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We consider the design of a passive optical telecommunication access network, where clients have to be connected to an intermediate level of distribution points (DPs) and further on to some central offices (COs) in a tree-like fashion. Each client demands a given number of fiber connections to its CO. Passive optical splitters installed at the DPs allow k connections to share a single common fiber between the DP and the CO. We consider fixed charge costs for the use of an edge of the underlying street network, of a DP, and of a CO and variable costs for installing fibers along the street edges and for installing splitters at the DPs. We present two Lagrangian decomposition approaches that decompose the problem based on the network structure and on the cost structure, respectively. The subproblems are solved using MIP techniques. We report computational results for realistic instances and compare the efficiency of the Lagrangian approaches to the solutions of an integrated MIP model.
Motivation. Modelling, parameter identification, and simulation play an important role in systems biology. Usually, the goal is to determine parameter values that minimise the difference between experimental measurement values and model predictions in a least-squares sense. Large-scale biological networks, however, often suffer from missing data for parameter identification. Thus, the least-squares problems are rank-deficient and solutions are not unique. Many common optimisation methods ignore this detail because they do not take into account the structure of the underlying inverse problem. These algorithms simply return a “solution” without additional information on identifiability or uniqueness. This can yield misleading results, especially if parameters are co-regulated and data are noisy.
Results. The Gauss-Newton method presented in this paper monitors the numerical rank of the Jacobian and converges locally, for the class of adequate problems, to a solution that is unique within the subspace of identifiable parameters. This method has been implemented in BioPARKIN, a software package that combines state-of-the-art numerical algorithms with compliance to system biology standards, most importantly SBML, and an accessible interface.
Availability. The software package BioPARKIN is available for download at http://bioparkin.zib.de .
A basic task in signal analysis is to character-
ize data in a meaningful way for analysis and classification
purposes. Time-frequency transforms are powerful strategies
for signal decomposition, and important recent generalizations
have been achieved in the setting of frame theory. In parallel
recent developments, tools from algebraic topology, traditionally
developed in purely abstract settings, have provided new insights
in applications to data analysis. In this report, we investigate some
interactions of these tools, both theoretically and with numerical
experiments, in order to characterize signals and their frame
transforms. We explain basic concepts in persistent homology
as an important new subfield of computational topology, as well
as formulations of time-frequency analysis in frame theory. Our
objective is to use persistent homology for constructing topo-
logical signatures of signals in the context of frame theory. The
motivation is to design new classification and analysis methods by
combining the strength of frame theory as a fundamental signal
processing methodology, with persistent homology as a new tool
in data analysis.
We derive a formula for the backward error of a complex number $\lambda$ when considered as an approximate eigenvalue
of a Hermitian matrix pencil or polynomial with respect to Hermitian perturbations. The same are also obtained for approximate
eigenvalues of matrix pencils and polynomials with related structures like skew-Hermitian, $*$-even and $*$-odd.
Numerical experiments suggest that in many cases there is a significant difference between the backward
errors with respect to perturbations that preserve structure and those with respect to arbitrary perturbations.
An existence result is proved for a nonlinear diffusion problem of phase-field type, consisting of a parabolic system of two partial differential equations, complemented by Neumann homogeneous boundary conditions and initial
conditions. This system is meant to model two-species phase segregation on an atomic lattice under the presence of diffusion. A similar system has been recently
introduced and analyzed in [3]. Both systems conform to the general theory developed in [5]: two parabolic PDEs, interpreted as balances of microforces and microenergy,
are to be solved for the order parameter rho and the chemical potential mu. In the system studied in this note, a phase-field equation in rho fairly more general than in [3] is coupled with a highly nonlinear diffusion equation for mu, in which the conductivity coefficient is allowed to depend nonlinearly on both variables.
Global existence and uniqueness for a singular/degenerate Cahn-Hilliard system with viscosity
(2013)
Existence and uniqueness are investigated for a nonlinear diffusion problem of phase-field type, consisting of a parabolic system of two partial differential equations, complemented by Neumann homogeneous boundary conditions and initial conditions. This system aims to model two-species phase segregation on an atomic lattice [19]; in the balance equations of microforces and microenergy, the two
unknowns are the order parameter rho and the chemical potential mu. A simpler version of the same system has recently been discussed in [8]. In this paper, a fairly more general phase-field equation for rho is coupled with a genuinely nonlinear diffusion equation for mu. The existence of a global-in-time solution is proved with the help of suitable a priori estimates. In the case of constant atom mobility, a new and rather unusual uniqueness
proof is given, based on a suitable combination of variables.
We are concerned with a nonstandard phase field model of
Cahn-Hilliard type. The model, which was introduced by Podio-Guidugli (Ric. Mat. 2006), describes two-species phase segregation and consists of a system of two highly nonlinearly coupled PDEs. It has been recently investigated
by Colli, Gilardi, Podio-Guidugli, and Sprekels in a series of papers: see, in particular, SIAM J. Appl. Math. 2011,
and Boll. Unione Mat. Ital. 2012. In the latter contribution, the authors can treat the very general case in which the diffusivity coefficient of the parabolic PDE
is allowed to depend nonlinearly on both variables. In the same framework, this paper investigates the asymptotic limit of the solutions to the initial-boundary value problems as the diffusion coefficient sigma in the equation governing the evolution of the order parameter tends to zero. We prove that such a limit actually exists and solves the limit problem, which couples a nonlinear PDE of parabolic type with an ODE accounting for the phase dynamics. In the case of a constant diffusivity, we are able to show uniqueness and to improve the regularity of the solution.
The present note deals with a nonstandard systems of differential equations describing a two-species phase segregation. This system naturally arises in the asymptotic analysis carried out recently by the same authors,
as the diffusion coefficient in the equation governing
the evolution of the order parameter tends to zero. In particular, an existence result has been proved for the limit system in a very general framework. On the contrary, uniqueness was shown by assuming a constant mobility coefficient. Here, we generalize this result and prove
a continuous dependence property in the case that the mobility coefficient suitably depends on the chemical potential.
In this paper we propose a time discretization of a system of two parabolic equations describing diffusion-driven atom rearrangement in crystalline matter. The equations express the balances of microforces and microenergy; the two phase fields are the order parameter and the chemical potential. The initial and boundary-value problem for the evolutionary system is known to be well posed. Convergence of the discrete scheme to the solution of the continuous problem is proved by a careful development of uniform estimates, by weak compactness and a suitable treatment of
nonlinearities. Moreover, for the difference of discrete
and continuous solutions we prove an error estimate of
order one with respect to the time step.
We study the incremental facility location problem, wherein we are given an instance of the uncapacitated facility location problem. We seek an incremental sequence of opening facilities and an incremental sequence of serving customers along with their fixed assignments to facilities open in the partial sequence. Our aim is to have the solution obtained for serving the first l customers in the sequence be competitive with the optimal solution to serve any l customers. We provide an incremental framework that provides an overall competitive factor of 8 and a worst case instance that provides the lower bound of 3. The problem has applications in multi-stage network planning.
We consider a generalized version of the rooted connected facility location problem which occurs in planning of telecommunication networks with both survivability and hop-length constraints. Given a set of client nodes, a set of potential facility nodes including one predetermined root facility, a set of optional Steiner nodes, and the set of the potential connections among these nodes, that task is to decide which facilities to open, how to assign the clients to the open facilities, and how to interconnect the open facilities in such a way, that the resulting network contains at least edge-disjoint paths, each containing at most H edges, between the root and each open facility and that the total cost for opening facilities and installing connections is minimal. We study two IP models for this problem and present a branch-and-cut algorithm based on Benders decomposition for nding its solution. Finally, we report computational results.
In the connected facility location problem with buy-at-bulk edge costs we are given a set of clients with positive demands and a set of potential facilities with opening costs in an undirected graph with edge lengths obeying the triangle inequality. Moreover, we are given a set of access cable types, each with a cost per unit length and a capacity such that the cost per capacity decreases from small to large cables, and a core cable type of innite capacity. The task is to open some facilities and to connect them by a Steiner tree using core cables, and to build a forest network using access cables such that the edge capacities suce to simultaneously route all client demands unsplit to the open facilities. The objective is to minimize the total cost of opening facilities, building the core Steiner tree, and installing the access cables. In this paper, we devise a constant-factor approximation algorithm for this problem based on a random sampling technique.
