TY - GEN A1 - Galliat, Tobias A1 - Deuflhard, Peter A1 - Roitzsch, Rainer A1 - Cordes, Frank T1 - Automatic Identification of Metastable Conformations via Self-Organized Neural Networks N2 - As has been shown recently, the identification of metastable chemical conformations leads to a Perron cluster eigenvalue problem for a reversible Markov operator. Naive discretization of this operator would suffer from combinatorial explosion. As a first remedy, a pre-identification of essential degrees of freedom out of the set of torsion angles had been applied up to now. The present paper suggests a different approach based on neural networks: its idea is to discretize the Markov operator via self-organizing (box) maps. The thus obtained box discretization then serves as a prerequisite for the subsequent Perron cluster analysis. Moreover, this approach also permits exploitation of additional structure within embedded simulations. As it turns out, the new method is fully automatic and efficient also in the treatment of biomolecules. This is exemplified by numerical results. T3 - ZIB-Report - 00-51 KW - biochemical conformations KW - cluster analysis KW - Molecular Dynamics KW - Monte-Carlo methods KW - operator discretization KW - Perron cluster Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6197 ER - TY - GEN A1 - Kober, Cornelia A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian A1 - Prohaska, Steffen A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Anisotrope Materialmodellierung für den menschlichen Unterkiefer N2 - Im Rahmen der biomechanischen Simulation knöcherner Organe ist die Frage nach einer befriedigenden Materialbeschreibung nach wie vor ungelöst. Computertomographische Datensätze liefern eine räumliche Verteilung der (Röntgen-)Dichte und ermöglichen damit eine gute Darstellung der individuellen Geometrie. Weiter können die verschiedenen Materialbestandteile des Knochens, Spongiosa und Kortikalis, voneinander getrennt werden. Aber die richtungsabängige Information der Materialanisotropie ist verloren. In dieser Arbeit wird ein Ansatz für eine anisotrope Materialbeschreibung vorgestellt, die es ermöglicht, den Einfluss der individuellen knöchernen Struktur auf das makroskopische Materialverhalten abzuschätzen. T3 - ZIB-Report - 01-31 KW - menschlicher Unterkiefer KW - Simulation mit der Methode der finiten Elemente KW - innerer Aufbau des Knochens KW - anisotrope Elastizität Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6574 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin T1 - Progress Towards a Combined MRI/Hyperthermia System N2 - Regional hyperthermia, a clinical cancer therapy, is the main topic of the Sonderforschungsbereich Hyperthermia: Scientific Methods and Clinical Applications'' at Berlin. In recent years, technological improvements towards a better concentration of heat to the desired target region have been achieved. These include a rather sophisticated integrated software environment for therapy planning and a new hyperthermia applicator. In a next step, a detailed closed loop monitoring of the actual treatment is to be developed. For this purpose the hyperthermia applicator is combined with an MRI system, which will allow to check the positioning of the patients and to measure individual blood perfusion as well as the 3D temperature distribution. The measurements will then be employed for an on-line control of the whole treatment. In this intended setting, new fast feedback control algorithms will come into play. T3 - ZIB-Report - 00-07 KW - hyperthermia KW - medical therapy planning KW - applicator design KW - interventional MRI Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5755 ER - TY - GEN A1 - Deuflhard, Peter A1 - Reich, Sebastian T1 - 2nd International Symposium Algorithms for Macromolecular Modelling N2 - The report contains the program and the collected abstracts of the 2nd International Symposium ``Algorithms for Macromolecular Modelling''. T3 - ZIB-Report - TR-97-03 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5455 ER - TY - GEN A1 - Deuflhard, Peter A1 - Louis, Alfred A1 - Schlegel, W. A1 - Seebass, Martin T1 - Workshop "Scientific Computing in der Medizin" SCMED '97 N2 - Die Arbeitstagung \glqq Scientific Computing in der Medizin\grqq , kurz SCMED \grq 97, findet vom 22. - 23. September 1997 im neu errichteten Gebäude des Konrad-Zuse-Zentrums auf dem Dahlemer naturwissenschaftlichen Campus der Freien Universtät Berlin statt. T3 - ZIB-Report - TR-97-05 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5474 ER - TY - GEN A1 - Deuflhard, Peter T1 - Adaptive Pseudo-transient Continuation for Nonlinear Steady State Problems N2 - Pseudo--transient continuation methods are quite popular for the numerical solution of steady state problems, typically in PDEs. They are based on an embedding into a time dependent initial value problem. In the presence of dynamical invariants the Jacobian matrix of the nonlinear equation system is bound to be singular. The paper presents a convergence analysis which takes this property into account -- in contrast to known approaches. On the basis of the new analysis adaptive algorithms are suggested in detail. These include a variant with Jacobian approximations as well as inexact pseudo--transient continuation, both of which play an important role in discretized PDEs. Numerical experiments are left to future work. T3 - ZIB-Report - 02-14 KW - pseudo--transient continuation KW - linearly implicit KW - Euler discretization KW - stiff integration KW - contractivity of ordinary differential equations KW - lar Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6814 ER - TY - GEN A1 - Deuflhard, Peter T1 - From Molecular Dynamics to Conformational Dynamics in Drug Design N2 - Computational drug design studies molecular recognition in the {\em virtual lab}. The arising Hamiltonian dynamics is known to be chaotic and ill-conditioned already after picoseconds, whereas times are $msec$ up to $min$. Classical molecular dynamics with long term trajectory computation gives, at best, information about time and statistical ensemble averages. The present paper surveys a recent new modeling approach called {\em conformational dynamics}, which is due to the author and Ch. Schütte. This approach achieves information about the dy time scales by telescoping a short term deterministic model with a statistical model. Examples of small biomolecules are included. T3 - ZIB-Report - 02-20 KW - molecular dynamics KW - conformational dynamics KW - drug design KW - Hamiltonian