7,864 research outputs found
Model reduction of controlled Fokker--Planck and Liouville-von Neumann equations
Model reduction methods for bilinear control systems are compared by means of
practical examples of Liouville-von Neumann and Fokker--Planck type. Methods
based on balancing generalized system Gramians and on minimizing an H2-type
cost functional are considered. The focus is on the numerical implementation
and a thorough comparison of the methods. Structure and stability preservation
are investigated, and the competitiveness of the approaches is shown for
practically relevant, large-scale examples
emgr - The Empirical Gramian Framework
System Gramian matrices are a well-known encoding for properties of
input-output systems such as controllability, observability or minimality.
These so-called system Gramians were developed in linear system theory for
applications such as model order reduction of control systems. Empirical
Gramian are an extension to the system Gramians for parametric and nonlinear
systems as well as a data-driven method of computation. The empirical Gramian
framework - emgr - implements the empirical Gramians in a uniform and
configurable manner, with applications such as Gramian-based (nonlinear) model
reduction, decentralized control, sensitivity analysis, parameter
identification and combined state and parameter reduction
Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits
We present a Python-based software package to automatically obtain phenomenological models of input-controlled synthetic biological circuits that guide the design using chemical reaction-level descriptive models. From the parts and mechanism description of a synthetic biological circuit, it is easy to obtain a chemical reaction model of the circuit under the assumptions of mass-action kinetics using various existing tools. However, using these models to guide design decisions during an experiment is difficult due to a large number of reaction rate parameters and species in the model. Hence, phenomenological models are often developed that describe the effective relationships among the circuit inputs, outputs, and only the key states and parameters. In this paper, we present an algorithm to obtain these phenomenological models in an automated manner using a Python package for circuits with inputs that control the desired outputs. This model reduction approach combines the common assumptions of time-scale separation, conservation laws, and species' abundance to obtain the reduced models that can be used for design of synthetic biological circuits. We consider an example of a simple gene expression circuit and another example of a layered genetic feedback control circuit to demonstrate the use of the model reduction procedure
Methods of model reduction for large-scale biological systems: a survey of current methods and trends
Complex models of biochemical reaction systems have become increasingly common in the systems biology literature. The complexity of such models can present a number of obstacles for their practical use, often making problems difficult to intuit or computationally intractable. Methods of model reduction can be employed to alleviate the issue of complexity by seeking to eliminate those portions of a reaction network that have little or no effect upon the outcomes of interest, hence yielding simplified systems that retain an accurate predictive capacity. This review paper seeks to provide a brief overview of a range of such methods and their application in the context of biochemical reaction network models. To achieve this, we provide a brief mathematical account of the main methods including timescale exploitation approaches, reduction via sensitivity analysis, optimisation methods, lumping, and singular value decomposition-based approaches. Methods are reviewed in the context of large-scale systems biology type models, and future areas of research are briefly discussed
Low-rank updates and a divide-and-conquer method for linear matrix equations
Linear matrix equations, such as the Sylvester and Lyapunov equations, play
an important role in various applications, including the stability analysis and
dimensionality reduction of linear dynamical control systems and the solution
of partial differential equations. In this work, we present and analyze a new
algorithm, based on tensorized Krylov subspaces, for quickly updating the
solution of such a matrix equation when its coefficients undergo low-rank
changes. We demonstrate how our algorithm can be utilized to accelerate the
Newton method for solving continuous-time algebraic Riccati equations. Our
algorithm also forms the basis of a new divide-and-conquer approach for linear
matrix equations with coefficients that feature hierarchical low-rank
structure, such as HODLR, HSS, and banded matrices. Numerical experiments
demonstrate the advantages of divide-and-conquer over existing approaches, in
terms of computational time and memory consumption
Inexact Solves in Interpolatory Model Reduction
We investigate the use of inexact solves for interpolatory model reduction
and consider associated perturbation effects on the underlying model reduction
problem. We give bounds on system perturbations induced by inexact solves and
relate this to termination criteria for iterative solution methods. We show
that when a Petrov-Galerkin framework is employed for the inexact solves, the
associated reduced order model is an exact interpolatory model for a nearby
full-order system; thus demonstrating backward stability. We also give evidence
that for \h2-optimal interpolation points, interpolatory model reduction is
robust with respect to perturbations due to inexact solves. Finally, we
demonstrate the effecitveness of direct use of inexact solves in optimal
approximation. The result is an effective model reduction
strategy that is applicable in realistically large-scale settings.Comment: 42 pages, 5 figure
Asymptotology of Chemical Reaction Networks
The concept of the limiting step is extended to the asymptotology of
multiscale reaction networks. Complete theory for linear networks with well
separated reaction rate constants is developed. We present algorithms for
explicit approximations of eigenvalues and eigenvectors of kinetic matrix.
Accuracy of estimates is proven. Performance of the algorithms is demonstrated
on simple examples. Application of algorithms to nonlinear systems is
discussed.Comment: 23 pages, 8 figures, 84 refs, Corrected Journal Versio
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