We consider a generalization of the connected facility location problem where the clients must be connected to the open facilities via shared capacitated (tree) networks instead of independent shortest paths. This problem arises in the planning of ber optic telecommunication access networks, for example. Given a set of clients with positive demands, a set of potential facilities with opening costs, a set of capacitated access cable types, and a core cable type of innite capacity, one has to decide which facilities to open, how to interconnect them using a Steiner tree of innite capacity core cables, and which access cable types to install on which potential edges such that these edges form a forest and the installed capacities suce to simultaneously route the client demands to the open facilities via single paths. The objective is to minimize the total cost of opening facilities, building the core Steiner tree among them, and installing the access cables. In this paper, we devise a constant-factor approximation algorithm for problem instances where the access cable types obey economies of scale. In the special case where only multiples of a single cable type can be installed on the access edges, a variant of our algorithm achieves a performance guarantee of 6.72.
This paper presents efficient computational techniques for solving an optimization problem in cardiac defibrillation governed by the monodomain equations. Time-dependent electrical currents injected at different spatial positions act as the control. Inexact Newton-CG methods are used, with reduced gradient computation by adjoint solves. In order to reduce the computational complexity, adaptive mesh refinement for state and adjoint equations is performed. To reduce the high storage and bandwidth demand imposed by adjoint gradient and Hessian-vector evaluations, a lossy compression technique for storing trajectory data is applied. An adaptive choice of quantization tolerance based on error estimates is developed in order to ensure convergence. The efficiency of the proposed approach is demonstrated on numerical examples.
In this paper a condition number for linear-quadratic two-stage stochastic optimization problems is introduced as the Lipschitz modulus of the multifunction assigning to a (discrete) probability distribution the solution set of the problem. Being the outer norm of the Mordukhovich coderivative of this multifunction, the condition number can be estimated from above explicitly in terms of the problem data by applying appropriate calculus rules. Here, a chain rule for the extended partial second-order subdifferential recently proved by Mordukhovich and Rockafellar plays a crucial role. The obtained results are illustrated for the example of two-stage stochastic optimization problems with simple recourse.
The chemical master equation is a fundamental equation in chemical kinetics. It is an adequate substitute for the classical reaction-rate equations whenever stochastic effects become relevant. In the present paper we give a simple argument showing that the solutions of a large class of chemical master equations, including all those in which elementary reactions between two and more molecules do not generate a larger number of molecules than existed before,
are bounded in weighted $\ell_1$-spaces. As an illustration for the implications of this kind of regularity we analyze the effect of truncating the state space. This leads to an error analysis of the finite state projection of the chemical master equation, an approximation that underlies many numerical methods.
A mixed-integer stochastic nonlinear optimization problem with joint probabilistic constraints
(2013)
We illustrate the solution of a mixed-integer stochastic nonlinear optimization problem in an application of power management. In this application, a coupled system consisting of a hydro power station and a wind farm is considered. The objective is to satisfy the local energy demand and sell any surplus energy on a spot market for a short time horizon. Generation of wind energy is assumed to be random, so that demand satisfaction is modeled by a joint probabilistic constraint taking into account the multivariate distribution. The turbine is forced to either operate between given positive limits or to be shut down. This introduces additional binary decisions. The numerical solution procedure is presented and results are illustrated.
We present new residual estimates based on Kato's square root theorem for spectral approximations of diagonalizable non-self-adjoint differential operators of convection-diffusion-reaction type. These estimates are incorporated as part of an hp-adaptive finite element algorithm for practical spectral computations, where it is shown that the
resulting a posteriori error estimates are reliable. Provided experiments demonstrate the efficiency and reliability of our approach.
The huge number of elementary flux modes (EFM) in genome-scale metabolic networks makes analysis based on elementary flux modes intrinsically difficult. However, it has been shown that the elementary flux modes with optimal yield often contain highly redundant information. The set of optimal-yield elementary flux modes can be compressed using modules. Up to now, this compression was only possible by first enumerating the whole set of all optimal-yield elementary flux modes.
We present a direct method for computing modules of the thermodynamically constrained optimal flux space of a metabolic network. This method can be used to decompose the set of optimal-yield elementary flux modes in a modular way and to speed up their computation. In addition, it provides a new form of coupling information that is not obtained by classical flux coupling analysis. We illustrate our approach on a set of model organisms.
Constraint-based analysis of metabolic networks has become a widely used approach in computational systems biology.
In the simplest form, a metabolic network is represented by a stoichiometric matrix and thermodynamic information on the irreversibility of certain reactions.
Then one studies the set of all steady-state flux vectors satisfying these stoichiometric and thermodynamic constraints.
We introduce a new lattice-theoretic framework for the computational analysis of metabolic networks, which focuses on the support of the flux vectors,
i.e., we consider only the qualitative information whether or not a certain reaction is active, but not its specific flux rate.
Our lattice-theoretic view includes classical metabolic pathway analysis as a special case, but turns out to be much more flexible and general,
with a wide range of possible applications.
We show how important concepts from metabolic pathway analysis, such as blocked reactions, flux coupling, or elementary modes, can be generalized to arbitrary lattice-based models. We develop corresponding general algorithms and present a number of computational results.
Multi-Level Monte-Carlo Finite Element Methods for stochastic elliptic variational inequalities
(2013)
Multi-Level Monte-Carlo Finite Element (MLMC--FE) methods
for the solution of stochastic elliptic variational inequalities
are introduced, analyzed, and numerically investigated.
Under suitable assumptions on the random diffusion coefficient,
the random forcing function, and the deterministic obstacle,
we prove existence and uniqueness of solutions of ``mean-square''
and ``pathwise'' formulations.
Suitable regularity results for deterministic,
elliptic obstacle problems lead
to uniform pathwise error bounds, providing
optimal-order error estimates of the statistical error
and upper bounds for the
corresponding computational cost for
classical Monte--Carlo and novel MLMC--FE methods.
Utilizing suitable multigrid solvers for the occurring sample problems,
in two space dimensions
MLMC--FE methods then provide numerical
approximations of the expectation of the random solution
with the same order of efficiency as for a corresponding
deterministic problem, up to logarithmic terms.
Our theoretical findings are illustrated by numerical experiments.
We introduce and analyze nonsmooth Schur-Newton methods for a class of nonsmooth saddle point problems. The method is able to solve problems where the primal energy decomposes into a convex smooth part and a convex separable but nonsmooth part. The method is based on nonsmooth Newton techniques for an equivalent unconstrained dual problem. Using this we show that it is globally convergent even for inexact evaluation of the linear subproblems.
We introduce a new operator for stabilizing error that arises from the weak enforcement of mass conservation in finite element simulations of incompressible flow problems. We show this new operator has a similar positive effect on velocity error as the well-known and very successful grad-div stabilization operator, but the new operator is more attractive from an implementation standpoint because it yields a sparser block structure matrix. That is, while grad-div produces fully coupled block matrices (i.e. block-full), the matrices arising from the new operator are block-upper triangular in two dimensions, and in three dimensions the 2,1 and 3,1 blocks are empty. Moreover, the diagonal blocks of the new operator's matrices are identical to those of grad-div. We provide error estimates and numerical examples for finite element simulations with the new operator, which reveals the significant improvement in accuracy it can provide. Solutions found using the new operator are also compared to those using usual grad-div stabilization, and in all cases, solutions are found to be very similar.
The computation of guided modes in photonic crystal wave-guides is a key issue in the process of designing devices in photonic communications. Existing methods, such as the super-cell method, provide an efficient computation of well-confined modes. However, if the modes are not well-confined, the modelling error of the super-cell method becomes prohibitive and advanced methods applying transparent boundary conditions for periodic media are needed. In this work we demonstrate the numerical realization of a recently proposed Dirichlet-to-Neumann approach and compare the results with those of the super-cell method. For the resulting non-linear eigenvalue problem we propose an iterative solution based on Newton's method and a direct solution using Chebyshev interpolation of the non-linear operator. Based on the Dirichlet-to-Neumann approach, we present a formula for the group velocity of guided modes that can serve as an objective function in the optimization of photonic crystal wave-guides.
We study the perturbation theory of structured matrices under structured
rank one perturbations, with emphasis on matrices that are unitary, orthogonal, or symplectic
with respect to an indefinite inner product. The rank one perturbations are not necessarily of
arbitrary small size (in the sense of norm).
