisatorischer Natur, die die Fremddatennutzung in der dezentralen Struktur des Kooperativen Bibliotheksverbundes Berlin-Brandenburg (KOBV) beeinflussen. Die Ausführungen stützen sich im Wesentlichen auf eine Umfrage, die die Autoren im Mai / Juni 2002 unter KOBV-Mitgliedsbibliotheken zum Thema Fremddatennutzung durchgeführt haben. Dargelegt wird, wie komfortabel die in den KOBV-Bibliotheken eingesetzten Bibliotheksinformationssysteme eine fremddatengestützte Katalogisierung erlauben. Diskutiert wird zudem die Software ZACK, die sich als Alternative zu einem eigenen Z39.50-Client zur Datenübernahme anbietet. Erstmals seit Bestehen des Verbundes werden Zahlen veröffentlicht über den Anteil der Bibliotheken, die Fremddaten nutzen und denjenigen, die dieses Angebot nicht wahrnehmen. Dabei wird die Fremddatenutzung differenziert sowohl für den Bereich der Neuaufnahmen als auch für die Retrokatalogisierung. In der weiteren Analyse werden zusätzliche Aspekte betrachtet wie z.B. die verfügbaren bzw. gewünschten Datenbanken im Verhältnis zum sprachlichen Spektrum des erworbenen Katalogisierungsgutes. Eingegangen wird auch auf die von den Bibliotheken genannten Hauptproblemen und die gewünschten zusätzlichen Serviceleistungen auf Seiten der KOBV-Verbundzentrale. Als Ergebnis dieses Status-Quo-Berichts legt das Autorenteam eine Reihe von Empfehlungen vor, die darauf abzielen, auch für KOBV-Bibliotheken in Zukunft eine Fremddatennutzungsquote von 70 - 75 % zu erreichen.
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  • 31
    Publication Date: 2014-02-26
    Description: Substellar atmospheres are cool and dense enough that dust forms very efficiently. As soon as these particles are formed, they sizedependently precipitate due to the large gravity of the objects. Arriving in hot atmospheric layers, the dust evaporates and enriches the gas by those elements from which it has formed. The upper atmospheric layers are depleted by the same elements. Non-continuous and spatially inhomogeneous convective element replenishment, generating a turbulent fluid field, completes the circuit of dust. The formation of dust in substellar atmosphere is described by extending the classical theory of Gail\plus Sedlmayr for the case of different gas and dust velocities. Turbulence is modeled in different scale regimes which reveals turbulence as trigger for dust formation in hot environments. Both mechanisms cause the dust to be present in else wise dust-hostile region: precipitation transports the dust into hot regions, and turbulence allows the formation of dust in there.
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  • 32
    Publication Date: 2014-02-26
    Description: The talk given by the author at the CRM workshop on Superintegrability in Sep.\ 2002 and this related paper report on work in two subjects. One is the collaboration with Vladimir Sokolov and Takayuki Tsuchida in an effort to classify polynomial integrable vector evolution equations. The other is the computer algebra package {\sc Crack} which did the main computations in solving large bi-linear algebraic systems. Although originally designed to solve over-determined systems of partial differential equations a number of extensions made {\sc Crack} a powerful tool for solving systems of bi-linear algebraic equations. Such systems turn up in many different classification problems some of which were investigated by other participants of this workshop. Two additional applications are outlined. In the talk on which this article is based a method to reduce the length of equations was presented which proved to be useful in solving the bi-linear algebraic systems. Due to numerous asked questions about the computer program, a more complete overview is given in the appendix.
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  • 33
    Publication Date: 2020-11-13
    Description: Die KOBV-Suchmaschine hat seit ihrer Inbetriebnahme Ende 1999 entscheidend zur Verbesserung der Informationsinfrastruktur in Berlin und Brandenburg beigetragen. Auf der Basis der offenen Plattform KOBV-Suchmaschine wird die KOBV-Zentrale gemeinsam mit den Bibliotheken in den nächsten Jahren das Dienstleistungsangebot des KOBV und seiner Bibliotheken kontinuierlich erweitern. Dabei sollen die Prinzipien des KOBV - Offenheit, Heterogenität und Dezentralität auf technischer und organisatorischer Ebene - gewahrt bleiben. Die einzelnen KOBV-Bibliotheken werden sich mit ihren Angeboten in unterschiedlicher Weise im Web positionieren. Die Integration auf regionaler Ebene kann und soll die lokalen Angebote nicht künstlich vereinheitlichen. Das kooperative Portal, das in der Region aufgebaut wird, ist als System geplant, in dem zentrales Portal und lokale Portale nicht hierarchisch einander zugeordnet, sondern miteinander vernetzt sind. Das \glqq KOBV-Informationsportal \grqq soll in der KOBV-Zentrale im Rahmen eines wissenschaftlichen Projektes von Mitte 2001 bis Ende 2003 aufgebaut werden. Das vorliegende Papier gibt einen ersten allgemeinen Einblick, welche Funktionen das \glqq KOBV-Informationsporta \grqq umfassen soll und stellt die Teilprojekte der 1. Stufe vor.
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  • 34
    Publication Date: 2014-11-10
    Description: Oriented matroids are combinatorial structures that encode the combinatorics of point configurations. The set of all triangulations of a point configuration depends only on its oriented matroid. We survey the most important ingredients necessary to exploit oriented matroids as a data structure for computing all triangulations of a point configuration, and report on experience with an implementation of these concepts in the software package TOPCOM. Next, we briefly overview the construction and an application of the secondary polytope of a point configuration, and calculate some examples illustrating how our tools were integrated into the {\sc polymake} framework.
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  • 35
    Publication Date: 2014-11-10
    Description: For all perfect graphs, the stable set polytope STAB$(G)$ coincides with the fractional stable set polytope QSTAB$(G)$, whereas STAB$(G) \subset$ QSTAB$(G)$ holds iff $G$ is imperfect. Padberg asked in the early seventies for ``almost'' perfect graphs. He characterized those graphs for which the difference between STAB$(G)$ and QSTAB$(G)$ is smallest possible. We develop this idea further and define three polytopes between STAB$(G)$ and QSTAB$(G)$ by allowing certain sets of cutting planes only to cut off all the fractional vertices of QSTAB$(G)$. The difference between QSTAB$(G)$ and the largest of the three polytopes coinciding with STAB$(G)$ gives some information on the stage of imperfectness of the graph~$G$. We obtain a nested collection of three superclasses of perfect graphs and survey which graphs are known to belong to one of those three superclasses. This answers the question: which graphs are ``almost'' perfect?
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  • 36
    Publication Date: 2020-11-13
    Description: Die Automatisierung von innerbetrieblicher Logistik erfordert -- über die physikalische Steuerung von Geräten hinaus -- auch eine effiziente Organisation der Transporte: ein Aufgabenfeld der kombinatorischen Optimierung. Dieser Artikel illustriert anhand von konkreten Aufgabenstellungen die Online-Problematik (unvollständiges Wissen) sowie die Echtzeit-Problematik (beschränkte Rechenzeit), auf die man in der innerbetrieblichen Logistik trifft. Der Text gibt einen Überblick über allgemeine Konstruktionsprinzipien für Online-Algorithmen und Bewertungsmethoden, die bei der Entscheidung helfen, welche Algorithmen für eine vorliegende Problemstellung geeignet sind.
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    Language: German
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  • 37
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    Publication Date: 2014-11-10
    Description: \We discuss a nested collection of three superclasses of perfect graphs: near-perfect, rank-perfect, and weakly rank-perfect graphs. For that, we start with the description of the stable set polytope for perfect graphs and allow stepwise more general facets for the stable set polytopes of the graphs in each superclass. Membership in those three classes indicates how far a graph is away from being perfect. We investigate for webs and antiwebs to which of the three classes they belong. We provide a complete description of the facets of the stable set polytope for antiwebs (with help of a result due to Shepherd on near-bipartite graphs). The main result is that antiwebs are rankperfect.
