A Symbolic Transformation Language and its Application to a Multiscale Method

The context of this work is the design of a software, called MEMSALab, dedicated to the automatic derivation of multiscale models of arrays of micro- and nanosystems. In this domain a model is a partial differential equation. Multiscale methods approximate it by another partial differential equation which can be numerically simulated in a reasonable time. The challenge consists in taking into account a wide range of geometries combining thin and periodic structures with the possibility of multiple nested scales. In this paper we present a transformation language that will make the development of MEMSALab more feasible. It is proposed as a Maple package for rule-based programming, rewriting strategies and their combination with standard Maple code. We illustrate the practical interest of this language by using it to encode two examples of multiscale derivations, namely the two-scale limit of the derivative operator and the two-scale model of the stationary heat equation.Comment: 36 page

Computer-Aided Derivation of Multi-scale Models: A Rewriting Framework

We introduce a framework for computer-aided derivation of multi-scale models. It relies on a combination of an asymptotic method used in the field of partial differential equations with term rewriting techniques coming from computer science. In our approach, a multi-scale model derivation is characterized by the features taken into account in the asymptotic analysis. Its formulation consists in a derivation of a reference model associated to an elementary nominal model, and in a set of transformations to apply to this proof until it takes into account the wanted features. In addition to the reference model proof, the framework includes first order rewriting principles designed for asymptotic model derivations, and second order rewriting principles dedicated to transformations of model derivations. We apply the method to generate a family of homogenized models for second order elliptic equations with periodic coefficients that could be posed in multi-dimensional domains, with possibly multi-domains and/or thin domains.Comment: 26 page

Lazy AC-Pattern Matching for Rewriting

We define a lazy pattern-matching mechanism modulo associativity and commutativity. The solutions of a pattern-matching problem are stored in a lazy list composed of a first substitution at the head and a non-evaluated object that encodes the remaining computations. We integrate the lazy AC-matching in a strategy language: rewriting rule and strategy application produce a lazy list of terms.Comment: In Proceedings WRS 2011, arXiv:1204.531

Formal methods for Multiscale models derivation

We are currently developing a software dedicated to multiscale and multiphysics model derivation oriented to arrays of micro and nanosystems. The software is based on the two-scale transform, together with formal specification and verification techniques in computer science. It helps to derive multiphysics models for complex geometries including thin or periodic structures or combinations of them. Final models are correct by construction since human errors are avoided and model derivation effort is dramatically reduced

Prospects for Declarative Mathematical Modeling of Complex Biological Systems

Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation program, in a general-purpose programming language. Examples of such computations on models include model analysis, relatively general-purpose model-reduction maps, and the initial phases of model implementation, all of which should preserve or approximate the mathematical semantics of a complex biological model. The potential advantages are particularly relevant in the case of developmental modeling, wherein complex spatial structures exhibit dynamics at molecular, cellular, and organogenic levels to relate genotype to multicellular phenotype. Multiscale modeling can benefit from both the expressive power of declarative modeling languages and the application of model reduction methods to link models across scale. Based on previous work, here we define declarative modeling of complex biological systems by defining the operator algebra semantics of an increasingly powerful series of declarative modeling languages including reaction-like dynamics of parameterized and extended objects; we define semantics-preserving implementation and semantics-approximating model reduction transformations; and we outline a "meta-hierarchy" for organizing declarative models and the mathematical methods that can fruitfully manipulate them

Nested Integrals and Rationalizing Transformations

A brief overview of some computer algebra methods for computations with nested integrals is given. The focus is on nested integrals over integrands involving square roots. Rewrite rules for conversion to and from associated nested sums are discussed. We also include a short discussion comparing the holonomic systems approach and the differential field approach. For simplification to rational integrands, we give a comprehensive list of univariate rationalizing transformations, including transformations tuned to map the interval $[0,1]$ bijectively to itself.Comment: manuscript of 25 February 2021, in "Anti-Differentiation and the Calculation of Feynman Amplitudes", Springe

An iterative semi-implicit scheme with robust damping

An efficient, iterative semi-implicit (SI) numerical method for the time integration of stiff wave systems is presented. Physics-based assumptions are used to derive a convergent iterative formulation of the SI scheme which enables the monitoring and control of the error introduced by the SI operator. This iteration essentially turns a semi-implicit method into a fully implicit method. Accuracy, rather than stability, determines the timestep. The scheme is second-order accurate and shown to be equivalent to a simple preconditioning method. We show how the diffusion operators can be handled so as to yield the property of robust damping, i.e., dissipating the solution at all values of the parameter \mathcal D\dt, where $\mathcal D$ is a diffusion operator and \dt the timestep. The overall scheme remains second-order accurate even if the advection and diffusion operators do not commute. In the limit of no physical dissipation, and for a linear test wave problem, the method is shown to be symplectic. The method is tested on the problem of Kinetic Alfv\'en wave mediated magnetic reconnection. A Fourier (pseudo-spectral) representation is used. A 2-field gyrofluid model is used and an efficacious k-space SI operator for this problem is demonstrated. CPU speed-up factors over a CFL-limited explicit algorithm ranging from $\sim20$ to several hundreds are obtained, while accurately capturing the results of an explicit integration. Possible extension of these results to a real-space (grid) discretization is discussed.Comment: Submitted to the Journal of Computational Physics. Clarifications and caveats in response to referees, numerical demonstration of convergence rate, generalized symplectic proo