@misc{NowakWeimann1992, author = {Nowak, Ulrich and Weimann, Lutz}, title = {A Family of Newton Codes for Systems of Highly Nonlinear Equations.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4855}, number = {TR-91-10}, year = {1992}, abstract = {This report presents new codes for the numerical solution of highly nonlinear systems. They realize the most recent variants of affine invariant Newton Techniques due to Deuflhard. The standard method is implemented in the code NLEQ1, whereas the code NLEQ2 contains a rank reduction device additionally. The code NLEQ1S is the sparse version of NLEQ1, i.e. the arising linear systems are solved with sparse matrix techniques. Within the new implementations a common design of the software in view of user interface and internal modularization is realized. Numerical experiments for some rather challenging examples illustrate robustness and efficiency of algorithm and software.}, language = {en} } @misc{DeuflhardNowakPoehleetal.1991, author = {Deuflhard, Peter and Nowak, Ulrich and P{\"o}hle, Uwe and Schmidt, B. Ch. and Weyer, J.}, title = {Die Ausbreitung von HIV/AIDS in Ballungsgebieten.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4844}, number = {TR-91-09}, year = {1991}, abstract = {The rapidly increasing number of AIDS cases requires a realistic estimation of the future development of the HIV/AIDS disease. For that purpose we develop a large system of coupled nonlinear differential equations describing simultaneously the dynamics of the development of the disease, the population size, the gender and age structure. A set of 1650 coupled equations are linked by balanced parameters. The balancing procedure is described by a set of (formally) 2,178,000 additional algebraic conditions. As the considered system is stiff, it requires new special extrapolation methods combined with techniquees of dynamical sparsing for the solution of sparsely filled systems. According to our simulations we expect 19,0,000 deaths caused by AIDS in the Federal Republic of Germany (former territories) in the year 2000. Such an epidemical spread would tie up about 4-7 percent of the actual health care workers.}, language = {de} } @misc{GajewskiEdDeuflhardMarkowiched1991, author = {Gajewski(Ed.), Herbert and Deuflhard, Peter and Markowich(ed.), A.}, title = {Tagung NUMSIM '91 5.-08. Mai 1991. Collected Abstracts and Papers.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4838}, number = {TR-91-08}, year = {1991}, abstract = {NUMSIM 91 fand vom 6.-08. Mai 1991 im Wissenschaftlichen Kommunikations- \& Konferenz- Zentrum der Humboldt-Universit{\"a}t in Gosen bei Berlin statt. Im Mittelpunkt dieses Seminars standen Probleme der numerischen Simulation von Ladungstransport- und Technologieprozessen der Mikro- und Optoelektronik. Es f{\"u}hrte Spezialisten der physikalischen Modellierung, der numerischen Mathematik und mathematischen Analysis sowie Nutzer von Simulationsprogrammen aus dem deutschsprachigen Raum zusammen. Ziel war die Vermittlung und der Austausch von Erfahrungen, die Diskussion gemeinsamer Aufgabenstellungen und Projekte und - in Anbetracht der deutschen Vereinigung nicht zuletzt - das gegenseitige Kennen- und Verstehenlernen.}, language = {en} } @misc{Bornemann1991, author = {Bornemann, Folkmar A.}, title = {An Adaptive Multilevel Approach to Parabolic Equations in Two Space Dimensions.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4821}, number = {TR-91-07}, year = {1991}, abstract = {A new adaptive multilevel approach for linear partial differential equations is presented, which is able to handle complicated space geometries, discontinuous coefficients, inconsistent initial data. Discretization in time first (Rothe's method) with order and stepsize control is perturbed by an adaptive finite element discretization of the elliptic subproblems, whose errors are controlled independently. Thus the high standards of solving adaptively ordinary differential equations and elliptic boundary value problems are combined. A theory of time discretization in Hilbert space is developed which yields to an optimal variable order method based on a multiplicative error correction. The problem of an efficient solution of the singularly perturbed elliptic subproblems and the problem of error estimation for them can be uniquely solved within the framework of preconditioning. A Multilevel nodal basis preconditioner is derived, which allows the use of highly nonuniform triangulations. Implementation issues are discussed in detail. Numerous numerical examples in one and two space dimensions clearly show the significant perspectives opened by the new algorithmic approach. Finally an application of the method is given in the area of hyperthermia, a recent clinical method for cancer therapy.}, language = {en} } @misc{Schoeffel1991, author = {Sch{\"o}ffel, Klaus}, title = {Computational Chemistry Software for CRAY X-MP/2.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4816}, number = {TR-91-06}, year = {1991}, abstract = {The following report intends to provide a survey over the computational chemistry molecular structure software installed on CRAY X-MP/24 at ZIB. It shows what kind of problems can be tackled with the existing chemistry software, which covers a wide range of ab initio, semiempirical, molecular mechanics, and dynamics applications.}, language = {en} } @misc{Gottschewski1991, author = {Gottschewski, J{\"u}rgen}, title = {Supercomputing During the German Reunification.