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  • 38
    Publication Date: 2021-01-21
    Description: \textsf{\itshape{GuiGen}} is a comprehensive set of tools for creating customized graphical user interfaces (GUIs). It draws from the concept of computing portals, which are here seen as interfaces to application-specific computing services for user communities. While \textsf{\itshape{GuiGen}} was originally designed for the use in computational grids, it can be used in client/server environments as well. Compared to other GUI generators, \textsf{\itshape{GuiGen}} is more versatile and more portable. It can be employed in many different application domains and on different target platforms. With \textsf{\itshape{GuiGen}}, application experts (rather than computer scientists) are able to create their own individually tailored GUIs.
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  • 39
    Publication Date: 2014-02-26
    Description: The purpose of the paper is to formulate and use syzygies for systems of linear PDEs. The computation of an equivalent of a GCD for linear partial differential operators will save us their factorization which is otherwise only possible algorithmically in special cases. After showing the computation with the new and the traditional method and comparing both in the next three sections, the algorithm is explained in general and an overview is given.
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  • 40
    Publication Date: 2020-11-13
    Description: Telekommunikation ist seit Jahren \glqq in\grqq. Zunächst gab es einen enormen Aufschwung; neue Technologien und Dienste haben eine überwältigende, nicht vorhersehbare Akzeptanz gefunden. Derzeit ist -- ausgelöst durch die UMTS-Lizenzversteigerungen, Rezessions- und Sättigungstendenzen -- eine Krise zu verzeichnen. Viele (auch wir) sind davon überzeugt, dass technischer Fortschritt und nützliche Dienste demnächst die Stimmung wieder ändern werden. Wenigen ist allerdings bewusst, welche Rolle Mathematik bei der Entwicklung und dem effizienten Einsatz vieler der neuen Kommunikationstechnologien spielt. In diesem Artikel soll kein Überblick über diesen umfangreichen Themenkreis gegeben werden. Wir zeigen lediglich an einem konkreten Beispiel aus dem Mobilfunk, der Frequenzplanung in GSM-Funknetzen, was man durch geeignete Modellierung der praktischen Fragestellung und den Einsatz problemadäquater Algorithmen erreichen kann.
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    Language: German
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  • 41
    Publication Date: 2020-03-09
    Description: Wir beschreiben einen Ansatz zur integrierten Umlauf- und Dienstplanung im öffentlichen Nahverkehr. Der Ansatz zielt auf die Verbesserung des Gesamtwirkungsgrades dieser beiden Planungsschritte und auf die besondere Planungsproblematik im Regionalverkehr. Wir entwickeln dazu mathematische Optimierungstechniken für den Einsatz in den Planungssystemen MICROBUS II und DIVA.
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  • 42
    Publication Date: 2014-02-26
    Description: A graph property is called elusive (or evasive) if every algorithm for testing this property has to read in the worst case $n\choose 2$ entries of the adjacency matrix of the given graph. Several graph properties have been shown to be elusive, e.g. planarity (Best et al) or $k$-colorability (Bollobas). A famous conjecture of Karp says that every non-trivial monotone graph property is elusive. We prove that a non-monotone but hereditary graph property is elusive: perfectness.
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  • 43
    Publication Date: 2014-02-26
    Description: Recently, a novel approach for the analysis of molecular dynamics on the basis of a transfer operator has been introduced. Therein conformations are considered to be disjoint metastable clusters within position space of a molecule. These clusters are defined by almost invariant characteristic functions that can be computed via {\em Perron Cluster} analysis. The present paper suggests to replace crisp clusters with {\em fuzzy} clusters, i.e. to replace characteristic functions with membership functions. This allows a more sufficient characterization of transiton states between different confor conformations and therefore leads to a better understanding of molecular dynamics. Fur thermore, an indicator for the uniqueness of metastable fuzzy clusters and a fast algorithm for the computation of these clusters are described. Numerical examples are included.
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  • 44
    Publication Date: 2019-01-29
    Description: The paper provides a detailed analysis of a short step interior point algorithm applied to linear control constrained optimal control problems. Using an affine invariant local norm and an inexact Newton corrector, the well-known convergence results from finite dimensional linear programming can be extended to the infinite dimensional setting of optimal control. The present work complements a recent paper of Weiser and Deuflhard, where convergence rates have not been derived. The choice of free parameters, i.e. the corrector accuracy and the number of corrector steps, is discussed.
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  • 45
    Publication Date: 2017-02-21
    Description: Pseudo--transient continuation methods are quite popular for the numerical solution of steady state problems, typically in PDEs. They are based on an embedding into a time dependent initial value problem. In the presence of dynamical invariants the Jacobian matrix of the nonlinear equation system is bound to be singular. The paper presents a convergence analysis which takes this property into account -- in contrast to known approaches. On the basis of the new analysis adaptive algorithms are suggested in detail. These include a variant with Jacobian approximations as well as inexact pseudo--transient continuation, both of which play an important role in discretized PDEs. Numerical experiments are left to future work.
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  • 46
    Publication Date: 2014-02-26
    Description: A beautiful result of Bröcker and Scheiderer on the stability index of basic closed semi-algebraic sets implies, as a very special case, that every $d$-dimensional polyhedron admits a representation as the set of solutions of at most $d(d+1)/2$ polynomial inequalities. Even in this polyhedral case, however, no constructive proof is known, even if the quadratic upper bound is replaced by any bound depending only on the dimension. Here we give, for simple polytopes, an explicit construction of polynomials describing such a polytope. The number of used polynomials is exponential in the dimension, but in the 2- and 3-dimensional case we get the expected number $d(d+1)/2$.
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  • 47
    Publication Date: 2014-11-10
    Description: TOPCOM is a package for computing triangulations of point configurations and oriented matroids. For example, for a point configuration one can compute the chirotope, components of the flip graph of triangulations, enumerate all triangulations. The core algorithms implemented in TOPCOM are described, and implentation issues are discussed.
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  • 48
    Publication Date: 2020-11-13
    Description: A model for the optimisation of the location and configuration of base stations in a UMTS network is described. The focus is primarily on modelling the configuration problem sufficiently accurate using mixed-integer variables and (essentially) linear constraints. These constraints reflect the limited downlink code capacity in each cell, the interference limitations for successful up- and downlink transmissions, the need for sufficiently strong (cell) pilot signals, and the potential gain for mobiles from being in soft(er) hand-over. It is also explained how to use the model as a basis for rating network configurations.
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  • 49
    Publication Date: 2016-06-09
    Description: Computational drug design studies molecular recognition in the {\em virtual lab}. The arising Hamiltonian dynamics is known to be chaotic and ill-conditioned already after picoseconds, whereas times are $msec$ up to $min$. Classical molecular dynamics with long term trajectory computation gives, at best, information about time and statistical ensemble averages. The present paper surveys a recent new modeling approach called {\em conformational dynamics}, which is due to the author and Ch. Schütte. This approach achieves information about the dy time scales by telescoping a short term deterministic model with a statistical model. Examples of small biomolecules are included.
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  • 50
    Publication Date: 2021-02-19
    Description: Combinatorial online optimization is an area with lots of applications and potential for significant progress, both in theory and practice. In this short note we sketch the ADACproblem, a typical large-scale online optimization problem, discuss some theoretical and pratical issues coming up, and explain, very briefly, how we approach this problem mathematically. Online problems are a battlefield of heuristics with many strong claims about their solution quality. We indicate that a stronger problem orientation and the use of a little more mathematics may yield.
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  • 51
    Publication Date: 2014-02-26
    Description: A subset ${\cal C}$ of the power set of a finite set $E$ is called cardinality homogeneous if, whenever ${\cal C}$ contains some set $F$, ${\cal C}$ contains all subsets of $E$ of cardinality $|F|$. Examples of such set systems ${\cal C}$ are the sets of circuits and the sets of cycles of uniform matroids and the sets of all even or of all odd cardinality subsets of $E$. With each cardinality homogeneous set system ${\cal C}$, we associate the polytope $P({\cal C})$, the convex hull of the incidence vectors of all sets in ${\cal C}$, and provide a complete and nonredundant linear description of $P({\cal C})$. We show that a greedy algorithm optimizes any linear function over $P({\cal C})$, give an explicit optimum solution of the dual linear program, and provide a polynomial time separation algorithm for the class of polytopes of type $P({\cal C})$.
