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  • 2000-2004  (56)
  • 1980-1984  (7,092)
  • 1950-1954
  • 1900-1904
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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
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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
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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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  • 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
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    Biopolymers 20 (1981), S. 169-185 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The IR data for the R1 CO-O-CHR2-CO-NHR3 derivatives are interpreted in terms of a H…π interaction involving the N—H bond and the π orbitals of the ester function and giving rise to a high ν(C=O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values φ # -90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C=O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
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  • 58
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    New York : Wiley-Blackwell
    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 59
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    Biopolymers 20 (1981), S. 251-268 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
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  • 60
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of L-3,4-dehydroproline, t-butoxycarbonyl-L-3,4-dehydroproline amide, and acetyl-L-3,4-dehydroproline amide have been determined. L-3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L-3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L-3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L-3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L-3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L-3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L-3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present φ and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have φ and ψ values corresponding to a collagenlike conformation (conformation F).
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  • 61
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    Biopolymers 20 (1981), S. 359-371 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10-7, 1.000 ± 0.05 × 10-7, and 0.835 ± 0.04 × 10-7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
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  • 62
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    Biopolymers 20 (1981), S. 387-397 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (φ,ψ) over the range -180° ≤ φ ≤ -60°, -60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (φ,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.
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  • 63
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T1ρoff), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine-DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
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  • 64
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    Biopolymers 20 (1981), S. 345-357 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In carbonate buffer at pH 10.5, a transparent solution of poly(L-lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L-lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
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  • 65
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    Biopolymers 20 (1981), S. 707-718 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2-pyridone and 2,6-dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L-Pro-X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the -CONH- of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m-1 for the secondary amide and 50m-1 for the tertiary amide. For pyridone the binding constant is about 45m-1 for either the secondary or tertiary amide. For comparison self-dimerization constants determined by vapor-pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m-1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L-Pro-Gly), respectively.
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  • 66
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    Biopolymers 20 (1981), S. 803-816 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and phosphorus nmr have been used to investigate the double-helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH 〈 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71-86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half-protonated state. Although the base-stacking arrangement of this state is similar to that observed in the more extensively protonated low-pH state, the phosphate backbone conformation is different from that found in either the neutral or low-pH structures.
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  • 67
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 68
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    Biopolymers 20 (1981), S. 39-51 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod-Wyman-Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
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  • 69
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    Biopolymers 20 (1981), S. 65-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200-320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first-approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
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  • 70
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA2Glu and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M-1 in the absence of magnesium to 1.5 × 106M-1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
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  • 71
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    Biopolymers 20 (1981), S. 231-235 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
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  • 72
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    Biopolymers 20 (1981), S. 237-240 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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  • 73
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    Biopolymers 20 (1981), S. 243-247 
    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
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A conformational quantum-mechanical study of (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple-helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly-Pro-Pro and Gly-Phe-Pro indicates that phenylalanyl in the second position favors the triple-helix formation.
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  • 75
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    Biopolymers 20 (1981), S. 327-343 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full-contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core-particle models have been compared with the observed functions and show that the neutron-scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4-7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
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  • 76
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-L-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well-defined N- and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°-8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
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  • 77
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
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  • 78
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    Biopolymers 20 (1981), S. 2121-2136 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton-induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103-178], we have obtained an expression that may be computer-fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill-defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
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  • 79
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    Biopolymers 20 (1981), S. 2137-2142 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso-propanol, n-propanol, formamide, acetamide, N-methyl-formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
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  • 80
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    Biopolymers 20 (1981), S. 2195-2202 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preparations have been made of acid-soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
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  • 81
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    Biopolymers 20 (1981), S. 2225-2241 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present an alternative to the common lattice model for nonspecific DNA-protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one-dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding-site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee-von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single-stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
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  • 82
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
    Additional Material: 21 Ill.
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  • 83
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro-molecule with unusually large positive ellipticity in the 250-300-nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples - via a series of intermediate forms with CD spectra resembling those of A-DNA, then B-DNA - into Ψ(-) states having anomalously large negative ellipticity similar to the well-known Ψ(-) forms produced by above-critical concentrations of poly-(ethylene oxide) and salt. These ethanol/salt-induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B-form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(-) interconversion has been reported. A “skein-of-yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.
    Additional Material: 7 Ill.
