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  • 1
    Publikationsdatum: 2014-11-10
    Beschreibung: Graphs with circular symmetry, called webs, are relevant w.r.t. describing the stable set polytopes of two larger graph classes, quasi-line graphs and claw-free graphs. Providing a decent linear description of the stable set polytopes of claw-free graphs is a long-standing problem. However, even the problem of finding all facets of stable set polytopes of webs is open. So far, it is only known that stable set polytopes of webs with clique number $\leq 3$ have rank facets only while there are examples with clique number $〉4$ having non-rank facets.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 2
    Publikationsdatum: 2014-02-26
    Beschreibung: The bio-heat transfer equation is a macroscopic model for describing the heat transfer in microvascular tissue. In [{\sl Deuflhard, Hochmuth 2002}] the authors applied homogenization techniques to derive the bio-heat transfer equation as asymptotic result of boundary value problems which provide a microscopic description for microvascular tissue. Here those results are generalized to a geometrical setting where the regions of blood are allowed to be connected. Moreover, asymptotic corrector results are derived.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 3
    Publikationsdatum: 2014-11-10
    Beschreibung: Stable multi-sets are an evident generalization of the well-known stable sets. As integer programs, they constitute a general structure which allows for a wide applicability of the results. Moreover, the study of stable multi-sets provides new insights to well-known properties of stable sets. In this paper, we continue our investigations started in [{\sl Koster and Zymolka 2002}] and present results of three types: on the relation to other combinatorial problems, on the polyhedral structure of the stable multi-set polytope, and on the computational impact of the polyhedral results. First of all, we embed stable multi-sets in a framework of generalized set packing problems and point out several relations. The second part discusses properties of the stable multi-set polytope. We show that the vertices of the linear relaxation are half integer and have a special structure. Moreover, we strengthen the conditions for cycle inequalities to be facet defining, show that the separation problem for these inequalities is polynomial time solvable, and discuss the impact of chords in cycles. The last result allows to interpret cliques as cycles with many chords. The paper is completed with a computational study to the practical importance of the cycle inequalities. The computations show that the performance of state-of-the-art integer programming solvers can be improved significantly by including these inequalities.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 4
    Publikationsdatum: 2014-02-26
    Beschreibung: In this paper, first solutions of the dust moment equations developed in [{\sl Woitke & Helling 2002}] for the description of dust formation and precipitation in brown dwarf and giant gas planet atmospheres are presented. We consider the special case of a static brown dwarf atmosphere, where dust particles continuously nucleate from the gas phase, grow by the accretion of molecules, settle gravitationally and re-evaporate thermally. Applying a kinetic description of the relevant microphysical and chemical processes for TiO$_2$-grains, the model makes predictions about the large-scale stratification of dust in the atmosphere, the depletion of molecules from the gas phase, the supersaturation of the gas in the atmosphere as well as the mean size and the mass fraction of dust grains as function of depth. Our results suggest that the nucleation occu in the upper atmosphere where the gas is cool, strongly depleted, but nevertheless highly supersaturated ($S\!\gg\!1$). These particles settle gravitationally and populate the warmer layers below, where the in-situ formation (nucleation) is ineffective or even not possible. During their descent, the particles grow up to radii $\approx\!0.3\,\mu{\rm m}\,...\,150\,\mu{\rm m}$, depending gas around the cloud base. The particles finally sink into layers which are sufficiently hot to cause their thermal evaporation. Hence, an effective transport mechanism for condensable elements exi considered solid/liquid material. In the stationary case studied here, this downward directed element transport by precipitating dust grains is balanced by an upward directed flux of condensable elements from the deep interior of the star via convective mixing (no dust without mixing). We find a self-regulation mechanism which leads to an approximate phase equilibrium ($S\!\approx\!1$) around the cloud base. The mass fraction of dust present in the atmosphere results be to approximately given by the mass fraction of condensable elements in the gas being mixed up.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 5
    Publikationsdatum: 2020-03-09
    Beschreibung: Analysis of phenomena that simultaneously occur on quite different spatial and temporal scales require adaptive, hierarchical schemes to reduce computational and storage demands. For data represented as grid functions, the key are adaptive, hierarchical, time-dependent grids that resolve spatio-temporal details without too much redundancy. Here, so-called AMR grids gain increasing popularity. For visualization and feature identification/tracking, the underlying continuous function has to be faithfully reconstructed by spatial and temporal interpolation. Well designed interpolation methods yield better results and help to reduce the amount of data to be stored. We address the problem of temporal interpolation of AMR grid data, e.g.\ for creation of smooth animations or feature tracking. Intermediate grid hierarchies are generated by merging the cells on all refinement levels that are present in the key frames considered. Utilizing a clustering algorithm a structure of nested grids is induced on the resulting collection of cells. The grid functions are mapped to the intermediate hierarchy, thus allowing application of appropriate interpolation techniques.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 6
    facet.materialart.
