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  • 1
    Publication Date: 2014-11-10
    Description: An edge of a perfect graph $G$ is critical if $G-e$ is imperfect. We would like to decide whether $G - e$ is still {\sl almost perfect} or already {\sl very imperfect}. Via relaxations of the stable set polytope of a graph, we define two superclasses of perfect graphs: rank-perfect and weakly rank-perfect graphs. Membership in those two classes indicates how far an imperfect graph is away from being perfect. We study the cases, when a critical edge is removed from the line graph of a bipartite graph or from the complement of such a graph.
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    Language: English
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  • 2
    Publication Date: 2020-03-06
    Description: Collection of abstracts of the first SIAM-EMS conference Applied Mathematics in our Changing World'' in Berlin, September 2-6, 2001.
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    Language: English
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  • 3
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    Publication Date: 2020-02-11
    Description: {\sc Zimpl} is a little language to translate the mathematical model of a problem into a linear or (mixed-)integer mathematical program expressed in {\tt lp} or {\tt mps} file format which can be read by a LP or MIP solver.
    Keywords: ddc:000
    Language: English
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  • 4
    Publication Date: 2014-02-26
    Description: Im ersten Teil des folgenden Aufsatzes werden allgemeine Überlegungen zur Entwicklung von Bibliotheken hin zu Informationsvermittlungsstellen für sowohl elektronische wie auch gedruckte Medien angestellt. Basierend auf den Ergebnissen der Evaluation digitaler Bibliotheken und Informationsportale in Deutschland wird ein erster Kriterienkatalog für ein Verbund-Informationsportal für den Kooperativen Bibliotheksverbund Berlin-Brandenburg entwickelt. Im Anhang befindet sich der Statusbericht über Informationsportale und digitale Bibliotheken in Deutschland. Dazu wurden sieben digitale Bibliotheken auf Verbundebene und 21 Bibliotheken nach Bundesländern evaluiert.
    Keywords: ddc:000
    Language: German
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  • 5
    Publication Date: 2020-11-13
    Description: Given a set of service requests (events), a set of guided servers (units), and a set of unguided service contractors (conts), the vehicle dispatching problem {\sl vdp} is the task to find an assignment of events to units and conts as well as tours for all units starting at their current positions and ending at their home positions (dispatch) such that the total cost of the dispatch is minimized. The cost of a dispatch is the sum of unit costs, cont costs, and event costs. Unit costs consist of driving costs, service costs and overtime costs; cont costs consist of a fixed cost per service; event costs consist of late costs linear in the late time, which occur whenever the service of the event starts later than its deadline. The program \textsf{ZIBDIP} based on dynamic column generation and set partitioning yields solutions on heavy-load real-world instances (215 events, 95 units) in less than a minute that are no worse than 1\% from optimum on state-of-the-art personal computers.
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  • 6
    Publication Date: 2021-02-01
    Description: Scenario tree models of stochastic programs arise naturally under standard nonanticipativity assumptions. We demonstrate how tree-sparse programs cover the general case, with \emph{arbitrary} information constraints. Detailed examples and intuitive interpretations illuminate the basic thoughts behind the abstract but elementary construction.
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    Language: English
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  • 7
    Publication Date: 2020-03-09
    Description: In this paper we present an algorithm that accelerates 3D texture-based volume rendering of large and sparse data sets. A hierarchical data structure (known as AMR tree) consisting of nested uniform grids is employed in order to efficiently encode regions of interest. The hierarchies resulting from this kind of space partitioning yield a good balance between the amount of volume to render and the number of texture bricks -- a prerequisite for fast rendering. Comparing our approach to an octree based algorithm we show that our algorithm increases rendering performance significantly for sparse data. A further advantage is that less parameter tuning is necessary.
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  • 8
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    Publication Date: 2019-10-24
    Keywords: ddc:000
    Language: German
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  • 9
    Publication Date: 2021-02-01
    Description: Mathematical optimization techniques are on their way to becoming a standard tool in chemical process engineering. While such approaches are usually based on deterministic models, uncertainties such as external disturbances play a significant role in many real-life applications. The present article gives an introduction to practical issues of process operation and to basic mathematical concepts required for the explicit treatment of uncertainties by stochastic optimization.
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    Language: English
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  • 10
    Publication Date: 2014-02-26
    Description: Uncoupling-coupling Monte Carlo (UCMC) combines uncoupling techniques for finite Markov chains with Markov chain Monte Carlo methodology. UCMC aims at avoiding the typical metastable or trapping behavior of Monte Carlo techniques. From the viewpoint of Monte Carlo, a slowly converging long-time Markov chain is replaced by a limited number of rapidly mixing short-time ones. Therefore, the state space of the chain has to be hierarchically decomposed into its metastable conformations. This is done by means of combining the technique of conformation analysis as recently introduced by the authors, and appropriate annealing strategies. We present a detailed examination of the uncoupling-coupling procedure which uncovers its theoretical background, and illustrates the hierarchical algorithmic approach. Furthermore, application of the UCMC algorithm to the $n$-pentane molecule allows us to discuss the effect of its crucial steps in a typical molecular scenario.
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  • 11
    Publication Date: 2021-02-01
    Description: Standard model predictive control for real-time operation of industrial production processes may be inefficient in the presence of substantial uncertainties. To avoid overly conservative disturbance corrections while ensuring safe operation, random influences should be taken into account explicitly. We propose a multistage stochastic programming approach within the model predictive control framework and apply it to a distillation process with a feed tank buffering external sources. A preliminary comparison to a probabilistic constraints approach is given and first computational results for the distillation process are presented.
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  • 12
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    Publication Date: 2021-02-01
    Description: Dynamic stochastic programs are prototypical for optimization problems with an inherent tree structure inducing characteristic sparsity patterns in the KKT systems of interior methods. We propose an integrated modeling and solution approach for such tree-sparse programs. Three closely related natural formulations are theoretically analyzed from a control-theoretic viewpoint and compared to each other. Associated KKT solution algorithms with linear complexity are developed and comparisons to other interior approaches and related problem formulations are discussed.
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  • 13
    Publication Date: 2020-11-13
    Description: We introduce a new problem that was motivated by a (more complicated) problem arising in a robotized assembly enviroment. The bin coloring problem is to pack unit size colored items into bins, such that the maximum number of different colors per bin is minimized. Each bin has size~$B\in\mathbb{N}$. The packing process is subject to the constraint that at any moment in time at most $q\in\mathbb{N}$ bins may be partially filled. Moreover, bins may only be closed if they are filled completely. An online algorithm must pack each item must be packed without knowledge of any future items. We investigate the existence of competitive online algorithms for the online uniform binpacking problem. We show upper bounds for the bin coloring problem. We prove an upper bound of $3q$ - 1 and a lower bound of $2q$ for the competitive ratio of a natural greedy-type algorithm, and show that surprisingly a trivial algorithm which uses only one open bin has a strictly better competitive ratio of $2q$ - 1. Morever, we show that any deterministic algorithm has a competitive ratio $\Omega (q)$ and that randomization does not improve this lower bound even when the adversary is oblivious.
    Keywords: ddc:000
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  • 14
    Publication Date: 2014-02-26
    Description: In circuit switching networks call streams are characterized by their mean and peakedness (two-moment method). The $GI/M/C/0$ system is used to model a single link, where the $GI$-stream is determined by fitting moments appropriately. For the moments of the overflow traffic of a $GI/M/C/0$ system there are efficient numerical algorithms available. However, for the moments of the freed carried traffic, defined as the moments of a virtual link of infinite capacity to which the process of calls accepted by the link (carried arrival process) is virtually directed and where the virtual calls get fresh exponential i.i.d.\ holding times, only complex numerical algorithms are available. This is the reason why the concept of the freed carried traffic is not used rigorously. The main result of this paper is an efficient algorithm for computing the moments of the freed carried traffic, in particular an explicit formula for its peakedness. This result offers a unified handling of both overflow and carried traffics in networks. Furthermore, some refined characteristics for the overflow and freed carried streams are derived.
