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The paper presents a new affine invariant theory on asymptotic mesh
independence of Newton’s method for discretized nonlinear operator equations.
Compared to earlier attempts, the new approach is both much simpler
and more intuitive from the algorithmic point of view. The theory
is exemplified at collocation methods for ODE boundary value problems
and at finite element methods for elliptic PDE problems.
The key to molecular conformation dynamics is the direct identification of metastable conformations, which are almost invariant sets of molecular dynamical systems. Once some reversible Markov operator has been discretized, a generalized symmetric stochastic matrix arises. This matrix can be treated by Perron cluster analysis, a rather recent method involving a Perron cluster eigenproblem. The paper presents an improved Perron cluster analysis algorithm, which is more robust than earlier suggestions. Numerical examples are included.
The purpose of the paper is to apply monotone multigrid methods
to static and dynamic biomechanical contact problems.
In space, a finite element method involving a mortar
discretization of the contact conditions is used.
In time, a new contact--stabilized Newmark scheme is presented.
Numerical experiments for a two body Hertzian contact problem
and a biomechanical knee problem are reported.
This paper is intended to be a first step towards the continuous dependence of dynamical contact problems on the initial data as well as the uniqueness of a solution. Moreover, it provides the basis for a proof of the convergence of popular time integration schemes as the Newmark method.
We study a frictionless dynamical contact problem between both linearly elastic and viscoelastic bodies which is formulated via the Signorini contact conditions. For viscoelastic materials fulfilling the Kelvin-Voigt constitutive law, we find a characterization of the class of problems which satisfy a perturbation result in a non-trivial mix of norms in function space. This characterization is given in the form of a stability condition on the contact stresses at the contact boundaries.
Furthermore, we present perturbation results for two well-established approximations of the classical Signorini condition: The Signorini condition formulated in velocities and the model of normal compliance, both satisfying even a sharper version of our stability condition.
Whenever the invariant stationary density of metastable dynamical systems decomposes into almost invariant partial densities, its computation as eigenvector of some transition probability matrix is an ill-conditioned problem. In order to avoid this computational difficulty, we suggest to apply an aggregation/disaggregation method which only addresses wellconditioned sub-problems and thus results in a stable algorithm. In contrast to existing methods, the aggregation step is done via a sampling algorithm which covers only small patches of the sampling space. Finally, the theoretical analysis is illustrated by two biomolecular examples.
Bovine fertility is the subject of extensive research in animal sciences,
especially because fertility of dairy cows has declined during the last
decades. The regulation of estrus is controlled by the complex interplay
of various organs and hormones. Mathematical modeling of the bovine
estrous cycle could help in understanding the dynamics of this complex
biological system. In this paper we present a mechanistic mathematical
model of the bovine estrous cycle that includes the processes of follicle
and corpus luteum development and the key hormones that interact to
control these processes. The model generates successive estrous cycles of
21 days, with three waves of follicle growth per cycle. The model contains
12 differential equations and 54 parameters. Focus in this paper is on
development of the model, but also some simulation results are presented,
showing that a set of equations and parameters is obtained that describes
the system consistent with empirical knowledge. Even though the majority
of the mechanisms that are included in the model are based on relations
that in literature have only been described qualitatively (i.e. stimulation
and inhibition), the output of the model is surprisingly well in line with
empirical data. This model of the bovine estrous cycle could be used
as a basis for more elaborate models with the ability to study effects of
external manipulations and genetic differences.
The aim of this paper is to devise an adaptive timestep control in the contact--stabilized Newmark method (CONTACX) for dynamical contact problems between two viscoelastic bodies in the framework of Signorini's condition. In order to construct a comparative scheme of higher order accuracy, we extend extrapolation techniques. This approach demands a subtle theoretical investigation of an asymptotic error expansion of the contact--stabilized Newmark scheme. On the basis of theoretical insight and numerical observations, we suggest an error estimator and a timestep selection which also cover the presence of contact. Finally, we give a numerical example.
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.
The paper considers the time integration of frictionless dynamical contact problems between viscoelastic bodies in the frame of the Signorini condition. Among the numerical integrators, interest focuses on the contact-stabilized Newmark method recently suggested by Deuflhard et al., which is compared to the classical Newmark method and an improved energy dissipative version due to Kane et al. In the absence of contact, any such variant is equivalent to the Störmer-Verlet scheme, which is well-known to have consistency order 2. In the presence of contact, however, the classical approach to discretization errors would not show consistency at all because of the discontinuity at the contact. Surprisingly, the question of consistency in the constrained situation has not been solved yet. The present paper fills this gap by means of a novel proof technique using specific norms based on earlier perturbation results due to the authors. The corresponding estimation of the local discretization error requires the bounded total variation of the solution. The results have consequences for the construction of an adaptive timestep control, which will be worked out subsequently in a forthcoming paper.
This study presents a differential equation model for the feedback mechanisms between
Gonadotropin-releasing Hormone (GnRH), Follicle-Stimulating Hormone (FSH), Luteinizing
Hormone (LH), development of follicles and corpus luteum, and the production of estradiol
(E2), progesterone (P4), inhibin A (IhA), and inhibin B (IhB) during the female menstrual
cycle. In contrast to other models, this model does not involve delay differential equations
and is based on deterministic modelling of the GnRH pulse pattern, which allows for faster
simulation times and efficient parameter identification. These steps were essential to tackle
the task of developing a mathematical model for the administration of GnRH analogues. The
focus of this paper is on model development for GnRH receptor binding and the integration of
a pharmacokinetic/pharmacodynamic model for the GnRH agonist Nafarelin and the GnRH
antagonist Cetrorelix into the menstrual cycle model. The final mathematical model describes
the hormone profiles (LH, FSH, P4, E2) throughout the menstrual cycle in 12 healthy women.
Moreover, it correctly predicts the changes in the cycle following single and multiple dose
administration of Nafarelin or Cetrorelix at different stages in the cycle.
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 .