Literature DB >> 25067852

A conservative algorithm for parabolic problems in domains with moving boundaries.

Igor L Novak1, Boris M Slepchenko1.   

Abstract

We describe a novel conservative algorithm for parabolic problems in domains with moving boundaries developed for modeling in cell biology. The spatial discretization is accomplished by applying Voronoi decomposition to a fixed rectangular grid. In the vicinity of the boundary, the procedure generates irregular Voronoi cells that conform to the domain shape and merge seamlessly with regular control volumes in the domain interior. Consequently, our algorithm is free of the CFL stability issue due to moving interfaces and does not involve cell-merging or mass redistribution. Local mass conservation is ensured by finite-volume discretization and natural-neighbor interpolation. Numerical experiments with two-dimensional geometries demonstrate exact mass conservation and indicate an order of convergence in space between one and two. The use of standard meshing techniques makes extension of the method to three dimensions conceptually straightforward.

Entities:  

Keywords:  cell migration; exact mass conservation; moving boundaries; numerical algorithm; parabolic equations

Year:  2014        PMID: 25067852      PMCID: PMC4107334          DOI: 10.1016/j.jcp.2014.03.014

Source DB:  PubMed          Journal:  J Comput Phys        ISSN: 0021-9991            Impact factor:   3.553


  20 in total

1.  Form and function in cell motility: from fibroblasts to keratocytes.

Authors:  Marc Herant; Micah Dembo
Journal:  Biophys J       Date:  2010-04-21       Impact factor: 4.033

2.  A Simple 1-D Physical Model for the Crawling Nematode Sperm Cell.

Authors:  A Mogilner; D W Verzi
Journal:  J Stat Phys       Date:  2003-03-01       Impact factor: 1.548

3.  MULTISCALE TWO-DIMENSIONAL MODELING OF A MOTILE SIMPLE-SHAPED CELL.

Authors:  B Rubinstein; K Jacobson; A Mogilner
Journal:  Multiscale Model Simul       Date:  2005       Impact factor: 1.930

Review 4.  Mechanical forces and feedbacks in cell motility.

Authors:  Enas Abu Shah; Kinneret Keren
Journal:  Curr Opin Cell Biol       Date:  2013-07-13       Impact factor: 8.382

5.  Diffusion on a Curved Surface Coupled to Diffusion in the Volume: Application to Cell Biology.

Authors:  Igor L Novak; Fei Gao; Yung-Sze Choi; Diana Resasco; James C Schaff; Boris M Slepchenko
Journal:  J Comput Phys       Date:  2007-10-01       Impact factor: 3.553

Review 6.  Mathematics of cell motility: have we got its number?

Authors:  Alex Mogilner
Journal:  J Math Biol       Date:  2008-05-07       Impact factor: 2.259

7.  A general computational framework for modeling cellular structure and function.

Authors:  J Schaff; C C Fink; B Slepchenko; J H Carson; L M Loew
Journal:  Biophys J       Date:  1997-09       Impact factor: 4.033

8.  Numerical studies of unreactive contractile networks.

Authors:  M Dembo; M Maltrud; F Harlow
Journal:  Biophys J       Date:  1986-07       Impact factor: 4.033

9.  Cell motion, contractile networks, and the physics of interpenetrating reactive flow.

Authors:  M Dembo; F Harlow
Journal:  Biophys J       Date:  1986-07       Impact factor: 4.033

Review 10.  How nematode sperm crawl.

Authors:  Dean Bottino; Alexander Mogilner; Tom Roberts; Murray Stewart; George Oster
Journal:  J Cell Sci       Date:  2002-01-15       Impact factor: 5.285

View more
  4 in total

1.  A biochemo-mechano coupled, computational model combining membrane transport and pericellular proteolysis in tissue mechanics.

Authors:  A-T Vuong; A D Rauch; W A Wall
Journal:  Proc Math Phys Eng Sci       Date:  2017-03-08       Impact factor: 2.704

2.  Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.

Authors:  M E Johnson; A Chen; J R Faeder; P Henning; I I Moraru; M Meier-Schellersheim; R F Murphy; T Prüstel; J A Theriot; A M Uhrmacher
Journal:  Mol Biol Cell       Date:  2020-11-25       Impact factor: 4.138

3.  A free-boundary model of a motile cell explains turning behavior.

Authors:  Masoud Nickaeen; Igor L Novak; Stephanie Pulford; Aaron Rumack; Jamie Brandon; Boris M Slepchenko; Alex Mogilner
Journal:  PLoS Comput Biol       Date:  2017-11-14       Impact factor: 4.475

Review 4.  A Review of Cell-Based Computational Modeling in Cancer Biology.

Authors:  John Metzcar; Yafei Wang; Randy Heiland; Paul Macklin
Journal:  JCO Clin Cancer Inform       Date:  2019-02
  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.