Numerical analysis of optimization-constrained differential equations

The modeling of a system composed by a gas phase and organic aerosol particles, and its numerical resolution are studied. The gas-aerosol system is modeled by ordinary differential equations coupled with a mixed-constrained optimization problem. This coupling induces discontinuities when inequality constraints are activated or deactivated. Two approaches for the solution of the optimization-constrained differential equations are presented. The first approach is a time splitting scheme together with a fixed-point method that alternates between the differential and optimization parts. The ordinary differential equations are approximated by the Crank-Nicolson scheme and a primal-dual interior-point method combined with a warm-start strategy is used to solve the minimization problem. The second approach considers the set of equations as a system of differential algebraic equations after replacing the minimization problem by its first order optimality conditions. An implicit 5th-order Runge-Kutta method (RADAU5) is then used. Both approaches are completed by numerical techniques for the detection and computation of the events (activation and deactivation of inequality constraints) when the system evolves in time. The computation of the events is based on continuation techniques and geometric arguments. Moreover the first approach completes the computation with extrapolation polynomials and sensitivity analysis, whereas the second approach uses dense output formulas. Numerical results for gas-aerosol system made of several chemical species are proposed for both approaches. These examples show the efficiency and accuracy of each method. They also indicate that the second approach is more efficient than the first one. Furthermore theoretical examples show that the method for the computation of the activation is of second order for the first approach and exact for the second one.

Solving Optimization-Constrained Differential Equations With Discontinuity Points, With Application To Atmospheric Chemistry

Alexandre Caboussat, Chantal Landry

Ordinary differential equations are coupled with mixed constrained optimization problems when modeling the thermodynamic equilibrium of a system evolving with time. A particular application arises in the modeling of atmospheric particles. Discontinuity points are created by the activation/deactivation of inequality constraints. A numerical method for the solution of optimization-constrained differential equations is proposed by coupling an implicit Runge-Kutta method (RADAU5), with numerical techniques for the detection of the events (activation and deactivation of constraints). The computation of the events is based on dense output formulas, continuation techniques, and geometric arguments. Numerical results are presented for the simulation of the time-dependent equilibrium of organic atmospheric aerosol particles, and show the efficiency and accuracy of the approach.

2009

Propagation Models for Biochemical Reaction Networks

Maria-Emanuela-Canini Mateescu

In this thesis we investigate different ways of approximating the solution of the chemical master equation (CME). The CME is a system of differential equations that models the stochastic transient behaviour of biochemical reaction networks. It does so by describing the time evolution of probability distribution over the states of a Markov chain that represents a biological network, and thus its stochasticity is only implicit. The transient solution of a CME is the vector of probabilities over the states of the corresponding Markov chain at a certain time point t, and it has traditionally been obtained by applying methods that are general to continuous-time Markov chains: uniformization, Krylov subspace methods, and general ordinary differential equation (ODE) solvers such as the fourth order Runge-Kutta method. Even though biochemical reaction networks are the main application of our work, some of our results are presented in the more general framework of propagation models (PM), a computational formalism that we introduce in the first part of this thesis. Each propagation model N has two associated propagation processes, one in discrete-time and a second one in continuous-time. These propagation processes propagate a generic mass through a discrete state space. For example, in order to model a CME, N propagates probability mass. In the discrete-time case the propagation is done step-wise, while in the continuous-time case it is done in a continuous flow defined by a differential equation. Again, in the case of the chemical master equation, this differential equation is the equivalent of the chemical master equation itself where probability mass is propagated through a discrete state space. Discrete-time propagation processes can encode methods such as the uniformization method and the fourth order Runge-Kutta integration method that we have mentioned above, and thus by optimizing propagation algorithms we optimize both of these methods simultaneously. In the second part of our thesis, we define stochastic hybrid models that approximate the stochastic behaviour of biochemical reaction networks by treating some variables of the system deterministically. This deterministic approximation is done for species with large populations, for which stochasticity does not play an important role. We propose three such hybrid models, which we introduce from the coarsest to the most refined one: (i) the first one replaces some variables of the system with their overall expectations, (ii) the second one replaces some variables of the system with their expectations conditioned on the values of the stochastic variables, (iii) and finally, the third one, splits each variable into a stochastic part (for low valuations) and a deterministic part (for high valuations), while tracking the conditional expectation of the deterministic part. For each of these algorithms we give the corresponding propagation models that propagate not only probabilities but also the respective continuous approximations for the deterministic variables.

EPFL2011

Optimization Problem Coupled with Differential Equations: A Numerical Algorithm Mixing an Interior-Point Method and Event Detection

Alexandre Caboussat, Christian Landry, Jacques Rappaz

The numerical analysis of a dynamic constrained optimization problem is presented. It consists of a global minimization problem that is coupled with a system of ordinary differential equations. The activation and the deactivation of inequality constraints induce discontinuity points in the time evolution. A numerical method based on an operator splitting scheme and a fixed point algorithm is advocated. The ordinary differential equations are approximated by the Crank-Nicolson scheme, while a primal-dual interior-point method with warm-starts is used to solve the minimization problem. The computation of the discontinuity points is based on geometric arguments, extrapolation polynomials and sensitivity analysis. Second order convergence of the method is proved when an inequality constraint is activated. Numerical results for atmospheric particles confirm the theoretical investigations.

2010

Propagation Models for Biochemical Reaction Networks

Maria-Emanuela-Canini Mateescu

EPFL2011