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  • 2005-2009  (51)
  • 1995-1999  (1,274)
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  • 1
    facet.materialart.
    Unknown
    Publication Date: 2019-10-24
    Keywords: ddc:000
    Language: German
    Type: annualzib , doc-type:report
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  • 2
    Publication Date: 2014-02-26
    Description: We propose a variant of the control reduced interior point method for the solution of state constrained problems. We show convergence of the corresponding interior point pathfollowing algorithm in function space. Morever, we provide error bounds for the iterates.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 3
    Publication Date: 2014-02-26
    Description: This paper aims at presenting the complex coupled network of the human menstrual cycle to the interested community. Beyond the presently popular smaller models, where important network components arise only as extremely simplified source terms, we add: the GnRH pulse generator in the hypothalamus, receptor binding, and the biosynthesis in the ovaries. Simulation and parameter identification are left to a forthcoming paper.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 4
    Publication Date: 2014-02-26
    Description: This work explores two applications of a classical result on the continuity of Nemyckii operators to optimal control with PDEs. First, we present an alternative approach to the analysis of Newton's method for function space problems involving semi-smooth Nemyckii operators. A concise proof for superlinear convergence is presented, and sharpened bounds on the rate of convergence are derived. Second, we derive second order sufficient conditions for problems, where the underlying PDE has poor regularity properties. We point out that the analytical structure in both topics is essentially the same.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 5
    Publication Date: 2014-02-26
    Description: In this paper, we study the efficiency of Nash equilibria for a sequence of nonatomic routing games. We assume that the games are played consecutively in time in an online fashion: by the time of playing game $i$, future games $i+1,\dots,n$ are not known, and, once players of game $i$ are in equilibrium, their corresponding strategies and costs remain fixed. Given a sequence of games, the cost for the sequence of Nash equilibria is defined as the sum of the cost of each game. We analyze the efficiency of a sequence of Nash equilibria in terms of competitive analysis arising in the online optimization field. Our main result states that the online algorithm $\sl {SeqNash}$ consisting of the sequence of Nash equilibria is $\frac{4n}{2+n}$-competitive for affine linear latency functions. For $n=1$, this result contains the bound on the price of anarchy of $\frac{4}{3}$ for affine linear latency functions of Roughgarden and Tardos [2002] as a special case. Furthermore, we analyze a problem variant with a modified cost function that reflects the total congestion cost, when all games have been played. In this case, we prove an upper bound of $\frac{4n}{2+n}$ on the competitive ratio of $\sl {SeqNash}$. We further prove a lower bound of $\frac{3n-2}{n}$ of $\sl {SeqNash}$ showing that for $n=2$ our upper bound is tight.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 6
    Publication Date: 2016-06-09
    Description: To approximate convolutions which occur in evolution equations with memory terms, a variable-stepsize algorithm is presented for which advancing $N$ steps requires only $O(N\log N)$ operations and $O(\log N)$ active memory, in place of $O(N^2)$ operations and $O(N)$ memory for a direct implementation. A basic feature of the fast algorithm is the reduction, via contour integral representations, to differential equations which are solved numerically with adaptive step sizes. Rather than the kernel itself, its Laplace transform is used in the algorithm. The algorithm is illustrated on three examples: a blow-up example originating from a Schrödinger equation with concentrated nonlinearity, chemical reactions with inhibited diffusion, and viscoelasticity with a fractional order constitutive law.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 7
    Publication Date: 2020-11-13
    Description: This paper deals with MIP-based primal heuristics to be used within a branch-and-cut approach for solving multi-layer telecommunication network design problems. Based on a mixed-integer programming formulation for two network layers, we present three heuristics for solving important subproblems, two of which solve a sub-MIP. On multi-layer planning instances with many parallel logical links, we show the effectiveness of our heuristics in finding good solutions early in the branch-and-cut search tree.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 8
    Publication Date: 2019-05-10
    Description: The dynamics of ventricular fibrillation caused by irregular excitation is simulated in the frame of the monodomain model with an action potential model due to Aliev-Panfilov for a human 3D geometry. The numerical solution of this multiscale reaction-diffusion problem is attacked by algorithms which are fully adaptive in both space and time (code library {\sc Kardos}). The obtained results clearly demonstrate an accurate resolution of the cardiac potential during the excitation and the plateau phases (in the regular cycle) as well as after a reentrant excitation (in the irregular cycle).
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 9
    Publication Date: 2020-12-15
    Description: The topic of this paper are integer programming models in which a subset of 0/1-variables encode a partitioning of a set of objects into disjoint subsets. Such models can be surprisingly hard to solve by branch-and-cut algorithms if the permutation of the subsets of the partition is irrelevant. This kind of symmetry unnecessarily blows up the branch-and-cut tree. We present a general tool, called orbitopal fixing, for enhancing the capabilities of branch-and-cut algorithms in solving this kind of symmetric integer programming models. We devise a linear time algorithm that, applied at each node of the branch-and-cut tree, removes redundant parts of the tree produced by the above mentioned permutations. The method relies on certain polyhedra, called orbitopes, which have been investigated in (Kaibel and Pfetsch (2006)). However, it does not add inequalities to the model, and thus, it does not increase the difficulty of solving the linear programming relaxations. We demonstrate the computational power of orbitopal fixing at the example of a graph partitioning problem motivated from frequency planning in mobile telecommunication networks.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 10
    Publication Date: 2014-11-10
    Description: In this paper, we discuss the relation of unsplittable shortest path routing (USPR) to other routing schemes and study the approximability of three USPR network planning problems. Given a digraph $D=(V,A)$ and a set $K$ of directed commodities, an USPR is a set of flow paths $\Phi_{(s,t)}$, $(s,t)\in K$, such that there exists a metric $\lambda=(\lambda_a)\in \mathbb{Z}^A_+$ with respect to which each $\Phi_{(s,t)}$ is the unique shortest $(s,t)$-path. In the \textsc{Min-Con-USPR} problem, we seek for an USPR that minimizes the maximum congestion over all arcs. We show that this problem is hard to approximate within a factor of $\mathcal{O}(|V|^{1-\epsilon})$, but easily approximable within min$(|A|,|K|)$ in general and within $\mathcal{O}(1)$ if the underlying graph is an undirected cycle or a bidirected ring. We also construct examples where the minimum congestion that can be obtained by USPR is a factor of $\Omega(|V|^2)$ larger than that achievable by unsplittable flow routing or by shortest multi-path routing, and a factor of $\Omega(|V|)$ larger than by unsplittable source-invariant routing. In the CAP-USPR problem, we seek for a minimum cost installation of integer arc capacities that admit an USPR of the given commodities. We prove that this problem is $\mathcal{NP}$-hard to approximate within $2-\epsilon$ (even in the undirected case), and we devise approximation algorithms for various special cases. The fixed charge network design problem \textsc{Cap-USPR}, where the task is to find a minimum cost subgraph of $D$ whose fixed arc capacities admit an USPR of the commodities, is shown to be $\mathcal{NPO}$-complete. All three problems are of great practical interest in the planning of telecommunication networks that are based on shortest path routing protocols. Our results indicate that they are harder than the corresponding unsplittable flow or shortest multi-path routing problems.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 11
    Publication Date: 2014-11-11
    Description: In this paper, we investigate the connection availabilities for the new protection scheme Demand-wise Shared Protection (DSP) and describe an appropriate approach for their computation. The exemplary case study on two realistic network scenarios shows that in most cases the availabilities for DSP are comparable with that for 1+1 path protection and better than in case of shared path protection.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 12
    Publication Date: 2016-06-30
    Description: THESEUS, the ZIB threading environment, is a parallel implementation of a protein threading based on a multi-queued branch-and-bound optimal search algorithm to find the best sequence-to-structure alignment through a library of template structures. THESEUS uses a template core model based on secondary structure definition and a scoring function based on knowledge-based potentials reflecting pairwise interactions and the chemical environment, as well as pseudo energies for homology detection, loop alignment, and secondary structure matching. The threading core is implemented in C++ as a SPMD parallization architecture using MPI for communication. The environment is designed for generic testing of different scoring functions, e.g. different secondary structure prediction terms, different scoring matrices and information derived from multiple sequence alignments. A validaton of the structure prediction results has been done on the basis of standard threading benchmark sets. THESEUS successfully participated in the 6th Critical Assessment of Techniques for Protein Structure Prediction (CASP) 2004.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 13
    Publication Date: 2014-02-26
    Description: We consider a multi-queue multi-server system with $n$ servers (processors) and $m$ queues. At the system there arrives a stationary and ergodic stream of $m$ different types of requests with service requirements which are served according to the following $k$-limited head of the line processor sharing discipline: The first $k$ requests at the head of the $m$ queues are served in processor sharing by the $n$ processors, where each request may receive at most the capacity of one processor. By means of sample path analysis and Loynes' monotonicity method, a stationary and ergodic state process is constructed, and a necessary as well as a sufficient condition for the stability of the $m$ separate queues are given, which are tight within the class of all stationary ergodic inputs. These conditions lead to tight necessary and sufficient conditions for the whole system, also in case of permanent customers, generalizing an earlier result by the authors for the case of $n$=$k$=1.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 14
    Publication Date: 2014-02-26
    Description: In order to compute the thermodynamic weights of the different metastable conformations of a molecule, we want to approximate the molecule's Boltzmann distribution in a reasonable time. This is an essential issue in computational drug design. The energy landscape of active biomolecules is generally very rough with a lot of high barriers and low regions. Many of the algorithms that perform such samplings (e.g. the hybrid Monte Carlo method) have difficulties with such landscapes. They are trapped in low-energy regions for a very long time and cannot overcome high barriers. Moving from one low-energy region to another is a very rare event. For these reasons, the distribution of the generated sampling points converges very slowly against the thermodynamically correct distribution of the molecule. The idea of ConfJump is to use $a~priori$ knowledge of the localization of low-energy regions to enhance the sampling with artificial jumps between these low-energy regions. The artificial jumps are combined with the hybrid Monte Carlo method. This allows the computation of some dynamical properties of the molecule. In ConfJump, the detailed balance condition is satisfied and the mathematically correct molecular distribution is sampled.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 15
    Publication Date: 2020-02-11
    Description: "`Volkssport Sudoku"' titelt der Stern in seiner Ausgabe vom 24. Mai2006. In der Tat traut sich derzeit kaum noch eine Zeitung, ohne Sudoku zu erscheinen. Die Begeisterung am Lösen dieser Zahlenrätsel offenbart eine unvermutete Freude am algorithmischen Arbeiten. Mathematisch kann man Sudokus als lineare diophantische Gleichungssysteme mit Nichtnegativitätsbedingungen formulieren. Solche ganzzahligen linearen Programme sind die wichtigsten Modellierungswerkzeuge in zahlreichen Anwendungsgebieten wie z.B. der Optimierung von Telekommunikations- und Verkehrsnetzen. Moderne Verfahren zur Lösung dieser Optimierungsprobleme sind durch Sudokus allerdings deutlich weniger zu beeindrucken als Zeitungsleser.