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  • 84
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    Biopolymers 20 (1981), S. 2623-2633 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H-Nmr was used to measure the rate of cis-trans interconversion of X-Pro bonds in linear and cyclic oligopeptides. k(cis → trans) = 2.5 × 10-3 s-1 at 25°C was found for the zwitterionic form of H-Ala-Pro-OH, in good agreement with earlier measurements. Replacement of Ala by Phe, Tyr, or Trp resulted in a 10-fold slower interconversion rate, whereas after substitution of Ala by His or Glu, the rate decreased only slightly. Independent of the residues X, the interconversion rate was increased by a factor of ca. 20 when the peptide chain was elongated by addition of Ala to the C-terminal Pro. An additional increase by a factor of 6 was observed when going from the protected linear peptide CF3CO-Gly-Gly-Pro-Ala-OCH3 to the closely related cyclic compound c[-Gly-Gly-Pro-Gly-Ala-]. These data are evaluated with regard to their possible use in future studies on the role of X-Pro cis-trans isomerization in the kinetics of protein folding.
    Additional Material: 6 Ill.
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  • 85
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As a model compound for the growing chain in the activated-NCA type of polymerization of α-amino acid N-carboxyanhydride (NCA), 3-[ω-acetylglycyl-poly(α-amino acid) acyl]-α-amino acid NCA (called the prepolymer) having various degrees of polymerization (DPs) was synthesized by the polymerization of Phe, Val, Glu(OEt), and Asp(OBzl) NCA in the presence of AcGly NCA by the tertiary amine. Activated (S)-Phe, Val, Glu(OEt), and Asp(OBzl) NCA were added to the terminal cyclic group of the corresponding (S)- or (R)- prepolymer, and the enantiomer selectivity in the reaction was investigated. With prepolymers having DPs ranging from 1 to 15, the addition reaction always took place preferentially between species having the same configuration, and the degree of the enantiomer selection increased with increasing DP of the prepolymer. With prepolymers having DP = 1 and 2, we found contributions from the chiral terminal unit and the chiral penultimate unit to the enantiomer selection, respectively. Prepolymer having DP = 5 was shown to take a β-type conformation, which led to higher enantiomer selection; and prepolymers having DP = 10 and 15 were shown to take an α-helix conformation, which led to much higher enantiomer selection than did the β-type conformation. In the present investigation the mechanisms of terminal-unit control, penultimate-unit control and conformational control of the enantiomer selection in the activated-NCA type of polymerization were clearly observed.
    Additional Material: 7 Ill.
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  • 86
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The helix-coil transition and conformational structure of poly(8-bromoadenylic acid) [poly(8BrA)] have been investigated using 1H- and 13C-nmr, CD, and ir spectroscopy. The results have been compared with the structure of the related 5′-mono- and polynucleotides. The chemical shifts of H(2′), H(3′), C(2′), and C(3′) nmr signals show an interesting correlation with both the puckering of ribose ring and glycosidic bond torsion angle. Poly(8BrA) shows an upfield shift of the C(3′) signal and a downfield shift of the H(3′) signal compared to the chemical shifts in poly(A). These shifts are consistent with a C(3′) endo-syn conformation for poly(8BrA). A similar effect has been reported previously and is also observed here on the C(2′) and H(2′) signals when the preferred conformation is C(2′)endo-syn (e.g., in 5′-8BrAMP). The chemical-shift parameters thus act as a probe for studying syn ⇄ anti and N ⇄ S equilibria in solutions. The three-bond 1H-′13C coupling constants between H(1′) and C(8) and C(4) have been measured in poly(8BrA) and 5′-8BrAMP and their structural implications have been discussed. The observed preference of a C(3′)endo-syn conformation for poly(8BrA), coupled with other evidence, throws doubt on the validity of a correlation previously reported whereby a syn conformation is associated with a C(2′)endo ribose pucker. The backbone conformation of randomly coiled poly(8BrA) is very similar to the structures found in polyribonucleotides: poly(A) and poly(U). All three polymers show strong preferences for the backbone angles found in RNA helices. The CD spectrum of poly(8BrA) has a striking relationship to that of poly(A). The signs of all extrema are inverted, and the magnitudes are related by a constant factor. We suggest that these differences result from a change in the angle between coupled transition moment vectors in the two polymers. Infrared spectra of poly(8BrA) in H2O and D2O solution are reported for the frequency range below 1400 cm-1. The antisymmetric 〉PO2- stretching vibration is observed at an unusually low frequency in the helix (1214 cm-1). The symmetric 〉PO2- stretch occurs at ∼1095 cm-1 but is not resolved from a ring vibration near this frequency. A conformationally sensitive band, characteristic of helical RNA structures, is observed at 817 cm-1 and disappears when the helix is melted. This observation confirms the conclusion that ordered poly(8BrA) has a regular helical structure with an RNA backbone conformation. A stereochemical explanation is provided for the failure of poly(8BrA) (or other syn polymers) to form double helices with anti-polyribonucleotides.
    Additional Material: 11 Ill.