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  • 52
    Publication Date: 2014-02-26
    Description: Die Bibliotheken des KOBV haben im Jahr 2001 die Entwicklung der KOBV-Suchmaschine zu einem gemeinsamen Informationsportal Berlin-Brandenburg und den Aufbau lokaler Bibliotheksportale als Hauptentwicklungsziele des KOBV definiert. Diese Informationsportale sollen mit Standardsoftware realisiert werden. Um die Auswahl eines Systems zu unterstützen, wurde in der Zentrale des KOBV ausgewählte Systeme untersucht. In der Arbeit werden zahlreiche Kriterien vorgestellt, auf Grund derer die betreffenden Systeme beurteilt werden. Die Kriterien umfassen sowohl Aspekte aus der Sicht der Benutzer als auch Kriterien aus der Sicht der Betreiber eines solchen Systems. Wesentliche Funktionen und die Realisierung von verschiedenen Merkmalen werden im Bericht ausführlich beschrieben. Daneben liefert eine Tabelle mit allen betrachteten Kriterien eine Übersicht über vorhandene Merkmale und der Art der Realisierung.
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    Language: German
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  • 53
    Publication Date: 2021-03-16
    Description: In the cake cutting problem, $n\ge2$ players want to cut a cake into $n$ pieces so that every player gets a ``fair'' share of the cake by his own measure. We describe a protocol with $n-1$~cuts in which each player can enforce to get a share of at least~$1/(2n-2)$. Moreover we show that no protocol with $n-1$~cuts can guarantee a better fraction.
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  • 54
    Publication Date: 2022-07-07
    Description: We present a new efficient algorithm for the solution of direct time-harmonic scattering problems based on the Laplace transform. This method does not rely on an explicit knowledge of a Green function or a series representation of the solution, and it can be used for the solution of problems with radially symmetric potentials and problems with waveguides. The starting point is an alternative characterization of outgoing waves called \emph{pole condition}, which is equivalent to Sommerfeld's radiation condition for problems with radially symmetric potentials. We obtain a new representation formula, which can be used for a numerical evaluation of the exterior field in a postprocessing step. Based on previous theoretical studies, we discuss the numerical realization of our algorithm and compare its performance to the PML method.
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  • 55
    Publication Date: 2022-07-07
    Description: The aim of this paper is to develop fast methods for the solution of nonlinear Schrödinger type equations in fiber optics. Using the method of lines we have to solve a stiff system of ordinary differential equations where the eigenvalues of the Jacobian are close to the imaginary axis. This is usually done by a Split Step method. Here we consider the extrapolation of Split Step methods with adaptive order and step size control. For more complicated nonlinearities, in particular stimulated Raman scattering, Split Step methods are less efficient since symmetry is either destroyed or requires much additional effort. In this case we use implicit Runge Kutta formulas of Gauß type. The key point for the efficient implementation of these methods is that the system of nonlinear algebraic equations can be solved without setting up the Jacobian. The proposed methods are compared to other methods, in particular exponential integrators, the method of Marcuse, and the method of Blow and Wood.
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  • 56
    Publication Date: 2022-07-07
    Description: The work presents a new approach to the numerical solution of time-harmonic and time-dependent scattering problems. We replace Sommerfeld's radiation condition valid for the Helmholtz equation by a more general concept called pole condition. The pole condition is based on the Laplace transform of the exterior solution and allows a characterization of outgoing waves. Both new insight into the analysis of scattering problems as well as new numerical algorithms are obtained.
    Keywords: ddc:000
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
    Format: application/postscript
    Format: application/pdf
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  • 57
    Electronic Resource
    Electronic Resource
    Springer
    Calcified tissue international 7 (1971), S. 150-162 
    ISSN: 1432-0827
    Keywords: Uranium ; Bone ; Distribution ; Fission ; Chemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Description / Table of Contents: Résumé Une concentration moyenne de 2.4×10−8 g U/g de cendre a été obtenue à partir de l'os humain normal. La microdistribution de l'uranium dans l'os indique que cet élément est surtout limité à surface de l'endoste et, en particulier, aux surfaces de l'os lamellaire et aux parois des canaux de Havers, ouverts dans l'os corticol. Cette répartition suggère que l'uranium se présente sous une forme chimique impropre à son incorporation dans l'apatite osseux: il ne semble donc pas exister une distribution diffuse significative de l'uranium dans l'os.
    Abstract: Zusammenfassung Eine mittlere Konzentration von 2,4×10−8 g Uran/g Asche wurde in normalen menschlichen Knochen gefunden. Die Feinverteilung von Uran im Knochen zeigt, daß dieses Element hauptsächlich an der endostalen Oberfläche vorkommt, insbesondere an der Oberfläche des trabeculären Knochens und an den Wänden der offenen Haversschen Kanäle im kortikalen Knochen. Diese Verteilung läßt vermuten, daß Uran in einer chemischen Form vorliegt, welche sich für den Einbau in das Knochenapatit nicht eignet. Daraus folgt, daß keine signifikante diffuse Verteilung des Urans innerhalb des Knochens vorliegt.
    Notes: Abstract A mean concentration of 2.4×10−8 g U/g ash has been obtained for normal human bone The microdistribution of uranium in bone indicates that this element is mainly restricted to endosteal surfaces; in particular the surfaces of trabecular bone and the walls of open Haversian canals in cortical bone. This distribution suggests that uranium is present in a chemical form that is not acceptable for incorporation into bone apatite and consequently there does not appear to be a significant diffuse distribution of uranium throughout bone.
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  • 58
    ISSN: 1432-0827
    Keywords: Morphology ; Glycosaminoglycans ; Cartilage ; Chemistry ; Audioradiography ; Healing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Description / Table of Contents: Résumé Une perte de substance ostéo-cartilagineuse, de taille limitée et identique, est réalisée chez le lapin adulte et la cicatrisation est étudiée histologiquement et par autoradiographie après marquagein vitro au35S-sulfate. Une analyse microchimique est pratiquée pour le contenu et la composition en glycosaminoglycanes. 1. Entre la première semaine et la 4ème et 8ème semaine, un tissu conjonctif non-métachromatique se différencie en un cartilage métachromatique et la quantité de sulfate de chondroitine augmente de façon significative aux dépens des glycoprotéines. 2. Jusqu'à la 4ème semaine, la perte de substance est surtout comblée par de l'os néoformé: après cette période, la région est comblée au delà de la limite de la surface articulaire. 3. Le cartilage hyalin, ressemblant morphologiquement, autoradiographiquement et chimiquement au cartilage articulaire, en ce qui concerne la distribution en glycosaminoglycanes, constitute la surface articulaire de la perte de substance comblée dans un tiers des cas après 8 semaines. Le cartilage hyalin s'observe surtout dans les régions où de l'os néoformé a comblé la cavité médullaire. 4. Dans les deux tiers des cas, après 8 semaines, les surfaces articulaires des zones comblées comportent, non seulement du cartilage, mais aussi du tissu fibreux se formant essentiellement sur les parties latérales et dans les régions, où la cavité médullaire, fliant face, à la surface articulaire, n'a pas été comblée par du tissue osseux. La fraction glycoprotéique augmente par rapport à la fraction chondroitine sulfate. 5. Dans la majorité des cas, après 20 semaines, le cartilage néoformé subit des phénomènes dégénératifs, qui se traduisent par une diminution en chondroitine sulfate.
