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  • 1
    Publication Date: 2020-08-05
    Description: This article is about the optimal track allocation problem (OPTRA) to find, in a given railway network, a conflict free set of train routes of maximum value. We study two types of integer programming formulations: a standard formulation that models block conflicts in terms of packing constraints, and a new extended formulation that is based on additional configuration' variables. We show that the packing constraints in the standard formulation stem from an interval graph, and that they can be separated in polynomial time. It follows that the LP relaxation of a strong version of this model, including all clique inequalities from block conflicts, can be solved in polynomial time. We prove that the extended formulation produces the same LP bound, and that it can also be computed with this model in polynomial time. Albeit the two formulations are in this sense equivalent, the extended formulation has advantages from a computational point of view, because it features a constant number of rows and is therefore amenable to standard column generation techniques. Results of an empirical model comparison on mesoscopic data for the Hannover-Fulda-Kassel region of the German long distance railway network are reported.
    Keywords: ddc:000
    Language: English
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  • 2
    Publication Date: 2016-06-09
    Description: We study barrier methods for state constrained optimal control problems with PDEs. In the focus of our analysis is the path of minimizers of the barrier subproblems with the aim to provide a solid theoretical basis for function space oriented path-following algorithms. We establish results on existence, continuity and convergence of this path. Moreover, we consider the structure of barrier subdifferentials, which play the role of dual variables.
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    Language: English
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  • 3
    Publication Date: 2016-06-09
    Description: For the treatment of equilibrated molecular systems in a heat bath we propose a transition state theory that is based on conformation dynamics. In general, a set-based discretization of a Markov operator ${\cal P}^\tau$ does not preserve the Markov property. In this article, we propose a discretization method which is based on a Galerkin approach. This discretization method preserves the Markov property of the operator and can be interpreted as a decomposition of the state space into (fuzzy) sets. The conformation-based transition state theory presented here can be seen as a first step in conformation dynamics towards the computation of essential dynamical properties of molecular systems without time-consuming molecular dynamics simulations.
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    Language: English
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  • 4
    Publication Date: 2021-01-22
    Description: We present a middleware to store multidimensional data sets on Internet-scale distributed systems and to efficiently perform range queries on them. Our structured overlay network \emph{SONAR (Structured Overlay Network with Arbitrary Range queries)} puts keys which are adjacent in the key space on logically adjacent nodes in the overlay and is thereby able to process multidimensional range queries with a single logarithmic data lookup and local forwarding. The specified ranges may have arbitrary shapes like rectangles, circles, spheres or polygons. Empirical results demonstrate the routing performance of SONAR on several data sets, ranging from real-world data to artificially constructed worst case distributions. We study the quality of SONAR's routing information which is based on local knowledge only and measure the indegree of the overlay nodes to find potential hot spots in the routing process. We show that SONAR's routing table is self-adjusting, even under extreme situations, keeping always a maximum of $\lceil \log N \rceil$ routing entries.
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  • 5
    Publication Date: 2016-06-09
    Description: \begin{abstract} In systems biology, the stochastic description of biochemical reaction kinetics is increasingly being employed to model gene regulatory networks and signalling pathways. Mathematically speaking, such models require the numerical solution of the underlying evolution equat ion, also known as the chemical master equation (CME). Up to now, the CME has almost exclusively been treated by Monte-Carlo techniques, the most prominent of which is the simulation algorithm suggest ed by Gillespie in 1976. Since this algorithm requires an update for each single reaction event, realizations can be computationally very costly. As an alternative, we here propose a novel approach, which focuses on the discrete partial differential equation (PDE) structure of the CME and thus allows to adopt ideas from adaptive discrete Galerkin methods (as designed by two of the present authors in 1989), which have proven to be highly efficient in the mathematical modelling of polyreaction kinetics. Among the two different options of discretizing the CME as a discrete PDE, the method of lines approach (first space, then time) and the Rothe method (first time, then space), we select the latter one for clear theoretical and algorithmic reasons. First numeric al experiments at a challenging model problem illustrate the promising features of the proposed method and, at the same time, indicate lines of necessary further research. \end{abstract}
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  • 6
    Publication Date: 2014-02-26
    Description: Chvatal-Gomory cuts are among the most well-known classes of cutting planes for general integer linear programs (ILPs). In case the constraint multipliers are either 0 or $\frac{1}{2}$, such cuts are known as $\{0,\frac{1}{2}\}$-cuts. It has been proven by Caprara and Fischetti (1996) that separation of $\{0,\frac{1}{2}\}$-cuts is NP-hard. In this paper, we study ways to separate $\{0,\frac{1}{2}\}$-cuts effectively in practice. We propose a range of preprocessing rules to reduce the size of the separation problem. The core of the preprocessing builds a Gaussian elimination-like procedure. To separate the most violated $\{0,\frac{1}{2}\}$-cut, we formulate the (reduced) problem as integer linear program. Some simple heuristic separation routines complete the algorithmic framework. Computational experiments on benchmark instances show that the combination of preprocessing with exact and/or heuristic separation is a very vital idea to generate strong generic cutting planes for integer linear programs and to reduce the overall computation times of state-of-the-art ILP-solvers.
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  • 7
    Publication Date: 2014-02-26
    Description: In this paper a Godunov-type projection method for computing approximate solutions of the zero Froude number (incompressible) shallow water equations is presented. It is second-order accurate and locally conserves height (mass) and momentum. To enforce the underlying divergence constraint on the velocity field, the predicted numerical fluxes, computed with a standard second order method for hyperbolic conservation laws, are corrected in two steps. First, a MAC-type projection adjusts the advective velocity divergence. In a second projection step, additional momentum flux corrections are computed to obtain new time level cell-centered velocities, which satisfy another discrete version of the divergence constraint. The scheme features an exact and stable second projection. It is obtained by a Petrov-Galerkin finite element ansatz with piecewise bilinear trial functions for the unknown incompressible height and piecewise constant test functions. The stability of the projection is proved using the theory of generalized mixed finite elements, which goes back to Nicola{\"i}des (1982). In order to do so, the validity of three different inf-sup conditions has to be shown. Since the zero Froude number shallow water equations have the same mathematical structure as the incompressible Euler equations of isentropic gas dynamics, the method can be easily transfered to the computation of incompressible variable density flow problems.
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  • 8
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    Publication Date: 2019-10-24
    Keywords: ddc:000
    Language: German
    Type: annualzib , doc-type:report
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  • 9
    Publication Date: 2020-12-15
    Description: We provide information on the Survivable Network Design Library (SNDlib), a data library for fixed telecommunication network design that can be accessed at http://sndlib.zib.de. In version 1.0, the library contains data related to 22 networks which, combined with a set of selected planning parameters, leads to 830 network planning problem instances. In this paper, we provide a mathematical model for each planning problem considered in the library and describe the data concepts of the SNDlib. Furthermore, we provide statistical information and details about the origin of the data sets.
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  • 10
    Publication Date: 2020-08-05
    Description: The \emph{optimal track allocation problem} (\textsc{OPTRA}), also known as the train routing problem or the train timetabling problem, is to find, in a given railway network, a conflict-free set of train routes of maximum value. We propose a novel integer programming formulation for this problem that is based on additional configuration' variables. Its LP-relaxation can be solved in polynomial time. These results are the theoretical basis for a column generation algorithm to solve large-scale track allocation problems. Computational results for the Hanover-Kassel-Fulda area of the German long distance railway network involving up to 570 trains are reported.
