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1. Fast and Accuracy-Preserving Domain Decomposition Methods for Reduced Fracture Models with Nonconforming Time Grids

   https://doi.org/10.1007/s10915-023-02251-0  

   Huynh, Phuoc-Toan ; Cao, Yanzhao ; Hoang, Thi-Thao-Phuong ( July 2023 , Journal of Scientific Computing)

   This paper is concerned with the numerical solution of compressible fluid flow in a fractured porous medium. The fracture represents a fast pathway (i.e., with high permeability) and is modeled as a hypersurface embedded in the porous medium. We aim to develop fast-convergent and accurate global-in-time domain decomposition (DD) methods for such a reduced fracture model, in which smaller time step sizes in the fracture can be coupled with larger time step sizes in the subdomains. Using the pressure continuity equation and the tangential PDEs in the fracture-interface as transmission conditions, three different DD formulations are derived; each method leads to a space-time interface problem which is solved iteratively and globally in time. Efficient preconditioners are designed to accelerate the convergence of the iterative methods while preserving the accuracy in time with nonconforming grids. Numerical results for two-dimensional problems with non-immersed and partially immersed fractures are presented to show the improved performance of the proposed methods. 

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2. Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints

   https://doi.org/10.1093/bioinformatics/bty446  

   Chan, Siu H. J. ; Wang, Lin ; Dash, Satyakam ; Maranas, Costas D. ; Wren, ed., Jonathan ( June 2018 , Bioinformatics)

   Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models.

   We aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10–150 compared to the original loopless constraints and by 4–20 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35 h to less than 2 h for a model with more than104 reactions.

   Matlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA

   Supplementary data are available at Bioinformatics online.

    

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3. Coupled and decoupled stabilized mixed finite element methods for nonstationary dual‐porosity‐Stokes fluid flow model

   https://doi.org/10.1002/nme.6158  

   Al Mahbub, Md. Abdullah ; He, Xiaoming ; Nasu, Nasrin Jahan ; Qiu, Changxin ; Zheng, Haibiao ( July 2019 , International Journal for Numerical Methods in Engineering)

   In this paper, we propose and analyze two stabilized mixed finite element methods for the dual‐porosity‐Stokes model, which couples the free flow region and microfracture‐matrix system through four interface conditions on an interface. The first stabilized mixed finite element method is a coupled method in the traditional format. Based on the idea of partitioned time stepping, the four interface conditions, and the mass exchange terms in the dual‐porosity model, the second stabilized mixed finite element method is decoupled in two levels and allows a noniterative splitting of the coupled problem into three subproblems. Due to their superior conservation properties and convenience of the computation of flux, mixed finite element methods have been widely developed for different types of subsurface flow problems in porous media. For the mixed finite element methods developed in this article, no Lagrange multiplier is used, but an interface stabilization term with a penalty parameter is added in the temporal discretization. This stabilization term ensures the numerical stability of both the coupled and decoupled schemes. The stability and the convergence analysis are carried out for both the coupled and decoupled schemes. Three numerical experiments are provided to demonstrate the accuracy, efficiency, and applicability of the proposed methods.

    

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4. A discontinuous Galerkin method for sequences of earthquakes and aseismic slip on multiple faults using unstructured curvilinear grids

   https://doi.org/10.1093/gji/ggac467  

   Uphoff, Carsten ; May, Dave A ; Gabriel, Alice-Agnes ( November 2022 , Geophysical Journal International)