In the case of sesquilinear forms, results on selfadjoint matrices can be applied to
unitary matrices by using the Cayley transformation, but
in the case of real or complex symmetric or skew-symmetric bilinear forms
additional considerations are necessary. For complex symplectic matrices, it turns out that
generically (with respect to the perturbations) the behavior of the Jordan form of the
perturbed matrix follows the pattern established earlier for unstructured matrices and their unstructured perturbations, provided the specific properties of the Jordan
form of complex symplectic matrices are accounted for. For instance,
the number of Jordan blocks of fixed odd size corresponding to the eigenvalue $1$ or $-1$ have to be even.
For complex orthogonal matrices, it is shown that the behavior of
the Jordan structures corresponding to the original eigenvalues that are not moved by
perturbations follows again the pattern established earlier for unstructured matrices,
taking into account the specifics of Jordan forms of complex orthogonal
matrices.
The proofs are based on general results developed in the paper concerning Jordan forms of
structured matrices (which include in particular the classes of orthogonal and symplectic matrices)
under structured rank one perturbations. These results are presented and proved in the framework of
real as well as of complex matrices.
Periodic Solutions to Dissipative Hyperbolic Systems. II: Hopf Bifurcation for Semilinear Problems
(2013)
We consider boundary value problems for semilinear hyperbolic systems of the type
$$
\partial_tu_j + a_j(x,\la)\partial_xu_j + b_j(x,\la,u) = 0, \; x\in(0,1), \;j=1,\dots,n
$$
with smooth coefficient functions $a_j$
and $b_j$
such that
$b_j(x,\la,0) = 0$ for all $x \in [0,1]$, $\la \in \R$, and $j=1,\ldots,n$.
We state conditions for Hopf bifurcation, i.e.,
for existence, local uniqueness (up to phase shifts), smoothness and smooth dependence
on $\la$
of time-periodic solutions bifurcating from the zero stationary solution. Furthermore,
we derive a formula which determines the bifurcation direction.
The proof is done by means of a Liapunov-Schmidt reduction procedure.
For this purpose, Fredholm properties of the linearized
system and implicit function
theorem techniques are used.
There are at least two distinguishing features of Hopf bifurcation theorems for hyperbolic PDEs in comparison with those for parabolic PDEs or for ODEs:
First, the question if a non-degenerate time-periodic solution depends smoothly on the system parameters
is much more delicate. And second,
a sufficient amount of dissipativity is needed in the system, and a priori
it is not clear how to verify this in terms of the data of the PDEs and of the boundary conditions.
Periodic Solutions to Dissipative Hyperbolic Systems. I: Fredholm Solvability of Linear Problems
(2013)
This paper concerns linear first-order hyperbolic systems in one space dimension of the type
$$
\partial_tu_j + a_j(x,t)\partial_xu_j + \sum\limits_{k=1}^nb_{jk}(x,t)u_k = f_j(x,t),\; x \in (0,1),\; j=1,\ldots,n,
$$
with periodicity conditions in time and reflection boundary conditions in space. We state a kind of dissipativity condition (depending on the coefficients $a_j$ and $b_{jj}$ and the boundary reflection coefficients), which implies Fredholm solvability of the problem, i.e., either there is a nontrivial solution to the homogeneous problem (in this case the space of such solutions has finite dimension) or the nonhomogeneous problem is uniquely solvable for any right-hand side (in this case the solution depends continuously on the right-hand side). In particular, under those conditions no small denominator effects occur.
Our results work for many non-strictly hyperbolic systems, but they are new even in the case of strict hyperbolicity.
Finally, in the case that all coefficients $a_j$ are $t$-independent, we show that the solutions are $C^\infty$-smooth if the data are $C^\infty$-smooth.
We examine robustness of exponential dichotomies of boundary value problems for general linear first-order one-dimensional hyperbolic systems. The boundary conditions are supposed to be of types ensuring smoothing solutions in finite time, which includes reflection boundary conditions. We show that the dichotomy survives in the space of continuous functions under small perturbations of all coefficients in the differential equations.
We give an exposition of recent results on regularity and Fredholm properties for first-order one-dimensional hyperbolic PDEs. We show that large classes of boundary operators cause an effect that smoothness increases with time. This property is the key in finding regularizers
(parametrices) for hyperbolic problems. We construct regularizers for periodic problems for dissipative first-order linear hyperbolic PDEs and show that these problems are modeled by Fredholm operators of index zero.
We consider systems of reaction-diffusion equations as gradient systems with respect to an entropy functional and a dissipation metric given in terms of a so-called Onsager operator, which is a sum of a diffusion part of Wasserstein type and a reaction part. We provide methods for establishing geodesic $\lambda$-convexity of the entropy functional by purely differential methods, thus circumventing arguments from mass transportation. Finally, several examples, including a drift-diffusion system, provide a survey on the applicability of the theory.
Grad-div stabilization has been proved to be a very useful tool in discretizations
of incompressible flow problems. Standard error analysis for inf-sup stable conforming pairs of
finite element spaces predicts that the stabilization parameter should be optimally chosen
to be $\mathcal O(1)$. This paper revisits this choice for the Stokes equations on the basis
of minimizing the $H^1(\Omega)$ error of the velocity and the $L^2(\Omega)$ error of the pressure.
It turns out, by applying a refined error analysis, that the optimal parameter choice is more subtle
than known so far in the literature. It depends on the used norm,
the solution, the family of finite
element spaces, and the type of mesh. Depending on the situation, the
optimal
stabilization parameter might range from being very small to very large.
The analytic results
are supported by numerical examples.
Complete damage in linear elastic materials — Modeling, weak formulation and existence results
(2013)
In this work, we introduce a degenerating PDE system with a time-depending
domain for complete damage processes under time-varying
Dirichlet boundary conditions. The evolution of the system is
described by a doubly nonlinear differential inclusion for the damage
process and a degenerating quasi-static balance equation for the displacement field
which are strongly nonlinearly coupled.
In our proposed model, the material
may completely disintegrate which is indispensable for a realistic modeling of
damage processes in elastic materials. Complete damage theories
lead to several mathematical problems since, for instance, coercivity properties
of the free energy are lost and, therefore, several difficulties arise.
For the introduced complete damage model, we propose a classical
formulation and a corresponding suitable weak formulation in an
$SBV$-framework. The main aim is to prove existence of weak solutions
for the introduced degenerating model. In addition, we show that the classical
differential inclusion can be regained from the notion of weak solutions under
certain regularity assumptions which is a novelty in the theory of complete damage
models of this type.
For the existence results, we had to handle the following problem:
During the damage process it might occur that not completely damaged material regions are isolated
from the Dirichlet boundary. In this case, the
deformation field cannot be controlled in the transition from incomplete
to complete damage. To tackle this problem, we consider the evolution
process on a time-depending domain. In this context, two major challenges
arise:
Firstly, the time-dependent domain approach leads to jumps in the energy
which have to be accounted for in the energy inequality of the notion of
weak solutions. To handle this problem, several energy estimates are established
by $\Gamma$-convergence techniques. Secondly, the time-depending domain
might have bad smoothness properties such that Korn's inequality cannot be
applied. To this end, a covering result for such sets with smooth
compactly embedded domains has been shown.
This paper discusses adaptive finite element methods (AFEMs) for the solution of elliptic eigenvalue problems associated with partial differential operators. An adaptive method based on nodal-patch refinement leads to an asymptotic error reduction property for the computed sequence of simple eigenvalues and eigenfunctions. This justifies the use of the proven saturation property for a class of reliable and efficient hierarchical a posteriori error estimators. Numerical experiments confirm that the saturation property is present even for very coarse meshes for many examples; in other cases the smallness assumption on the initial mesh may be severe.
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.
We discuss the possibility of computing eigenpairs of some prototypical linear second-order self-adjoint elliptic partial differential operator (or its high-resolution finite element discretization) by numerical upscaling techniques. We compute a low-dimensional generalized finite element space that preserves small eigenvalues in a superconvergent way. The approximate eigenpairs are then obtained by solving the corresponding low-dimensional algebraic eigenvalue problem. The rigorous error bounds are based on two-scale decompositions of H1 by means of a certain Clement-type quasi-interpolation operator.
