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Two novel parallel Newton-Krylov Balancing Domain Decomposition by Constraints (BDDC) and Dual-Primal Finite Element Tearing and Interconnecting (FETI-DP) solvers are here constructed, analyzed and tested numerically for implicit time discretizations of the three-dimensional Bidomain system of equations. This model represents the most advanced mathematical description of the cardiac bioelectrical activity and it consists of a degenerate system of two non-linear reaction-diffusion partial differential equations (PDEs), coupled with a stiff system of ordinary differential equations (ODEs). A finite element discretization in space and a segregated implicit discretization in time, based on decoupling the PDEs from the ODEs, yields at each time step the solution of a non-linear algebraic system. The Jacobian linear system at each Newton iteration is solved by a Krylov method, accelerated by BDDC or FETI-DP preconditioners, both augmented with the recently introduced {\em deluxe} scaling of the dual variables. A polylogarithmic convergence rate bound is proven for the resulting parallel Bidomain solvers. Extensive numerical experiments on linux clusters up to two thousands processors confirm the theoretical estimates, showing that the proposed parallel solvers are scalable and quasi-optimal.

This work presents a numerical formulation to model isotropic viscoelastic material behavior for membranes and thin shells. The surface and the shell theory are formulated within a curvilinear coordinate system, which allows the representation of general surfaces and deformations. The kinematics follow from Kirchhoff-Love theory and the discretization makes use of isogeometric shape functions. A multiplicative split of the surface deformation gradient is employed, such that an intermediate surface configuration is introduced. The surface metric and curvature of this intermediate configuration follow from the solution of nonlinear evolution laws - ordinary differential equations (ODEs) - that stem from a generalized viscoelastic solid model. The evolution laws are integrated numerically with the implicit Euler scheme and linearized within the Newton-Raphson scheme of the nonlinear finite element framework. The implementation of surface and bending viscosity is verified with the help of analytical solutions and shows ideal convergence behavior. The chosen numerical examples capture large deformations and typical viscoelasticity behavior, such as creep, relaxation, and strain rate dependence. It is shown that the proposed formulation can also be straightforwardly applied to model boundary viscoelasticity of 3D bodies.

Molecular dynamics (MD) has long been the \emph{de facto} choice for modeling complex atomistic systems from first principles, and recently deep learning become a popular way to accelerate it. Notwithstanding, preceding approaches depend on intermediate variables such as the potential energy or force fields to update atomic positions, which requires additional computations to perform back-propagation. To waive this requirement, we propose a novel model called ScoreMD by directly estimating the gradient of the log density of molecular conformations. Moreover, we analyze that diffusion processes highly accord with the principle of enhanced sampling in MD simulations, and is therefore a perfect match to our sequential conformation generation task. That is, ScoreMD perturbs the molecular structure with a conditional noise depending on atomic accelerations and employs conformations at previous timeframes as the prior distribution for sampling. Another challenge of modeling such a conformation generation process is that the molecule is kinetic instead of static, which no prior studies strictly consider. To solve this challenge, we introduce a equivariant geometric Transformer as a score function in the diffusion process to calculate the corresponding gradient. It incorporates the directions and velocities of atomic motions via 3D spherical Fourier-Bessel representations. With multiple architectural improvements, we outperforms state-of-the-art baselines on MD17 and isomers of C7O2H10. This research provides new insights into the acceleration of new material and drug discovery.

We describe a numerical algorithm for approximating the equilibrium-reduced density matrix and the effective (mean force) Hamiltonian for a set of system spins coupled strongly to a set of bath spins when the total system (system+bath) is held in canonical thermal equilibrium by weak coupling with a "super-bath". Our approach is a generalization of now standard typicality algorithms for computing the quantum expectation value of observables of bare quantum systems via trace estimators and Krylov subspace methods. In particular, our algorithm makes use of the fact that the reduced system density, when the bath is measured in a given random state, tends to concentrate about the corresponding thermodynamic averaged reduced system density. Theoretical error analysis and numerical experiments are given to validate the accuracy of our algorithm. Further numerical experiments demonstrate the potential of our approach for applications including the study of quantum phase transitions and entanglement entropy for long-range interaction systems.

