Multiscale Modeling & Simulation最新文献_第3页

Pattern Formation of a Pathway-Based Diffusion Model: Linear Stability Analysis and an Asymptotic Preserving Method 基于路径的扩散模型的模式形成:线性稳定性分析和渐近保持方法

4区数学

Multiscale Modeling & Simulation Pub Date : 2023-03-15 DOI: 10.1137/22m1490958

Yaming Zhang, Ning Jiang, Jiangyan Liang, Yi-Long Luo, Min Tang

引用次数: 0

A Fast Butterfly-Compressed Hadamard–Babich Integrator for High-Frequency Helmholtz Equations in Inhomogeneous Media with Arbitrary Sources 非齐次介质中高频Helmholtz方程的快速蝴蝶压缩Hadamard-Babich积分器

4区数学

Multiscale Modeling & Simulation Pub Date : 2023-02-25 DOI: 10.1137/21m1450422

Yang Liu, Jian Song, Robert Burridge, Jianliang Qian

{"title":"A Fast Butterfly-Compressed Hadamard–Babich Integrator for High-Frequency Helmholtz Equations in Inhomogeneous Media with Arbitrary Sources","authors":"Yang Liu, Jian Song, Robert Burridge, Jianliang Qian","doi":"10.1137/21m1450422","DOIUrl":"https://doi.org/10.1137/21m1450422","url":null,"abstract":"We present a butterfly-compressed representation of the Hadamard–Babich (HB) ansatz for the Green’s function of the high-frequency Helmholtz equation in smooth inhomogeneous media. For a computational domain discretized with discretization cells, the proposed algorithm first solves and tabulates the phase and HB coefficients via eikonal and transport equations with observation points and point sources located at the Chebyshev nodes using a set of much coarser computation grids, and then butterfly compresses the resulting HB interactions from all cell centers to each other. The overall CPU time and memory requirement scale as for any bounded two-dimensional (2D) domains with arbitrary excitation sources. A direct extension of this scheme to bounded 3D domains yields an CPU complexity, which can be further reduced to quasi-linear complexities with proposed remedies. The scheme can also efficiently handle scattering problems involving inclusions in inhomogeneous media. Although the current construction of our HB integrator does not accommodate caustics, the resulting HB integrator itself can be applied to certain sources, such as concave-shaped sources, to produce caustic effects. Compared to finite-difference frequency domain methods, the proposed HB integrator is free of numerical dispersion and requires fewer discretization points per wavelength. As a result, it can solve wave propagation problems well beyond the capability of existing solvers. Remarkably, the proposed scheme can accurately model wave propagation in 2D domains with 640 wavelengths per direction and in 3D domains with 54 wavelengths per direction on a state-of-the-art supercomputer at Lawrence Berkeley National Laboratory.","PeriodicalId":49791,"journal":{"name":"Multiscale Modeling & Simulation","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136080825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

OPTIMIZING WEIGHTED ENSEMBLE SAMPLING OF STEADY STATES. 优化稳定状态的加权集合采样。

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2020-01-01 Epub Date: 2020-05-06 DOI: 10.1137/18m1212100

David Aristoff, Daniel M Zuckerman

引用次数: 0

A MATHEMATICAL MODEL OF PLATELET AGGREGATION IN AN EXTRAVASCULAR INJURY UNDER FLOW. 流下血管外损伤中血小板聚集的数学模型。

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2020-01-01 Epub Date: 2020-11-18 DOI: 10.1137/20m1317785

Kathryn G Link, Matthew G Sorrells, Nicholas A Danes, Keith B Neeves, Karin Leiderman, Aaron L Fogelson

