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We propose two efficient energetic spectral-element methods in time for marching nonlinear gradient systems with the phase-field Allen--Cahn equation as an example: one fully implicit nonlinear method and one semi-implicit linear method. Different from other spectral methods in time using spectral Petrov-Galerkin or weighted Galerkin approximations, the presented implicit method employs an energetic variational Galerkin form that can maintain the mass conservation and energy dissipation property of the continuous dynamical system. Another advantage of this method is its superconvergence. A high-order extrapolation is adopted for the nonlinear term to get the semi-implicit method. The semi-implicit method does not have superconvergence, but can be improved by a few Picard-like iterations to recover the superconvergence of the implicit method. Numerical experiments verify that the method using Legendre elements of degree three outperforms the 4th-order implicit-explicit backward differentiation formula and the 4th-order exponential time difference Runge-Kutta method, which were known to have best performances in solving phase-field equations. In addition to the standard Allen--Cahn equation, we also apply the method to a conservative Allen--Cahn equation, in which the conservation of discrete total mass is verified. The applications of the proposed methods are not limited to phase-field Allen--Cahn equations. They are suitable for solving general, large-scale nonlinear dynamical systems., Comment: 28 pages, 10 figures

Computed tomography (CT) relies on precise patient immobilization during image acquisition. Nevertheless, motion artifacts in the reconstructed images can persist. Motion compensation methods aim to correct such artifacts post-acquisition, often incorporating temporal smoothness constraints on the estimated motion patterns. This study analyzes the influence of a spline-based motion model within an existing rigid motion compensation algorithm for cone-beam CT on the recoverable motion frequencies. Results demonstrate that the choice of motion model crucially influences recoverable frequencies. The optimization-based motion compensation algorithm is able to accurately fit the spline nodes for frequencies almost up to the node-dependent theoretical limit according to the Nyquist-Shannon theorem. Notably, a higher node count does not compromise reconstruction performance for slow motion patterns, but can extend the range of recoverable high frequencies for the investigated algorithm. Eventually, the optimal motion model is dependent on the imaged anatomy, clinical use case, and scanning protocol and should be tailored carefully to the expected motion frequency spectrum to ensure accurate motion compensation.

We study Lyapunov exponents of tracers in compressible homogeneous isotropic turbulence at different turbulent Mach number $M_t$ and Taylor-scale Reynolds number $Re_\lambda$. We demonstrate that statistics of finite-time Lyapunov exponents have the same form as in incompressible flow due to density-velocity coupling. Modulus of the smallest Lyapunov exponent $\lambda_3$ provides the principal Lyapunov exponent of the time-reversed flow, which usually is wrong in a compressible flow. This exponent, along with the principal Lyapunov exponent $\lambda_1$, determines all the exponents due to the vanishing of the sum of all Lyapunov exponents. Numerical results by high-order schemes for solving the Navier-Stokes equations and tracking particles verify these theoretical predictions. We found that: 1) The largest normalized Lyapunov exponent $\lambda_1 \tau_\eta$, where $\tau_\eta$ is the Kolmogorov time scale, is a decreasing function of $M_t$. Its dependence on $Re_\lambda$ is weak when the driving force is solenoidal, while it is an increasing function of $Re_\lambda$ when the solenoidal and compressible forces are comparable. Similar facts hold for $|\lambda_3|$, in contrast with well-studied short-correlated model; 2) The ratio of the first two Lyapunov exponents $\lambda_1/\lambda_2$ decreases with $Re_\lambda$, and is virtually independent of $M_t$ for $M_t \le 1$ in the case of solenoidal force but decreases as $M_t$ increases when solenoidal and compressible forces are comparable; 3) For purely solenoidal force, $\lambda_1 :\lambda_2 :\lambda_3 \approx 4:1:-5$ for $Re_\lambda > 80$, which is consistent with incompressible turbulence studies; 4) The ratio of dilation-to-vorticity is a more suitable parameter to characterize LEs than $M_t$., Comment: 25 pages, 18 figures