This paper proposes a numerical method based on the Adomian decomposition approach for the time discretization, applied to Euler equations. A recursive property is demonstrated that allows to formulate the method in an appropriate and efficient way. To obtain a fully numerical scheme, the space discretization is achieved using the classical DG techniques. The efficiency of the obtained numerical scheme is demonstrated through numerical tests by comparison to exact solution and the popular Runge-Kutta DG method results.

We study an implicit finite-volume scheme for non-linear, non-local aggregation-diffusion equations which exhibit a gradient-flow structure, recently introduced by Bailo, Carrillo, and Hu (2020). Crucially, this scheme keeps the dissipation property of an associated fully discrete energy, and does so unconditionally with respect to the time step. Our main contribution in this work is to show the convergence of the method under suitable assumptions on the diffusion functions and potentials involved.

We study the numerical approximation by space-time finite element methods of a multi-physics system coupling hyperbolic elastodynamics with parabolic transport and modelling poro- and thermoelasticity. The equations are rewritten as a first-order system in time. Discretizations by continuous Galerkin methods in space and time with inf-sup stable pairs of finite elements for the spatial approximation of the unknowns are investigated. Optimal order error estimates of energy-type are proven. Superconvergence at the time nodes is addressed briefly. The error analysis can be extended to discontinuous and enriched Galerkin space discretizations. The error estimates are confirmed by numerical experiments.

In this paper, we consider the constrained energy minimizing generalized multiscale finite element method (CEM-GMsFEM) with discontinuous Galerkin (DG) coupling for the linear elasticity equations in highly heterogeneous and high contrast media. We will introduce the construction of a DG version of the CEM-GMsFEM, such as auxiliary basis functions and offline basis functions. The DG version of the method offers some advantages such as flexibility in coarse grid construction and sparsity of resulting discrete systems. Moreover, to our best knowledge, this is the first time where the proof of the convergence of the CEM-GMsFEM in the DG form is given. Some numerical examples will be presented to illustrate the performance of the method.

Convection-diffusion-reaction equations model the conservation of scalar quantities. From the analytic point of view, solution of these equations satisfy under certain conditions maximum principles, which represent physical bounds of the solution. That the same bounds are respected by numerical approximations of the solution is often of utmost importance in practice. The mathematical formulation of this property, which contributes to the physical consistency of a method, is called Discrete Maximum Principle (DMP). In many applications, convection dominates diffusion by several orders of magnitude. It is well known that standard discretizations typically do not satisfy the DMP in this convection-dominated regime. In fact, in this case, it turns out to be a challenging problem to construct discretizations that, on the one hand, respect the DMP and, on the other hand, compute accurate solutions. This paper presents a survey on finite element methods, with a main focus on the convection-dominated regime, that satisfy a local or a global DMP. The concepts of the underlying numerical analysis are discussed. The survey reveals that for the steady-state problem there are only a few discretizations, all of them nonlinear, that at the same time satisfy the DMP and compute reasonably accurate solutions, e.g., algebraically stabilized schemes. Moreover, most of these discretizations have been developed in recent years, showing the enormous progress that has been achieved lately. Methods based on algebraic stabilization, nonlinear and linear ones, are currently as well the only finite element methods that combine the satisfaction of the global DMP and accurate numerical results for the evolutionary equations in the convection-dominated situation.

The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used schemes to compute MEPs numerically. It approximates an MEP by a discrete set of configuration images, where the discretization size determines both computational cost and accuracy of the simulations. In this paper, we consider a discrete MEP to be a stationary state of the NEB method and prove an optimal convergence rate of the discrete MEP with respect to the number of images. Numerical simulations for the transitions of some several proto-typical model systems are performed to support the theory.