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    Publikationsdatum: 2020-03-09
    Beschreibung: An improved general-purpose technique for the visualization of symmetric positive definite tensor fields of rank two is described. It is based on a splatting technique that is built from tiny transparent glyph primitives which are capable to incorporate the full directional information content of a tensor. The result is an information-rich image that allows to read off the preferred directions in a tensor field at each point of a three-dimensional volume or two-dimensional surface. It is useful for analyzing slices or volumes of a three-dimensional tensor field and can be overlayed with standard volume rendering or color mapping. The application of the rendering technique is demonstrated on general relativistic data and the diffusion tensor field of a human brain.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 7
    Publikationsdatum: 2014-11-10
    Beschreibung: Graphs with circular symmetry, called webs, are relevant for describing the stable set polytopes of two larger graph classes, quasi-line graphs [{\sl Giles and Trotter 1981, Oriolo 2001}] and claw-free graphs [{\sl Galluccio and Sassano 1997, Giles and Trotter 1981}]. Providing a decent linear description of the stable set polytopes of claw-free graphs is a long-standing problem [{\sl Grötschel, Lov\'asz, and Schrijver 1988}]. However, even the problem of finding all facets of stable set polytopes of webs is open. So far, it is only known that stable set polytopes of webs with clique number $\leq 3$ have rank facets only [{\sl Dahl 1999, Trotter 1975}] while there are examples with clique number $\geq 4$ having non-rank facets [{\sl e.g. Liebling et al. 2003, Oriolo 2001, P\^echer and Wagler 2003}]. In this paper, we provide a construction for non-rank facets of stable set polytopes of webs. We use this construction to prove, for several fixed values of $\omega$ including all odd values at least 5, that there are only finitely many webs with clique number $\omega$ whose stable set polytopes admit rank facets only.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 8
    Publikationsdatum: 2020-11-13
    Beschreibung: We present an algorithm that constructs parametrizations of boundary and interface surfaces automatically. Starting with high-resolution triangulated surfaces describing the computational domains, we iteratively simplify the surfaces yielding a coarse approximation of the boundaries with the same topological type. While simplifying we construct a function that is defined on the coarse surface and whose image is the original surface. This function allows access to the correct shape and surface normals of the original surface as well as to any kind of data defined on it. Such information can be used by geometric multigrid solvers doing adaptive mesh refinement. Our algorithm runs stable on all types of input surfaces, including those that describe domains consisting of several materials. We have used our method with success in different fields and we discuss examples from structural mechanics and biomechanics.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 9
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    Publikationsdatum: 2020-08-05
    Beschreibung: This article investigates a certain class of combinatorial packing problems and some polyhedral relations between such problems and the set packing problem.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 10
    Publikationsdatum: 2014-02-26
    Beschreibung: We construct non-constructible simplicial $d$-spheres with $d+10$ vertices and non-constructible, non-realizable simplicial $d$-balls with $d+9$ vertices for $d\geq 3$.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 11
    Publikationsdatum: 2014-11-11
    Beschreibung: We consider the problem of designing a network that employs a non-bifurcated shortest path routing protocol. The network's nodes and the set of potential links are given together with a set of forecasted end-to-end traffic demands. All relevant hardware components installable at links or nodes are considered. The goal is to simultaneously choose the network's topology, to decide which hardware components to install on which links and nodes, and to find appropriate routing weights such that the overall network cost is minimized. In this paper, we present a mathematical optimization model for this problem and an algorithmic solution approach based on a Lagrangian relaxation. Computational results achieved with this approach for several real-world network planning problems are reported.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 12
    Publikationsdatum: 2014-02-26
    Beschreibung: We investigate the impact of link and path restoration on the cost of telecommunication networks. The surprising result is the following: the cost of an optimal network configuration is almost independent of the restoration concept if (i) the installation of network elements (ADMs, DXCs, or routers) and interface cards, (ii) link capacities, and (iii) working and restoration routings are simultaneously optimized. We present a mixed-integer programming model which integrates all these decisions. Using a branch-and-cut algorithm (with column generation to deal with all potential routing paths), we solve structurally different real-world problem instances and show that the cost of optimal solutions is almost independent of the used restoration concept. In addition, we optimize spare capacities for given shortest working paths which are predetermined with respect to different link metrics. In comparison to simultaneous optimization of working and restoration routings, it turns out that this approach does not allow to obtain predictably good results.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 13
    Publikationsdatum: 2020-11-13
    Beschreibung: In the dial-a-ride-problem (DARP) objects have to be moved between given sources and destinations in a transportation network by means of a server. The goal is to find a shortest transportation for the server. We study the DARP when the underlying transportation network forms a caterpillar. This special case is strongly NP-hard in the worst case. We prove that in a probabilistic setting there exists a polynomial time algorithm which almost surely finds an optimal solution. Moreover, with high probability the optimality of the solution found can be certified efficiently. We also examine the complexity of the DARP in a semi-random setting and in the unweighted case.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 14
    Publikationsdatum: 2019-01-29
    Beschreibung: The paper presents a new affine invariant theory on asymptotic mesh independence of Newton's method in nonlinear PDEs. Compared to earlier attempts, the new approach is both much simpler and more natural from the algorithmic point of view. The theory is exemplified at collocation methods for ODE boundary value problems and at finite element methods for elliptic PDE problems.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 15
    Publikationsdatum: 2014-02-26
