TY - GEN A1 - Yevick, David A1 - Friese, Tilmann A1 - Schmidt, Frank T1 - A Comparison of Transparent Boundary Conditions for the Fresnel Equation N2 - We establish the relationship between the transparent boundary condition (BPP) of Baskakov and Popov [Wave Motion 14 (1991) 121-128] and Pakpadakis et. al. [J. Acoust. Soc. Am. 92 (1992) 2030-2038] and a second boundary condition (SDY) introduced by Schmidt and Deuflhard [Comp. Math. Appl. 29 (1995) 53-76] and Schmidt and Yevick [J. Compu. Phys. 134 (1997) 96-107], that is explicitly tailored to the form of the underlying numerical propagation scheme. Our analysis demonstrates that if the domain is first discretized in the propagation direction, the SDY expression can be obtained by applying the exact sequence of steps used to derive the BPP procedure. The BPP method is thus an approximate realization of the computationally far simpler and unconditionally stable SDY boundary condition. T3 - ZIB-Report - 00-05 KW - Fresnel equation KW - transparent boundary condition Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5738 ER - TY - GEN A1 - Schmidt, Frank T1 - Discrete Nonreflecting Boundary Conditions for the Helmholtz Equation N2 - We derive exact discrete nonreflecting boundary conditions for time-harmonic scattering problems modeled by the Helmholtz equation. The main idea is to consider the exterior problem as an initial value problem with initial data given on the boundary of the computational domain. The solution of the exterior problem is obtained via Laplace transformation techniques which supply the boundary conditions in terms of discrete Dirichlet-to-Neumann operators. T3 - ZIB-Report - 00-06 KW - Helmholtz equation KW - transparent boundary consitions KW - finite element method Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5744 ER - TY - GEN A1 - Hohage, Thorsten A1 - Schmidt, Frank T1 - On the Numerical Solution of Nonlinear Schrödinger type equations in fiber optics N2 - The aim of this paper is to develop fast methods for the solution of nonlinear Schrödinger type equations in fiber optics. Using the method of lines we have to solve a stiff system of ordinary differential equations where the eigenvalues of the Jacobian are close to the imaginary axis. This is usually done by a Split Step method. Here we consider the extrapolation of Split Step methods with adaptive order and step size control. For more complicated nonlinearities, in particular stimulated Raman scattering, Split Step methods are less efficient since symmetry is either destroyed or requires much additional effort. In this case we use implicit Runge Kutta formulas of Gauß type. The key point for the efficient implementation of these methods is that the system of nonlinear algebraic equations can be solved without setting up the Jacobian. The proposed methods are compared to other methods, in particular exponential integrators, the method of Marcuse, and the method of Blow and Wood. T3 - ZIB-Report - 02-04 KW - nonlinear Schroedinger equation KW - split step methods KW - extrapolation KW - collocation methods Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6715 ER - TY - GEN A1 - Cordes, Frank A1 - Weber, Marcus A1 - Schmidt-Ehrenberg, Johannes T1 - Metastable Conformations via successive Perron-Cluster Cluster Analysis of dihedrals N2 - Decomposition of the high dimensional conformational space of bio-molecules into metastable subsets is used for data reduction of long molecular trajectories in order to facilitate chemical analysis and to improve convergence of simulations within these subsets. The metastability is identified by the Perron-cluster cluster analysis of a Markov process that generates the thermodynamic distribution. A necessary prerequisite of this analysis is the discretization of the conformational space. A combinatorial approach via discretization of each degree of freedom will end in the so called ''curse of dimension''. In the following paper we analyze Hybrid Monte Carlo simulations of small, drug-like biomolecules and focus on the dihedral degrees of freedom as indicators of conformational changes. To avoid the ''curse of dimension'', the projection of the underlying Markov operator on each dihedral is analyzed according to its metastability. In each decomposition step of a recursive procedure, those significant dihedrals, which indicate high metastability, are used for further decomposition. The procedure is introduced as part of a hierarchical protocol of simulations at different temperatures. The convergence of simulations within metastable subsets is used as an ''a posteriori'' criterion for a successful identification of metastability. All results are presented with the visualization program AmiraMol. T3 - ZIB-Report - 02-40 KW - metastability KW - Perron-Cluster Cluster Analysis KW - curse of dimension KW - Hybrid Monte Carlo KW - significant dihedrals Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7074 ER - TY - GEN A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Solving time-harmonic scattering problems based on the pole condition: Convergence of the PML method N2 - In this paper we study the PML method for Helmholtz-type scattering problems with radially symmetric potential. The PML method consists in surrounding the computational domain by a \textbf{P}erfectly \textbf{M}atched sponge \textbf{L}ayer. We prove that the approximate solution obtained by the PML method converges exponentially fast to the true solution in the computational domain as the thickness of the sponge layer tends to infinity. This is a generalization of results by Lassas and Somersalo based on boundary integral eqaution techniques. Here we use techniques based on the pole condition instead. This makes it possible to treat problems without an explicitly known fundamental solution. T3 - ZIB-Report - 01-23 KW - transparent boundary conditions KW - PML KW - pole condition Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6494 ER - TY - GEN A1 - Hohage, Thorsten A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - A new method for the