clustervoronoicode
This is an addition to the cellGPU code which adds a concertation gradient which alters the cells' mechanical properties.
https://github.com/manning-research-group/clustervoronoicode
Science Score: 28.0%
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Low similarity (6.3%) to scientific vocabulary
Repository
This is an addition to the cellGPU code which adds a concertation gradient which alters the cells' mechanical properties.
Basic Info
- Host: GitHub
- Owner: Manning-Research-Group
- License: other
- Language: C++
- Default Branch: main
- Size: 16.5 MB
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- Stars: 0
- Watchers: 0
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Concentration gradient inside cellGPU
This work adds a dynamically updating biochemical signaling gradient to the cellGPU code which was created and maintained by Daniel Sussman. The original open-source code is found at https://github.com/sussmanLab/cellGPU. The paper describing this code in more detail can currently be found on the arXiv (https://arxiv.org/abs/1702.02939), or in print (http://www.sciencedirect.com/science/article/pii/S0010465517301832). While this addition uses the cellGPU code as a base the new additions are not currently able to be used on a GPU.
The signal gradient is a scalar field superimposed on top of the Voronoi model. This field is divided into a grid which evolves according to the advection-diffusion equation using the central finite difference method. At each time step, the cells will calculate a signal strength by taking the average concentration of each gridpoint within their cell walls. Then this can be coupled to any of the cell mechanical properties. The paper describing the gradient in more detail can be found on arXiv at (arxiv link once we have it).
Additions and alterations to the cellGPU code
The primary additions to the code are the following:
Main: voronoi_cluster.cpp
Model: voronoiQuadraticEnergyWithConc.cpp / voronoiQuadraticEnergyWithConc.h
Updater: gradientinteractions.cpp / gradientinteractions.h
Database: DatabaseNetCDFSPVConc.cpp / DatabaseNetCDFSPVConc.h
With minor changes to the following:
Simple2DModel.h
Simple2DActiveCell.cpp
Simple2DCell.cpp / Simple2DCell.h
voronoiModelBase.cpp / voronoiModelBase.h
Owner
- Name: Manning-Research-Group
- Login: Manning-Research-Group
- Kind: organization
- Repositories: 1
- Profile: https://github.com/Manning-Research-Group
Citation (CITATIONS.md)
# Citations for ConcGrad cellGPU {#cite}
If you use this code for a publication or project, please cite our paper and the main cellGPU paper:
(1) "Collective chemotaxis in a Voronoi model for confluent clusters" Elizabeth Lawson-Keister and M. Lisa Manning, (arXiv link)
(2) "cellGPU: massively parallel simulations of dynamic vertex models" Daniel M. Sussman; Computer Physics Communications, volume 219, pages 400-406, (2017)
Here are some additional citation to consider, according to what parts of the code you use and your
taste on how much to cite:
(3) Chen and Gotsman ''Localizing the delaunay triangulation and its parallel implementation,''
[Transactions on Computational Science XX (M. L. Gavrilova, C.J.K. Tan, and B. Kalantari, eds.),Lecture Notes in Computer Science, vol. 8110, Springer Berlin Heidelberg, 2013, Extended abstract in ISVD 2012, pp. 24–31, pp. 39–55 (English)]
The local ''test-and-repair'' part of the code used in the SPV branch is parallelized using an idea
from this paper. In particular, it points out a locality condition for the Delaunay neighborhood of a given point
(Given a polygon formed by other vertices that encloses the target point, the possible set of Delaunay
neighbors of the target point are those points contained in any of the circumcircles that can be
formed by that point and consecutive vertices of the polygon).
(4) CGAL,Computational Geometry Algorithms Library, http://www.cgal.org
The default triangulation library, used in the Voronoi branch of the code
(5) paulbourke.net/papers/triangulate (Pan-Pacific Computer Conference, Beijing, China)
Staying on the "Delaunay" branch, there are two underlying routines for computing full Delaunay
triangulation of non-periodic and periodoc point sets. In default operation of the code, the
routines called are all part of the CGAL library, and that should be cited. In less-ideal operations
the user can call a naive $(O(N^{1.5}))$ Bowyer-Watson algorithm based off of the Paul Bourke Triangulate
code: paulbourke.net/papers/triangulate (Pan-Pacific Computer Conference, Beijing, China). This is
never used by the code if you do not explicitly invoke it in the DelaunayLoc class.
(6) [E. Bitzek et al. Phys. Rev. Lett. 97, 170201 (2006)](http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.97.170201)
One of the energy minimizer uses a straightforward implementation of the FIRE minimization algorithm,
which is described in the above paper.
(7) [G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein; Mol. Phys. 87, 1117 (1996)](http://www.tandfonline.com/doi/abs/10.1080/00268979600100761)
The NoseHooverChainNVT class integrates the Nose-Hoover equations of motion with a chain of thermostats,
and does so using an update scheme that is explicitly time-reversible. The algorithm to do this is
described in Martyna et al., (see also the nice algorithmic pseudo-code in the Frenkel & Smit textbook)
(8) [J. Ramirez, S. K. Sukumaran, B. Vorselaars, and A. E. Likhtman; J. Chem. Phys. 133, 154103 (2010)](http://aip.scitation.org/doi/abs/10.1063/1.3491098)
The "autocorrelator" class in the analysis tools section is entirely based around this Ramirez et al. paper.
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