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4803}, number = {TR-91-05}, year = {1991}, abstract = {The success of the German Reunification requires a unique migration from the traditional Eastern Block system to a modern free society. The successful migration must include a shift from a low state of the art in technology to the high level of science and technology present in the Western Community. The role of supercomputing in this transition will include leading the process of organizational change in research and development. The paper contains a short overview on the current state of this evolution, on the currently used political and administrative tools to keep this evolution on track, and on the influence on the Konrad-Zuse-Zentrum, which is, as a Berlin institution, in the geographical and cultural center of this transformation.}, language = {en} } @misc{Lang1991, author = {Lang, Jens}, title = {An Adaptive Finite Element Method for Convection-Diffusion Problems by Interpolation Techniques.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4795}, number = {TR-91-04}, year = {1991}, abstract = {For adaptive solution of convection- difussion problems with the streamline-diffusion finite element method, an error estimator based on interpolation techniques is developed. It can be shown that for correctness of this error estimator a restriction of the maximum angle is to be sufficient. Compared to usual methods, the adaptive process leads to more accurate solutions at much less computational cost. Numerical tests are enclosed. {\bf Keywords: } Adaptive finite elements, convection- diffusion equation, internal and boundary layers, streamline-diffusion. {\bf Subject Classifications:} AMS(MOS): 65N15, 65N30}, language = {en} } @misc{Noelle1991, author = {Noelle, Sebastian W. C.}, title = {On the Limits of Operator Splitting: Numerical Experiments for the Complex Burgers Equation.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4789}, number = {TR-91-03}, year = {1991}, abstract = {A high resolution Godunov-type method is developed and applied to a two-dimensional version of the Burgers equation. On one-dimensional testproblems the scheme is second order accurate for smooth flow and resolves discontinuities sharply. On two-dimensional problems, however, large numerical oscillations are introduced when discontinuities traveling obliquely to the grid directions are present. These oscillations are caused by a Strang- type operator splitting, and cannot be eliminated using flux limiters or small timesteps. {\bf Keywords:} High resolution methods, Godunovs method, operator splitting, complex Burgers equation. {\bf AMS:} 35: A40, L45, L60, L65, L, 67. 65: M05, M10.}, language = {en} } @misc{LueggerDalitz1991, author = {L{\"u}gger, Joachim and Dalitz, Wolfgang}, title = {Verteilung mathematischer Software mittels elektronischer Netze: Die elektronische Softwarebibliothek eLib.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4774}, number = {TR-91-02}, year = {1991}, abstract = {Mit zunehmender Dezentralisierung im Bereich des Wissenschaftlichen Rechnens steigt auch der Bedarf an Softwarequellen qualitativ hochwertiger mathematischer Algorithmen. F{\"u}r den Software- und Informationsaustausch wird die Einrichtung {\"o}ffentlicher, elektronischer Softwarebibliotheken vorgeschlagen. Am Beispiel der eLib des ZIB werden die notwendigen technischen Konzepte, die u.a. auch in den heutigen Gegebenheiten der technischen Kommunikation begr{\"u}ndet sind, diskutiert. Die eLib ist fenster- und men{\"u}orientiert aufgebaut und folglich im Dialog sehr einfach zu benutzen. Sie kann aber auch mit ihrer Kommandosprache allein auf dem Wege {\"u}ber elektronische Post abgefragt werden. {\"U}ber die eLib sind, nach dem Verbund mit den Netzbibliotheken NetLib und Reduce-NetLib jetzt etwa 6000 mathematische Programme und allgemeine Dokumente verf{\"u}gbar. Das Dienstleistungsangebot der eLib setzt Beitr{\"a}ge aus einer aktiven Benutzergemeinschaft voraus. Es besteht die Hoffnung, daß durch den {\"o}ffentlichen Softwareaustausch sich Entwickler und Anwender wechselseitig in ihrer Arbeit befruchten.}, language = {de} } @misc{BornemannErdmannRoitzsch1991, author = {Bornemann, Folkmar A. and Erdmann, Bodo and Roitzsch, Rainer}, title = {KASKADE - Numerical Experiments.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4762}, number = {TR-91-01}, year = {1991}, abstract = {The C-implementation of KASKADE, an adaptive solver for linear elliptic differential equations in 2D, is object of a set of numerical experiments to analyze the use of resources (time and memory) with respect to numerical accuracy. We study the dependency of the reliability, robustness, and efficiency of the program from the parameters controlling the algorithm.}, language = {en} } @misc{Giloi1990, author = {Giloi, Wolfgang K.}, title = {Konrad Zuses Plankalk{\"u}l als Vorl{\"a}ufer moderner Programmier-modelle. (Vortrag)}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4759}, number = {TR-90-13}, year = {1990}, language = {de} } @misc{NowakWeimann1990, author = {Nowak, Ulrich and Weimann, Lutz}, title = {GIANT - A Software Package for the Numerical Solution of Very Large Systems of Highly Nonlinear Equations.