A Training Set Subsampling Strategy for the Reduced Basis Method

We present a subsampling strategy for the offline stage of the Reduced Basis Method. The approach is aimed at bringing down the considerable offline costs associated with using a finely-sampled training set. The proposed algorithm exploits the potential of the pivoted QR decomposition and the discrete empirical interpolation method to identify important parameter samples. It consists of two stages. In the first stage, we construct a low-fidelity approximation to the solution manifold over a fine training set. Then, for the available low-fidelity snapshots of the output variable, we apply the pivoted QR decomposition or the discrete empirical interpolation method to identify a set of sparse sampling locations in the parameter domain. These points reveal the structure of the parametric dependence of the output variable. The second stage proceeds with a subsampled training set containing a by far smaller number of parameters than the initial training set. Different subsampling strategies inspired from recent variants of the empirical interpolation method are also considered. Tests on benchmark examples justify the new approach and show its potential to substantially speed up the offline stage of the Reduced Basis Method, while generating reliable reduced-order models.

A Monolithic and a Partitioned, Reduced Basis Method for Fluid–Structure Interaction Problems

The aim of this work is to present an overview about the combination of the Reduced Basis Method (RBM) with two different approaches for Fluid–Structure Interaction (FSI) problems, namely a monolithic and a partitioned approach. We provide the details of implementation of two reduction procedures, and we then apply them to the same test case of interest. We first implement a reduction technique that is based on a monolithic procedure where we solve the fluid and the solid problems all at once. We then present another reduction technique that is based on a partitioned (or segregated) procedure: the fluid and the solid problems are solved separately and then coupled using a fixed point strategy. The toy problem that we consider is based on the Turek–Hron benchmark test case, with a fluid Reynolds number Re=100.

Fast solution of the linearized Poisson–Boltzmann equation with nonaffine parametrized boundary conditions using the reduced basis method

The Poisson–Boltzmann equation (PBE) is a nonlinear elliptic parametrized partial differential equation that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges immersed in an ionic solution. Efficient numerical computation of the PBE yields a high number of degrees of freedom in the resultant algebraic system of equations, ranging from several hundred thousand to millions. Coupled with the fact that in most cases the PBE requires to be solved multiple times for a large number of system configurations, for example, in Brownian dynamics simulations or in the computation of similarity indices for protein interaction analysis, this poses great computational challenges to conventional numerical techniques. To accelerate such onerous computations, we suggest to apply the reduced basis method (RBM) and the (discrete) empirical interpolation method ((D)EIM) to the PBE with a special focus on simulations of complex biomolecular systems, which greatly reduces this computational complexity by constructing a reduced order model (ROM) of typically low dimension. In this study, we employ a simple version of the PBE for proof of concept and discretize the linearized PBE (LPBE) with a centered finite difference scheme. The resultant linear system is solved by the aggregation-based algebraic multigrid (AGMG) method at different samples of ionic strength on a three-dimensional Cartesian grid. The discretized LPBE, which we call the high-fidelity full order model (FOM), yields solution as accurate as other LPBE solvers. We then apply the RBM to the FOM. DEIM is applied to the Dirichlet boundary conditions which are nonaffine in the parameter (ionic strength), to reduce the complexity of the ROM. From the numerical results, we notice that the RBM reduces the model order from $${\mathcal {N}} = 2\times 10^{6}$$ N = 2 × 10 6 to $$N = 6$$ N = 6 at an accuracy of $${\mathcal {O}}(10^{-9})$$ O ( 10 - 9 ) and reduces the runtime by a factor of approximately 7600. DEIM, on the other hand, is also used in the offline-online phase of solving the ROM for different values of parameters which provides a speed-up of 20 for a single iteration of the greedy algorithm.