Reliable evaluations of geotechnical hazards like landslides and debris flow require accurate simulation of granular flow dynamics. Traditional numerical methods can simulate the complex behaviors of such flows that involve solid-like to fluid-like transitions, but they are computationally intractable when simulating large-scale systems. Surrogate models based on statistical or machine learning methods are a viable alternative, but they are typically empirical and rely on a confined set of parameters in evaluating associated risks. Due to their permutation-dependent learning, conventional machine learning models require an unreasonably large amount of training data for building generalizable surrogate models. We employ a graph neural network (GNN), a novel deep learning technique, to develop a GNN-based simulator (GNS) for granular flows to address these issues. Graphs represent the state of granular flows and interactions, like the exchange of energy and momentum between grains, and GNN learns the local interaction law. GNS takes the current state of the granular flow and estimates the next state using Euler explicit integration. We train GNS on a limited set of granular flow trajectories and evaluate its performance in a three-dimensional granular column collapse domain. GNS successfully reproduces the overall behaviors of column collapses with various aspect ratios that were not encountered during training. The computation speed of GNS outperforms high-fidelity numerical simulators by 300 times.
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In this work, we present the physics-informed neural network (PINN) model applied particularly to dynamic problems in solid mechanics. We focus on forward and inverse problems. Particularly, we show how a PINN model can be used efficiently for material identification in a dynamic setting. In this work, we assume linear continuum elasticity. We show results for two-dimensional (2D) plane strain problem and then we proceed to apply the same techniques for a three-dimensional (3D) problem. As for the training data we use the solution based on the finite element method. We rigorously show that PINN models are accurate, robust and computationally efficient, especially as a surrogate model for material identification problems. Also, we employ state-of-the-art techniques from the PINN literature which are an improvement to the vanilla implementation of PINN. Based on our results, we believe that the framework we have developed can be readily adapted to computational platforms for solving multiple dynamic problems in solid mechanics.
In this article, we propose an interval constraint programming method for globally solving catalog-based categorical optimization problems. It supports catalogs of arbitrary size and properties of arbitrary dimension, and does not require any modeling effort from the user. A novel catalog-based contractor (or filtering operator) guarantees consistency between the categorical properties and the existing catalog items. This results in an intuitive and generic approach that is exact, rigorous (robust to roundoff errors) and can be easily implemented in an off-the-shelf interval-based continuous solver that interleaves branching and constraint propagation. We demonstrate the validity of the approach on a numerical problem in which a categorical variable is described by a two-dimensional property space. A Julia prototype is available as open-source software under the MIT license at //github.com/cvanaret/CateGOrical.jl
By conceiving physical systems as 3D many-body point clouds, geometric graph neural networks (GNNs), such as SE(3)/E(3) equivalent GNNs, have showcased promising performance. In particular, their effective message-passing mechanics make them adept at modeling molecules and crystalline materials. However, current geometric GNNs only offer a mean-field approximation of the many-body system, encapsulated within two-body message passing, thus falling short in capturing intricate relationships within these geometric graphs. To address this limitation, tensor networks, widely employed by computational physics to handle manybody systems using high-order tensors, have been introduced. Nevertheless, integrating these tensorized networks into the message-passing framework of GNNs faces scalability and symmetry conservation (e.g., permutation and rotation) challenges. In response, we introduce an innovative equivariant Matrix Product State (MPS)-based message-passing strategy, through achieving an efficient implementation of the tensor contraction operation. Our method effectively models complex many-body relationships, suppressing mean-field approximations, and captures symmetries within geometric graphs. Importantly, it seamlessly replaces the standard message-passing and layer-aggregation modules intrinsic to geometric GNNs. We empirically validate the superior accuracy of our approach on benchmark tasks, including predicting classical Newton systems and quantum tensor Hamiltonian matrices. To our knowledge, our approach represents the inaugural utilization of parameterized geometric tensor networks.
A well-balanced second-order finite volume scheme is proposed and analyzed for a 2 X 2 system of non-linear partial differential equations which describes the dynamics of growing sandpiles created by a vertical source on a flat, bounded rectangular table in multiple dimensions. To derive a second-order scheme, we combine a MUSCL type spatial reconstruction with strong stability preserving Runge-Kutta time stepping method. The resulting scheme is ensured to be well-balanced through a modified limiting approach that allows the scheme to reduce to well-balanced first-order scheme near the steady state while maintaining the second-order accuracy away from it. The well-balanced property of the scheme is proven analytically in one dimension and demonstrated numerically in two dimensions. Additionally, numerical experiments reveal that the second-order scheme reduces finite time oscillations, takes fewer time iterations for achieving the steady state and gives sharper resolutions of the physical structure of the sandpile, as compared to the existing first-order schemes of the literature.