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4746}, number = {TR-90-11}, year = {1990}, abstract = {This report presents the final realization and implementation of a global inexact Newton method proposed by Deuflhard. In order to create a complete piece of software, a recently developed iterative solver (program GBIT) due to Deuflhard, Freund, Walter is adapted and serves as the standard iterative linear solver. Alternative linear iterative solvers may be adapted as well, e.g. the widely distributed code GMRES. The new software package GIANT (Global Inexact Affine Invariant Newton Techniques) allows an efficient and robust numerical solution of very large scale highly nonlinear systems. Due to the user friendly interface and its modular design, the software package is open for an easy adaptation to specific problems. Numerical experiments for some selected problems illustrate performance and usage of the package.}, language = {en} } @misc{RoitzschKornhuber1990, author = {Roitzsch, Rainer and Kornhuber, Ralf}, title = {BOXES - a Program to Generate Triangulations from a Rectangular Domain Description.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4738}, number = {TR-90-09}, year = {1990}, abstract = {BOXES computes a triangulation from a 2D domain description which consists of an arbitrary set of rectangles. Each rectangle may have attributes to control the triangulating process, define subdomain classes, or specify boundary conditions. The output of the program can be used as a coarse grid for KASKADE or one of its variants. Additional features are extensive checking of the user input, graphical display, and simple editing.}, language = {en} } @misc{Wulkow1990, author = {Wulkow, Michael}, title = {Numerical Treatment of Countable Systems of Ordinary Differential Equations.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4728}, number = {TR-90-08}, year = {1990}, abstract = {Countable systems of ordinary differential equations appear frequently in chemistry, physics, biology and medicine. They can be considered as ordinary differential equations in sequence spaces. In this work, a full adaptive algorithm for the computational treatment of such systems is developed. The method combines time discretization with extrapolation in Hilbert spaces with a discrete Galerkin approach as discretization of the stationary subproblems. The Galerkin method is based on orthogonal functions of a discrete variable , which are generated by certain weight functions. A theory of countable systems in the associated weighted sequence spaces is developed as well as a theory of the Galerkin method. The Galerkin equations can be assembled either by use of analytical properties of the orthogonal functions or numerically by a multilevel summation algorithm. The resulting algorithm CODEX is applied to many examples of technological interest, in particular from polymer chemistry.}, language = {en} } @misc{Deuflhard1990, author = {Deuflhard, Peter}, title = {Zuses Werk weiterdenken. (Vortrag)}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4717}, number = {TR-90-07}, year = {1990}, language = {de} } @misc{DeuflhardHohmann1990, author = {Deuflhard, Peter and Hohmann, Andreas}, title = {Einf{\"u}hrung in die Numerische Mathematik.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4704}, number = {TR-90-06}, year = {1990}, abstract = {Diese Vorlesung ist eine Einf{\"u}hrung in die Numerische Mathematik als einem der drei Bereiche (neben den Naturwissenschaften und der Informatik) des am besten mit dem Begriff Scientific Computing charakterisierten Forschungsgebietes. Aufgabe dieser relativ jungen Wissenschaft ist die Entwicklung von Rechenverfahren f{\"u}r Probleme aus den Naturwissenschaften mit Hilfe mathematischer Methoden.}, language = {de} } @misc{GrammelMaierhoeferSkorobohatyj1989, author = {Grammel, Martin and Maierh{\"o}fer, Gerhard and Skorobohatyj, Georg}, title = {Trapex in POOL-Implementierung eines numerischen Algorithmus in einer parallelen objektorientierten Sprache.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4696}, number = {TR-90-05}, year = {1989}, abstract = {Die Parallelisierung eines vorhandenen sequentiellen Programmes erfolgt im allgemeinen in der Weise, daß es auf Grund einer Analyse der Datenabh{\"a}ngigkeiten in mehrere parallel ausf{\"u}hrbare Teile zerlegt wird, die ihrerseits sequentiell ablaufen und untereinander Daten austauschen. Eine parallele Programmiersprache sollte diese Vorgehensweise unterst{\"u}tzen, indem sie Sprachmittel zur Verf{\"u}gung stellt, mittels derer sich die Modularisierung und Kommunikation bequem formulieren l{\"a}ßt. Nun l{\"a}ßt sich prinzipiell jede vorhandene sequentielle Programmiersprache um solche Konstrukte erweitern; g{\"u}nstiger in Hinblick auf die Strukturierung eines parallelen Programmes erscheint es aber m{\"o}glicherweise, eine solche Programmiersprache zu verwenden, die die genannten Konzepte als elementare zur Verf{\"u}gung stellt. Dies ist offensichtlich bei objektorientierten Programmiersprachen der Fall. Im vorliegenden Bericht wird an Hand eines Beispiels - TRAPEX -, das in POOL-T implementiert wurde, untersucht, inwieweit eine objektorientierte Sprache zur effektiven Programmierung eines numerischen Algorithmus geeignet ist. {\bf Key Words:} parallele objektorientierte Programmiersprache, Message Passing, Abstract Data Typing, Klassenhierarchi, Modul-Import-Mechanismus, Client/Server-Prinzip, Load Balancing, adaptive numerische Algorithmen, Ordnungs- und Schrittweitensteuerung, Romberg-Quadratur.