solution of scattering problems N2 - We present a new efficient algorithm for the solution of direct time-harmonic scattering problems based on the Laplace transform. This method does not rely on an explicit knowledge of a Green function or a series representation of the solution, and it can be used for the solution of problems with radially symmetric potentials and problems with waveguides. The starting point is an alternative characterization of outgoing waves called \emph{pole condition}, which is equivalent to Sommerfeld's radiation condition for problems with radially symmetric potentials. We obtain a new representation formula, which can be used for a numerical evaluation of the exterior field in a postprocessing step. Based on previous theoretical studies, we discuss the numerical realization of our algorithm and compare its performance to the PML method. T3 - ZIB-Report - 02-01 KW - transparent boundary conditions KW - inhomogeneous exterior domains KW - Laplace transform Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6683 ER - TY - THES A1 - Schmidt, Frank T1 - A New Approach to Coupled Interior-Exterior Helmholtz-Type Problems: Theory and Algorithms N2 - The work presents a new approach to the numerical solution of time-harmonic and time-dependent scattering problems. We replace Sommerfeld's radiation condition valid for the Helmholtz equation by a more general concept called pole condition. The pole condition is based on the Laplace transform of the exterior solution and allows a characterization of outgoing waves. Both new insight into the analysis of scattering problems as well as new numerical algorithms are obtained. T3 - ZIB-Report - 02-45 KW - Pole condition KW - Helmholtz equation KW - Wide angle one-way equation KW - Schroedinger equation KW - Transparent boundary conditions KW - Unbounded domains KW - Fini Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7128 ER - TY - GEN A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank T1 - A new Finite Element realization of the Perfectly Matched Layer Method for Helmholtz scattering problems on polygonal domains in 2D N2 - In this paper we propose a new finite element realization of the Perfectly Matched Layer method (PML-method). Our approach allows to deal with arbitrary shaped polygonal domains and with certain types of inhomogeneous exterior domains. Among the covered inhomogeneities are open waveguide structures playing an essential role in integrated optics. We give a detailed insight to implementation aspects. Numerical examples show exponential convergence behavior to the exact solution with the thickness of the PML sponge layer. T3 - ZIB-Report - 03-44 KW - transparent boundary conditions KW - perfectly matched layer KW - pole condition Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7662 ER - TY - GEN A1 - May, Andreas A1 - Eisenhardt, Steffen A1 - Schmidt-Ehrenberg, Johannes A1 - Cordes, Frank T1 - Rigid body docking for Virtual Screening N2 - A recently developed algorithm allows Rigid Body Docking of ligands to proteins, regardless of the accessibility and location of the binding site. The Docking procedure is divided into three subsequent optimization phases, two of which utilize rigid body dynamics. The last one is applied with the ligand already positioned inside the binding pocket and accounts for full flexibility. Initially, a combination of geometrical and force-field based methods is used as a Coarse Docking strategy, considering only Lennard-Jones interactions between the target and pharmaceutically relevant atoms or functional groups. The protein is subjected to a Hot Spot Analysis, which reveals points of high affinity in the protein environment towards these groups. The hot spots are distributed into different subsets according to their group affiliation. The ligand is described as a complementary point set, consisting of the same subsets. Both sets are matched in $\mathrm{I\!R}^{3}$, by superimposing members of the same subsets. In the first instance, steric inhibition is nearly neglected, preventing the system's trajectory from trapping in local minima and thus from finding false positive solutions. Hence the exact location of the binding site can be determined fast and reliably without any additional information. Subsequently, errors resulting from approximations are minimized via finetuning, this time considering both Lennard-Jones and Coulomb forces. Finally, the potential energy of the whole complex is minimized. In a first evaluation, results are rated by a reduced scoring function considering only noncovalent interaction energies. Exemplary Screening results will be given for specific ligands. T3 - ZIB-Report - 03-47 KW - docking KW - point matching KW - identification of active sites Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7690 ER - TY - GEN A1 - Ruprecht, Daniel A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Transparent boundary conditons for time-dependent problems N2 - A new approach to derive transparent boundary conditions (TBCs) for wave, Schrödinger, heat and drift-diffusion equations is presented. It relies on the pole condition and distinguishes between physical reasonable and unreasonable solutions by the location of the singularities of the spatial Laplace transform of the exterior solution. To obtain a numerical algorithm, a Möbius transform is applied to map the Laplace transform onto the unit disc. In the transformed coordinate the solution is expanded into a power series. Finally, equations for the coefficients of the power series are derived. These are coupled to the equation in the interior, and yield transparent boundary conditions. Numerical results are presented in the last section, showing that the error introduced by the new approximate TBCs decays exponentially in the number of coefficients. T3 - ZIB-Report - 07-12 KW - transparent boundary condition KW - non-reflecting boundary condition KW - pole condition KW - wave equation KW - Schrödinger equation KW - drift diffusion equation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9558 ER -