@inproceedings{FischerSchuetteDeuflhardetal.2002, author = {Fischer, Alexander and Sch{\"u}tte, Christof and Deuflhard, Peter and Cordes, Frank}, title = {Hierarchical Uncoupling-Coupling of Metastable Conformations}, volume = {24}, booktitle = {Computational Methods for Macromolecules}, editor = {Schlick, T. and Gan, H.}, publisher = {Springer}, pages = {235 -- 259}, year = {2002}, language = {en} } @inproceedings{SchuetteHuisingaDeuflhard2001, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm and Deuflhard, Peter}, title = {Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems}, booktitle = {Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems}, editor = {Fiedler, B.}, publisher = {Springer}, pages = {191 -- 223}, year = {2001}, language = {en} } @article{DeuflhardRoeblitzStoetzel2010, author = {Deuflhard, Peter and R{\"o}blitz, Susanna and St{\"o}tzel, Claudia}, title = {Mathematical Systems Biology at Zuse Institute Berlin (ZIB)}, volume = {39}, journal = {BioTOPics - Journal of Biotechnology in Berlin-Brandenburg}, year = {2010}, language = {en} } @misc{Deuflhard2017, author = {Deuflhard, Peter}, title = {The Grand Four}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66038}, year = {2017}, abstract = {This paper gives a concise synopsis and some new insights concerning four affine invariant globalizations of the local Newton method. The invariance classes include: affine covariance, affine contravariance, affine conjugacy, and affine similarity. In view of algorithmic robustness, each of these classes of algorithms is particularly suitable for some corresponding problem class.}, language = {en} } @misc{DeuflhardHerothMaas1996, author = {Deuflhard, Peter and Heroth, J{\"o}rg and Maas, Ulrich}, title = {Towards Dynamical Dimension Reduction in Reactive Flow Problems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2383}, number = {SC-96-27}, year = {1996}, abstract = {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.}, language = {en} } @misc{DeuflhardWeiser1996, author = {Deuflhard, Peter and Weiser, Martin}, title = {Local Inexact Newton Multilevel FEM for Nonlinear Elliptic Problems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2401}, number = {SC-96-29}, year = {1996}, abstract = {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.}, language = {en} } @misc{DeuflhardSeebassStallingetal.1997, author = {Deuflhard, Peter and Seebass, Martin and Stalling, Detlev and Beck, Rudolf and Hege, Hans-Christian}, title = {Hyperthermia Treatment Planning in Clinical Cancer Therapy: Modelling, Simulation and Visualization}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2958}, number = {SC-97-26}, year = {1997}, abstract = {\noindent The speaker and his co-workers in Scientific Computing and Visualization have established a close cooperation with medical doctors at the Rudolf--Virchow--Klinikum of the Humboldt University in Berlin on the topic of regional hyperthermia. In order to permit a patient--specific treatment planning, a special software system ({\sf\small HyperPlan}) has been developed. \noindent A mathematical model of the clinical system ({\it radio frequency applicator with 8 antennas, water bolus, individual patient body}) involves Maxwell's equations in inhomogeneous media and a so--called bio--heat transfer PDE describing the temperature distribution in the human body. The electromagnetic field and the thermal phenomena need to be computed at a speed suitable for the clinical environment. An individual geometric patient model is generated as a quite complicated tetrahedral ``coarse'' grid (several thousands of nodes). Both Maxwell's equations and the bio--heat transfer equation are solved on that 3D--grid by means of {\em adaptive} multilevel finite element methods, which automatically refine the grid where necessary in view of the required accuracy. Finally optimal antenna parameters for the applicator are determined . \noindent All steps of the planning process are supported by powerful visualization methods. Medical images, contours, grids, simulated electromagnetic fields and temperature distributions can be displayed in combination. A number of new algorithms and techniques had to be developed and implemented. Special emphasis has been put on advanced 3D interaction methods and user interface issues.}, language = {en} } @misc{BeckDeuflhardHegeetal.1996, author = {Beck, Rudolf and Deuflhard, Peter and Hege, Hans-Christian and Seebass, Martin and Stalling, Detlev}, title = {Numerical Algorithms and Visualization in Medical Treament Planning}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2643}, number = {SC-96-54}, year = {1996}, abstract = {After a short summary on therapy planning and the underlying technologies we discuss quantitative medicine by giving a short overview on medical image data, summarizing some applications of computer based treatment planning, and outlining requirements on medical planning systems. Then we continue with a description of our medical planning system {\sf HyperPlan}. It supports typical working steps in therapy planning, like data aquisition, segmentation, grid generation, numerical simulation and optimization, accompanying these with powerful visualization and interaction techniques.