}, language = {de} } @misc{Hege1990, author = {Hege, Hans-Christian}, title = {Datenabh{\"a}ngigkeitsanalyse und Programmtransformationen auf CRAY-Rechnern mit dem Fortran-Pr{\"a}prozessor fpp}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4685}, number = {TR-90-04}, year = {1990}, abstract = {The FORTRAN preprocessor fpp in the newly introduced Autotasking System of CRAY Research allows automatic vectorization and parallelization on basis of a data dependence analysis. An introduction into data dependence analysis is given, showing how data dependence graphs unveil opportunities for program transformations like vectorization and concurrentization. The report contains a complete description of the preprocessors functionality, its options and directives for increasing the effectiveness of the dependence analyzer and steering the code transformations. Finally, some advice is given for the practical use of fpp on CRAY computers.}, language = {de} } @misc{OPUS4-467, title = {CRAY-Handbuch. Einf{\"u}hrung in die Benutzung der CRAY X-MP unter UNICOS 5.1}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4679}, number = {TR-90-03}, year = {1990}, abstract = {Das CRAY-Handbuch des ZIB beschreibt nach einer grundlegenden bersicht detailliert die Handhabung von UNICOS-Dateien, die Verwendung von UNICOS-Kommandos und schließlich die (f{\"u}r Benutzer allein zugelassene) Ausf{\"u}hrung von Batchjobs auf der CRAY. Neben der Erreichbarkeit der CRAY {\"u}ber das TCP/IP-Netz werden die Compiler FORTRAN, PASCAL und C beschrieben und schließlich auf die Optimierung der Rechenzeit ebenso wie auf die Fehlersuche eingegangen. Ein umfangreicher Anhang f{\"u}hrt bereitgestellte Programmpakete, weiterf{\"u}hrende Literatur, Zahlenbereiche und Zeichendarstellung an der CRAY auf.}, language = {de} } @misc{MaierhoeferSkorobohatyj1990, author = {Maierh{\"o}fer, Gerhard and Skorobohatyj, Georg}, title = {Implementierung von parallelen Versionen der Gleichungsl{\"o}ser EULEX und EULSIM auf Transputern.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4666}, number = {TR-90-02}, year = {1990}, abstract = {Im vorliegenden Bericht wird die Parallelisierung zweier numerischer Algorithmen zur L{\"o}sung gew{\"o}hnlicher Differentialgleichungssysteme 1.Ordnung (explizite und semi-implizite Euler- Diskretisierung und \$h\$-Extrapolation) beschrieben. Implementiert wurden die Algorithmen mit OCCAM2 unter TDS (Transputer Development System) mit bis zu 4 Transputern T800. Meßwerte f{\"u}r die erreichten Beschleunigungen werden anhand mehrer Beispiele von Differentialgleichungs-systemen angegeben. {\bf Schl{\"u}sselw{\"o}rter:} Adaptive, parallele Systeme; OCCAM2; Transputer; numerische Gleichungsl{\"o}ser; Euler-Diskretisierung; \$h\$-Extrapolation.}, language = {de} } @misc{Gatermann1990, author = {Gatermann, Karin}, title = {Gruppentheoretische Konstruktion von symmetrischen Kubaturformeln.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4652}, number = {TR-90-01}, year = {1990}, abstract = {\$G\$-invariant cubature formulas for numerical integration over n-dimensional, \$G\$- invariant integration regions are computed symbolically. The nodes are the common zeros of some \$d\$-orthogonal polynomials which build an \$H\$-basis of an ideal. Approaches for these polynomials depending on parameters are made with the help of the theory of linear representations of a group \$G\$. This theory is also used for the effective computation of necessary conditions which determines the parameters. Another approach uses invariant theory and gr{\"o}bner bases.}, language = {de} } @misc{MaierhoeferSkorobohatyj1989, author = {Maierh{\"o}fer, Gerhard and Skorobohatyj, Georg}, title = {Implementierung des parallelen TRAPEX auf Transputern.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4649}, number = {TR-89-08}, year = {1989}, abstract = {Der folgende Bericht ist eine Erg{\"a}nzung des ZIB Technical Report TR 88-05. Entsprechend wird hier nicht auf die grunds{\"a}tzlichen Fragen der Parallelisierbarkeit des sequentiellen TRAPEX eingegangen. Diese sind im TR 88-5 er{\"o}rtert, die dort beschriebenen Algorithmen (vertikale und horizontale Parallelisierung) werden auch f{\"u}r die Transputerarchitektur verwendet. Meßergebnisse sind im letzten Teil angef{\"u}gt.}, language = {de} } @misc{Bornemann1989, author = {Bornemann, Folkmar A.}, title = {Adaptive multilevel discretization in time and space for parabolic partial differential equations.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4638}, number = {TR-89-07}, year = {1989}, abstract = {The present paper developes an adaptive multilevel approach for parabolic PDE's - as a first step, for one linear scalar equation. Full adaptivity of the algorithm is conceptually realized by simultaneous multilevel discretization in both time and space. Thus the approach combines multilevel time discretization, better known as extrapolation methods, and multilevel finite element space discretization such as the hierarchical basis method. The algorithmic approach is theoretically backed by careful application of fundamental results from semigroup theory. These results help to establish the existence of asymptotic expansions (in terms of time-steps) in Hilbert space. Finite element approximation then leads to perturbed expansions, whose perturbations, however, can be pushed below a necessary level by means of an adaptive grid control. The arising space grids are not required to satisfy any quasi- uniformity assumption. Even though the theoretical presentation is independent of space dimension details of the algorithm and numerical examples are given for the 1-D case only. For the 1-D elliptic solver, which is used, an error estimator is established, which works uniformly well for a family of elliptic problems. The numerical results clearly show the significant perspectives opened by the new algorithmic approach.}, language = {en} } @misc{MelenkNeun1989, author = {Melenk, Herbert and Neun, Winfried}, title = {Implementation of Portable Standard LISP for the SPARC Processor.