   SUMMARY Physics-based simulations provide a path to overcome the lack of observational data hampering a holistic understanding of earthquake faulting and crustal deformation across the vastly varying space–time scales governing the seismic cycle. However, simulations of sequences of earthquakes and aseismic slip (SEAS) including the complex geometries and heterogeneities of the subsurface are challenging. We present a symmetric interior penalty discontinuous Galerkin (SIPG) method to perform SEAS simulations accounting for the aforementioned challenges. Due to the discontinuous nature of the approximation, the spatial discretization natively provides a means to impose boundary and interface conditions. The method accommodates 2-D and 3-D domains, is of arbitrary order, handles subelement variations in material properties and supports isoparametric elements, that is, high-order representations of the exterior boundaries, interior material interfaces and embedded faults. We provide an open-source reference implementation, Tandem, that utilizes highly efficient kernels for evaluating the SIPG linear and bilinear forms, is inherently parallel and well suited to perform high-resolution simulations on large-scale distributed memory architectures. Additional flexibility and efficiency is provided by optionally defining the displacement evaluation via a discrete Green’s function approach, exploiting advantages of both the boundary integral and volumetric methods. The optional discrete Green’s functions are evaluated once in a pre-computation stage using algorithmically optimal and scalable sparse parallel solvers and pre-conditioners. We illustrate the characteristics of the SIPG formulation via an extensive suite of verification problems (analytic, manufactured and code comparison) for elastostatic and quasi-dynamic problems. Our verification suite demonstrates that high-order convergence of the discrete solution can be achieved in space and time and highlights the benefits of using a high-order representation of the displacement, material properties and geometries. We apply Tandem to realistic demonstration models consisting of a 2-D SEAS multifault scenario on a shallowly dipping normal fault with four curved splay faults, and a 3-D intersecting multifault scenario of elastostatic instantaneous displacement of the 2019 Ridgecrest, CA, earthquake sequence. We exploit the curvilinear geometry representation in both application examples and elucidate the importance of accurate stress (or displacement gradient) representation on-fault. This study entails several methodological novelties. We derive a sharp bound on the smallest value of the SIPG penalty ensuring stability for isotropic, elastic materials; define a new flux to incorporate embedded faults in a standard SIPG scheme; employ a hybrid multilevel pre-conditioner for the discrete elasticity problem; and demonstrate that curvilinear elements are specifically beneficial for volumetric SEAS simulations. We show that our method can be applied for solving interesting geophysical problems using massively parallel computing. Finally, this is the first time a discontinuous Galerkin method is published for the numerical simulations of SEAS, opening new avenues to pursue extreme scale 3-D SEAS simulations in the future. 

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5. The Impact of Climate Change on Ocean Submesoscale Activity

   https://doi.org/10.1029/2020JC016750  

   Richards, K. J. ; Whitt, D. B. ; Brett, G. ; Bryan, F. O. ; Feloy, K. ; Long, M. C. ( April 2021 , Journal of Geophysical Research: Oceans)

   Global warming may modify submesoscale activity in the ocean through changes in the mixed layer depth (MLD) and lateral buoyancy gradients. As a case study we consider a region in the NE Atlantic under present and future climate conditions, using a time‐slice method and global and nested regional ocean models. The high resolution regional model reproduces the strong seasonal cycle in submesoscale activity observed under present‐day conditions. Focusing on the well‐resolved winter months, in the future, with a reduction in the MLD, there is a substantial reduction in submesoscale activity, an associated decrease in kinetic energy (KE) at the mesoscale, and the vertical buoyancy flux induced by submesoscale activity is reduced by a factor of 2. When submesoscale activity is suppressed, by increasing the parameterized lateral mixing in the model, the climate change induces a larger reduction in winter MLDs while there is less of a change in KE at the mesoscale. A scaling for the vertical buoyancy flux proposed by (Fox‐Kemper et al., 2008; doi:10.1175/2007JPO3792.1) based on the properties of mixed layer instability (MLI), is found to capture much of the seasonal and future changes to the flux in terms of regional averages as well as the spatial structure, although it over predicts the reduction in the flux in the winter months. The vertical buoyancy flux when the mixed layer is relatively shallow is significantly greater than that given by the scaling based on MLI, suggesting during these times other processes (besides MLI) may dominate submesoscale buoyancy fluxes.

    

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