dynamics KW - almost invariant sets KW - transition operator KW - Markov chain KW - Perro Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6878 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hochmuth, Reinhard T1 - Multiscale Analysis of Thermoregulation in the Human Microvascular System N2 - The bio-heat transfer equation is a macroscopic model for describing the heat transfer in microvascular tissue. So far the deduction of the Helmholtz term in the bio-heat transfer equation is not co role. In view of a future numerical application of this new mathematical model to treatment planning in hyperthermia we derive asymptotic estimates for first and second order correctors. T3 - ZIB-Report - 02-31 KW - bio-heat equation KW - hyperthermia KW - homogenization Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6985 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Weiser, Martin T1 - Affine Invariant Adaptive Newton Codes for Discretized PDEs N2 - The paper deals with three different Newton algorithms that have recently been worked out in the general frame of affine invariance. Of particular interest is their performance in the numerical solution of discretized boundary value problems (BVPs) for nonlinear partial differential equations (PDEs). Exact Newton methods, where the arising linear systems are solved by direct elimination, and inexact Newton methods, where an inner iteration is used instead, are synoptically presented, both in affine invariant convergence theory and in numerical experiments. The three types of algorithms are: (a) affine covariant (formerly just called affine invariant) Newton algorithms, oriented toward the iterative errors, (b) affine contravariant Newton algorithms, based on iterative residual norms, and (c) affine conjugate Newton algorithms for convex optimization problems and discrete nonlinear elliptic PDEs. T3 - ZIB-Report - 02-33 KW - Affine invariant Newton methods KW - global Newton methods KW - inexact Newton methods KW - adaptive trust region methods KW - nonlinear partial differential equa Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7005 ER - TY - GEN A1 - Ehrig, Rainald A1 - Ofenloch, Oliver A1 - Schaber, Karlheinz A1 - Deuflhard, Peter T1 - Modelling and Simulation of Aerosol Formation by Heterogeneous Nucleation in Gas-Liquid Contact Devices N2 - This paper describes a new simulation tool for the prediction of aerosol formation and behavior in gas--liquid contact devices such as absorbers, scrubbers, quench coolers, and condensers as well as multistage gas cleaning processes, respectively. Aerosol formation can impact severely the separation efficiency of gas cleaning processes. Aerosol or fog formation can arise by spontaneous condensation or desublimation in supersaturated gas phases. The rigorous description of the mass and energy transfer between the gas phase, the liquid phase, and the growing aerosol droplets leads to a system of partial differential and algebraic equations. For the solution of these systems we have developed the plant simulation tool AerCoDe. This program bases upon the linearly--implicit Euler discretisation, which in combination with extrapolation permits an adaptive step size and order control. Typical simulation results of a multistage industrial flue gas scrubbing process are presented. It is shown, that experimental data can be confirmed if the number concentration of condensation nuclei as an input parameter is roughly known. T3 - ZIB-Report - 01-15 KW - aerosols KW - heterogeneous nucleation KW - two-phase flow KW - balance equations KW - extrapolation methods Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6416 ER - TY - GEN A1 - Weiser, Martin A1 - Deuflhard, Peter T1 - The Central Path towards the Numerical Solution of Optimal Control Problems N2 - A new approach to the numerical solution of optimal control problems including control and state constraints is presented. Like hybrid methods, the approach aims at combining the advantages of direct and indirect methods. Unlike hybrid methods, however, our method is directly based on interior-point concepts in function space --- realized via an adaptive multilevel scheme applied to the complementarity formulation and numerical continuation along the central path. Existence of the central path and its continuation towards the solution point is analyzed in some theoretical detail. An adaptive stepsize control with respect to the duality gap parameter is worked out in the framework of affine invariant inexact Newton methods. Finally, the performance of a first version of our new type of algorithm is documented by the successful treatment of the well-known intricate windshear problem. T3 - ZIB-Report - 01-12 KW - optimal control KW - interior point methods KW - affine invariance Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6380 ER - TY - GEN A1 - Erdmann, Bodo A1 - Kober, Cornelia A1 - Lang, Jens A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian A1 - Deuflhard, Peter T1 - Efficient and Reliable Finite Element Methods for Simulation of the Human Mandible N2 - By computed tomography data (CT), the individual geometry of the mandible is quite well reproduced, also the separation between cortical and trabecular bone. Using anatomical knowledge about the architecture and the functional potential of the masticatory muscles, realistic situations were approximated. The solution of the underlying partial differential equations describing linear elastic material behaviour is provided by an adaptive finite element method. Estimations of the discretization error, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method. T3 - ZIB-Report - 01-14 KW - mandible KW - sensitivity analysis KW - finite element method KW - adaptive grid refinement Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6403 ER - TY - GEN A1 - Deuflhard, Peter T1 - A Comparison of Related Concepts in Computational Chemistry and Mathematics N2 - This article studies the relation of the two scientific languages Chemistry and Mathematics via three selected comparisons: (a) QSSA versus dynamic ILDM in reaction kinetics, (b) lumping versus discrete Galerkin methods in polymer chemistry, and (c) geometrical conformations versus metastable conformations in drug design. The common clear message from these comparisons is that chemical intuition may pave the way for mathematical concepts just as chemical concepts may gain from mathematical precisioning. Along this line, significant improvements in chemical research and engineering have already