{"title":"A MATHEMATICAL MODEL OF PLATELET AGGREGATION IN AN EXTRAVASCULAR INJURY UNDER FLOW.","authors":"Kathryn G Link, Matthew G Sorrells, Nicholas A Danes, Keith B Neeves, Karin Leiderman, Aaron L Fogelson","doi":"10.1137/20m1317785","DOIUrl":"10.1137/20m1317785","url":null,"abstract":"We present the first mathematical model of flow-mediated primary hemostasis in an extravascular injury which can track the process from initial deposition to occlusion. The model consists of a system of ordinary differential equations (ODEs) that describe platelet aggregation (adhesion and cohesion), soluble-agonist-dependent platelet activation, and the flow of blood through the injury. The formation of platelet aggregates increases resistance to flow through the injury, which is modeled using the Stokes-Brinkman equations. Data from analogous experimental (microfluidic flow) and partial differential equation models informed parameter values used in the ODE model description of platelet adhesion, cohesion, and activation. This model predicts injury occlusion under a range of flow and platelet activation conditions. Simulations testing the effects of shear and activation rates resulted in delayed occlusion and aggregate heterogeneity. These results validate our hypothesis that flow-mediated dilution of activating chemical adenosine diphosphate hinders aggregate development. This novel modeling framework can be extended to include more mechanisms of platelet activation as well as the addition of the biochemical reactions of coagulation, resulting in a computationally efficient high throughput screening tool of primary and secondary hemostasis.","PeriodicalId":49791,"journal":{"name":"Multiscale Modeling & Simulation","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8051825/pdf/nihms-1681040.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38817792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational model of electrode-induced microenvironmental effects on pH measurements near a cell membrane. 电极诱导微环境对细胞膜附近pH值测量影响的计算模型。

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2020-01-01 Epub Date: 2020-05-28 DOI: 10.1137/19m1262875

D Calvetti, J Prezioso, R Occhipinti, W F Boron, E Somersalo

{"title":"Computational model of electrode-induced microenvironmental effects on pH measurements near a cell membrane.","authors":"D Calvetti, J Prezioso, R Occhipinti, W F Boron, E Somersalo","doi":"10.1137/19m1262875","DOIUrl":"https://doi.org/10.1137/19m1262875","url":null,"abstract":"The mechanism of gas transport across cell membranes remains a topic of considerable interest, particularly regarding the extent to which lipids vs. specific membrane proteins provide conduction pathways. Studies of transmembrane (CO2) transport often rely on data collected under controlled conditions, using pH-sensitive microelectrodes at the extracellular surface to record changes due to extracellular CO2 diffusion and reactions. Although recent detailed computational models can predict a qualitatively correct behavior, a mismatch between the dynamical ranges of the predicted and observed pH curves raises the question whether the discrepancy may be due to a bias introduced by the pH electrode itself. More specifically, it is reasonable to ask whether bringing the electrode tip near or in contact with the membrane creates a local microenvironment between the electrode tip and the membrane, so that the measured data refer to the microenvironment rather than to the free surface. Here, we introduce a detailed computational model, designed to address this question. We find that, as long as a zone of free diffusion exists between the tip and the membrane, the microenvironment behaves effectively as the free membrane. However, according to our model, when the tip contacts the membrane, partial quenching of extracellular diffusion by the electrode rim leads to a significant increase in the pH dynamics under the electrode, matching values measured in physiological experiments. The computational schemes for the model predictions are based on semi-discretization by a finite-element method, and an implicit-explicit time integration scheme to capture the different time scales of the system.","PeriodicalId":49791,"journal":{"name":"Multiscale Modeling & Simulation","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1137/19m1262875","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39363587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

RIGID GRAPH COMPRESSION: MOTIF-BASED RIGIDITY ANALYSIS FOR DISORDERED FIBER NETWORKS. 刚性图压缩:无序光纤网络的基于图案的刚性分析。

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2018-01-01 Epub Date: 2018-08-21 DOI: 10.1137/17M1157271