We present a discretization for dynamic large deformation contact problems without friction. Our model is based on Hamilton’s principle, which avoids the explicit appearance of the contact forces. The resulting differential inclusion is discretized in time using a modified midpoint rule. This modification, which concerns the evaluation of the generalized gradient, allows to achieve energy dissipativity. For the space discretization we use a dual-basis mortar method. The resulting spatial algebraic
problems are nonconvex minimization problems with nonconvex inequality constraints. These can be solved efficiently using a trust-region SQP framework with a monotone multigrid inner solver.
In this paper we propose and analyze a new Multiscale Method for solving semi-linear elliptic problems with heterogeneous and highly variable coeffcient functions. For this purpose we construct a generalized finite element basis that spans a low dimensional multiscale space. The basis is assembled by performing localized linear finescale computations in small patches that have a diameter of order H |log(H)| where H is the coarse mesh size. Without any assumptions on the type of the oscillations in the coeffcients, we give a rigorous proof for a linear convergence of the H1-error with respect to the coarse mesh
size. To solve the arising equations, we propose an algorithm that is based on a damped Newton scheme in the multiscale space.
We discuss shape optimization problems for cylindrical tubes that are loaded by time-dependent applied force. This is a problem of shape optimization that leads to optimal control in linear elasticity theory. We determine the optimal thickness of a cylindrical tube minimizing the deformation of the tube under the influence of the external force. The main difficulty is that the state equation is a hyperbolic partial differential equation of 4th order. First order necessary conditions for the optimal solution are derived. Based on them, a numerical method is set up and numerical examples are presented.
Optimal Thickness of a Cylindrical Shell -- An Optimal Control Problem in Linear Elasticity Theory
(2012)
In this paper we discuss optimization problems for cylindrical tubes which are loaded by an applied force. This is a problem of optimal control in linear elasticity theory (shape optimization). We are looking for an optimal thickness minimizing the deflection (deformation) of the tube under the influence of an external force.
From basic equations of mechanics, we derive the equation of deformation. We apply the displacement approach from shell theory and make use of the hypotheses of
Mindlin and Reissner. A corresponding optimal control problem is formulated and first order necessary conditions for the optimal solution (optimal thickness) are derived.
We present numerical examples which were solved by the finite element method.
In incompressible flows with vanishing
normal velocities at the boundary, irrotational forces in the momentum
equations should be balanced
completely by the pressure gradient.
Unfortunately, nearly all available discretization methods for incompressible flows violate this property.
The origin of the problem is that discrete velocity approximations
of incompressible flows are usually not
divergence-free. Hence, the use of divergence-free velocity reconstructions is
proposed wherever an $L^2$ scalar product appears in the discrete
variational formulation.
The approach is illustrated and applied to a nonconforming MAC-like discretization for unstructured Delaunay grids.
It is numerically demonstrated that a divergence-free velocity reconstruction based on the lowest-order Raviart-Thomas element
increases the robustness and accuracy of an existing convergent discretization, when irrotational forces appear in the momentum equations.
A novel Finite Element Method (FEM) for the computational simulation in particle reinforced composite materials with many inclusions is presented. It is based on an adapted mesh which consists of triangles and parametric quadrilaterals in 2D. The number of elements and, hence, the number of degrees of freedom are proportional to the number of inclusions. The error of the method is independent of the distance of the neighboring inclusions. While being related to network methods, the approach can tackle more general settings. We present an efficient residual a posteriori error estimator which enables to compute reliable upper and lower error bounds. Several numerical examples illustrate the performance of the method and the error estimator. Moreover, it is demonstrated that the assumption of a lattice structure of inclusions can easily lead to incorrect predictions about material properties.
We formulate the static mechanical coupling of a geometrically exact Cosserat rod
to a nonlinearly elastic continuum. In this setting, appropriate coupling conditions have
to connect a one-dimensional model with director variables to a three-dimensional
model without directors.
Two alternative coupling conditions are proposed,
which correspond to two different configuration trace spaces.
For both we show existence of solutions of the coupled problems, using the direct
method of the calculus of variations. From the first-order optimality conditions
we also derive the corresponding conditions for the dual variables. These are
then interpreted in mechanical terms.
Recent research has shown that
in some practically relevant situations like multi-physics flows[11]
divergence-free mixed finite elements may have a significantly
smaller discretization error than standard non-divergence-free
mixed finite elements. In order to judge the overall performance of
divergence-free mixed finite elements, we
investigate linear solvers for the saddle point linear systems arising in $((P_k)^d,P_{k-1}^{disc})$ Scott-Vogelius finite element implementations of the incompressible Navier-Stokes equations. We investigate both direct and iterative solver methods.
Due to discontinuous pressure elements in the case of Scott-Vogelius elements, considerably more solver strategies seem to deliver promising results than in the case of standard mixed finite elements like
Taylor-Hood elements. For direct methods, we extend recent preliminary work using sparse banded solvers on the penalty method formulation to finer meshes, and discuss extensions. For iterative methods, we test augmented Lagrangian and H-LU preconditioners with GMRES, on both full and statically condensed systems.
Several numerical experiments are provided that show these classes of solvers are well suited for use with Scott-Vogelius elements, and could deliver an interesting overall performance in several applications.
We consider discretizations for reaction-diffusion systems with nonlinear
diffusion in two space dimensions. The applied model allows to handle heterogeneous
materials and uses the chemical potentials of the involved species as primary variables.
We propose an implicit Voronoi finite volume discretization on regular Delaunay
meshes that allows to prove uniform, mesh-independent global upper and lower L1
bounds for the chemical potentials. These bounds provide the main step for a convergence
analysis for the full discretized nonlinear evolution problem. The fundamental
ideas are energy estimates, a discrete Moser iteration and the use of discrete
Gagliardo-Nirenberg inequalities. For the proof of the Gagliardo-Nirenberg inequalities
we exploit that the discrete Voronoi finite volume gradient norm in 2d coincides
with the gradient norm of continuous piecewise linear finite elements.
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.
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.
Piecewise linear convex functions arise as integrands in stochastic programs. They are Lipschitz continuous on their domain, but do not belong to tensor product Sobolev spaces. Motivated by applying Quasi-Monte Carlo methods we show that all terms of their ANOVA decomposition, except the one of highest order, are smooth if the underlying densities are smooth and certain geometric condition is satisfied. The latter condition is generically satisfied in the normal case.
We consider convex optimization problems with $k$th order stochastic dominance constraints for $k\ge 2$. We discuss distances of random variables that are relevant for the dominance relation and establish quantitative stability results for optimal values and solution sets in terms of a suitably selected probability metrics.Moreover, we provide conditions ensuring that the optimal value function is Hadamard directionally differentiable. Finally, we discuss some implications of the results for empirical (Monte Carlo,
sample average) approximations of dominance constrained optimization models.
Logical modeling of biological regulatory networks gives rise to a representation of the system's dynamics as a so-called state transition graph. Analysis of such a graph in its entirety allows for a comprehensive understanding of the functionalities and behavior of the modeled system. However, the size of the vertex set of the graph is exponential in the number of the network components making analysis costly, motivating development of reduction methods. In this paper, we present results allowing for a complete description of an asynchronous state transition graph of a Thomas network solely based on the analysis of the subgraph induced by certain extremal states. Utilizing this notion, we compare the behavior of a simple multi-valued network and a corresponding Boolean network and analyze the conservation of dynamical properties between them. Understanding the relation between such coarser and finer models is a necessary step towards meaningful network reduction as well as model refinement methods.
We develop a model for the dynamic evolution of default-free and defaultable interest rates in a LIBOR framework. Utilizing the class of affine processes, this model produces positive LIBOR rates and spreads, while the dynamics are analytically tractable under defaultable forward measures. This leads to explicit formulas for CDS spreads, while semi-analytical formulas are derived for other credit derivatives. Finally, we give an application to counterparty risk.
Scalable Frames
(2012)
Tight frames can be characterized as those frames which possess optimal numerical stability properties. In this paper, we consider the question of modifying a general frame to generate a tight frame by rescaling its frame vectors; a process which can also be regarded as perfect preconditioning of a frame by a diagonal operator. A frame is called scalable, if such a diagonal operator exists. We derive various characterizations of scalable frames, thereby including the infinite-dimensional situation. Finally, we provide a geometric interpretation of scalability in terms of conical surfaces.