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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  • 16
    Publication Date: 2020-02-11
    Description: This article surveys mathematical models and methods used for physical PCB layout, i.e., component placement and wire routing. The main concepts are briefly described together with relevant references.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 17
    Publication Date: 2020-12-15
    Description: We study online multicommodity minimum cost routing problems in networks, where commodities have to be routed sequentially. Arcs are equipped with load dependent price functions defining the routing weights. We discuss an online algorithm that routes each commodity by minimizing a convex cost function that depends on the demands that are previously routed. We present a competitive analysis of this algorithm showing that for affine linear price functions this algorithm is $4K/2+K$-competitive, where $K$ is the number of commodities. For the parallel arc case this algorithm is optimal. Without restrictions on the price functions and network, no algorithm is competitive. Finally, we investigate a variant in which the demands have to be routed unsplittably.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 18
    Publication Date: 2021-03-16
    Description: Perfect graphs constitute a well-studied graph class with a rich structure, reflected by many characterizations w.r.t different concepts. Perfect graphs are, e.g., characterized as precisely those graphs $G$ where the stable set polytope STAB$(G)$ coincides with the clique constraint stable set polytope QSTAB$(G)$. For all imperfect graphs STAB$(G) \subset$ QSTAB$(G)$ holds and, therefore, it is natural to measure imperfection in terms of the difference between STAB$(G)$ and QSTAB$(G)$. Several concepts have been developed in this direction, for instance the dilation ratio of STAB$(G)$ and QSTAB$(G)$ which is equivalent to the imperfection ratio imp$(G)$ of $G$. To determine imp$(G)$, both knowledge on the facets of STAB$(G)$ and the extreme points of QSTAB$(G)$ is required. The anti-blocking theory of polyhedra yields all {\em dominating} extreme points of QSTAB$(G)$, provided a complete description of the facets of STAB$(\overline G)$ is known. As this is typically not the case, we extend the result on anti-blocking polyhedra to a {\em complete} characterization of the extreme points of QSTAB$(G)$ by establishing a 1-1 correspondence to the facet-defining subgraphs of $\overline G$. We discuss several consequences, in particular, we give alternative proofs of several famous results.
    Keywords: ddc:000
    Language: English
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  • 19
    Publication Date: 2014-11-10
    Description: We give experimental and theoretical results on the problem of computing the treewidth of a graph by exact exponential time algorithms using exponential space or using only polynomial space. We first report on an implementation of a dynamic programming algorithm for computing the treewidth of a graph with running time $O^\ast(2^n)$. This algorithm is based on the old dynamic programming method introduced by Held and Karp for the {\sc Tra veling Salesman} problem. We use some optimizations that do not affect the worst case running time but improve on the running time on actual instances and can be seen to be practical for small instances. However, our experiments show that the space use d by the algorithm is an important factor to what input sizes the algorithm is effective. For this purpose, we settle the problem of computing treewidth under the restriction that the space used is only polynomial. In this direction we give a simple $O^\ast(4^n)$ al gorithm that requires {\em polynomial} space. We also show that with a more complicated algorithm, using balanced separators, {\sc Treewidth} can be computed in $O^\ast(2.9512^n)$ time and polynomial space.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 20
    Publication Date: 2014-03-10
    Description: The dynamic behavior of molecules can often be described by Markov processes. From computational molecular simulations one can derive transition rates or transition probabilities between subsets of the discretized conformational space. On the basis of this dynamic information, the spatial subsets are combined into a small number of so-called metastable molecular conformations. This is done by clustering methods like the Robust Perron Cluster Analysis (PCCA+). Up to now it is an open question how this coarse graining in space can be transformed to a coarse graining of the Markov chain while preserving the essential dynamic information. In the following article we aim at a consistent coarse graining of transition probabilities or rates on the basis of metastable conformations such that important physical and mathematical relations are preserved. This approach is new because PCCA+ computes molecular conformations as linear combinations of the dominant eigenvectors of the transition matrix which does not hold for other clustering methods.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 21
    Publication Date: 2014-02-26
    Description: Das deutschsprachige Bibliothekswesen verfügt mit den \glqq Regeln für den Schlagwortkatalog \grqq (RSWK) unter Verwendung der \glqq Schlagwortnormdatei \grqq (SWD) über ein Instrumentarium, welches zusammen mit einem \glqq Faceted Browsing \grqq das bisher bestehende Angebot für ein Information Retrieval optimal ergänzen kann. Die Verbindung zwischen Standardvokabular (SWD) und Kettenbildung (RSWK) einerseits und eine nach Facetten-Eigenschaften gegliederte Navigation andererseits unterstützt bestmöglich eine inhaltlich bezogene Recherche. Die Stärken und Schwächen der RSWK/SWD werden erörtert und auch Klassifikationen (DDC und RVK) als mögliche Facetten diskutiert.
    Keywords: ddc:000
    Language: German
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  • 22
    Publication Date: 2016-06-09
    Keywords: ddc:000
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 23
    Publication Date: 2022-03-14
    Description: A lot of problems arising in Combinatorial Optimization and Operations Research can be formulated as Mixed Integer Programs (MIP). Although MIP-solving is an NP-hard optimization problem, many practically relevant instances can be solved in reasonable time. In modern MIP-solvers like the branch-cut-and-price-framework SCIP, primal heuristics play a major role in finding and improving feasible solutions at the early steps of the solution process. This helps to reduce the overall computational effort, guides the remaining search process, and proves the feasibility of the MIP model. Furthermore, a heuristic solution with a small gap to optimality often is sufficient in practice. We investigate 16 different heuristics, all of which are available in SCIP. Four of them arise from the literature of the last decade, nine are specific implementations of general heuristic ideas, three have been newly developed. We present an improved version of the feasibility pump heuristic by Fischetti et al., which in experiments produced solutions with only a third of the optimality gap compared to the original version. Furthermore, we introduce two new Large Neighborhood Search (LNS) heuristics. Crossover is an LNS improvement heuristic making use of similarities of diverse MIP solutions to generate new incumbent solutions. RENS is an LNS rounding heuristic which evaluates the space of all possible roundings of a fractional LP-solution. This heuristic makes it possible to determine whether a point can be rounded to an integer solution and which is the best possible rounding. We conclude with a computational comparison of all described heuristics. It points out that a single heuristic on its own has only a slight impact on the overall performance of SCIP, but the combination of all of them reduces the running time by a factor of two compared to a version without any heuristics.
    Keywords: ddc:000
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 24
    Publication Date: 2014-02-26
    Description: We present a finite volume method for the solution of the two-dimensional Poisson equation $ \nabla\cdot( \beta( {\mbox{\boldmath $x$}}) \nabla u({\mbox{\boldmath $x$}})) = f(\mbox{\boldmath $x$}) $ with variable, discontinuous coefficients and solution discontinuities on irregular domains. The method uses bilinear ansatz functions on Cartesian grids for the solution $u({\mbox{\boldmath $x$})$ resulting in a compact nine-point stencil. The resulting linear problem has been solved with a standard multigrid solver. Singularities associated with vanishing partial volumes of intersected grid cells or the dual bilinear ansatz itself are removed by a two-step asymptotic approach. The method achieves second order of accuracy in the $L^\infty$ and $L^2$ norm.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 25
    Publication Date: 2014-11-11
    Description: In this article we aim at an efficient sampling of the stationary distribution of dynamical systems in the presence of metastabilities. In the past decade many sophisticated algorithms have been inven ted in this field. We do not want to simply add a further one. We address the problem that one has applied a sampling algorithm for a dynamical system many times. This leads to different samplings which more or less represent the stationary distribution partially very well, but which are still far away from ergodicity or from the global stationary distribution. We will show how these samplings can be joined together in order to get one global sampling of the stationary distribution.
    Keywords: ddc:000
    Language: English
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  • 26
    Publication Date: 2014-02-26
    Description: The concept of jump system, introduced by Buchet and Cunningham (1995), is a set of integer points with a certain exchange property. In this paper, we discuss several linear and convex optimization problems on jump systems and show that these problems can be solved in polynomial time under the assumption that a membership oracle for a jump system is available. We firstly present a polynomial-time implementation of the greedy algorithm for the minimization of a linear function. We then consider the minimization of a separable-convex function on a jump system, and propose the first polynomial-time algorithm for this problem. The algorithm is based on the domain reduction approach developed in Shioura (1998). We finally consider the concept of M-convex functions on constant-parity jump systems which has been recently proposed by Murota (2006). It is shown that the minimization of an M-convex function can be solved in polynomial time by the domain reduction approach.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 27
    Publication Date: 2020-12-15
    Description: We introduce orbitopes as the convex hulls of 0/1-matrices that are lexicographically maximal subject to a group acting on the columns. Special cases are packing and partitioning orbitopes, which arise from restrictions to matrices with at most or exactly one 1-entry in each row, respectively. The goal of investigating these polytopes is to gain insight into ways of breaking certain symmetries in integer programs by adding constraints, e.g., for a well-known formulation of the graph coloring problem. We provide a thorough polyhedral investigation of packing and partitioning orbitopes for the cases in which the group acting on the columns is the cyclic group or the symmetric group. Our main results are complete linear inequality descriptions of these polytopes by facet-defining inequalities. For the cyclic group case, the descriptions turn out to be totally unimodular, while for the symmetric group case, both the description and the proof are more involved. The associated separation problems can be solved in linear time.
    Keywords: ddc:000
    Language: English
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  • 28
    Publication Date: 2014-11-21
    Description: The standard computational methods for computing the optimal value functions of Markov Decision Problems (MDP) require the exploration of the entire state space. This is practically infeasible for applications with huge numbers of states as they arise, e.\,g., from modeling the decisions in online optimization problems by MDPs. Exploiting column generation techniques, we propose and apply an LP-based method to determine an $\varepsilon$-approximation of the optimal value function at a given state by inspecting only states in a small neighborhood. In the context of online optimization problems, we use these methods in order to evaluate the quality of concrete policies with respect to given initial states. Moreover, the tools can also be used to obtain evidence of the impact of single decisions. This way, they can be utilized in the design of policies.
