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For regular matrix pencils the distance in norm to the nearest singular pencil
under low rank perturbation is studied. Characterizations of this distance are derived via the Weyl function of the perturbation. Special attention is paid to the Hermitian pencil case.
Estimates for the distance of a given pencil to the set of singular pencils are obtained.
A Branch-Cut-And-Price Algorithm for a Combined Buy-at-Bulk Network Design Facility Location Problem
(2014)
In the combined buy-at-bulk network design facility location
problem we are given an undirected network with a set of potential facilities and a set of clients with demands. In addition, we are also provided a set of cable types with each cable type having a capacity and cost per unit length. The cost to capacity ratio decreases from large to small
cables following economies of scale. A network planner is expected to determine a set of facilities to open and install cables along the edges of the network in order to route the demands of the clients to some open facility. The capacities of the installed cable must be able to support the demands of the clients routed along that edge.The objective is to minimize the cost that is paid for opening facilities and installing cables. We model the problem as an integer program and propose a branch-cut-and-price algorithm for solving it. We study the effect of two family of valid inequalities that naturally emerge from the model. We present the results of our implementation that were tested on a set of large real world instances.
Asymptotic behavior is often of particular interest when analyzing asynchronous Boolean networks representing biological systems such as signal transduction or gene regulatory networks. Methods based on a generalization of the steady state notion, the so-called symbolic steady states, can be exploited to investigate attractor properties as well as for model reduction techniques conserving attractors. In this paper, we propose a novel optimization-based method for computing all maximal symbolic steady states and motivate their use. In particular, we add a new result yielding a lower bound for the number of cyclic attractors and illustrate the methods with a short study of a MAPK pathway model.
Constraint-based modeling of genome-scale metabolic network reconstructions has become a widely used approach in computational biology. Flux coupling analysis is a constraint-based method that analyses the impact of single reaction knockouts on other reactions in the network.We present an extension of flux coupling analysis for double and multiple gene or reaction knockouts, and develop corresponding algorithms for an in silico simulation. To evaluate our method, we perform a full single and double knockout analysis on a selection of genome-scale metabolic network reconstructions and compare the results.
Flux coupling analysis (FCA) has become a useful tool for aiding metabolic reconstructions and guiding genetic manipulations. Originally, it was introduced for constraint-based models of metabolic networks that are based on the steady-state assumption. Recently, we have shown that the steady-state assumption can be replaced by a much weaker lattice-theoretic property related to the supports of metabolic fluxes. In this paper, we further extend our approach and delevelop an efficient algorithm for general qualitative flux coupling analysis (QFCA). We illustrate our method by thermodynamic flux coupling analysis (tFCA), which allows studying steady-state metabolic models with loop-law thermodynamic constraints. These models do not satisfy the lattice-theoretic properties required in our previous work. For a selection of genome-scale metabolic network reconstructions, we discuss both theoretically and practically, how thermodynamic constraints strengthen the coupling results that can be obtained with classical FCA.
Transitive reductions and minimal equivalent subgraphs have proven to be a powerful concept to simplify networks and to measure their redundancy. Here we consider a generalization of the minimal equivalent subgraph problem where a set of arcs is already given. For two digraphs D = (V,A), D′ = (V,A′) with A′ ⊆ A, we ask for the minimal set of edges of D that have to be added to D′ such that the transitive closure of D equals the transitive closure of D′.
We present a method to compute such an extension and show that if D is transitively closed, this problem can be solved in polynomial time.
The long standing problem is discussed of how to deflate the part associated with the eigenvalue infinity in a structured matrix pencil using structure preserving unitary transformations. We derive such a deflation procedure and apply this new technique to symmetric, Hermitian or alternating pencils and in a modified form to (anti)-palindromic pencils. We present a detailed error and perturbation analysis of this and other deflation procedures and demonstrate the properties of the new algorithm with several numerical examples.