been possible -- and can be further expected in the future from the dialogue between the two scientific languages. T3 - ZIB-Report - 02-46 KW - dimension reduction KW - model reduction KW - QSSA KW - ILDM KW - reaction kinetics KW - polyreaction kinetics KW - Hamilton systems KW - conformations KW - metastability KW - d Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7138 ER - TY - GEN A1 - Weiser, Martin A1 - Schiela, Anton A1 - Deuflhard, Peter T1 - Asymptotic Mesh Independence of Newton's Method Revisited N2 - The paper presents a new affine invariant theory on asymptotic mesh independence of Newton's method in nonlinear PDEs. Compared to earlier attempts, the new approach is both much simpler and more natural from the algorithmic point of view. The theory is exemplified at collocation methods for ODE boundary value problems and at finite element methods for elliptic PDE problems. T3 - ZIB-Report - 03-13 KW - mesh independence KW - nonlinear partial differential equations KW - Newton method KW - finite element method KW - collocation method Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7352 ER - TY - GEN A1 - Hochmuth, Reinhard A1 - Deuflhard, Peter T1 - Multiscale Analysis for the Bio-Heat Transfer Equation N2 - The bio-heat transfer equation is a macroscopic model for describing the heat transfer in microvascular tissue. In [{\sl Deuflhard, Hochmuth 2002}] the authors applied homogenization techniques to derive the bio-heat transfer equation as asymptotic result of boundary value problems which provide a microscopic description for microvascular tissue. Here those results are generalized to a geometrical setting where the regions of blood are allowed to be connected. Moreover, asymptotic corrector results are derived. T3 - ZIB-Report - 03-08 KW - bio-heat equation KW - hyperthermia KW - homogenization KW - correctors KW - heat transfer KW - Robin boundary conditions Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7302 ER - TY - GEN A1 - Deuflhard, Peter A1 - Weber, Marcus T1 - Robust Perron Cluster Analysis in Conformation Dynamics N2 - The key to molecular conformation dynamics is the direct identification of metastable conformations, which are almost invariant sets of molecular dynamical systems. Once some reversible Markov operator has been discretized, a generalized symmetric stochastic matrix arises. This matrix can be treated by Perron cluster analysis, a rather recent method involving a Perron cluster eigenproblem. The paper presents an improved Perron cluster analysis algorithm, which is more robust than earlier suggestions. Numerical examples are included. T3 - ZIB-Report - 03-19 KW - Markov chains KW - cluster algorithms KW - Perron cluster analysis KW - conformation dynamics Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7415 ER - TY - GEN A1 - Deuflhard, Peter A1 - Schütte, Christof T1 - Molecular Conformation Dynamics and Computational Drug Design N2 - The paper surveys recent progress in the mathematical modelling and simulation of essential molecular dynamics. Particular emphasis is put on computational drug design wherein time scales of $msec$ up to $min$ play the dominant role. Classical long-term molecular dynamics computations, however, would run into ill-conditioned initial value problems already after time spans of only $psec=10^{-12} sec$. Therefore, in order to obtain results for times of pharmaceutical interest, a combined deterministic-stochastic model is needed. The concept advocated in this paper is the direct identification of metastable conformations together with their life times and their transition patterns. It can be interpreted as a {\em transfer operator} approach corresponding to some underlying hybrid Monte Carlo process, wherein short-term trajectories enter. Once this operator has been discretized, which is a hard problem of its own, a stochastic matrix arises. This matrix is then treated by {\em Perron cluster analysis}, a recently developed cluster analysis method involving the numerical solution of an eigenproblem for a Perron cluster of eigenvalues. In order to avoid the 'curse of dimension', the construction of appropriate boxes for the spatial discretization of the Markov operator requires careful consideration. As a biomolecular example we present a rather recent SARS protease inhibitor. T3 - ZIB-Report - 03-20 KW - conformation dynamics KW - Monte Carlo methods KW - transfer operations KW - Hamiltonian dynamics KW - Smoluchowski dynamics KW - metastable sets KW - Perron cluster an Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7427 ER - TY - GEN A1 - Weiser, Martin A1 - Deuflhard, Peter A1 - Erdmann, Bodo T1 - Affine conjugate adaptive Newton methods for nonlinear elastomechanics N2 - The paper extends affine conjugate Newton methods from convex to nonconvex minimization, with particular emphasis on PDE problems originating from compressible hyperelasticity. Based on well-known schemes from finite dimensional nonlinear optimization, three different algorithmic variants are worked out in a function space setting, which permits an adaptive multilevel finite element implementation. These algorithms are tested on two well-known 3D test problems and a real-life example from surgical operation planning. T3 - ZIB-Report - 04-01 KW - affine conjugate Newton methods KW - nonconvex minimization KW - nonlinear elastomechnics KW - cranio-maxillofacial surgery KW - soft tissue simulation KW - multilev Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7768 ER - TY - GEN A1 - Deuflhard, Peter A1 - (Chairs), Hyung Yong Ra T1 - Korean-German Bilateral Symposium on Scientific Computing N2 - Collection of abstracts of the Korean-German Bilateral Symposium on Scientific Computing, Berlin January 15/16, 2004 T3 - ZIB-Report - 04-02 KW - Abstracts Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7778 ER - TY - GEN A1 - Klapproth, Corinna A1 - Schiela, Anton A1 - Deuflhard, Peter T1 - Consistency Results for the Contact-Stabilized Newmark Method N2 - The paper considers the time integration of frictionless dynamical contact problems between viscoelastic bodies in the frame of the Signorini condition. Among the numerical integrators, interest focuses on the contact-stabilized Newmark method recently suggested by Deuflhard et al., which is compared to the classical Newmark method and an improved energy dissipative version due to Kane et al. In the absence of contact, any such variant is equivalent to the Störmer-Verlet scheme, which is well-known to have consistency order 2. In the presence