Samuel Heroy, Dane Taylor, F Bill Shi, M Gregory Forest, Peter J Mucha

{"title":"RIGID GRAPH COMPRESSION: MOTIF-BASED RIGIDITY ANALYSIS FOR DISORDERED FIBER NETWORKS.","authors":"Samuel Heroy, Dane Taylor, F Bill Shi, M Gregory Forest, Peter J Mucha","doi":"10.1137/17M1157271","DOIUrl":"https://doi.org/10.1137/17M1157271","url":null,"abstract":"Using particle-scale models to accurately describe property enhancements and phase transitions in macroscopic behavior is a major engineering challenge in composite materials science. To address some of these challenges, we use the graph theoretic property of rigidity to model mechanical reinforcement in composites with stiff rod-like particles. We develop an efficient algorithmic approach called rigid graph compression (RGC) to describe the transition from floppy to rigid in disordered fiber networks (\"rod-hinge systems\"), which form the reinforcing phase in many composite systems. To establish RGC on a firm theoretical foundation, we adapt rigidity matroid theory to identify primitive topological network motifs that serve as rules for composing interacting rigid particles into larger rigid components. This approach is computationally efficient and stable, because RGC requires only topological information about rod interactions (encoded by a sparse unweighted network) rather than geometrical details such as rod locations or pairwise distances (as required in rigidity matroid theory). We conduct numerical experiments on simulated two-dimensional rod-hinge systems to demonstrate that RGC closely approximates the rigidity percolation threshold for such systems, through comparison with the pebble game algorithm (which is exact in two dimensions). Importantly, whereas the pebble game is derived from Laman's condition and is only valid in two dimensions, the RGC approach naturally extends to higher dimensions.","PeriodicalId":49791,"journal":{"name":"Multiscale Modeling & Simulation","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1137/17M1157271","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36693127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

EIGENVECTOR-BASED CENTRALITY MEASURES FOR TEMPORAL NETWORKS^. 基于特征向量的时间网络中心性测度。

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2017-01-01 Epub Date: 2017-03-28 DOI: 10.1137/16M1066142

Dane Taylor, Sean A Myers, Aaron Clauset, Mason A Porter, Peter J Mucha

{"title":"EIGENVECTOR-BASED CENTRALITY MEASURES FOR TEMPORAL NETWORKS.","authors":"Dane Taylor, Sean A Myers, Aaron Clauset, Mason A Porter, Peter J Mucha","doi":"10.1137/16M1066142","DOIUrl":"https://doi.org/10.1137/16M1066142","url":null,"abstract":"Numerous centrality measures have been developed to quantify the importances of nodes in time-independent networks, and many of them can be expressed as the leading eigenvector of some matrix. With the increasing availability of network data that changes in time, it is important to extend such eigenvector-based centrality measures to time-dependent networks. In this paper, we introduce a principled generalization of network centrality measures that is valid for any eigenvector-based centrality. We consider a temporal network with N nodes as a sequence of T layers that describe the network during different time windows, and we couple centrality matrices for the layers into a supra-centrality matrix of size NT × NT whose dominant eigenvector gives the centrality of each node i at each time t. We refer to this eigenvector and its components as a joint centrality, as it reflects the importances of both the node i and the time layer t. We also introduce the concepts of marginal and conditional centralities, which facilitate the study of centrality trajectories over time. We find that the strength of coupling between layers is important for determining multiscale properties of centrality, such as localization phenomena and the time scale of centrality changes. In the strong-coupling regime, we derive expressions for time-averaged centralities, which are given by the zeroth-order terms of a singular perturbation expansion. We also study first-order terms to obtain first-order-mover scores, which concisely describe the magnitude of nodes' centrality changes over time. As examples, we apply our method to three empirical temporal networks: the United States Ph.D. exchange in mathematics, costarring relationships among top-billed actors during the Golden Age of Hollywood, and citations of decisions from the United States Supreme Court.","PeriodicalId":49791,"journal":{"name":"Multiscale Modeling & Simulation","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1137/16M1066142","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35522511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 152

A Non-Markovian Phase Space Approach to Schroźdinger Dynamics Schroźdinger动力学的非马尔可夫相空间方法

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2016-01-01 DOI: 10.1137/15M101899X

Joseź Luis Loźpez, J. Soler

引用次数: 1

The Random Schroźdinger Equation 随机Schroźdinger方程

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2016-01-01 DOI: 10.1137/15M1024986

Yu Gu, L. Ryzhik

引用次数: 3

MESOSCOPIC MODELING OF STOCHASTIC REACTION-DIFFUSION KINETICS IN THE SUBDIFFUSIVE REGIME. 亚扩散状态下随机反应扩散动力学的介观模拟。

IF 1.6 4区数学

Multiscale Modeling & Simulation Pub Date : 2016-01-01 Epub Date: 2016-05-03 DOI: 10.1137/15M1013110

Emilie Blanc, Stefan Engblom, Andreas Hellander, Per Lötstedt

引用次数: 9