}, language = {en} } @misc{DeuflhardDellnitzJungeetal.1996, author = {Deuflhard, Peter and Dellnitz, Michael and Junge, Oliver and Sch{\"u}tte, Christof}, title = {Computation of Essential Molecular Dynamics by Subdivision Techniques I: Basic Concept}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2553}, number = {SC-96-45}, year = {1996}, abstract = {The paper presents the concept of a new type of algorithm for the numerical computation of what the authors call the {\em essential dynamics\/} of molecular systems. Mathematically speaking, such systems are described by Hamiltonian differential equations. In the bulk of applications, individual trajectories are of no specific interest. Rather, time averages of physical observables or relaxation times of conformational changes need to be actually computed. In the language of dynamical systems, such information is contained in the natural invariant measure (infinite relaxation time) or in almost invariant sets ("large" finite relaxation times). The paper suggests the direct computation of these objects via eigenmodes of the associated Frobenius-Perron operator by means of a multilevel subdivision algorithm. The advocated approach is different to both Monte-Carlo techniques on the one hand and long term trajectory simulation on the other hand: in our setup long term trajectories are replaced by short term sub-trajectories, Monte-Carlo techniques are just structurally connected via the underlying Frobenius-Perron theory. Numerical experiments with a first version of our suggested algorithm are included to illustrate certain distinguishing properties. A more advanced version of the algorithm will be presented in a second part of this paper.}, language = {en} } @misc{DeuflhardWeiser1996, author = {Deuflhard, Peter and Weiser, Martin}, title = {Global Inexact Multilevel FEM for Nonlinear Elliptic Problems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2430}, number = {SC-96-33}, year = {1996}, abstract = {The paper deals with the multilevel solution of {\em elliptic} partial differential equations (PDEs) in a {\em finite element} setting: {\em uniform ellipticity} of the PDE then goes with {\em strict monotonicity} of the derivative of a nonlinear convex functional. A {\em Newton multigrid method} is advocated, wherein {\em linear residuals} are evaluated within the multigrid method for the computation of the Newton corrections. The globalization is performed by some {\em damping} of the ordinary Newton corrections. The convergence results and the algorithm may be regarded as an extension of those for local Newton methods presented recently by the authors. An {\em affine conjugate} global convergence theory is given, which covers both the {\em exact} Newton method (neglecting the occurrence of approximation errors) and {\em inexact} Newton--Galerkin methods addressing the crucial issue of accuracy matching between discretization and iteration errors. The obtained theoretical results are directly applied for the construction of adaptive algorithms. Finally, illustrative numerical experiments with a~{\sf NEWTON--KASKADE} code are documented.}, language = {en} } @misc{DeuflhardHeroth1995, author = {Deuflhard, Peter and Heroth, J{\"o}rg}, title = {Dynamic Dimension Reduction in ODE Models}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1951}, number = {SC-95-29}, year = {1995}, abstract = {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.}, language = {en} } @misc{DeuflhardLangNowak1995, author = {Deuflhard, Peter and Lang, Jens and Nowak, Ulrich}, title = {Adaptive Algorithms in Dynamical Process Simulation}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1823}, number = {SC-95-16}, year = {1995}, abstract = {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.}, language = {en} } @misc{FroehlichDeuflhard1994, author = {Fr{\"o}hlich, Jochen and Deuflhard, Peter}, title = {Moving Weight Galerkin Methods for Turbulent Reactive Flows}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1646}, number = {SC-94-36}, year = {1994}, abstract = {Adopting a statistical approach for the computation of turbulent combustion flows an approximation for the probability density function (PDF) of the composition variables is often required to treat the highly non-linear reaction term in a satisfactory way. One class of methods currently being used are the moment methods which employ transport equations for low order statistical moments and use a parametrized shape of the PDF. A second class solves a transport equation for the joint PDF by a Monte Carlo method. In the present paper we develop an intermediate algorithm based on a Galerkin method for the PDF transport equation. The solution is developed in terms of an orthogonal or bi-orthogonal basis of a suitable Hilbert space. The unconventional use of the related weight function as a prefactor (moving weight approach) permits adaptivity and results in a generalization of the \$\beta-\$closure for bounded scalar quantities. We present the approximation procedure in detail and apply it to the evolution of the composition in a homogeneous well-stirred reactor. The extension to non-homogeneous flow simulations is straightforward.}, language = {en} } @misc{DeuflhardAckermann1993, author = {Deuflhard, Peter and Ackermann, J{\"o}rg}, title = {Adaptive Discrete Galerkin-Methods for Macromolecular Processes.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1180}, number = {SC-93-22}, year = {1993}, abstract = {In this paper, a rather recent algorithmic approac to the numerical simulation of macromolecula processes is surveyed. It avoids the numerical stiff integration o thousands up to millions of ODE's by constructing a scale of discret Hilbert spaces, especially weighted sequence spaces, and establishing corresponding Galerkin method. Examples including polyreactions o industrial relevance and ecological waste management by biochemica recycling illustrate the importance and efficiency of the algorithm.