    Beschreibung: In this paper we introduce the notion of smoothed competitive analysis of online algorithms. Smoothed analysis has been proposed by [{\sl Spielman and Teng} STOC 2001] to explain the behaviour of algorithms that work well in practice while performing very poorly from a worst case analysis point of view. We apply this notion to analyze the Multi-Level Feedback (MLF) algorithm to minimize the total flow time on a sequence of jobs released over time when the processing time of a job is only known at time of completion. The initial processing times are integers in the range $[1,2^K]$. We use a partial bit randomization model, where the initial processing times are smoothened by changing the $k$ least significant bits under a quite general class of probability distributions. We show that MLF admits a smoothed competitive ratio of $O(max((2^k/\sigma)^3, (2^k/\sigma)^2 2^K-k))$, where $\sigma$ denotes the standard deviation of the distribution. In particular, we obtain a competitive ratio of $O(2^K-k)$ if $\sigma = \Theta(2^k)$. %The analysis holds for an oblivious as well as for a stronger adaptive %adversary. We also prove an $\Omega(2^{K-k})$ lower bound for any deterministic algorithm that is run on processing times smoothened according to the partial bit randomization model. For various other smoothening models, including the additive symmetric smoothening model used by [{\sl Spielman and Teng}], we give a higher lower bound of $\Omega(2^K)$. A direct consequence of our result is also the first average case analysis of MLF. We show a constant expected ratio of the total flow time of MLF to the optimum under several distributions including the uniform distribution.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 16
    Publikationsdatum: 2014-11-11
    Beschreibung: For the general G/G/1 processor sharing (PS) system a sample path result for the sojourn times in a busy period is proved, which yields a relation between the sojourn times under PS and FCFS discipline. In particular, the result provides a formula for the mean sojourn time in G/D/1-PS in terms of the mean sojourn time in the corresponding G/D/1-FCFS, generalizing known results for GI/M/1 and M/GI/1. Extensions of the formula provide the basis for a two-moment approximation of the mean sojourn time in G/GI/1-PS in terms of a related G/D/1-FCFS.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 17
    Publikationsdatum: 2014-02-26
    Beschreibung: The paper surveys recent progress in the mathematical modelling and simulation of essential molecular dynamics. Particular emphasis is put on computational drug design wherein time scales of $msec$ up to $min$ play the dominant role. Classical long-term molecular dynamics computations, however, would run into ill-conditioned initial value problems already after time spans of only $psec=10^{-12} sec$. Therefore, in order to obtain results for times of pharmaceutical interest, a combined deterministic-stochastic model is needed. The concept advocated in this paper is the direct identification of metastable conformations together with their life times and their transition patterns. It can be interpreted as a {\em transfer operator} approach corresponding to some underlying hybrid Monte Carlo process, wherein short-term trajectories enter. Once this operator has been discretized, which is a hard problem of its own, a stochastic matrix arises. This matrix is then treated by {\em Perron cluster analysis}, a recently developed cluster analysis method involving the numerical solution of an eigenproblem for a Perron cluster of eigenvalues. In order to avoid the 'curse of dimension', the construction of appropriate boxes for the spatial discretization of the Markov operator requires careful consideration. As a biomolecular example we present a rather recent SARS protease inhibitor.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 18
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    Publikationsdatum: 2021-02-01
    Beschreibung: The operative planning problem in natural gas distribution networks is addressed. An optimization model focusing on the governing PDE and other nonlinear aspects is presented together with a suitable discretization for transient optimization in large networks by SQP methods. Computational results for a range of related dynamic test problems demonstrate the viability of the approach.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 19
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    Publikationsdatum: 2014-02-26
    Beschreibung: This article presents a new computational approach to the three-dimensional (3D) modeling of ribonucleic acid (RNA) sequences with unknown spatial structure. The main concept is a mapping of the query sequence onto the 3D structures of a suitable template RNA molecule. This technique called \textit{threading} has originally been developed for the modeling of protein 3D structures. The application to RNA systems bridges the information gap between the growing mass of RNA sequence data and the relatively limited number of available 3D structures. The new RNA threading method is demonstrated on a tRNA model system because sufficient representative 3D structures have experimentally been elucidated and deposited in the public databases. Nevertheless, the method is in principle transferable on all other RNA species. Algorithms are developed that decompose these template structures into their secondary structure elements and gather this information in a specific template database. The best template is chosen with public alignment and secondary structure prediction tools which are integrated in the RNA modeling module. The structural information gathered from the template and the best alignment is combined to establish a comprehensive 3D model of the query sequence. A range of complete tRNA structures has successfully been modeled with the RNA threading method. The prototype module visualizes the models and provides convenient access to the proposed 3D structures. Therefore, the method could give new insight into a variety of RNA systems which in the recent years have become increasingly important as potential new pharmaceutical agents.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 20
    Publikationsdatum: 2014-02-26
    Beschreibung: Collection of abstracts of the Korean-German Bilateral Symposium on Scientific Computing, Berlin January 15/16, 2004
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 21
    Publikationsdatum: 2014-11-11
    Beschreibung: Beim Entwurf und Ausbau von Informations- und Kommunikationsnetzwerken m{ü}ssen zahlreiche interdependente Entscheidungen getroffen und gleichzeitig mannigfaltige Bedingungen ber{ü}cksichtigt werden. Die verf{ü}gbaren technischen und organisatorischen Alternativm{ö}glichkeiten sind normalerweise so vielf{ä}ltig und komplex, dass eine manuelle Planung praktisch nicht m{ö}glich ist. In diesem Artikel wird das Potential und die Methodik der mathematischen Optimierung bei der kostenoptimalen Planung von Kommunikationsnetzen vorgestellt. Als Ausgangspunkt wird exemplarisch eine typische praktische Aufgabe, die Struktur- und Konfigurationsplanung mehrstufiger Telekommunikationsnetzwerke, dargestellt. Anschließend werden kurz die wesentlichen Modellierungstechniken und Verfahrensans{ä}tze der mathematischen Optimierung skizziert. Abschließend gehen wir auf die Planung einer ad{ä}quaten Informations- und Kommunikations- Infrastruktur f{ü}r ein dezentrales Energieversorgungsnetz ein.
