Journal of Computational Physics: X最新文献

A computational model of self-organized shape dynamics of active surfaces in fluids 流体中活性表面自组织形状动力学的计算模型

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-04-28 DOI: 10.1016/j.jcpx.2023.100126

Lucas D. Wittwer , Sebastian Aland

{"title":"A computational model of self-organized shape dynamics of active surfaces in fluids","authors":"Lucas D. Wittwer , Sebastian Aland","doi":"10.1016/j.jcpx.2023.100126","DOIUrl":"https://doi.org/10.1016/j.jcpx.2023.100126","url":null,"abstract":"<div><p>Mechanochemical processes on surfaces such as the cellular cortex or epithelial sheets, play a key role in determining patterns and shape changes of biological systems. To understand the complex interplay of hydrodynamics and material flows on such active surfaces requires novel numerical tools. Here, we present a finite-element method for an active deformable surface interacting with the surrounding fluids. The underlying model couples surface and bulk hydrodynamics to surface flow of a diffusible species which generates active contractile forces. The method is validated with previous results based on linear stability analysis and shows almost perfect agreement regarding predicted patterning. Away from the linear regime we find rich non-linear behavior, such as the presence of multiple stationary states. We study the formation of a contractile ring on the surface and the corresponding shape changes. Finally, we explore mechanochemical pattern formation on various surface geometries and find that patterning strongly adapts to local surface curvature. The developed method provides a basis to analyze a variety of systems that involve mechanochemical pattern formation on active surfaces interacting with surrounding fluids.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"17 ","pages":"Article 100126"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50191203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Corrected ALE-ISPH with novel Neumann boundary condition and density-based particle shifting technique 用新的Neumann边界条件和基于密度的粒子移位技术校正ALE-ISPH

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-03-15 DOI: 10.1016/j.jcpx.2023.100125

Daniel Shigueo Morikawa , Kumpei Tsuji , Mitsuteru Asai

{"title":"Corrected ALE-ISPH with novel Neumann boundary condition and density-based particle shifting technique","authors":"Daniel Shigueo Morikawa , Kumpei Tsuji , Mitsuteru Asai","doi":"10.1016/j.jcpx.2023.100125","DOIUrl":"https://doi.org/10.1016/j.jcpx.2023.100125","url":null,"abstract":"<div><p>It is well-known in the Smoothed Particle Hydrodynamics (SPH) community that correction in the gradient and Laplacian operators have the potential to drastically increase the accuracy of the method at the expense of computational stability. This paper proposes a stable implementation of such corrections in all derivative operators to the Arbitrary Lagrangian Eulerian incompressible SPH (ALE-ISPH) method, in addition to a novel Neumann boundary condition (BC) applied directly on the velocity (as opposed to traditional BCs where the constraint is applied on the acceleration). In this way, the pressure is solved for both water and wall particles simultaneously, leading to a pressure field that obeys non-penetration BC and divergence-free at the same time. Furthermore, to stabilize the method, we have developed a novel density-based particle shifting technique (PST), specifically designed to deal with incompressible fluids. In this formulation, the numerical density is given as one of the most critical constraint variables. As a result, the proposed density-based PST can maintain the fluid's overall volume for the whole simulation. In addition, it also provides numerical stability as it prevents particle clustering and leads the fluid domain to an isotropic composition. First, we verified the proposed corrected formulation with the novel Neumann BC for both non-penetration and non-slip conditions with the simulation of hydrostatic pressure and Poisenuille flow, respectively. Then, we tested the proposed density-based PST with the rotating square patch problem with results comparable to previous studies. Lastly, we verified the proposed method for the dam break with an obstacle test, a highly dynamic problem.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"17 ","pages":"Article 100125"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50191215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Relative acceleration of orthonormal basis vectors for the geometric conduction blocks of the cardiac electric signal propagation on anisotropic curved surfaces 各向异性曲面上心电信号几何传导块正交基向量的相对加速度

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-11-10 DOI: 10.1016/j.jcpx.2023.100135

Sehun Chun

{"title":"Relative acceleration of orthonormal basis vectors for the geometric conduction blocks of the cardiac electric signal propagation on anisotropic curved surfaces","authors":"Sehun Chun","doi":"10.1016/j.jcpx.2023.100135","DOIUrl":"10.1016/j.jcpx.2023.100135","url":null,"abstract":"<div><p>Geometric conduction blocks stop cardiac electric propagation due to the shape or conductivity properties of the domain. The blocks are considered to cause many abnormal cardiac electric propagations, leading to cardiac electrophysiological pathologies, such as cardiac fibrillation and arrhythmia. Locating such multidimensional conduction blocks is challenging, particularly in a complex domain with a complex shape and strong anisotropy, such as the heart. To address this problem, we propose a novel mathematical model of the geometric conduction block using the relative acceleration adopted from space-time physics. An efficient numerical scheme for the mathematical model is also proposed to predict the unidirectional conduction block effectively, even in a complex domain. The relative acceleration in the cardiac electric propagation corresponds to the sink-source relationship between the excited (after repolarization) and excitable (before depolarization) cardiac cells, representing the geometric growth rate of the volume of metric balls. The trajectory is constructed from the wavefront of diffusion-reaction equations by aligning orthonormal basis vectors along the gradient of the action potential. Relative acceleration is computed along the propagational direction from the connection 1-form of the basis vectors. The proposed mathematical model and numerical scheme are applied to demonstrate geometric conduction blocks in two-dimensional (2D) simple curved domains with strong anisotropy.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"17 ","pages":"Article 100135"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590055223000136/pdfft?md5=ab2847b27f86f9bb7689e05fdaa1d88d&pid=1-s2.0-S2590055223000136-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135566404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Natural grid stretching for DNS of compressible wall-bounded flows 可压缩壁有界流DNS的自然网格拉伸

