Literature DB >> 24427530

Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations.

D Groen1, J Borgdorff2, C Bona-Casas2, J Hetherington1, R W Nash1, S J Zasada1, I Saverchenko3, M Mamonski4, K Kurowski4, M O Bernabeu1, A G Hoekstra2, P V Coveney1.   

Abstract

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from laptops to petascale supercomputers, including combinations of these. Our work features two multiscale applications, in-stent restenosis and cerebrovascular bloodflow, which combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1-10% of the total execution time.

Entities:  

Keywords:  blood flow; cerebrovascular bloodflow; distributed computing; high performance computing; in-stent restenosis; multiscale modelling

Year:  2013        PMID: 24427530      PMCID: PMC3638484          DOI: 10.1098/rsfs.2012.0087

Source DB:  PubMed          Journal:  Interface Focus        ISSN: 2042-8898            Impact factor:   3.906


  18 in total

Review 1.  Modeling the heart--from genes to cells to the whole organ.

Authors:  Denis Noble
Journal:  Science       Date:  2002-03-01       Impact factor: 47.728

2.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

Review 3.  Computational modeling of vascular anastomoses.

Authors:  Francesco Migliavacca; Gabriele Dubini
Journal:  Biomech Model Mechanobiol       Date:  2005-03-17

4.  The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery.

Authors:  D J W Evans; P V Lawford; J Gunn; D Walker; D R Hose; R H Smallwood; B Chopard; M Krafczyk; J Bernsdorf; A Hoekstra
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2008-09-28       Impact factor: 4.226

Review 5.  Multi-scale modelling in computational biomedicine.

Authors:  Peter M A Sloot; Alfons G Hoekstra
Journal:  Brief Bioinform       Date:  2009-12-22       Impact factor: 11.622

6.  Choice of boundary condition for lattice-Boltzmann simulation of moderate-Reynolds-number flow in complex domains.

Authors:  Rupert W Nash; Hywel B Carver; Miguel O Bernabeu; James Hetherington; Derek Groen; Timm Krüger; Peter V Coveney
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2014-02-18

7.  Percutaneous and surgical interventions for in-stent restenosis: long-term outcomes and effect of diabetes mellitus.

Authors:  A Moustapha; A R Assali; S Sdringola; W K Vaughn; R D Fish; O Rosales; G Schroth; Z Krajcer; R W Smalling; H V Anderson
Journal:  J Am Coll Cardiol       Date:  2001-06-01       Impact factor: 24.094

Review 8.  Restenosis after PCI. Part 1: pathophysiology and risk factors.

Authors:  J Wouter Jukema; Jeffrey J W Verschuren; Tarek A N Ahmed; Paul H A Quax
Journal:  Nat Rev Cardiol       Date:  2011-09-13       Impact factor: 32.419

9.  Long-term outcome after coronary stenting.

Authors:  Adnan Kastrati; Donald Hall; Albert Schömig
Journal:  Curr Control Trials Cardiovasc Med       Date:  2000

10.  Systems biology and the virtual physiological human.

Authors:  Peter Kohl; Denis Noble
Journal:  Mol Syst Biol       Date:  2009-07-28       Impact factor: 11.429

View more
  7 in total

1.  A framework for multi-scale modelling.

Authors:  B Chopard; Joris Borgdorff; A G Hoekstra
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2014-08-06       Impact factor: 4.226

Review 2.  Systems Modeling to Quantify Safety Risks in Early Drug Development: Using Bifurcation Analysis and Agent-Based Modeling as Examples.

Authors:  Carmen Pin; Teresa Collins; Megan Gibbs; Holly Kimko
Journal:  AAPS J       Date:  2021-05-20       Impact factor: 4.009

3.  Evaluating a common semi-mechanistic mathematical model of gene-regulatory networks.

Authors:  Alexandru Mizeranschi; Huiru Zheng; Paul Thompson; Werner Dubitzky
Journal:  BMC Syst Biol       Date:  2015-09-01

4.  Performance of distributed multiscale simulations.

Authors:  J Borgdorff; M Ben Belgacem; C Bona-Casas; L Fazendeiro; D Groen; O Hoenen; A Mizeranschi; J L Suter; D Coster; P V Coveney; W Dubitzky; A G Hoekstra; P Strand; B Chopard
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2014-08-06       Impact factor: 4.226

5.  A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data.

Authors:  Pavel S Zun; Tatiana Anikina; Andrew Svitenkov; Alfons G Hoekstra
Journal:  Front Physiol       Date:  2017-05-23       Impact factor: 4.566

6.  Impact of blood rheology on wall shear stress in a model of the middle cerebral artery.

Authors:  Miguel O Bernabeu; Rupert W Nash; Derek Groen; Hywel B Carver; James Hetherington; Timm Krüger; Peter V Coveney
Journal:  Interface Focus       Date:  2013-04-06       Impact factor: 3.906

7.  Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface.

Authors:  Alfons G Hoekstra; Saad Alowayyed; Eric Lorenz; Natalia Melnikova; Lampros Mountrakis; Britt van Rooij; Andrew Svitenkov; Gábor Závodszky; Pavel Zun
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-11-13       Impact factor: 4.226

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.