    Abstract: Zusammenfassung Bei ausgewachsenen Kaninchen wurde ein begrenzter, standardisierter, osteochondraler Defekt hervorgerufen, und das regenerierte Gewebe wurde histologisch und autoradiographisch durch Markierung in vitro mit35S-Sulfat und durch mikrochemische Bestimmung des Gehaltes und der Zusammensetzung der Glykosaminglykane untersucht. Die wichtigsten Befunde waren: 1. Zwischen 1 und 4–8 Wochen veränderte sich nichtmetachromatisches Bindegewebe zu metachromatisch gefärbtem Knorpel, und der Anteil an Chondroitin-Sulfat nahm auf Kosten der Glykoproteine signifikant zu. 2. Bis zu 4 Wochen war der Hauptteil des defekten Gebietes mit neugebildetem Knochen gefüllt; nach dieser Zeit lag dieser Bezirk oberhalb der Verknöcherungsgrenze in Richtung der Gelenkoberfläche. 3. Nach 8 Wochen bestand die Gelenkoberfläche des defekten Gebietes in einem Drittel der Fälle aus hyalinem Knorpel, der morphologisch, autoradiographisch und chemisch dem Gelenkknorpel in Bezug auf die Verteilung von Glykosaminoglykanen glich. Hyaliner Knorpel wurde hauptsächlich an Stellen beobachtet, wo neugebildeter Knochen die Markhöhle geschlossen hatte. 3. Nach 8 Wochen bestand die Gelenkoberfläche des defekten Gebietes in einem Drittel der Fälle aus hyalinem Knorpel, der morphologisch, autoradiographisch und chemisch dem Gelenkknorpel in Bezug auf die Verteilung von Glykosaminoglykanen glich. Hyaliner Knorpel wurde hauptsächlich an Stellen beobachtet, wo neugebildeter Knochen die Markhöhle geschlossen hatte. 4. Nach 8 Wochen bestanden Teile der Gelenkoberfläche des Defektes in zwei Dritteln der Fälle nicht nur aus Knorpel, sondern auch aus fibrösem Gewebe, welches vor allem in den seitlichen Teilen des Defektes und an Stellen vorlag, wo die Markhöhle gegenüber der Gelenkoberfläche nicht mit Knochengewebe verschlossen worden war. Die Glykoproteinfraktion nahm im Vergleich zur Chondroitin-Sulfatfraktion zu. 5. Nach 20 Wochen zeigten sich in den meisten Fällen bei neugebildetem Knorpel degenerative Veränderungen, welche durch eine gewisse Abnahme des Chondroitin-Sulfats wiedergegeben wurden.
    Notes: Abstract A limited, standardized osteochondral defect was created in adult rabbits and the regenerated tissue was examined histologically and autoradiographically after labellingin vitro with35S-sulphate, and microchemically for its content and composition of glycosaminoglycans. The principal findings were: 1. Between 1 week and 4 to 8 weeks, non-metachromatic connective tissue differentiated to metachromatically stained cartilage, and the proportion of the chondroitin sulphate increased significantly at the expense of the glycoproteins. 2. Up to 4 weeks, the major part of the defect area was filled with newly formed bone; after this time, the area lay above the level of the “tidemark”, towards the articular surface. 3. Hyaline cartilage with morphological, autoradiographic and chemical resemblance to the articular cartilage in terms of the distribution of glycosaminoglycans constituted the articular surface of the defect area in one-third of the cases at observation times after 8 weeks. Hyaline cartilage was observed mainly in areas where newly formed bone had closed the medullary cavity. 4. In two-thirds of the cases, after 8 weeks, parts of the articular surface of the defect consisted not only of cartilage but also of fibrous tissue, occurring mainly in the lateral parts of the defect and in areas where the medullary cavity facing the articular surface had not been sealed by bone tissue. The glycoprotein fraction increased relative to the chondroitin sulphate fraction. 5. In most cases after 20 weeks, newly-formed cartilage underwent degenerative changes, which were reflected in some reduction of the chondroitin sulphate.
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  • 59
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    Springer
    Calcified tissue international 8 (1971), S. 228-236 
    ISSN: 1432-0827
    Keywords: Skin ; Calcinosis ; Keratin ; Chemistry ; X-ray diffraction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Description / Table of Contents: Résumé Des études histologiques antérieures ont montré que le follicle pileux est particulièrement susceptible de se calcifier, lorsque la peau de rats hypercalcémiques est lésée. Des analyses chimiques et par diffraction aux rayons X du follicule ont confirmé ce résultat. — En se basant sur l'augmentation du calcium et du phosphore, les calcifications débutent dans le tissue folliculaire 6–12 h après une blessure d'intensité moyenne de la peau de rats, ayant reçu du dihydrotachysterol (DHT), et 24–48 h après une blessure similaire chez des rats non injectés. Les diagrammes de diffraction aux rayons X sont diffus. Trois heures après la blessure, on note une augmentation du calcium du tissu folliculaire qui ne semble pas en rapport avec le DHT qui traduit probablement une liaison de calcium plutôt qu'un dépot minéral.
    Abstract: Zusammenfassung Frühere histologische Untersuchungen haben gezeigt, daß der Haarfollikel besonders anfällig für Verkalkungen ist, wenn die Haut von hypercalcämischen Ratten verletzt wird. Dieses Resultat wurde nun durch direkte chemische Bestimmungen und Röntgendiffraktions-analysen von Follikelgewebe bestätigt. Aufgrund der erhöhten Calcium- und Phosphatwerte kann gesagt werden, daß nach einer leichten Quetschung der Haut von Ratten, die mit Dihydrotachysterol (DHT) behandelt wurden, im Haarfollikelgewebe nach 6–12 Std Mineral-ablagerungen stattfanden, wogegen Kontrollratten mit der gleichen leichten Hautverletzung diese Ablagerungen erst nach 24–48 Std zeigten. Röntgendiffraktionsanalysen ergaben ein diffuses Apatit-Muster. Innerhalb 3 Std nach der Verletzung wurde ein Anstieg des Calcium-gehaltes im Follikelgewebe beobachtet, der nicht im Zusammenhang mit der DHT-Behandlung stand, also nicht eine Mineralablagerung, sondern eher eine Bindung von Calcium widerspiegelte.
    Notes: Abstract Previous histological investigations have shown that the hair follicle is particularly susceptible to mineralization when the skin of hypercalcaemic rats is injured. Direct chemical and X-ray diffraction analyses of follicle tissue have now confirmed this finding. As judged by increases in both calcium and phosphorus, mineral deposits began to form in hair follicle tissue 6–12 h after a mild crush injury to the skin of rats dosed with dihydrotachysterol (DHT), and 24–48 h after a similar injury to the skin of non-dosed rats. X-ray diffraction gave a diffuse apatite pattern. Within 3 h of injury there was a rise in the calcium content of follicle tissue which was not related to DHT-dosing and which was probably a reflection of calcium binding rather than mineral deposition.
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  • 60
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    Calcified tissue international 8 (1971), S. 304-319 
    ISSN: 1432-0827
    Keywords: Chemistry ; Calcium ; Phosphate ; Solubility ; Computer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Description / Table of Contents: Résumé Un programme d'ordinateur a été mis au point pour calculer les activités ioniques du calcium et l'orthophosphate dans un grand nombre de solutions. Dans le cas de solutions synthétiques, les calculs sont vérifiés en comparant les valeurs de pH, obtenues par ordinateur, avec celles observées expérimentalement. Des essais de ce type, avec des solutions possèdant des concentrations de calcium et d'orthophosphate trouvées dans les liquides biologiques et à des valeurs de pH variant de 3.00 à 10.00, indiquent que le programme est adapté pour des applications biologiques. Le programme n'est pas effectif pour des solutions, dans les lesquelles l'ion bromure est la source principale de la force ionique, sans doute, par manque d'équation étendue de Debye-Hückel dans ces circonstances. Aucune formation de complexe de phosphate de sodium n'a été notée à des concentrations biologiques normales.
    Abstract: Zusammenfassung Es wurde ein Computer-Programm ausgearbeitet, um die Ionenaktivitäten von Calcium und Orthophosphat in einer breiten Varietät von Lösungen zu berechnen. Die Berechnungen wurden bei synthetischen Lösungen durch Vergleiche zwischen den auf diese Weise errechneten pH-Werten und den experimentell gefundenen kontrolliert. Diese Art Kontrollen mit Calcium-und Orthophosphatkonzentrationen, wie sie in biologischen Flüssigkeiten gefunden werden, und mit pH-Werten zwischen 3,0 und 10,0 wies darauf hin, daß das Programm für biologische Anwendungen geeignet war. Das Programm konnte nicht benützt werden für solche Lösungen, bei welchen hauptsächlich das Bromidion zur Einstellung der Ionenstärke verwendet wurde, vermutlich weil die erweiterte Debye-Hückel-Gleichung unter diesen Umständen nicht anwendbar ist. Die Bildung eines Natriumphosphat-Komplexes unter normalen biologischen Konzentrationen konnte nicht nachgewiesen werden.