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  • 15
    Publication Date: 2014-02-26
    Description: In this work we concentrate on developing methods which determine good lower bounds for set partitioning problems (SPP) in an appropriate amount of time. We found out that it makes sense to use the Lagrangian relaxation method for this task. The Lagrangian relaxed problem of SPP has a simple structure, which leads to algorithms and heuristics, whose total complexity per iteration depends linearly on the number of non-zeros of the problem matrix of SPP. In contrast, other methods like simplex methods or interior point methods have a complexity of higher order. Because the problem matrices of our tested instances are sparse, the linear dependence becomes an advantage for the algorithms and heuristics mentioned above. As a reference for the state-of-the-art we have applied the dual simplex method and the barrier function method, implemented in CPLEX. The methods, which we have developed and compared with those of CPLEX, are SBM, CAM, CCBM, and CBM. SBM is a subgradient bundle method derived from the basic subgradient method, which is a global convergent method for determining the maximum of concave functions. CAM is a coordinate ascent method, where the convex coordinate bundle method CCBM and the coordinate bundle method CBM are derivatives from CAM. We observed that the basic subgradient and the coordinate ascent method are improved if bundling techniques can be used. But the motivation for bundling differs for both approaches. In the former case bundling helps to approximate a minimum norm subgradient, which provides a steepest ascent direction, in order to speed up the performance. In the latter case bundling enables proceeding along directions, which are not restricted on the coordinate directions. By this the performance is accelerated. Among all used techniques stabilization is worth mentioning. Stabilization improves the performance especially at the beginning by avoiding too big steps during the proceeding. This leads to a more stabilized progression. Stabilization was successfully applied to SBM, CAM, CCBM, and CBM. As an overall result we conclude the following: \begin{enumerate} \item CPLEX computes the optimal objective values, whereas SBM and CBM has on average a gap of under $1.5\%$. \item In comparison to CPLEX baropt, SBM, CAM, and CBM the algorithm CCBM has a slow convergence because of the convex combination of ascent coordinate directions. An alternative is to relax the convex combination to a simple sum of the corresponding directions. This idea is realized in CBM. \item If we focus on the running time rather than on optimality then CBM is on average the fastest algorithm. \end{enumerate} Note that methods like SBM or CBM are applied on static SPP instances in order to determine a good lower bound. For solving SPP we need dynamical methods. Due to the complex topic of dynamical methods we will not discuss them, but a certain technique is worth mentioning. It is called column generation. We have indicated that this technique needs good Lagrangian multipliers of the corresponding SPP instances in order to generate further columns (in our case duties), which are added to the current SPP instance. Those multipliers are by-products of methods like our six considered methods. Due to the large number of such generation steps the running time depends on the computation time of these methods. Therefore, CBM fits more to this technique than CPLEX baropt or SBM. To sum it up it can be said that applications such as a duty scheduling can be described as set partitioning problems, whose lower bound can be solved by simplex, interior points, subgradient, or coordinate ascent methods. It turns out that the interior points method CPLEX baropt and the heuristic CBM have good performances. Furthermore, good Lagrangian multipliers, which are by-products of these methods, can be used by techniques like column generation. For this particular technique it also turns out that among our tested algorithms CBM is the most efficient one. In general we can state that real-world applications, which have to solve a large number of Lagrangian relaxed SPP instances can improve their performance by using CBM.
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  • 16
    Publication Date: 2014-02-26
    Description: The success of large-scale multi-national projects like the forthcoming analysis of the LHC particle collision data at CERN relies to a great extent on the ability to efficiently utilize computing a management software (Datagrid, Globus, etc.), while the effective integration of computing nodes has been largely neglected up to now. This is the focus of our work. We present a framework for a high-performance cluster that can be used as a reliable computing node in the Grid. We outline the cluster architecture, the management of distributed data and the seamless intergration of the cluster into the Grid environment.
    Keywords: ddc:000
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  • 17
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    Publication Date: 2020-11-13
    Description: Der Aufsatz ist die ausgearbeitete Fassung eines Vortrages, gehalten am 05.04.2001 auf dem 91. Deutschen Bibliothekartag in Bielefeld. Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) ist im Rahmen eines wissenschaftlichen Projektes in den Jahren 1997 bis 2000 am Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) aufgebaut worden. Nachdem das Projekt erfolgreich abgeschlossen ist, wird der KOBV 2001 institutionalisiert. In dem Vortrag hat die Verfasserin einen Überblick über das bisher Erreichte, den derzeitigen Stand und die Perspektiven des neuen Verbundes gegeben. Der KOBV stellt eine neue Art von Bibliotheksverbund dar. Sein technisches Konzept und sein organisatorischer Aufbau basieren auf der {\sl Internetphilosophie}. Den informationstechnischen Kern bildet eine Suchmaschine, die die heterogenen lokalen Bibliothekssysteme miteinander verbindet. Die KOBV-Organisation ist dezentral. Sie wird getragen von der Kooperation der Bibliotheken in Berlin und Brandenburg. Eine kleine Verbundzentrale koordiniert dieses Geflecht vernetzter lokaler Einheiten, vertritt den KOBV nach außen und arbeitet - in Form von Projekten - an seiner Weiterentwicklung. Der Entwicklungsaspekt und die Nutzerorientierung sind zwei wesentliche Komponenten in der Verbundarbeit. Berlin und Brandenburg haben auf engem Raum zahlreiche Bibliotheken mit großen, reichhaltigen Medienbeständen. Mittel- bis langfristig sollen Bibliotheken aller Sparten und Größen in den KOBV integriert werden, seien es wissenschaftliche Universalbibliotheken, universitäre Bibliothekssysteme, Spezialbibliotheken, Behörden- und Parlamentsbibliotheken oder öffentliche Bibliotheken. Auch regionale Bibliotheksverbünde können als Subverbünde am KOBV teilnehmen. Mit der KOBV-Suchmaschine ist eine offene Plattform geschaffen worden, auf der weitere Entwicklungen aufsetzen können. Der Aufbau einer virtuellen Regionalbibliothek mit Bestell- und Lieferkomponenten ist eines der Ziele. Darüber hinaus ist es die Vision, in der Region ein virtuelles {\sl Wissensportal} aufzubauen, das dem Nutzer unter einer Adresse den umfassenden Zugang und die umfassende Bereitstellung von Informationen aller Art bietet.
    Keywords: ddc:000
    Language: German
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  • 18
    Publication Date: 2019-01-29
    Description: A new approach to the numerical solution of optimal control problems including control and state constraints is presented. Like hybrid methods, the approach aims at combining the advantages of direct and indirect methods. Unlike hybrid methods, however, our method is directly based on interior-point concepts in function space --- realized via an adaptive multilevel scheme applied to the complementarity formulation and numerical continuation along the central path. Existence of the central path and its continuation towards the solution point is analyzed in some theoretical detail. An adaptive stepsize control with respect to the duality gap parameter is worked out in the framework of affine invariant inexact Newton methods. Finally, the performance of a first version of our new type of algorithm is documented by the successful treatment of the well-known intricate windshear problem.
    Keywords: ddc:000
    Language: English
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  • 19
    Publication Date: 2014-02-26
    Description: Das \emph{Committee on Electronic Information and Communication} (CEIC) der \emph{International Mathematical Union} (IMU) hat die Aufgabe, sich über die langfristige Informationsversorgung in der Mathematik Gedanken zu machen und Lösungsvorschläge hierfür zu erarbeiten. Das Kernthema ist natürlich "`Elektronisches Publizieren"'. Dazu gehören auch Copyright-Regelungen. % Sie sind -- % neben einer Andeutung der weiteren CEIC-Pläne -- der Fokus dieses % kurzen Artikels. Er schließt mit einem von der IMU verabschiedeten % Aufruf zu vernünftigem Verhalten bei Copyright-Vereinbarungen. Eine % nachhaltige Befolgung dieses Aufrufs -- verbunden mit weiteren % Aktivitäten -- könnte die (derzeit kaum noch bezahlbare und % dadurch gefährdete) Literaturversorgung nachhaltig zum Positiven % verändern. Mit diesem Artikel beginnt eine kleine Serie von Aufsätzen, in denen ich (in meiner Funktion als eines von elf CEIC-Mitgliedern) die Empfehlungen des CEIC erläutern werde. % Das heutige Thema sind die % CEIC-Vorschläge zum Copyright
    Keywords: ddc:000
    Language: German
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  • 20
    Publication Date: 2019-05-10
    Description: By computed tomography data (CT), the individual geometry of the mandible is quite well reproduced, also the separation between cortical and trabecular bone. Using anatomical knowledge about the architecture and the functional potential of the masticatory muscles, realistic situations were approximated. The solution of the underlying partial differential equations describing linear elastic material behaviour is provided by an adaptive finite element method. Estimations of the discretization error, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method.
    Keywords: ddc:000
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  • 21
    Publication Date: 2021-03-19
    Description: Optimization is the task of finding an optimum solution to a given problem. When the decision variables are discrete we speak of a combinatorial optimization problem. Such a problem is online when decisions have to be made before all data of the problem are known. And we speak of a real-time online problem when online decisions have to be computed within very tight time bounds. This paper surveys the are of combinatorial online and real-time optimization, it discusses, in particular, the concepts with which online and real-time algorithms can be analyzed.
    Keywords: ddc:000
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  • 22
    Publication Date: 2014-02-26
    Description: This paper describes a new simulation tool for the prediction of aerosol formation and behavior in gas--liquid contact devices such as absorbers, scrubbers, quench coolers, and condensers as well as multistage gas cleaning processes, respectively. Aerosol formation can impact severely the separation efficiency of gas cleaning processes. Aerosol or fog formation can arise by spontaneous condensation or desublimation in supersaturated gas phases. The rigorous description of the mass and energy transfer between the gas phase, the liquid phase, and the growing aerosol droplets leads to a system of partial differential and algebraic equations. For the solution of these systems we have developed the plant simulation tool AerCoDe. This program bases upon the linearly--implicit Euler discretisation, which in combination with extrapolation permits an adaptive step size and order control. Typical simulation results of a multistage industrial flue gas scrubbing process are presented. It is shown, that experimental data can be confirmed if the number concentration of condensation nuclei as an input parameter is roughly known.
