Coupling vs decoupling approaches for PDE/ODE systems modeling intercellular signaling

被引:5
作者
Carraro, Thomas [1 ]
Friedmann, Elfriede [1 ]
Gerecht, Daniel [1 ]
机构
[1] Heidelberg Univ, Inst Appl Math, INF 293-294, D-69120 Heidelberg, Germany
关键词
Coupled PDE/ODE systems; Sensitivity analysis; Multilevel preconditioner; Intercellular signaling; MESH INDEPENDENCE; BLOOD; FLOW;
D O I
10.1016/j.jcp.2016.03.020
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
We consider PDE/ODE systems for the simulation of intercellular signaling in multicellular environments. The intracellular processes for each cell described here by ODEs determine the long-time dynamics, but the PDE part dominates the solving effort. Thus, it is not clear if commonly used decoupling methods can outperform a coupling approach. Based on a sensitivity analysis, we present a systematic comparison between coupling and decoupling approaches for this class of problems and show numerical results. For biologically relevant configurations of the model, our quantitative study shows that a coupling approach performs much better than a decoupling one. (C) 2016 Elsevier Inc. All rights reserved.
引用
收藏
页码:522 / 537
页数:16
相关论文
共 39 条
[1]   APPLICATION OF THE MESH INDEPENDENCE PRINCIPLE TO MESH REFINEMENT STRATEGIES [J].
ALLGOWER, EL ;
BOHMER, K .
SIAM JOURNAL ON NUMERICAL ANALYSIS, 1987, 24 (06) :1335-1351
[2]  
[Anonymous], 1978, STUDIES MATH ITS APP
[3]  
[Anonymous], 1993, MULTIGRID METHODS
[4]  
Bangerth W., ARCH NUMERICAL SOFTW
[5]  
BRANDT A, 1977, MATH COMPUT, V31, P333, DOI 10.1090/S0025-5718-1977-0431719-X
[6]   Competing feedback loops shape IL-2 signaling between helper and regulatory T lymphocytes in cellular microenvironments [J].
Busse, Dorothea ;
de la Rosa, Maurus ;
Hobiger, Kirstin ;
Thurley, Kevin ;
Flossdorf, Michael ;
Scheffold, Alexander ;
Hoefer, Thomas .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (07) :3058-3063
[7]   Non-linear additive Schwarz preconditioners and application in computational fluid dynamics [J].
Cai, XC ;
Keyes, DE ;
Marcinkowski, L .
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, 2002, 40 (12) :1463-1470
[8]   On the computational efficiency and implementation of block-iterative algorithms for nonlinear coupled problems [J].
Cervera, M ;
Codina, R ;
Galindo, M .
ENGINEERING COMPUTATIONS, 1996, 13 (06) :4-&
[9]  
[COllaborative VIsualization and Simulation Environment (COVISE) HLRS High Performance Computing Center Stuttgart], COLLABORATIVE VISUAL
[10]   Algorithm 832: UMFPACK V4.3 - An unsymmetric-pattern multifrontal method [J].
Davis, TA .
ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE, 2004, 30 (02) :196-199