    Notes: Abstract A computer program has been designed to calculate the ionic activities of calcium and orthophosphate in a wide variety of solutions. In the case of synthetic solutions the calculations were checked by comparing the computed pH values with those observed experimentally. Tests of this type with solutions having the concentrations of calcium and orthophosphate found in biological fluids and with pH values ranging from pH 3.0–10.0 indicated that the program was suitable for biological applications. The program was not effective for solutions in which the bromide ion was a principal source of ionic strength probably because of the failure of the extended Debye-Hückel equation under those circumstances. No evidence for the formation of any sodium phosphate complex at normal biological concentrations could be found.
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  • 61
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    Calcified tissue international 8 (1971), S. 197-210 
    ISSN: 1432-0827
    Keywords: Fluorescence ; Calcium ; Collagen ; Chemistry ; Bone ; Dentine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Description / Table of Contents: Résumé Des composants fluorescents de l'os et la dentine sont séparés des hydrolysats alcalins de leur marice sur des colonnes Sephadex C25 CM d'échange cationique. Les concentrations en fluorescence et le spectre d'excitation (λ max 330 nm) et d'émission (λ max 395 nm) sont les mêmes que ceux observés au niveau des matrices intactes et gélatinisées. Les paramètres de fluorescence ne sont pas altérés par hydrolyse. La filtration sur gel à l'aide de colonnes Sephadex G 10 perment de différencier le matériel isolé en deux composants, ayant la même fluorescence et la même absorption UV. La fluorescence est indépendante de pH de 3.5–9.5. Des études de dialyse et de filtration sur gel de matrices gélatinisées indiquent une association étroite du matériel fluorescent avec les chaines polypeptidiques de collagène.
    Abstract: Zusammenfassung Fluorescierende Bestandteile aus Knochen und Dentin wurden in Sephadex C25 CM Kationen-Austauschersäulen von alkalischen Hydrolysaten ihrer Matrices getrennt. Die Fluorescenzintensitäten sowie die Erregungs- (λ max 330 nm) und Emissions- (λ max 395 nm) Spektren waren dieselben wie bei intakten und gelatinisierten Matrices. Die Fluorescenzparameter wurden durch die Hydrolyse nicht verändert. Eine Gelfiltration über Sephadex-G10-Säulen trennte das isolierte Material in 2 Komponenten auf, welche gleiche Fluorescenz- und UV-Absorptionseigenschaften zeigten. Im pH-Bereich zwischen 3,5 und 9,5 war die Fluorescenz unabhängig vom pH. Dialysierversuche sowie Gelfiltrationsexperimente mitden gelatinisierten Matrices zeigten eine starkgefügte Bindung des fluorescierenden Materials mit den Polypeptidketten des Kollagens.
    Notes: Abstract Fluorescent components in bone and dentine were separated from alkaline hydrolysates of their matrices on Sephadex C25 CM cationic exchange columns. The fluorescence levels, and the excitation (λ max 330 nm) and emission (λ max 395 nm) spectra, were the same as those observed in the intact and gelatinised matrices. The fluorescence parameters were unaltered by the hydrolysis procedure. Gel filtration on Sephadex G. 10 columns further resolved the isolated material into two components with the same fluorescence and UV absorption properties. The fluorescence was independent of pH over the range 3.5–9.5. Dialysis and gel filtration studies on the gelatinised matrices indicated a firmly-bonded association of the fluorescent material with the collagen polypeptide chains.
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  • 62
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    Biopolymers 10 (1971), S. 1049-1057 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ultrastructural morphology and x-ray and electron diffraction of poly (Gly-Gly-Ala) have been studied. The polymer has two forms; the first, form I possesses a super-folded cross-β structure, long fibers of which show some twisting and intertwining. Form II precipitates in a less distinct fibrous form from aqueous solution. The x-ray diffraction and oriented electron diffraction data suggest that form II is a polyglycine II helix situated in a monoclinic cell with dimensions a = 8.86 Å, b = 22.0 Å, c = 9.42 Å, and β = 90°. Combined with the morphological evidence it appears likely that form II is also in an antiparallel superfolded array.
    Additional Material: 5 Ill.
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  • 63
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    Biopolymers 10 (1971), S. 1099-1101 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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  • 64
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A statistical mechanical model was developed for use in connection with the problem of preferential binding of solvent components to proteins and of conformational transition in water-organic solvent systems. The model is a statistical one for the conformational transition of globular proteins induced by the adsorption of solutes in the solution, considered as a nearest-neighbor problem in statistical mechanics. Although a few illustrative examples are given, the actual interpretations of the experimental data using this theory are reserved for a later paper.
    Additional Material: 7 Ill.
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  • 65
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    Biopolymers 10 (1971), S. 1103-1103 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 66
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    Biopolymers 10 (1971), S. 1121-1138 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The concept and representation of a logical tree as defined in computer science is applied to obtain a suitable representation of protein molecules in computer programs which handle or calculate atomic coordinates of protein molecules. On the basis of this analysis and of the analysis of the calculation and modification of the structure of a protein from bond lengths, bond angles, and dihedral angles, which is reproduced in an appendix, program modules which accomplish the various required computations are described. Three such modules are given in Iverson notation; in fact, it is hoped that this article will serve as a reasonably complete basis for the preparation of machine programs by moderately proficient programmers.
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  • 67
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    Biopolymers 10 (1971), S. 1207-1212 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism spectrum obtained from a dilute aqueous solution of poly (ala-gly-gly) resembles that described for charged polypeptides such as the salt form of poly glutamic acid. A similar spectrum is found for films cast from aqueous solution where x-ray studies reported elsewhere have indicated a poly-glycinc II conformation. Evidence is presented for a heat induced poly-glycine II to unordered state transition similar to that described for collagen. The interpretation of this, the first observation of the optical properties of a poly-amino acid in the poly glycine II conformation, is further rationalized on the basis of spectra obtained from a number of polypeptides whose conformation approaches that of a 31 helix.
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  • 68
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    Biopolymers 10 (1971), S. 1229-1242 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of cupric ion on the emission of tryptophan, tyrosine, and serum albumins is studied by emission spectroscopy and lifetime measurements. It is found that whenever cupric ion is bound to tryptophan or tyrosine, their emissions are quenched completely. The quenching may be due to an electron transfer mechanism. The fluorescence of complexes of cupric ions with serum albumins is partially quenched; this is because energy is transferred from tryptophan to the complexed cupric ions by a dipolar energy transfer mechanism. It is deduced from the present study that the tryptophan in the human serum albumin molecule is between 11 and 16 Å from the nearest eupric ion binding sites (assumed to be at the surface of the protein) and that one of the tryptophan in the bovine serum albumin molecule is very close to the cupric ion binding sites and the other is near the center of the bovine serum albumin molecule. It is also found that the deuterium solvent effect on serum albumin fluorescence is very small, and that the quenching of bovine serum albumin fluorescence at the N-F transition is the result of quenching of the fluorescence of both tryptophans. The phosphorescence lifetime apparatus, capable of measuring decay times of signals with intensities changing over a few orders of magnitude, and the ratio spectrofluorometer, both of which were constructed in this laboratory, are also described.
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  • 69
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    Biopolymers 10 (1971), S. 1253-1260 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The measurements were made for the volume and the sound velocity changes (ΔV and ΔU) on titrating the sodium salt of poly (S-carboxymethyl L-cysteine) with dilute HCl. For the reaction, —COO- + H+ → —COOH, ΔV per mole of H+ bound was + 12. 7 ml and +11. 4 ml in salt-free and 0. 2 M NaCl solutions, respectively. Corresponding ΔU was about -13 cm/sec in salt-free polymer solution where 11.5 mM carboxylate ion reacts with equimolar hydrogen ion. ΔV associated with the coil-to-β transition was found to be +2. 35 ml in H2O and +1. 90 ml in 0. 2 M NaCl per mole of amino acid residue, respectively. These values are larger than those obtained for the coil-to-helix transition of poly (L-glutamic acid). ΔU for the transition was about -30 cm/sec in salt-free solution of polymer concentration 0.0115 mole/liter. Possible sources of ΔV and ΔU for reaction; coil → β, are (1) the formation of void volume and (2) the changes in the extent of solvation in amide linkage and in side chain.