    Keywords: ddc:000
    Language: English
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  • 11
    Publication Date: 2020-12-15
    Description: We consider a multicommodity routing problem, where demands are released \emph{online} and have to be routed in a network during specified time windows. The objective is to minimize a time and load dependent convex cost function of the aggregate arc flow. First, we study the fractional routing variant. We present two online algorithms, called Seq and Seq$^2$. Our first main result states that, for cost functions defined by polynomial price functions with nonnegative coefficients and maximum degree~$d$, the competitive ratio of Seq and Seq$^2$ is at most $(d+1)^{d+1}$, which is tight. We also present lower bounds of $(0.265\,(d+1))^{d+1}$ for any online algorithm. In the case of a network with two nodes and parallel arcs, we prove a lower bound of $(2-\frac{1}{2} \sqrt{3})$ on the competitive ratio for Seq and Seq$^2$, even for affine linear price functions. Furthermore, we study resource augmentation, where the online algorithm has to route less demand than the offline adversary. Second, we consider unsplittable routings. For this setting, we present two online algorithms, called U-Seq and U-Seq$^2$. We prove that for polynomial price functions with nonnegative coefficients and maximum degree~$d$, the competitive ratio of U-Seq and U-Seq$^2$ is bounded by $O{1.77^d\,d^{d+1}}$. We present lower bounds of $(0.5307\,(d+1))^{d+1}$ for any online algorithm and $(d+1)^{d+1}$ for our algorithms. Third, we consider a special case of our framework: online load balancing in the $\ell_p$-norm. For the fractional and unsplittable variant of this problem, we show that our online algorithms are $p$ and $O{p}$ competitive, respectively. Such results where previously known only for scheduling jobs on restricted (un)related parallel machines.
    Keywords: ddc:000
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  • 12
    Publication Date: 2014-02-26
    Description: Die Zentrale des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV) betreibt seit Januar 2004 das KOBV-Portal, in dem u.a. vielfältige Open-Linking-Dienste eingebunden sind. Dieser Beitrag erläutert Open-Linking allgemein und stellt die KOBV spezifischen Dienste im Detail vor. Dabei wird auch die Zugriffsentwicklung auf die KOBV-Open-Linking-Dienste evaluiert. Ein Ergebnis ist, dass signifikante Steigerungen der Nutzung erst dann bewirkt werden, wenn Maßnahmen durchgeführt werden, die erstens die Open-Linking-Dienste stärker ins Bewusstsein der NutzerInnen rücken und zweitens den Weg dorthin im KOBV-Portal verkürzen. Vor allem muss ein schneller Weg zu den Open-Linking-Diensten gewährleistet sein, um die Nutzung deutlich zu steigern. Um zusätzlich den Bekanntheitsgrad der Open-Linking-Dienste bundesweit zu erhöhen, regt die KOBV-Zentrale andere Bibliotheken und Verbünde dazu an, analoge Open-Linking-Dienste einzurichten. Auf diese Weise wird die Handhabung von Open-Linking selbstverständlicher.
    Keywords: ddc:000
    Language: German
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  • 13
    Publication Date: 2014-02-26
    Description: Dieser Artikel berichtet über eine erfolgreiche Schüleraktivität, die seit Jahren am Zuse-Institut Berlin (ZIB) bei Besuchen von Schülergruppen erprobt und verfeinert worden ist. Das hier zusammengestellte Material ist gedacht als Basis für eine Unterrichtseinheit in Leistungskursen Mathematik an Gymnasien. Inhaltlich wird von einem zwar für Schüler (wie auch Lehrer) neuen, aber leicht fasslichen Gegenstand ausgegangen: der Drei-Term-Rekursion für Besselfunktionen. Die Struktur wird erklärt und in ein kleines Programm umgesetzt. Dazu teilen sich die Schüler selbstorganisierend in Gruppen ein, die mit unterschiedlichen Taschenrechnern "um die Wette" rechnen. Die Schüler und Schülerinnen erfahren unmittelbar die katastrophale Wirkung von an sich kleinen'' Rundungsfehlern, sie landen -- ebenso wie der Supercomputer des ZIB -- im Bessel'schen Irrgarten''. Die auftretenden Phänomene werden mathematisch elementar erklärt, wobei lediglich auf das Konzept der linearen Unabhängigkeit zurückgegriffen wird. Das dabei gewonnene vertiefte Verständnis fließt ein in die Konstruktion eines klassischen Algorithmus sowie eines wesentlich verbesserten Horner-artigen Algorithmus.
    Keywords: ddc:000
    Language: German
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  • 14
    Publication Date: 2017-08-01
    Description: In this paper we study capacitated network design problems, differentiating directed, bidirected and undirected link capacity models. We complement existing polyhedral results for the three variants by new classes of facet-defining valid inequalities and unified lifting results. For this, we study the restriction of the problems to a cut of the network. First, we show that facets of the resulting cutset polyhedra translate into facets of the original network design polyhedra if the two subgraphs defined by the network cut are (strongly) connected. Second, we provide an analysis of the facial structure of cutset polyhedra, elaborating the differences caused by the three different types of capacity constraints. We present flow-cutset inequalities for all three models and show under which conditions these are facet-defining. We also state a new class of facets for the bidirected and undirected case and it is shown how to handle multiple capacity modules by Mixed Integer Rounding (MIR).
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    Language: English
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  • 15
    Publication Date: 2020-12-15
    Description: In this paper we study online multicommodity routing problems in networks, in which commodities have to be routed sequentially. The flow of each commodity can be split on several paths. Arcs are equipped with load dependent price functions defining routing costs, which have to be minimized. We discuss a greedy online algorithm that routes each commodity by minimizing a convex cost function that only depends on the demands previously routed. We present a competitive analysis of this algorithm showing that for affine linear price functions this algorithm is 4K2 (1+K)2 -competitive, where K is the number of commodities. For the single-source single-destination case, this algorithm is optimal. Without restrictions on the price functions and network, no algorithm is competitive. Finally, we investigate a variant in which the demands have to be routed unsplittably.
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    Language: English
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  • 16
    Publication Date: 2020-12-15
    Description: In this paper, we empirically investigate the NP-hard problem of finding sparse solutions to linear equation systems, i.e., solutions with as few nonzeros as possible. This problem has received considerable interest in the sparse approximation and signal processing literature, recently. We use a branch-and-cut approach via the maximum feasible subsystem problem to compute optimal solutions for small instances and investigate the uniqueness of the optimal solutions. We furthermore discuss five (modifications of) heuristics for this problem that appear in different parts of the literature. For small instances, the exact optimal solutions allow us to evaluate the quality of the heuristics, while for larger instances we compare their relative performance. One outcome is that the basis pursuit heuristic performs worse, compared to the other methods. Among the best heuristics are a method due to Mangasarian and a bilinear approach.
    Keywords: ddc:000
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  • 17
    Publication Date: 2014-02-26
    Description: The performance evaluation of W-CDMA networks is intricate as cells are strongly coupled through interference. Pole equations have been developed as a simple tool to analyze cell capacity. Numerous scientific contributions have been made on their basis. In the established forms, the pole equations rely on strong assumptions such as homogeneous traffic, uniform users, and constant downlink orthogonality factor. These assumptions are not met in realistic scenarios. Hence, the pole equations are typically used during initial network dimensioning only. Actual network (fine-) planning requires a more faithful analysis of each individual cell's capacity. Complex analytical analysis or Monte-Carlo simulations are used for this purposes. In this paper, we generalize the pole equations to include inhomogeneous data. We show how the equations can be parametrized in a cell-specific way provided the transmit powers are known. This allows to carry over prior results to realistic settings. This is illustrated with an example: Based on the pole equation, we investigate the accuracy of average snapshot'' approximations for downlink transmit powers used in state-of-the-art network optimization schemes. We confirm that the analytical insights apply to practice-relevant settings on the basis of results from detailed Monte-Carlo simulation on realistic datasets.
