Petascale simulations of Complex Biological Behavior in Fluctuating Environments

波动环境中复杂生物行为的千万亿次模拟

• 批准号: 0941360
• 负责人: Ilias Tagkopoulos
• 金额: $ 4万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-10-01 至 2014-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0941360&HistoricalAwards=false
• 关键词: Petascale; simulations; Complex; Biological; Behavior

This award is for a provisional allocation of time on the Blue Waters computer system, due to become operational in 2011, and for travel funds to support technical coordination by various collaborators with the Blue Waters project team and vendor technical team.The project involves studies in bacterial ecology, gene regulatory networks and intracellular biochemical networks with a view to understanding the way in which populations of unicellular organisms evolve and adapt as their environment changes. This involves multi-scale biological systems where processes ranging from gene expression and intracellular biochemistry to ecosystem dynamics are in play. A key aim is to understand how, by considering the genetic and biochemical processes within a cell, unicellular organisms evolve to develop adaptive responses to recurring changes in their environments. The study will look at the influence of parameters such as nutrient concentrations and mutation on adaptation, compare the efficacy of different strategies for survival in static and fluctuating environments, and examine how unicellular organisms internalize the correlation structure of their environment by modifying their internal networks to facilitate such changes. The role of genetic and molecular information transfer processes will also be studied.The modeling approach has been developed and previously used for scientific research using an implementation on contemporary computing systems. It is inherently multi-scale, including representations of molecular processes within cells and scaling up to ecosystems of unicellular organisms. In prior work, the limitations of computer power have necessitated a number of simplifying assumptions. It is anticipated that the use of Blue Waters will allow some of these to be relaxed, so that more biological processes can be included in the simulations. Results will be tested against the outcomes of in vivo experiments in the UC Davis Genome Center.The principal investigator is a recent Ph.D. Progress in this research area could find application in bioengineering and biotechnology.

该合同是为定于2011年投入运行的蓝色沃茨计算机系统临时分配的时间，以及为支持各合作者与蓝色沃茨项目小组和供应商技术小组进行技术协调提供的差旅费。基因调控网络和细胞内生物化学网络，以了解单细胞生物种群进化和适应的方式，环境变化。 这涉及多尺度生物系统，其中从基因表达和细胞内生物化学到生态系统动力学的过程都在发挥作用。 一个关键的目标是了解如何通过考虑细胞内的遗传和生物化学过程，单细胞生物进化以发展适应性反应，以应对环境中的反复变化。 该研究将研究营养浓度和突变等参数对适应的影响，比较静态和波动环境中不同生存策略的功效，并研究单细胞生物如何通过修改其内部网络来促进这种变化，从而内化其环境的相关结构。 遗传和分子信息传递过程的作用也将被研究。建模方法已经开发出来，以前用于科学研究，使用当代计算系统的实现。 它本质上是多尺度的，包括细胞内的分子过程的表示和单细胞生物生态系统的放大。 在以前的工作中，计算机能力的限制需要一些简化的假设。 预计使用蓝色沃茨将使其中一些得以放松，以便更多的生物过程可以包括在模拟中。 研究结果将与加州大学戴维斯分校基因组中心的体内实验结果进行对比。 这一研究领域的进展可以应用于生物工程和生物技术。