}, language = {en} } @misc{Deuflhard1993, author = {Deuflhard, Peter}, title = {Cascadic Conjugate Gradient Methods for Elliptic Partial Differential Equations I. Algorithm and Numerical Results.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1197}, number = {SC-93-23}, year = {1993}, abstract = {Cascadic conjugate gradient methods for the numerical solution of elliptic partial differential equations consists of Galerkin finite element methods as outer iteration and (possibly preconditioned) conjugate gradient methods as inner iteration. Both iterations are known to minimize the energy norm of the arising iterations errors. A simple but efficient strategy to control the discretization errors versus the PCG iteration errors in terms of energy error norms is derived and worked out in algorithmic detail. In a unified setting, the relative merits of different preconditioners versus the case of no preconditioning is compared. Surprisingly, it appears that the cascadic conjugate gradient method without any preconditioning is not only simplest but also fastest. The numerical results seem to indicate that the cascade principle in itself already realizes some kind of preconditioning. A theoretical explanation of these observations will be given in Part II of this paper.}, language = {en} } @misc{DeuflhardSchmidt1993, author = {Deuflhard, Peter and Schmidt, Frank}, title = {Discrete Transparent Boundary Conditions for the Numerical Solution of Fresnel's Equation.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1205}, number = {SC-93-24}, year = {1993}, abstract = {The paper presents a construction scheme of deriving transparent , i. e. reflection-free, boundary conditions for the numerical solution of Fresnel's equation (being formally equivalent to Schr{\"o}dinger's equation). These boundary conditions appear to be of a nonlocal Cauchy type. As it turns out, each kind of linear implicit discretization induces its own discrete transparent boundary conditions.}, language = {en} } @misc{WulffHohmannDeuflhard1994, author = {Wulff, Claudia and Hohmann, Andreas and Deuflhard, Peter}, title = {Numerical Continuation of Periodic Orbits with Symmetry.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1421}, number = {SC-94-12}, year = {1994}, abstract = {We consider periodic orbits of autonomous parameter dependent ODE's. Starting from a shooting algorithm for the numerical computation of periodic orbits via an adaptive Poincar\'e-section we develop a pathfollowing algorithm for periodic solutions based on a tangential continuation method with implicit reparametrization. For ODE's equivariant w.r.t. a finite group we show that spatial as well as spatio-temporal symmetries of periodic orbits can be exploited within the (multiple) shooting context. We describe how turning points, period doubling bifurcations and Hopf points along the branch of periodic solutions can be handled. Furthermore equivariant Hopf points and generic secondary bifurcations of periodic orbits with \$ Z_m\$-symmetry are treated. We tested the code with standard examples, e.g., the period doubling cascade in the Lorenz equations. To show the efficiency of the described methods we also used the program for an application from electronics, a ring oscillator with \$n \$ inverters. In this example the exploitation of symmetry reduces the amount of work for the continuation of periodic orbits from \${\cal O}(n^2)\$ to \${\cal O}(n)\$}, language = {en} } @misc{DeuflhardWulkow1994, author = {Deuflhard, Peter and Wulkow, Michael}, title = {Simulationsverfahren f{\"u}r die Polymerchemie}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1502}, number = {SC-94-22}, year = {1994}, abstract = {Die enorme algorithmische Beschleunigung durch diskrete Galerkin-Methoden f{{\"u}}r abz{{\"a}}hlbare Differentialgleichungssysteme hat der Simulation von Polymerisationsprozessen neue, industriell relevante Problembereiche er{{\"o}}ffnet, die mit den bis dahin verf{{\"u}}gbaren Methoden nicht zug{{\"a}}nglich waren.}, language = {de} } @misc{DeuflhardNowakWeyer1994, author = {Deuflhard, Peter and Nowak, Ulrich and Weyer, J.}, title = {Prognoserechnung zur AIDS-Ausbreitung in der Bundesrepublik Deutschland}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1511}, number = {SC-94-23}, year = {1994}, abstract = {Die Autoren sind sich dar{{\"u}}ber im klaren, daß zahlreiche Imponderabilien die Ergebnisse der vorgelegten Modellrechnungen beeinflussen k{{\"o}}nnen. Immerhin repr{\"a}sentiert jedoch das vorgelegte mathematische Modell die Summe unserer derzeitigen Kenntnisse zur Fragestellung AIDS--Epidemie; neu hinzukommende Erkenntnisse lassen sich rasch einarbeiten und in ihren Konsequenzen {\"u}berschauen. Die Entwicklung neuer effizienter numerischer Methoden spielte eine Schl{\"u}sselrolle bei der tats{\"a}chlichen Simulation dieses umfangreichen realit{\"a}tsnahen mathematischen Modells.}, language = {de} } @misc{Deuflhard1993, author = {Deuflhard, Peter}, title = {A Study of Lanczos-Type Iterations for Symmetric Indefinite Linear Systems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-1029}, number = {SC-93-06}, year = {1993}, abstract = {The Lanczos iteration for symmetric indefinite linear systems seems to be well--known for quite a while. However, in order to modify it with the aim of improved performance, the present paper studies certain aspects in terms of an adjoint scalar three--term recurrence. Thus, at least a different view is opened. Moreover, an alternative \$3n\$--implementation in terms of the Euclidean orthogonal basis has been found that easily permits generalizations. The study is understood as a start--off for further numerical investigations and experiments.}, language = {en} }