    Keywords: ddc:000
    Language: English
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  • 29
    Publication Date: 2014-11-21
    Description: Wir beschäftigen uns mit dem Problem der Betriebsplanung von Laserschweißrobotern im Karosseriebau. Gegeben ist eine Menge von Schweißnähten, die innerhalb einer Fertigungszelle an einem Karosserieteil gefertigt werden müssen. Die Schweißnähte werden durch mehrere parallel betriebene Roboter bearbeitet. Die Aufgabe besteht darin, für jeden Roboter eine Reihenfolge und eine zeitliche Koordinierung seiner Bewegungen zu finden, so dass alle Schweißnähte innerhalb der Taktzeit der Fertigungszelle bearbeitet werden und so wenig Laserquellen wie möglich eingesetzt werden. Dabei müssen einige Nebenbedingungen berücksichtigt werden. Für dieses spezielle Schweißproblem haben wir eine Formulierung als gemischt-ganzzahliges lineares Programm entwickelt, welches sich für die untersuchten praktischen Fälle sehr schnell lösen lässt.
    Keywords: ddc:000
    Language: German
    Type: reportzib , doc-type:preprint
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  • 30
    Publication Date: 2021-08-05
    Description: Modern applications of mathematical programming must take into account a multitude of technical details, business demands, and legal requirements. Teaching the mathematical modeling of such issues and their interrelations requires real-world examples that are well beyond the toy sizes that can be tackled with the student editions of most commercial software packages. We present a new tool, which is freely available for academic use including complete source code. It consists of an algebraic modeling language and a linear mixed integer programming solver. The performance and features of the tool are in the range of current state-of-the-art commercial tools, though not in all aspects as good as the best ones. Our tool does allow the execution and analysis of large real-world instances in the classroom and can therefore enhance the teaching of problem solving issues. Teaching experience has been gathered and practical usability was tested in classes at several universities and a two week intensive block course at TU Berlin. The feedback from students and teachers has been very positive.
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    Language: English
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  • 31
    Publication Date: 2014-11-21
    Description: The Bottleneck Shortest Path Problem is a basic problem in network optimization. The goal is to determine the limiting capacity of any path between two specified vertices of the network. This is equivalent to determining the unsplittable maximum flow between the two vertices. In this note we analyze the complexity of the problem, its relation to the Shortest Path Problem, and the impact of the underlying machine/computation model.
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    Language: English
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  • 32
    Publication Date: 2014-02-26
    Description: We introduce a new and rich class of graph coloring manifolds via the Hom complex construction of Lov\´{a}sz. The class comprises examples of Stiefel manifolds, series of spheres and products of spheres, cubical surfaces, as well as examples of Seifert manifolds. Asymptotically, graph coloring manifolds provide examples of highly connected, highly symmetric manifolds.
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  • 33
    Publication Date: 2014-02-26
    Description: We give coordinate-minimal geometric realizations in general position for 17 of the 20 vertex-minimal triangulations of the orientable surface of genus 3 in the 5x5x5-cube.
    Keywords: ddc:000
    Language: English
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  • 34
    Publication Date: 2014-02-26
    Description: Biochemical interactions are determined by the 3D-structure of the involved components - thus the identification of conformations is a key for many applications in rational drug design. {\sf ConFlow} is a new multilevel approach to conformational analysis with main focus on completeness in investigation of conformational space. In contrast to known conformational analysis, the starting point for design is a space-based description of conformational areas. A tight integration of sampling and analysis leads to an identification of conformational areas simultaneously during sampling. An incremental decomposition of high-dimensional conformational space is used to guide the analysis. A new concept for the description of conformations and their path connected components based on convex hulls and {\em Hypercubes}is developed. The first results of the {\sf ConFlow} application constitute a 'proof of concept' and are further more highly encouraging. In comparison to conventional industrial applications, {\sf ConFlow} achieves higher accuracy and a specified degree of completeness with comparable effort.
    Keywords: ddc:000
    Language: English
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  • 35
    Publication Date: 2014-02-26
    Description: We consider linear inverse problems where the solution is assumed to fulfill some general homogeneous convex constraint. We develop an algorithm that amounts to a projected Landweber iteration and that provides and iterative approach to the solution of this inverse problem. For relatively moderate assumptions on the constraint we can always prove weak convergence of the iterative scheme. In certain cases, i.e. for special families of convex constraints, weak convergence implies norm convergence. The presented approach covers a wide range of problems, e.g. Besov- or BV-restoration for which we present also numerical experiments in the context of image processing.
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    Language: English
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  • 36
    Publication Date: 2014-03-10
    Description: Whenever the invariant stationary density of metastable dynamical systems decomposes into almost invariant partial densities, its computation as eigenvector of some transition probability matrix is an ill-conditioned problem. In order to avoid this computational difficulty, we suggest to apply an aggregation/disaggregation method which only addresses wellconditioned sub-problems and thus results in a stable algorithm. In contrast to existing methods, the aggregation step is done via a sampling algorithm which covers only small patches of the sampling space. Finally, the theoretical analysis is illustrated by two biomolecular examples.
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    Language: English
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  • 37
    Publication Date: 2016-02-29
    Description: \noindent We give a partial description of the $(s,t)-p$-path polytope of a directed graph $D$ which is the convex hull of the incidence vectors of simple directed $(s,t)$-paths in $D$ of length $p$. First, we point out how the $(s,t)-p$-path polytope is located in the family of path and cycle polyhedra. Next, we give some classes of valid inequalities which are very similar to inequalities which are valid for the $p$-cycle polytope, that is, the convex hull of the incidence vectors of simple cycles of length $p$ in $D$. We give necessary and sufficient conditions for these inequalities to be facet defining. Furthermore, we consider a class of inequalities that has been identifie d to be valid for $(s,t)$-paths of cardinality at most $p$. Finally, we transfer the results to related polytopes, in particular, the undirected counterpart of the $(s,t)-p$-path polytope.
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    Language: English
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  • 38
    Publication Date: 2020-11-13
    Description: The numerical integration of dynamical contact problems often leads to instabilities at contact boundaries caused by the non-penetration condition between bodies in contact. Even a recent energy dissipative modification due to Kane et al. (1999), which discretizes the non-penetration constraints implicitly, is not able to circumvent artificial oscillations. For this reason, the present paper suggests a contact stabilization which avoids artificial oscillations at contact interfaces and is also energy dissipative. The key idea of this contact stabilization is an additional $L^2$-projection at contact interfaces, which can easily be added to any existing time integration scheme. In case of a lumped mass matrix, this projection can be carried out completely locally, thus creating only negligible additional numerical cost. For the new scheme, an elementary analysis is given, which is confirmed by numerical findings in an illustrative test example (Hertzian two body contact).
    Keywords: ddc:000
    Language: English
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  • 39
    Publication Date: 2016-06-30
    Keywords: ddc:000
    Language: German
    Type: masterthesis , doc-type:masterThesis
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  • 40
    Publication Date: 2014-02-26
    Description: We discuss different approaches for the enumeration of triangulated surfaces. In particular, we enumerate all triangulated surfaces with 9 and 10 vertices. We also show how geometric realizations of orientable surfaces with few vertices can be obtained by choosing coordinates randomly.
    Keywords: ddc:000
    Language: English
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  • 41
    Publication Date: 2014-02-26
    Description: The concept of L##-convexity is introduced by Fujishige--Murota (2000) as a discrete convexity for functions defined over the integer lattice. The main aim of this note is to understand the difference of the two algorithms for L##-convex function minimization: Murota's steepest descent algorithm (2003) and Kolmogorov's primal algorithm (2005).
    Keywords: ddc:000
    Language: English
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  • 42
    Publication Date: 2014-02-26
    Description: In this survey on combinatorial properties of triangulated manifolds we discuss various lower bounds on the number of vertices of simplicial and combinatorial manifolds. Moreover, we give a list of all known examples of vertex-minimal triangulations.
    Keywords: ddc:000
    Language: English
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  • 43
    Publication Date: 2020-02-11
    Description: This paper concerns the problem of operating a landside container exchange area that is serviced by multiple semi-automated rail mounted gantry cranes (RMGs) that are moving on a single bi-directional traveling lane. Such a facility is being built by Patrick Corporation at the Port Botany terminal in Sydney. The gantry cranes are a scarce resource and handle the bulk of container movements. Thus, they require a sophisticated analysis to achieve near optimal utilization. We present a three stage algorithm to manage the container exchange facility, including the scheduling of cranes, the control of associated short-term container stacking, and the allocation of delivery locations for trucks and other container transporters. The key components of our approach are a time scale decomposition, whereby an integer program controls decisions across a long time horizon to produce a balanced plan that is fed to a series of short time scale online subproblems, and a highly efficient space-time divisioning of short term storage areas. A computational evaluation shows that our heuristic can find effective solutions for the planning problem; on real-world data it yields a solution at most~8\% above a lower bound on optimal RMG utilization.
    Keywords: ddc:000
    Language: English
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  • 44
    Publication Date: 2014-02-26
    Description: We describe an algorithm for the enumeration of (candidates of) vertex-transitive combinatorial $d$-manifolds. With an implementation of our algorithm, we determine, up to combinatorial equivalence, all combinatorial manifolds with a vertex-transitive automorphism group on $n\leq 13$ vertices. With the exception of actions of groups of small order, the enumeration is extended to 14 and 15 vertices.
    Keywords: ddc:000
    Language: English
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  • 45
    Publication Date: 2014-02-26
    Description: We give coordinate-minimal geometric realizations in general position of all 865 vertex-minimal triangulations of the orientable surface of genus 2 in the 4x4x4-cube.
    Keywords: ddc:000
    Language: English
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  • 46
    Publication Date: 2014-02-26
    Description: We give a complete enumeration of combinatorial 3-manifolds with 10 vertices: There are precisely 247882 triangulated 3-spheres with 10 vertices as well as 518 vertex-minimal triangulations of the sphere product $S^2 x S^1$ and 615 triangulations of the twisted sphere product $S^2 \underline{x} S^1$. An analysis of the 3-spheres with up to 10 vertices shows that all these spheres are shellable, but that there are 29 vertex-minimal non-shellable 3-balls with 9 vertices.
    Keywords: ddc:000
    Language: English
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  • 47
    Publication Date: 2019-05-10
    Description: Adaptive numerical methods in time and space are introduced and studied for linear poroelastic models in two and three space dimensions. We present equivalent models for linear poroelasticity and choose both the {\em displacement--pressure} and the {\em stress--pressure} formulation for our computations. Their discretizations are provided by means of linearly implicit schemes in time and linear finite elements in space. Our concept of adaptivity opens a way to a fast and reliable simulation of different loading cases defined by corresponding boundary conditions. We present some examples using our code {\sf Kardos} and show that the method works efficiently. In particular, it could be used in the simulation of some bone healing models.