    Keywords: ddc:000
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  • 23
    Publication Date: 2020-11-13
    Description: This paper discusses online optimization of real-world transportation systems. We concentrate on transportation problems arising in production and manufacturing processes, in particular in company internal logistics. We describe basic techniques to design online optimization algorithms for such systems, but our main focus is decision support for the planner: which online algorithm is the most appropriate one in a particular setting? We show by means of several examples that traditional methods for the evaluation of online algorithms often do not suffice to judge the strengths and weaknesses of online algorithms. We present modifications of well-known evaluation techniques and some new methods, and we argue that the selection of an online algorithm to be employed in practice should be based on a sound combination of several theoretical and practical evaluation criteria, including simulation.
    Keywords: ddc:000
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  • 24
    Publication Date: 2014-02-26
    Description: Wireless communication networks employ radio frequencies to establish communication links. The available radio spectrum is very limited. To meet today's radio communication demand, this resource has to be administered and reused carefully in order to control mutual interference. The reuse can be organized via separation in space, time, or frequency, for example. The problem, therefore, arises to distribute frequencies to links in a ``reasonable manner''. This is the basic form of the frequency assignment problem. What ``reasonable'' means, how to quantify this measure of quality, which technical side constraints to consider cannot be answered in general. The exact specification of this task and its mathematical model depend heavily on the particular application considered. In this paper we discuss this issue with respect to the GSM standard for mobile communication.
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  • 25
    Publication Date: 2014-02-26
    Description: This paper is a summary of the Round Table: ``The Impact of Mathematical Research on Industry and Vice Versa'' held at 3ecm in Barcelona on July 11, 2000. The round table started with contributions of the three panelists. Irene Fonseca, the panel chair, opened the discussion by stating six questions addressing the main issues of the round table topic. She presented the panel's answers to these questions, drawing on many examples from her own academic experience. In the following additional presentations, the other two panel members added further points of view based on their personal involvement with industry. The round table ended with a lively discussion with members from the audience. This written summary of the oral presentations follows the structure of the round table indicated above.
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  • 26
    Publication Date: 2020-03-09
    Description: This article is about \emph{adaptive column generation techniques} for the solution of duty scheduling problems in public transit. The current optimization status is exploited in an adaptive approach to guide the subroutines for duty generation, LP resolution, and schedule construction toward relevant parts of a large problem. Computational results for three European scenarios are reported.
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  • 27
    Publication Date: 2014-02-26
    Description: The recent spectral bundle method allows to compute, within reasonable time, approximate dual solutions of large scale semidefinite quadratic 0-1 programming relaxations. We show that it also generates a sequence of primal approximations that converge to a primal optimal solution. Separating with respect to these approximations gives rise to a cutting plane algorithm that converges to the optimal solution under reasonable assumptions on the separation oracle and the feasible set. We have implemented a practical variant of the cutting plane algorithm for improving semidefinite relaxations of constrained quadratic 0-1 programming problems by odd-cycle inequalities. We also consider separating odd-cycle inequalities with respect to a larger support than given by the cost matrix and present a heuristic for selecting this support. Our preliminary computational results for max-cut instances on toroidal grid graphs and balanced bisection instances indicate that warm start is highly efficient and that enlarging the support may sometimes improve the quality of relaxations considerably.
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  • 28
    Publication Date: 2014-02-26
    Description: Der Wissenschaftsrat hat in seiner Juli-Sitzung 2001 \glqq Empfehlungen zur digitalen Informationsversorgung durch Hochschulbibliotheken \grqq verabschiedet. Einige der Vorschläge des Wissenschaftsrates können, falls sie von den angesprochenen Institutionen aufgenommen werden, zu einer nachhaltigen Veränderung der wissenschaftlichen Informationslandschaft führen. In meinem kurzen Kommentar zu diesem Papier möchte ich auf einige dieser Anregungen hinweisen.
    Keywords: ddc:000
    Language: German
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  • 29
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    Unknown
    Publication Date: 2014-02-26
    Description: Von welcher "Informationsumwelt" träumt jemand, der für seine wissenschaftliche (und sonstige) Arbeit digitale Informationstechnologie intensiv einsetzt? In diesem Artikel beschreibe ich meinen "digitalen Traum". Er ist ganz einfach zu formulieren:"Ich will alles und zwar sofort, jederzeit, "überall" und kostenlos zur Verfügung haben." Ich schildere, was davon heute schon (fast) realisiert ist und was noch fehlt. Ich skizziere einige zentrale Schwierigkeiten der vollständigen Realisierung und skizziere mögliche Lösungen.
    Keywords: ddc:000
    Language: German
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  • 30
    Publication Date: 2019-01-24
    Description: Im Rahmen der biomechanischen Simulation knöcherner Organe ist die Frage nach einer befriedigenden Materialbeschreibung nach wie vor ungelöst. Computertomographische Datensätze liefern eine räumliche Verteilung der (Röntgen-)Dichte und ermöglichen damit eine gute Darstellung der individuellen Geometrie. Weiter können die verschiedenen Materialbestandteile des Knochens, Spongiosa und Kortikalis, voneinander getrennt werden. Aber die richtungsabängige Information der Materialanisotropie ist verloren. In dieser Arbeit wird ein Ansatz für eine anisotrope Materialbeschreibung vorgestellt, die es ermöglicht, den Einfluss der individuellen knöchernen Struktur auf das makroskopische Materialverhalten abzuschätzen.
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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  • 31
    Publication Date: 2020-03-09
    Description: Many phenomena in nature and engineering happen simultaneously on rather diverse spatial and temporal scales, i.e.\ exhibit a multi-scale character. Therefore various hierarchical data structures and numerical schemes have been devised to represent quantitatively such phenomena. A special numerical multilevel technique, associated with a particular hierarchical data structure, is so-called Adaptive Mesh Refinement (AMR). This scheme achieves locally very high spatial and temporal resolutions. Due to its popularity, many scientists are in need of interactive visualization tools for AMR data. In this article we present a 3D texture-based volume rendering algorithm for AMR data, that directly utilizes the hierarchical structure. Thereby interactive rendering even for large data sets is achieved. In particular the problems of interpolation artifacts, opacity corrections, and texture memory limitations are addressed. The algorithm's value in practice is demonstrated with simulation and image data.
    Keywords: ddc:000
    Language: English
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  • 32
    Publication Date: 2020-03-09
    Description: By combining techniques of preparation, histology, confocal microscopy, data visualization and data processing, we have created and recently published a standard brain model for drosophila and honey bee brains. This report describes the algorithms and implementation of the corresponding software modules. At the same time it serves as a user's guide for scientist who want to reproduce the results for differerent species or mutants.
    Keywords: ddc:000
    Language: English
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  • 33
    Publication Date: 2014-02-26
    Description: Several classes of systems of evolution equations with one or two vector unknowns are considered. We investigate also systems with one vector and one scalar unknown. For these classes all equations having the simplest higher symmetry are listed.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 34
    Publication Date: 2014-02-26
    Description: Two traffic streams $\Phi_1$, $\Phi_2$ are offered a link. The calls of $\Phi_i$ require exponential holding times with parameter $\mu$ and are accepted if less than $C_i$ trunks are occupied. Approximating the $\Phi_i$ by appropriate renewal processes meeting their first two moments, defined as the moments of the numbers of calls in virtual links of infinite capacity to which the traffic streams as freed traffics are virtually directed and where the calls get fresh exponential i.i.d.\ holding times with parameter $\mu$, stable recursive algorithms of complexity $O(\max(C_1,C_2))$ are derived for the first two defined as above moments of the individual overflow and freed carried traffics. The results offer a unified handling of both overflow and carried traffics in circuit switching networks with trunk reservation, providing a basis for new two-moment network dimensioning algorithms.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 35
    Publication Date: 2014-02-26
    Description: We study the performance of QCD simulations with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering on $10^4$ and $12^4$ lattices. In order to compare tempered with standard simulations, covariance matrices between sub-ensembles have to be formulated and evaluated using the general properties of autocorrelations of the parallel tempering algorithm. We find that rendering the hopping parameter $\kappa$ dynamical does not lead to an essential improvement. We point out possible reasons for this observation and discuss more suitable ways of applying parallel tempering to QCD.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 36
    Publication Date: 2020-11-13
    Description: Dem vorliegenden Aufsatz liegt ein Vortrag zugrunde, den die Verfasserin auf der Ersten Gemeinsamen Fachtagung der DBV-Landesverbände Berlin und Brandenburg "Wir machen den Weg frei : Fusionen - Kooperationen in Berlin und Brandenburg" am 17. Oktober 2001 gehalten hat, in der Vortragsreihe "Möglichkeiten und Grenzen von Ausleih- und bibliographischen Verbünden - VÖB Berlin, VÖB Brandenburg, KOBV". Der Kooperative Bibliotheksverbund Berlin-Brandenburg (KOBV) ist angetreten, um auf der Basis neuer Technologien zeitgemäße, nutzerorientierte Dienstleistungen für den Informationsbereich zu entwickeln und die Informationsinfrastruktur in der Region Berlin-Brandenburg neu zu organisieren. Dabei setzt der KOBV insbesondere auf das Internet. Die Verfasserin beschreibt die einzelnen Stufen, in denen die Dienste des KOBV aufgebaut wurden und kontinuierlich weiter ausgebaut werden. Dabei zeigt sie Vorteile auf, die Nutzern und Bibliotheken durch den Verbund entstehen, und lotet gleichzeitig die Grenzen aus, die dem Verbund gesetzt sind.