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  • 87
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    Biopolymers 20 (1981), S. 1103-1112 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The arginine and lysine residues of calf thymus histone H1 were modified with large molar excesses of 2,3-butanedione and O-methylisourea, respectively. Kinetic study of the modification reaction of the arginine residue revealed that the reaction is divided into the two pseudo-first-order processes. About a third (1 Arg) of the total arginine residues of the H1 molecule was rapidly modified without causing any detectable structural change of the molecule, and the slow modification of the remaining arginine residues (2 Arg) led to a loss of the folded structure of H1. In the case of lysine residue modification, 93% (56 Lys) of the total lysine residues of the H1 was modified with the same rate constant, while 7% (4 Lys) of lysine residue remained unmodified. When the reaction was performed in the presence of 6M guanidine-HCl, all of lysine residues were modified. It is concluded that the 2 arginine and 4 lysine residues resistant to modification are buried in interior regions of the H1 molecule and play an important role in the formation of the H1 globular structure, while the other 1 arginine and 56 lysine residues are exposed to solvent.
    Additional Material: 5 Ill.
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  • 88
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    Biopolymers 20 (1981), S. 1191-1209 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molar Kerr constants mK, molar refractions mR, and dipole moments μ are reported for the N-methylacetamides CX3CONHCH3 (X = H, CH3, F. CI, Br) and acetamides CX3CONH2 (X = H, F, Cl, Br). The components of the polarizability tensor α are deduced for N-methylacetamide and acetamide on the basis of the bond additivity approximation. This α is found to be considerably more anisotropic than was indicated in previous determinations by other methods. The data for N-methylacetamide were used to calculate mK, μ, and γ2 (anisotropy squared) of N-acetyl-N′-methylglycine amide and N-acetyl-N′-methyl-alanine amide as functions of the torsional angles (φ,Ψ). The statistical mechanical averages of mK, μ, and γ2 were calculated from conformational energies obtained by the methods of Scheraga.
    Additional Material: 4 Ill.
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  • 89
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    Biopolymers 20 (1981), S. 1247-1260 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The physical properties of single, 5-8-μm diameter, water-swollen elastin fibers have been investigated on a microtest apparatus attached to a polarizing microscope. Analysis of the mechanical and optical properties at extensions below 100% indicate that the elastic modulus (G) has a value of 4.1 × 105 N m-2, the average molecular weight of chains between crosslinks is in the range of 6000-7100, and the stress optical coefficient (C′) is 1 × 10-9 m2 N-1 at 24°C. Analysis of the temperature dependence of the stress optical coefficient indicates that the polarizability of the random link decreases with increasing temperature, with an apparent activation energy for this process of the order of 1.6 kcal/mol. Analysis of the non-Gaussian mechanical and optical properties at extensions above about 100% suggest that the chains between crosslinks contain approximately 10 “effective” random links, with each link consisting of 7-8 amino acid residues. These parameters for the random chains in the elastin network have been used to predict the dimensions of other random proteins. The close correlation of these predictions with published values for the dimensions of a series of proteins in solution in 6M guanidinium hydrochloride provides an independent test of the appropriateness of our analysis.
    Additional Material: 4 Ill.
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  • 90
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    Biopolymers 20 (1981), S. 1333-1335 
    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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  • 91
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    Biopolymers 20 (1981), S. 1399-1411 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Heavy meromyosin binding to F-actin saturated with tropomyosin is studied theoretically. The problem is formulated as a special case of n-mer adsorption to a one-dimensional Ising lattice which is divided into m-site-long blocks.
    Additional Material: 9 Ill.
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  • 92
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    Biopolymers 20 (1981), S. 1481-1502 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field-free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio 〉 20; 0.1 〈 L/P 〈 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
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  • 93
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    Biopolymers 20 (1981), S. 1537-1547 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solvents which accelerate DNA renaturation rates have been investigated. Addition of NaCl or LiCl to DNA in 2.4M Et4NCl initially increases renaturation rates at 45°C and then leads to a loss of second-order behavior. The greatest accelerations are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most effective method of accelerating DNA renaturation with concentrated DNA. Addition of dextran sulfate beyond 10-12% in 2.4M Et4NCl fails to increase the acceleration beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35-40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to be more effective, although acceleration may be achieved in solvents containing formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of the normal concentration and temperature dependence of DNA renaturation and is also independent of dextran sulfate concentration if sufficient dextran sulfate is used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.