of contact, however, the classical approach to discretization errors would not show consistency at all because of the discontinuity at the contact. Surprisingly, the question of consistency in the constrained situation has not been solved yet. The present paper fills this gap by means of a novel proof technique using specific norms based on earlier perturbation results due to the authors. The corresponding estimation of the local discretization error requires the bounded total variation of the solution. The results have consequences for the construction of an adaptive timestep control, which will be worked out subsequently in a forthcoming paper. T3 - ZIB-Report - 09-06 KW - Dynamical contact problems KW - viscoelasticity KW - Signorini condition KW - consistency KW - Newmark method Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11164 SN - 1438-0064 ER - TY - GEN A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Deuflhard, Peter T1 - On Efficiency and Accuracy in Cardioelectric Simulation N2 - Reasons for the failure of adaptive methods to deliver improved efficiency when integrating monodomain models for myocardiac excitation are discussed. Two closely related techniques for reducing the computational complexity of linearly implicit integrators, deliberate sparsing and splitting, are investigated with respect to their impact on computing time and accuracy. T3 - ZIB-Report - 08-41 KW - elektrische Herzanregung KW - Diskretisierungsfehler KW - splitting KW - mass lumping KW - cardioelectric excitation KW - discretization error KW - splitting KW - mass lumping Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10934 SN - 1438-0064 ER - TY - GEN A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - Mehr Mathematik wagen in der Medizin N2 - Der Artikel gibt einen Einblick in das reiche Feld der Zusammenarbeit zwischen Mathematik und Medizin. Beispielhaft werden drei Erfolgsmodelle dargestellt: Medizinische Bildgebung, mathematische Modellierung und Biosignalverarbeitung im Bereich der Dynamik des Herzens sowie mathematische Modellierung und Simulation in der Krebstherapie Hyperthermie und der Mund-Kiefer-Gesichts-Chirurgie. In allen Fällen existiert ein Gleichklang der Interessen von Medizin und Mathematik: Beide Disziplinen wollen die Resultate schnell und zuverlässig. Für die Klinik heißt das, dass notwendige Rechnungen in möglichst kurzer Zeit, und zwar auf dem PC, ablaufen müssen und dass die Resultate so genau und belastbar sein müssen, dass medizinische Entscheidungen darauf aufbauen können. Für die Mathematik folgt daraus, dass höchste Anforderungen an die Effizienz der verwendeten Algorithmen und die darauf aufbauende Software in Numerik und Visualisierung zu stellen sind. Jedes Kapitel endet mit einer Darstellung der Perspektive des jeweiligen Gebietes. Abschließend werden mögliche Handlungsoptionen für Politik und Wirtschaft diskutiert. T3 - ZIB-Report - 08-25 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10776 SN - 1438-0064 ER - TY - GEN A1 - Klapproth, Corinna A1 - Deuflhard, Peter A1 - Schiela, Anton T1 - A Perturbation Result for Dynamical Contact Problems N2 - This paper is intended to be a first step towards the continuous dependence of dynamical contact problems on the initial data as well as the uniqueness of a solution. Moreover, it provides the basis for a proof of the convergence of popular time integration schemes as the Newmark method. We study a frictionless dynamical contact problem between both linearly elastic and viscoelastic bodies which is formulated via the Signorini contact conditions. For viscoelastic materials fulfilling the Kelvin-Voigt constitutive law, we find a characterization of the class of problems which satisfy a perturbation result in a non-trivial mix of norms in function space. This characterization is given in the form of a stability condition on the contact stresses at the contact boundaries. Furthermore, we present perturbation results for two well-established approximations of the classical Signorini condition: The Signorini condition formulated in velocities and the model of normal compliance, both satisfying even a sharper version of our stability condition. T3 - ZIB-Report - 08-27 KW - Dynamical contact problems KW - stability KW - (visco-)elasticity KW - Signorini condition KW - Newmark method Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10793 SN - 1438-0064 ER - TY - GEN A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo N2 - Recently, a novel concept for the computation of essential features of the dynamics of Hamiltonian systems (such as molecular dynamics) has been proposed. The realization of this concept had been based on subdivision techniques applied to the Frobenius--Perron operator for the dynamical system. The present paper suggests an alternative but related concept that merges the conceptual advantages of the dynamical systems approach with the appropriate statistical physics framework. This approach allows to define the phrase ``conformation'' in terms of the dynamical behavior of the molecular system and to characterize the dynamical stability of conformations. In a first step, the frequency of conformational changes is characterized in statistical terms leading to the definition of some Markov operator $T$ that describes the corresponding transition probabilities within the canonical ensemble. In a second step, a discretization of $T$ via specific hybrid Monte Carlo techniques is shown to lead to a stochastic matrix $P$. With these theoretical preparations, an identification algorithm for conformations is applicable. It is demonstrated that the discretization of $T$ can be restricted to few essential degrees of freedom so that the combinatorial explosion of discretization boxes is prevented and biomolecular systems can be attacked. Numerical results for the n-pentane molecule and the triribonucleotide adenylyl\emph{(3'-5')}cytidylyl\emph{(3'-5')}cytidin are given and interpreted. T3 - ZIB-Report - SC-98-45 KW - conformation KW - conformational dynamics KW - hybrid Monte Carlo KW - reweighting KW - essential degrees of freedom KW - transition probabilities KW - Markov operator Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3889 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hohmann, Andreas T1 - Einführung in die Numerische Mathematik. N2 - Diese Vorlesung ist eine Einführung 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 für Probleme aus den Naturwissenschaften mit Hilfe mathematischer Methoden. T3 - ZIB-Report - TR-90-06 