The Computational Microscope

本提案是关于预定于2011年投入运行的蓝色沃茨计算机系统的临时时间分配，以及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的差旅费。病毒感染、细胞内膜的形态发生和光合色素。 这些生物过程的作用随着时间的推移而展开，很难用晶体学来跟踪这种演变。 分子动力学模拟将为这些过程的演变提供深入的见解。计划中的脊髓灰质炎病毒研究工作包括使用数值模拟来研究脊髓灰质炎病毒进入细胞过程中原子水平的变化。 据认为，这将是一类病毒，无包膜RNA病毒，包括疾病如甲型肝炎，普通感冒和病毒性脑膜炎的代理人的这一过程的代表。 对蛋白质如何塑造细胞内膜的计划研究将为细胞器和囊泡形成的一个重要方面提供见解。 光合作用的研究涉及紫色细菌中色素细胞的研究，这是一个涉及200多种蛋白质的系统，也是能够模拟细胞器的沿着一步。 这将使研究人员能够确定醌类化合物与远距离蛋白质偶联时的统计学首选路线，以及光生电势在驱动ATP合成和细胞运输时如何传播。这项工作中使用的分子模拟代码将广泛提供，为化学，生物化学和材料研究领域的其他研究人员提供工具。 博士后研究人员和研究生将大量参与申请拨款的项目。 这项工作的结果应该在医学和生物工程中有用。

This proposal 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 molecular dynamics simulations of three cellular systems and processes: viral infection, morphogenesis of intra-cellular membranes, and the photosynthetic chromatophore. The actions of these biological processes unfold in time and it is difficult to follow such evolution with crystallography. Molecular dynamics simulations will provide insights into the evolution of these processes.Planned work with the poliovirus involves the use of numerical simulation to study the changes at the atomic level that are responsible for the process by which a poliovirus enters a cell. It is thought that this will be representative of this process for a class of viruses, the non-enveloped RNA viruses, that include the agents of diseases such as hepatitis A, the common cold, and viral meningitis. The planned studies of how proteins shape intracellular membranes will provide insights into an important aspect of organelle and vesicle formation. The work on photosynthesis involves studies of the chromatophore in purple bacteria, a system involving over 200 proteins and a step along the route of being able to model an organelle. This will allow researchers to determine the statistically preferred routes for quinones as they couple distant proteins, and how the light-generated electrical potential spreads as it drives ATP synthesis and cellular transport.The molecular simulation codes used in this work will be made widely available, providing tools for other researchers in the chemistry, biochemistry and materials research communities. There will be substantial involvement of post-doctoral researchers and graduate students in the projects for which the allocation is requested. The results of the work should be of use in medicine and bio-engineering.