## ZIB-Report

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18-54

The paper investigates the efficient use of a linearly implicit stiff integrator for the numerical solution of density driven flow problems. Upon choosing a one-step method of extrapolation type (code LIMEX), the use of full Jacobians and reduced approximations are discussed. Numerical experiments include nonlinear density flow problems such as diffusion from a salt dome (2D), a (modified) Elder problem (3D), the saltpool benchmark (3D) and a real life salt dome problem (2D). The arising linear equations are solved using either a multigrid preconditioner from the software package UG4 or the sparse matrix solver SuperLU.

18-45

18-53

We show how biologically coherent mesh models of animals can be created from μCT data to generate artificial yet naturally looking intermediate objects. The whole pipeline of processing algorithms is presented, starting from generating topologically equivalent surface meshes, followed by solving the correspondence problem, and, finally, creating a surface morphing. In this pipeline, we address all the challenges that are due to dealing with complex biological, non-isometric objects. For biological objects it is often particularly important to obtain deformations that look as realistic as possible. In addition, spatially non-uniform shape morphings that only change one part of the surface and keep the rest as stable as possible are of interest for evolutionary studies, since functional modules often change independently from one another. We use Poisson interpolation for this purpose and show that it is well suited to generate both global and local shape deformations.

18-51

Calculation of clinch and elimination numbers for sports leagues with multiple tiebreaking criteria
(2018)

The clinch (elimination) number is a minimal number of future wins (losses) needed to clinch (to be eliminated from) a specified place in a sports league. Several optimization models and computational results are shown in this paper for calculating clinch and elimination numbers in the presence of predefined multiple tiebreaking criteria. The main subject of this paper is to provide a general algorithmic framework based on integer programming with utilizing possibly multilayered upper and lower bounds.

18-47

Dieses Dokument fasst den Stand der mathematischen Modellierung von
Preissystemen des öV mittels eines am ZIB entwickelten Tarifgraphenmodells zusammen. Damit sind sehr einfache und konzise
Beschreibungen von Tarifstrukturen möglich, die sich algorithmisch
behandeln lassen: Durch das zeitgleiche Tracken eines Pfades im
Routinggraphen im Tarifgraphen kann schon während einer Routenberechnung der Preis bestimmt werden. Wir beschreiben
zunächst das Konzept. Die konkrete Realisierung wird im Folgenden
beispielhaft an den Tarifsystemen der Verkehrsverbünde Warnow,
MDV, Vogtland, Bremen/Niedersachsen, Berlin/Brandenburg und Mittelsachsen erläutert. Anschließend folgen Überlegungen zur konkreten Implementierung von Kurzstrecken-Tarifen und zur Behandlung des Verbundübergriffs.

18-52

Gene Regulatory Networks are powerful models for describing the mechanisms and dynamics inside a cell. These networks are generally large in dimension and seldom yield analytical formulations. It was shown that studying the conditional expectations between dimensions (vertices or species) of a network could lead to drastic dimension reduction. These conditional expectations were classically given by solving equations of motions derived from the Chemical Master Equation. In this paper we deviate from this convention and take an Algebraic approach instead. That is, we explore the consequences of conditional expectations being described by a polynomial function. There are two main results in this work. Firstly: if the conditional expectation can be described by a polynomial function, then coefficients of this polynomial function can be reconstructed using the classical moments. And secondly: there are dimensions in Gene Regulatory Networks which inherently have conditional expectations with algebraic forms. We demonstrate through examples, that the theory derived in this work can be used to develop new and effective numerical schemes for forward simulation and parameter inference. The algebraic line of investigation of conditional expectations has considerable scope to be applied to many different aspects of Gene Regulatory Networks; this paper serves as a preliminary commentary in this direction.

18-24

We present an extension of Taylor’s theorem towards nonsmooth evalua-
tion procedures incorporating absolute value operaions. Evaluations procedures are
computer programs of mathematical functions in closed form expression and al-
low a different treatment of smooth operations and calls to the absolute value value
function. The well known classical Theorem of Taylor defines polynomial approx-
imation of sufficiently smooth functions and is widely used for the derivation and
analysis of numerical integrators for systems of ordinary differential or differential
algebraic equations, for the construction of solvers for the continuous nonlinear op-
timization of finite dimensional objective functions and for root solving of nonlinear
systems of equations. The herein provided proof is construtive and allow efficiently
designed algorithms for the execution and computation of generalized piecewise
polynomial expansions. As a demonstration we will derive a k-step method on the
basis of polynomial interpolation and the proposed generalized expansions.

18-43

Recent research has shown that piecewise smooth (PS) functions can be approximated by piecewise linear functions with second order error in the distance to
a given reference point. A semismooth Newton type algorithm based on successive application of these piecewise linearizations was subsequently developed
for the solution of PS equation systems. For local bijectivity of the linearization
at a root, a radius of quadratic convergence was explicitly calculated in terms
of local Lipschitz constants of the underlying PS function. In the present work
we relax the criterium of local bijectivity of the linearization to local openness.
For this purpose a weak implicit function theorem is proved via local mapping
degree theory. It is shown that there exist PS functions f:IR^2 --> IR^2 satisfying the weaker
criterium where every neighborhood of the root of f contains a point x such that
all elements of the Clarke Jacobian at x are singular. In such neighborhoods
the steps of classical semismooth Newton are not defined, which establishes
the new method as an independent algorithm. To further clarify the relation between a PS function and its piecewise linearization,
several statements about structure correspondences between the two are proved.
Moreover, the influence of the specific representation of the local piecewise linear models
on the robustness of our method is studied.
An example application from cardiovascular mathematics is given.

18-50

A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo-pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo-pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (> 300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo-pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3 % and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed.

18-49

We establish a general computational framework for Chvátal’s conjecture based on exact rational integer programming. As a result we prove Chvátal’s conjecture holds for all downsets whose union of sets contains seven elements or less. The computational proof relies on an exact branch-and-bound certificate that allows for elementary verification and is independent of the integer programming solver used.