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4704 ER - TY - GEN A1 - Deuflhard, Peter A1 - Nowak, Ulrich A1 - Lutz-Westphal, Brigitte T1 - Bessel'scher Irrgarten N2 - Dieser Artikel berichtet über eine erfolgreiche Schüleraktivität, die seit Jahren am Zuse-Institut Berlin (ZIB) bei Besuchen von Schülergruppen erprobt und verfeinert worden ist. Das hier zusammengestellte Material ist gedacht als Basis für eine Unterrichtseinheit in Leistungskursen Mathematik an Gymnasien. Inhaltlich wird von einem zwar für Schüler (wie auch Lehrer) neuen, aber leicht fasslichen Gegenstand ausgegangen: der Drei-Term-Rekursion für Besselfunktionen. Die Struktur wird erklärt und in ein kleines Programm umgesetzt. Dazu teilen sich die Schüler selbstorganisierend in Gruppen ein, die mit unterschiedlichen Taschenrechnern "um die Wette" rechnen. Die Schüler und Schülerinnen erfahren unmittelbar die katastrophale Wirkung von an sich kleinen'' Rundungsfehlern, sie landen -- ebenso wie der Supercomputer des ZIB -- im Bessel'schen Irrgarten''. Die auftretenden Phänomene werden mathematisch elementar erklärt, wobei lediglich auf das Konzept der linearen Unabhängigkeit zurückgegriffen wird. Das dabei gewonnene vertiefte Verständnis fließt ein in die Konstruktion eines klassischen Algorithmus sowie eines wesentlich verbesserten Horner-artigen Algorithmus. T3 - ZIB-Report - 07-09 KW - Rundungsfehler KW - Drei-Term-Rekursionen KW - Bessel-Rekursion Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9525 ER - TY - GEN A1 - Weber, Marcus A1 - Walter, Lionel A1 - Kube, Susanna A1 - Deuflhard, Peter T1 - Stable computation of probability densities for metastable dynamical systems N2 - 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. T3 - ZIB-Report - 06-39 KW - dynamical systems KW - metastability KW - molecular conformations KW - cluster analysis KW - sampling KW - aggregation/disaggregation KW - domain decomposition Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9331 ER - TY - GEN A1 - Deuflhard, Peter A1 - Krause, Rolf A1 - Ertel, Susanne T1 - A Contact-Stabilized Newmark Method for Dynamical Contact Problems N2 - 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). T3 - ZIB-Report - 06-42 KW - Numerical problems in dynamical systems KW - nonlinear stabilities Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9361 ER - TY - GEN A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Jahnke, Tobias A1 - Wulkow, Michael T1 - Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation N2 - \begin{abstract} In systems biology, the stochastic description of biochemical reaction kinetics is increasingly being employed to model gene regulatory networks and signalling pathways. Mathematically speaking, such models require the numerical solution of the underlying evolution equat ion, also known as the chemical master equation (CME). Up to now, the CME has almost exclusively been treated by Monte-Carlo techniques, the most prominent of which is the simulation algorithm suggest ed by Gillespie in 1976. Since this algorithm requires an update for each single reaction event, realizations can be computationally very costly. As an alternative, we here propose a novel approach, which focuses on the discrete partial differential equation (PDE) structure of the CME and thus allows to adopt ideas from adaptive discrete Galerkin methods (as designed by two of the present authors in 1989), which have proven to be highly efficient in the mathematical modelling of polyreaction kinetics. Among the two different options of discretizing the CME as a discrete PDE, the method of lines approach (first space, then time) and the Rothe method (first time, then space), we select the latter one for clear theoretical and algorithmic reasons. First numeric al experiments at a challenging model problem illustrate the promising features of the proposed method and, at the same time, indicate lines of necessary further research. \end{abstract} T3 - ZIB-Report - 07-04 KW - adaptive discrete Galerkin methods KW - adaptive Rothe method KW - discrete Chebyshev polynomials KW - stochastic reactions kinetics KW - chemical master equation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9471 ER - TY - GEN A1 - Reinecke, Isabel A1 - Deuflhard, Peter T1 - A Complex Mathematical Model of the Human Menstrual Cycle N2 - 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. T3 - ZIB-Report - 06-18 Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9112 ER - TY - GEN A1 - Deuflhard, Peter A1 - Heroth, Jörg A1 - Maas, Ulrich T1 - Towards Dynamical Dimension Reduction in Reactive Flow Problems N2 - The paper addresses the possibilities of reducing the overall number of degrees of freedom in large scale reactive flow computations. Attention focusses on the dimension reduction technique ILDM due to {\sc Maas and Pope}, which treats certain automatically detected fast dynamic components as algebraic equations (so-called slow manifold). In earlier papers, the dimension of the reduction had been kept constant throughout each computation. Recently, a mathematically sound and nevertheless cheap dimension monitor for the chemistry part only has been suggested by {\sc Deuflhard and Heroth}. The present paper reports about first steps taken towards the implementation of that monitor into a flame code. Moreover, a sparse grid storage scheme is advocated and analyzed in view of the construction of efficient table look--ups for nested manifolds. T3 - ZIB-Report - SC-96-27 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2383 ER - TY - GEN A1 - Deuflhard, Peter A1 - Weiser, Martin T1 - Local Inexact Newton Multilevel FEM for Nonlinear Elliptic Problems N2 - The finite element setting for nonlinear elliptic PDEs directly leads to the minimization of convex functionals. Uniform ellipticity of the underlying PDE shows up as strict convexity of the arising nonlinear functional. The paper analyzes computational variants of Newton's method for convex optimization in an affine conjugate setting, which reflects the appropriate affine transformation behavior for this class of problems. First, an affine conjugate Newton--Mysovskikh type theorem on the local quadratic convergence of the exact Newton method in Hilbert spaces is given. It can be easily extended to inexact Newton methods, where the inner iteration is only approximately solved. For fixed finite dimension, a special implementation of a Newton--PCG algorithm is worked out. In this case, the suggested monitor for the inner iteration guarantees quadratic convergence of the outer