    Schlagwort(e): ddc:000
    Sprache: Deutsch
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  • 22
    Publikationsdatum: 2020-08-05
    Beschreibung: Point-to-Multipoint systems are one kind of radio systems supplying wireless access to voice/data communication networks. Such systems have to be run using a certain frequency spectrum, which typically causes capacity problems. Hence it is, on the one hand, necessary to reuse frequencies but, on the other hand, no interference must be caused thereby. This leads to the bandwidth allocation problem, a special case of so-called chromatic scheduling problems. Both problems are NP-hard, and there exist no polynomial time approximation algorithms with a guaranteed quality. One kind of algorithms which turned out to be successful for many other combinatorial optimization problems uses cutting plane methods. In order to apply such methods, knowledge on the associated polytopes is required. The present paper contributes to this issue, exploring basic properties of chromatic scheduling polytopes and several classes of facet-defining inequalities.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 23
    Publikationsdatum: 2020-02-11
    Beschreibung: The UMTS radio network planning problem poses the challenge of designing a cost-effective network that provides users with sufficient coverage and capacity. We describe an optimization model for this problem that is based on comprehensive planning data of the EU project MOMENTUM. We present heuristic mathematical methods for this realistic model, including computational results.
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    Sprache: Englisch
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  • 24
    Publikationsdatum: 2014-02-26
    Beschreibung: Relaying -- allowing multiple wireless hops -- is a protocol extension for cellular networks conceived to improve data throughput. Its benefits have only been quantified for small example networks. For assessing its general potential, we define a complex resource allocation\slash{}scheduling problem. Several mathematical models are presented for this problem; while a time-expanded MIP approach turns out intractable, a sophisticated column generation scheme leads to good computational results. We thereby show that for selected cases relaying can increase data throughput by 30\% on the average.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 25
    Publikationsdatum: 2014-02-26
    Beschreibung: Finding conflict-free wavelength assignments with a minimum number of required conversions for a routing of the lightpaths is one of the important tasks within the design of all-optical networks. We consider this problem in multi-fiber networks with different types of WDM systems. We give a detailed description of the problem and derive its theoretical complexity. For practical application, we propose several sequential algorithms to compute appropriate wavelength assignments. We also perform computational experiments to evaluate their performance. For the iterative algorithms, we identify characteristic patterns of progression. Two of these algorithms qualify for application in practice.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 26
    Publikationsdatum: 2014-09-30
    Beschreibung: A recently developed algorithm allows Rigid Body Docking of ligands to proteins, regardless of the accessibility and location of the binding site. The Docking procedure is divided into three subsequent optimization phases, two of which utilize rigid body dynamics. The last one is applied with the ligand already positioned inside the binding pocket and accounts for full flexibility. Initially, a combination of geometrical and force-field based methods is used as a Coarse Docking strategy, considering only Lennard-Jones interactions between the target and pharmaceutically relevant atoms or functional groups. The protein is subjected to a Hot Spot Analysis, which reveals points of high affinity in the protein environment towards these groups. The hot spots are distributed into different subsets according to their group affiliation. The ligand is described as a complementary point set, consisting of the same subsets. Both sets are matched in $\mathrm{I\!R}^{3}$, by superimposing members of the same subsets. In the first instance, steric inhibition is nearly neglected, preventing the system's trajectory from trapping in local minima and thus from finding false positive solutions. Hence the exact location of the binding site can be determined fast and reliably without any additional information. Subsequently, errors resulting from approximations are minimized via finetuning, this time considering both Lennard-Jones and Coulomb forces. Finally, the potential energy of the whole complex is minimized. In a first evaluation, results are rated by a reduced scoring function considering only noncovalent interaction energies. Exemplary Screening results will be given for specific ligands.
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    Sprache: Englisch
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  • 27
    Publikationsdatum: 2014-02-26
    Beschreibung: We suggest a new model for the design of telecommunication networks which integrates decisions about the topology, configuration of the switching hardware, link dimensioning, and protected routing of communication demands. Applying the branch-and-cut-algorithm implemented in our network planning and optimization tool DISCNET, we demonstrate that real-world based network planning instances of such an enhanced model can be solved.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 28
    Publikationsdatum: 2020-02-11
    Beschreibung: Dieser Bericht beschreibt die Erfahrungen und Schlussfolgerungen,die im Rahmen der VDS-Vorstudie bei der Speicherung der vom Friedrich-Althoff-Konsortium lizenzierten Zeitschriften des Kluwer-Verlages gewonnen wurden.