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  • 70
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    Biopolymers 10 (1971), S. 1317-1329 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of three aromatic molecules to apomyoglobin has been investigated. In each case equilibrium dialysis studies and tryptophan fluorescence quenching studies indicate that a one to one complex has been formed. The fluorescence quenching studies further suggest that the binding of the aromatic molecules is at the heme site with possible involvement of the arginine CD3. Xenon, which is known to quench the fluorescence of aromatic hydrocarbons, is found to be bound to apomyoglobin-aromatic molecule complexes and quenches the emission of the aromatic molecule in the complexes. Oxygen quenches pyrene fluorescence in water solution but does not quench the pyrene fluorescence from the apomyoglobin-pyrene complex. This is explained by a slower rate of diffusion of oxygen to pyrene in the apomyoglobin-pyrene complex.
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  • 71
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    Biopolymers 10 (1971), S. 1365-1369 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rotor speed-dependent aggregation of T4 DNA in the analytical ultracentrifuge is studied in the presence of high pressure generated by compressed nitrogen gas in the cell. The extents of aggregation at various speeds are found to be practically the same in the presence and absence of pressure.
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  • 72
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    Biopolymers 10 (1971), S. 1331-1349 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The time-dependent theory developed in Part I is specialized to treat tetrameric hemoglobin, and the results of the theory for dimeric-and tetrameric hemoglobin are compared with data on the kinetics of the reactions of hemoglobin with carbon monoxide and oxygen at various salt concentrations for the case of large concentration of ligand relative to that of hemoglobin. The fit of the theoretical results to the data suggests that hemoglobin at a 2 M salt concentration is predominantly dimeric and that the tetramer should be taken as the functional unit to explain the kinetics of the reactions of normal hemoglobin. A relationship is established between the time-dependent theory arid Adair's Intermediate Compound Hypothesis (I.C.H.) for hemoglobin, as brought to its present state by Gibson and Roughton. A generalization (G.I.C.H.) of the I.C.H. is presented and is shown to be equivalent to the time-dependent theory in the limit of infinite ligand concentration. The I.C.H. is shown to be an excellent approximation to the centralized theory (G.I.C.H.) in this limit.
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  • 73
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    Biopolymers 10 (1971), S. 1421-1425 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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  • 74
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    Biopolymers 10 (1971), S. 1427-1428 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 75
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    Biopolymers 10 (1971), S. 1429-1454 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ability of oligodesoxyribonucleotides of various chain lengths to form complexes has been compared with that of oligoribonucleotides. Four series of oligonucleotidcs were prepared and investigated, i.e., dCn at acid pH versus rCn, dAn and dTn versus. rAn and rUn at neutral pH. The results indicate that in dilute solution, the formation of complexes is greatly facilitated in the case of desoxyoligomers and occurs for shorter oligomere than in the corresponding ribooligomers. The spectrophotometric titration of deoxyribooligo C indicates the appearance of two pK values in the 4-5 pH region characteristic of the double-stranded form, which occurs for much shorter dCn than rCn. The circular dichroism (CD.) spectra of deoxycytidylies in dilute solution starting from the trimer are conservative, characteristic of the double-stranded helical form of poly C at acid pH. In contrast, the CD spectra of a series of corresponding ribo Cn, under identical conditions is of nonconservative character similar to that of the single-stranded form of poly C at neutral pH, but differs in the band position. This spectrum is called intermediate. Only at higher concentrations of oligonucleotidcs (i.e., 10-3Minstead of 10-4M) does the circular dichroism spectrum of longer ribocytidylics assume conservative character. Thermal denaturation of deoxycytidylces at acid pH are strongly dependent on chain length and concentration, its one would expect for a cooperative helix-coil transition. The circular dichroism spectra measured at different temperatures shows one isosbestic point. In dilute solution, the standard-state enthalpy change found was 5-6 kcal/mole for higher oligomers (dC7). These properties are all in agreement with a structural transition from the d-Cn double-stranded form to a coil for n 〉 3. Studies of dAn and dTn in solutions of high ionic strength at low temperature indicate that complex formation occurs already at the level of trimer and for high oligomers. Under identical conditions a complex between rAn and rUn is detected only for oligomers longer than the hexamer. The nature of the “intermediate” form of oligoribo C at acid pH and low temperature was investigated by sedimentation and circular dichroism. A model of rCn is proposed of linear molecules which are partially double-stranded and partially single-stranded, which probably are slowly rearranged by “slippage” into a regular-double-stranded helical form.
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  • 76
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The number average molecular weight, Mn, of low molecular weight dextran was determined through endgroup analysis, and the intrinsic, viscosities of these materials in aqueous solution were determined at 25°C. The ultrasonic velocities in their aqueous solutions were also measured at 25 and 45°C. As concerns the molecular weight dependence of the intrinsic viscosity, partial specific compressibility of solute and the hound water around the solute, the following results were obtained. (1) log [η]-log Mn and [η]/Mn0.5 - Mn0.5 plots were in accord with the Mark-Houwink and Stockmayer-Fix-man equations respectively for Mn 〉 2, 000, but these plots deviated from the equations for Mn 〈 2, 000. (2)The partial specific compressibility, β1°, of dextran is expressed by following equation for Mn 〈 2,000: β1° = 10-12 × (13.6 log Mn - 51.7) (cm2/dyne). In contrast, it, becomes the constant value, -- 7.3 × 10-12 cm2/dyne, for Mn 〉 2,000. (3) The amount of bound water of dextran calculated from the sound velocity measurement lakes constant value of 0.17 ml g for Mn 〉 2, 000, but the amount of hydration increase with decreasing molecular weight for Mn 〈 2,000. From these results, a dextran molecule in aqueous solution is expected to change its conformation from random coiling to uncoiling stretched form at the molecular weight of around 2, 000 or about 12 glucose units.
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  • 77
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    Biopolymers 10 (1971), S. 1559-1581 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Optical rotation studies were performed on five compounds containing two peptide groups. Four of the molecules were confined to restricted regions of conformational space by the presence of closed rings. Solvent and temperature were varied, and theoretical calculations were done for each compound covering the appropriate conformational space. The interpretation which results is qualitatively successful over the conformational regions covered by the compounds. Quantitative correlation between theory and experiment will require compounds of high rigidity.
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  • 78
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    Biopolymers 10 (1971), S. 1617-1623 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational energy maps have been calculated for α-D-mannuronic acid (1-4) α-L-guluronic acid and for α-L-guluronic acid (1-4) β-D-mannuronic acid. These have been used, together with maps previously calculated for the homomonomeric dimers, to estimate the characteristic ratios and Kuhn lengths of the alternating copolymer and of a stochastic copolymer similar in composition to that extracted from L. digitata.The results show that the alternating copolymer is less extended than either homopolymer. Kuhn lengths calculated for the stochastic copolymer agree well with experimental results on high ionic strength solutions of alginate isolated from L digitata.
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  • 79
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    Biopolymers 10 (1971), S. 1635-1648 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly-S-carboxyethyl-L-cysteine, a higher side-chain homolog of poly-S-carboxymethyl-L-cysteine, has been prepared from poly-S-carbobenzoxyethyl-L-cysteine with hydrogen bromide in chloroform or acetic acid. The polymer is found to be in the β-conformation of an antiparallel arrangement of polypeptide chains in solid films, both in acid and salt forms, when examined by infrared spectra. Aqueous solutions of t he polymer have been investigated by measurements of rotatory dispersion and circular dichroism as well as by infrared spectra in D2O. These properties show sharp changes around pH 5.5, as the pH of solution is varied. At higher ionization the polymer is randomly coiled, but at lower ionization it is in the β-conformation. Dependence of the rotatory properties upon polymer concentration as well as on ionic strength has been observed even at the lowest degree of ionization attained, and this has been attributed to the formation of intermolecular β-conformation in solutions. The β-structure is characterized by a negative circular dichroic band at 223 mμ and a positive dichroic band at a wavelength lower than 200 mμ, and furt her by a negative bo value, -140°. The pH-induced coil-β transition of the polymer is compared with that of poly-S-carboxymethl-L-cysteine.
