Molecular mechanics (MM) force fields -- the models that characterize the energy landscape of molecular systems via simple pairwise and polynomial terms -- have traditionally relied on human expert-curated, inflexible, and poorly extensible discrete chemical parameter assignment rules, namely atom or valence types. Recently, there has been significant interest in using graph neural networks to replace this process, while enabling the parametrization scheme to be learned in an end-to-end differentiable manner directly from quantum chemical calculations or condensed-phase data. In this paper, we extend the Espaloma end-to-end differentiable force field construction approach by incorporating both energy and force fitting directly to quantum chemical data into the training process. Building on the OpenMM SPICE dataset, we curate a dataset containing chemical spaces highly relevant to the broad interest of biomolecular modeling, covering small molecules, proteins, and RNA. The resulting force field, espaloma 0.3.0, self-consistently parametrizes these diverse biomolecular species, accurately predicts quantum chemical energies and forces, and maintains stable quantum chemical energy-minimized geometries. Surprisingly, this simple approach produces highly accurate protein-ligand binding free energies when self-consistently parametrizing protein and ligand. This approach -- capable of fitting new force fields to large quantum chemical datasets in one GPU-day -- shows significant promise as a path forward for building systematically more accurate force fields that can be easily extended to new chemical domains of interest.
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We applied physics-informed neural networks to solve the constitutive relations for nonlinear, path-dependent material behavior. As a result, the trained network not only satisfies all thermodynamic constraints but also instantly provides information about the current material state (i.e., free energy, stress, and the evolution of internal variables) under any given loading scenario without requiring initial data. One advantage of this work is that it bypasses the repetitive Newton iterations needed to solve nonlinear equations in complex material models. Additionally, strategies are provided to reduce the required order of derivative for obtaining the tangent operator. The trained model can be directly used in any finite element package (or other numerical methods) as a user-defined material model. However, challenges remain in the proper definition of collocation points and in integrating several non-equality constraints that become active or non-active simultaneously. We tested this methodology on rate-independent processes such as the classical von Mises plasticity model with a nonlinear hardening law, as well as local damage models for interface cracking behavior with a nonlinear softening law. In order to demonstrate the applicability of the methodology in handling complex path dependency in a three-dimensional (3D) scenario, we tested the approach using the equations governing a damage model for a three-dimensional interface model. Such models are frequently employed for intergranular fracture at grain boundaries. We have observed a perfect agreement between the results obtained through the proposed methodology and those obtained using the classical approach. Furthermore, the proposed approach requires significantly less effort in terms of implementation and computing time compared to the traditional methods.
We consider the numerical evaluation of a class of double integrals with respect to a pair of self-similar measures over a self-similar fractal set (the attractor of an iterated function system), with a weakly singular integrand of logarithmic or algebraic type. In a recent paper [Gibbs, Hewett and Moiola, Numer. Alg., 2023] it was shown that when the fractal set is "disjoint" in a certain sense (an example being the Cantor set), the self-similarity of the measures, combined with the homogeneity properties of the integrand, can be exploited to express the singular integral exactly in terms of regular integrals, which can be readily approximated numerically. In this paper we present a methodology for extending these results to cases where the fractal is non-disjoint but non-overlapping (in the sense that the open set condition holds). Our approach applies to many well-known examples including the Sierpinski triangle, the Vicsek fractal, the Sierpinski carpet, and the Koch snowflake.
This paper concerns SLAM and exploration for a swarm of nano-UAVs. The laser range finder-based tinySLAM algorithm is used to build maps of the environment. The maps are synchronized using an iterative closest point algorithm. The UAVs then explore the map by steering to points selected by a modified dynamic coverage algorithm, for which we prove a stability result. Both algorithms inform each other, allowing the UAVs to map out new areas of the environment and move into them for exploration. Experimental findings using the nano-UAV Crazyflie 2.1 platform are presented. A key challenge is to implement all algorithms on the hardware limited experimental platform.
This article presents a high-order accurate numerical method for the evaluation of singular volume integral operators, with attention focused on operators associated with the Poisson and Helmholtz equations in two dimensions. Following the ideas of the density interpolation method for boundary integral operators, the proposed methodology leverages Green's third identity and a local polynomial interpolant of the density function to recast the volume potential as a sum of single- and double-layer potentials and a volume integral with a regularized (bounded or smoother) integrand. The layer potentials can be accurately and efficiently evaluated everywhere in the plane by means of existing methods (e.g. the density interpolation method), while the regularized volume integral can be accurately evaluated by applying elementary quadrature rules. We describe the method both for domains meshed by mapped quadrilaterals and triangles, introducing for each case (i) well-conditioned methods for the production of certain requisite source polynomial interpolants and (ii) efficient translation formulae for polynomial particular solutions. Compared to straightforwardly computing corrections for every singular and nearly-singular volume target, the method significantly reduces the amount of required specialized quadrature by pushing all singular and near-singular corrections to near-singular layer-potential evaluations at target points in a small neighborhood of the domain boundary. Error estimates for the regularization and quadrature approximations are provided. The method is compatible with well-established fast algorithms, being both efficient not only in the online phase but also to set-up. Numerical examples demonstrate the high-order accuracy and efficiency of the proposed methodology; applications to inhomogeneous scattering are mentioned.
