WHOLE CELL SIMULATION

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 该资源已经开始开发新的软件包，以实现高效的模拟 反应扩散主方程，命名为“晶格微生物”。发展 专注于优化全细胞模型的模拟软件 包括近似的活体拥挤。通过使用图形处理 单位(GPU)我们能够将模拟大小和时间扩展到 细胞和细胞周期。新软件将允许计算生物学家 充分利用有关蜂窝架构的数据 低温电子断层扫描(CET)和单分子、单细胞等实验 荧光。与胡里奥·奥尔蒂斯和沃尔夫冈·鲍迈斯特合作 马丁斯里德的马克斯·普朗克研究所的资源研究人员使用了单细胞 CET重建作为建立E。 Coli细胞。利用这个模型，他们研究了空间异质性对基因的影响。 在细菌中表达[1]。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The Resource has begun development of a new software package for efficient simulation of the reaction-diffusion master equation, named "Lattice Microbes". Development is focused on optimizing the software for the simulation of whole-cell models including approximated in vivo crowding. Through the use of graphics processing units (GPUs) we have been able to extend simulation sizes and times to the scale of cells and cell cycles. The new software will allow computational biologists to take advantage of data regarding the cellular architecture now being collected from experiments such as cryoelectron tomography (CET) and single-molecule, singlecell fluorescence. In collaboration with Julio Ortiz and Wolfgang Baumeister at the Max Planck Institute in Martinsreid, Resource researchers have used single-cell CET reconstructions as the basis for building a three-dimensional model of an E. coli cell. Using this model they studied the effect of spatial heterogeneity on gene expression in bacteria [1].