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  • 80
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    Biopolymers 10 (1971), S. 1681-1699 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The specific heat, of rat tail tendon at various water contents was measured as a function of temperature. The resulting graphs showed peaks arising from the melting, near 50°C, of helical material in the collagen, and from the melting of absorbed water in the range -40°C to 0°C. The heat of melting of helical material was 11.7 cal per gram of dry tendon. Determination of the heat and temperature of fusion of the absorbed water allowed resolution of the water into four states in the case of tendon before denaturation, and three states after denaturation. The four states are (1) water not freezable on cooling to - 70°C, (2) freezable water with-both heat and temperature of fusion different from the values for ordinary water, (3) freezable water with the heat of fusion of ordinary water, but a different temperature of fusion, and (4) water not distinguished from ordinary water. The fourth state was absent in denatured tendon. The results are discussed in terms of increasing size of clusters of absorbed water molecules.
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  • 81
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    Biopolymers 10 (1971) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 82
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    Biopolymers 10 (1971), S. 1743-1757 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The absorption and rotatory properties of acridine orange-poly-S-carboxymethyl-L-cysteine system in water and in 0.2 M NaCl have been measured at different pH and polymer-to-dye mixing ratios. The absorption spectra indicate that the dyes are bound to the polymer in dimeric or highly aggregated forms. At neutral pH where the polymer is randomly coiled, no optical activity is induced on the absorption bands of bound acridine orange. At acid pH where the polymer has the β-conformation, a pair of positive and negative circular dichroic bands occur at each of the absorption bands, centered around 458 and 261 mμ. The signs of those bands are opposite to those found for α-helical poly-L-glutamic acid. A model for the binding of dye to the β-form polymer is presented, in which dimeric dyes are attached to ionized carboxyl groups and slack one another to form linear arrays on both sides of an extended polypeptide chain. The observed circular dichroism spectra can be explained by the Tinoco's exciton mechanism, based on this model. Low molecular weight poly-S-carboxymethyl-L-cysteine induces quite a different circular dichroism on bound acridine orange.
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  • 83
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    Biopolymers 10 (1971), S. 1853-1863 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dicrosim (CD) spectra of complexes of DNA with ethidiun bromnide, profiavine, 9-aminoacridine and 4-etliyl-9-amino-acridine have been determined between 220 and 450 nm, the range lieing extended to 600 nm for ethidiufm bromide. The variation of the magnitude of the visible and near - ultraviolet CD spectra of ethidium bromide - DNA complexes with the amount of ligand bound (r) suggests a common binding position with profiavine. On the other hand, 4-ethyl-9-aminoacndine complexed to DNA shows CD spectra not distinguishable from those of 9-aminnoacnidmc in both the visible and ultraviolet. The interpretation of these results with respect to the stereochemistry of the DNA-ligand complexes is discussed.
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  • 84
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    Biopolymers 10 (1971), S. 1901-1924 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The various treatments of sedimentation equilibrium are compared on a theoretical and an experimental basis. Particular attention is paid to the polyelectrolyte nature of the problem and the choice of a neutral component. The effective density gradients of several cesium salts for DNA are measured. Two previous theories for the effective density gradient are shown to be equivalent, and the experimental values are interpreted with respect to these theories. It is clear t hat sedimentation equilibrium in a density gradient may be used for the determination of unambiguous molecular weights.
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  • 85
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    Biopolymers 10 (1971), S. 1949-1972 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The theory of friction-limited DNA unwinding is developed explicitly for moderate tind large perturbations. This extension of the earlier theory of the relaxation kinetics is necessary because of the complex nature of the rate limitation for small perturbations. The assumption of the theory that is violated under relaxation conditions is that base pairing reactions occurring at a constant local degree of twist of the strands are fast compared to the net unwinding of the molecule. However, these reactions that are slow for small perturbations have a large activation energy, and become faster than friction-limited un winding for large enough temperature jumps and sufficiently large DXA molecules. Thus only the rate for moderate and large perturbations is clearly limited by frictional resistance to turning the molecule in solution. The model used is a diffusional unwinding of the two strands, driven by the accompanying decrease in free energy. For large perturbations a numerical solution of the diffusion equation is required, since the diffusion coefficient is not constant. Two new parameters must be introduced into the equilibrium statistical theory to describe friction-limited unwinding kinetics. These are the force constant b, for winding up coil regions and the frictional coefficient per base pair βcfor rotating coil regions in solution. We find by fitting the theory to experiment that b = 1.8 × 10-13 ergs/ rad2- and βc = 3.5 × 10-21 erg see/base pair, both for DNA melted in alkali at 0.4.M Na + and ∼30 °C. The latter value is in agreement with predictions based on the viscosity of single stranded DNA in alkali. The quoted value of bcan be interpreted to mean that the number of conformational states of a nucleolide is reduced by an average factor of 1.55 when it is wound around another strand to the degree of twist in a double helix, but without forming a base pair.
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  • 86
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The properties of oligonucleotide helices of adeuylic- and uridylic acid oligomers have been investigated by measurements of hypo-and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix-coil transition can be studied (without interference by triple helices) only at low ionic-strength. A “phase diagram” is given representing the Tm-values of the various transitions at different ionic strengths for the system A(pA)17 + U(pU)17. Oligonucleolides of chain lengths 〈8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix-coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the Tm-value and the broader the helix-coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x. The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting xwas computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix-coil equilibria of poly A + poly U at neutral pH are calculated (ΔHA = -7.9 kcal/mole for the poly A stacking and ΔH12 = -10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.
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  • 87
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    Biopolymers 10 (1971), S. 2049-2049 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 88
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    Biopolymers 10 (1971), S. 2071-2077 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The data on the band widths and band shapes of several DNA's at various concentrations in sedimentation equilibrium in a CsCl density gradient have recently become available. In the present report, these literature data are treated in the following manner: (1) based on a theory of isotope-substitution, calculations are made of the molecular weights at infinite dilution, and (2) to explain the concentration dependence of band widths and band shapes, a theory of charge and hydration is put forth, and it is shown that by retaining the terms involving the charge of the macromolecules, it is possible to account for most of the concentration dependence.
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  • 89
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    Biopolymers 10 (1971), S. 2083-2094 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The mechanism of the unique and specific association of a given amino acid to its t-RNA is investigated by theoretical methods. Several possible schemes are proposed to explain specificity. The physical forces which act within these mechanisms are illustrated by the computer simulation of probable interactions between glycine and nucleotide bases and base pairs. It is demonstrated that glycine has direct and selective affinities for the nucleotide bases and that these interactions are principally determined by the polar groups. Energies have been calculated for the interaction of glycine with several base pairs. From these, the possibility that specificity arises through direct complexing of an amino acid with its anticodon is evaluated.
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  • 90
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    Biopolymers 10 (1971), S. 2147-2160 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Equations are developed to describe the shift in the temperature of the helix-coil transition when small molecules bind to nucleic acids. Included are high polymers, oligonucleotides, and oligomer-polymer interactions. The equations prescribe simple ways of plotting experimental data to evaluate transition and binding parameters.
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  • 91
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    Biopolymers 10 (1971), S. 2181-2197 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The helix-coil transitions for poly-L-lysine (PL) were investigated by the methods of spectropolarimetry, viscometry and potentiometric titration in 0.2M NaCl at different temperatures as well as in 0.2MNaBr, 1MKCl, and in mixtures of 0.2MNaCl or NaBr with methanol at room temperature. The enthalpy and entropy differences between the helical and coillike states of uncharged PL molecules in 0.2.M NaCl were determined from the potentiometric titration curves. The cooperativity parameters σ for PL in different solvents were determined by two methods (from the sharpness of the transition and from the dependence of the intrinsic viscosity on the helical content in the transition region). In 0.2MNaCl σ has a value of (2.3 ± 0.5) × 10-4 and does not depend on temperature, i.e., the cooperativity of the helix-coil transition, as for PGA, is mainly of an entropy origin (the initiating of the helical region is accompanied by the entropy decrease ΔSi = -12 eu/mole of helical regions). A comparison of the obtained results for PGA and PL with the molecular theories of the helix-coil transitions shows that the role of dipole-dipole interactions of nonneighboring peptide groups is greatly overestimated in these theories, leading to a considerable enthalpy contribution to the free energy of initiating helical regions which is not observed in the experiment.