    Schlagwort(e): ddc:000
    Sprache: Deutsch
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  • 29
    Publikationsdatum: 2020-11-13
    Beschreibung: Der KOBV setzt für die endnutzerbasierte Online-Fernleihe den Sisis ZFL-Server (Zentraler Fernleih-Server) ein. Mit dem Einsatz des ZFL-Servers können in den Bibliotheken echte Rationalisierungseffekte erzielt werden: Der Server ist in der Lage, Fernleih-Bestellungen an lokale Systeme zu übergeben, so dass sie im lokalen System automatisch - ohne Eingreifen von Bibliotheksmitarbeitern - weiterverarbeitet werden können. Im KOBV können derzeit Sisis- und Aleph-Lokalsysteme diese Schnittstelle voll bedienen. Andere Bibliothekssysteme im KOBV, die diese Schnittstelle nicht bedienen können, werden mittels eines E-Mail-Verfahrens in die Online-Fernleihe integriert. Die vorliegende Kurzbeschreibung der Online-Fernleihe im KOBV soll - im Gegensatz zur Spezifikation, die möglichst vollständig sein sollte - einen leicht verständlichen Einblick in die Abläufe der Online-Fernleihe vermitteln. Nach einem Überblick über zu erwartende Rationalisierungseffekte ist der Ablauf einer Online-Fernleih-Bestellung - veranschaulicht durch eine Graphik mit dem technischen Aufbau im KOBV - kurz dargestellt. \vspace{6mm} {\it Hinweis:} Die von einer Arbeitsgruppe des KOBV erstellte Spezifikation zur Online-Fernleihe ist als ZIB Report 02-30 auf dem Preprint-Server des ZIB veröffentlicht. Siehe: Monika Kuberek (Red.) {\begin{rawhtml} 〈a href="http://www.zib.de/Publications/Reports/ZR-02-30.pdf"〉 〈i〉 Spezifikation für eine Verbund-Fernleih-Software im KOBV〈/i〉 〈/a〉 \end{rawhtml}}
    Schlagwort(e): ddc:000
    Sprache: Deutsch
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  • 30
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    Unbekannt
    Publikationsdatum: 2014-02-26
    Beschreibung: The problem of clustering data can often be transformed into the problem of finding a hidden block diagonal structure in a stochastic matrix. Deuflhard et al. have proposed an algorithm that state s the number $k$ of clusters and uses the sign structure of $k$ eigenvectors of the stochastic matrix to solve the cluster problem. Recently Weber and Galliat discovered that this system of eigenvectors can easily be transformed into a system of $k$ membership functions or soft characteristic functions describing the clusters. In this article we explain the corresponding cluster algorithm and point out the underlying theory. By means of numerical examples we explain how the grade of membership can be interpreted.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 31
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    Publikationsdatum: 2014-02-26
    Beschreibung: Mit der Entwicklung des KOBV-Informationsportals soll den Benutzern in der Region Berlin-Brandenburg ein verbesserter Zugang zu Informationsressourcen geboten werden. Einen wesentlichen Anteil diese Auf der Grundlage der Analyse der Rahmenbedingungen werden Anforderungen an die Zugriffskontrolle im KOBV definiert und Lösungsmöglichkeiten auf der Ebene allgemeiner Modelle diskutiert.
    Schlagwort(e): ddc:000
    Sprache: Deutsch
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  • 32
    Publikationsdatum: 2014-02-26
    Beschreibung: The KOBV Informationsportal aims to be a universal gateway to the sources of information hosted by the partner libraries from the Berlin-Brandenburg area. Due to the large number of these sources, an intuitive navigation is an essential component of the portal. The navigation-component should preserve the partner libraries? independence and overcome their administrative and technical differences. This paper proposes a collection-level navigation with four dimensions: the sources? subject areas (e.g. the first two levels of DDC), the sources? type (e.g. e-journals, databases, OPACs, etc.), the sources? location (e.g. Berlin, Brandenburg) / the library that hosts that source and the sources? accessing state (e.g. free, restricted, etc.).
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 33
    Publikationsdatum: 2014-02-26
    Beschreibung: Our main result is that every n-dimensional polytope can be described by at most (2n-1) polynomial inequalities and, moreover, these polynomials can explicitly be constructed. For an n-dimensional pointed polyhedral cone we prove the bound 2n-2 and for arbitrary polyhedra we get a constructible representation by 2n polynomial inequalities.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 34
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    Publikationsdatum: 2020-02-11
    Beschreibung: The NETLIB has now served for 18 years as a repository of LP problem instances. From the beginning to the present day there was some uncertainness about the precise values of the optimal solutions. We implemented a program using exact rational arithmetic to compute proofs for the feasibility and optimality of an LP solution. This paper reports the \emph{exact} optimal objective values for all NETLIB problems.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 35
    Publikationsdatum: 2014-02-26
    Beschreibung: Based on the knowledge gained from direct numerical simulations which are only possible in the microscale regime, a concept of driven turbulence is presented which allows to enter the mesoscopic scale regime. Here, dust formation under stochastic hydro- and thermodynamic conditions is studied: constructively superimposed stochastic waves initiate dust formation by the creation of singular nucleation events. It, hence, results a varying mean grain size and dust density in space and time. The newly formed dust changes the thermodynamic behavior from almost isotherm to adiabatic and chemically depletes the gas phase.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 36
    Publikationsdatum: 2014-11-11
    Beschreibung: Der scharfe Wettbewerb innerhalb der Telekommunikationsbranche zwingt die Netzbetreiber dazu, ihre Investitionen genau zu planen und immer wieder Einsparungsmanahmen durchzuführen. Gleichzeitig ist es jedoch wichtig, die Qualität der angebotenen Dienste zu verbessern, um neue Kunden zu gewinnen und langfristig an sich zu binden. Die mathematische Optimierung bietet sich für viele solcher Aufgabenstellungen als hervorragend geeignetes Planungswerkzeug an. Ziel dieses Artikels ist es, ihre Methodik und ihre Anwendung speziell zur Kosten- und Qualitätsoptimierung in Kommunikationsnetzen vorzustellen. Anhand von vier konkreten Planungsaufgaben aus dem Bereich der Festnetzplanung wird aufgezeigt, wie sich komplexe Zusammenhänge in flexiblen mathematischen Modellen abbilden lassen und welche Verfahren zur automatisierten Bearbeitung der Probleme eingesetzt werden können. Die hier vorgestellten Methoden zeichnen sich insbesondere dadurch aus, dass sie neben hochwertigen Lösungen auch eine Qualittsgarantie liefern, mit der sich die Lsungen fundiert bewerten lassen. Die dokumentierten Ergebnisse aus verschiedenen Industrieprojekten belegen die Eignung und Güte der mathematischen Optimierung für die Praxis.