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4625}, number = {TR-89-06}, year = {1989}, abstract = {The SPARC processor is a RISC (Reduced Instruction Set Computer) microcomputer, built into the SUN4 workstations. Since RISC processors are very well-suited for LISP processing, the implementation of a dialect of LISP (Portable Standard LISP, PSL) boded well for a great speed-up in comparison with other types of microcomputers. A first approach was done at The RAND Corporation in Santa Monica, which was derived from classical processor types like MC68000 or VAX. At the Konrad- Zuse-Zentrum f{\"u}r Informationstechnik Berlin (ZIB) that initial implementation was redesigned in order to adapt PSL to the specific features of the SPARC processor. The present implementation, in some parts, is very close to Cray PSL version also done in ZIB. Some timing informations are given in the appendix.}, language = {en} } @misc{Roitzsch1989, author = {Roitzsch, Rainer}, title = {KASKADE Programmer's Manual.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4617}, number = {TR-89-05}, year = {1989}, abstract = {The Programmers Manual contains the documentation of the C-KASKADE implementation. KASKADE is an adaptive finite element code (see SC ). The interfaces of all modules are described.}, language = {en} } @misc{Roitzsch1989, author = {Roitzsch, Rainer}, title = {KASKADE User's Manual.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4605}, number = {TR-89-04}, year = {1989}, abstract = {The Users Manual contains an introduction to the usage of the C-KASKADE implementation. KASKADE is an adaptive finite element code (see SC ). The manual includes a description of all commands, a simple recipe to define a new problem by changing the KASKADE source and a complete example.}, language = {en} } @misc{Walter1989, author = {Walter, Artur}, title = {Ein Finite-Element-Verfahren zur numerischen L{\"o}sung von Erhaltungsgleichungen.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4597}, number = {TR-89-03}, year = {1989}, abstract = {A new approach for the discretisation of hyperbolic conservation laws via a finite element method is developed and analysed. Appropriate forms of the Eulers equation of gas dynamic are considered to employ the algorithm in a reasonable way for this system of nonlinear equations. Both mathematical and physical stability results are obtained. A main part of the paper is devoted to the convergence proof with energy methods under strong regularity of the solution of a scalar nonlinear conservation law. Some hints on the implementation and numerical results for the calculation of transonic gasflow through a Laval nozzle are given. The necessary amount of numerical work is compared to an established finite difference method and the efficiency of the algorithm is shown. A survey on recent literature about finite element methods for hyperbolic problem is included.}, language = {de} } @misc{Deuflhard1989, author = {Deuflhard, Peter}, title = {Numerik von Anfangswertmethoden f{\"u}r gew{\"o}hnliche Differentialgleichungen.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4580}, number = {TR-89-02}, year = {1989}, abstract = {Das voliegende Skriptum entstand aus einer Vorlesung, die ich im WS 87/88 an der Freien Universit{\"a}t Berlin im Fachbereich Mathematik gehalten habe. Mein urspr{\"u}ngliches Vorlesungsmanuskript wurde von Herrn F. Bornemann in weiten Teilen {\"u}berarbeitet, reorganisiert und substantiell erg{\"a}nzt. Der Inhalt stammt gr{\"o}ßtenteils aus Originalarbeiten j{\"u}ngeren Datums. Dar{\"u}berhinaus finden sich zahlreiche Teile, die aus meiner jahrelangen Besch{\"a}ftigung mit dem Thema entstanden aber unpubliziert geblieben sind. Das Skriptum erhebt nicht den Anspruch, ein Lehrbuch zu sein. Es war zun{\"a}chst als Ausarbeitung f{\"u}r meinen studentischen H{\"o}rerkreis sowie als internes Arbeitspapier f{\"u}r das ZIB bestimmt. Die Kunde von der bloßen Existenz eines solchen Skriptums hat jedoch zu einer derart regen Nachfrage gef{\"u}hrt, daß es hiermit als Technischer Report des ZIB einer breiteren ffentlichkeit zug{\"a}nglich gemacht werden soll. In der vorliegenden Form richtet es sich in erster Linie an Mathematiker; es soll sich jedoch auch f{\"u}r Naturwissenschaftler und Ingenieure eignen, die sich einen Einblick in den theoretischen und algorithmischen Hintergrund der von ihnen verwendeten wissenschaftlichen Software verschaffen wollen.}, language = {de} } @misc{OPUS4-457, title = {CRAY-HANDBUCH. Einf{\"u}hrung in die Benutzung der CRAY X-MP unter UNICOS. (veraltet)}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4574}, number = {TR-89-01}, year = {1989}, language = {de} } @misc{MaierhoeferSkorobohatyj1988, author = {Maierh{\"o}fer, Gerhard and Skorobohatyj, Georg}, title = {Parallel-TRAPEX (Ein paralleler adaptiver Algorithmus zur numerischen Integration; seine Implementierung f{\"u}r SUPRENUM-artige Architekturen mit SUSI).}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4560}, number = {TR-88-05}, year = {1988}, abstract = {This paper describes some ways of transforming a sequential adaptive algorithm for numerical evaluation of an integral (Romberg- Quadrature with polynomial Extrapolation method) to a parallel one, such as have been implementad by the authors. We developed an algorithm which preserves the sequential adaptivity and is capable of running on various architectures, dynamically controlling the number of avtive processors depending on the problem. To study the time behaviour, we used the simulator SUSI(SUprenum SImulatur) which is able to simulate SUPRENUM-like architectures. Results are given in part 3. {\bf Keywords:} Romberg quadrature; numerical integration; parallel adaptive algorithm; SUSI; simulation; SUPRENUM; MIMD-Fortran; computer architecture; granularity; load balacing; master-slave-principle.