A mathematical model for instationary magnetization
processes is considered, where the underlying spatial domain
includes electrically conducting and nonconducting regions. The
model accounts for the magnetic induction law that couples the given
electrical voltage with the induced electrical current in the
induction coil. By a theorem of Showalter on degenerate parabolic
equations, theorems on existence, uniqueness, and regularity of the
solution to the associated Maxwell integrodifferential system are
proved.
Cubature methods, a powerful alternative to Monte Carlo due to Kusuoka [Adv. Math. Econ. 6, 69–83, 2004] and Lyons–Victoir [Proc. R. Soc. Lond. Ser. A 460, 169–198, 2004], involve the solution to numerous auxiliary ordinary differential equations. With focus on the Ninomiya-Victoir algorithm [Appl. Math. Fin. 15, 107–121, 2008], which corresponds to a concrete level 5 cubature method, we study some parametric diffusion models motivated from financial applications, and exhibit structural conditions under which all involved ODEs can be solved explicitly and efficiently. We then enlarge the class of models for which this technique applies, by introducing a (model-dependent) variation of the Ninomiya-Victoir method. Our method remains easy to implement; numerical examples illustrate the savings in computation time.
Density expansions for hypoelliptic diffusions (X1^,...,X^d) are revisited. In particular, we are interested in density expansions of the projection (X^1_T,...,X^l_T) at time $T>0$, with $l \le d$. Global conditions are found which replace the well-known ”not-in-cutlocus” condition known from heat-kernel asymptotics; cf. G. Ben Arous (88). Our small noise expansion allows for a ”second order” exponential factor. Applications include tail and implied volatility asymptotics in some correlated stochastic volatility models; in particular, we solve a problem left open by A. Gulisashvili and E.M. Stein (2009).
A robust implementation of a Dupire type local volatility model is an important issue for every option trading floor. In the present note we provide new analytic insights into the asymptotic behavior of local volatility in the wings. We present a general approximation formula and specialize it to the Heston model, showing that local variance is linear in the wings. This further justifies the choice of certain local volatility parametrizations.
Flows over time generalize classical ``static'' network flows by introducing a temporal dimension. They can thus be used to model non-instantaneous travel times for flow and variation of flow values over time, both of which are crucial characteristics in many real-world routing problems. There exist two different models of flows over time with respect to flow conservation: one where flow might be stored temporarily at intermediate nodes and a stricter model where flow entering an intermediate node must instantaneously progress to the next arc. While the first model is in general easier to handle, the second model is often more realistic since in applications like, e.\,g., road traffic, storage of flow at intermediate nodes is undesired or even prohibited. The main contribution of this paper is a fully polynomial time approximation scheme (FPTAS) for (min-cost) multi-commodity flows over time without intermediate storage. This improves upon the best previously known $(2+\varepsilon)$-approximation algorithm presented 10 years ago by Fleischer and Skutella (IPCO~2002).
Some mathematical problems related to the 2nd order optimal shape of a crystallization interface
(2012)
We consider the problem to optimize the stationary temperature distribution and the equilibrium shape of the solid-liquid interface in a two-phase system subject to a temperature gradient. The interface satisfies the minimization principle of the free energy, while the temperature is solving the heat equation with a radiation boundary conditions at the outer wall. Under the condition that the temperature gradient is uniformly negative in the direction of crystallization, the interface is expected to have a global graph representation. We reformulate this condition as a pointwise constraint on the gradient of the state, and we derive the first order optimality system for a class of objective functionals that account for the second surface derivatives, and for the surface temperature gradient.
We characterize the Smith form of skew-symmetric matrix polynomials
over an arbitrary field $\F$,
showing that all elementary divisors occur with even multiplicity.
Restricting the class of equivalence transformations to unimodular congruences,
a Smith-like skew-symmetric canonical form
for skew-symmetric matrix polynomials is also obtained.
These results are used to analyze the eigenvalue and elementary divisor structure
of matrices expressible as products of two skew-symmetric matrices,
as well as the existence of structured linearizations
for skew-symmetric matrix polynomials.
By contrast with other classes of structured matrix polynomials
(e.g., alternating or palindromic polynomials),
every regular skew-symmetric matrix polynomial
is shown to have a structured strong linearization.
While there are singular skew-symmetric polynomials of even degree
for which a structured linearization is impossible,
for each odd degree we develop a skew-symmetric companion form
that uniformly provides a structured linearization
for every regular and singular skew-symmetric polynomial
of that degree.
Finally, the results are applied to the construction of minimal
symmetric factorizations of skew-symmetric rational matrices.
We consider the solution of a system of stochastic generalized equations (SGE) where the underlying functions are mathematical expectation of random set-valued mappings. SGE has many applications such as characterizing optimality conditions of a nonsmooth stochastic optimization problem and a stochastic equilibrium problem. We derive quantitative continuity of expected value of the set-valued mapping with respect to the variation of the underlying
probability measure in a metric space. This leads to the subsequent qualitative and quantitative stability analysis of solution set mappings of the SGE. Under some metric regularity conditions, we derive Aubin's property of the solution set mapping with respect to the change of probability measure. The established results are
applied to stability analysis of stationary points of classical one stage and two stage stochastic minimization problems, two stage stochastic mathematical programs with equilibrium constraints and stochastic programs with second order dominance constraints.
Quasi-Monte Carlo algorithms are studied for designing discrete approximations of two-stage linear stochastic programs. Their integrands are piecewise linear, but neither smooth nor of bounded variation in the sense of Hardy and Krause. We show that under some weak geometric condition on the two-stage model all terms of their
ANOVA decomposition, except the one of highest order, are smooth and, hence, certain Quasi-Monte Carlo algorithms may achieve the optimal rate of convergence $O(n^{-1+\delta})$ with $\delta\in(0,\frac{1}{2})$ and a constant not depending on the dimension if the integrands belong to weighted tensor product Sobolev spaces with properly selected weights. The geometric condition is generically (i.e., almost everywhere) satisfied if the underlying distribution is normal. We also discuss sensitivity
indices and efficient dimensions of two-stage integrands, and suggest a dimension reduction heuristic for such integrands.
We consider risk-averse formulations of multistage stochastic linear programs. For these formulations, based on convex combinations of spectral risk measures, risk-averse dynamic programming equations can be written. As a result, the Stochastic Dual Dynamic Programming
(SDDP) algorithm can be used to obtain approximations of
the corresponding risk-averse recourse functions. This allows us to define a risk-averse nonanticipative feasible policy for thestochastic linear program. Formulas for the cuts that approximate the recourse functions are given.
We present a time-dependent finite element model of the human knee joint of full 3D geometric complexity together with advanced numerical algorithms needed for its simulation. The model comprises bones, cartilage and the major ligaments, while patella and menisci are still missing. Bones are modeled by linear elastic materials, cartilage by linear viscoelastic materials, and ligaments by one-dimensional nonlinear Cosserat rods. In order to capture the dynamical contact problems correctly, we solve the full PDEs of elasticity with strict contact inequalities. The spatio--temporal discretization follows a time layers approach (first time, then space discretization). For the time discretization of the elastic and viscoelastic parts we use a new contact-stabilized Newmark method, while for the Cosserat rods we choose an energy--momentum method. For the space discretization, we use linear finite elements for the elastic and viscoelastic parts and novel geodesic finite elements for the Cosserat rods. The coupled system is solved by a Dirichlet--Neumann method. The large algebraic systems of the bone--cartilage contact problems are solved efficiently by the truncated non-smooth Newton multigrid method.
Hybrid systems are often used to describe many complex dynamic phenomena by combining multiple modes of
dynamics into whole systems. In this paper, we present a flat Dirichlet process switching (FDPS) model that defines
a prior on mode switching dynamics of hybrid systems. Compared with the classical Markovian jump system (MJS)
models, the FDPS model is nonparametric and can be applied to the hybrid systems with an unbounded number of
potential modes. On the other hand, the probability structure of the new model is simpler and more flexible than the
recently proposed hierarchical Dirichlet process (HDP) based MJS. Furthermore, we develop a Markov chain Monte
Carlo (MCMC) method for estimating the states of hybrid systems with FDPS prior. And the numerical simulations
of a hybrid system in different conditions are employed to show the effectiveness of the proposed approach.