    Schlagwort(e): ddc:000
    Sprache: Deutsch
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  • 37
    Publikationsdatum: 2014-02-26
    Beschreibung: Dust formation {in brown dwarf atmospheres} is studied by utilizing a model for driven turbulence in the mesoscopic scale regime. We apply a pseudo-spectral method where waves are created and superimposed {within} a {limited} wavenumber interval. The turbulent kinetic energy distribution follows the Kolmogoroff spectrum which is assumed to be the most likely value. Such superimposed, stochastic waves may occur in a convectively active environment. They cause nucleation fronts and nucleation events and thereby initiate the dust formation process which { continues until} all condensible material is consumed. Small disturbances {are found to} have a large impact on the dust forming system. An initially dust-hostile region, which may originally be optically thin, becomes optically thick in a patchy way showing considerable variations in the dust properties during the formation process. The dust appears in lanes and curls as a result of the interaction with waves, i.e. turbulence, which form larger and larger structures with time. Aiming on a physical understanding of the variability of brown dwarfs, related to structure formation in substellar atmospheres, we work out first necessary criteria for small-scale closure models to be applied in macroscopic simulations of dust forming astrophysical systems.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 38
    Publikationsdatum: 2014-02-26
    Beschreibung: Substellar atmospheres are observed to be irregularly variable for which the formation of dust clouds is the most promising candidate explanation. The atmospheric gas is convectively unstable and, last but not least, colliding convective cells are seen as cause for a turbulent fluid field. Since dust formation depends on the local properties of the fluid, turbulence influences the dust formation process and may even allow the dust formation in an initially dust-hostile gas. A regime-wise investigation of dust forming substellar atmospheric situations reveals that the largest scales are determined by the interplay between gravitational settling and convective replenishment which results in a dust-stratified atmosphere. The regime of small scales is determined by the interaction of turbulent fluctuations. Resulting lane-like and curled dust distributions combine to larger and larger structures. We compile necessary criteria for a subgrid model in the frame of large scale simulations as result of our study on small scale turbulence in dust forming gases.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 39
    Publikationsdatum: 2019-01-24
    Beschreibung: The solution of scattering problems described by the Helmholtz equation on unbounded domains is of importance for a wide variety of applications, for example in electromagnetics and acoustics. An implementation of a solver for scattering problems based on the programming language Matlab is introduced. The solver relies on the finite-element-method and on the perfectly-matched-layer-method, which allows for the simulation of scattering problems on complex geometries surrounded by inhomogeneous exterior domains. This report gives a number of detailed examples and can be understood as a user manual to the freely accessible code of the solver HelmPole.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 40
    Publikationsdatum: 2020-03-09
    Beschreibung: \noindent The size of data sets produced on remote supercomputer facilities frequently exceeds the processing capabilities of local visualization workstations. This phenomenon increasingly limits scientists when analyzing results of large-scale scientific simulations. That problem gets even more prominent in scientific collaborations, spanning large virtual organizations, working on common shared sets of data distributed in Grid environments. In the visualization community, this problem is addressed by distributing the visualization pipeline. In particular, early stages of the pipeline are executed on resources closer to the initial (remote) locations of the data sets. \noindent This paper presents an efficient technique for placing the first two stages of the visualization pipeline (data access and data filter) onto remote resources. This is realized by exploiting the ``extended retrieve'' feature of GridFTP for flexible, high performance access to very large HDF5 files. We reduce the number of network transactions for filtering operations by utilizing a server side data processing plugin, and hence reduce latency overhead compared to GridFTP partial file access. The paper further describes the application of hierarchical rendering techniques on remote uniform data sets, which make use of the remote data filtering stage.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 41
    Publikationsdatum: 2014-02-26
    Beschreibung: Relaying is a protocol extension for cellular wireless computer networks; in order to utilize radio resources more efficiently, several hops are allowed within one cell. This paper investigates the principle potential of relaying by casting transmission scheduling as a mathematical optimization problem, namely, a linear program. We analyze the throughput gains showing that, irrespective of the concrete scheduling algorithm, performance gains of up to 30\% on average for concrete example networks are achievable.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 42
    Publikationsdatum: 2014-02-26