    Keywords: ddc:000
    Language: German
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  • 37
    Publication Date: 2014-02-26
    Description: We report numerical results for SBmethod --- a publically available implementation of the spectral bundle method --- applied to the 7$^{th}$ DIMACS challenge test sets that are semidefinite relaxations of combinatorial optimization problems. The performance of the code is heavily influenced by parameters that control bundle update and eigenvalue computation. Unfortunately, no mathematically sound guidelines for setting them are known. Based on our experience with SBmethod, we propose heuristics for dynamically updating the parameters as well as a heuristc for improving the starting point. These are now the default settings of SBmethod Version 1.1. We compare their performance on the DIMACS instances to our previous best choices for Version 1.0. SBmethod Version 1.1 is also part of the independent DIMACS benchmark by H.~Mittelmann. Based on these results we try to analyze strengths and weaknesses of our approach in comparison to other codes for large scale semidefinite programming.
    Keywords: ddc:000
    Language: English
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  • 38
    Publication Date: 2014-11-10
    Description: Many {\cal NP}-hard graph problems can be solved in polynomial time for graphs with bounded treewidth. Equivalent results are known for pathwidth and branchwidth. In recent years, several studies have shown that this result is not only of theoretical interest but can successfully be applied to find (almost) optimal solutions or lower bounds for diverse optimization problems. To apply a tree decomposition approach, the treewidth of the graph has to be determined, independently of the application at hand. Although for fixed $k$, linear time algorithms exist to solve the decision problem ``treewidth $\leq k$'', their practical use is very limited. The computational tractability of treewidth has been rarely studied so far. In this paper, we compare four heuristics and two lower bounds for instances from applications such as the frequency assignment problem and the vertex coloring problem. Three of the heuristics are based on well-known algorithms to recognize triangulated graphs. The fourth heuristic recursively improves a tree decomposition by the computation of minimal separating vertex sets in subgraphs. Lower bounds can be computed from maximal cliques and the minimum degree of induced subgraphs. A computational analysis shows that the treewidth of several graphs can be identified by these methods. For other graphs, however, more sophisticated techniques are necessary.
    Keywords: ddc:000
    Language: English
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  • 39
    Publication Date: 2014-02-26
    Description: The currently most efficient algorithm for inference with a probabilistic network builds upon a triangulation of a network's graph. In this paper, we show that pre-processing can help in finding good triangulations for probabilistic networks, that is, triangulations with a minimal maximum clique size. We provide a set of rules for stepwise reducing a graph, without losing optimality. This reduction allows us to solve the triangulation problem on a smaller graph. From the smaller graph's triangulation, a triangulation of the original graph is obtained by reversing the reduction steps. Our experimental results show that the graphs of some well-known real-life probabilistic networks can be triangulated optimally just by preprocessing; for other networks, huge reductions in their graph's size are obtained.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 40
    Publication Date: 2014-11-11
    Description: {\begin{rawhtml} 〈a href="http://dx.doi.org/10.1007/s10479-007-0178-0"〉 Revised Version unter http://dx.doi.org/10.1007/s10479-007-0178-0〈/a〉 \end{rawhtml}} Wireless communication is used in many different situations such as mobile telephony, radio and TV broadcasting, satellite communication, and military operations. In each of these situations a frequency assignment problem arises with application specific characteristics. Researchers have developed different modelling ideas for each of the features of the problem, such as the handling of interference among radio signals, the availability of frequencies, and the optimization criterion. This survey gives an overview of the models and methods that the literature provides on the topic. We present a broad description of the practical settings in which frequency assignment is applied. We also present a classification of the different models and formulations described in the literature, such that the common features of the models are emphasized. The solution methods are divided in two parts. Optimization and lower bounding techniques on the one hand, and heuristic search techniques on the other hand. The literature is classified according to the used methods. Again, we emphasize the common features, used in the different papers. The quality of the solution methods is compared, whenever possible, on publicly available benchmark instances.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 41
    facet.materialart.
    Unknown
    Publication Date: 2014-02-26
    Description: Telota ist ein Kunstwort, das für alle Aktivitäten der Berlin-Brandenburgischen Akademie der Wissenschaften steht, die der Förderung von Forschung, Kommunikation und Präsentation durch elektronische Medien dienen. In diesem Artikel werden die Entstehung des Telota-Projektes geschildert und die Ziele diskutiert, die mit diesem Projekt erreicht werden sollen. Es geht darum, moderne Informationstechnik bewusst, geplant und nachhaltig für alle Belange der {\rm BBAW} einzusetzen. Informationstechnische Werkzeuge sollen für die wissenschaftliche Arbeit effizient genutzt werden; die Information nach innen und nach außen soll deutlich verbessert werden; eine bessere Kommunikationsinfrastuktur soll die Zusammenarbeit fördern.
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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  • 42
    Publication Date: 2022-07-07
    Description: The pole condition is a general concept for the theoretical analysis and the numerical solution of a variety of wave propagation problems. It says that the Laplace transform of the physical solution in radial direction has no poles in the lower complex half-plane. In the present paper we show that for the Helmholtz equation with a radially symmetric potential the pole condition is equivalent to Sommerfeld's radiation condition. Moreover, a new representation formula based on the pole condition is derived and used to prove existence, uniqueness and asymptotic properties of solutions. This lays the foundations of a promising new algorithm to solve time-harmonic scattering problems numerically and provides a new approach for analyzing existing algorithms such as the Perfectly Matched Layer (PML) method and the Bayliss-Gunzburger-Turkel (BGT) algorithm.
    Keywords: ddc:000
    Language: English
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  • 43
    Publication Date: 2022-07-07
    Description: In this paper we study the PML method for Helmholtz-type scattering problems with radially symmetric potential. The PML method consists in surrounding the computational domain by a \textbf{P}erfectly \textbf{M}atched sponge \textbf{L}ayer. We prove that the approximate solution obtained by the PML method converges exponentially fast to the true solution in the computational domain as the thickness of the sponge layer tends to infinity. This is a generalization of results by Lassas and Somersalo based on boundary integral eqaution techniques. Here we use techniques based on the pole condition instead. This makes it possible to treat problems without an explicitly known fundamental solution.
    Keywords: ddc:000
    Language: English
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  • 44
    Electronic Resource
    Electronic Resource
    Springer
    Surgical and radiologic anatomy 4 (1982), S. 197-204 
    ISSN: 1279-8517
    Keywords: Finite element method ; Engineering ; Mandible ; Stress ; Honeycomb
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé Nous avons, dans le précédent travail, attiré l'attention sur le fait que l'application des méthodes modernes utilisées en engineering pour la création et la vérification des structures mécaniques complexes à la recherche en anatomie semblait d'avérer une voie de recherche nouvelle et fructueuse, précisant bien que cette méthodologie n'était appliquable qu'à certains types de recherche bien définis et que son domaine de choix était l'ostéologie fonctionnelle. Nous avons donc procédé à une ≪modélisation≫ de la mandibule et à une expérimentation sur le modèle ainsi obtenu à l'aide de la ≪méthode des éléments finis≫ parce que l'étude de celle-ci nous semblait un moyen commode de tester notre méthodologie et sa fiabilité (la traumatologie de la mandibule est en effet bien connue), mais aussi et surtout parce que les conceptions généralement admises, relatives à la structure de la mandibule, ne nous semblaient pas pleinement satisfaisantes eu égard aux progrès actuels des connaissances en résistance des matériaux.
    Notes: Summary In a previous article we drew attention to the application of modern methods used in engineering to the development and verification of complex mechanical structures in anatomical research. This approach was new and appeared to be fruitful, showing clearly that this technique was only applicable to certain types of well-defined research, in particular functional osteology. We therefore developed a model of the mandible and performed a series of experiments using the concepts of finite structures which provided a convenient means of testing our approach and its validity. More particularly, however, there are a number of widely held ideas regarding the structure of the mandible which strike us as not altogether consistent with current developments in the knowledge of resistance in materials.
    Type of Medium: Electronic Resource
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  • 45
    ISSN: 1432-0827
    Keywords: Bacterial amphophile ; Purification ; Chemistry ; Resorption ; Ca influx ; Cyclic AMP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Summary The bone resorptive factor and amphipathic antigen (AcA) previously identified by us in preparations fromActinomyces viscosus have been partially purified, characterized chemically, and compared. They elute at the same location on chromatography with Ac 22. The fatty acid composition of AcA and the bone resorptive factor is the same. Some differences in carbohydrate composition are observed. TheActinomyces factor does not affect calcium influx or cyclic AMP in isolated bone cells. Therefore it is concluded that AcA stimulates resorption either by gaining entrance into bone cells or by way of a yet undetermined second messenger.
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  • 46
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 17-24 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Computer simulation shows that the time required to attain near sedimentation equilbrium is dramatically reduced by a two-step initial loading in which a macromolecular solution at low or zero concentration is layered above one at a higher concentration. To achieve the minimum time requires a good estimate of the molecular weight, but at least a 50% reduction in time can be achieved if the molecular weight of the macromolecule is known only within a factor of 2. Numerical solutions to the differential equation of the ultracentrifuge are calculated using the finite element method. An efficient Gaussian elimination algorithm can be used to minimize calculation time and computer storage requirements.
    Additional Material: 4 Ill.
