1,759 research outputs found
Minimal Curvature Trajectories: Riemannian Geometry Concepts for Model Reduction in Chemical Kinetics
In dissipative ordinary differential equation systems different time scales
cause anisotropic phase volume contraction along solution trajectories. Model
reduction methods exploit this for simplifying chemical kinetics via a time
scale separation into fast and slow modes. The aim is to approximate the system
dynamics with a dimension-reduced model after eliminating the fast modes by
enslaving them to the slow ones via computation of a slow attracting manifold.
We present a novel method for computing approximations of such manifolds using
trajectory-based optimization. We discuss Riemannian geometry concepts as a
basis for suitable optimization criteria characterizing trajectories near slow
attracting manifolds and thus provide insight into fundamental geometric
properties of multiple time scale chemical kinetics. The optimization criteria
correspond to a suitable mathematical formulation of "minimal relaxation" of
chemical forces along reaction trajectories under given constraints. We present
various geometrically motivated criteria and the results of their application
to three test case reaction mechanisms serving as examples. We demonstrate that
accurate numerical approximations of slow invariant manifolds can be obtained.Comment: 22 pages, 18 figure
A variational principle for computing slow invariant manifolds in dissipative dynamical systems
A key issue in dimension reduction of dissipative dynamical systems with
spectral gaps is the identification of slow invariant manifolds. We present
theoretical and numerical results for a variational approach to the problem of
computing such manifolds for kinetic models using trajectory optimization. The
corresponding objective functional reflects a variational principle that
characterizes trajectories on, respectively near, slow invariant manifolds. For
a two-dimensional linear system and a common nonlinear test problem we show
analytically that the variational approach asymptotically identifies the exact
slow invariant manifold in the limit of both an infinite time horizon of the
variational problem with fixed spectral gap and infinite spectral gap with a
fixed finite time horizon. Numerical results for the linear and nonlinear model
problems as well as a more realistic higher-dimensional chemical reaction
mechanism are presented.Comment: 16 pages, 5 figure
Fast computation of multi-scale combustion systems
In the present work, we illustrate the process of constructing a simplified model for complex multi-scale combustion systems. To this end, reduced models of homogeneous ideal gas mixtures of methane and air are first obtained by the novel Relaxation Redistribution Method (RRM) and thereafter used for the extraction of all the missing variables in a reactive flow simulation with a global reaction mode
Reduction of dynamical biochemical reaction networks in computational biology
Biochemical networks are used in computational biology, to model the static
and dynamical details of systems involved in cell signaling, metabolism, and
regulation of gene expression. Parametric and structural uncertainty, as well
as combinatorial explosion are strong obstacles against analyzing the dynamics
of large models of this type. Multi-scaleness is another property of these
networks, that can be used to get past some of these obstacles. Networks with
many well separated time scales, can be reduced to simpler networks, in a way
that depends only on the orders of magnitude and not on the exact values of the
kinetic parameters. The main idea used for such robust simplifications of
networks is the concept of dominance among model elements, allowing
hierarchical organization of these elements according to their effects on the
network dynamics. This concept finds a natural formulation in tropical
geometry. We revisit, in the light of these new ideas, the main approaches to
model reduction of reaction networks, such as quasi-steady state and
quasi-equilibrium approximations, and provide practical recipes for model
reduction of linear and nonlinear networks. We also discuss the application of
model reduction to backward pruning machine learning techniques
Model reduction of biochemical reactions networks by tropical analysis methods
We discuss a method of approximate model reduction for networks of
biochemical reactions. This method can be applied to networks with polynomial
or rational reaction rates and whose parameters are given by their orders of
magnitude. In order to obtain reduced models we solve the problem of tropical
equilibration that is a system of equations in max-plus algebra. In the case of
networks with nonlinear fast cycles we have to solve the problem of tropical
equilibration at least twice, once for the initial system and a second time for
an extended system obtained by adding to the initial system the differential
equations satisfied by the conservation laws of the fast subsystem. The two
steps can be reiterated until the fast subsystem has no conservation laws
different from the ones of the full model. Our method can be used for formal
model reduction in computational systems biology
A geometric method for model reduction of biochemical networks with polynomial rate functions
Model reduction of biochemical networks relies on the knowledge of slow and
fast variables. We provide a geometric method, based on the Newton polytope, to
identify slow variables of a biochemical network with polynomial rate
functions. The gist of the method is the notion of tropical equilibration that
provides approximate descriptions of slow invariant manifolds. Compared to
extant numerical algorithms such as the intrinsic low dimensional manifold
method, our approach is symbolic and utilizes orders of magnitude instead of
precise values of the model parameters. Application of this method to a large
collection of biochemical network models supports the idea that the number of
dynamical variables in minimal models of cell physiology can be small, in spite
of the large number of molecular regulatory actors
Tropicalization and tropical equilibration of chemical reactions
Systems biology uses large networks of biochemical reactions to model the
functioning of biological cells from the molecular to the cellular scale. The
dynamics of dissipative reaction networks with many well separated time scales
can be described as a sequence of successive equilibrations of different
subsets of variables of the system. Polynomial systems with separation are
equilibrated when at least two monomials, of opposite signs, have the same
order of magnitude and dominate the others. These equilibrations and the
corresponding truncated dynamics, obtained by eliminating the dominated terms,
find a natural formulation in tropical analysis and can be used for model
reduction.Comment: 13 pages, 1 figure, workshop Tropical-12, Moskow, August 26-31, 2012;
in press Contemporary Mathematic
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