WHOLE CELL SIMULATION

全细胞模拟

• 批准号: 8363668
• 负责人: Zaida Luthey-Schulten
• 金额: $ 4.97万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2012-09-09
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363668
• 关键词: Architecture; Bacteria; Bioinformatics; Cell Cycle; Cell model; Cells; Collaborations; Computer software; Crowding; Data; Development; Diffusion; Equation; Escherichia coli; Fluorescence; Funding; Gene Expression; Grant; Heterogeneity; Institutes; Microbe; Modeling; Names; National Center for Research Resources; Principal Investigator; Process; Reaction; Research; Research Infrastructure; Research Personnel; Resources; Source; Study models; Time; United States National Institutes of Health; base; cost; in vivo; reconstruction; research study; simulation; simulation software; single molecule; three-dimensional modeling; tomography

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].

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其他NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， NCRR赠款不直接向子项目或子项目工作人员提供资金。 资源已开始开发一个新的软件包，以进行有效的模拟。 反应-扩散主方程的一部分，名为“晶格微生物”。发展 专注于优化全细胞模型模拟的软件 包括近似的体内拥挤。通过使用图形处理 单元（GPU），我们已经能够扩展模拟大小和时间的规模 细胞和细胞周期。新软件将允许计算生物学家 利用目前正在收集的有关蜂窝结构的数据， 实验，如冷冻电子断层扫描（CET）和单分子，电子束 荧光。与Julio Ortiz和Wolfgang Baumeister合作， 在马丁斯里德的马克斯·普朗克研究所，资源研究人员使用单细胞 以CET重建为基础，建立了一个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， 在细菌中的表达[1]。