    Beschreibung: We call an edge $e$ of a perfect graph $G$ critical if $G-e$ is imperfect and call $e$ anticritical if $G+e$ is imperfect. The present paper surveys several questions in this context. We ask in which perfect graphs critical and anticritical edges occur and how to detect such edges. The main result by [{\sl Wagler, PhD thesis 2000}] shows that a graph does not admit any critical edge if and only if it is Meyniel. The goal is to order the edges resp.~non-edges of certain perfect graphs s.t. deleting resp.~adding all edges in this order yields a sequence of perfect graphs only. Results of [{\sl Hayward 1985}] and [{\sl Spinrad & Sritharan 1995}] show the existence of such edge orders for weakly triangulated graphs; the line-perfect graphs are precisely these graphs where all edge orders are perfect [{\sl Wagler 2001}]. Such edge orders cannot exist for every subclass of perfect graphs that contains critically resp.~anticritically perfect graphs where deleting resp.~adding an arbitrary edge yields an imperfect graph. We present several examples and properties of such graphs, discuss constructions and characterizations from [{\sl Wagler 1999, Wagler PhD thesis 2000}]. An application of the concept of critically and anticritically perfect graphs is a result due to [{\sl Hougardy & Wagler 2002}] showing that perfectness is an elusive graph property.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 43
    Publikationsdatum: 2014-02-26
    Beschreibung: Hasenbusch has proposed splitting the pseudo-fermionic action into two parts, in order to speed-up Hybrid Monte Carlo simulations of QCD. We have tested a different splitting, also using clover-improved Wilson fermions. An additional speed-up between 5 and 20\% over the original proposal was achieved in production runs.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 44
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    Publikationsdatum: 2014-11-10
    Beschreibung: A set of vertices $S\subseteq V$ is called a safe separator for treewidth, if $S$ is a separator of $G$, and the treewidth of $G$ equals the maximum of the treewidth over all connected components $W$ of $G-S$ of the graph, obtained by making $S$ a clique in the subgraph of $G$, induced by $W\cup S$. We show that such safe separators are a very powerful tool for preprocessing graphs when we want to compute their treewidth. We give several sufficient conditions for separators to be safe, allowing such separators, if existing, to be found in polynomial time. In particular, every minimal separator of size one or two is safe, every minimal separator of size three that does not split off a component with only one vertex is safe, and every minimal separator that is an almost clique is safe; an almost clique is a set of vertices $W$ such that there is a $v\in W$ with $W-\{v\}$ a clique. We report on experiments that show significant reductions of instance sizes for graphs from proba! bilistic networks and frequency assignment.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 45
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    Publikationsdatum: 2019-01-29
    Beschreibung: A primal-dual interior point method for optimal control problems is considered. The algorithm is directly applied to the infinite dimensional problem. Existence and convergence of the central path are analyzed, and linear convergence of a short step pathfollowing method is established.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 46
    Publikationsdatum: 2014-02-26
    Beschreibung: We explicitly construct small triangulations for a number of well-known $3$-dimensional manifolds and give a brief outline of some aspects of the underlying theory of $3$-manifolds and its historical development.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 47
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    Publikationsdatum: 2016-06-30
    Beschreibung: Peer-to-Peer (P2P) Systeme werden u.a. zur Verwaltung von großen Datenmengen benutzt, die auf verschiedene Rechner verteilt sind. Benutzern soll damit der Zugriff auf Daten innerhalb des Systems leicht ermöglicht werden. Damit in P2P Systemen die Daten effizient verteilt und gesucht werden können, existieren Distributed Hash Tables. Distributed Hash Tables (DHT) sind eine Methode, um globale Informationen persistent speichern zu können. Der Wertebereich der Hashfunktion, welche die zu veröffentlichenden Einträge auf Werte abbildet, wird in Abschnitte aufgeteilt, die einzelnen Knoten zugeteilt werden. Die meisten DHTs haben aber ein Problem bei der Verteilung der Last. Die verschiedenen DHT Systeme beruhen meist auf einem identischen Ansatz der Lastverteilung. Die Last wird nur mit Hilfe einer Hashfunktion verteilt. Es wird davon ausgegangen, dass diese Funktion die Last gleichmäßig verteilt. Im Rahmen dieser Arbeit wurde ein Verfahren zur Last Verteilung entwickelt, simuliert und implementiert. Bei dem Verfahren wird die Last wie bei der Verteilung von Wärme an die Umgebung abgegeben. Es wird mit existierenden Lastbalancierungsalgorithmen verglichen. Mit diesem neuen Verfahren ist es möglich, Last in DHTs besser zu verteilen ohne große Änderungen an den DHTs vorzunehmen. Es wird gezeigt, wie mit dem Verfahren zusätzlich die Fehlertoleranz des P2P Systems erhöht werden kann.
    Beschreibung: One of the many uses of Peer-to-Peer (P2P) systems is the administration of large data sets that are distributed across different computers, with the goal of facilitating user access to files within the system. Distributed Hash Tables (DHT) are designed to enable the efficient distribution and search of files, by allowing global information to be persistently stored. The range of values of the hash function (the possible entries in the published hash table) are assigned to individual nodes. Most DHTs, however, have a problem with load distribution. The various DHT systems usually operate by distributing load equally among nodes. Thus the load is distributed using the help of the hash function. One assumes this function distributes the load evenly. In the context of this work a method of distributing load has been developed, simulated and implemented. With this method load is transferred in a fashion analogous to the dissipation of heat into the environment. Comparisons with existing algorithms for load balancing are drawn. With the new procedure it is possible to better distribute load in DHTs without requiring major changes to the DHTs themselves. It is shown that with the procedure the fault tolerance of P2P systems may also be increased.
