Petascale simulations of Complex Biological Behavior in Fluctuating Environments

该奖项用于临时分配 Blue Waters 计算机系统的时间（预计将于 2011 年投入运行），以及用于支持各合作者与 Blue Waters 项目团队和供应商技术团队进行技术协调的旅费。该项目涉及细菌生态学、基因调控网络和细胞内生化网络的研究，旨在了解单细胞生物种群随着环境变化而进化和适应的方式。 这涉及多尺度生物系统，其中从基因表达、细胞内生物化学到生态系统动力学等过程都在发挥作用。 一个关键目标是通过考虑细胞内的遗传和生化过程，了解单细胞生物如何进化以对其环境中反复发生的变化产生适应性反应。 该研究将着眼于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。 还将研究遗传和分子信息传递过程的作用。该建模方法已经开发出来，并且之前通过当代计算系统的实现用于科学研究。 它本质上是多尺度的，包括细胞内分子过程的表示以及扩展到单细胞生物的生态系统。 在之前的工作中，计算机能力的限制需要进行一些简化的假设。 预计 Blue Waters 的使用将使其中一些问题得到缓解，以便更多的生物过程可以包含在模拟中。 结果将根据加州大学戴维斯分校基因组中心的体内实验结果进行测试。主要研究员是最近的博士生。 该研究领域的进展可以在生物工程和生物技术中得到应用。

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.