A fast and convergent combined Newton and gradient descent method for computing steady states of chemical reaction networks

In this work we present a fast, globally convergent, iterative algorithm for computing the asymptotically stable states of nonlinear large--scale systems of quadratic autonomous Ordinary Differential Equations (ODEs) modeling, e.g., the dynamic of complex chemical reaction networks. Towards this aim...

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Bibliographic Details
Published in:arXiv.org 2022-12
Main Authors: Berra, Silvia, Alessandro La Torraca, Benvenuto, Federico, Sommariva, Sara
Format: Article
Language:English
Subjects:
Algorithms
Asymptotic properties
Cauchy problems
Chemical reactions
Computation
Constraints
Convergence
Differential equations
Iterative algorithms
Iterative methods
Mathematical models
Modelling
Nonlinear equations
Nonlinear systems
Operators (mathematics)
Optimization
Ordinary differential equations
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Summary:In this work we present a fast, globally convergent, iterative algorithm for computing the asymptotically stable states of nonlinear large--scale systems of quadratic autonomous Ordinary Differential Equations (ODEs) modeling, e.g., the dynamic of complex chemical reaction networks. Towards this aim, we reformulate the problem as a box--constrained optimization problem where the roots of a set of nonlinear equations need to be determined. Then, we propose to use a projected Newton's approach combined with a gradient descent algorithm so that every limit point of the sequence generated by the overall algorithm is a stationary point. More importantly, we suggest replacing the standard orthogonal projector with a novel operator that ensures the final solution to satisfy the box constraints while lowering the probability that the intermediate points reached at each iteration belong to the boundary of the box where the Jacobian of the objective function may be singular. The effectiveness of the proposed approach is shown in a practical scenario concerning a chemical reaction network modeling the signaling network of colorectal cancer cells. Specifically, in this scenario the proposed algorithm is proven to be faster and more accurate than a classical dynamical approach where the asymptotically stable states are computed as the limit points of the flux of the Cauchy problem associated with the ODEs system.
ISSN:2331-8422