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  • 92
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    Biopolymers 10 (1971), S. 2029-2037 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The variation of the polarized components of fluorescence of a rodlike particle bearing a fluorescent label upon partial orientation is calculated for some special geometry of the dye macromolecules complexes. Explicit expressions are given for the case where the energy of the molecule in the field depends only on one angle θ, showing that the result is a function of both 〈sin2θ〉 and 〈sin4θ〉. For the case of orientation in an electric field through an anisotropic induced moment, the expressions allow the calculation of this anisotropy of polarizability. The method is applied to the measurement of the polarizability of rodlike fragments of DNA labeled by intercalated molecules of Acridine Orange.
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  • 93
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    Biopolymers 10 (1971), S. 2039-2048 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As the temperature of solid poly(β-benzyl-L-aspartate) (PBLA), (CO.NH.CH.-CH2COOCH2C6H5)n, in the α-helieal form is raised from -150 °C, tlie line width and second moment of the proton magnetic resonance (PMR) signal decrease in stages until the conformational transition to the ω-helix occurs at about 90 °C. A similar temperature dependence of the PMR parameters is observed as the transformed polymer is cooled. Below -100°C (where the lattice is presumed to be rigid), the measured second moments are 9.5 Oe2 and 10.7 Oe2 for the α and ω forms, respectively. Second moments, calculated from the Van Vleck formula for the rigid lattice and also estimated for possible motional cases in which the polymer is taken to be in the ω form, are compared with the PMH data. By combination with the results of X-ray diffraction and infrared spectroscopic measurements, a tentative explanation can be made of the types of motion occurring in PBLA.
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  • 94
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    Biopolymers 10 (1971), S. 2133-2145 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have performed potentiometric titrations of poly-L-lysine. From these data we have calculated the free energy and enthalpy changes for the folding of the random coil to the α-helix in 10% ethanol (-120 and -120 cal/mole) and from the random coil to the β-structure in water (-140 and 870 cal/mole) and in 10% ethanol (-180 and 980 cal mole). Comparison of these values with each other and with values for the coil → α- helix transition in water (-78 and -880 cal/mole) led to the following conclusions. The stabilization by ethanol of ethanol of the α-helix with respect to the coil is that predicted from the known free energy of transfer of the peptide group from water to 10% ethanol. Similar data to explain the enthalpy difference are not available. The thermodynamic functions for the transition from α-helix to β-structure, obtained by subtracting those for the coil → α-helix and coil → β-structure transitions, are explained from a consideration of the structural differences: non bonded interactions of the polypeptide backbone are less favorable in the β-structure than in the α-helix, causing an increase in the energy, while hydrophobic contacts between side chains raise the entropy of the β-structure as compared with the α-helix, so that the free energy difference between the two structures is small, but enthalpy and entropy differences are large. The observation of only small differences in the free energy and enthalpy changes for the transition from coil β-structure upon going from water to 10% ethanol is expected by considering both the free energy of transfer of the peptide group (as for the α-helix) and the free energy and enthalpy of transfer of the apolar part of the side chain involved in hydrophobic bond formation.
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  • 95
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    Biopolymers 10 (1971), S. 2209-2221 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Valine specific transfer RNA (tRNAVal) was isolated from Bacillus stearothermophilus and Escherichia coli by chromatography on benzoylated DEAE-cellulose (BD-cellulose). Likewise isoleucine specific transfer RNA (tRNAIle) was isolated from B. stearothermophilus and from Mycoplasma sp. Kid. The thermal denaturation profiles (melting curves) of the two tRNAVal species in the presence of Mg+ + were nearly identical. However, the Tm for the Kid tRNAIle was about 10°C lower than that for the B. stearothermophilus tRNAIle. A nuclease and tRNA-free aminoacyl-tRNA synthetase (AA-tRNA synthetase) preparation from B. stearothermophilus was able to function efficiently at temperatures up to 80°C in the aminoacylation of all four tRNA species. Determination of the amino acid-acceptor activity of each tRNA species as a function of temperature of the aminoacylation reaction showed in each case a strong correlation between the loss of acceptor activity and the thermal denaturation profile of the tRNA. Evidence is presented that the loss in acceptor activity is most likely due to a change in structure of the tRNA as opposed to denaturation of the enzyme. These results further support the idea that correct secondary and/or tertiary structure must be maintained for tRNA to be active as a substrate for the AA-tRNA synthetase.
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  • 96
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    Biopolymers 10 (1971), S. 2275-2281 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Cotton effects of N-acetoacetyl amino acids and derivatives were examined by a circular dichroism technique. A correlation has been established between the sign of the Cotton effect and the absolute configuration of the asymmetric center. The L derivatives show, in dioxane, negative circular dichroism curves, whereas the D antipodes present positive curves. The effect of solvent and pH and influence of alkylation at the amide nitrogen are also discussed.
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  • 97
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    Biopolymers 10 (1971), S. 2345-2358 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The anisotropy of electrical polarizability of rodlike fragments of DNA has been studied by a number of electro-optical methods: Kerr effect (combined with flow birefringence), light scattering, diehroism, and fluorescence in an electric field. The most sensitive technique (Kerr effect) has been used to study the variation of the polarizability with the nature and concentration of counteroins. DNA fragments constitute a truly rigid polyelectrolyte of known structure. The value obtained can then be quantitatively compared to the predictions of those of the theories of the longitudinal polarizability of rigid polyelectrolytes which are based on true molecular parameters. The comparison emphasizes the role of the counterion-counterion repulsion. Oosawa's theory seems to represent the best approach but fails to explain the differences observed between monovalent and divalent ions.
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  • 98
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    Biopolymers 10 (1971) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 99
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    Biopolymers 10 (1971), S. 2537-2553 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The MCD (magnetic circular dichroism) spectra of Ap, ApA, ApApA, poly A, Up, UpU, poly U and double-stranded poly A:U alternating copoly A-U and alternating deoxyribopoly A-T were measured with a Cary 61 spectropolarimeter fitted with a Varian superconducting magnet at a field strength of 50 Kgauss. The MCD spectra of T2 and T5 DNA at various stages of heal denaturation were measured as a function of hyperchromicity of the sample. MCD spectra of the intact and degraded T2 and T5 phages were used to study the degree of alteration of the DNA inside the phages versus the DNA in vitro. The results for the adenine polymers show that the main MCD bands, B2u(271 nm), B1u(252 nm), and E1u(212 nm), show a decrease in specific magnitude as the length of the polymer is increased, reflecting the degree of stacking of the polymer. In contrast, the uridine series of polymers shows little change of the MCD bands, indicating that there is little interaction between the bases regardless of the length of the polymers. The MCD spectra of poly A:U, alternating poly r(A-U): (A-U), and alternating poly d(A-T):(A-T) show significant differences among themselves in the magnitude of the B2u band and when compared with the sum of the spectrum for the poly A plus poly U. This may indicate the selective effect of hydrogen bonding on the B2u band. Alternatively, the difference may be due to the absence of an n → π* transition in the double-stranded polymer. Measurements of denatured T2 and To DNA's show increases in all MCD bands. The T2 DNA internally packed in phage shows an increase of the B2u and E1ubands, the B2u remaining unchanged. The internal T5 DNA shows an increase of the B1u band only. Thus, the internal DNA structure is altered in a manner quite different from a simple denaturation caused by hydrogen bond breaking. Furthermore, different MCD bands indicate that different modes of DNA packing exist for T2 and T5 phages.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 10 (1971), S. 2591-2596 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The infrared absorption of poly-L-proline in concentrated aqueous salt solutions was measured in the fundamental region. Of primary interest were the carbonyl absorption of the peptide linkage and the methylene C-H bending absorption of the pyrrolidine ring. These spectral regions each show an additional component in the concentrated salt solutions. Using the position of the absorptions of poly-L-proline I (cis) and II (trans) as models, we conclude that both cis-trans linkages are present in the peptide in salt solutions. Increasing the temperature shifts the equilibrium slightly in favor of cis.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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