An efficient method of computing power expansions of algebraic functions is the method of Kung and Traub and is based on exact arithmetic. This paper shows a numeric approach is both feasible and accurate while also introducing a performance improvement to Kung and Traub's method based on the ramification extent of the expansions. A new method is then described for computing radii of convergence using a series comparison test. Series accuracies are then fitted to a simple log-linear function in their domain of convergence and found to have low variance. Algebraic functions up to degree 50 were analyzed and timed. A consequence of this work provided a simple method of computing the Riemann surface genus and was used as a cycle check-sum. Mathematica ver. 13.2 was used to acquire and analyze the data on a 4.0 GHz quad-core desktop computer.
This paper aims to address two issues of integral equations for the scattering of time-harmonic electromagnetic waves by a perfect electric conductor with Lipschitz continuous boundary: resonant instability and dense discretization breakdown. The remedy to resonant instability is a combined field integral equation, and dense discretization breakdown is eliminated by means of operator preconditioning. The exterior traces of single and double layer potentials are complemented by their interior counterparts of a pure imaginary wave number. We derive the corresponding variational formulation in the natural trace space for electromagnetic fields and establish its well-posedness for all wave numbers. A Galerkin discretization scheme is employed using conforming edge boundary elements on dual meshes, which produces well-conditioned discrete linear systems of the variational formulation. Some numerical results are also provided to support the numerical analysis.
The analysis of a delayed generalized Burgers-Huxley equation (a non-linear advection-diffusion-reaction problem) with weakly singular kernels is carried out in this work. Moreover, numerical approximations are performed using the conforming finite element method (CFEM). The existence, uniqueness and regularity results for the continuous problem have been discussed in detail using the Faedo-Galerkin approximation technique. For the numerical studies, we first propose a semi-discrete conforming finite element scheme for space discretization and discuss its error estimates under minimal regularity assumptions. We then employ a backward Euler discretization in time and CFEM in space to obtain a fully-discrete approximation. Additionally, we derive a prior error estimates for the fully-discrete approximated solution. Finally, we present computational results that support the derived theoretical results.
Applying parallel-in-time algorithms to multiscale Hamiltonian systems to obtain stable long time simulations is very challenging. In this paper, we present novel data-driven methods aimed at improving the standard parareal algorithm developed by Lion, Maday, and Turinici in 2001, for multiscale Hamiltonian systems. The first method involves constructing a correction operator to improve a given inaccurate coarse solver through solving a Procrustes problem using data collected online along parareal trajectories. The second method involves constructing an efficient, high-fidelity solver by a neural network trained with offline generated data. For the second method, we address the issues of effective data generation and proper loss function design based on the Hamiltonian function. We show proof-of-concept by applying the proposed methods to a Fermi-Pasta-Ulum (FPU) problem. The numerical results demonstrate that the Procrustes parareal method is able to produce solutions that are more stable in energy compared to the standard parareal. The neural network solver can achieve comparable or better runtime performance compared to numerical solvers of similar accuracy. When combined with the standard parareal algorithm, the improved neural network solutions are slightly more stable in energy than the improved numerical coarse solutions.
We consider the coupled system of the Landau--Lifshitz--Gilbert equation and the conservation of linear momentum law to describe magnetic processes in ferromagnetic materials including magnetoelastic effects in the small-strain regime. For this nonlinear system of time-dependent partial differential equations, we present a decoupled integrator based on first-order finite elements in space and an implicit one-step method in time. We prove unconditional convergence of the sequence of discrete approximations towards a weak solution of the system as the mesh size and the time-step size go to zero. Compared to previous numerical works on this problem, for our method, we prove a discrete energy law that mimics that of the continuous problem and, passing to the limit, yields an energy inequality satisfied by weak solutions. Moreover, our method does not employ a nodal projection to impose the unit length constraint on the discrete magnetisation, so that the stability of the method does not require weakly acute meshes. Furthermore, our integrator and its analysis hold for a more general setting, including body forces and traction, as well as a more general representation of the magnetostrain. Numerical experiments underpin the theory and showcase the applicability of the scheme for the simulation of the dynamical processes involving magnetoelastic materials at submicrometer length scales.
Assouad-Nagata dimension addresses both large and small scale behaviors of metric spaces and is a refinement of Gromov's asymptotic dimension. A metric space $M$ is a minor-closed metric if there exists an (edge-)weighted graph $G$ in a fixed minor-closed family such that the underlying space of $M$ is the vertex-set of $G$, and the metric of $M$ is the distance function in $G$. Minor-closed metrics naturally arise when removing redundant edges of the underlying graphs by using edge-deletion and edge-contraction. In this paper, we determine the Assouad-Nagata dimension of every minor-closed metric. It is a common generalization of known results for the asymptotic dimension of $H$-minor free unweighted graphs and the Assouad-Nagata dimension of some 2-dimensional continuous spaces (e.g.\ complete Riemannian surfaces with finite Euler genus) and their corollaries.
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