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  • 47
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 79-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aldehydes present in acid-soluble type I collagen react with pyrenebutyrylhydrazine to form various types of complexes under different reaction conditions. These complexes exhibit one or more of three different pyrene fluorescence bands: monomer, excimer, and aggregate fluorescence. Collagen, whose aldehydes have been reduced with NaBH4, does not react with this fluorescent hydrazine, confirming that the hydrazine reacts specifically with aldehyde groups to form hydrazones. The absence of a reaction with pepsin-treated collagen also shows that the fluorescent labels are primarily in the nonhelical terminal telopeptides. Upon dialysis, the pyrene label bound to a saturated aldehyde in an α-chain is lost; whereas that bound to an unsaturated aldehyde remains on the protein. The pyrene monomer fluorescence in the β-chain of old collagen is stronger than that of young collagen. The formation of the pyrene excimer fluorescence implies the proximity of two pyrene molecules, probably attached to two adjacent aldehydes. Upon changing from acidic to neutral pH, both excimer and aggregate fluorescence bands disappear within a few seconds, revealing a very rapid alteration at the telopeptides.
    Additional Material: 6 Ill.
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  • 48
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 147-157 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe conditions which lead to complete helix formation of poly(I) in the presence of NH4+. Binding of NH4+ is shown to be specific in the presence of Li+, which does not by itself support helix formation under these conditions. The NH4+-poly(I) complex is characterized by uv, CD, and ir spectroscopy. The CD spectrum is strikingly different from those of the Na+ or K+ complexes, the first extremum being changed from negative for the metal ions to positive for NH4+. A stereospecific model is proposed for the NH4+-poly(I) helix in which the N of NH4+ is located on the axis of the four-stranded helix, midway between planar tetramers formed by the bases. The model is consistent with the tetrahedral symmetry of NH4+, the requirement for four acceptable hydrogen bonds, the observed stability of the helix, and the accepted geometry of the backbone.
    Additional Material: 8 Ill.
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  • 49
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 159-167 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It has recently been proven that the counterion condensate around an isolated line charge in an electrolyte, as characterized by nonlinear Poisson-Boltzmann theory, is an encapsulating δ-function. Here the identical result is shown to hold in the framework of the polyelectrolyte theory of Fuoss, Katchalsky, and Lifson. The proof fully exploits analytic solutions to the differential equation which are not available for the nonlinear, cylindrical Poisson-Boltzmann equation.
    Type of Medium: Electronic Resource
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  • 50
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 203-218 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The extent and modes of binding of the divalent metal ions Mn2+ and Co2+ to DNA and the effects of salt on the binding have been studied by measurements of the effects of these paramagnetic metal ions on the longitudinal and transverse relaxation rates of the protons of the solvent water molecules, a technique that is sensitive to overall binding. The number of water molecules coordinated to the DNA-bound Mn2+ and Co2+ is found to be between five and six, and the electron spin relaxation times and the electron-nuclear hyperfine constants associated with Mn2+ and Co2+ are little or not affected by the binding. These observations indicate little disturbance of the hydration sphere of Mn2+ and Co2+ upon binding to DNA. An average 2-3-fold reduction in the exchange rate of the water of hydration of the bound metal ions and an order-of-magnitude increase in their rotational correlation time are attributed to hydrogen-bond formation with the DNA. The binding constants of Mn2+ to DNA, at metal concentrations approaching zero, are found to be inversely proportional to the second power of the salt concentration, in agreement with the predictions of Manning's polyelectrolyte theory. A remarkable quantitative agreement with the polyelectrolyte theory is also obtained for the anticooperativity in the binding of Mn2+ to DNA, although the experimental results can be well accounted for by another simple electrostatic model. The various modes of binding of divalent metal ions to DNA are discussed.
    Additional Material: 6 Ill.
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  • 51
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 265-275 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dc electrical conductivity of films of the polyelectrolyte complexes of glycol chitosan (GlChi) with the sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) was measured at temperatures above and below room temperature. The maximum field strength in the thinnest film used amounted to 3 × 104 V/cm. A plot of normalized current against the reciprocal of the absolute temperature revealed two regions with different slopes, and activation energies in these two regions have been obtained for all the complexes. The activation energies in the high-temperature region vary from 0.85 to 1.18 eV and in the low-temperature region from 0 to 0.22 eV. Reasons are given to show that the conductivity is probably ionic. Near room temperature, the current-voltage relation is almost linear in the GlChi-DS complex, while in the other three complexes the current varies as a power n of the voltage with the value of n ranging from 1.7 to 2.5. A rise in temperatures causes an increase in the slope of the log I vs log V plot in GlChi-DS and GlChi-CMC complexes. The nonlinear current-voltage relation is ascribed to a space-charge-limited conductivity.
    Additional Material: 9 Ill.
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  • 52
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 301-319 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Five different glucomannan samples were recrystallized from dilute solution. Depending on the experimental conditions, the crystals obtained could be identified as corresponding to the mannan I (anhydrous precipitate of more or less regular lozenge-shaped crystals) or mannan II (hydrated gel-forming pseudo-fibrillar precipitate). High-molecular-weight material, low temperature of crystallization, or a polar crystallization medium favored the mannan II polymorph, whereas a low-molecular weight, a high temperature of crystallization, and a crystallization medium of low polarity yielded the mannan I polymorph. Since the base-plane unit-cell dimensions are fairly constant with respect to variation of glucose, it is likely that isomorphous replacement of mannose by glucose occurs in glucomannan crystallization; the data also indicate that perfection of the glucomannan crystals was reduced in specimens having a high glucose:mannose ratio. The oriented crystallization of glucomannan on cellulose microfibrils was also studied under conditions where the mannan I polymorph was obtained. This gave shish-kebab structures that were characterized.
    Additional Material: 10 Ill.
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  • 53
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer-water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (hp′ = 0.06-0.1 g H2O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ∼20% of the primary hydration sphere. In order to test this model, detailed sorption-desorption scanning experiments were performed on a globular protein (α-chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.
    Additional Material: 6 Ill.
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  • 54
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 451-458 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The light scattering of bovine serum albumin (BSA) has been measured at protein concentration up to 90 g/L and at pH values between 4.4 and 7.6. The dependence of scattering on both protein concentration and pH may be quantitatively accounted for by a simple extension of the hard-sphere model for protein solutions [Ross, P. D. & Minton, A. P. (1977) J. Mol. Biol. 112, 437-452] allowing for electrostatic repulsions between molecules. According to the extended model, the radius of the effective hard spherical particle representing BSA varies with the net electrical charge of the BSA molecule in a manner which may be calculated from electrostatic theory.
    Additional Material: 4 Ill.
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  • 55
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 475-497 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ3), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C2-Cβ-exo-Cγ-endo. For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.
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  • 56
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    Biopolymers 21 (1982), S. 547-563 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectrum of the enzyme adenylate kinase has been investigated. Theoretical calculations, based on the x-ray crystal structure, have been carried out by means of an origin independent matrix formalism. The entire molecule was included in the calculations in the sense that essentially all electronic transitions that occur at wavelengths longer than 185 nm were included in the basis set. A linear dielectric function was utilized to evaluate the intertransition coupling potentials. The results of the theoretical calculations were in reasonable agreement with experimental CD spectra of the molecule.
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  • 57
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    Biopolymers 21 (1982), S. 633-652 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The mode of action of many antitumor agents entails the inhibition of nucleic acid synthesis. Because many of the drugs can intercalate, it is assumed that intercalation is an important step in the mechanism of biological activity. As intercalants contain a planar chromophore as an ingredient essential for intercalation, chromophores that should fit into DNA are desired. This is the main theme of this investigation. Binding to DNA of fundamental moieties, protonated pyridine, aniline, phenol, quinone, and 4H-thiopyran-4-one, is studied to determine their optimum placement in DNA. The optimum orientations for each moiety are superimposed to form polyaromatic systems that can intercalate in a manner in which functional groups on these chromophores are oriented as in the moieties themselves. Ideal intercalants proposed contain three and four fused ring system, have protonated ring nitrogen atoms located to maximize the electrostatic interactions with DNA, hydroxy and amino groups that can hydrogen bond to the OII and O5′ phosphate backbone atoms, and carbonyl and sulfur groups in the central position of the ring system to provide variations in the chromophore and to interact with the relatively positive region in the intercalation site. The optimum orientation occurs when the chromophore and the base pairs overlap to the maximum extent. The ideal intercalants are fundamentally of the type:
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  • 58
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    Biopolymers 21 (1982), S. 665-677 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA reassociation kinetics using the phenol emulsion reassociation technique (PERT) [Kohne, D. E., Levison, S. A. & Byers, M. J. (1977) Biochemistry 16, 5329-5341] has been investigated at high DNA concentrations using an endonuclease S1 assay of reaction progress. Apparent second-order rate constants fall on two intersecting straight lines when presented as a function of DNA concentrations on a log-log plot. In the low DNA concentration range, the rate constants drop about 10-fold when concentration increases 1000-fold. In the high DNA concentration range, the rate constants drop more than 10-fold when concentration increases 10-fold. The slopes of these lines are the same in different solvents and at different temperatures. The intersection between the lines occurs when the available catalytic surface is saturated. At high DNA concentrations, high-complexity heterologous denatured DNA apparently competes 2-4 times better for the surface than homologous DNA because it does not participate in a reassociation reaction. Native and partially native DNA molecules cannot compete with single-stranded DNA for a saturated surface. At high DNA concentrations, reactions using PERT become dependent on the single-strand DNA length. Increasing length lowers reassociation rates.