iteration. In infinite dimensional problems, the PCG method may be just formally replaced by any Galerkin method such as FEM for linear elliptic problems. Instead of the algebraic inner iteration errors we now have to control the FE discretization errors, which is a standard task performed within any adaptive multilevel method. A careful study of the information gain per computational effort leads to the result that the quadratic convergence mode of the Newton--Galerkin algorithm is the best mode for the fixed dimensional case, whereas for an adaptive variable dimensional code a special linear convergence mode of the algorithm is definitely preferable. The theoretical results are then illustrated by numerical experiments with a {\sf NEWTON--KASKADE} algorithm. T3 - ZIB-Report - SC-96-29 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2401 ER - TY - GEN A1 - Deuflhard, Peter A1 - Friese, Tilmann A1 - Schmidt, Frank A1 - März, Reinhard A1 - Nolting, Hans-Peter T1 - Effiziente Eigenmodenberechnung für den Entwurf integriert-optischer Chips N2 - {\bf Efficient eigenmode computation for the design of integrated optical chips.}The paper deals with adaptive multigrid methods for 2D Helmholtz eigenvalue problems arising in the design of integrated optical chips. Typical features of the technological problem are its geometric complexity, its multiscale structure, the possible occurrence of eigenvalue clusters, and the necessity of quite stringent required relative error tolerances. For reasons of sheer computational complexity, multigrid methods must be used to solve the discretized eigenvalue problems and adaptive grids must be automatically constructed to avoid an undesirable blow-up of the required number of nodes for these accuracies. In view of the problem specifications, an adaptive multigrid method based on Rayleigh quotient minimization, simultaneous eigenspace iteration, and conjugate gradient method as smoother is carefully selected. Its performance in the numerical simulation of a component of a rather recent optical chip (heterodyne receiver of HHI) is documented. T3 - ZIB-Report - SC-96-02 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2131 ER - TY - GEN A1 - Ehrig, Rainald A1 - Nowak, Ulrich A1 - Deuflhard, Peter T1 - Highly scalable parallel linearly-implicit extrapolation algorithms N2 - We present parallel formulations of the well established extrapolation algorithms EULSIM and LIMEX and its implementation on a distributed memory architecture. The discretization of partial differential equations by the method of lines yields large banded systems, which can be efficiently solved in parallel only by iterative methods. Polynomial preconditioning with a Neumann series expansion combined with an overlapping domain decomposition appears as a very efficient, robust and highly scalable preconditioner for different iterative solvers. A further advantage of this preconditioner is that all computation can be restricted to the overlap region as long as the subdomain problems are solved exactly. With this approach the iterative algorithms operate on very short vectors, the length of the vectors depends only on the number of gridpoints in the overlap region and the number of processors, but not on the size of the linear system. As the most reliable and fast iterative methods based on this preconditioning scheme appeared GMRES or FOM and BICGSTAB. To further reduce the number of iterations in GMRES or FOM we can reuse the Krylov-spaces constructed in preceeding extrapolation steps. The implementation of the method within the program LIMEX results in a highly parallel and scalable program for solving differential algebraic problems getting an almost linear speedup up to 64 processors even for medium size problems. Results are presented for a difficult application from chemical engineering simulating the formation of aerosols in industrial gas exhaust purification. T3 - ZIB-Report - TR-96-11 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5405 ER - TY - GEN A1 - Deuflhard, Peter T1 - Numerik von Anfangswertmethoden für gewöhnliche Differentialgleichungen. N2 - Das voliegende Skriptum entstand aus einer Vorlesung, die ich im WS 87/88 an der Freien Universität Berlin im Fachbereich Mathematik gehalten habe. Mein ursprüngliches Vorlesungsmanuskript wurde von Herrn F. Bornemann in weiten Teilen überarbeitet, reorganisiert und substantiell ergänzt. Der Inhalt stammt größtenteils aus Originalarbeiten jüngeren Datums. Darüberhinaus finden sich zahlreiche Teile, die aus meiner jahrelangen Beschäftigung mit dem Thema entstanden aber unpubliziert geblieben sind. Das Skriptum erhebt nicht den Anspruch, ein Lehrbuch zu sein. Es war zunächst als Ausarbeitung für meinen studentischen Hörerkreis sowie als internes Arbeitspapier für das ZIB bestimmt. Die Kunde von der bloßen Existenz eines solchen Skriptums hat jedoch zu einer derart regen Nachfrage geführt, daß es hiermit als Technischer Report des ZIB einer breiteren ffentlichkeit zugänglich gemacht werden soll. In der vorliegenden Form richtet es sich in erster Linie an Mathematiker; es soll sich jedoch auch für Naturwissenschaftler und Ingenieure eignen, die sich einen Einblick in den theoretischen und algorithmischen Hintergrund der von ihnen verwendeten wissenschaftlichen Software verschaffen wollen. T3 - ZIB-Report - TR-89-02 Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4580 ER - TY - GEN A1 - Deuflhard, Peter A1 - Bölling, Reinhard A1 - Bott, Raoul H. T1 - Materialien zur Euler-Vorlesung in Sanssouci. N2 - Aus dem Inhalt: Vorwort; Leonhard Euler - aus der Zeit seines Wirkens in Berlin; Introductory Remarks. T3 - ZIB-Report - TR-93-10 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5029 ER - TY - GEN A1 - Deuflhard, Peter A1 - Gottschewski, Jürgen T1 - Das Konrad-Zuse-Zentrum für Informationstechnik Berlin. Struktur, wissenschaftliches Konzept und Einbettung in die Region N2 - Die Arbeit beschreibt Konzept, Struktur und Ausstattung des ZIB. Übergeordnetes Ziel des ZIB ist die Beschleunigung des {\it Know-how Transfers} aus der mathematischen Grundlagenforschung über die Entwicklung von Algorithmen und Software bis hin zur tatsächlichen Nutzung in der Industrie. In der Tat ist Computational Mathematics inzwischen zu einer der wichtigsten {\it Schlüsseltechnologien} geworden, die nicht zuletzt im Zusammenhang mit der Standort-Diskussion eine wichtige Rolle spielt und vermehrt spielen wird. Dazu müssen Methodenentwicklung und Rechenzentrum auf höchstem Niveau sowie interdisziplinäre