101,681 research outputs found
Identifiable reparametrizations of linear compartment models
Identifiability concerns finding which unknown parameters of a model can be
quantified from given input-output data. Many linear ODE models, used in
systems biology and pharmacokinetics, are unidentifiable, which means that
parameters can take on an infinite number of values and yet yield the same
input-output data. We use commutative algebra and graph theory to study a
particular class of unidentifiable models and find conditions to obtain
identifiable scaling reparametrizations of these models. Our main result is
that the existence of an identifiable scaling reparametrization is equivalent
to the existence of a scaling reparametrization by monomial functions. We also
provide partial results beginning to classify graphs which possess an
identifiable scaling reparametrization.Comment: 5 figure
Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models
We use the Litvinov-Maslov correspondence principle to reduce and hybridize
networks of biochemical reactions. We apply this method to a cell cycle
oscillator model. The reduced and hybridized model can be used as a hybrid
model for the cell cycle. We also propose a practical recipe for detecting
quasi-equilibrium QE reactions and quasi-steady state QSS species in
biochemical models with rational rate functions and use this recipe for model
reduction. Interestingly, the QE/QSS invariant manifold of the smooth model and
the reduced dynamics along this manifold can be put into correspondence to the
tropical variety of the hybridization and to sliding modes along this variety,
respectivelyComment: conference SASB 2011, to be published in Electronic Notes in
Theoretical Computer Scienc
h-multigrid agglomeration based solution strategies for discontinuous Galerkin discretizations of incompressible flow problems
In this work we exploit agglomeration based -multigrid preconditioners to
speed-up the iterative solution of discontinuous Galerkin discretizations of
the Stokes and Navier-Stokes equations. As a distinctive feature -coarsened
mesh sequences are generated by recursive agglomeration of a fine grid,
admitting arbitrarily unstructured grids of complex domains, and agglomeration
based discontinuous Galerkin discretizations are employed to deal with
agglomerated elements of coarse levels. Both the expense of building coarse
grid operators and the performance of the resulting multigrid iteration are
investigated. For the sake of efficiency coarse grid operators are inherited
through element-by-element projections, avoiding the cost of numerical
integration over agglomerated elements. Specific care is devoted to the
projection of viscous terms discretized by means of the BR2 dG method. We
demonstrate that enforcing the correct amount of stabilization on coarse grids
levels is mandatory for achieving uniform convergence with respect to the
number of levels. The numerical solution of steady and unsteady, linear and
non-linear problems is considered tackling challenging 2D test cases and 3D
real life computations on parallel architectures. Significant execution time
gains are documented.Comment: 78 pages, 7 figure
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