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  • 59
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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  • 60
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    Biopolymers 21 (1982), S. 859-872 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Classical potential functions (CPF) calculations on 3′-mononucleotides, the building blocks of nucleic acids, predict a correlation between the sugar ring pucker and the torsion angle Φ′ around the C3′—O3′ bond. In ribonucleotides, the value of Φ′ depends on the sugar pucker, viz. the C2′-endo sugar pucker is associated with Φ′ = 210° and 270°, while the C3′-endo sugar pucker favors only Φ′ = 210°. On the other hand, in deoxyribonucleotides, both sugar puckers show a preference for Φ′ = 180°. These theoretical predictions are fully corroborated by the results obtained from x-ray and nmr studies on mono-, di-, and polynucleotides.
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  • 61
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of several surfactants on the secondary structure of bovine β-lactoglobulin B was determined from the circular dichroism spectra. The spectra were measured at several concentrations of surfactant ranging from 1 mg/mL to the critical micelle concentration. The surfactants studied were sodium dodecyl, decyl, and octyl sulfate, sodium dodecyl sarcosinate, dodecyltrimethylammonium bromide. The data were analyzed using the method of Chen et al. [Biochemistry (1974) 13, 3350-3359] to determine the percentage of α-helix, β-sheet, and unordered form at each surfactant concentration. In every case, an increase in structured form and a 20-25% decrease in the amount of unordered form was noted when the surfactant concentration reached the critical micelle concentration. However, the relative amounts of the two structured forms present depend on the surfactant used. The profile of the secondary structure of the protein also varied from surfactant to surfactant as the protein was titrated, probably reflecting the delicate balance between ionic and nonionic forces that governs the secondary structure of β-lactoglobulin and most other globular proteins in aqueous solution.
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  • 62
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amino acids are known to differ in their individual preferences for each of the four positions of the β-turn conformation formed by tetrapeptide segments. Proline and glycine show relatively high preferences for positions 2 and 3, respectively, of the β-turn. Using tripeptides of the type N-acetyl-Pro-Gly-X-OH, where X = Gly, Ala, Leu, Ile, and Phe, we have sought to study the influence of the 4th residue X on the stability of the β-turn conformation in these tripeptides. Our nmr and CD results show that the β-turn stability is quite significantly governed by the nature of the amino acid residue at this position in the following order: Leu 〉 Ala 〉 Ile, Gly 〉 Phe.
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  • 63
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    Biopolymers 21 (1982), S. 1153-1166 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Thermodynamic studies of the binding of adamantanecarboxylate to cyclodextrins have been made as a function of temperature and added organic cosolvent (methanol) using flow microcalorimetry. The negative heat capacity change associated with the adamantanecar-boxylate/β-cyclodextrin interaction and the fact that the interaction is weakened by the addition of methanol implicate the binding process as being a hydrophobically driven one. The negative enthalpy change (ΔH0 = -5.5 kcal/mol) and near-zero entropy change (ΔS0 = 1.5 cal/mol deg) are quite different from the values normally expected for a hydrophobic bond, indicating that other bonding forces are important in addition to the hydrophobic effect. The relative contribution of the hydrophobic effect and other bonding forces (most likely van der Waals forces) to the overall binding was judged from an analysis of the dependence of the thermodynamics of the association process on the surface tension of the water-methanol mixtures following a model for “solvophobic” bonding described by Sinanoglu [Molecular Associations in Biology (1968) Academic Press, New York, pp. 427-445]. From this analysis, adamantane-carboxylate/cyclodextrin complex formation is found to be driven to the extent of -1.9 kcal/mol by the hydrophobic effect. Furthermore, the hydrophobic driving force is found to be characterized by a positive ΔS0 of 10 cal/mol deg. The remaining free energy of binding (and the ΔH0 of binding of ∼-6 kcal/mol) is then due to the intrinsic (surface-tension-independent) van der Waals interaction between the ligand and cyclodextrin cavity.
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  • 64
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    Biopolymers 21 (1982) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 65
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pivaloyl-L-Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H-nmr methods, suggesting the existence of β-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II β-turn conformations are about 2 kcal mol-1 more stable than Type III structures. A crystallographic study has established the Type II β-turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β-turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are φPro = -57.8°, ψPro = 139.3°, φAib = 61.4°, and ψAib = 25.1°. The Type II β-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.
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  • 66
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    Biopolymers 21 (1982), S. 1333-1363 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The folding-unfolding process of reduced bovine pancreatic trypsin inhibitor was investigated with an idealized model employing approximate free energies. The protein is regarded to consist of only Cα and Cβ atoms. The backbone dihedral angles are the only conformational variables and are permitted to take discrete values at every 10°. Intraresidue energies consist of two terms: an empirical part taken from the observed frequency distributions of (φ,ψ) and an additional favorable energy assigned to the native conformation of each residue. Interresidue interactions are simplified by assuming that there is an attractive energy operative only between residue pairs in close contact in the native structure. A total of 230,000 molecular conformations, with no atomic overlaps, ranging from the native state to the denatured state, are randomly generated by changing the sampling bias. Each conformation is classified according to its conformational energy, F; a conformational entropy, S(F) is estimated for each value of F from the number of samples. The dependence of S(F) on energy reveals that the folding-unfolding transition for this idealized model is an “all-or-none” type; this is attributable to the specific long-range interactions. Interresidue contact probabilities, averaged over samples representing various stages of folding, serve to characterize folding intermediates. Most probable equilibrium pathways for the folding-unfolding transition are constructed by connecting conformationally similar intermediates. The specific details obtained for bovine pancreatic trypsin inhibitor are as follows: (1) Folding begins with the appearance of nativelike medium-range contacts at a β-turn and at the α-helix. (2) These grow to include the native pair of interacting β-strands. This state includes intact regular secondary conformations, as well as the interstrand sheet contacts, and corresponds to an activated state with the highest free energy on the pathway. (3) Additional native long-range contacts are completely formed either toward the amino terminus or toward the carboxyl terminus. (4) In a final step, the missing contacts appear. Although these folding pathways for this model are not consistent with experimental reports, it does indicate multiple folding pathways. The method is general and can be applied to any set of calculated conformational energies and furthermore permits investigation of gross folding features.
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  • 67
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aib-OMe in CDCl3 (0.001-0.06M) and (CD3)2SO (0.001-0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen-bonding pattern in the decapeptide.
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  • 68
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    Biopolymers 21 (1982), S. 1469-1472 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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  • 69
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    Biopolymers 21 (1982), S. 1479-1487 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A formalism for extracting the conformations of a proline ring based on the bistable jump model of R. E. London [(1978) J. Am. Chem. Soc. 100, 2678-2685] from 13C spin-lattice relaxation times (T1) is given. The method is such that the relaxation data are only partially used to generate the conformations; these conformations are constrained to satisfy the rest of the relaxation data and to yield acceptable ring geometry. An alternate equation for T1 of 13C nuclei to that of London is given. The formalism is illustrated through an example.
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  • 70
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    Biopolymers 21 (1982), S. 1521-1534 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have used broadline proton magnetic resonance to study molecular motion in cellulose, a sodium pectate solution, a calcium pectate gel, and isolated bean cell walls. All samples were prepared in D2O to minimize the contribution of water to the observed signals. For each sample, a free induction decay was obtained, and the second moment, spin-lattice relaxation, and dipolar relaxation were measured. Our results show that the large majority of protons in cellulose are immobile. Rigid and mobile domains were also observed in the pectate samples. We have shown that gelation induces large-scale changes in the free induction decay, the second moment, and the relaxation behavior of the pectate. As with the other samples, rigid and more mobile domains were found in bean cell walls. The fraction in the rigid domains is much larger than the fraction of cellulose in the sample, suggesting that the noncellulosic wall components are also organized into rigid and mobile domains.
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  • 71
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational energy computations were carried out on collagenlike triple-stranded conformations of several poly(tripeptide)s with the general structure CH3CO—(Gly—X—Y)3—NHCH3. The sequences considered had various amino acid residues in position X or Y of the central tripeptide, with either Pro or Ala as a neighbor, i.e., Gly-X-Pro, Gly-X-Ala, Gly-Pro-Y, and Gly-Ala-Y. Minimum-energy conformations were computed for the side chains, and their distributions were compared for the four sequences. The residues used were Abu (= α-aminobutyric acid), Leu, Phe, Ser, Asp, Asn, Val, Ile, and Thr. The conformational energy of a —Ch2—CH3 side chain in Abu was mapped as a function of the dihedral angle χ1. Intrastrand interactions with neighboring residues do not affect the conformations of a side chain in position Y, and they have a minor effect on it in the X-Ala sequence, but they strongly restrict the conformational freedom of the side chain in the X-Pro sequence. Conversely, interstrand interactions do not affect side chains in position X, but they strongly restrict the conformational freedom of a side chain in position Y if there is a nearby Pro residue in a neighboring strand. Hydrogen bonds with the backbone can be formed in some conformations of long polar side chains, such as Asp, Asn, or Gln. All amino acid residues can be accommodated in collagen. Because of the interactions mentioned above, steric and energetic constraints can be correlated with observed preferences of certain amino acids for positions X or Y in collagen. Hence, these preferences may be explained, in part, in terms of differences in the conformational freedom of the side chains in the triple-stranded structure.