Forschung möglichst vereint in einer Institution mit enger Anbindung an ein universitäres Umfeld realisiert sein. Das Konrad-Zuse-Zentrum hat die wesentlichen Voraussetzungen als SC Zentrum bereits geschaffen; ein Ausbau zum HPSC Zentrum wäre eine natürliche Entwicklung - falls die Politik diese Chance rechtzeitig begreift! T3 - ZIB-Report - TR-95-12 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5274 ER - TY - GEN A1 - Deuflhard, Peter T1 - Zuses Werk weiterdenken. (Vortrag) T3 - ZIB-Report - TR-90-07 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4717 ER - TY - GEN A1 - Braess, Dietrich A1 - Deuflhard, Peter A1 - Lipnikov, Konstantin T1 - A Subspace Cascadic Multigrid Method for Mortar Elements N2 - A cascadic multigrid (CMG) method for elliptic problems with strong material jumps is proposed and analyzed. Non--matching grids at interfaces between subdomains are allowed and treated by mortar elements. The arising saddle point problems are solved by a subspace confined conjugate gradient method as smoother for the CMG. Details of algorithmic realization including adaptivity are elaborated. Numerical results illustrate the efficiency of this CMG algorithm. T3 - ZIB-Report - SC-99-07 KW - Finite Elements KW - Rayleigh-Ritz and Galerkin Methods KW - Multigrid Methods KW - Domain Decomposition Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3954 ER - TY - GEN A1 - Deuflhard, Peter A1 - Heroth, Jörg T1 - Dynamic Dimension Reduction in ODE Models N2 - The paper analyzes a splitting technique into fast and slow dynamical components of ODE systems as suggested by {\sc Maas and Pope} recently. Their technique is based on a real block -- Schur decomposition of the Jacobian of the right hand side of the ODE. As a result of the analysis, a computationally cheap monitor for the possible necessary recovering of the splitting is derived by singular perturbation theory. Numerical experiments on moderate size, but challenging reaction kinetics problems document the efficiency of the new device within a linearly-implicit stiff integrator. T3 - ZIB-Report - SC-95-29 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1951 ER - TY - GEN A1 - Ehrig, Rainald A1 - Nowak, Ulrich A1 - Deuflhard, Peter T1 - Massively Parallel Linearly-Implicit Extrapolation Algorithms as a Powerful Tool in Process Simulation. N2 - We study the parallelization of linearly--implicit extrapolation codes for the solution of large scale PDE systems and differential algebraic equations on distributed memory machines. The main advantage of these algorithms is that they enable adapativity both in time and space. Additive Krylov--Schwarz methods yield high parallel perfomance for such extrapolation methods. Our approach combines a slightly overlapping domain decomposition together with a polynomial block Neumann preconditioner and a reduced system technique. Furthermore we get important advantages through the explicit computation of the matrix--products of the preconditioner and the matrix of the linear system. The parallel algorithms exhibit scalability up to 64 processors already for medium--sized test problems. We show that the codes are really efficient in large application systems for chemical engineering problems. T3 - ZIB-Report - SC-97-43 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3127 ER - TY - GEN A1 - Deuflhard, Peter A1 - Lang, Jens A1 - Nowak, Ulrich T1 - Adaptive Algorithms in Dynamical Process Simulation N2 - Dynamical simulation of industrially relevant processes strongly advises the use of algorithms, which are {\em adaptive} both in time and in space discretization. The paper presents two alternatives: (a) a fully adaptive method of lines approach, which is based on finite difference methods and essentially applicable to 1D problems; (b) a fully adaptive Rothe method, which is based on a fast multilevel finite element method and applicable to 1D up to 3D. T3 - ZIB-Report - SC-95-16 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1823 ER - TY - GEN A1 - Deuflhard, Peter T1 - Differential Equations in Technology and Medicine. Computational Concepts, Adaptive Algorithms, and Virtual Labs N2 - This series of lectures has been given to a class of mathematics postdocs at a European summer school on Computational Mathematics Driven by Industrial Applications in Martina Franca, Italy (organized by CIME). It deals with a variety of challenging real life problems selected from clinical cancer therapy, communication technology, polymer production, and pharmaceutical drug design. All of these problems from rather diverse application areas share two common features: (a) they have been modelled by various differential equations -- elliptic, parabolic, or Schrödinger--type partial differential equations, countable ordinary diffential equations, or Hamiltonian systems, (b) their numerical solution has turned out to be real challenge to computational mathematics. T3 - ZIB-Report - SC-99-34 KW - differential equations: KW - ordinary KW - partial KW - countable KW - hamiltonian KW - finite element methods: KW - adaptive KW - multilevel KW - grid generation KW - medical t Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4223 ER - TY - GEN A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems N2 - The article surveys the development of novel mathematical concepts and algorithmic approaches based thereon in view of their possible applicability to biomolecular design. Both a first deterministic approach, based on the Frobenius-Perron operator corresponding to the flow of the Hamiltonian dynamics, and later stochastic approaches, based on a spatial Markov operator or on Langevin dynamics, can be subsumed under the unified mathematical roof of the transfer operator approach to effective dynamics of molecular systems. The key idea of constructing specific transfer operators especially taylored for the purpose of conformational dynamics appears as the red line throughout the paper. Different steps of the algorithm are exemplified by a trinucleotide molecular system as a small representative of possible RNA drug molecules. T3 - ZIB-Report - SC-99-36 KW - Transfer operator KW - Markov process KW - Markov chain KW - molecular dynamics KW - biomolecular conformations KW - canonical ensemble KW - transition prohability KW - Ha Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4247 ER - TY - GEN A1 - Galliat, Tobias A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification N2 - One of the important tasks in Data Mining is automated cluster analysis. Self-Organizing Maps (SOMs) introduced by {\sc Kohonen} are, in principle, a powerful tool for this task. Up to now, however, its cluster identification part is still open to personal bias. The present paper suggests a new approach towards automated cluster identification based on a combination of SOMs with an eigenmode analysis that has recently been developed by {\sc Deuflhard et al.