Recently, linear computed tomography (LCT) systems have actively attracted attention. To weaken projection truncation and image the region of interest (ROI) for LCT, the backprojection filtration (BPF) algorithm is an effective solution. However, in BPF for LCT, it is difficult to achieve stable interior reconstruction, and for differentiated backprojection (DBP) images of LCT, multiple rotation-finite inversion of Hilbert transform (Hilbert filtering)-inverse rotation operations will blur the image. To satisfy multiple reconstruction scenarios for LCT, including interior ROI, complete object, and exterior region beyond field-of-view (FOV), and avoid the rotation operations of Hilbert filtering, we propose two types of reconstruction architectures. The first overlays multiple DBP images to obtain a complete DBP image, then uses a network to learn the overlying Hilbert filtering function, referred to as the Overlay-Single Network (OSNet). The second uses multiple networks to train different directional Hilbert filtering models for DBP images of multiple linear scannings, respectively, and then overlays the reconstructed results, i.e., Multiple Networks Overlaying (MNetO). In two architectures, we introduce a Swin Transformer (ST) block to the generator of pix2pixGAN to extract both local and global features from DBP images at the same time. We investigate two architectures from different networks, FOV sizes, pixel sizes, number of projections, geometric magnification, and processing time. Experimental results show that two architectures can both recover images. OSNet outperforms BPF in various scenarios. For the different networks, ST-pix2pixGAN is superior to pix2pixGAN and CycleGAN. MNetO exhibits a few artifacts due to the differences among the multiple models, but any one of its models is suitable for imaging the exterior edge in a certain direction., Comment: 13 pages, 13 figures

One of the most exciting applications of artificial intelligence (AI) is automated scientific discovery based on previously amassed data, coupled with restrictions provided by known physical principles, including symmetries and conservation laws. Such automated hypothesis creation and verification can assist scientists in studying complex phenomena, where traditional physical intuition may fail. Here we develop a platform based on a generalized Onsager principle to learn macroscopic dynamical descriptions of arbitrary stochastic dissipative systems directly from observations of their microscopic trajectories. Our method simultaneously constructs reduced thermodynamic coordinates and interprets the dynamics on these coordinates. We demonstrate its effectiveness by studying theoretically and validating experimentally the stretching of long polymer chains in an externally applied field. Specifically, we learn three interpretable thermodynamic coordinates and build a dynamical landscape of polymer stretching, including the identification of stable and transition states and the control of the stretching rate. Our general methodology can be used to address a wide range of scientific and technological applications., Comment: Fix figure visibility issue

Micro-computed tomography (micro-CT) is a widely used state-of-the-art instrument employed to study the morphological structures of objects in various fields. However, its small field-of-view (FOV) cannot meet the pressing demand for imaging relatively large objects at high spatial resolutions. Recently, we devised a novel scanning mode called multiple source translation CT (mSTCT) that effectively enlarges the FOV of the micro-CT and correspondingly developed a virtual projection-based filtered backprojection (V-FBP) algorithm for reconstruction. Although V-FBP skillfully solves the truncation problem in mSTCT, it requires densely sampled projections to arrive at high-resolution reconstruction, which reduces imaging efficiency. In this paper, we developed two backprojection-filtration (BPF)-based algorithms for mSTCT, i.e., S-BPF (derivatives along source) and D-BPF (derivatives along detector). D-BPF can achieve high-resolution reconstruction with fewer projections than V-FBP and S-BPF. Through simulated and real experiments conducted in this paper, we demonstrate that D-BPF can reduce source sampling by 75% compared with V-FBP at the same spatial resolution, which makes mSTCT more feasible in practice. Meanwhile, S-BPF can yield more stable results than D-BPF, which is similar to V-FBP., Comment: 23 pages, 13 figures

Laguerre polynomials are orthogonal polynomials defined on positive half line with respect to weight $e^{-x}$. They have wide applications in scientific and engineering computations. However, the exponential growth of Laguerre polynomials of high degree makes it hard to apply them to complicated systems that need to use large numbers of Laguerre bases. In this paper, we introduce modified three-term recurrence formula to reduce the round-off error and to avoid overflow and underflow issues in generating generalized Laguerre polynomials and Laguerre functions. We apply the improved Laguerre methods to solve an elliptic equation defined on the half line. More than one thousand Laguerre bases are used in this application and meanwhile accuracy close to machine precision is achieved. The optimal scaling factor of Laguerre methods are studied and found to be independent of number of quadrature points in two cases that Laguerre methods have better convergence speeds than mapped Jacobi methods., Comment: 19pages, 8 figures