    Keywords: ddc:000
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  • 18
    Publication Date: 2017-08-01
    Description: This paper deals with directed, bidirected, and undirected capacitated network design problems. Using mixed integer rounding (MIR), we generalize flow-cutset inequalities to these three link types and to an arbitrary modular link capacity structure, and propose a generic separation algorithm. In an extensive computational study on 54 instances from the Survivable Network Design Library (SNDlib), we show that the performance of cplex can significantly be enhanced by this class of cutting planes. The computations reveal the particular importance of the subclass of cutset-inequalities.
    Keywords: ddc:000
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  • 19
    Publication Date: 2020-02-04
    Description: Wigner transformation provides a one-to-one correspondence between functions on position space (wave functions) and functions on phase space (Wigner functions). Weighted integrals of Wigner functions yield quadratic quantities of wave functions like position and momentum densities or expectation values. For molecular quantum systems, suitably modified classical transport of Wigner functions provides an asymptotic approximation of the dynamics in the high energy regime. The article addresses the computation of Wigner functions by Monte Carlo quadrature. An ad aption of the Metropolis algorithm for the approximation of signed measures with disconnected support is systematically tested in combination with a surface hopping algorithm for non-adiabatic quantum dynamics. The numerical experiments give expectation values and level populations with an error of two to three percent, which agrees with the theoretically expected accuracy.
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  • 20
    Publication Date: 2020-11-13
    Description: We study a planning problem arising in SDH/WDM multi-layer telecommunication network design. The goal is to find a minimum cost installation of link and node hardware of both network layers such that traffic demands can be realized via grooming and a survivable routing. We present a mixed-integer programming formulation that takes many practical side constraints into account, including node hardware, several bitrates, and survivability against single physical node or link failures. This model is solved using a branch-and-cut approach with problem-specific preprocessing and cutting planes based on either of the two layers. On several realistic two-layer planning scenarios, we show that these cutting planes are still useful in the multi-layer context, helping to increase the dual bound and to reduce the optimality gaps.
    Keywords: ddc:000
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  • 21
    Publication Date: 2020-08-05
    Description: In \emph{classical optimization} it is assumed that full information about the problem to be solved is given. This, in particular, includes that all data are at hand. The real world may not be so nice'' to optimizers. Some problem constraints may not be known, the data may be corrupted, or some data may not be available at the moments when decisions have to be made. The last issue is the subject of \emph{online optimization} which will be addressed here. We explain some theory that has been developed to cope with such situations and provide examples from practice where unavailable information is not the result of bad data handling but an inevitable phenomenon.
    Keywords: ddc:000
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  • 22
    Publication Date: 2020-12-11
    Description: Die Intention ist der kooperative Aufbau einer Infrastruktur durch die Bibliotheksverbünde, um den Nutzern Volltext-Angebote dauerhaft und komfortabel zur Verfügung zu stellen: Zeitschriftenartikel und elektronische Dokumente werden mittels Suchmaschinentechnologie indexiert und unter Berücksichtigung von Zugriffsrechten zugänglich gemacht. Realisiert ist dies bereits im KOBV-Volltextserver, der seit Ende 2005 im Routinebetrieb läuft. Vorstellbar ist ein überregionales Netz von Volltextservern der Verbünde, die mittels Suchmaschinentechnologie indiziert und nahtlos in das regionale und lokale Literaturangebot integriert werden. Bei den lizenzierten Materialien sind insbesondere auch die Rechte der Verlage zu wahren und entsprechende Rechtemanagement-Verfahren einzusetzen. Es gilt, transparente Verfahren zu konzipieren und umzusetzen, um für die Verlage die notwendige Vertrauensbasis zu schaffen und gleichzeitig den Einrichtungen ihren berechtigten Zugriff auf die Volltexte zu sichern. Der vorliegende Text ist die schriftliche Fassung eines Vortrages auf dem 3. Leipziger Kongress für Information und Bibliothek "Information und Ethik", der vom 19.-22. März 2007 im Congress Center Leipzig stattfand.
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    Language: German
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  • 23
    Publication Date: 2020-12-11
    Description: Zur Unterstützung der Bibliotheken bei ihren Open-Access-Aktivitäten betreibt die KOBV-Zentrale seit Anfang 2005 den Service "Opus- und Archivierungsdienste". Die KOBV-Zentrale agiert als Application Service Provider (ASP) für sämtliche technischen Komponenten des Publikationsprozesses, indem sie die gesamte technische Infrastruktur bereitstellt und betreibt – angefangen bei den lokalen Publikationsservern bis hin zu lokalen Repositories zur Archivierung der elektronischen Dokumente. Der vorliegende Text ist die schriftliche Fassung eines gleichnamigen Vortrages auf der 31. ASpB-Tagung "Kooperation versus Eigenprofil?" der Arbeitsgemeinschaft der Spezialbibliotheken, die vom 25.-28. September 2007 in der Technischen Universität Berlin stattfand.
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    Language: German
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  • 24
    Publication Date: 2022-07-07
    Description: A new approach to derive transparent boundary conditions (TBCs) for wave, Schrödinger, heat and drift-diffusion equations is presented. It relies on the pole condition and distinguishes between physical reasonable and unreasonable solutions by the location of the singularities of the spatial Laplace transform of the exterior solution. To obtain a numerical algorithm, a Möbius transform is applied to map the Laplace transform onto the unit disc. In the transformed coordinate the solution is expanded into a power series. Finally, equations for the coefficients of the power series are derived. These are coupled to the equation in the interior, and yield transparent boundary conditions. Numerical results are presented in the last section, showing that the error introduced by the new approximate TBCs decays exponentially in the number of coefficients.
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  • 25
    Publication Date: 2022-07-19
    Description: We present a unified approach for consistent remeshing of arbitrary non-manifold triangle meshes with additional user-defined feature lines, which together form a feature skeleton. Our method is based on local operations only and produces meshes of high regularity and triangle quality while preserving the geometry as well as topology of the feature skeleton and the input mesh.
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  • 26
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    Publication Date: 2019-10-24
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    Language: German
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  • 27
    Publication Date: 2014-02-26
    Description: We propose a variant of the control reduced interior point method for the solution of state constrained problems. We show convergence of the corresponding interior point pathfollowing algorithm in function space. Morever, we provide error bounds for the iterates.
    Keywords: ddc:000
    Language: English
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  • 28
    Publication Date: 2014-02-26
    Description: This paper aims at presenting the complex coupled network of the human menstrual cycle to the interested community. Beyond the presently popular smaller models, where important network components arise only as extremely simplified source terms, we add: the GnRH pulse generator in the hypothalamus, receptor binding, and the biosynthesis in the ovaries. Simulation and parameter identification are left to a forthcoming paper.
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  • 29
    Publication Date: 2014-02-26
    Description: This work explores two applications of a classical result on the continuity of Nemyckii operators to optimal control with PDEs. First, we present an alternative approach to the analysis of Newton's method for function space problems involving semi-smooth Nemyckii operators. A concise proof for superlinear convergence is presented, and sharpened bounds on the rate of convergence are derived. Second, we derive second order sufficient conditions for problems, where the underlying PDE has poor regularity properties. We point out that the analytical structure in both topics is essentially the same.