    Schlagwort(e): ddc:000
    Sprache: Deutsch
    Materialart: masterthesis , doc-type:masterThesis
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  • 48
    Publikationsdatum: 2014-02-26
    Beschreibung: The key to molecular conformation dynamics is the direct identification of metastable conformations, which are almost invariant sets of molecular dynamical systems. Once some reversible Markov operator has been discretized, a generalized symmetric stochastic matrix arises. This matrix can be treated by Perron cluster analysis, a rather recent method involving a Perron cluster eigenproblem. The paper presents an improved Perron cluster analysis algorithm, which is more robust than earlier suggestions. Numerical examples are included.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 49
    Publikationsdatum: 2014-11-11
    Beschreibung: In this paper, a new shared protection mechanism for meshed optical networks is presented. Significant network design cost reductions can be achieved in comparison to the well-known 1+1 protection scheme. Demand-wise Shared Protection (DSP) bases on the diversification of demand routings and exploits the network connectivity to restrict the number of backup lightpaths needed to provide the desired level of prorection. Computational experiments approve the benefits of the concept DSP for cost efficient optical network designs.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 50
    Publikationsdatum: 2019-05-10
    Beschreibung: The correlation of the inner architecture of bone and its functional loading was already stated by Wolff in 1892. Our objective is to demonstrate this interdependence in the case of the human mandible. For this purpose, stress/strain profiles occuring at a human lateral bite were simulated. Additionally, by a combination of computer graphics modules, a three--dimensional volumetric visualization of bone mineral density could be given. Qualitative correspondences between the density profile of the jaw and the simulated stress/strain profiles could be pointed out. In the long run, this might enable the use of the simulation for diagnosis and prognosis. The solution of the underlying partial differential equations describing linear elastic material behaviour was provided by an adaptive finite element method. Estimates of the discretization errors, local grid refinement, and multilevel techniques guaranteed the reliability and efficiency of the method.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 51
    Publikationsdatum: 2014-02-26
    Beschreibung: UMTS is a 3rd generation mobile telecommunication system which enables multi-service and multi-bit rate communication going beyond the possibilities of previous systems. The simulator MoDySim models UMTS in great detail. Characteristics of UMTS such as soft hand-over and the interdependency of load and capacity among neighbouring cells are challenges for the parallelisation of such a system. In this paper we explain how the software was parallelised and present performance results of a UMTS simulation for the city of Berlin.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 52
    Publikationsdatum: 2014-02-26
    Beschreibung: We report on a numerical reinvestigation of the Aoki phase in lattice QCD with two flavors of Wilson fermions where the parity-flavor symmetry is spontaneously broken. For this purpose the Hybrid Monte Carlo algorithm was used and an explicit symmetry-breaking source term $h\bar{\psi} i \gamma_{5} \tau^{3}\psi$ was added to the Wilson fermion action. The order parameter $\langle\bar{\psi}i\gamma_{5}\tau^{3}\psi\rangle$ was studied at several values of $(\beta,\kappa,h)$ on lattices of sizes $4^4$ to $12^4$. Our largest lattices can be considered as infintely large allowing to extrapolate to $h=0$. The existence of a parity-flavor-breaking phase can be confirmed at $\beta=4.0$ and $\beta=4.3$ while we find no sign of parity-flavor-breaking at $\beta=4.6$ and $\beta=5.0$.
    Schlagwort(e): ddc:000
    Sprache: Englisch
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  • 53
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    Publikationsdatum: 2014-02-26
    Beschreibung: In this paper we interpret clustering as a mapping of data into a simplex. If the data itself has simplicial struture this mapping becomes linear. Spectral analysis is an often used tool for clustering data. We will show that corresponding singular vectors or eigenvectors comprise simplicial structure. Therefore they lead to a cluster algorithm, which consists of a simple linear mapping. An example for this kind of algorithms is the Perron cluster analysis (PCCA). We have applied it in practice to identify metastable sets of molecular dynamical systems. In contrast to other algorithms, this kind of approach provides an a priori criterion to determine the number of clusters. In this paper we extend the ideas to more general problems like clustering of bipartite graphs.
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    Sprache: Englisch
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  • 54
    Publikationsdatum: 2016-06-09
    Schlagwort(e): ddc:000
    Sprache: Deutsch
    Materialart: masterthesis , doc-type:masterThesis
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  • 55
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    Publikationsdatum: 2019-10-24
    Schlagwort(e): ddc:000
    Sprache: Deutsch
    Materialart: annualzib , doc-type:report
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  • 56
    Publikationsdatum: 2022-04-11
    Beschreibung: The Web of the future will provide a huge amount of information. We need better ways for dealing with and managing the information. A qualified semantic annotation of the information plays a key role for the Web of the future. This article gives an overview about the efforts of the mathematical community to build up a distributed and open information and communication system for mathematics: the Math-Net. The Math-Net Initiative has developed metadata schemas for some classes of Web resources which are relevant in mathematics. Math-Net Services process this information and enable the user to efficiently search and access the information.
    Schlagwort(e): ddc:000
    Sprache: Englisch
    Materialart: reportzib , doc-type:preprint
    Format: application/postscript
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  • 57
    Publikationsdatum: 2022-07-07
    Beschreibung: In this paper we propose a new finite element realization of the Perfectly Matched Layer method (PML-method). Our approach allows to deal with arbitrary shaped polygonal domains and with certain types of inhomogeneous exterior domains. Among the covered inhomogeneities are open waveguide structures playing an essential role in integrated optics. We give a detailed insight to implementation aspects. Numerical examples show exponential convergence behavior to the exact solution with the thickness of the PML sponge layer.
    Schlagwort(e): ddc:000
    Sprache: Englisch
    Materialart: reportzib , doc-type:preprint
    Format: application/postscript
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  • 58
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 169-185 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 59
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Materialart: Digitale Medien
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  • 60
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 251-268 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 61
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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).
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 62
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 359-371 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 63
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 387-397 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 64
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 65
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 345-357 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 66
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 707-718 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 67
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 803-816 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 68
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Materialart: Digitale Medien
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  • 69
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 39-51 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 70
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 65-88 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 71
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 155-168 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 72
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 231-235 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 73
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 237-240 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 74
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 243-247 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 75
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 269-282 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 76
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 327-343 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 77
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
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  • 78
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1305-1328 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 79
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2121-2136 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 80
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2137-2142 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 81
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2195-2202 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 82
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2225-2241 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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).
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 83
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 21 Ill.
    Materialart: Digitale Medien
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  • 84
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 85
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2623-2633 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 86
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 87
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 11 Ill.
    Materialart: Digitale Medien
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  • 88
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1103-1112 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 89
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1191-1209 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 90
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1247-1260 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 91
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1333-1335 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 92
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1399-1411 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 93
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1481-1502 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 94
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1537-1547 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 95
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1503-1535 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 17 Ill.
    Materialart: Digitale Medien
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  • 96
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1575-1588 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 97
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1625-1633 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 98
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1707-1725 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 99
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 100
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2011-2020 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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