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-05-30 DOI: 10.1016/j.jcpx.2023.100128

Alessandro Ceci, Sergio Pirozzoli

引用次数: 0

Fast hierarchical low-rank view factor matrices for thermal irradiance on planetary surfaces 行星表面热辐照度的快速分层低阶视图因子矩阵

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-07-22 DOI: 10.1016/j.jcpx.2023.100130

Samuel F. Potter , Stefano Bertone , Norbert Schörghofer , Erwan Mazarico

{"title":"Fast hierarchical low-rank view factor matrices for thermal irradiance on planetary surfaces","authors":"Samuel F. Potter , Stefano Bertone , Norbert Schörghofer , Erwan Mazarico","doi":"10.1016/j.jcpx.2023.100130","DOIUrl":"https://doi.org/10.1016/j.jcpx.2023.100130","url":null,"abstract":"<div><p>We present an algorithm for compressing the radiosity view factor model commonly used in radiation heat transfer and computer graphics. We use a format inspired by the hierarchical off-diagonal low rank format, where elements are recursively partitioned using a quadtree or octree and blocks are compressed using a sparse singular value decomposition—the hierarchical matrix is assembled using dynamic programming. The motivating application is time-dependent thermal modeling on vast planetary surfaces, with a focus on permanently shadowed craters which receive energy through indirect irradiance. In this setting, shape models are comprised of a large number of triangular facets which conform to a rough surface. At each time step, a quadratic number of triangle-to-triangle scattered fluxes must be summed; that is, as the sun moves through the sky, we must solve the same view factor system of equations for a potentially unlimited number of time-varying righthand sides. We first conduct numerical experiments with a synthetic spherical cap-shaped crater, where the equilibrium temperature is analytically available. We also test our implementation with triangle meshes of planetary surfaces derived from digital elevation models recovered by orbiting spacecraft. Our results indicate that the compressed view factor matrix can be assembled in quadratic time, which is comparable to the time it takes to assemble the full view matrix itself. Memory requirements during assembly are reduced by a large factor. Finally, for a range of compression tolerances, the size of the compressed view factor matrix and the speed of the resulting matrix vector product both scale linearly (as opposed to quadratically for the full matrix), resulting in orders of magnitude savings in processing time and memory space.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"17 ","pages":"Article 100130"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50191210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Monte Carlo radiative transfer peel off mechanism for spatially extended detectors 空间扩展探测器的蒙特卡罗辐射传递剥离机制

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-10-29 DOI: 10.1016/j.jcpx.2023.100132

Christian Peest, Oliver Reich, Lena Bressel

引用次数: 0

Ensemble transport smoothing. Part I: Unified framework 集合输运平滑。第一部分:统一框架

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-11-13 DOI: 10.1016/j.jcpx.2023.100134

Maximilian Ramgraber , Ricardo Baptista , Dennis McLaughlin , Youssef Marzouk

{"title":"Ensemble transport smoothing. Part I: Unified framework","authors":"Maximilian Ramgraber , Ricardo Baptista , Dennis McLaughlin , Youssef Marzouk","doi":"10.1016/j.jcpx.2023.100134","DOIUrl":"10.1016/j.jcpx.2023.100134","url":null,"abstract":"<div><p>Smoothers are algorithms for Bayesian time series re-analysis. Most operational smoothers rely either on affine Kalman-type transformations or on sequential importance sampling. These strategies occupy opposite ends of a spectrum that trades computational efficiency and scalability for statistical generality and consistency: non-Gaussianity renders affine Kalman updates inconsistent with the true Bayesian solution, while the ensemble size required for successful importance sampling can be prohibitive. This paper revisits the smoothing problem from the perspective of measure transport, which offers the prospect of consistent prior-to-posterior transformations for Bayesian inference. We leverage this capacity by proposing a general ensemble framework for transport-based smoothing. Within this framework, we derive a comprehensive set of smoothing recursions based on nonlinear transport maps and detail how they exploit the structure of state-space models in fully non-Gaussian settings. We also describe how many standard Kalman-type smoothing algorithms emerge as special cases of our framework. A companion paper <span>[35]</span> explores the implementation of nonlinear ensemble transport smoothers in greater depth.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"17 ","pages":"Article 100134"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590055223000124/pdfft?md5=5628d601649f468d0e56d36b3987da03&pid=1-s2.0-S2590055223000124-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135714752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Ensemble transport smoothing. Part II: Nonlinear updates 整体传输平滑。第二部分:非线性更新

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-11-14 DOI: 10.1016/j.jcpx.2023.100133

Maximilian Ramgraber , Ricardo Baptista , Dennis McLaughlin , Youssef Marzouk

引用次数: 3

Numerical simulation of temperature-driven free surface flows, with application to laser melting and polishing 温度驱动自由表面流动的数值模拟及其在激光熔化和抛光中的应用

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-06-01 DOI: 10.1016/j.jcpx.2023.100127

Alexandre Caboussat , Julien Hess , Alexandre Masserey , Marco Picasso

引用次数: 2

Numerical simulations of the nonlinear quantum vacuum in the Heisenberg-Euler weak-field expansion 海森堡-欧拉弱场展开中非线性量子真空的数值模拟

Journal of Computational Physics: X Pub Date : 2023-11-01 Epub Date: 2023-01-13 DOI: 10.1016/j.jcpx.2023.100124

Andreas Lindner, Baris Ölmez, Hartmut Ruhl

引用次数: 2