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  • 30
    Publication Date: 2014-02-26
    Description: In this paper, we study the efficiency of Nash equilibria for a sequence of nonatomic routing games. We assume that the games are played consecutively in time in an online fashion: by the time of playing game $i$, future games $i+1,\dots,n$ are not known, and, once players of game $i$ are in equilibrium, their corresponding strategies and costs remain fixed. Given a sequence of games, the cost for the sequence of Nash equilibria is defined as the sum of the cost of each game. We analyze the efficiency of a sequence of Nash equilibria in terms of competitive analysis arising in the online optimization field. Our main result states that the online algorithm $\sl {SeqNash}$ consisting of the sequence of Nash equilibria is $\frac{4n}{2+n}$-competitive for affine linear latency functions. For $n=1$, this result contains the bound on the price of anarchy of $\frac{4}{3}$ for affine linear latency functions of Roughgarden and Tardos [2002] as a special case. Furthermore, we analyze a problem variant with a modified cost function that reflects the total congestion cost, when all games have been played. In this case, we prove an upper bound of $\frac{4n}{2+n}$ on the competitive ratio of $\sl {SeqNash}$. We further prove a lower bound of $\frac{3n-2}{n}$ of $\sl {SeqNash}$ showing that for $n=2$ our upper bound is tight.
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    Language: English
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  • 31
    Publication Date: 2016-06-09
    Description: To approximate convolutions which occur in evolution equations with memory terms, a variable-stepsize algorithm is presented for which advancing $N$ steps requires only $O(N\log N)$ operations and $O(\log N)$ active memory, in place of $O(N^2)$ operations and $O(N)$ memory for a direct implementation. A basic feature of the fast algorithm is the reduction, via contour integral representations, to differential equations which are solved numerically with adaptive step sizes. Rather than the kernel itself, its Laplace transform is used in the algorithm. The algorithm is illustrated on three examples: a blow-up example originating from a Schrödinger equation with concentrated nonlinearity, chemical reactions with inhibited diffusion, and viscoelasticity with a fractional order constitutive law.
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  • 32
    Publication Date: 2020-11-13
    Description: This paper deals with MIP-based primal heuristics to be used within a branch-and-cut approach for solving multi-layer telecommunication network design problems. Based on a mixed-integer programming formulation for two network layers, we present three heuristics for solving important subproblems, two of which solve a sub-MIP. On multi-layer planning instances with many parallel logical links, we show the effectiveness of our heuristics in finding good solutions early in the branch-and-cut search tree.
    Keywords: ddc:000
    Language: English
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  • 33
    Publication Date: 2019-05-10
    Description: The dynamics of ventricular fibrillation caused by irregular excitation is simulated in the frame of the monodomain model with an action potential model due to Aliev-Panfilov for a human 3D geometry. The numerical solution of this multiscale reaction-diffusion problem is attacked by algorithms which are fully adaptive in both space and time (code library {\sc Kardos}). The obtained results clearly demonstrate an accurate resolution of the cardiac potential during the excitation and the plateau phases (in the regular cycle) as well as after a reentrant excitation (in the irregular cycle).
    Keywords: ddc:000
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  • 34
    Publication Date: 2020-12-15
    Description: The topic of this paper are integer programming models in which a subset of 0/1-variables encode a partitioning of a set of objects into disjoint subsets. Such models can be surprisingly hard to solve by branch-and-cut algorithms if the permutation of the subsets of the partition is irrelevant. This kind of symmetry unnecessarily blows up the branch-and-cut tree. We present a general tool, called orbitopal fixing, for enhancing the capabilities of branch-and-cut algorithms in solving this kind of symmetric integer programming models. We devise a linear time algorithm that, applied at each node of the branch-and-cut tree, removes redundant parts of the tree produced by the above mentioned permutations. The method relies on certain polyhedra, called orbitopes, which have been investigated in (Kaibel and Pfetsch (2006)). However, it does not add inequalities to the model, and thus, it does not increase the difficulty of solving the linear programming relaxations. We demonstrate the computational power of orbitopal fixing at the example of a graph partitioning problem motivated from frequency planning in mobile telecommunication networks.
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  • 35
    Publication Date: 2014-11-10
    Description: In this paper, we discuss the relation of unsplittable shortest path routing (USPR) to other routing schemes and study the approximability of three USPR network planning problems. Given a digraph $D=(V,A)$ and a set $K$ of directed commodities, an USPR is a set of flow paths $\Phi_{(s,t)}$, $(s,t)\in K$, such that there exists a metric $\lambda=(\lambda_a)\in \mathbb{Z}^A_+$ with respect to which each $\Phi_{(s,t)}$ is the unique shortest $(s,t)$-path. In the \textsc{Min-Con-USPR} problem, we seek for an USPR that minimizes the maximum congestion over all arcs. We show that this problem is hard to approximate within a factor of $\mathcal{O}(|V|^{1-\epsilon})$, but easily approximable within min$(|A|,|K|)$ in general and within $\mathcal{O}(1)$ if the underlying graph is an undirected cycle or a bidirected ring. We also construct examples where the minimum congestion that can be obtained by USPR is a factor of $\Omega(|V|^2)$ larger than that achievable by unsplittable flow routing or by shortest multi-path routing, and a factor of $\Omega(|V|)$ larger than by unsplittable source-invariant routing. In the CAP-USPR problem, we seek for a minimum cost installation of integer arc capacities that admit an USPR of the given commodities. We prove that this problem is $\mathcal{NP}$-hard to approximate within $2-\epsilon$ (even in the undirected case), and we devise approximation algorithms for various special cases. The fixed charge network design problem \textsc{Cap-USPR}, where the task is to find a minimum cost subgraph of $D$ whose fixed arc capacities admit an USPR of the commodities, is shown to be $\mathcal{NPO}$-complete. All three problems are of great practical interest in the planning of telecommunication networks that are based on shortest path routing protocols. Our results indicate that they are harder than the corresponding unsplittable flow or shortest multi-path routing problems.
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  • 36
    Publication Date: 2014-11-11
    Description: In this paper, we investigate the connection availabilities for the new protection scheme Demand-wise Shared Protection (DSP) and describe an appropriate approach for their computation. The exemplary case study on two realistic network scenarios shows that in most cases the availabilities for DSP are comparable with that for 1+1 path protection and better than in case of shared path protection.
    Keywords: ddc:000
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  • 37
    Publication Date: 2016-06-30
    Description: THESEUS, the ZIB threading environment, is a parallel implementation of a protein threading based on a multi-queued branch-and-bound optimal search algorithm to find the best sequence-to-structure alignment through a library of template structures. THESEUS uses a template core model based on secondary structure definition and a scoring function based on knowledge-based potentials reflecting pairwise interactions and the chemical environment, as well as pseudo energies for homology detection, loop alignment, and secondary structure matching. The threading core is implemented in C++ as a SPMD parallization architecture using MPI for communication. The environment is designed for generic testing of different scoring functions, e.g. different secondary structure prediction terms, different scoring matrices and information derived from multiple sequence alignments. A validaton of the structure prediction results has been done on the basis of standard threading benchmark sets. THESEUS successfully participated in the 6th Critical Assessment of Techniques for Protein Structure Prediction (CASP) 2004.
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  • 38
    Publication Date: 2014-02-26
    Description: We consider a multi-queue multi-server system with $n$ servers (processors) and $m$ queues. At the system there arrives a stationary and ergodic stream of $m$ different types of requests with service requirements which are served according to the following $k$-limited head of the line processor sharing discipline: The first $k$ requests at the head of the $m$ queues are served in processor sharing by the $n$ processors, where each request may receive at most the capacity of one processor. By means of sample path analysis and Loynes' monotonicity method, a stationary and ergodic state process is constructed, and a necessary as well as a sufficient condition for the stability of the $m$ separate queues are given, which are tight within the class of all stationary ergodic inputs. These conditions lead to tight necessary and sufficient conditions for the whole system, also in case of permanent customers, generalizing an earlier result by the authors for the case of $n$=$k$=1.