With the development of computed tomography (CT) imaging technology, it is possible to acquire multi-energy data by spectral CT. Being different from conventional CT, the X-ray energy spectrum of spectral CT is cutting into several narrow bins which leads to the result that only a part of photon can be collected in each individual energy channel, which cause the image qualities to be severely degraded by noise and artifacts. To address this problem, we propose a spectral CT reconstruction algorithm based on low-rank representation and structure preserving regularization in this paper. To make full use of the prior knowledge about both the inter-channel correlation and the sparsity in gradient domain of inner-channel data, this paper combines a low-rank correlation descriptor with a structure extraction operator as priori regularization terms for spectral CT reconstruction. Furthermore, a split-Bregman based iterative algorithm is developed to solve the reconstruction model. Finally, we propose a multi-channel adaptive parameters generation strategy according to CT values of each individual energy channel. Experimental results on numerical simulations and real mouse data indicate that the proposed algorithm achieves higher accuracy on both reconstruction and material decomposition than the methods based on simultaneous algebraic reconstruction technique (SART), total variation minimization (TVM), total variation with low-rank (LRTV), and spatial-spectral cube matching frame (SSCMF). Compared with SART, our algorithm improves the feature similarity (FSIM) by 40.4% on average for numerical simulation reconstruction, whereas TVM, LRTV, and SSCMF correspond to 26.1%, 28.2%, and 29.5%, respectively., Comment: 21 pages, 9 figures

Quasi-equilibrium approximation is a widely used closure approximation approach for model reduction with applications in complex fluids, materials science, etc. It is based on the maximum entropy principle and leads to thermodynamically consistent coarse-grain models. However, its high computational cost is a known barrier for fast and accurate applications. Despite its good mathematical properties, there are very few works on the fast and efficient implementations of quasi-equilibrium approximations. In this paper, we give efficient implementations of quasi-equilibrium approximations for antipodally symmetric problems on unit circle and unit sphere using polynomial and piecewise polynomial approximations. Comparing to the existing methods using linear or cubic interpolations, our approach achieves high accuracy (double precision) with much less storage cost. The methods proposed in this paper can be directly extended to handle other moment closure approximation problems.

We propose a systematic method for learning stable and physically interpretable dynamical models using sampled trajectory data from physical processes based on a generalized Onsager principle. The learned dynamics are autonomous ordinary differential equations parameterized by neural networks that retain clear physical structure information, such as free energy, diffusion, conservative motion and external forces. For high dimensional problems with a low dimensional slow manifold, an autoencoder with metric preserving regularization is introduced to find the low dimensional generalized coordinates on which we learn the generalized Onsager dynamics. Our method exhibits clear advantages over existing methods on benchmark problems for learning ordinary differential equations. We further apply this method to study Rayleigh-Benard convection and learn Lorenz-like low dimensional autonomous reduced order models that capture both qualitative and quantitative properties of the underlying dynamics. This forms a general approach to building reduced order models for forced dissipative systems., Comment: 29 pages, 19 figures

We propose and analyze a linearly stabilized semi-implicit diffusive Crank--Nicolson scheme for the Cahn--Hilliard gradient flow. In this scheme, the nonlinear bulk force is treated explicitly with two second-order stabilization terms. This treatment leads to linear elliptic system with constant coefficients and provable discrete energy dissipation. Rigorous error analysis is carried out for the fully discrete scheme. When the time step-size and the space step-size are small enough, second order accuracy in time is obtained with a prefactor controlled by some lower degree polynomial of $1/\varepsilon$. {Here $\varepsilon$ is the thickness of the interface}. Numerical results together with an adaptive time stepping are presented to verify the accuracy and efficiency of the proposed scheme., Comment: arXiv admin note: text overlap with arXiv:1710.03604, arXiv:1708.09763

In a previous study [B. Li, S. Tang and H. Yu, Commun. Comput. Phy. 27(2):379-411, 2020], it is shown that deep neural networks built with rectified power units (RePU) as activation functions can give better approximation for sufficient smooth functions than those built with rectified linear units, by converting polynomial approximations using power series into deep neural networks with optimal complexity and no approximation error. However, in practice, power series approximations are not easy to obtain due to the associated stability issue. In this paper, we propose a new and more stable way to construct RePU deep neural networks based on Chebyshev polynomial approximations. By using a hierarchical structure of Chebyshev polynomial approximation in frequency domain, we obtain efficient and stable deep neural network construction, which we call ChebNet. The approximation of smooth functions by ChebNets is no worse than the approximation by deep RePU nets using power series. On the same time, ChebNets are much more stable. Numerical results show that the constructed ChebNets can be further fine-tuned to obtain much better results than those obtained by tuning deep RePU nets constructed by power series approach. As spectral accuracy is hard to obtain by direct training of deep neural networks, ChebNets provide a practical way to obtain spectral accuracy, it is expected to be useful in real applications that require efficient approximations of smooth functions., Comment: 6 figures, 3 tables, to appear on Communications in Mathematics and Statistics