We discuss Möbius transformations for general matrix polynomials over arbitrary
elds, analyzing their in
uence on regularity, rank, determinant, constructs such as compound
matrices, and on structural features including sparsity and symmetry. Results on
the preservation of spectral information contained in elementary divisors, partial multiplicity
sequences, invariant pairs, and minimal indices are presented. The eect on canonical
forms such as Smith forms and local Smith forms, on relationships of strict equivalence
and spectral equivalence, and on the property of being a linearization or quadratication
are investigated. We show that many important transformations are special instances
of Möbius transformations, and analyze a Möbius connection between alternating and
palindromic matrix polynomials. Finally, the use of Möbius transformations in solving
polynomial inverse eigenproblems is illustrated.
This paper focuses on
rate-independent damage in elastic bodies. Since the driving energy is nonconvex,
solutions may have jumps as a function of time, and in this situation it is known that the classical concept
of energetic solutions for rate-independent systems
may fail to accurately describe the
behavior of the system at jumps.
Therefore, we resort to the (by now well-established) vanishing viscosity approach to rate-independent modeling
and approximate the model by its viscous regularization.
In fact, the analysis of the latter PDE system presents
remarkable difficulties, due to its highly nonlinear character.
We tackle it by combining a variational approach to a class of abstract doubly nonlinear evolution equations, with
careful regularity estimates tailored to this specific system relying on a q-Laplacian type gradient regularization of the damage variable.
Hence, for the viscous problem we conclude the existence of weak solutions satisfying a
suitable energy-dissipation inequality that is the starting point for the vanishing viscosity analysis.
The latter leads to the notion of (weak) parameterized
solution to our rate-independent system,
which encompasses the influence of viscosity in the description of the jump regime.
We study the approximation of Wasserstein gradient structures
by their finite-dimensional analog. We show that simple
finite-volume discretizations of the linear Fokker-Planck
equation exhibit the recently established entropic gradient-flow
structure for reversible Markov chains. Then we reprove the
convergence of the discrete scheme in the limit of vanishing
mesh size using only the involved gradient-flow structures.
In particular, we make no use of the linearity of the equations
nor of the fact that the Fokker-Planck equation is of second order.
Spectral deferred correction methods for solving stiff ODEs are known to
converge rapidly towards the collocation limit solution on equidistant grids,
but show a much less favourable contraction on non-equidistant grids such as
Radau-IIa points. We interprete SDC methods as fixed point iterations for the
collocation system and propose new DIRK-type sweeps for stiff problems based
on purely linear algebraic considerations. Good convergence is recovered also
on non-equidistant grids. The properties of different variants are explored on
a couple of numerical examples.
The well-known structure theorem of Hadamard-Zol\'esio states that the derivative of a shape functional is a distribution on the boundary of the domain depending only on the normal perturbations of a smooth enough boundary. However a volume representation (distributed shape derivative) is more general than the boundary form and allows to work with shapes having a lower regularity.
It is customary in the shape optimization literature to assume regularity of the domains and use the boundary expression of the shape derivative for numerical algorithm. In this paper we describe the numerous advantages of the distributed shape derivative in terms of generality, easiness of computation and numerical implementation. We give several examples of numerical applications such as the inverse conductivity problem and the level set method.
For the solution of optimal control problems governed by nonlinear parabolic PDEs, methods working on the reduced objective functional are often employed to avoid a full
spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of
the adjoint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories
have to be stored. To get numerical results which are accurate enough, in many case very fine discretizations in time and space are necessary, which leads to a significant
amount of data to be stored and transmitted to mass storage. Lossy compression methods were developed to overcome the storage problem by reducing the accuracy of the stored
trajectories. The inexact data induces errors in the reduced gradient and reduced Hessian. In this paper, we analyze the influence of such a lossy trajectory compression
method on Newton-CG methods for optimal control of parabolic PDEs and design an adaptive strategy for choosing appropriate quantization tolerances.