    Keywords: ddc:000
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  • 39
    Publication Date: 2014-02-26
    Description: In order to compute the thermodynamic weights of the different metastable conformations of a molecule, we want to approximate the molecule's Boltzmann distribution in a reasonable time. This is an essential issue in computational drug design. The energy landscape of active biomolecules is generally very rough with a lot of high barriers and low regions. Many of the algorithms that perform such samplings (e.g. the hybrid Monte Carlo method) have difficulties with such landscapes. They are trapped in low-energy regions for a very long time and cannot overcome high barriers. Moving from one low-energy region to another is a very rare event. For these reasons, the distribution of the generated sampling points converges very slowly against the thermodynamically correct distribution of the molecule. The idea of ConfJump is to use $a~priori$ knowledge of the localization of low-energy regions to enhance the sampling with artificial jumps between these low-energy regions. The artificial jumps are combined with the hybrid Monte Carlo method. This allows the computation of some dynamical properties of the molecule. In ConfJump, the detailed balance condition is satisfied and the mathematically correct molecular distribution is sampled.
    Keywords: ddc:000
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  • 40
    Publication Date: 2020-02-11
    Description: "`Volkssport Sudoku"' titelt der Stern in seiner Ausgabe vom 24. Mai2006. In der Tat traut sich derzeit kaum noch eine Zeitung, ohne Sudoku zu erscheinen. Die Begeisterung am Lösen dieser Zahlenrätsel offenbart eine unvermutete Freude am algorithmischen Arbeiten. Mathematisch kann man Sudokus als lineare diophantische Gleichungssysteme mit Nichtnegativitätsbedingungen formulieren. Solche ganzzahligen linearen Programme sind die wichtigsten Modellierungswerkzeuge in zahlreichen Anwendungsgebieten wie z.B. der Optimierung von Telekommunikations- und Verkehrsnetzen. Moderne Verfahren zur Lösung dieser Optimierungsprobleme sind durch Sudokus allerdings deutlich weniger zu beeindrucken als Zeitungsleser.
    Keywords: ddc:000
    Language: German
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  • 41
    Publication Date: 2020-02-11
    Description: This article surveys mathematical models and methods used for physical PCB layout, i.e., component placement and wire routing. The main concepts are briefly described together with relevant references.
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  • 42
    Publication Date: 2020-12-15
    Description: We study online multicommodity minimum cost routing problems in networks, where commodities have to be routed sequentially. Arcs are equipped with load dependent price functions defining the routing weights. We discuss an online algorithm that routes each commodity by minimizing a convex cost function that depends on the demands that are previously routed. We present a competitive analysis of this algorithm showing that for affine linear price functions this algorithm is $4K/2+K$-competitive, where $K$ is the number of commodities. For the parallel arc case this algorithm is optimal. Without restrictions on the price functions and network, no algorithm is competitive. Finally, we investigate a variant in which the demands have to be routed unsplittably.
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  • 43
    Publication Date: 2021-03-16
    Description: Perfect graphs constitute a well-studied graph class with a rich structure, reflected by many characterizations w.r.t different concepts. Perfect graphs are, e.g., characterized as precisely those graphs $G$ where the stable set polytope STAB$(G)$ coincides with the clique constraint stable set polytope QSTAB$(G)$. For all imperfect graphs STAB$(G) \subset$ QSTAB$(G)$ holds and, therefore, it is natural to measure imperfection in terms of the difference between STAB$(G)$ and QSTAB$(G)$. Several concepts have been developed in this direction, for instance the dilation ratio of STAB$(G)$ and QSTAB$(G)$ which is equivalent to the imperfection ratio imp$(G)$ of $G$. To determine imp$(G)$, both knowledge on the facets of STAB$(G)$ and the extreme points of QSTAB$(G)$ is required. The anti-blocking theory of polyhedra yields all {\em dominating} extreme points of QSTAB$(G)$, provided a complete description of the facets of STAB$(\overline G)$ is known. As this is typically not the case, we extend the result on anti-blocking polyhedra to a {\em complete} characterization of the extreme points of QSTAB$(G)$ by establishing a 1-1 correspondence to the facet-defining subgraphs of $\overline G$. We discuss several consequences, in particular, we give alternative proofs of several famous results.
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  • 44
    Publication Date: 2014-11-10
    Description: We give experimental and theoretical results on the problem of computing the treewidth of a graph by exact exponential time algorithms using exponential space or using only polynomial space. We first report on an implementation of a dynamic programming algorithm for computing the treewidth of a graph with running time $O^\ast(2^n)$. This algorithm is based on the old dynamic programming method introduced by Held and Karp for the {\sc Tra veling Salesman} problem. We use some optimizations that do not affect the worst case running time but improve on the running time on actual instances and can be seen to be practical for small instances. However, our experiments show that the space use d by the algorithm is an important factor to what input sizes the algorithm is effective. For this purpose, we settle the problem of computing treewidth under the restriction that the space used is only polynomial. In this direction we give a simple $O^\ast(4^n)$ al gorithm that requires {\em polynomial} space. We also show that with a more complicated algorithm, using balanced separators, {\sc Treewidth} can be computed in $O^\ast(2.9512^n)$ time and polynomial space.
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  • 45
    Publication Date: 2014-03-10
    Description: The dynamic behavior of molecules can often be described by Markov processes. From computational molecular simulations one can derive transition rates or transition probabilities between subsets of the discretized conformational space. On the basis of this dynamic information, the spatial subsets are combined into a small number of so-called metastable molecular conformations. This is done by clustering methods like the Robust Perron Cluster Analysis (PCCA+). Up to now it is an open question how this coarse graining in space can be transformed to a coarse graining of the Markov chain while preserving the essential dynamic information. In the following article we aim at a consistent coarse graining of transition probabilities or rates on the basis of metastable conformations such that important physical and mathematical relations are preserved. This approach is new because PCCA+ computes molecular conformations as linear combinations of the dominant eigenvectors of the transition matrix which does not hold for other clustering methods.
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  • 46
    Publication Date: 2014-02-26
    Description: Das deutschsprachige Bibliothekswesen verfügt mit den \glqq Regeln für den Schlagwortkatalog \grqq (RSWK) unter Verwendung der \glqq Schlagwortnormdatei \grqq (SWD) über ein Instrumentarium, welches zusammen mit einem \glqq Faceted Browsing \grqq das bisher bestehende Angebot für ein Information Retrieval optimal ergänzen kann. Die Verbindung zwischen Standardvokabular (SWD) und Kettenbildung (RSWK) einerseits und eine nach Facetten-Eigenschaften gegliederte Navigation andererseits unterstützt bestmöglich eine inhaltlich bezogene Recherche. Die Stärken und Schwächen der RSWK/SWD werden erörtert und auch Klassifikationen (DDC und RVK) als mögliche Facetten diskutiert.