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  • 72
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    Biopolymers 21 (1982), S. 1657-1666 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ionization constants of the tyrosyl groups of chymotrypsinogen and of nitrated-chymotrypsinogen (two tyrosyl residues nitrated) have been determined by difference spectrophotometry. In chymotrypsinogen, two of the four tyrosyl groups ionize without any time dependence. Above pH greater than ca. 12.5, time-dependent spectral changes are seen for 0.7 group equivalent. The data can be fitted to the values of pK′1 9.75 ± 0.07, pK′2 11.55 ± 0.05, pK′3 13.30 ± 0.05. In nitrated-chymotrypsinogen, the two nitrated tyrosyl residues have pK′1 6.44 and pK′2 8.30. For both proteins, these pK′ values are in agreement with those evaluated from potentiometric titration and calorimetric data using computer-assisted curve-fitting analysis.
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  • 73
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    Biopolymers 21 (1982), S. 2195-2203 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of several samples of poly(α,β-L-Asp) with a molar fraction of β-bonds ranging from 0.1 to 0.55 was investigated by means of ir and CD spectroscopy and potentiometric titration and compared with the results obtained previously with poly(α-L-Asp). All samples investigated underwent a conformational change induced by changes in their degree of ionization: unpronounced ir absorption of amide V at 650 cm-1 was shifted to 620 cm-1 and substantially increased on deionization; CD spectra changed with the degree of ionization, passing through an isosbestic point; and the pattern of the titration curves was more complex than that of a simple polyelectrolyte. The conformation developing with the decreasing degree of ionization may be considered to be α-helix, as deduced according to the analogous behavior of other polypeptides. The extent of the conformational change in the individual samples depends on the molar fraction of β-bonds: the higher it is, the lower is the helix-forming ability of the sample.
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  • 74
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    Biopolymers 21 (1982), S. 2225-2239 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of 1H-nmr spectroscopy is demonstrated to be a useful analytical method to characterize the structure of synthetic peptides attached to soluble, macromolecular polyoxyethylene (POE) supports in the liquid-phase method (LPM) of peptide synthesis. We report an extensive 360-MHz 1H-nmr study of POE-bound homo-oligo-L-methionine peptides. A combination of high field and selective saturation or Redfield pulse methods allows resolution of individual backbone NH and α-CH resonances of dilute peptides in the presence of strong resonances from macromolecular POE and/or protonated solvents. The nmr spectra for the POE-bound peptides in CDCl3 are qualitatively similar to those of the low-molecular-weight Boc-L-Metn-OMe peptide esters. This corroborates other observations that POE has little effect on peptide stucture. The backbone α-CH region of peptides is overlapped by signals from the terminal oxyethylene group of POE, but the peptide side-chain and low-field backbone NH resonances are well resolved. In trifluoroethanol the Boc-(L-Met)n-NH-POE heptamer and octamer adopt the right-handed α-helical structure, and the present nmr studies provide evidence for two strong intramolecular hydrogen bonds to stabilize the helices. In water, the N-deblocked derivatives, (L-Met)n-NH-POE oligomers adopt β-sheet structure and manifest well-resolved nonequivalent NH resonances with 6-7 Hz 3JNH-CH coupling constants.
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  • 75
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    Biopolymers 21 (1982), S. 2241-2252 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The concerted model of Monod, Wyman, and Changeux is generalized so that all effects of interactions for an enzyme operating at a nonequilibrium stationary state are considered. In contrast to the original model, which is based on an analogy to equilibrium ligand binding, the generalization may show both “positive” and “negative cooperativity” in both catalytic binding and conformational processes. Furthermore, in contrast to any equilibrium binding model, the Hill coefficients may be greater than the number of sites n. For catalysis, the maximum value is 2n, and for conformational changes, n + 1. These points are illustrated by two cases that yield simpler analytic expressions. The first obtains when catalysis occurs on a much faster time scale than the conformational changes, and the second, when this situation is reversed.
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  • 76
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    Biopolymers 21 (1982), S. 2315-2316 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 77
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    Biopolymers 21 (1982), S. 1473-1477 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 78
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    Biopolymers 21 (1982) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 79
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    Biopolymers 21 (1982), S. 1503-1520 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: By combining gel permeation chromatography (GPC) and light-scattering spectroscopy, including photon correlation and angular distribution of absolute scattered intensity, we were able to characterize immunologically active Haemophilus influenzae type b polysaccharide (HIB Ps) bovine serum albumin (BSA) conjugates in terms of equivalent hydrodynamic radius rh ∼ (6.2 ± 0.6) × 102 Å, apparent radius of gyration rg ∼ (5.4 ± 0.3) × 102 Å, apparent molecular weight Mw ∼ (3.5 ± 0.4) × 106 g/mol, and a second virial coefficient A2 ∼ (1.9 ± 0.3) × 10-4 cm3 mol/g2. We could study the effects of each of the processes in the conjugate formation according to the following procedure: BSA (dialysis, modification, fractionation) + HIB Ps → HIB Ps/BSA conjugate (conjugate formation, fractionation). Narrow distributions of HIB Ps BSA conjugate formation can be achieved using fractionated BSA.
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  • 80
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    Biopolymers 21 (1982), S. 1569-1586 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ∼25 to ∼500 cm-1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out-of-plane deformation of the bases contributes strongly to vibrations near 200 cm-1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm-1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200-cm-1 region and sharpening of the features assigned to the low-frequency ribose-ring vibrations.
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  • 81
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    Biopolymers 21 (1982), S. 1735-1747 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the oxygen replacement reaction of carbon monoxide-saturated hemoglobin (HbA0) was carried out using spectroscopic, calorimetric, and pH titration methods. Under fully saturated conditions the replacement reaction can be defined by a single partition constant over all ratios of bound oxygen to carbon monoxide. This indicates that under saturating conditions Haldane's first law for the ligand binding of gas mixtures holds for any CO/O2 ratio. It further shows that there is no appreciable difference in relative CO-O2 affinity between the α- and β-chains. The same partition coefficient was found to hold for different pH, buffer, and allosteric effector conditions. The lack of any pH dependence of the partition coefficient was confirmed by the absence of proton changes for the replacement reaction. The temperature dependence of the partition coefficient and calorimetric results yield a value for the enthalpy of the reaction of -3.65 ± 0.29 kcal/mol/heme.
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  • 82
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    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 1763-1780 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We demonstrate that the isotropic absorption and linear dichroism in an unknown flow field can be used to determine base tilt in polynucleotides if three transitions are measured and the directions of the corresponding dipoles are known. The method is applied here to reach conclusions about the base tilt in poly(rA), poly(rA)+·poly(rA), and poly(rC). The respective values are: 28° tilt about the axis + 50° toward C8 from the C1′ → N9, and 25° tilt about the axis + 118° toward C5 from C1′ → N1. The results for poly(rA)+·poly(rA) are consistent with the accepted model. Spectra were measured for poly(rC)+·poly(rC), but definite conclusions must await reliable directions for transition dipoles. The dipole direction for the 218-nm transition in rC is found to be +13° or +43° toward C5 from C1′ → N1. The CD spectra to about 168 nm are presented and discussed.
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  • 83
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    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 1811-1832 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements of stress relaxation in uniaxial extension and associated time-dependent birefringence have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 13-22% fibrin plasticized with either aqueous buffer or glycerol. Both unligated and ligated (i.e., with α-α and γ-γ ligation by fibrinoligase, factor XIIIa) films were studied. Both types showed two stages of stress relaxation, with time scales of approximately 10 and 103-104 s, respectively, with a plateau region between. In the plateau, the nominal (engineering) stress for ligated glycerol-plasticized film is proportional to In λ, where λ is the stretch ratio, up to λ ≅ 2, and it decreases with increasing temperature. For unligated glycerol-plasticized film, the stresses are smaller by a factor of one-half to one-third. For ligated film, the second stage of relaxation is relatively slight, and recovery after release of stress is often nearly complete. For unligated film, the second stage involves a substantial drop in stress, and after recovery there is a significant permanent set. A second relaxation for ligated film reproduces the first, but for unligated film it reproduces the first only if the initial relaxation is terminated before the second stage; otherwise, the second relaxation shows a weaker structure. The behavior of water-plasticized film is similar to that of glycerol-plasticized except that the second stage of relaxation occurs at shorter times. During the first stage of stress relaxation, up to about 100 s, the birefringence and the stress-optical coefficient increase; during the plateau zone of stress relaxation, the birefringence of ligated films is approximately constant and is proportional to 2λ2/(λ2 + 1) - 1, where λ is the stretch ratio. This dependence is predicted by a two-dimensional model in which rodlike elements in the plane of the film are oriented with independent alignment. During the final stage of stress relaxation, the birefringence of ligated films decreases slightly; that of unligated films decreases substantially, but less rapidly than the stress, corresponding to a further increase in the stress-optical coefficient. With additional information from small-angle x-ray scattering reported in an accompanying paper, the first stage of relaxation is attributed to partial release of bending forces in the fibers by orientation, accompanied by increased birefringence. The second stage is attributed, for ligated films, to an internal transition in the fibrin units accompanied by elongation of some of the fibers; and in the unligated films, to a combination of the latter transition with slippage of protofibrils lengthwise within the fiber bundles that causes some loss of orientation, which diminishes the birefringence.
