Abstract

FZJ-2025-01064

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Dynamic collagen matrix model for tissue simulations on distributed memory systems

Brinkmeier, P. (Corresponding author) ; Herold, J. M. ; Behle, E.FZJ* ; Schug, A. H.FZJ*

2024

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Please use a persistent id in citations: doi:10.1016/j.bpj.2023.11.1732

Abstract: Recent research suggests that the extracellular matrix (ECM) has a significant influence on the development of cancer. However, most computational models of cancer pay little attention to the mechanical properties of the ECM. We introduce an elastic lattice model (ELM) as an extension to the cellular Potts model (CPM) and employ the Zener model of viscoelasticity to simulate the ECM. To seamlessly integrate the ELM with the CPM, we propose a flexible formalization of their interactions. The choice of the ELM is motivated by its reliance on local particle interactions, allowing us to implement it efficiently as a stencil code within cells in silico (CiS), our massively parallel CPM implementation. We conduct extensive computational experiments on both CPUs and GPUs, evaluating factors such as execution time, memory usage, and scalability. Finally, we assess the model’s utility by attempting to replicate experimental findings, thereby demonstrating its potential in advancing our understanding of cancer development and the ECM’s crucial role.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)

Research Program(s):

1. 5111 - Domain-Specific Simulation & Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) (POF4-511)

Appears in the scientific report 2024

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Database coverage:
; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; Essential Science Indicators ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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