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    Language: German
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  • 47
    Publication Date: 2016-06-09
    Keywords: ddc:000
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 48
    Publication Date: 2022-03-14
    Description: A lot of problems arising in Combinatorial Optimization and Operations Research can be formulated as Mixed Integer Programs (MIP). Although MIP-solving is an NP-hard optimization problem, many practically relevant instances can be solved in reasonable time. In modern MIP-solvers like the branch-cut-and-price-framework SCIP, primal heuristics play a major role in finding and improving feasible solutions at the early steps of the solution process. This helps to reduce the overall computational effort, guides the remaining search process, and proves the feasibility of the MIP model. Furthermore, a heuristic solution with a small gap to optimality often is sufficient in practice. We investigate 16 different heuristics, all of which are available in SCIP. Four of them arise from the literature of the last decade, nine are specific implementations of general heuristic ideas, three have been newly developed. We present an improved version of the feasibility pump heuristic by Fischetti et al., which in experiments produced solutions with only a third of the optimality gap compared to the original version. Furthermore, we introduce two new Large Neighborhood Search (LNS) heuristics. Crossover is an LNS improvement heuristic making use of similarities of diverse MIP solutions to generate new incumbent solutions. RENS is an LNS rounding heuristic which evaluates the space of all possible roundings of a fractional LP-solution. This heuristic makes it possible to determine whether a point can be rounded to an integer solution and which is the best possible rounding. We conclude with a computational comparison of all described heuristics. It points out that a single heuristic on its own has only a slight impact on the overall performance of SCIP, but the combination of all of them reduces the running time by a factor of two compared to a version without any heuristics.
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    Type: masterthesis , doc-type:masterThesis
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  • 49
    Publication Date: 2014-02-26
    Description: We present a finite volume method for the solution of the two-dimensional Poisson equation $ \nabla\cdot( \beta( {\mbox{\boldmath $x$}}) \nabla u({\mbox{\boldmath $x$}})) = f(\mbox{\boldmath $x$}) $ with variable, discontinuous coefficients and solution discontinuities on irregular domains. The method uses bilinear ansatz functions on Cartesian grids for the solution $u({\mbox{\boldmath $x$})$ resulting in a compact nine-point stencil. The resulting linear problem has been solved with a standard multigrid solver. Singularities associated with vanishing partial volumes of intersected grid cells or the dual bilinear ansatz itself are removed by a two-step asymptotic approach. The method achieves second order of accuracy in the $L^\infty$ and $L^2$ norm.
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  • 50
    Publication Date: 2014-11-11
    Description: In this article we aim at an efficient sampling of the stationary distribution of dynamical systems in the presence of metastabilities. In the past decade many sophisticated algorithms have been inven ted in this field. We do not want to simply add a further one. We address the problem that one has applied a sampling algorithm for a dynamical system many times. This leads to different samplings which more or less represent the stationary distribution partially very well, but which are still far away from ergodicity or from the global stationary distribution. We will show how these samplings can be joined together in order to get one global sampling of the stationary distribution.
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  • 51
    Publication Date: 2014-02-26
    Description: The concept of jump system, introduced by Buchet and Cunningham (1995), is a set of integer points with a certain exchange property. In this paper, we discuss several linear and convex optimization problems on jump systems and show that these problems can be solved in polynomial time under the assumption that a membership oracle for a jump system is available. We firstly present a polynomial-time implementation of the greedy algorithm for the minimization of a linear function. We then consider the minimization of a separable-convex function on a jump system, and propose the first polynomial-time algorithm for this problem. The algorithm is based on the domain reduction approach developed in Shioura (1998). We finally consider the concept of M-convex functions on constant-parity jump systems which has been recently proposed by Murota (2006). It is shown that the minimization of an M-convex function can be solved in polynomial time by the domain reduction approach.
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  • 52
    Publication Date: 2020-12-15
    Description: We introduce orbitopes as the convex hulls of 0/1-matrices that are lexicographically maximal subject to a group acting on the columns. Special cases are packing and partitioning orbitopes, which arise from restrictions to matrices with at most or exactly one 1-entry in each row, respectively. The goal of investigating these polytopes is to gain insight into ways of breaking certain symmetries in integer programs by adding constraints, e.g., for a well-known formulation of the graph coloring problem. We provide a thorough polyhedral investigation of packing and partitioning orbitopes for the cases in which the group acting on the columns is the cyclic group or the symmetric group. Our main results are complete linear inequality descriptions of these polytopes by facet-defining inequalities. For the cyclic group case, the descriptions turn out to be totally unimodular, while for the symmetric group case, both the description and the proof are more involved. The associated separation problems can be solved in linear time.
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  • 53
    Publication Date: 2014-11-21
    Description: The standard computational methods for computing the optimal value functions of Markov Decision Problems (MDP) require the exploration of the entire state space. This is practically infeasible for applications with huge numbers of states as they arise, e.\,g., from modeling the decisions in online optimization problems by MDPs. Exploiting column generation techniques, we propose and apply an LP-based method to determine an $\varepsilon$-approximation of the optimal value function at a given state by inspecting only states in a small neighborhood. In the context of online optimization problems, we use these methods in order to evaluate the quality of concrete policies with respect to given initial states. Moreover, the tools can also be used to obtain evidence of the impact of single decisions. This way, they can be utilized in the design of policies.
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  • 54
    Publication Date: 2014-11-21
    Description: Wir beschäftigen uns mit dem Problem der Betriebsplanung von Laserschweißrobotern im Karosseriebau. Gegeben ist eine Menge von Schweißnähten, die innerhalb einer Fertigungszelle an einem Karosserieteil gefertigt werden müssen. Die Schweißnähte werden durch mehrere parallel betriebene Roboter bearbeitet. Die Aufgabe besteht darin, für jeden Roboter eine Reihenfolge und eine zeitliche Koordinierung seiner Bewegungen zu finden, so dass alle Schweißnähte innerhalb der Taktzeit der Fertigungszelle bearbeitet werden und so wenig Laserquellen wie möglich eingesetzt werden. Dabei müssen einige Nebenbedingungen berücksichtigt werden. Für dieses spezielle Schweißproblem haben wir eine Formulierung als gemischt-ganzzahliges lineares Programm entwickelt, welches sich für die untersuchten praktischen Fälle sehr schnell lösen lässt.
    Keywords: ddc:000
    Language: German
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  • 55
    Publication Date: 2021-08-05
    Description: Modern applications of mathematical programming must take into account a multitude of technical details, business demands, and legal requirements. Teaching the mathematical modeling of such issues and their interrelations requires real-world examples that are well beyond the toy sizes that can be tackled with the student editions of most commercial software packages. We present a new tool, which is freely available for academic use including complete source code. It consists of an algebraic modeling language and a linear mixed integer programming solver. The performance and features of the tool are in the range of current state-of-the-art commercial tools, though not in all aspects as good as the best ones. Our tool does allow the execution and analysis of large real-world instances in the classroom and can therefore enhance the teaching of problem solving issues. Teaching experience has been gathered and practical usability was tested in classes at several universities and a two week intensive block course at TU Berlin. The feedback from students and teachers has been very positive.
    Keywords: ddc:000
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  • 56
    Publication Date: 2014-11-21
    Description: The Bottleneck Shortest Path Problem is a basic problem in network optimization. The goal is to determine the limiting capacity of any path between two specified vertices of the network. This is equivalent to determining the unsplittable maximum flow between the two vertices. In this note we analyze the complexity of the problem, its relation to the Shortest Path Problem, and the impact of the underlying machine/computation model.
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    Language: English
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  • 57
    Publication Date: 2014-02-26
    Description: We introduce a new and rich class of graph coloring manifolds via the Hom complex construction of Lov\´{a}sz. The class comprises examples of Stiefel manifolds, series of spheres and products of spheres, cubical surfaces, as well as examples of Seifert manifolds. Asymptotically, graph coloring manifolds provide examples of highly connected, highly symmetric manifolds.