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  • 84
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    Biopolymers 21 (1982), S. 1899-1908 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A microscope capable of measuring the CD of intact single eukaryotic cells, DNA microcrystals, and other microscopic structures has been constructed and tested. It can measure the CD spectra in the 200- and 800-nm wavelength range and consists of a modification to a standard Cary 60 CD machine in combination with a Zeiss uv microspectrometer. Preliminary CD spectra of red blood cells and lymphocytes are presented.
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  • 85
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    Biopolymers 21 (1982), S. 1909-1926 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of fibers in agarose gels has been studied by electron-microscopic examination of replicas formed from freeze-fracture surfaces. For gels set in water, the results obtained support the model proposed for the gel structure by Arnott et al. (1974) of a random array of long, straight, connected fibers, with each fiber having a diameter equivalent to that of an aggregate of approximately 10-30 agarose helixes, depending on the initial agarose concentration. The density of these fibers, their water content, and the total length of fibers per unit volume have been derived from the measured distribution of intersections per unit area of freeze-fracture surfaces. For gels set in the presence of salt, the distribution of fibers becomes distinctly non-Poissonian, leading to larger interfiber spaces and a gel of greater effective pore size. The larger pore size of gels set in the presence of salt also has been revealed by electrophoretic measurements in which the relative migration rates of plasmid DNA molecules of varying conformations have been determined.
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  • 86
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    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 1933-1943 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Energy embedding has been shown recently to be a useful extension of the distance geometry approach to conformational calculations in the case of very small molecules and simple energy functions. This paper tests the ability of energy embedding to locate low energy conformations satisfying both weak and strong geometric constraints when the molecule is the small protein, bovine pancreatic trypsin inhibitor, and the energy function is the complicated Oobatake-Crippen residue-residue potential. Using the potential function alone, the algorithm reaches a structure with energy lower than that of the native conformation, but with little resemblance to it. Aided by numerous geometric constraints, such as preformed secondary structure segments, the algorithm again finds a local minimum with energy better than that of the native, and with only 3.3 Å rms deviation from it. This is significantly closer to the native value than can be obtained using standard distance geometry and the geometric constraints alone. Thus, energy embedding using the Oobatake-Crippen potential function is a significant help in finding native conformations of proteins. However, additional trials on a hairpin bend fragment of trypsin inhibitor demonstrate the potential's shortcomings in encouraging proper secondary structure.
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  • 87
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model-built Arnott B-DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x-ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 2179-2185].We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′-O3′-P-O5′ (ω) torsion angles to change from gauche- to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double-helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche- to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base-base hydrogen-bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.
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  • 88
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The microwave absorption of aqueous solutions of DNA extracted from E. coli has been studied between 8 and 12 GHz by the use of an optical heterodyne technique. By measuring optically the temperature rise produced in an absorbing sample by pulsed microwave radiation, unambiguous, direct measurement of the microwave absorption is possible. Our results show that E. coli DNA absorbs microwaves in the 8-12-GHz region substantially more efficiently than water, which is itself an extremely efficient absorber. The observed absorption is featureless and decreases slightly with increasing frequency. These observations are consistent with an explanation involving direct absorption by longitudinal acoustic modes of the double helix.
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  • 89
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    Biopolymers 21 (1982), S. 251-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formation of polyelectrolyte complexes of glycol chitosan (GlChi) with sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) has been studied. The number of ionizable groups per pyranose ring and the degree of dissociation as a function of pH in the polycation and polyanions have been determined using conductometric and potentiometric titrations. The formation of the complexes at different pH values has been followed by turbidity measurements. It is found that stoichiometric complexes of the polycation with CMC, (GalUA)n, and AlgA are formed at a mixing ratio of 0.5, indicating that the conformation may correspond to chains of equal lengths. In the case of the complex of GlChi with DS, the stoichiometric composition corresponds to a mixing ratio of 0.62. Thin transparent films of the complexes have been obtained by dehydration under reduced pressure on a layer of mercury. The dielectric constant ε′ and loss ε″ of thin films of these complexes have been measured in the range of frequencies of 1-100 kHz at different temperatures above and below room temperature. The GlChi-DS complex shows very little change in the values of ε′ and ε″ with frequency or temperature. On the other hand, films of GlChi-CMC and GlChi-(GalUA)n complexes show a significant increase in ε′ and ε″ as the temperature is increased above room temperature. The increase is more prominent at low frequencies. This behavior is attributed to the Maxwell-Wagner interfacial polarization. In the case of GlChi-AlgA film, the values of ε′ and ε″ increase enormously as the temperature increases. This behavior is similar to the increase in ε′ and ε″ observed by Michels et al. [(1965) J. Phys. Chem. 69, 1456-1465] as the salt concentration increases in another polyelectrolyte complex studied by them. The electric double-layer mechanism proposed by Schwarz [(1962) J. Phys. Chem. 66, 2636-2642] to account for the dielectric properties of biocolloids is shown to account quantitatively for the observations on the GlChi-AlgA film.
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  • 90
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    Chemie in unserer Zeit 16 (1982) 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 91
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    Chemie in unserer Zeit 16 (1982), S. 35-45 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 16 Ill.
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  • 92
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    Chemie in unserer Zeit 16 (1982), S. 69-70 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 93
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    Chemie in unserer Zeit 16 (1982), S. 94-100 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 7 Ill.
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  • 94
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    Chemie in unserer Zeit 16 (1982), S. A32 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 95
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    Chemie in unserer Zeit 16 (1982), S. 116-123 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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  • 96
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    Chemie in unserer Zeit 16 (1982), S. A46 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 97
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    Chemie in unserer Zeit 16 (1982), S. 149-159 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 7 Ill.
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  • 98
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    Biopolymers 21 (1982), S. 117-129 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A melting experiment was performed on the whole set of populations of the replicative form of φX174 DNA, which can be obtained treating this DNA with rat liver nicking-closing enzyme in the presence of ethidium bromide. Gel electrophoresis performed by loading the DNA samples at neutral and alkaline pH allows separation of these populations in discrete sets of bands, which can then be compared. The outcome of the experiments indicates that in the range of electrophoretic mobilities which can be explored, no band is formed exclusively by circular complementary strands which can be separated by alkaline denaturation. These results are compared with what would be expected if double-stranded closed circular DNA had structures other than the canonical double helix. Under nonrestrictive hypotheses, the experiments reported allow one to obtain a minimum estimate of the absolute value of the linking number of a closed circular double-stranded DNA: for native φX174 RF DNA, the linking number appears to be greater than 12 (in absolute value). Some data on the electrophoretic mobility of denatured closed circular duplexes are reported, which still wait for a physicochemical interpretation.
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  • 99
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    Biopolymers 21 (1982), S. 169-179 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthetic cyclic octapeptides of general structure cyclo[Glu(γOBzl)-Sar-Gly-(N-R)Gly]2 (R = n-hexyl and cyclohexyl) transport calcium ions selectively across organic phases and phospholipid membranes. We have now used proton nmr spectroscopy (360 MHz) to study the solution conformation(s) of their calcium complexes. When Ca(ClO4)2 was added to solutions of these peptides in CDCl3, nmr spectra of the resulting calcium complexes were characteristic of a single C2-symmetric conformer. From a Karplus-Bystrov analysis of vicinal coupling constants in both the peptide backbone and Glu side chain (treated as an ABCC′MX spin system), in conjuction with model-building studies, a structure was proposed in which the calcium ion is bound in an octahedral-type complex by the four (coplanar) carbonyl groups of the (all-trans) Glu-Sar and Gly-(N-R)Gly peptide bonds. Occurrence of preferred rotamers about Glu side chain Cα-Cβ bonds indicated that restricted rotation in peptide side chains arises upon calcium binding.
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  • 100
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    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 25-42 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (L-Cys)n + N-base systems and (L-Cys)n + (L-Lys)n systems were studied by ir spectroscopy. It is shown that in the water-free systems, SH⃛N ⇌ S-⃛H+N hydrogen bonds are formed. With the (L-Cys)n + N-base systems, both proton-limiting structures in the SH⃛N ⇌ S-⃛H+N bonds have equal weight when the pKa of the protonated N-base is 2 pKa units larger than that of (L-Cys)n. The same is true with the water-free (L-Cys)n + (L-Lys)n system. Thus, with regard to the type of proton potentials present, these hydrogen bonds are proton-transfer hydrogen bonds showing very large proton polarizabilities. This is confirmed by the occurrence of continua in the ir spectra. Small amounts of water open these hydrogen bonds and increase the transfer of the proton to (L-Lys)n. In the (L-Lys)n + N-base systems, with increasing proton transfer the backbone of (L-Cys)n changes from antiparallel β-structure to coil. In (L-Cys)n + (L-Lys)n, the conformation is determined by the (L-Lys)n conformation and changes depending on the chain length of (L-Lys)n. Finally, the reactivity increase in the active center of fatty acid synthetase, which should be caused by the shift of a proton, is discussed on the basis of the great proton polarizability of the cysteine-lysine hydrogen bonds.
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