Elementary flux mode (EM) analysis is an important tool in the constraint-based analysis of genome-scale metabolic networks. Due to the combinatorial complexity of these networks, as well as the advances in the level of detail to which they can be reconstructed, an exhaustive enumeration of all EMs is often not practical. Therefore, in recent years interest has shifted towards searching EMs with specific properties. We present a novel method that allows computing EMs containing a given set of target reactions. This generalizes previous algorithms where the set of target reactions consists of a single reaction. In the one-reaction case, our method compares favorably to the previous approaches. In addition, we present several applications of our algorithm for computing EMs containing two target reactions in genome-scale metabolic networks.
Resolving thin conducting sheets for shielding or even skin layers inside by the mesh of numerical methods like the finite element method (FEM) can be avoided by using impedance transmission conditions (ITCs). Those ITCs shall provide an accurate approximation for small sheet thicknesses $d$, where the accuracy is best possible independent of the conductivity or the frequency being small or large -- this we will call robustness. We investigate the accuracy and robustness of popular and recently developed ITCs, and propose robust ITCs which are accurate up to $O(d^2)$.
We consider multiscale Hamiltonian systems in which harmonic oscillators with several high frequencies are coupled to a slow system. It is shown that the oscillatory energy is nearly preserved over long times eps^{-N} for arbitrary N>1, where eps^{-1} is the size of the smallest high frequency. The result is uniform in the frequencies and does not require non-resonance conditions.
Sobolev stability of plane wave solutions to the cubic nonlinear Schrödinger equation on a torus
(2013)
It is shown that plane wave solutions to the cubic nonlinear Schrödinger equation on a torus behave orbitally stable under generic perturbations of the initial data that are small in a high-order Sobolev norm, over long times that extend to arbitrary negative powers of the smallness parameter. The perturbation stays small in the same Sobolev norm over such long times. The proof uses a Hamiltonian reduction and transformation and, alternatively, Birkhoff normal forms or modulated Fourier expansions in time.
Coarsening in solder alloys is a widely accepted indicator for
possible failure of joints in electronic devices.
Based on the well-established Cahn--Larch\'e model
with logarithmic chemical energy density (see, e.g., Dreyer and Mueller 2001),
we present a numerical environment for the efficient
and reliable simulation of coarsening in binary alloys.
Main features are adaptive mesh refinement based on hierarchical error estimates,
fast and reliable algebraic solution by multigrid and Schur--Newton multigrid methods,
and the quantification of the coarsening speed by the temporal growth of mean phase radii.
We provide a detailed description and a numerical assessment of the algorithm and its different components,
together with a practical application to a eutectic AgCu brazing alloy.
We investigate the convergence of an implicit Voronoi finite volume
method for reaction-diffusion problems including nonlinear diffusion
in two space dimensions. The model allows to handle heterogeneous
materials and uses the chemical potentials of the involved species as
primary variables. The numerical scheme uses boundary conforming Delaunay
meshes and preserves positivity and the dissipative property of the
continuous system. Starting from a result on the global stability of
the scheme (uniform, mesh-independent global upper and lower bounds),
we prove strong convergence of the chemical activities and their gradients
to a weak solution of the continuous problem. In order to illustrate the
preservation of qualitative properties by the numerical scheme, we present
a long-term simulation of the Michaelis-Menten-Henri system. Especially,
we investigate the decay properties of the relative free energy and the
evolution of the dissipation rate over several magnitudes of time, and
obtain experimental orders of convergence for these quantities.
In this work we present a complete algorithm for the exact computation of the guided mode band structure in photonic crystal (PhC) wave-guides. In contrast to the supercell method, the used approach does not introduce any modelling error and is hence independent of the confinement of the modes. The approach is based on Dirichlet-to-Neumann (DtN) transparent boundary conditions that yield a nonlinear eigenvalue problem. For the solution of this nonlinear eigenvalue problem we present a direct technique using Chebyshev interpolation that requires a band gap calculation of the PhC in advance. For this band gap calculation –- we introduce as a very efficient tool –- a Taylor expansion of the PhC band structure. We show that our algorithm –- like the supercell method –- converges exponentially, however, its computational costs –- in comparison to the supercell method –- only increase moderately since the size of the matrix to be inverted remains constant.