    Keywords: ddc:000
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  • 58
    Publication Date: 2014-02-26
    Description: We give coordinate-minimal geometric realizations in general position for 17 of the 20 vertex-minimal triangulations of the orientable surface of genus 3 in the 5x5x5-cube.
    Keywords: ddc:000
    Language: English
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  • 59
    Publication Date: 2014-02-26
    Description: Biochemical interactions are determined by the 3D-structure of the involved components - thus the identification of conformations is a key for many applications in rational drug design. {\sf ConFlow} is a new multilevel approach to conformational analysis with main focus on completeness in investigation of conformational space. In contrast to known conformational analysis, the starting point for design is a space-based description of conformational areas. A tight integration of sampling and analysis leads to an identification of conformational areas simultaneously during sampling. An incremental decomposition of high-dimensional conformational space is used to guide the analysis. A new concept for the description of conformations and their path connected components based on convex hulls and {\em Hypercubes}is developed. The first results of the {\sf ConFlow} application constitute a 'proof of concept' and are further more highly encouraging. In comparison to conventional industrial applications, {\sf ConFlow} achieves higher accuracy and a specified degree of completeness with comparable effort.
    Keywords: ddc:000
    Language: English
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  • 60
    Publication Date: 2014-02-26
    Description: We consider linear inverse problems where the solution is assumed to fulfill some general homogeneous convex constraint. We develop an algorithm that amounts to a projected Landweber iteration and that provides and iterative approach to the solution of this inverse problem. For relatively moderate assumptions on the constraint we can always prove weak convergence of the iterative scheme. In certain cases, i.e. for special families of convex constraints, weak convergence implies norm convergence. The presented approach covers a wide range of problems, e.g. Besov- or BV-restoration for which we present also numerical experiments in the context of image processing.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 61
    Publication Date: 2014-03-10
    Description: Whenever the invariant stationary density of metastable dynamical systems decomposes into almost invariant partial densities, its computation as eigenvector of some transition probability matrix is an ill-conditioned problem. In order to avoid this computational difficulty, we suggest to apply an aggregation/disaggregation method which only addresses wellconditioned sub-problems and thus results in a stable algorithm. In contrast to existing methods, the aggregation step is done via a sampling algorithm which covers only small patches of the sampling space. Finally, the theoretical analysis is illustrated by two biomolecular examples.
    Keywords: ddc:000
    Language: English
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  • 62
    Publication Date: 2016-02-29
    Description: \noindent We give a partial description of the $(s,t)-p$-path polytope of a directed graph $D$ which is the convex hull of the incidence vectors of simple directed $(s,t)$-paths in $D$ of length $p$. First, we point out how the $(s,t)-p$-path polytope is located in the family of path and cycle polyhedra. Next, we give some classes of valid inequalities which are very similar to inequalities which are valid for the $p$-cycle polytope, that is, the convex hull of the incidence vectors of simple cycles of length $p$ in $D$. We give necessary and sufficient conditions for these inequalities to be facet defining. Furthermore, we consider a class of inequalities that has been identifie d to be valid for $(s,t)$-paths of cardinality at most $p$. Finally, we transfer the results to related polytopes, in particular, the undirected counterpart of the $(s,t)-p$-path polytope.
    Keywords: ddc:000
    Language: English
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  • 63
    Publication Date: 2020-11-13
    Description: The numerical integration of dynamical contact problems often leads to instabilities at contact boundaries caused by the non-penetration condition between bodies in contact. Even a recent energy dissipative modification due to Kane et al. (1999), which discretizes the non-penetration constraints implicitly, is not able to circumvent artificial oscillations. For this reason, the present paper suggests a contact stabilization which avoids artificial oscillations at contact interfaces and is also energy dissipative. The key idea of this contact stabilization is an additional $L^2$-projection at contact interfaces, which can easily be added to any existing time integration scheme. In case of a lumped mass matrix, this projection can be carried out completely locally, thus creating only negligible additional numerical cost. For the new scheme, an elementary analysis is given, which is confirmed by numerical findings in an illustrative test example (Hertzian two body contact).
    Keywords: ddc:000
    Language: English
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  • 64
    Publication Date: 2016-06-30
    Keywords: ddc:000
    Language: German
    Type: masterthesis , doc-type:masterThesis
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  • 65
    Publication Date: 2014-02-26
    Description: We discuss different approaches for the enumeration of triangulated surfaces. In particular, we enumerate all triangulated surfaces with 9 and 10 vertices. We also show how geometric realizations of orientable surfaces with few vertices can be obtained by choosing coordinates randomly.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 66
    Publication Date: 2014-02-26
    Description: The concept of L##-convexity is introduced by Fujishige--Murota (2000) as a discrete convexity for functions defined over the integer lattice. The main aim of this note is to understand the difference of the two algorithms for L##-convex function minimization: Murota's steepest descent algorithm (2003) and Kolmogorov's primal algorithm (2005).
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 67
    Publication Date: 2014-02-26
    Description: In this survey on combinatorial properties of triangulated manifolds we discuss various lower bounds on the number of vertices of simplicial and combinatorial manifolds. Moreover, we give a list of all known examples of vertex-minimal triangulations.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 68
    Publication Date: 2020-02-11
    Description: This paper concerns the problem of operating a landside container exchange area that is serviced by multiple semi-automated rail mounted gantry cranes (RMGs) that are moving on a single bi-directional traveling lane. Such a facility is being built by Patrick Corporation at the Port Botany terminal in Sydney. The gantry cranes are a scarce resource and handle the bulk of container movements. Thus, they require a sophisticated analysis to achieve near optimal utilization. We present a three stage algorithm to manage the container exchange facility, including the scheduling of cranes, the control of associated short-term container stacking, and the allocation of delivery locations for trucks and other container transporters. The key components of our approach are a time scale decomposition, whereby an integer program controls decisions across a long time horizon to produce a balanced plan that is fed to a series of short time scale online subproblems, and a highly efficient space-time divisioning of short term storage areas. A computational evaluation shows that our heuristic can find effective solutions for the planning problem; on real-world data it yields a solution at most~8\% above a lower bound on optimal RMG utilization.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 69
    Publication Date: 2014-02-26
    Description: We describe an algorithm for the enumeration of (candidates of) vertex-transitive combinatorial $d$-manifolds. With an implementation of our algorithm, we determine, up to combinatorial equivalence, all combinatorial manifolds with a vertex-transitive automorphism group on $n\leq 13$ vertices. With the exception of actions of groups of small order, the enumeration is extended to 14 and 15 vertices.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 70
    Publication Date: 2014-02-26
    Description: We give coordinate-minimal geometric realizations in general position of all 865 vertex-minimal triangulations of the orientable surface of genus 2 in the 4x4x4-cube.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 71
    Publication Date: 2014-02-26
    Description: We give a complete enumeration of combinatorial 3-manifolds with 10 vertices: There are precisely 247882 triangulated 3-spheres with 10 vertices as well as 518 vertex-minimal triangulations of the sphere product $S^2 x S^1$ and 615 triangulations of the twisted sphere product $S^2 \underline{x} S^1$. An analysis of the 3-spheres with up to 10 vertices shows that all these spheres are shellable, but that there are 29 vertex-minimal non-shellable 3-balls with 9 vertices.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 72
    Publication Date: 2019-05-10
    Description: Adaptive numerical methods in time and space are introduced and studied for linear poroelastic models in two and three space dimensions. We present equivalent models for linear poroelasticity and choose both the {\em displacement--pressure} and the {\em stress--pressure} formulation for our computations. Their discretizations are provided by means of linearly implicit schemes in time and linear finite elements in space. Our concept of adaptivity opens a way to a fast and reliable simulation of different loading cases defined by corresponding boundary conditions. We present some examples using our code {\sf Kardos} and show that the method works efficiently. In particular, it could be used in the simulation of some bone healing models.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 73
    Publication Date: 2016-06-30
    Description: During the last few years more and more functionalities of RNA have been discovered that were previously thought of being carried out by proteins alone. One of the most striking discoveries was the de tection of microRNAs, a class of noncoding RNAs that play an important role in post-transcriptional gene regulation. Large-scale analyses are needed for the still increasingly growing amount of sequen ce data derived from new experimental technologies. In this paper we present a framework for the detection of the distinctive precursor structure of microRNAS that is based on the well-known Smith-Wat erman algorithm and various filtering steps. We conducted experiments on real genomic data and we found several new putative hits for microRNA precursor structures.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 74
    Publication Date: 2014-02-26