    Keywords: ddc:000
    Language: English
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  • 48
    Publication Date: 2016-06-30
    Description: During the last few years more and more functionalities of RNA have been discovered that were previously thought of being carried out by proteins alone. One of the most striking discoveries was the de tection of microRNAs, a class of noncoding RNAs that play an important role in post-transcriptional gene regulation. Large-scale analyses are needed for the still increasingly growing amount of sequen ce data derived from new experimental technologies. In this paper we present a framework for the detection of the distinctive precursor structure of microRNAS that is based on the well-known Smith-Wat erman algorithm and various filtering steps. We conducted experiments on real genomic data and we found several new putative hits for microRNA precursor structures.
    Keywords: ddc:000
    Language: English
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  • 49
    Publication Date: 2014-02-26
    Description: Wir erleben zu Beginn des aufkommenden Informationszeitalters mit dem Siegeszug von Google und anderen Internet-Technologien einen Wandel im Verhalten von Wissenschaftlern und Studenten, der mit dem Einsatz von {\sl Google Scholar} und {\sl Google Book Search} einen Paradigmenwechsel für Bibliotheken und Informationsversorger gleichkommt. Der Artikel untersucht die technischen Hintergründe für den Erfolg dieser besonderen Art des Information Retrievals: Fulltext Indexing und Citation Ranking als besondere Form des Information Minig. Er diskutiert Stärken und auch Schwächen des Google-Ansatzes. Der Autor stellt sich auch der Frage, unter welchen Bedingungen es möglich ist, ein zu {\sl Google Scholar} und der {\sl Google Book Search} konkurrenzfähiges Retrieval in der Landschaft der Bibliotheken und Bibliotheksverbünde zu entrichten. Die These ist, dass dieses unter Einsatz des {\sl Open Source} Indexierers {\sl Lucene} und des Web-Robots {\sl Nutch} möglich ist. Bibliotheken können durch gezielten Einsatz solcher Internet-Technologien dem Nutzer die Leistungen, welche Google uns mit seinen Tools im {\sl Visible Web} und mit Referenzen auf {\sl Citations} in der Welt der Literatur zur Verfügung stellt, in vergleichbarer Art auch für ihre eigenen durch Lizenzen geschützten digitalen Journale und ihre speziellen lokal verfügbaren Ressourcen, auf die Internet-Suchmaschinen keine Zugriff haben, anbieten. Es besteht die Hoffnung, dass Nutzer dann nicht - wie in einer kürzlichen Studie des OCLC konstatiert - überwiegend im Internet verbleiben, sondern bei ihrer Suche auch den Weg zu den Angeboten der örtlichen Bibliothek attraktiv finden.
    Keywords: ddc:000
    Language: German
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  • 50
    Publication Date: 2014-02-26
    Description: We consider a system where the arrivals form a Poisson process and the required service times of the requests are exponentially distributed. According to the generalized processor sharing discipline, each request in the system receives a fraction of the capacity of one processor which depends on the actual number of requests in the system. We derive systems of ordinary differential equations for the LST and for the moments of the conditional waiting time of a request with given required service time as well as a stable and fast recursive algorithm for the LST of the second moment of the conditional waiting time, which in particular yields the second moment of the unconditional waiting time. Moreover, asymptotically tight upper bounds for the moments of the conditional waiting time are given. The presented numerical results for the first two moments of the sojourn times in the $M/M/m-PS$ system show that the proposed algorithms work well.
    Keywords: ddc:000
    Language: English
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  • 51
    Publication Date: 2022-07-07
    Description: We present a domain decomposition approach for the computation of the electromagnetic field within periodic structures. We use a Schwarz method with transparent boundary conditions at the interfaces of the domains. Transparent boundary conditions are approximated by the perfectly matched layer method (PML). To cope with Wood anomalies appearing in periodic structures an adaptive strategy to determine optimal PML parameters is developed. We focus on the application to typical EUV lithography line masks. Light propagation within the multi-layer stack of the EUV mask is treated analytically. This results in a drastic reduction of the computational costs and allows for the simulation of next generation lithography masks on a standard personal computer.
    Keywords: ddc:000
    Language: English
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  • 52
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 204-216 
    ISSN: 0006-3592
    Keywords: expanded bed adsorption ; bakers' yeast ; G6PDH ; STREAMLINE ion exchange adsorbents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The use of expanded beds of STREAMLINE ion exchange adsorbents for the direct extraction of an intracellular enzyme glucose-6-phosphate dehydrogenase (G6PDH) from unclarified yeast cell homogenates has been investigated. It has been demonstrated that such crude feedstocks can be applied to the bed without prior clarification steps. The purification of G6PDH from an unclarified yeast homogenate was chosen as a model system containing the typical features of a direct extraction technique. Optimal conditions for the purification were determined in small scale, packed bed experiments conducted with clarified homogenates. Results from these experiments were used to develop a preparative scale separation of G6PDH in a STREAMLINE 50 EBA apparatus. The use of an on-line rotameter for measuring and controlling the height of the expanded bed when operated in highly turbid feedstocks was demonstrated. STREAMLINE DEAE has been shown to be successful in achieving isolation of G6PDH from an unclarified homogenate with a purification factor of 12 and yield of 98% in a single step process. This ion exchange adsorbent is readily cleaned using simple cleaning-in-place procedures without affecting either adsorption or the bed expansion properties of the adsorbent after many cycles of operation. The ability of combining clarification, capture, and purification in a single step will greatly simplify downstream processing flowsheets and reduce the costs of protein purification. © 1996 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 53
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 259-265 
    ISSN: 0006-3592
    Keywords: hepatocytes ; lactose-derivatized polystyrene ; polystyrene ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Hepatocytes isolated from male Fisher 344VF rats were cultured on two substrates, collagen I and a lactose-derivatized polystyrene (PS-lactose), to compare morphological and functional differences. Hepatocyte morphology changed dramatically depending upon the substrate, shown through actin cytoskeletal staining and scanning electron microscopy. Functional assays performed included albumin secretion, reduced glutathione content, UDP-glucuronosyl transferase, and cytochrome P4501A1 activity. The presence of dexamethasone and dimethylsulfoxide (DMSO) in the media was required for the maintenance of several differentiated functions for cells cultured on collagen. In general, cells cultured on the PS-lactose substrate showed a much slower loss of function over the same period of time. The maintenance of differentiated function of cells on PS-lactose was enhanced with the addition of dexamethasone and DMSO. This is the first report of a culture system in which hepatocytes, cultured on a polymer substrate without additional protein coatings or media additives, have been able to maintain differentiated functions for up to 1 week. © 1996 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 54
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 290-299 
    ISSN: 0006-3592
    Keywords: proteins, modified ; partitioning in aqueous system ; thaumatin ; β-lactoglobulin ; BSA ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Relatively conservative modifications of three proteins were carried out to alter their surface properties. The protein properties modified were hydrophobicity and charge. This was done by acylation of amino groups with anhydrides. For the hydrophobic modification experiments, two proteins (β-lactoglobulin and bovine serum albumin [BSA]) and four anhydrides (hexanoic, butyric, succinic, acetic) were used. For the modification of surface charge the protein thaumatin was selected and various proportions of the free amino groups were blocked with acetic anhydride to give a series of proteins with differing isoelectric points. Detailed characterization and purification of selected modified proteins was carried out including molecular weight measurements and conformational analysis. The criteria used for selecting the modified proteins for subsequent investigation of their partitioning in aqueous two-phase systems (ATPS) is described. With a judicious choice of starting material it was found that limited chemical modifications to proteins could effectively alter surface hydrophobicity or charge almost independently, with little effect on other molecular properties. It appears, however, that the method for chemical modification and the reaction conditions must also be carefully controlled. © 1996 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 55
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 309-315 
    ISSN: 0006-3592
    Keywords: surface charge ; proteins, modified ; partitioning in aqueous system ; thaumatin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A series of charge-modified thaumatins with different values of surface charge were partitioned in aqueous two-phase systems (ATPS) to study the effect of surface charge as a single property on partitioning. Electrophoretic mobility of the proteins in titration curves was used as a measure of surface charge. Four modified proteins derived from thaumatin with the following values of isoelectric point: 8.70, 8.15, 5.60, and 4.50 were used for partitioning. The resolution of the systems in terms of protein surface charge was calculated. Partitioning of modified thaumatins in PEG 4000/dextran systems with phosphate buffer, Tris buffer, NaCl, KCl, and sulfate salts was carried out. Among the sulfate salts tested, the addition of 50 mM Li2SO4 to the system buffered with phosphate gave the highest value of resolution for differences in surface protein charge (RSPC). It shows a decrease in the value of K (partition coefficient) with an increase in the protein's charge. The addition of 100 mM KCl to the system promoted the opposite effect on the RSPC value. Charge-modified proteins were partitioned in PEG/salt systems to investigate the ability of these systems for resolving differences in surface charge. The PEG/citrate system seemed to have almost no ability for resolving proteins on the basis of surface charge differences; PEG/phosphate systems had some capability for resolving differently charged proteins. The more negative proteins tended to have higher values of K than the more positively charged fractions. The use of charge-modified proteins allowed the investigation of the effect of protein surface charge on partitioning in aqueous two-phase systems independently from other protein parameters as they were prepared from a common parent protein thaumatin. This technique provides an interesting novel tool to investigate the effect of protein surface charge on partitioning in ATPS taking protein charge as an independent parameter. © 1996 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 56
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 348-354 
    ISSN: 0006-3592
    Keywords: oxygenator ; NMR spectroscopy ; organ perfusion ; mammalian cell culture ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A compact, reusable membrane oxygenator has been constructed for the perfusion of cultured cells and isolated organs. While the oxygenator was designed to be compatible with nuclear magnetic resonance (NMR) spectroscopy studies, it can also be used for any experiment which requires warming and oxygenation of perfusates. For the NMR studies, the oxygenator can be positioned at the opening of the magnet bore which allows oxygenation and warming of the perfusate immediately prior to delivery to the tissue, therefore eliminating problems with heat or oxygen loss which may occur with the long perfusion lines. © 1996 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 57
    ISSN: 0006-3592
    Keywords: c-fos protein ; endothelium ; hemodynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The c-fos protein belongs to a family of transcriptional cofactors that can complex with proteins of the Jun family and activate mRNA transcription from gene promoters containing an activator protein 1 (AP-1) binding element. The shear stress inducibility of the c-fos protein was studied in human and animal cell lines of vastly different origins. Primary human umbilical vein endothelial cells (HUVEC), bovine aortic endothelial cells (BAEC, passage 2-14), HeLa cells, and Chinese hamster ovary (CHO) cells were subjected to steady laminar shear stress using a parallel plate flow apparatus. After 1 h of flow exposure at 25 dyn/cm2, the c-fos levels in nuclei of shear stress HUVEC, BAEC, HeLa, and CHO were 5.4 ± 2.0 (n = 3), 2.25 ± 1.38 (n = 6), 2.14 ± 0.07 (n = 8), 1.92 ± 0.58 (n = 2) times higher, respectively, than in matched stationary controls. Flow exposure at 4 dyn/cm2 caused no enhancement of c-fos levels in any of the cell lines tested, but caused significant reduction in c-fos expression in the HeLa cells. The c-fos induction by shear stress could be blocked by pharmacological agents. For example, the flow induction of the c-fos protein levels was blocked by 50% with the preincubation of HUVEC with a protein kinase C inhibitor, H7 (10 μM) and blocked completely in HeLa cells preincubated with the phospholipase C inhibitor, neomycin (5 mM). The minimum time of shear stress exposure required to induce the c-fos protein expression in HeLa cells was found to be as low as 1 min. By Northern analysis, the c-fos mRNA levels were found to be elevated in BAEC, CHO, and HeLa cells exposed to 25 dyn/cm2 for 30 min. These studies indicate that c-fos induction is a consistent genetic response in a variety of mammalian cells that may alter cellular phenotype in mechanical environments. © 1996 John Wiley & Sons, Inc.