Diffusion processes are relevant for a variety of phenomena in the natural sciences, including
diffusion of cells or biomolecules within cells, diffusion of molecules on a membrane or surface,
diffusion of a molecular conformation within a complex energy landscape. Many experimental
tools exist now to track such diffusive motions in single cells or molecules, including high-resolution
light microscopy, optical tweezers, fluorescence quenching, and Förster resonance energy transfer
(FRET). Experimental observations are most often indirect and incomplete: (1) They do not
directly reveal the potential or diffusion constants that govern the diffusion process, (2) they have
limited time and space resolution, and (3) the highest-resolution experiments do not track the
motion directly but rather probe it stochastically by recording single events, such as photons,
whose properties depend on the state of the system under investigation.
Here, we propose a general Bayesian framework to model diffusion processes with nonlinear
drift based on incomplete observations as generated by various types of experiments. A maximum
penalized likelihood estimator is given as well as a Gibbs sampling method that allows to estimate
the trajectories that have caused the measurement, the nonlinear drift or potential function and
the noise or diffusion matrices, as well as uncertainty estimates of these properties. The approach
is illustrated on numerical simulations of FRET experiments where it is shown that trajectories,
potentials and diffusion constants can be efficiently and reliably estimated even in cases with little
statistics or non-equilibrium measurement conditions.
In many fields of physics, chemistry and biology the characterization of dynamical processes
between states or species is of fundamental interest. The central mathematical function in such sit-
uations is the committor probability - a generalized reaction coordinate that measures the progress
of the process of interest as the probability of proceeding towards the target state rather than re-
lapsing to the source state. Here, we present methodology for the efficient computation of com-
mittor probabilities for large-scale systems, such as, for example simuations of biomolecular fold-
ing. A method is derived for computing the committor for discrete state spaces using eigenvectors
with expressions for the sensitivity and a Bayesian error model for the committor. The concepts
are illustrated on two examples of diffusive dynamics with a very large number of states: a two-
dimensional model potential with three minima, and a three-dimensional model representing
protein-ligand binding. The method can finally be used to compute committor probabilities in-
cluding error estimations for medium and large system sizes allowing access to the apparatus of
transition path theory and its applications.
Resolving the apparent gap in complexity between
simulated and measured kinetics of biomolecules
(2012)
Molecular simulations of biomolecules often reveal a complex picture of the their kinetics,
whereas kinetic experiments typically seem to indicate considerably simpler two- or three-state
kinetics. Markov state models (MSM) provide a tool to link between simulation and experi-
ment, and to resolve this apparent contradiction.
Markov State Models (MSMs) have become the tool of choice to analyze large amounts of molec-
ular dynamics data by approximating them as a Markov jump process between suitably predefined
states. Here we investigate ”Core Set MSMs”, a new type of MSMs that builds on metastable core
sets acting as milestones for tracing the rare event kinetics. We present a thorough analysis of Core
Set MSMs based on the existing milestoning framework, Bayesian estimation methods and Transi-
tion Path Theory (TPT). As a result, Core Set MSMs can now be used to extract phenomenological
rate constants between the metastable sets of the system and to approximate the evolution of certain
key observables. The performance of Core Set MSMs in comparison to standard MSMs is analyzed
and illustrated on a model potential and the torsion angle dynamics of Alanine dipeptide.
RENS – the optimal rounding
(2012)
This article introduces RENS, the relaxation enforced neighborhood search, a large neighborhood search algorithm for mixed integer nonlinear programming (MINLP) that uses a sub-MINLP to explore the set of feasible roundings of an optimal solution x' of a linear or nonlinear relaxation. The sub-MINLP is constructed by fixing integer variables x_j with x'_j in Z and bounding the remaining integer variables to x_j in {floor(x'_j), ceil(x'_j)}. We describe two different applications of RENS: as a standalone algorithm to compute an optimal rounding of the given starting solution and as a primal heuristic inside a complete MINLP solver.
We use the former to compare different kinds of relaxations and the impact of cutting planes on the roundability of the corresponding optimal solutions. We further utilize RENS to analyze the performance of three rounding heuristics implemented in the branch-cut-and-price framework SCIP. Finally, we study the impact of RENS when it is applied as a primal heuristic inside SCIP.
All experiments were performed on three publically available test sets of mixed integer linear programs (MIPs), mixed integer quadratically constrained programs (MIQCPs), and MINLPs, using solely software which is available in source code.
It turns out that for these problem classes 60% to 70% of the instances have roundable relaxation optima and that the success rate of RENS does not depend on the percentage of fractional variables. Last but not least, RENS applied as primal heuristic complements nicely with existing root node heuristics in SCIP and improves the overall performance.
In this paper, we study the influence of technology, traffic properties and price trends on optimized
design of a reference IP-over-WDM network with rich underlying fiber topology. In each network node,
we investigate the optimal degree of traffic switching in an optical (lambda) domain versus an electrical
(packet) domain, also known as measure of \emph{node transparency}. This measure is studied in connection to changes in
traffic volume,
demand affinity, optical circuit speeds and equipment cost. By applying variable design constraints,
we assess the relative roles of the two distinct equipment groups, IP routers and optical
cross-connects, with respect to resulting changes in cost-sensitive network architectures
Persistence of rogue waves in extended nonlinear Schrödinger equations: Integrable Sasa-Satsuma case
(2012)
We present the lowest order rogue wave solution of the Sasa-Satsuma equation (SSE) which is one of the integrable extensions of the nonlinear Schrödinger equation (NLSE). In contrast to the Peregrine solution of the NLSE, it is significantly more involved and contains polynomials of fourth order rather than second order in the corresponding expressions. The correct limiting case of Peregrine solution appears when the extension parameter of the SSE is reduced to zero.
When simulating isolated resonators, the application of transparent boundary conditions causes the approximated spectrum to be polluted with spurious solutions. Distinguishing these artificial solutions from solutions with a physical meaning is often difficult and requires a priori knowledge of the spectrum or the expected field distribution of resonant states. We present an implementation of the pole condition that distinguishes between incoming and outgoing waves by the location of the poles of their Laplace transform as transparent boundary condition. This implementation depends on one tuning parameter. We will use the sensitivity of the computed solutions to perturbations of this parameter as a means to identify spurious solutions. To obtain global statements, we will combine this technique with a convergence monitor for the boundary condition.
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.
The hypergraph assignment problem (HAP) is the generalization of assignments
from directed graphs to directed hypergraphs. It serves, in particular,
as a universal tool to model several train composition rules in vehicle rotation
planning for long distance passenger railways. We prove that even for problems
with a small hyperarc size and hypergraphs with a special partitioned structure
the HAP is NP-hard and APX-hard. Further, we present an extended integer
linear programming formulation which implies, e. g., all clique inequalities.
We consider a semilinear parabolic equation subject to a nonlinear dynamical boundary condition that is related to the so-calles Wentzell boundary condition. First, we prove the existence and uniqueness of global solutions as well as the existence of a global attractor. Then we derive a suitable Lojasiewicz-Simon-type inequality to show the convergence of global solutions to single steady states as time tends to infinity under the assumption that the nonlinear terms $f$, $g$ are real analytic. Moreover, we provide an estimate for the convergence rate.
We investigate a distributed optimal control problem for a phase field
model of Cahn-Hilliard type. The model describes two-species phase segregation
on an atomic lattice under the presence of diffusion; it has been introduced recently in
[4], on the basis of the theory developed in [15], and consists of a system of two
highly nonlinearly coupled PDEs. For this reason, standard arguments of optimal control theory do not apply
directly, although the control constraints and the cost functional are of standard type.
We show that the problem admits a solution, and we derive the first-order
necessary conditions of optimality.
A nonlocal quasilinear multi-phase system with nonconstant specific heat and heat conductivity
(2012)
In this paper, we prove the existence
and global boundedness from above for a solution to an
integrodifferential model for nonisothermal multi-phase
transitions under nonhomogeneous third type boundary conditions.
The system couples a quasilinear internal energy balance
ruling the evolution of the absolute temperature with a vectorial
integro-differential inclusion governing the vectorial
phase-parameter dynamics. The specific heat and the heat
conductivity k are allowed to depend both on the order parameter
$\chi$ and on the absolute temperature $\teta$ of the system, and
the convex component of the free energy may or may not be
singular. Uniqueness and continuous data dependence are
also proved under additional assumptions.