    Description: Wir erleben zu Beginn des aufkommenden Informationszeitalters mit dem Siegeszug von Google und anderen Internet-Technologien einen Wandel im Verhalten von Wissenschaftlern und Studenten, der mit dem Einsatz von {\sl Google Scholar} und {\sl Google Book Search} einen Paradigmenwechsel für Bibliotheken und Informationsversorger gleichkommt. Der Artikel untersucht die technischen Hintergründe für den Erfolg dieser besonderen Art des Information Retrievals: Fulltext Indexing und Citation Ranking als besondere Form des Information Minig. Er diskutiert Stärken und auch Schwächen des Google-Ansatzes. Der Autor stellt sich auch der Frage, unter welchen Bedingungen es möglich ist, ein zu {\sl Google Scholar} und der {\sl Google Book Search} konkurrenzfähiges Retrieval in der Landschaft der Bibliotheken und Bibliotheksverbünde zu entrichten. Die These ist, dass dieses unter Einsatz des {\sl Open Source} Indexierers {\sl Lucene} und des Web-Robots {\sl Nutch} möglich ist. Bibliotheken können durch gezielten Einsatz solcher Internet-Technologien dem Nutzer die Leistungen, welche Google uns mit seinen Tools im {\sl Visible Web} und mit Referenzen auf {\sl Citations} in der Welt der Literatur zur Verfügung stellt, in vergleichbarer Art auch für ihre eigenen durch Lizenzen geschützten digitalen Journale und ihre speziellen lokal verfügbaren Ressourcen, auf die Internet-Suchmaschinen keine Zugriff haben, anbieten. Es besteht die Hoffnung, dass Nutzer dann nicht - wie in einer kürzlichen Studie des OCLC konstatiert - überwiegend im Internet verbleiben, sondern bei ihrer Suche auch den Weg zu den Angeboten der örtlichen Bibliothek attraktiv finden.
    Keywords: ddc:000
    Language: German
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  • 75
    Publication Date: 2014-02-26
    Description: We consider a system where the arrivals form a Poisson process and the required service times of the requests are exponentially distributed. According to the generalized processor sharing discipline, each request in the system receives a fraction of the capacity of one processor which depends on the actual number of requests in the system. We derive systems of ordinary differential equations for the LST and for the moments of the conditional waiting time of a request with given required service time as well as a stable and fast recursive algorithm for the LST of the second moment of the conditional waiting time, which in particular yields the second moment of the unconditional waiting time. Moreover, asymptotically tight upper bounds for the moments of the conditional waiting time are given. The presented numerical results for the first two moments of the sojourn times in the $M/M/m-PS$ system show that the proposed algorithms work well.
    Keywords: ddc:000
    Language: English
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  • 76
    Publication Date: 2022-07-07
    Description: We present a domain decomposition approach for the computation of the electromagnetic field within periodic structures. We use a Schwarz method with transparent boundary conditions at the interfaces of the domains. Transparent boundary conditions are approximated by the perfectly matched layer method (PML). To cope with Wood anomalies appearing in periodic structures an adaptive strategy to determine optimal PML parameters is developed. We focus on the application to typical EUV lithography line masks. Light propagation within the multi-layer stack of the EUV mask is treated analytically. This results in a drastic reduction of the computational costs and allows for the simulation of next generation lithography masks on a standard personal computer.
    Keywords: ddc:000
    Language: English
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  • 77
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 169-185 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The IR data for the R1 CO-O-CHR2-CO-NHR3 derivatives are interpreted in terms of a H…π interaction involving the N—H bond and the π orbitals of the ester function and giving rise to a high ν(C=O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values φ # -90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C=O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
    Additional Material: 8 Ill.
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  • 78
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 79
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 251-268 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
    Additional Material: 1 Ill.
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  • 80
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of L-3,4-dehydroproline, t-butoxycarbonyl-L-3,4-dehydroproline amide, and acetyl-L-3,4-dehydroproline amide have been determined. L-3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L-3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L-3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L-3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L-3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L-3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L-3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present φ and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have φ and ψ values corresponding to a collagenlike conformation (conformation F).
    Additional Material: 6 Ill.
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  • 81
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 359-371 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10-7, 1.000 ± 0.05 × 10-7, and 0.835 ± 0.04 × 10-7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
    Additional Material: 6 Ill.
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  • 82
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 387-397 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (φ,ψ) over the range -180° ≤ φ ≤ -60°, -60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (φ,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.
    Additional Material: 1 Ill.
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  • 83
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 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.
    Additional Material: 5 Ill.
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  • 84
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 345-357 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In carbonate buffer at pH 10.5, a transparent solution of poly(L-lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L-lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
    Additional Material: 7 Ill.
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  • 85
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 707-718 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2-pyridone and 2,6-dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L-Pro-X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the -CONH- of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m-1 for the secondary amide and 50m-1 for the tertiary amide. For pyridone the binding constant is about 45m-1 for either the secondary or tertiary amide. For comparison self-dimerization constants determined by vapor-pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m-1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L-Pro-Gly), respectively.
    Additional Material: 6 Ill.
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  • 86
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 803-816 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and phosphorus nmr have been used to investigate the double-helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH 〈 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71-86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half-protonated state. Although the base-stacking arrangement of this state is similar to that observed in the more extensively protonated low-pH state, the phosphate backbone conformation is different from that found in either the neutral or low-pH structures.
    Additional Material: 8 Ill.
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  • 87
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 88
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 39-51 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod-Wyman-Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
    Additional Material: 4 Ill.
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  • 89
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 65-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200-320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first-approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
    Additional Material: 6 Ill.
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  • 90
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA2Glu and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M-1 in the absence of magnesium to 1.5 × 106M-1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
    Additional Material: 2 Ill.
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  • 91
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 231-235 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
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  • 92
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 237-240 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 93
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 243-247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 94
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A conformational quantum-mechanical study of (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple-helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly-Pro-Pro and Gly-Phe-Pro indicates that phenylalanyl in the second position favors the triple-helix formation.
    Additional Material: 7 Ill.
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  • 95
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 327-343 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full-contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core-particle models have been compared with the observed functions and show that the neutron-scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4-7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
    Additional Material: 8 Ill.
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  • 96
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-L-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well-defined N- and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°-8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
    Additional Material: 5 Ill.
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  • 97
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
    Additional Material: 7 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2121-2136 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton-induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103-178], we have obtained an expression that may be computer-fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill-defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
    Additional Material: 3 Ill.
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  • 99
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2137-2142 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso-propanol, n-propanol, formamide, acetamide, N-methyl-formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
    Additional Material: 1 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2195-2202 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preparations have been made of acid-soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
    Additional Material: 2 Ill.
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