}, language = {de} } @misc{BuhtzLangendorfPaetsch1988, author = {Buhtz, Danuta Anna and Langendorf, Jens and Paetsch, Olaf}, title = {GRAZIL - 3D. Ein graphisches Anwendungsprogramm zur Darstellung von Kurven- und Funktionsverl{\"a}ufen im r{\"a}umlichen Koordinatensystem.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4556}, number = {TR-88-04}, year = {1988}, abstract = {GRAZIL - 3D ist ein interaktives Programmpaket zur graphischen Darstellung von dreidimensionalen Kurvenverl{\"a}ufen. Das Aussehen der r{\"a}umlichen Ausgabe des Bildes wird durch Angabe des Blickwinkels und der Perspektive festgelegt.}, language = {de} } @misc{MelenkNeun1988, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Installation Guide for CRAY 1 / X-MP Systems Running UNICOS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4541}, number = {TR-88-03}, year = {1988}, abstract = {This guide describes the CRAY/UNICOS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running UNICOS. This document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, publication CP84.}, language = {en} } @misc{MelenkNeun1988, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE User s Guide for the CRAY 1 / CRAY X-MP Series Running UNICOS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4539}, number = {TR-88-02}, year = {1988}, abstract = {This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the Operating System UNICOS. The document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, (CP85).}, language = {en} } @misc{BuhtzBuhtz1988, author = {Buhtz, Rainer and Buhtz, Danuta Anna}, title = {TDLG 3.1 - Ein interaktives Programm zur Darstellung dreidimensionaler Modelle auf Rastergraphikger{\"a}ten.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4522}, number = {TR-88-01}, year = {1988}, abstract = {TDLG 3.1 dient zur Darstellung von dreidimensionalen Objekten, die sich aus offenen Linienz{\"u}gen, Dreieck- und Viereckelementen zusammensetzen. Dabei k{\"o}nnen verschiedene Visualisierungstechniken benutzt werden: Drahtmodell, Schattierung mit und ohne Lichtquelle, Hidden Surface Removal. Durch Verwendung von Konvertierungsprogrammen k{\"o}nnen auch IGES- und VDAFS- Dateien dargestellt werden.}, language = {de} } @misc{LangendorfPaetsch1987, author = {Langendorf, Jens and Paetsch, Olaf}, title = {GRAZIL (Graphical ZIB Language).}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4518}, number = {TR-87-07}, year = {1987}, abstract = {GRAZIL ist ein interaktives Programmpaket zur graphischen Darstellung von zwei-dimensionalen Kurvenverl{\"a}ufen. Dem Benutzer stehen zahlreiche Kommandos zum Gestalten des Layouts der Zeichnung zur Verf{\"u}gung. Die Eingabedaten m{\"u}ssen dem ZUGRIFF- Konzept gen{\"u}gen, wodurch die genaue Struktur der Daten erst zur Laufzeit bekannt sein muß und somit eine hohe Flexibilit{\"a}t und eine große Bandbreite der Einsatzm{\"o}glichkeiten erreicht wird. GRAZIL wurde mit der graphischen Grundsoftware BIZEPS2 und GKS entwickelt. Dadurch kann ein breites Rechner- und Ausgabeger{\"a}tespektrum genutzt werden.}, language = {de} } @misc{BuhtzLangendorfPaetschetal.1987, author = {Buhtz, Rainer and Langendorf, Jens and Paetsch, Olaf and Buhtz, Danuta Anna}, title = {ZUGRIFF - Eine vereinheitlichte Datenspezifikation f{\"u}r graphische Darstellungen und ihre graphische Aufbereitung.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4506}, number = {TR-87-06}, year = {1987}, abstract = {ZUGRIFF ist eine Dateischnittstelle f{\"u}r Graphikausgabe speziell numerischer Anwenderprogramme. Dieser Report beschreibt den Leistungsumfang der Spezifikation sowie die interaktive graphische Verarbeitung von ZUGRIFF- Dateien.}, language = {de} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Users Guide for the CRAY 1 / X-MP Series Running COS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4498}, number = {TR-87-05}, year = {1987}, abstract = {This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the CRAY Operating System (COS). The document was derived from the corresponding document for Vax/UNIX prepared by A.C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, (CP85).}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Installation Guide for CRAY 1 / X-MP Systems Running COS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4486}, number = {TR-87-04}, year = {1987}, abstract = {This guide describes the CRAY/COS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running COS. This document was derived from the corresponding document for Vax/Unix prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, publication CP84.}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {Portable Common LISP Subset Implementation for CRAY X+MP Computers.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4479}, number = {TR-87-03}, year = {1987}, abstract = {This document describes the installation procedure and maintenance for the Portable Common LISP Subset (PCLS) developed at the University of Utah.}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {Portable Standard LISP Implementation for CRAY X+MP Computers. Release of PSL 3.4 for COS.