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  • 58
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 412-420 
    ISSN: 0006-3592
    Keywords: Amycolatopsis orientalis ; vancomycin production ; chemostat culture ; phosphate inhibition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Production of the glycopeptide antibiotic vancomycin by two Amycolatopsis orientalis strains was examined in batch shake flask culture in a semidefined medium with peptone as the nitrogen source. Different growth and production profiles were observed with the two strains; specific production (Yp/x) was threefold higher with strain ATCC 19795 than with strain NCIMB 12945. A defined medium with amino acids as the nitrogen source was developed by use of the Plackett-Burman statistical screening method. This technique identified certain amino acids (glycine, phenylalanine, tyrosine, and arginine) that gave significant increased specific production, whereas phosphate was identified as inhibitory for high specific vancomycin production. Experiments made with the improved medium and strain ATCC 19795 showed that vancomycin production kinetics were either growth dissociated or growth associated, depending on the amino acid concentration. In chemostat culture at a constant dilution rate (0.087 h-1), specific vancomycin production rate (qvancomycin) decreased linearly as the medium phosphate concentration was increased from 2 to 8 mM. In both phosphate and glucose limited chemostats, qvancomycin was a function of specific growth rate; the maximum value was observed at D = 0.087 h-1 (52% of the maximum specific growth rate). Under phosphate limited growth conditions, qvancomycin was threefold higher (0.37 mg/g dry weight/h) than under glucose limitation (0.12 mg/g dry weight/h). © 1996 John Wiley & Sons, Inc.
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  • 59
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 36-48 
    ISSN: 0006-3592
    Keywords: insect cell culture ; Sf-9 cells ; respiration ; bioreactor ; on-line monitoring ; baculovirus expression vector system ; recombinant proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Respiration rates in Spodoptera frugiperda (Sf-9) cell bioreactor cultures were successfully measured on-line using two methods: The O2 uptake rate (OUR) was determined using gas phase pO2 values imposed by a dissolved oxygen controller and the CO2 evolution rate (CER) was measured using an infrared detector. The measurement methods were accurate, reliable, and relatively inexpensive. The CER was routinely determined in bioreactor cultures used for the production of several recombinant proteins. Simple linear relationships between viable cell densities and both OUR and CER in exponentially growing cultures were used to predict viable cell density. Respiration measurements were also used to follow the progress of baculoviral infections in Sf-9 cultures. Infection led to increases in volumetric and per-cell respiration rates. The relationships between respiration and several other culture parameters, including viable cell density, cell protein, cell volume, glucose consumption, lactate production, viral titer, and recombinant β-galactosidase accumulation, were examined. The extent of the increase in CER following infection and the time postinfection at which maximum CER was attained were negatively correlated with the multiplicity of infection (MOI) at multiplicities below the level required to infect all the cells in a culture. Delays in the respiration peak related to the MOI employed were correlated with delays in the peak in recombinant protein accumulation. DO levels in the range 5-100% did not exert any major effects on viable cell densities, CER, or product titer in cultures infected with a baculovirus expressing recombinant β-galactosidase. © 1996 John Wiley & Sons, Inc.
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  • 60
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    Biotechnology and Bioengineering 50 (1996) 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
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  • 61
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    Biotechnology and Bioengineering 50 (1996), S. 169-183 
    ISSN: 0006-3592
    Keywords: liposomes ; biotin ; aggregation kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The aggregation of biotinylated phospholipid vesicles (liposomes) cross-linked by antibiotin IgG was studied experimentally and theoretically. The liposomes were either low density liposomes that contained 0.4 mol% biotinylated phospholipid (≈100 exposed biotin molecules per liposome), or high density liposomes that contained 2.7 mol% biotinylated phospholipid (≈1000 exposed biotin molecules per liposome). The solution turbidity and mean particle size measured by quasi-elastic light scattering (QLS) were monitored throughout the aggregation. Three different lots of antibiotin antibodies, each with different association constants and binding heterogeneities, were used. The antibody binding characteristics affected the aggregation rates. The aggregation kinetics were analyzed using a model based on the Smoluchowski theory of aggregation, fractal concepts of aggregate microstructure, and Rayleigh and Mie light scattering theory. The experimental conditions of liposome concentration, protein concentration, and ligand density under which aggregation occurred correlated well with calculated sticking probabilities based on isotherms describing the adsorption of antibiotin antibody to the liposomes. These results are compared with prior observations made when avidin was used as the cross-linking protein. © 1996 John Wiley & Sons, Inc.
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  • 62
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    Biotechnology and Bioengineering 50 (1996) 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
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  • 63
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    Biotechnology and Bioengineering 50 (1996), S. 211-216 
    ISSN: 0006-3592
    Keywords: microgravity ; bioprocessing ; sedimentation ; turbulence ; collagenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of a quiescent microgravity fluid environment on the activity of collagenase directed at demineralized bone fragments was investigated over a period of 10 days. Enzyme treatment resulted in greater mass loss in microgravity, with nearly three times the loss of mass during Space Shuttle mission STS-62 compared to the stationary ground control. Clinorotation enhanced the loss of mass relative to a stationary control, but this increase was still significantly less than the increase with exposure to microgravity. This suggests the detrimental influence of turbulence on the enzyme function and the benefit of using microgravity to provide both low turbulence and uniformity of unequally dense materials within the reaction chamber. The results are considered for their general applicability to a variety of bioprocessing applications that may be enhanced in microgravity. © 1996 John Wiley & Sons, Inc.
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  • 64
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    Biotechnology and Bioengineering 50 (1996), S. 430-437 
    ISSN: 0006-3592
    Keywords: cartilage ; tissue regeneration ; chondrocytes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In the last 5 to 10 years, tissue engineering has revolutionized the way in which medical researchers and clinicians are thinking of and, in some cases, actually treating diseases involving tissue damage and destruction. One such disease, osteoarthritis, results from progressive degeneration of articular cartilage, which has a limited ability to repair itself. With tissue engineering, scientists are now able to regenerate cartilage in vitro from isolated mature chondrocytes. While the regeneration process is still not fully understood, enough has been learned that physicians are already implanting cultured chondrocytes into humans and other animals in the hopes of effecting joint repair. One aspect which has not been fully explored is the effect of mechanical stress on developing and implanted cartilage, especially over the long term. This article will review in brief what is now known about the mechanical factors affecting cartilage regeneration in vitro and what still remains to be determined for optimum tissue engineering of cartilage constructs. © 1996 John Wiley & Sons, Inc.
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  • 65
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    Biotechnology and Bioengineering 50 (1996), S. 443-451 
    ISSN: 0006-3592
    Keywords: osteoblast ; migration ; poly(αhydroxy esters) ; poly(DL-lactic-co-glycolic acid) ; PLGA ; biodegradable polymers ; tissue engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We investigated the migration of rat calvaria osteoblast populations on poly(α-hydroxy ester) films for up to 14 days to determine effects of substrate composition and culture conditions on the migratory characteristics of osteoblasts. Initial osteoblast culture conditions included cell colonies formed by seeding a high (84,000 cells/cm2) or low (42,000 cells/cm2) density of isolated osteoblasts on the polymer films, and bone tissue cultures formed by plating bone chips directly on the substrates. High density osteoblast colonies cultured and allowed to migrate and proliferate radially on 85:15 poly(DL-lactic-co-glycolic acid) (PLGA) films, 75:25 PLGA films, and tissue culture polystyrene controls demonstrated that the copolymer ratio in the polymer films did not affect the rate of increase in substrate surface area (or culture area) covered by the growing cell colony. However, the rate of increase in culture area was dependent on the initial osteoblast seeding density. Initial cell colonies formed with a lower osteoblast seeding density on 75:25 PLGA resulted in a lower rate of increase in culture area, specifically 4.9 ± 0.3 mm2/day, versus 14.1 ± 0.7 mm2/day for colonies seeded with a higher density of cells on the same polymer films. The proliferation rate for osteoblasts in the high and low density seeded osteoblast colonies did not differ, whereas the proliferation rate for the osteoblasts arising from the bone chips was lower than either of these isolated cell colonies. Confocal and light microscopy revealed that the osteoblast migration occurred as a monolayer of individual osteoblasts and not a calcified tissue front. These results demonstrated that cell seeding conditions strongly affect the rates of osteoblast migration and proliferation on biodegradable poly(α-hydroxy esters). © 1996 John Wiley & Sons, Inc.
