Arjunan Satya N V, Takahashi Koichi
Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan.
Methods Mol Biol. 2017;1611:219-236. doi: 10.1007/978-1-4939-7015-5_16.
As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle simulator for biochemical reaction and diffusion processes. Simulations can be performed at single molecule and compartment spatial scales simultaneously. Molecules can diffuse and react in 1D (filament), 2D (membrane), and 3D (cytosol) compartments. The implications of crowded regions in the cell can be investigated because each diffusing molecule has spatial dimensions. Spatiocyte adopts multi-algorithm and multi-timescale frameworks to simulate models that simultaneously employ deterministic, stochastic, and particle reaction-diffusion algorithms. Comparison of light microscopy images to simulation snapshots is supported by Spatiocyte microscopy visualization and molecule tagging features. Spatiocyte is open-source software and is freely available at http://spatiocyte.org .
随着定量生物学家对细胞分裂和极化等空间调控系统的测量越来越多，利用这些数据对蛋白质的反应和扩散进行模拟，对于揭示这些系统背后的机制变得越来越重要。Spatiocyte是一种基于晶格的用于生化反应和扩散过程的随机粒子模拟器。模拟可以在单分子和区室空间尺度上同时进行。分子可以在一维（细丝）、二维（膜）和三维（胞质溶胶）区室中扩散和反应。由于每个扩散分子都具有空间维度，因此可以研究细胞中拥挤区域的影响。Spatiocyte采用多算法和多时间尺度框架来模拟同时采用确定性、随机性和粒子反应扩散算法的模型。Spatiocyte的显微镜可视化和分子标记功能支持将光学显微镜图像与模拟快照进行比较。Spatiocyte是开源软件，可从http://spatiocyte.org免费获取。