This paper is devoted to an optimal control problem of Maxwell's equations in the presence of pointwise state constraints. The control is given by a divergence--free three--dimensional vector function representing an applied current density. To cope with the divergence--free constraint on the control, we consider a vector potential ansatz. Due to the lack of regularity of the control--to--state mapping, existence of Lagrange multipliers cannot be guaranteed. We regularize the optimal control problem by penalizing the pointwise state constraints. Optimality conditions for the regularized problem can be derived straightforwardly. It also turns out that the solution of the regularized problem enjoys higher regularity which then allows us to establish its convergence towards the solution of the unregularized problem. The second part of the paper focuses on the numerical analysis of the regularized optimal control problem. Here the state and the control are discretized by N\'ed\'elec's curl--conforming edge elements. Employing the higher regularity property of the optimal control, we establish an a priori error estimate for the discretization error in the $\boldsymbol{H}(\bold{curl})$--norm. The paper ends by numerical results including a numerical verification of our theoretical results.
An optimal control problem arising in the context of 3D electromagnetic induction heating is investigated. The state equation is given by a quasilinear stationary heat equation coupled with a semilinear time-harmonic eddy current equation. The temperature-dependent electrical conductivity and the presence of pointwise inequality state-constraints represent the main challenge of the paper. In the first part of the paper, the existence and regularity of the state are addressed. The second part of the paper deals with the analysis of the corresponding linearized equation. Some sufficient conditions are presented which guarantee the solvability of the linearized system. The final part of the paper is concerned with the optimal control. The aim of the optimization is to find the optimal voltage such that a desired temperature can be achieved optimally. The corresponding first-order necessary optimality condition is presented.
This paper is concerned with a PDE-constrained optimization problem of induction heating, where the state equations consist of 3D time--dependent heat equations coupled with 3D time--harmonic eddy current equations. The control parameters are given by finite real numbers representing applied alternating voltages which enter the eddy current equations via impressed current. The optimization problem is to find optimal voltages so that, under certain constraints on the voltages and the temperature, a desired temperature can be optimally achieved. As there are finitely many control parameters but the state constraint has to be satisfied in an infinite number of points, the problem belongs to a class of semi--infinite programming problems. We present a rigorous analysis of the optimization problem and a numerical strategy based on our theoretical result.
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.
Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics
of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have
seen widespread use in recent years. This approach has many appealing characteristics compared
to straightforward molecular dynamics simulation and analysis, including the potential to mitigate
the sampling problem by extracting long-time kinetic information from short trajectories and the
ability to straightforwardly calculate expectation values and statistical uncertainties of various
stationary and dynamical molecular observables. In this article, we summarize the current state of
the art in generation and validation of MSMs and give some important new results. We describe
an upper bound for the approximation error made by modeling molecular dynamics with an MSM
and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast
to previous practice, it becomes clear that the best MSM is not obtained by the most metastable
discretization, but the MSM can be much improved if non-metastable states are introduced near
the transition states. Moreover, we show that it is not necessary to resolve all slow processes
by the state space partitioning, but individual dynamical processes of interest can be resolved
separately. We also present an efficient estimator for reversible transition matrices and a robust
test to validate that an MSM reproduces the kinetics of the molecular dynamics data.
Dynamical averages based on functionals of dynamical trajectories, such as time-correlation func-
tions, play an important role in determining kinetic or transport properties of matter. At temperatures
of interest, the expectations of these quantities are often dominated by contributions from rare events,
making the precise calculation of these quantities by molecular dynamics simulation difficult. Here,
we present a reweighting method for combining simulations from multiple temperatures (or from
simulated or parallel tempering simulations) to compute an optimal estimate of the dynamical prop-
erties at the temperature of interest without the need to invoke an approximate kinetic model (such as
the Arrhenius law). Continuous and differentiable estimates of these expectations at any temperature
in the sampled range can also be computed, along with an assessment of the associated statistical
uncertainty. For rare events, aggregating data from multiple temperatures can produce an estimate
of the desired precision at greatly reduced computational cost compared with simulations conducted
at a single temperature. Here, we describe use of the method for the canonical (NVT) ensemble us-
ing four common models of dynamics (canonical distribution of Hamiltonian trajectories, Andersen
thermostatting, Langevin, and overdamped Langevin or Brownian dynamics), but it can be applied to
any thermodynamic ensemble provided the ratio of path probabilities at different temperatures can be
computed. To illustrate the method, we compute a time-correlation function for solvated terminally-
blocked alanine peptide across a range of temperatures using trajectories harvested using a modified
parallel tempering protocol.
Dynamical fingerprints of macromolecules obtained from experiments often seem to indicate two- or
three state kinetics while simulations typically reveal a more complex picture. Markov state models of
molecular conformational dynamics can be used to predict these dynamical fingerprints and to reconcile
experiment with simulation. This is illustrated on two model systems: a one-dimensional energy surface
and a four-state model of a protein folding equilibrium. We show that (i) there might be no process
which corresponds to our notion of folding, (ii) often the experiment will be insensitive to some of the
processes present in the system, (iii) with a suitable combination the observable and initial conditions in
a relaxation experiment one can selectively measure specific processes. Furthermore, our method can be
used to design experiments such that specific processes appear with large amplitudes. We demonstrate
that for a fluorescence quenching experiment of the MR121-G9-W peptide.
Protein-ligand interactions are essential for nearly all biological processes, and yet the bio-
physical mechanism that enables potential binding partners to associate before specific binding
occurs remains poorly understood. Fundamental questions include which factors influence the
formation of protein-ligand encounter complexes, and whether designated association path-
ways exist. In this article we introduce a computational approach to systematically analyze
the complete ensemble of association pathways and to thus investigate these questions. This
approach is employed here to study the binding of a phosphate ion to the Escherichia coli
Phosphate Binding Protein. Various mutants of the protein are considered and their effects
on binding free energy profiles, association rates and association pathway distributions are
quantified. The results reveal the existence of two anion attractors, i.e. regions that initially
attract negatively charged particles and allow them to be efficiently screened for phosphate
which is specifically bound subsequently. Point mutations that affect the charge on these
attractors modulate their attraction strength and speed up association to a factor of 10 of
the diffusion limit and thus change the association pathways of the phosphate ligand. It is
demonstrated that a phosphate that pre-binds to such an attractor neutralizes its attraction
effect to the environment, making the simultaneous association of a second phosphate ion
unlikely. Our study suggests ways how structural properties can be used to tune molecular
association kinetics so as to optimize the efficiency of binding, and highlights the importance
of kinetic properties.
While studies of protein-ligand association have mostly focused on the native complex and its
stability (binding affinity), relatively little attention has been paid on the association process
that precedes the formation of the complex. Here we review approaches to study the kinet-
ics of association and association mechanisms, i.e. the probability distribution of association
pathways. Selected methods are described that allow these properties to be calculated quan-
titatively from simulation models. We summarize some applications of these methods and
finally propose a model mechanism by which proteins may efficiently screen potential ligands
for those that can be natively bound.
In this paper, we present a Gaussian Markov random field (GMRF) model for the transition
matrices (TMs) of Markov chains (MCs) by assuming the existence of a neighborhood relationship
between states, and develop the maximum a posteriori (MAP) estimators under different obser-
vation conditions. Unlike earlier work on TM estimation, our method can make full use of the
similarity between different states to improve the estimated accuracy, and the estimator can be
performed very efficiently by solving a convex programming problem. In addition, we discuss the
parameter choice of the proposed model, and introduce a Monte Carlo cross validation (MCCV)
method. The numerical simulations of a diffusion process are employed to show the effectiveness
of the proposed models and algorithms.
Optimal Identification of Semi-Rigid Domains in Macromolecules from Molecular Dynamics Simulation
(2012)
Biological function relies on the fact that biomolecules can switch between different conformations and aggregation states.
Such transitions involve a rearrangement of parts of the biomolecules involved that act as dynamic domains. The reliable
identification of such domains is thus a key problem in biophysics. In this work we present a method to identify semi-rigid
domains based on dynamical data that can be obtained from molecular dynamics simulations or experiments. To this end
the average inter-atomic distance-deviations are computed. The resulting matrix is then clustered by a constrained
quadratic optimization problem. The reliability and performance of the method are demonstrated for two artificial peptides.
Furthermore we correlate the mechanical properties with biological malfunction in three variants of amyloidogenic
transthyretin protein, where the method reveals that a pathological mutation destabilizes the natural dimer structure of the
protein. Finally the method is used to identify functional domains of the GroEL-GroES chaperone, thus illustrating the
efficiency of the method for large biomolecular machines.