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  • 94
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    Biopolymers 20 (1981), S. 1503-1535 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the preceding article, a Monte Carlo analysis was presented which provides a quantitative numerical relationship between the rotational diffusion coefficients, as measured by the decay of optical anisotropy following an electric field pulse, and the flexibility (persistence length) of short, wormlike chains. In the present article, the results of the foregoing analysis are applied to the observed rates of decay of birefringence for a series of sequenced DNA fragments ranging in size from 104 to 910 base pairs. Under the conditions used in this study, the DNA fragments exist as native, duplex molecules. Furthermore, conditions are defined in which the observed relaxation times are not dependent on DNA concentration, field strength, or the duration of the pulse. It is pointed out that the ionic atmosphere associated with a wormlike polyion does not exert any significant (direct) influence on the rotational diffusion of the polyion and, therefore, that the rotational relaxation times are a true measure of the configurations of the DNA molecules in solution. Moreover, excluded-volume effects are shown not to be significant for the moderately short molecules employed in this study. The major conclusion of this study is that there is no strong ionic strength dependence of the persistence length for ionic strengths above 1 mM and that the persistence length, under conditions where electrostatic contributions are negligible, is approximately 500 Å. For ionic strengths significantly lower than 1 mM, electrostatic contributions to the stiffness of DNA become significant.
    Additional Material: 17 Ill.
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  • 95
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    Biopolymers 20 (1981), S. 1575-1588 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aqueous and hydroalcoholic solutions of the heptenic macrolide amphotericin B display strong and variable signals in CD and absorption spectroscopies in the range of the π* ← π transition. An interpretation of the spectroscopic changes is proposed based on the equilibrium between two forms of the intermolecular organization: the aggregated one (A) with strong excitonic interaction and the nonaggregative one (B) whose spectra are like those of linear conjugated polyenes in true solution with a well-developed vibrational structure. The intermediate spectra are fitted by linear combination of the A- and B-form spectra. A two-level organization of the aggregates is proposed for the A-form: (1) a close packing of few molecules, which is the origin of the absorption maxima hypsochromic shift; and (2) interaction between the preceding small units inside the aggregates, which is spectroscopically expressed by the intense CD couplet.
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  • 96
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    Biopolymers 20 (1981), S. 1625-1633 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polypeptides of dicarboxylic amino acids having the monomer units linked in α- and ω-peptide bonds contain two kinds of carboxyls of different acidity. How well potentiometric titration can distinguish these two carboxyls and so characterize the nature of the peptide bonds is evaluated critically. An analysis of the equation describing the dependence of pH on the degree of neutralization based on neglecting the polymer effect and a discussion of the dissociation behavior of polyanions show that the method of evaluating experimental data found in the literature is incorrect. Nevertheless, if a conformational transition does not interfere, some useful and reliable information may be gained by this method; namely, an indication of the presence of two different peptide bonds, their mole ratio, and an approximate pK value for the carboxyl of the amino acid linked in the ω-peptide bond. The presence of two types of carboxyls complicates the evaluation of the titration curves in the conformation studies.
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  • 97
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    Biopolymers 20 (1981), S. 1707-1725 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational analysis of antiparallel double-helical polynucleotides with Watson-Crick base pairing was reduced to a four-dimensional problem using original mathematical methods. In the four-dimensional conformational space the family of structures, characterized by the base-pair stacking with the most stable conformations in water solution as well as in the solid state, was localized. For the C′2-endo sugar pucker, both right-handed and left-handed structures were found; right-handed structures only, however, seem to be allowed for the C′3-endo pucker, the only possible one for ribonucleotides with base stacking.
    Additional Material: 7 Ill.
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  • 98
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Angiotensin II and its competitive inhibitor [Sar1, Ile8]-angiotensin II, as well as several analogs of these two compounds specifically chosen for their well-defined pharmacological properties, were studied by circular dichroism and nuclear magnetic resonance methods at various pH values in aqueous solution and in d6-dimethylsulfoxide. The results were compared with their biological activities. This allowed us to establish relationships between conformation and pressor activity, explaining most of the properties of angiotensin II, its inhibitor, and the analogs successively substituted in positions 3 and 5.
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  • 99
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    Biopolymers 20 (1981), S. 2011-2020 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Peptide agonists covalently attached to tobacco mosaic virus exhibit such unusual properties as superpotency, superaffinity, enhanced resistance towards enzymic degradation, and prolonged action at the target cell. These properties can be exploited for the isolation by density-gradient centrifugation of membrane vesicles bearing specific receptors for the peptides and for radioactive and fluorescent labeling of cell-surface receptors. Our observations can be explained by cooperative-affinity phenomena caused by the deployment in space of the agonist molecules.
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  • 100
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    Biopolymers 20 (1981), S. 2035-2049 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The early steps of fibrin aggregation induced by low Reptilase concentrations were studied by means of static and dynamic light scattering. In order to obtain information on the size and shape of the first oligomers, the angular dependence of the scattered intensity and the mean Rayleigh line width were measured. Under physiological pH and ionic strength, oligomer formation was detectable immediately after enzymatic activation. Comparison of the calculated data for different models with experimental results shows that the early fibrin polymerization proceeds as an end-to-end aggregation of elongated and possibly flexible molecules approximately 75 nm long.
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