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  • 66
    ISSN: 0006-3592
    Keywords: bone marrow ; hematopoiesis ; perfusion ; culture optimization ; stroma ; stem cells ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Hematopoiesis, the formation of mature blood cells from stem (LTC-IC) and progenitor (CFU-GM) cells in the bone marrow, is a complex tissue-forming process that leads to many important physiological functionalities. Consequently, a functioning ex vivo hematopoietic system has a variety of basic scientific and clinical uses. The design and operation of such a system presents the tissue engineer with challenges and choices. In this study, three culture variables were used to control ex vivo human hematopoiesis. Systematic variation of inoculum density (ID), medium exchange interval (MEI), and the use of preformed stroma (PFS) showed that (1) all three variables significantly influenced culture performance, (2) the three variables interacted strongly, and (3) the variables could be manipulated to achieve the optimization of different performance criteria. Donor-to-donor variability in culture performance was great at low ID but was minimized at higher ID. PFS had a large positive effect on cell and CFU-GM output at low ID, but had minimal effect at higher ID. In fact, PFS caused a decrease in LTC-IC output at high ID. The effects of PFS indicated that stromal cell elements became more limiting than proliferative cell elements as ID was reduced.In cultures without PFS, maximum cell output was obtained with high ID using a short MEI, whereas the greatest cell expansion ratio was obtained at low ID with an intermediate MEI. Maximum CFU-GM output was obtained from cultures with high ID using a short to intermediate MEI, whereas the greatest CFU-GM expansion ratio was obtained at intermediate ID with an intermediate MEI. The addition of PFS altered the locations of these maxima. In general, PFS moved the maxima to lower ID, and culture output became more sensitive to MEI. Therefore, the optimization of one performance criterion always resulted in a decline of the others. This study demonstrates that ex vivo tissue function is sensitive to many culture variables in an interactive fashion and that systematic multivariable studies are required to characterize tissue function. Once the effects of individual variables and their interactions are known, this knowledge can be used to optimize tissue performance with respect to desired criteria. © 1996 John Wiley & Sons, Inc.
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  • 67
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    Biotechnology and Bioengineering 50 (1996) 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
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  • 68
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    Biotechnology and Bioengineering 51 (1996), S. 410-421 
    ISSN: 0006-3592
    Keywords: lysozyme ; thermal stability ; 1H NMR ; conformational flexibility ; melting temperature ; PEG ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The reversible folding destabilization of hen lysozyme has been confirmed by a melting temperature (Tm) decrease in aqueous poly(ethylene glycol) (PEG). The percent denatured, extracted from the histidine 15 C2H (H15 C2H) native and denatured peak areas from 500-MHz one-dimensional proton nuclear magnetic resonance (1D 1H NMR) spectra in D2O, was analyzed through denaturation temperatures at 0% and 20% (w/w) PEG 1000. The lysozyme (3.5 mM) Tm decreased by 4.2°C and 7.1°C in 20% (w/w) PEG 1000 at pH 3.8 and 3.0, respectively. The Tm decreased with increasing lysozyme concentration. Additionally, the temperature-induced resonance migrations of 17 protons from 8 residues indicate that the native lysozyme structure undergoes temperature-induced conformational changes. The changes were essentially identical in both 0% and 20% (w/w) PEG 1000 at both pH 3.0 and 3.8. This small, local restructuring of the hydrophobic box region may be a manifestation of temperature-dependent solution hydrophobicity, whereas active-site cleft fluctuations may be due to the inherent active-site flexibility. The lysozyme structure in PEG at 35°C was determined to be essentially native from the 1H nuclear Overhauser effect spectroscopy (NOESY) fingerprint regions. Additionally, lysozyme chemical shifts, from 1D spectra, in PEG 200, 300, and 1000 at 35°C and various concentrations were essentially identical, further confirming that the conformation remains native in various PEG solutions. © 1996 John Wiley & Sons, Inc.
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  • 69
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    Biotechnology and Bioengineering 51 (1996), S. 375-383 
    ISSN: 0006-3592
    Keywords: cellulase ; enzyme recycling ; enzyme adsorption ; lignocellulosic hydrolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Past technoeconomic modeling work has identified the relatively large contribution that enzymatic hydrolysis adds to the total cost of producing ethanol from lignocellulosic substrates. This cost was primarily due to the high concentration of enzyme and long incubation time that was required to obtain complete hydrolysis. Although enzyme and substrate concentration and end-product inhibition influenced the rate of hydrolysis, the effect was less pronounced during the initial stages of hydrolysis. During this time most of the cellulases were adsorbed onto the unhydrolyzed residue. By recycling the cellulases adsorbed to the residual substrate remaining after an initial 24 h, a high rate of hydrolysis, with low overall residence time and minimal cellulase input, could be achieved for several rounds of enzyme recycle. A comparison of the front end (pretreatment, fractionation, and hydrolysis) of a softwood/hardwood to ethanol process indicated that the lignin associated with the softwood-derived cellulose stream limited the number of times the cellulose containing residue could be recycled. © 1996 John Wiley & Sons, Inc.
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  • 70
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    Biotechnology and Bioengineering 51 (1996), S. 399-409 
    ISSN: 0006-3592
    Keywords: cell damage ; cell culture ; bubble aeration ; agitation ; bubble coalescence and breakup ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: It has been established that the forces resulting from bubbles rupturing at the free air (gas)/liquid surface injure animal cells in agitated and/or sparged bioreactors. Although it has been suggested that bubble coalescence and breakup within agitated and sparged bioreactors (i.e., away from the free liquid surface) can be a source of cell injury as well, the evidence has been indirect. We have carried out experiments to examine this issue. The free air/liquid surface in a sparged and agitated bioractor was eliminated by completely filling the 2-L reactor and allowing sparged bubbles to escape through an outlet tube. Two identical bioreactors were run in parallel to make comparisons between cultures that were oxygenated via direct air sparging and the control culture in which silicone tubing was used for bubble-free oxygenation. Thus, cell damage from cell-to-bubble interactions due to processes (bubble coalescence and breakup) occurring in the bulk liquid could be isolated by eliminating damage due to bubbles rupturing at the free air/liquid surface of the bioreactor. We found that Chinese hamster ovary (CHO) cells grown in medium that does not contain shear-protecting additives can be agitated at rates up to 600 rpm without being damaged extensively by cell-to bubble interactions in the bulk of the bioreactor. We verified this using both batch and high-density perfusion cultures. We tested two impeller designs (pitched blade and Rushton) and found them not to affect cell damage under similar operational conditions. Sparger location (above vs. below the impeller) had no effect on cell damage at higher agitation rates but may affect the injury process at lower agitation intensities (here, below 250 rpm). In the absence of a headspace, we found less cell damage at higher agitation intensities (400 and 600 rpm), and we suggest that this nonintuitive finding derives from the important effect of bubble size and foam stability on the cell damage process. © 1996 John Wiley & Sons, Inc.
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  • 71
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    Biotechnology and Bioengineering 51 (1996), S. 434-438 
    ISSN: 0006-3592
    Keywords: polyphosphate ; Escherichia coli ; phosphate starvation ; gene expression ; heterologous ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of intracellular polyphosphate on the phosphate-starvation response in Escherichia coli was studied by genetically manipulating the intracellular polyphosphate levels and by performing phosphate shifts on the genetically engineered strains. Strains that produced large quantities of polyphosphate and were able to degrade it induced the phosphate-starvation response to a lesser extent than wild-type strains, whereas strains that were unable to degrade a large intracellular polyphosphate pool induced the phosphate-starvation response to a greater extent than wild-type strains. These results have important implications for expression of heterologous genes under control of the phoA promoter. © 1996 John Wiley & Sons, Inc.
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  • 72
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    Biotechnology and Bioengineering 51 (1996), S. 458-465 
    ISSN: 0006-3592
    Keywords: concentric-cylinder shear device ; rotor/stator homogenization ; shear ; shear rate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Shear is present in almost all bioprocesses and high shear is associated with processes involving agitation and emulsification. The purpose of this study is to investigate the effect of high shear and high shear rate on proteins. Two concentric cylinder-based shear systems were used. One was a closed concentric-cylinder shear device (CCSD) and the other was a homogenizer with a rotor/stator assembly. Mathematical modeling of these systems allowed calculation of the shear rate and shear. The CCSD generated low shear rates (a few hundred s-1), whereas the homogenizer could generate very high shear rates (〉 105 s-1). High shear could be achieved in both systems by increasing the processing time. Recombinant human growth hormone (rhGH) and recombinant human deoxyribonuclease (rhDNase) were used as the model proteins in this study. It was found that neither high shear nor high shear rate had a significant effect on protein aggregation. However, a lower melting temperature and enthalpy were detected for highly sheared rhGH by using scanning microcalorimetry, presumably due to some changes in protein's conformation. Also, SDS-PAGE indicated the presence of low molecular-weight fragments, suggesting that peptide bond breakage occurred due to high shear. rhDNase was relatively more stable than rhGH under high shear. No conformational changes and protein fragments were observed. © 1996 John Wiley & Sons, Inc.
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  • 73
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    Biotechnology and Bioengineering 51 (1996), S. 494-499 
    ISSN: 0006-3592
    Keywords: cell metabolism ; baculovirus ; insect cells ; recombinant protein OSF-2 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The properties of Sf9 and Tn5 insect cells were analyzed comparatively under serum-free culture conditions. Sf9 cells in SF900II medium apparently utilized sucrose as a primary nutrient both before and after virus infection, yielding small amounts of lactate and ammonia. Tn5 cells in Excell 401 medium consumed all the nutrients examined, including sucrose. The productivity of a recombinant glycoprotein, OSF-2, by Tn5 cells, was moderate in both monolayer and spinner cultures, but the ability to secrete it was compromised in the former case. Relative to the Tn5 cultures, Sf9 produced 30-fold more OSF-2 in either culture mode. © 1996 John Wiley & Sons, Inc.
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  • 74
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    Biotechnology and Bioengineering 51 (1996), S. 538-543 
    ISSN: 0006-3592
    Keywords: NMR imaging ; biosorption ; alginate ; shrinking core model ; Laminaria ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this contribution, an NMR imaging study of heavy metal absorption in alginate, immobilized-cell biosorbents, and kombu (Laminaria japonica) algal biomass is presented. This method provides the good possibility of directly monitoring the time evolution of the spatial distribution of the ions in the materials. From these results, we demonstrate that rare earth ions are absorbed with a steep reaction front that can be described very well with a modified shrinking core model, while copper ions are absorbed with a more diffuse front.