Discrete-state Markov (or master equation) models provide a useful simplified representation for
characterizing the long-time statistical evolution of biomolecules in a manner that allows direct
comparison with experiments as well as the elucidation of mechanistic pathways for an inherently
stochastic process. A vital part of meaningful comparison with experiment is the characterization of
the statistical uncertainty in the predicted experimental measurement, which may take the form of
an equilibrium measurement of some spectroscopic signal, the time-evolution of this signal following
a perturbation, or the observation of some statistic (such as the correlation function) of the equilib-
rium dynamics of a single molecule. Without meaningful error bars (which arise due to the finite
quantity of data used to construct the model), there is no way to determine whether the deviations
between model and experiment are statistically meaningful. Previous work has demonstrated that
a Bayesian method that enforces microscopic reversibility can be used to characterize the correlated
uncertainties in state-to-state transition probabilities (and functions thereof) for a model inferred from
molecular simulation data. Here, we extend this approach to include the uncertainty in observables
that are functions of molecular conformation (such as surrogate spectroscopic signals) characteriz-
ing each state, permitting the full statistical uncertainty in computed spectroscopic experiments to be
assessed. We test the approach in a simple model system to demonstrate that the computed uncer-
tainties provide a useful indictor of statistical variation, and then apply it to the computation of the
fluorescence autocorrelation function measured for a dye-labeled peptide previously studied by both
experiment and simulation.
Markov (state) models (MSMs) have attracted a lot of interest recently as they (1) can probe
long-term molecular kinetics based on short-time simulations, (2) offer a way to analyze great
amounts of simulation data with relatively little subjectivity of the analyst, (3) provide insight into
microscopic quantities such as the ensemble of transition pathways, and (4) allow simulation data
to be reconciled with measurement data in a rigorous and explicit way. Here we sketch our current
perspective of Markov models and explain in short their theoretical basis and assumptions. We
describe transition path theory which allows the entire ensemble of protein folding pathways to be
investigated and that combines naturally with Markov models. Experimental observations can be
naturally linked to Markov models with the dynamical fingerprint theory, by which experimentally
observable timescales can be equipped with an understanding of the structural rearrangement
processes that take place at these timescales. The concepts of this paper are illustrated by a
simple kinetic model of protein folding.
Large-scale stochastic models are relevant in many different fields such as com- putational biology, finance, social sciences, communication and traffic networks. In order to both efficiently simulate and analyze such models and to understand the essential properties of the sys- tem, it is desirable to have model reduction techniques that much reduce the dimensionality of the model while at the same time preserving the system’s essential dynamical properties. In this paper, a general model reduction technique for the class of discrete space and time Hidden Markov Models is presented, thereby also including the more special class discrete Markov Chains. The method is illustrated on some model applications.
Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility.
Here, we present a model of the actin filament (F-actin) that incorporates the global structure
of the recently published model by Oda et al. but also conserves internal stereochemistry. A
comparison is made using molecular dynamics simulation of the model with other recent F-
actin models. A number of structural determents such as the protomer propeller angle, the
number of hydrogen bonds and the structural variation among the protomers are analyzed.
The MD comparison is found to reflect the evolution in quality of actin models over the last
six years. In addition, simulations of the model are carried out in states with both ADP or
ATP bound and local hydrogen-bonding differences characterized. The results point to the
significance of a direct interaction of Gln137 with ATP for activation of ATPase activity after
the G-to-F-actin transition.
This paper provides a generic formulation for rolling stock planning problems in the context of intercity passenger traffic. The main contributions are a graph theoretical model and a Mixed-Integer-Programming formulation that integrate all main requirements of the considered Vehicle-Rotation-Planning problem (VRPP). We show that it is possible to solve this model for real-world instances provided by our industrial partner DB Fernverkehr AG using modern algorithms and computers.
Rapid Branching
(2012)
We propose rapid branching (RB) as a general branch-and-bound heuristic for solving large scale optimization problems in traffic and transport. The key idea is to combine a special branching rule and a greedy node selection strategy in order to produce solutions of controlled quality rapidly and efficiently. We report on three successful applications of the method for integrated vehicle and crew scheduling, railway track allocation, and railway vehicle rotation planning.
Mathematical modeling of Czochralski type growth processes for semiconductor bulk single crystals
(2012)
This paper deals with the mathematical modeling and simulation of
crystal growth processes by the so-called Czochralski method and related methods,
which are important industrial processes
to grow large
bulk single crystals of semiconductor materials such as, e.g., gallium arsenide
(GaAs) or silicon (Si) from the melt.
In particular, we investigate a recently developed
technology in which traveling magnetic fields are applied in order to
control
the behavior of the turbulent melt flow. Since numerous different physical effects
like electromagnetic fields, turbulent melt flows, high temperatures, heat transfer via
radiation, etc., play an important role in the process, the corresponding mathematical
model leads to an extremely difficult system of initial-boundary value problems for
nonlinearly coupled partial differential equations. In this paper, we describe a mathematical
model that is under use for the simulation of real-life growth scenarios, and we give an overview
of mathematical results and numerical simulations that have been obtained for it in recent years.
In this paper a bottom-up approach of automatic simplification of a railway network is presented. Starting from a very detailed, microscopic level, as it is used in railway simulation, the network is transformed by an algorithm to a less detailed level (macroscopic network), that is sufficient for long-term planning and optimization. In addition running and headway times are rounded to a pre-chosen time discretization by a special cumulative method, which we will present and analyse in this paper. After the transformation we fill the network with given train requests to compute an optimal slot allocation. Then the optimized schedule is re-transformed into the microscopic level and can be simulated without any conflicts occuring between the slots. The algorithm is used to transform the network of the very dense Simplon corridor between Swiss and Italy. With our aggregation it is possible for the first time to generate a profit maximal and conflict free timetable for the corridor across a day by a simultaneously optimization run.
The track allocation problem, also known as train routing problem or train timetabling problem, is to find a conflict-free set of train routes of maximum value in a railway network. Although it can be modeled as a standard path packing problem, instances of sizes relevant for real-world railway applications could not be solved up to now. We propose a rapid branching column generation approach that integrates the solution of the LP relaxation of a path coupling formulation of the problem with a special rounding heuristic. The approach is based on and exploits special properties of the bundle method for the approximate solution of convex piecewise linear functions. Computational results for difficult instances of the benchmark library TTPLIB are reported.
Today the railway timetabling process and the track allocation is one of the most challenging problems to solve by a railway company. Especially due to the deregulation of the transport market in the recent years several suppliers of railway traffic have entered the market in Europe. This leads to more potential conflicts between trains caused by an increasing demand of train paths. Planning and operating railway transportation systems is extremely hard due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. In order to make best use of the infrastructure and to ensure economic operation, efficient planning of the railway operation is indispensable. Mathematical optimization models and algorithms can help to automatize and tackle these challenges. Our contribution in this paper is to present a renewed planning process due to the liberalization in Europe and an associated concept for track allocation, that consists of three important parts, simulation, aggregation, and optimization. Furthermore, we present results of our general framework for real world data.
We propose a model for the integrated optimization of vehicle rotations and vehicle compositions in long distance railway passenger transport. The main contribution of the paper is a hypergraph model that is able to handle the challenging technical requirements as well as very general stipulations with respect to the "regularity" of a schedule. The hypergraph model directly generalizes network flow models, replacing arcs with hyperarcs. Although NP-hard in general, the model is computationally well-behaved in practice. High quality solutions can be produced in reasonable time using high performance Integer Programming techniques, in particular, column generation and rapid branching. We show that, in this way, large-scale real world instances of our cooperation partner DB Fernverkehr can be solved.
Vehicle rotation planning is a fundamental problem in rail transport. It decides how the railcars, locomotives, and carriages are operated in order to implement the trips of the timetable. One important planning requirement is operational regularity, i.e., using the rolling stock in the same way on every day of operation. We propose to take regularity into account by modeling the vehicle rotation planning problem as a minimum cost hyperassignment problem (HAP). Hyperassignments are generalizations of assignments from directed graphs to directed hypergraphs. Finding a minimum cost hyperassignment is NP-hard. Most instances arising from regular vehicle rotation planning, however, can be solved well in practice. We show that, in particular, clique inequalities strengthen the canonical LP relaxation substantially.