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Mathematical modeling often helps to provide a systems perspective on gene regulatory networks. In particular, qualitative approaches are useful when detailed kinetic information is lacking. Multiple methods have been developed that implement qualitative information in different ways, e.g., in purely discrete or hybrid discrete/continuous models. In this paper, we compare the discrete asynchronous logical modeling formalism for gene regulatory networks due to R. Thomas with piecewise affine differential equation models.
We provide a local characterization of the qualitative dynamics of a piecewise affine differential equation model using the discrete dynamics of a corresponding Thomas model. Based on this result, we investigate the consistency of higher-level dynamical properties such as attractor characteristics and reachability. We show that although the two approaches are based on equivalent information, the resulting qualitative dynamics are different. In particular, the dynamics of the piecewise affine differential equation model is not a simple refinement of the dynamics of the Thomas model.
The authors propose a recycling MINRES scheme for a solution of subsequent self-adjoint linear systems as appearing, for example, in the Newton process for solving nonlinear equations. Ritz vectors are automatically extracted from one MINRES run and then used for self-adjoint deflation in the next. The method is designed to work with a preconditioner and arbitrary inner products. Numerical experiments with nonlinear Schrödinger equations indicate a substantial decrease in computation time when recycling is used.
We consider a shape implant design problem that arises in the context of facial surgery. We introduce a reformulation as an optimal control problem, where the control acts as a boundary force. The state is modelled as a minimizer of a polyconvex hyperelastic energy functional. We show existence of optimal solutions and derive - on a formal level - first order optimality conditions. Finally, preliminary numerical results are presented.
The pole condition approach for deriving transparent boundary conditions is extended to the time-dependent, two-dimensional case. Non-physical modes of the solution are identified by the position of poles of the solution's spatial Laplace transform in the complex plane. By requiring the Laplace transform to be analytic on some
problem dependent complex half-plane, these modes can be
suppressed. The resulting algorithm computes a finite number of coefficients of a series expansion of the Laplace transform, thereby providing an approximation to the exact boundary condition. The resulting error decays super-algebraically with the number of coefficients, so relatively few additional degrees of freedom are
sufficient to reduce the error to the level of the discretization error in the interior of the computational domain. The approach shows good results for the Schroedinger and the drift-diffusion equation
but, in contrast to the one-dimensional case, exhibits instabilities for the wave and Klein-Gordon equation. Numerical examples are shown that demonstrate the good performance in the former and the instabilities in the latter case.
Flux variability analysis (FVA) is an important tool to further analyze the results obtained by flux balance analysis (FBA) on genome-scale metabolic networks. Standard FVA may predict unbounded fluxes through some reactions in the network even if the nutrient uptake rate is bounded. These fluxes violate the second law of thermodynamics. They may be eliminated by extending flux variability analysis with thermodynamic constraints.
We present a new algorithm for efficient flux variability (and flux balance) analysis with thermodynamic constraints, suitable for analyzing genome-scale metabolic networks. We first show that flux balance analysis with thermodynamic constraints is NP-hard. Then we derive a theoretical tractability result, which can be applied to metabolic networks in practice. We use this result to develop a new constraint programming algorithm Fast-tFVA for fast flux variability analysis with thermodynamic constraints (tFVA). Computational comparisons with previous methods demonstrate the efficiency of the new method. For tFVA, a speed-up of factor 30-300 is achieved.
In an analysis of genome-scale metabolic networks in the BioModels database, we found that in 485 out of 716 networks additional irreversible or fixed reactions could be detected.
This article describes Fortran 77 subroutines for computing eigenvalues and invariant subspaces
of Hamiltonian and skew-Hamiltonian matrices. The implemented algorithms are based on orthogonal
symplectic decompositions, implying numerical backward stability as well as symmetry
preservation for the computed eigenvalues. These algorithms are supplemented with balancing and
block algorithms, which can lead to considerable accuracy and performance improvements. As a
by-product, an efficient implementation for computing symplectic QR decompositions is provided.
We demonstrate the usefulness of the subroutines for several, practically relevant examples.
Stewart's recently introduced Krylov-Schur algorithm
is a modification of the implicitly restarted Arnoldi algorithm which
employs reordered Schur decompositions to perform restarts and de-
ations in a numerically reliable manner. This paper describes a variant
of the Krylov-Schur algorithm suitable for addressing eigenvalue
problems associated with products of large and sparse matrices. It
performs restarts and de
ations via reordered periodic Schur decompositions
and, by taking the product structure into account, it is
capable to achieve qualitatively better approximations to the eigenvalues
of small magnitude.
The role of larger bulges in the QR algorithm is controversial. Large bulges are infamous
for having a strong, negative influence on the convergence of the implicit shifted QR algorithm.
This paper provides a new explanation of this shift blurring effect by connecting the computation of
the first column of the shift polynomial to the notoriously ill-conditioned pole placement problem.
To avoid shift blurring, modern variants of the QR algorithm employ chains of tightly coupled tiny
bulges instead of one large bulge. It turns out that larger bulges still play a positive role in these
variants; a slight increase of the bulge sizes often results in considerable performance improvements.
We investigate the condition number for a complex eigenvalue of a real matrix under
real perturbations. Based on an explicit formula, it is shown that this number is never
smaller than 1/
p
2 times the corresponding condition number with respect to complex
perturbations. This result can be generalized to the condition number of an arbitrary
complex-valued function under real perturbations. This extends to related condition
numbers.