CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions

Pranav Madhikar; Jan Åström; Jan Westerholm; Mikko Karttunen

doi:10.1016/j.cpc.2018.05.024

CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions

Pranav Madhikar, Jan Åström, Jan Westerholm, Mikko Karttunen

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Abstract

We present a new open source software package CellSim3D for computer simulations of mechanical aspects (that is, biochemical details are not accounted for) of cell division in three dimensions. It is also possible to use the software in the mode with cell division and growth turned off which allows for simulations of soft colloidal matter. The code is based on a previously introduced two dimensional mechanical model for cell division which is extended to full 3D. CellSim3D is written in C/C++ and CUDA and allows for simulations of 100,000 cells using standard desktop computers.

Original language	Undefined/Unknown
Pages (from-to)	206–213
Journal	Computer Physics Communications
Volume	232
DOIs	https://doi.org/10.1016/j.cpc.2018.05.024
Publication status	Published - 2018
MoE publication type	A1 Journal article-refereed

Access to Document

10.1016/j.cpc.2018.05.024

cell_paper-cpc-revision-may-2018-final.pdfAccepted author manuscript, 3.72 MBLicence: CC BY-NC-ND

http://urn.fi/URN:NBN:fi-fe2020100882493

Cite this

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title = "CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions",

abstract = "We present a new open source software package CellSim3D for computer simulations of mechanical aspects (that is, biochemical details are not accounted for) of cell division in three dimensions. It is also possible to use the software in the mode with cell division and growth turned off which allows for simulations of soft colloidal matter. The code is based on a previously introduced two dimensional mechanical model for cell division which is extended to full 3D. CellSim3D is written in C/C++ and CUDA and allows for simulations of 100,000 cells using standard desktop computers.",

author = "Pranav Madhikar and Jan {\AA}str{\"o}m and Jan Westerholm and Mikko Karttunen",

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journal = "Computer Physics Communications",

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T1 - CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions

AU - Madhikar, Pranav

AU - Åström, Jan

AU - Westerholm, Jan

AU - Karttunen, Mikko

PY - 2018

Y1 - 2018

N2 - We present a new open source software package CellSim3D for computer simulations of mechanical aspects (that is, biochemical details are not accounted for) of cell division in three dimensions. It is also possible to use the software in the mode with cell division and growth turned off which allows for simulations of soft colloidal matter. The code is based on a previously introduced two dimensional mechanical model for cell division which is extended to full 3D. CellSim3D is written in C/C++ and CUDA and allows for simulations of 100,000 cells using standard desktop computers.

AB - We present a new open source software package CellSim3D for computer simulations of mechanical aspects (that is, biochemical details are not accounted for) of cell division in three dimensions. It is also possible to use the software in the mode with cell division and growth turned off which allows for simulations of soft colloidal matter. The code is based on a previously introduced two dimensional mechanical model for cell division which is extended to full 3D. CellSim3D is written in C/C++ and CUDA and allows for simulations of 100,000 cells using standard desktop computers.

U2 - 10.1016/j.cpc.2018.05.024

DO - 10.1016/j.cpc.2018.05.024

M3 - Artikel

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JO - Computer Physics Communications

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