} in the context of molecular conformational dynamics. Details of the algorithm are worked out. Numerical examples from Data Mining and Molecular Dynamics are included. T3 - ZIB-Report - SC-99-38 KW - Self-Organizing Maps KW - cluster analysis Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4279 ER - TY - GEN A1 - Lipnikov, Konstantin A1 - Deuflhard, Peter T1 - Domain Decomposition with Subdomain CCG for Material Jump Elliptic Problems. N2 - A combination of the cascadic conjugate gradient (CCG) method for homogeneous problems with a non-overlapping domain decomposition (DD) method is studied. Mortar finite elements on interfaces are applied to permit non-matching grids in neighboring subdomains. For material jump problems, the method is designed as an alternative to the cascadic methods. T3 - ZIB-Report - SC-97-36 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3057 ER - TY - GEN A1 - Deuflhard, Peter A1 - Seebass, Martin T1 - Adaptive Multilevel FEM as Decisive Tools in the Clinical Cancer Therapy Hyperthermia N2 - The paper surveys recent progress in a joint mathematical-medical project on cancer therapy planning. Within so-called regional hyperthermia the computational task is to tune a set of coupled radiofrequency antennas such that a carefully measured tumor is locally heated, but any outside hot spots are avoided. A mathematical model of the whole clinical system -- air, applicator with antennas, water bolus, individual patient body -- involves Maxwell's equations in inhomogeneous media and a parabolic bioheat transfer equation, which represents a simplified model of heat transfer in the human body (ignoring strong blood vessel heat transport). Both PDEs need to be computed fast and to medical reliability (!) on a workstation within a clinical environment. This requirement triggered a series of new algorithmic developments to be reported here, among which is an adaptive multilevel FEM for Maxwell's equations, which dominates the numerical simulation time. In total, however, the main bulk of computation time (see Table 3 in Section 4 below) still goes into segmentation -- a necessary preprocessing step in the construction a 3D virtual patient from the input of a stack of 2D computed tomograms (left out here). T3 - ZIB-Report - SC-98-30 KW - hyperthermia KW - Maxwell's equations KW - nonlinear heat transfer KW - finite elements Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3739 ER - TY - GEN A1 - Deuflhard, Peter A1 - Weiser, Martin A1 - Seebass, Martin T1 - A New Nonlinear Elliptic Multilevel FEM Applied to Regional Hyperthermia N2 - In the clinical cancer therapy of regional hyperthermia nonlinear perfusion effects inside and outside the tumor seem to play a not negligible role. A stationary model of such effects leads to a nonlinear Helmholtz term within an elliptic boundary value problem. The present paper reports about the application of a recently designed adaptive multilevel FEM to this problem. For several 3D virtual patients, nonlinear versus linear model is studied. Moreover, the numerical efficiency of the new algorithm is compared with a former application of an adaptive FEM to the corresponding instationary model PDE. T3 - ZIB-Report - SC-98-35 KW - hyperthermia KW - nonlinear elliptic KW - multilevel FEM Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3785 ER - TY - GEN A1 - Schöpf, R. A1 - Deuflhard, Peter T1 - OCCAL: A mixed symbolic- numeric Optimal Control CALculator. N2 - The numerical solution of optimal control problems by indirect methods (such as multiple shooting or collocation) requires a considerable amount of analytic calculation to establish a numerically tractable system. These analytic calculations, though being rather tedious in realistic examples, are nowadays mostly still done by hand-and thus prone to calculation errors. The paper aims at automating this analytic processing to a reasonable extent by means of a modern symbolic manipulation language (here: REDUCE). In its present stage of development the package OCCAL (mnemotechnically for \underline{O}ptimal \underline{C}ontrol \underline{CAL}culator) permits an interactive use, covering tasks like automatic determination of control and, in case of a singular control, of its order. In simpler problems, the present version of OCCAL automatically produces the full subroutine input for a MULtiple shooting code (MULCON) with adaptive numerical CONtinuation. In more complicate problems where singular sub-arcs may occur or where the sequence of sub-arcs of the optimal trajectory is unclear OCCAL is a significant help in reducing analytic pre-processing. Numerical examples illustrate the performance of OCCAL/MULCON. T3 - ZIB-Report - SC-91-13 Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-638 ER - TY - GEN A1 - Deuflhard, Peter A1 - Leinen, P. A1 - Yserentant, Harry T1 - Concepts of an Adaptive Hierarchical Finite Element Code. N2 - The paper presents the mathematical concepts underlying the new adaptive finite element code KASKADE, which, in its present form, applies to linear scalar second-order 2-D elliptic problems on general domains. Starting point for the new development is the recent work on hierarchical finite element bases due to Yserentant (1986). It is shown that this approach permits a flexible balance between iterative solver, local error estimator, and local mesh refinement device - which are the main components of an adaptive PDE code. Without use of standard multigrid techniques, the same kind of computational complexity is achieved - independent of any uniformity restrictions on the applied meshes. In addition, the method is extremely simple and all computations are purely local - making the method particularly attractive in view of parallel computing. The algorithmic approach is illustrated by a well-known critical test problem. {\bf Keywords:} finite elements, hierarchical basis, adaptive mesh refinement, preconditioned conjugate gradient methods. T3 - ZIB-Report - SC-88-05 KW - finite elements KW - hierarchical basis KW - adaptive mesh refinement KW - preconditioned conjugate gradient methods Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-131 ER -