2023-09, Wirtz, Johannes

At the interface between Phylo- and Population Genetics, and recently heavily inspired by Epidemonology, the discipline of Phylogeography comprises modelling techniques from classical theoretical biology and combines them with a spatial (2D or 3D) aspect, with the purpose of utilizing geographical information in the analysis to understand the evolutionary history of a biological system or aspects of virology such as directionality and seasonality in pandemic outbreaks [1, 2, 3, 4]. An prime example of this are datasets that take into account the sampling locations of its components (geo-referenced genomic data). In this project, we have focused on the model called "spatial Lambda-Fleming-Viot process" ( V [5, 6]) and analzed its statistical properties forward in time as well as in the ancestral (dual) process, with results that may be used for parameter inference. Of particlar interest was the spatial variance, denoted , a parameter controlling the speed at which genetic information is spread across space and therefore an analog of the reproduction number (R0) used in epidemonology e.g. to assess the infectiousness of differing viral strains. We explored the relation of this parameter to the time to coalescence between lineage pairs in this model and described methods of estimating it from sampled data under different circumstances. We have furthermore investigated similarities and differences between this model and classical models in Population Genetics, particularly Birth-Death processes, which are heavily used for all kinds of biological inference problems, but do not by themselves feature a spatial component. We compared the Vto a variant of the Birth-Death process where the location of a live individual changes over the course of its lifetime according to a Brownian motion. This process is not as easily viewed backward in time as the V, but the genalogical process is accessible by Markov-Chain Monte Carlosimulation, as the likelihoods of ancestral positions and branch lengths are easily calculated, making this model easily applicable to data. Our analysis highlights the analogy between the two processes forward in time as well as backward in time; on the other hand, we also observed a divergent behavior of the two models when no prior on the phylogenetic time scale was assumed. Lastly, this project has given rise to a study of combinatorial properties of tree shapes relevant to the V, the Birth-Death and other biological processes. In particular, we were able to identify the combinatorial class genealogical trees generated from these processes belong to and verify a conjecture regarding their enumeration. Preliminary versions of software tools for the aforementioned inference have also been provided.

2016, Radziunas, Mindaugas

This report summarizes our scientific activities within the project MANUMIEL (BMBF Program “Förderung der Wissenschaftlich-Technologischen Zusammenarbeit (WTZ) mit der Republik Moldau”, FKZ 01DK13020A). Namely, we discuss modeling of external cavity diode lasers, numerical simulations and analysis of these devices using the software package LDSL-tool, as well as the development of this software.

2004, Schmidt, Gunther

This is the manual of the software package DIPOG, version 1.4, which can be used to simulate and optimize binary and multilevel optical gratings. The algorithms are based on the finite--element solution of a system of Helmholtz equations, which are equivalent to the timeharmonic electromagnetic field equations, and on gradient methods for solving optimization problems. The package offers several options to postprocess the calculated electromagnetic fields.

2003, Rathsfeld, A.

[no abstract available]

2010, Streckenbach, Timo

WPM is a command-line tool designed to support build and installation facilities. It is implemented as a collection of script files, written in Bourne shell syntax. For the sake of portability the code takes care of the common pitfalls of shell programming.

2002, Mucha, H.-J., Simon, U., Brüggemann, R.

Starting from well-known model-based clustering models equivalent formulations for some special models based on pairwise distances are presented. Moreover, these models can be generalized in order to taking into account both weights of observations and weights of variables. Well-known cluster analysis techniques like the iterative partitional K-means method or the agglomerative hierarchical Ward method are useful for discovering partitions or hierarchies in the underlying data. Here these methods are generalised in two ways, firstly by using weighted observations and secondly by allowing different volumes of clusters. Then a more general K-means approach based on pair-wise distances is recommended. Simulation studies are carried out in order to compare the new clustering techniques with the well-known ones. Afterwards a successful application in the field of freshwater ecology is presented. As an example, the cluster analysis of a snapshot from monitoring of phytoplankton (algae) is considered in more detail. Indeed, monitoring by microscope is very time- and work-consuming. Flow cytometry provides the opportunity to investigate algae communities in a semiautomatic way. Statistical data analysis and cluster analysis can at least support the investigations. Here a combination of agglomerative hierarchical clustering and iterative clustering is recommended. In order to give some insight into the data under investigation several univariate, bivariate and multivariate visualizations are proposed.

2016, Borchardt, Jürgen, Mathé, Peter, Printsypar, Galina

The WIAS software package BOP is used to simulate gas turbine models. In order to make accurate predictions the underlying models need to be calibrated. This study compares different strategies of model calibration. These are the deterministic optimization tools as nonlinear least squares (MSO) and the sparsity promoting variant LASSO, but also the probabilistic (Bayesian) calibration. The latter allows for the quantification of the inherent uncertainty, and it gives rise to a surrogate uncertainty measure in the MSO tool. The implementation details are accompanied with a numerical case study, which highlights the advantages and drawbacks of each of the proposed calibration methods.

2002, Si, Hang

This technical report describes the main features and the using of TetGen, a 3D Delaunay tetrahedral mesh generator. Based on the most recent developments in mesh generation algorithms, this program has been specifically designed to fulfill the task of automatically generating high quality tetrahedral meshes, which are suitable for scientific computing using numerical methods such as finite element and finite volume methods. In this document, the user will learn how to create 3D tetrahedral meshes using TetGen's input files and command line switches. Various examples were given for better understanding. This document describes the features of the version 1.2.

2013, Si, Hang

TetGen is a software for tetrahedral mesh generation. Its goal is to generate good quality tetrahedral meshes suitable for numerical methods and scientific computing. It can be used as either a standalone program or a library component integrated in other software. The purpose of this document is to give a brief explanation of the kind of tetrahedralizations and meshing problems handled by TetGen and to give a fairly detailed documentation about the usage of the program. Readers will learn how to create tetrahedral meshes using input files from the command line. Furthermore, the programming interface for calling TetGen from other programs is explained.

2002, Buchwalder, A., Hömberg, D., Jurke, Th., Spies, H.-J., Weiss, W.

Die Software WIAS-SHarP zur Simulation der Oberflaechenhaertung von Stahl mit Laser- und Elektronenstrahl wurde im Rahmen eines zweijaehrigen interdisziplinaeren Forschungsprojektes entwickelt. Das zugrunde liegende mathematische Modell besteht aus einem System gewoehnlicher Differentialgleichungen zur Beschreibung der Gefuegeumwandlungen, gekoppelt mit einer nichtlinearen Waermeleitungsgleichung sowie Komponenten zur Beschreibung der Energieeinkopplung. Um eine moeglichst breite Anwendbarkeit der Software zu gewaehrleisten, wurden werkstoffspezifische Kennwerte zum Umwandlungsverhalten fuer eine grosse Anzahl praxisrelevanter Staehle bereitgestellt. Zur Modellverifikation wurden experimentelle Untersuchungen bei beteiligten Industriepartnern durchgefuehrt und mit den entsprechenden Simulationsrechnungen verglichen.