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A wide variety of biological phenomena can be modeled by the collective activity of a population of individual units. A common strategy for simulating such a system, the population density approach, is to take the macroscopic limit and update its population density function. However, in many cases, the coupling between the units and noise gives rise to complex behaviors challenging to existing population density approach methods. To address these challenges, we develop the asymmetric particle population density (APPD) method that efficiently and accurately simulates such populations consist of coupled elements. The APPD is well-suited for a parallel implementation. We compare the performance of the method against direct Monte-Carlo simulation and verify its accuracy by applying it to the well-studied Hodgkin-Huxley model, with a range of challenging scenarios. We find that our method can accurately reproduce complex macroscopic behaviors such as inhibitory coupling-induced clustering and noise-induced firing while being faster than the direct simulation., 13 pages, 4 figures

Fluid dynamical simulations are often performed using cheap macroscopic models like the Euler equations. For rarefied gases under near-equilibrium conditions, however, macroscopic models are not sufficiently accurate and a simulation using more accurate microscopic models is often expensive. In this paper, we introduce a hierarchical micro-macro acceleration based on moment models that combines the speed of macroscopic models and the accuracy of microscopic models. The hierarchical micro-macro acceleration is based on a flexible four step procedure including a micro step, restriction step, macro step, and matching step. We derive several new micro-macro methods from that and compare to existing methods. In 1D and 2D test cases, the new methods achieve high accuracy and a large speedup.

Arising from averaging and linearizing over the original Vlasov-Maxwell system for magnetized plasmas, the quasilinear theory describes the resonant interaction between particles and waves. Such a model reduction in weak turbulence regime results in a kinetic diffusion process in momentum space for the particle probability density function(pdf ), where the diffusion coefficients are determined by the wave spectral energy density(sed). Meanwhile, a reaction equation in spectral space governs the time dynamics of the wave sed, with growth rates linearly dependent on the particle pdf. We propose a conservative Galerkin scheme for the quasilinear diffusion model in three-dimensional momentum space and three-dimensional spectral space, with cylindrical symmetry. The conservation laws are preserved by adopting the conservative discrete integro-differential operators and a consistent quadrature rule. We introduce a semi-implicit time discretization, and the stability condition is discussed. Numerical examples with applications in the electron runaway problem are provided, they show that the particle-wave interaction results in a strong anisotropic diffusion effect on the particle pdf., 20 pages, 3 figures

While deep learning algorithms demonstrate a great potential in scientific computing, its application to multi-scale problems remains to be a big challenge. This is manifested by the "frequency principle" that neural networks tend to learn low frequency components first. Novel architectures such as multi-scale deep neural network (MscaleDNN) were proposed to alleviate this problem to some extent. In this paper, we construct a subspace decomposition based DNN (dubbed SD$^2$NN) architecture for a class of multi-scale problems by combining traditional numerical analysis ideas and MscaleDNN algorithms. The proposed architecture includes one low frequency normal DNN submodule, and one (or a few) high frequency MscaleDNN submodule(s), which are designed to capture the smooth part and the oscillatory part of the multi-scale solutions, respectively. In addition, a novel trigonometric activation function is incorporated in the SD$^2$NN model. We demonstrate the performance of the SD$^2$NN architecture through several benchmark multi-scale problems in regular or irregular geometric domains. Numerical results show that the SD$^2$NN model is superior to existing models such as MscaleDNN., Comment: 19pages,11 figures

The solution of time dependent differential equations with neural networks has attracted a lot of attention recently. The central idea is to learn the laws that govern the evolution of the solution from data, which might be polluted with random noise. However, in contrast to other machine learning applications, usually a lot is known about the system at hand. For example, for many dynamical systems physical quantities such as energy or (angular) momentum are exactly conserved. Hence, the neural network has to learn these conservation laws from data and they will only be satisfied approximately due to finite training time and random noise. In this paper we present an alternative approach which uses Noether's Theorem to inherently incorporate conservation laws into the architecture of the neural network. We demonstrate that this leads to better predictions for three model systems: the motion of a non-relativistic particle in a three-dimensional Newtonian gravitational potential, the motion of a massive relativistic particle in the Schwarzschild metric and a system of two interacting particles in four dimensions., Comment: 24 pages, 16 figures; to appear in Journal of Computational Physics

We present a new discretization approach to advection-diffusion problems with Robin boundary conditions on complex, time-dependent domains. The method is based on second order cut cell finite volume methods introduced by Bochkov et al. [8] to discretize the Laplace operator and Robin boundary condition. To overcome the small cell problem, we use a splitting scheme along with a semi-Lagrangian method to treat advection. We demonstrate second order accuracy in the L 1 , L 2 , and L ∞ norms for both analytic test problems and numerical convergence studies. We also demonstrate the ability of the scheme to convert one chemical species to another across a moving boundary.