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4465}, number = {TR-87-02}, year = {1987}, abstract = {Portable Standard LISP (PSL) is a portable implementation of the programming language LISP constructed at the University of Utah. The version 3.4 of PSL was implemented for CRAY X-MP computers by Konrad Zuse-Zentrum Berlin; this implementation is based to an important part on the earlier implementation of PSL 3.2 at Salt Lake City, Los Alamos and Mendota Heights.}, language = {en} } @misc{BuschPoehleStech1987, author = {Busch, Hubert and P{\"o}hle, Uwe and Stech, Wolfgang}, title = {CRAY-Handbuch. - Einf{\"u}hrung in die Benutzung der CRAY.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4459}, number = {TR-87-01}, year = {1987}, abstract = {Das vorliegende Handbuch wendet sich an alle Benutzer des f{\"u}r den Norddeutschen Vektorrechnerverbund im ZIB installierten Rechners CRAY X-MP/24. Ein großer Teil der Darstellung ist der Optimierung von Programmen gewidmet, die in FORTRAN geschrieben sind. Gerade weil die CRAY einer der schnellsten Rechner der Welt ist, wird jeder Benutzer fr{\"u}her oder sp{\"a}ter selbst auf dieses Thema stoßen, denn die Maschine ist vornehmlich f{\"u}r Probleme bestimmt, die f{\"u}r die meisten anderen Rechner zu komplex sind. Maschinen der CRAY-Leistungsklasse beziehen einen erheblichen Teil ihrer Geschwindigkeit aus der parallelen Arbeit vieler Komponenten. Programme, die die jeweilige Architektur der Maschine ber{\"u}cksichtigen, k{\"o}nnen um Gr{\"o}ßenordnungen schneller (also wirtschaftlicher) sein als Programme, deren Autor beim Schreiben einen sogenannten "klassischen" Rechner vor seinem geistigen Auge hatte. Daher wird auch der technische Aufbau der CRAY X-MP im Handbuch erl{\"a}utert. Weitere Teile des Handbuches besch{\"a}ftigen sich mit den Vorrechnern und dem Rechnernetz.}, language = {de} } @misc{WitzigBeckenbachEifleretal.2016, author = {Witzig, Jakob and Beckenbach, Isabel and Eifler, Leon and Fackeldey, Konstantin and Gleixner, Ambros and Grever, Andreas and Weber, Marcus}, title = {Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes}, issn = {1438-0064}, doi = {10.1137/16M1091162}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60353}, year = {2016}, abstract = {In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst.}, language = {en} } @misc{EhlkeRammLameckeretal.2013, author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Hege, Hans-Christian and Zachow, Stefan}, title = {Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41896}, year = {2013}, abstract = {We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.}, language = {en} } @misc{WinkelmannSchuettevonKleist2013, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1}, issn = {1438-0064}, doi = {10.4310/CMS.2014.v12.n5.a4}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41955}, year = {2013}, abstract = {Markov Decision Processes (MDP) or Partially Observable MDPs (POMDP) are used for modelling situations in which the evolution of a process is partly random and partly controllable. These MDP theories allow for computing the optimal control policy for processes that can continuously or frequently be observed, even if only partially. However, they cannot be applied if state observation is very costly and therefore rare (in time). We present a novel MDP theory for rare, costly observations and derive the corresponding Bellman equation. In the new theory, state information can be derived for a particular cost after certain, rather long time intervals. The resulting information costs enter into the total cost and thus into the optimization criterion. This approach applies to many real world problems, particularly in the medical context, where the medical condition is examined rather rarely because examination costs are high. At the same time, the approach allows for efficient numerical realization. We demonstrate the usefulness of the novel theory by determining, from the national economic perspective, optimal therapeutic policies for the treatment of the human immunodefficiency virus (HIV) in resource-rich and resource-poor settings. Based on the developed theory and models, we discover that available drugs may not be utilized efficiently in resource-poor settings due to exorbitant diagnostic costs.}, language = {en} } @misc{WendeSteinke2013, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, issn = {1438-0064}, doi = {10.1145/2503210.2503254}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42187}, year = {2013}, abstract = {Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated.}, language = {en} } @misc{LieFackeldeyWeber2013, author = {Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus}, title = {A square root approximation of transition rates for a Markov State Model}, issn = {1438-0064}, doi = {10.1137/120899959}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42195}, year = {2013}, abstract = {Trajectory- or mesh-based methods for analyzing the dynamical behavior of large molecules tend to be impractical due to the curse of dimensionality - their computational cost increases exponentially with the size of the molecule. We propose a method to break the curse by a novel square root approximation of transition rates, Monte Carlo quadrature and a discretization approach based on solving linear programs. With randomly sampled points on the molecular energy landscape and randomly generated discretizations of the molecular configuration space as our initial data, we construct a matrix describing the transition rates between adjacent discretization regions. This transition rate matrix yields a Markov State Model of the molecular dynamics. We use Perron cluster analysis and coarse-graining techniques in order to identify metastable sets in configuration space and approximate the transition rates between the metastable sets. Application of our method to a simple energy landscape on a two-dimensional configuration space provides proof of concept and an example for which we compare the performance of different discretizations. We show that the computational cost of our method grows only polynomially with the size of the molecule. However, finding discretizations of higher-dimensional configuration spaces in which metastable sets can be identified remains a challenge.