Cell Scale Code

(Updated on 2013/2/4)

RICS Cell simulation integrated platform.
ID：C-1
Principal developer

Hideo YOKOTA, Team Leader, CSRP, RIKEN

General description

The code treats the intracellular biochemical reactions, the substance diffusion by the concentration gradient, and membrane functions (channel, pump, receptor), and those are coupled to solve the cell behaviors

Computational model

A coupled analysis of biochemical reaction, diffusion, and membrane function using the regular orthogonal grid (voxel)

Computational method
  • Finite difference method (spatial approximation)
  • Finite volume method (time integration)
  • Ordinary differential simultaneous equation (biochemical reaction)
Parallelization

SPHERE (MPI)

Required language and library

Fortran, C, C++, Sphere, E-Cell (Boost,GSL)

Status of code for public release

Source code is available through ISLIM download site.

Maximum computing size in present experiences
  • The number of voxels: 10243 (RICC's 8192 cores, 103 sec)
  • Required memory/disk storage: 2.6 TB/400 TB
Expected computing size in K computer
  • A multicell model (60 cells, 220 substances, 190 reactions)
  • The number of voxels: 20003 (640,000 cores)
  • Required memory/disk storage: 570 TB/3500 PB
Platypus-MM/CGイメージ

Figure 1. RICS input data. It is derived from a microscope image of a real HepG2 cell. (Blue: nucleus, green: mitochondria, red: cell shape）

What does the code enable?
  • A detailed simulation of a single cell, considering the complicated cell shape and the internal structure (organelle)
  • A multicell or tissue simulation considering the shape
  • Comparison and evaluation of the simulation results with experimental results, such as for intracellular substance, since the simulation's input data is given from the real shape data like a microscope image.