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  • 75
    ISSN: 0006-3592
    Keywords: oxidoreductase ; chiral alcohol ; racemic resolution ; membrane reactor ; continuous extraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Oxidations of alcohols by alcohol dehydrogenases often suffer from low conversions and slow reaction rates due to severe product inhibition. This can be overcome by continuous product extraction, because only the concentrations, but not the kinetic parameters, can be changed. As a consequence, it is favorable to apply a differential circulation reactor with continuous product extraction, where only a small amount of product is formed per cycle. The product is then directly extracted using a microporous hydrophobic hollow fiber membrane. This results in an increase of the relative activity of the dehydrogenase at a given conversion. The reaction investigated is the kinetic resolution of racemic 1-phenyl-1,2-ethanediol by glycerol dehydrogenase (GDH). The resulting oxidation product, 2-hydroxyacetophenone, causes a strong product inhibition. Additionally, it reacts in a chemical reaction with the cofactor lowering its active concentration. Because the GDH needs β-nicotinamide adenine dinucleotide (NAD+) as a cofactor, lactate dehydrogenase is used to regenerate NAD+ from NADH by reducing pyruvate to (L)-lactate. A conversion of 50% with respect to the racemate and an enantiomeric excess 〉99% of the (S)-enantiomer was reached.
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  • 76
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    Biotechnology and Bioengineering 51 (1996), S. 581-590 
    ISSN: 0006-3592
    Keywords: microfiber ; graft polymerization ; DNA immobilization ; immunoadsorbent ; DNA ; anti-DNA antibody ; systemic lupus erythematosus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Immobilization of DNA to the surface of poly(ethylene terephthalate) (PET) microfibers with a high specific surface area of 0.83 m2/g was carried out to give the fiber surface an affinity for anti-DNA antibody. Following ozone oxidation, the microfibers were subjected to graft polymerization of monomers including acrylic acid, methacryloyloxyethyl phosphate, N,N-dimethylaminoethyl methacrylate, N-vinylformamide, and glycidyl methacrylate. Calf thymus DNA was immobilized to the grafted fiber surface through either covalent binding or polyion complexation with the grafted polymer chains. The highest surface density of DNA immobilized (0.6 μg/cm2) was obtained when DNA was immobilized through formation of phosphodiester linkage between the hydroxyl group of DNA and the phosphate group in grafted poly(methacryloyloxyethyl phosphate) using 1,1-carbonyldiimidazole, or through polyion complexation between the anionic DNA and the cationic grafted poly(N,N-dimethylaminoethyl methacrylate) chains. Batch adsorption of anti-DNA antibody to the grafted PET fibers with and without DNA immobilized on their surface was conducted with serum obtained from systemic lupus erythematosus model mice. The DNA-immobilized PET fibers exhibited a higher adsorption capacity and specificity than the others. In addition, the DNA-immobilized fibers effectively adsorbed human anti-DNA antibody.
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  • 77
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 335-344 
    ISSN: 0887-3585
    Keywords: protein design ; synthetic heteropolymer design ; energy matrix ; sequence degeneracy ; structural encodability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proteins fold to unique compact native structures. Perhaps other polymers could be designed to fold in similar ways. The chemical nature of the monomer “alphabet” determines the “energy matrix” of monomer interactions - which defines the folding code, the relationship between sequence and structure. We study two properties of energy matrices using two-dimensional lattice models: uniqueness, the number of sequences that fold to only one structure, and encodability, the number of folds that are unique lowest-energy structures of certain monomer sequences. For the simplest model folding code, involving binary sequences of H (hydrophobic) and P (polar) monomers, only a small fraction of sequences fold uniquely, and not all structures can be encoded. Adding strong repulsive interactions results in a folding code with more sequences folding uniquely and more designable folds. Some theories suggest that the quality of a folding code depends only on the number of letters in the monomer alphabet, but we find that the energy matrix itself can be at least as important as the size of the alphabet. Certain multi-letter codes, including some with 20 letters, may be less physical or protein-like than codes with smaller numbers of letters because they neglect correlations among inter-residue interactions, treat only maximally compact conformations, or add arbitrary energies to the energy matrix.
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 345-351 
    ISSN: 0887-3585
    Keywords: energy landscape ; kinetic traps ; hydrophobic interaction ; multiple folding pathways ; chaperone action ; lattice models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Chaperonins are oligomeric proteins that help other proteins fold. They act, according to the “Anfinsen cage” or “box of infinite dilution” model, to provide private space, protected from aggregation, where a protein can fold. Recent evidence indicates, however, that proteins are often ejected from the GroEL chaperonin in nonnative conformations, and repeated cycles of binding and ejection are needed for successful folding. Some experimental evidence suggests that GroEL chaperonins can act as folding “catalysts” in an ATP-dependent manner even when no aggregation takes place. This implies that chaperonins must somehow recognize the kinetically trapped intermediate states of a protein. A central puzzle is how a chaperonin can catalyze the folding reaction of a broad spectrum of different proteins. We propose a physical mechanism by which chaperonins can flatten the energy barriers to folding in a nonspecific way. Using a lattice model, we illustrate how a chaperonin could provide a sticky surface that helps pull apart an incorrectly folded protein so it can try again to fold. Depending on the relative sizes of the protein and the chaperonin cavity, folding can proceed both inside and outside the chaperonin. Consistent with experiments, we find that the folding rate and amount of native protein can be considerably enhanced, or sometimes reduced, depending on the amino acid sequence, the chaperonin size, and the binding and ejection rates from the chaperonin.
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  • 79
    ISSN: 0887-3585
    Keywords: scorpion venom ; neurotoxin ; NMR ; structure-activity relationships ; calcium activated-potassium channel ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The venom of the North African scorpion Androctonus mauretanicus mauretanicus possesses numerous highly active neurotoxins that specifically bind to various ion channels. One of these, P05, has been found to bind specifically to calcium-activated potassium channels and also to compete with apamin, a toxin extracted from bee venom. Besides the highly potent ones, several of these peptides (including that of P01) have been purified and been found to possess only a very weak, although significant, activity in competition with apamin. The amino acid sequence of P01 shows that it is shorter than P05 by two residues. This deletion occurs within an α-helix stretch (residues 5-12). This α-helix has been shown to be involved in the interaction of P05 with its receptor via two arginine residues. These two arginines are absent in the P01 sequence. Furthermore, a proline residue in position 7 of the P01 sequence may act as an α-helix breaker. We have determined the solution structure of P01 by conventional two-dimensional 1H nuclear magnetic resonance and show that 1) the proline residue does not disturb the α-helix running from residues 5 to 12; 2) the two arginines are topologically replaced by two acidic residues, which explains the drop in activity; 3) the residual binding activity may be due to the histidine residue in position 9; and 4) the overall secondary structure is conserved, i.e., an α-helix running from residues 5 to 12, two antiparallel stretches of β-sheet (residues 15-20 and 23-27) connected by a type I′ β-turn, and three disulfide bridges connecting the α-helix to the β-sheet.
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 379-387 
    ISSN: 0887-3585
    Keywords: infrared spectroscopy ; protein structure ; unfolding ; RNase T1 ; RNase A ; histone-like protein HBsu ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Fourier-transform infrared (FTIR) spectroscopy has been used to study the thermally induced exchange characteristics of those backbone amide protons which persist H-D exchange at ambient conditions in ribonuclease A, in wild type ribonuclease T1 and some of its variants, and in the histone-like protein HBsu. The H-D exchange processes were induced by increasing the thermal energy of the protein solutions in two ways: (i) by linearly increasing the temperature, and (ii) by a temperature jump. To trace the H-D exchange in the proteins, various infrared absorption bands known to be sensitive to H-D exchange were used as specific monitors. Characteristic H-D exchange curves were obtained from which the endpoints (TH/D) of H-D exchange could be determined. The H-D exchange curves, the TH/D-values and the phase transition temperatures Tm were used to estimate the structural flexibility and stability of the given proteins. It is suggested that time-resolved FTIR spectroscopy can be used to determine global stability parameters of proteins.
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  • 81
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 394-401 
    ISSN: 0887-3585
    Keywords: cytokines ; homology modeling ; erythropoietin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of the structure of erythropoietin (Epo) is presented based on structural homology to other hemopoietic cytokines. A model of the erythropoietin receptor complex was made based on evidence that this includes a homodimer of the receptor chain with known sequence. Key interactions are noted which explain data from mutation experiments, although at not all residues believed to be important to binding of Epo are at the interface. This is consistent with the hypothesis that the Epo receptor complex includes proteins in addition to the cloned receptor chain that have been cross-linked to Epo (Todokoro et al., Proc. Natl. Acad. Sci. USA 84:4126-4130, 1987; Mayeux et al., J. Biol. Chem. 266:23380-23385, 1991) but not isolated.
    Additional Material: 5 Ill.
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  • 82
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 402-403 
    ISSN: 0887-3585
    Keywords: Tus ; terminus site ; protein-DNA interaction ; replication arrest ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the Escherichia coli replication terminator protein (Tus) complexed with its binding site DNA were obtained by a microdialysis method using PEG 4000. They belong to the tetragonal space group P41212 or P43212 with the unit cell parameter: a = 68.1 Å, c = 230.7 Å and contain one protein-DNA complex in an asymmetric unit. The native data set has been collected to 2.7 Å resolution.
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  • 83
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 404-406 
    ISSN: 0887-3585
    Keywords: DAHP synthase ; metalloenzyme ; shikimate pathway ; KDOP synthase ; affinity chromatography ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The phenylalanine-regulated isozyme of 3-deoxy-D-arabino-heptulosonate-7-phosphate- synthase (DAHPS) from Escherichia coli, its binary complexes with either substrate, phosphoenolpyruvate (PEP), or feedback inhibitor, Phe, and its ternary complexes with either PEP or Phe plus metal cofactor (either Mn2+, Cd2+, or Pb2+) were crystallized from polyethylglycol (PEG) solutions. All crystals of the DAHPS without Phe belong to space group C2, with cell parameters a = 213.5 Å, b = 54.3 Å, c = 149.0 Å, β = 116.6°. All crystals of the enzyme with Phe also belong to space group C2, but with cell parameters a = 297.1 Å, b = 91.4 Å, c = 256.5 Å, and β = 148.2°.
    Additional Material: 1 Tab.
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  • 84
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    Proteins: Structure, Function, and Genetics 24 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 85
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 1-1 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 86
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 87
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 410-410 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 88
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 427-432 
    ISSN: 0887-3585
    Keywords: GCN4 ; protein folding ; folding kinetics ; helix formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To determine when secondary structure forms as two chains coalesce to form an α-helical dimer, the folding rates of variants of the coiled coil region of GCN4 were compared. Residues at non-perturbing positions along the exterior length of the helices were substituted one at a time with alanine and glycine to vary helix propensity and therefore dimer stability. For all variants, the bimolecular folding rate remains largely unchanged; the unfolding rate changes to largely account for the change in stability. Thus, contrary to most folding models, widespread helix is not yet formed at the rate-limiting step in the folding pathway. The high-energy transition state is a collapsed form that contains little if any secondary structure, as suggested for the globular protein cytochrome c (Sosnick et al., Proteins 24:413-426, 1996).