}, language = {en} } @misc{DresslerSteinke2013, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {An Automated Approach for Estimating the Memory Footprint of Non-Linear Data Objects}, issn = {1438-0064}, doi = {10.1007/978-3-642-54420-0_25}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42224}, year = {2013}, abstract = {Current programming models for heterogeneous devices with disjoint physical memory spaces require explicit allocation of device memory and explicit data transfers. While it is quite easy to manually implement these operations for linear data objects like arrays, this task becomes more difficult for non-linear objects, e.g. linked lists or multiple inherited classes. The difficulties arise due to dynamic memory requirements at run-time and the dependencies between data structures. In this paper we present a novel method to build a graph-based static data type description which is used to create code for injectable functions that automatically determine the memory footprint of data objects at run-time. Our approach is extensible to implement automatically generated optimized data transfers across physical memory spaces.}, language = {en} } @misc{RammMorilloVictoriaTodtetal.2013, author = {Ramm, Heiko and Morillo Victoria, Oscar Salvador and Todt, Ingo and Schirmacher, Hartmut and Ernst, Arneborg and Zachow, Stefan and Lamecker, Hans}, title = {Visual Support for Positioning Hearing Implants}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42495}, year = {2013}, abstract = {We present a software planning tool that provides intuitive visual feedback for finding suitable positions of hearing implants in the human temporal bone. After an automatic reconstruction of the temporal bone anatomy the tool pre-positions the implant and allows the user to adjust its position interactively with simple 2D dragging and rotation operations on the bone's surface. During this procedure, visual elements like warning labels on the implant or color encoded bone density information on the bone geometry provide guidance for the determination of a suitable fit.}, language = {en} } @misc{HombergBaumWiebeletal.2013, author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42510}, year = {2013}, abstract = {An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.}, language = {en} } @misc{MeiselRoeblitz2013, author = {Meisel, Kristin and R{\"o}blitz, Susanna}, title = {Mathematische Modellierung der Knochenremodellierung}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42010}, year = {2013}, abstract = {Knochenremodellierung beinhaltet den Auf- und Abbau der Knochenmasse durch die verschiedenen Knochenzellen und findet fast {\"u}berall, auch am Skelett Erwachsener, statt. F{\"u}r die Erneuerung der Knochensubstanz sind die Osteoblasten zust{\"a}ndig. Sie ersetzen exakt die Menge der Knochenmasse, welche zuvor durch Osteoklasten abgebaut wurde. St{\"o}rungen dieses, durch viele Faktoren beeinflussten Prozesses f{\"u}hren zu pathologischen Ver{\"a}nderungen, beispielsweise zu Osteoporose oder Arthritis. Auf der Grundlage analysierter publizierter Modelle wurde ein Modell entwickelt, welches den Einfluss einiger dieser Faktoren realistisch abbildet. Auf diese Weise kann die Wirkung von basalem PTH, des RANKL-OPG-Systems ( RANKL: Receptor activator of nuclear factor kappa-B ligand, OPG: Osteoprotegerin) und des Estradiols auf den Knochenstoffwechsel am vorgestellten System untersucht werden. Außerdem wurde durch Estradiolmangel hervorgerufene Osteoporose und der kurative Effekt von synthetischen Medikamenten wie Estradiol oder intermittierend verabreichtem PTH modelliert. Mit der Parametersch{\"a}tzung anhand des Gauß-Newton-Verfahrens wird des Weiteren eine Methode vorgestellt, die es erm{\"o}glicht, mathematische Modelle bestm{\"o}glich durch Variation der Parameterwerte an experimentelle Daten anzupassen. Das am Zuse-Institut Berlin entwickelte Softwarepaket POEM wendet diesen Algorithmus an und wird ebenfalls erl{\"a}utert.}, language = {de} } @misc{Pyszkalski2013, author = {Pyszkalski, Wolfgang}, title = {{\"U}bersicht {\"u}ber die Datenhaltung im ZIB und die M{\"o}glichkeiten einer Nutzung durch Projekte}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42060}, year = {2013}, abstract = {Dieser Bericht beschreibt in allgemein verst{\"a}ndlicher Form die Struktur der Datenhaltung im Zuse-Institut Berlin (ZIB) und die aktuell verwendeten Strategien im Umgang mit immer st{\"a}rker wachsenden Datenmengen, sowie der Herausforderung der Speicherung unwiederbringlicher Daten {\"u}ber im Grunde unbegrenzte Zeit.}, language = {de} } @misc{BujotzekSchuettNielsenetal.2013, author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {Efficient Conformational Analysis by Partition-of-Unity Coupling}, journal = {Math Chem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42570}, year = {2013}, abstract = {Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.}, language = {en} }