We propose a semi-analytic Stokes expansion ansatz for finite-depth standing water waves and devise a recursive algorithm to solve the system of differential equations governing the expansion coefficients. We implement the algorithm on a supercomputer using arbitrary-precision arithmetic. The Stokes expansion introduces hyperbolic trigonometric terms that require exponentiation of power series. We handle this efficiently using Bell polynomials. Under mild assumptions on the fluid depth, we prove that there are no exact resonances, though small divisors may occur. Sudden changes in growth rate in the expansion coefficients are found to correspond to imperfect bifurcations observed when families of standing waves are computed using a shooting method. A direct connection between small divisors in the recursive algorithm and imperfect bifurcations in the solution curves is observed, where the small divisor excites higher-frequency parasitic standing waves that oscillate on top of the main wave. A 109th order Pad\'e approximation maintains 25--30 digits of accuracy on both sides of the first imperfect bifurcation encountered for the unit-depth problem. This suggests that even if the Stokes expansion is divergent, there may be a closely related convergent sequence of rational approximations.
We study Whitney-type estimates for approximation of convex functions in the uniform norm on various convex multivariate domains while paying a particular attention to the dependence of the involved constants on the dimension and the geometry of the domain.
Computational modeling of charged species transport has enabled the analysis, design, and optimization of a diverse array of electrochemical and electrokinetic devices. These systems are represented by the Poisson-Nernst-Planck (PNP) equations coupled with the Navier-Stokes (NS) equation. Direct numerical simulation (DNS) to accurately capture the spatio-temporal variation of ion concentration and current flux remains challenging due to the (a) small critical dimension of the diffuse charge layer (DCL), (b) stiff coupling due to fast charge relaxation times, large advective effects, and steep gradients close to boundaries, and (c) complex geometries exhibited by electrochemical devices. In the current study, we address these challenges by presenting a direct numerical simulation framework that incorporates (a) a variational multiscale (VMS) treatment, (b) a block-iterative strategy in conjunction with semi-implicit (for NS) and implicit (for PNP) time integrators, and (c) octree based adaptive mesh refinement. The VMS formulation provides numerical stabilization critical for capturing the electro-convective flows often observed in engineered devices. The block-iterative strategy decouples the difficulty of non-linear coupling between the NS and PNP equations and allows the use of tailored numerical schemes separately for NS and PNP equations. The carefully designed second-order, hybrid implicit methods circumvent the harsh timestep requirements of explicit time steppers, thus enabling simulations over longer time horizons. Finally, the octree-based meshing allows efficient and targeted spatial resolution of the DCL. These features are incorporated into a massively parallel computational framework, enabling the simulation of realistic engineering electrochemical devices. The numerical framework is illustrated using several challenging canonical examples.
Laguerre spectral approximations play an important role in the development of efficient algorithms for problems in unbounded domains. In this paper, we present a comprehensive convergence rate analysis of Laguerre spectral approximations for analytic functions. By exploiting contour integral techniques from complex analysis, we prove that Laguerre projection and interpolation methods of degree $n$ converge at the root-exponential rate $O(\exp(-2\rho\sqrt{n}))$ with $\rho>0$ when the underlying function is analytic inside and on a parabola with focus at the origin and vertex at $z=-\rho^2$. As far as we know, this is the first rigorous proof of root-exponential convergence of Laguerre approximations for analytic functions. Several important applications of our analysis are also discussed, including Laguerre spectral differentiations, Gauss-Laguerre quadrature rules, the scaling factor and the Weeks method for the inversion of Laplace transform, and some sharp convergence rate estimates are derived. Numerical experiments are presented to verify the theoretical results.
Detecting differences in gene expression is an important part of single-cell RNA sequencing experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression between two groups (e.g., treatment vs. control). But there is increasing interest in multi-condition differential expression analyses in which expression is measured in many conditions, and the aim is to accurately detect and estimate expression differences in all conditions. We show that directly modeling single-cell RNA-seq counts in all conditions simultaneously, while also inferring how expression differences are shared across conditions, leads to greatly improved performance for detecting and estimating expression differences compared to existing methods. We illustrate the potential of this new approach by analyzing data from a single-cell experiment studying the effects of cytokine stimulation on gene expression. We call our new method "Poisson multivariate adaptive shrinkage", and it is implemented in an R package available online at //github.com/stephenslab/poisson.mash.alpha.
This work focuses on the task of property targeting: that is, generating molecules conditioned on target chemical properties to expedite candidate screening for novel drug and materials development. DiGress is a recent diffusion model for molecular graphs whose distinctive feature is allowing property targeting through classifier-based (CB) guidance. While CB guidance may work to generate molecular-like graphs, we hint at the fact that its assumptions apply poorly to the chemical domain. Based on this insight we propose a classifier-free DiGress (FreeGress), which works by directly injecting the conditioning information into the training process. CF guidance is convenient given its less stringent assumptions and since it does not require to train an auxiliary property regressor, thus halving the number of trainable parameters in the model. We empirically show that our model yields up to 79% improvement in Mean Absolute Error with respect to DiGress on property targeting tasks on QM9 and ZINC-250k benchmarks. As an additional contribution, we propose a simple yet powerful approach to improve chemical validity of generated samples, based on the observation that certain chemical properties such as molecular weight correlate with the number of atoms in molecules.
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