The numerical prediction of two-phase flows with an interface is challenging, to a considerable extent because of the high density ratio at the interface. Numerical results become affected by momentum losses, diverging spurious interface velocities, free surface distortion, and even numerical instability. To prevent issues like these, consistent momentum and mass transport with an additional continuity equation were introduced. In this article, we describe how a consistent discretization was incorporated into our own method and extended for fluid-structure interaction (FSI) with moving rigid bodies. The new method was tested against benchmark simulations from literature confirming that consistent transport modeling gives a significant improvement compared to non-consistent modeling for the dynamics of two-phase flows. Newly devised proof of principle FSI simulations with momentum transfer from fluid to body in the presence of a high-density ratio between fluids are introduced that could serve as a benchmark for future studies. The simulations demonstrate that consistent modeling gives an order of magnitude improvement in terms of momentum conservation compared to non-consistent modeling. Simulations with the new method are also compared to FSI experiments from literature. Results obtained with the consistent method are closer to the measurements than results of the non-consistent method. The merit of consistent modeling with and without FSI becomes especially apparent for two-phase flows with a high-density ratio between fluids.

We present a new approach to compute and analyze the dynamical electro-geometric properties of proteins undergoing conformational changes. The molecular trajectory is obtained from Markov state models, and the electrostatic potential is calculated using the continuum Poisson-Boltzmann equation. The numerical electric potential is constructed using a parallel sharp numerical solver implemented on adaptive Octree grids. We introduce novel a posteriori error estimates to quantify the solution's accuracy on the molecular surface. To illustrate the approach, we consider the opening of the SARS-CoV-2 spike protein using the recent molecular trajectory simulated through the Folding@home initiative. We analyze our results, focusing on the characteristics of the receptor-binding domain and its vicinity. This work lays the foundation for a new class of hybrid computational approaches, producing high-fidelity dynamical computational measurements serving as a basis for protein bio-mechanism investigations. © 2021 The Author(s)

This paper presents a strategy to accelerate virtually any Poisson solver by taking advantage of s spatial reflection symmetries. More precisely, we have proved the existence of an inexpensive block diagonalisation that transforms the original Poisson equation into a set of 2s fully decoupled subsystems then solved concurrently. This block diagonalisation is identical regardless of the mesh connectivity (structured or unstructured) and the geometric complexity of the problem, therefore applying to a wide range of academic and industrial configurations. In fact, it simplifies the task of discretising complex geometries since it only requires meshing a portion of the domain that is then mirrored implicitly by the symmetries’ hyperplanes. Thus, the resulting meshes naturally inherit the exploited symmetries, and their memory footprint becomes 2s times smaller. Thanks to the subsystems’ better spectral properties, iterative solvers converge significantly faster. Additionally, imposing an adequate grid points’ ordering allows reducing the operators’ footprint and replacing the standard sparse matrix-vector products with the sparse matrixmatrix product, a higher arithmetic intensity kernel. As a result, matrix multiplications are accelerated, and massive simulations become more affordable. Finally, we include numerical experiments based on a turbulent flow simulation and making state-of-theart solvers exploit a varying number of symmetries. On the one hand, algebraic multigrid and preconditioned Krylov subspace methods require up to 23% and 72% fewer iterations, resulting in up to 1.7x and 5.6x overall speedups, respectively. On the other, sparse direct solvers’ memory footprint, setup and solution costs are reduced by up to 48%, 58% and 46%, respectively. This work has been financially supported by two competitive R+D projects: RETOtwin (PDC2021-120970-I00), given by MCIN/AEI/10.13039/501100011033 and European Union Next GenerationEU/PRTR, and FusionCAT (001-P-001722), given by Generalitat de Catalunya RIS3CAT-FEDER. Àdel Alsalti-Baldellou has also been supported by the predoctoral grants DIN2018-010061 and 2019-DI-90, given by MCIN/AEI/10.13039/501100011033 and the Catalan Agency for Management of University and Research Grants (AGAUR), respectively.