    Additional Material: 4 Ill.
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  • 89
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 433-438 
    ISSN: 0887-3585
    Keywords: structure refinement ; buried water ; free energy calculation ; molecular dynamics simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Water molecules inside cavities in proteins constitute integral parts of the structure. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating energies and free energies of introducing a water molecule into these cavities. A threshold value of the water-protein interaction energy at -12 kcal/mol was found to be able to distinguish hydrated from empty cavities. It follows that buried waters have entropy comparable to that of liquid water or ice. A simple consistent picture of the energetics of the buried waters provided by this study enabled us to address the reliability of buried waters assigned in experiments.
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  • 90
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 413-426 
    ISSN: 0887-3585
    Keywords: protein folding ; folding kinetics ; folding barriers ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Experiments with cytochrome c (cyt c) show that an initial folding event, molecular collapse, is not an energetically downhill continuum as commonly presumed but represents a large-scale, time-consuming, cooperative barrier-crossing process. In the absence of later misfold-reorganization barriers, the early collapse barrier limits cyt c folding to a time scale of milliseconds. The collapse process itself appears to be limited by an uphill search for some coarsely determined transition state structure that can nucleate subsequent energetically downhill folding events. An earlier “burst phase” event at strongly native conditions appears to be a non-specific response of the unfolded chain to reduced denaturant concentration. The molecular collapse process may or may not require the co-formation of the amino- and carboxyl-terminal helices, which are present in an initial metastable intermediate directly following the rate-limiting collapse. After the collapse-nucleation event, folding can proceed rapidly in an apparent two-state manner, probably by way of a predetermined sequence of metastable intermediates that leads to the native protein structure (Bai et al., Science 269:192-197, 1995).
    Additional Material: 6 Ill.
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  • 91
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 439-449 
    ISSN: 0887-3585
    Keywords: salt bridges ; hydrogen bonds ; secondary structure ; ionizable side chains ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In a selected set of 44 high-resolution, non-homologous protein structures, the intramolecular hydrogen bonds or salt bridges formed by ionizable amino acid side chains were identified and analyzed. The analysis was based on the investigation of several properties of the involved residues such as their solvent exposure, their belonging to a certain secondary structural element, and their position relative to the N- and C-termini of their respective structural element. It was observed that two-thirds of the interactions made by basic or acidic side chains are hydrogen bonds to polar uncharged groups. In particular, the majority (78%) of the hydrogen bonds between ionizable side chains and main chain polar groups (sch:mch bonds) involved at least one buried atom, and in 42% of the cases both interacting atoms were buried. In α-helices, the sch:mch bonds observed in the proximity of the C- and N-termini show a clear preference for acidic and basic side chains, respectively. This appears to be due to the partial charges of peptide group atoms at the termini of α-helices, which establish energetically favorable electrostatic interactions with side chain carrying opposite charge, at distances even greater than 4.5 Å. The sch:mch interactions involving ionizable side chains that belong either to β-strands or to the central part of α-helices are based almost exclusively on basic residues. This results from the presence of main chain carbonyl oxygen atoms in the protein core which have unsatisfied hydrogen bonding capabilities.
    Additional Material: 5 Ill.
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  • 92
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 467-484 
    ISSN: 0887-3585
    Keywords: heptad repeat ; alpha helix ; intermediate filament ; nuclear matrix ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We examined GenBank sequence files with a heptad repeat analysis program to assess the phylogenetic occurrence of coiled coil proteins, how heptad repeat domains are organized within them, and what structural/functional categories they comprise. Of 102,007 proteins analyzed, 5.95% (6,074) contained coiled coil domains; 1.26% (1,289) contained “extended” (〉 75 amino acid) domains. While the frequency of proteins containing coiled coils was surprisingly constant among all biota, extended coiled coil proteins were fourfold more frequent in the animal kingdom and may reflect early events in the divergence of plants and animals. Structure/function categories of extended coils also revealed phylogenetic differences. In pathogens and parasites, many extended coiled coil proteins are external and bind host proteins. In animals, the majority of extended coiled coil proteins were identified as constituents of two protein categories: 1) myosins and motors; or 2) components of the nuclear matrix-intermediate filament scaffold. This scaffold, produced by sequential extraction of epithelial monolayers in situ, contains only 1-2% of the cell mass while accurately retaining morphological features of living epithelium and is greatly enriched in proteins with extensive, interrupted coiled coil forming domains. The increased occurrence of this type of protein in Metazoa compared with plants or protists leads us to hypothesize a tissue-wide matrix of coiled coil interactions underlying metazoan differentiated cell and tissue structure.
    Additional Material: 9 Ill.
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  • 93
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 495-501 
    ISSN: 0887-3585
    Keywords: ab initio calculations ; density functional theory ; semiempirical calculations ; solvent reaction field ; phosphoserine ; phosphothreonine ; phosphotyrosine ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein phosphorylation is one of the major signal transduction mechanisms for controlling and regulating intracellular processes. Phosphorylation of specific hydroxylated amino acid side chains (Ser, Thr, Tyr) by protein kinases can activate numerous enzymes; this effect can be reversed by the action of protein phosphatases. Here we report ab initio (HF/6-31G* and Becke3LYP/6-31G*) and semiempirical (PM3) molecular orbital calculations pertinent to the ion pair formation of the phosphorylated amino acids with the basic side chains of Lys and Arg. Methyl-, ethyl-, and phenylphosphate, as well as methylamine and methylguanidinium were used as model compounds for the phosphorylated and basic amino acids, respectively. Phosphorylated amino acids were calculated as mono- and divalent anions. Our results indicate that the PSer/PThr ion pair interaction energies are stronger than those with PTyr. Moreover, the interaction energies with the amino group of Lys are generally more favorable than with the guanidinium group of Arg. The Lys amino groups form stable bifurcated hydrogen bonded structures; while the Arg guanidinium group can form a bidentate hydrogen bonded structure. Reasonable values for the interaction free energies in aqueous solution were obtained for some complexes by the inclusion of a solvent reaction field in the computation (PM3-SM3).
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  • 94
    ISSN: 0887-3585
    Keywords: de novo design ; protein structure ; inverse folding ; genetic algorithms ; 1H NMR ; CD ; peptide ; protein folding ; methanol ; ethylene glycol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In response to the Paracelsus Challenge (Rose and Creamer, Proteins, 19:1-3, 1994), we present here the design, synthesis, and characterization of a helical protein, whose sequence is 50% identical to that of an all-β protein. The new sequence was derived by applying an inverse protein folding approach, in which the sequence was optimized to “fit” the new helical structure, but constrained to retain 50% of the original amino acid residues. The program utilizes a genetic algorithm to optimize the sequence, together with empirical potentials of mean force to evaluate the sequence-structure compatibility. Although the designed sequence has little ordered (secondary) structure in water, circular dichroism and nuclear magnetic resonance data show clear evidence for significant helical content in water/ethylene glycol and in water/methanol mixtures at low temperatures, as well as melting behavior indicative of cooperative folding. We believe that this represents a significant step toward meeting the Paracelsus Challenge.
    Additional Material: 5 Ill.
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  • 95
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    Keywords: dehalogenase ; hydrolase ; Pseudomonas ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The dimeric L-2-haloacid dehalogenase from Pseudomonas sp. YL, (subunit mass, 26179 Da), has been crystallized by vapor diffusion, supplemented by repetitive seeding, against a 50 mM potassium dihydrogenphosphate solution (pH 4.5) containing 15% (w/v) polyethylene glycol 8,000 and 1% (v/v) n-propanol. The crystals belong to the monoclinic space group C2 with unit cell dimensions of a = 92.21 Å, b = 62.78 Angst; c = 50.84 Å, and β = 122.4°, and contain two dehalogenase dimers in the unit cell. They are of good quality and diffract up to 1.5 Å resolution.
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  • 96
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    Proteins: Structure, Function, and Genetics 24 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 97
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 525-527 
    ISSN: 0887-3585
    Keywords: naphtol reductase ; melanin synthesis ; rice blast disease ; fungicide ; rational drug design ; crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: 1,3,8-Trihydroxynaphthalene reductase was crystallized in the presence of NADPH and the inhibitor tricyclazole. The crystals are trigonal, space group P3121 or its enantiomorph P3221. Two crystal forms with slightly different cell dimensions were obtained. Form A has unit cell dimensions a = b = 142.6 Å, c = 70.1 Å and form B cell dimensions a = b = 142.6 Å, c = 72.9 Å. The diffraction pattern of the latter crystal form extends to 2.5 Å resolution.
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  • 98
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 1-11 
    ISSN: 0887-3585
    Keywords: HIV-1 gp120 ; secondary structure ; prediction ; multiple alignment ; CD4-binding site ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, β-strand, and coil was consistent with estimates from Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design of future HIV sub-unit vaccine candidates. © 1996 Wiley-Liss, Inc.
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  • 99
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 28-37 
    ISSN: 0887-3585
    Keywords: protein evolution ; structure prediction ; information theory ; amino acid substitution ; multiple sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using an information theoretic formalism, we optimize classes of amino acid substitution to be maximally indicative of local protein structure. Our statistically-derived classes are loosely identifiable with the heuristic constructions found in previously published work. However, while these other methods provide a more rigid idealization of physicochemically constrained residue substitution, our classes provide substantially more structural information with many fewer parameters. Moreover, these substitution classes are consistent with the paradigmatic view of the sequence-to-structure relationship in globular proteins which holds that the three-dimensional architecture is predominantly determined by the arrangement of hydrophobic and polar side chains with weak constraints on the actual amino acid identities. More specific constraints are imposed on the placement of prolines, glycines, and the charged residues. These substitution classes have been used in highly accurate predictions of residue solvent accessibility. They could also be used in the identification of homologous proteins, the construction and refinement of multiple sequence alignments, and as a means of condensing and codifying the information in multiple sequence alignments for secondary structure prediction and tertiary fold recognition. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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  • 100
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 79-88 
    ISSN: 0887-3585
    Keywords: weighted masses ; molecular dynamics ; adenylate kinase ; domain movement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The weighted masses molecular dynamics (WMMD) technique is applied to the protein adenylate kinase. A novel set of restraints has been developed to allow the use of this technique with proteins. The WMMD simulation is successful in predicting the flexibility of the two mobile domains of the protein. The end product of the simulation is similar to the known open and AMP bound forms of the enzyme. The biological relevance of the restraints used and potential methods of improving the technique are discussed. © 1996 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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