Inexpensive numerical methods are key to enable simulations of systems of a large number of particles of different shapes in Stokes flow. Several approximate methods have been introduced for this purpose. We study the accuracy of the multiblob method for solving the Stokes mobility problem in free space, where the 3D geometry of a particle surface is discretised with spherical blobs and the pair-wise interaction between blobs is described by the RPY-tensor. The paper aims to investigate and improve on the magnitude of the error in the solution velocities of the Stokes mobility problem using a combination of two different techniques: an optimally chosen grid of blobs and a pair-correction inspired by Stokesian dynamics. Optimisation strategies to determine a grid with a certain number of blobs are presented with the aim of matching the hydrodynamic response of a single accurately described ideal particle, alone in the fluid. Small errors in this self-interaction are essential as they determine the basic error level in a system of well-separated particles. With a good match, reasonable accuracy can be obtained even with coarse blob-resolutions of the particle surfaces. The error in the self-interaction is however sensitive to the exact choice of grid parameters and simply hand-picking a suitable blob geometry can lead to errors several orders of magnitude larger in size. The pair-correction is local and cheap to apply, and reduces on the error for more closely interacting particles. Two different types of geometries are considered: spheres and axisymmetric rods with smooth caps. The error in solutions to mobility problems is quantified for particles of varying inter-particle distances for systems containing a few particles, comparing to an accurate solution based on a second kind BIE-formulation where the quadrature error is controlled by employing quadrature by expansion (QBX)., 49 pages, 37 figures

We introduce a new electrostatic particle-in-cell algorithm capable of using large timesteps compared to particle gyro-period under a uniform external magnetic field. The algorithm extends earlier electrostatic fully implicit PIC implementations with a new asymptotic-preserving particle-push scheme that allows timesteps much larger than particle gyroperiods. In the large-timestep limit, the integrator preserves all particle drifts, while recovering the full orbit for small timesteps. The scheme allows for a seamless, efficient treatment of particles with coexisting magnetized and unmagnetized species, and conserves energy and charge exactly without spoiling implicit solver performance. We demonstrate by numerical experiment with several problems of variable species magnetization (diocotron instability, modified two-stream instability, and drift instability) that orders of magnitude wall-clock-time speedups vs. the standard fully implicit electrostatic PIC algorithm are possible without sacrificing solution accuracy.

In this paper, we propose a mesh-free numerical method for solving elliptic PDEs on unknown manifolds, identified with randomly sampled point cloud data. The PDE solver is formulated as a spectral method where the test function space is the span of the leading eigenfunctions of the Laplacian operator, which are approximated from the point cloud data. While the framework is flexible for any test functional space, we will consider the eigensolutions of a weighted Laplacian obtained from a symmetric Radial Basis Function (RBF) method induced by a weak approximation of a weighted Laplacian on an appropriate Hilbert space. Especially, we consider a test function space that encodes the geometry of the data yet does not require us to identify and use the sampling density of the point cloud. To attain a more accurate approximation of the expansion coefficients, we adopt a second-order tangent space estimation method to improve the RBF interpolation accuracy in estimating the tangential derivatives. This spectral framework allows us to efficiently solve the PDE many times subjected to different parameters, which reduces the computational cost in the related inverse problem applications. In a well-posed elliptic PDE setting with randomly sampled point cloud data, we provide a theoretical analysis to demonstrate the convergent of the proposed solver as the sample size increases. We also report some numerical studies that show the convergence of the spectral solver on simple manifolds and unknown, rough surfaces. Our numerical results suggest that the proposed method is more accurate than a graph Laplacian-based solver on smooth manifolds. On rough manifolds, these two approaches are comparable. Due to the flexibility of the framework, we empirically found improved accuracies in both smoothed and unsmoothed Stanford bunny domains by blending the graph Laplacian eigensolutions and RBF interpolator., 8 figures