Acquisition of a Multi-Processor Computer for Computational Physics and Structural Biology
购买用于计算物理和结构生物学的多处理器计算机
基本信息
- 批准号:9601845
- 负责人:
- 金额:$ 31.3万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Standard Grant
- 财政年份:1996
- 资助国家:美国
- 起止时间:1996-10-01 至 1998-09-30
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Project Summary This proposal seeks funding for a new multi-processor computer for structural biology and computational physics at The Rockefeller University. Structural biologists need increasingly faster computers with memories in excess of 256 MB because of the size of data sets from X-ray crystallography, NMR spectroscopy, and electron microscopy that need to be processed and fitted by complicated models. In addition, the main subject of structural biology, understanding the relation between structure and function, frequently depends on large computer simulations such as molecular dynamics and protein structure modeling. Likewise, calculations in computational physics also require more computing power and memory than currently available in order to simulate larger systems at a higher resolution and to explore larger parameter spaces. The projects of the eleven major users include crystallographic, NMR, and electron microscopic studies of structure, dynamics and function of proteins. The proteins under study are involved in signal transduction, chromosomal replication, transcription, and transmission of signals through cell membranes. Additional work by the major users includes protein identification and characterization by mass spectrometry, simulations of protein, DNA, and chromosome structure and dynamics, and modeling of neuron function and visual cortex architecture. The researchers are currently using small workstations, many of which are more than three years old and have less than 64 MB of memory. Speed and memory of these workstations are increasingly restricting. The existing and future needs can best be met by a multi-processor computer such as the Silicon Graphics Power Challenge XL system with 12 R10000 processors and 1.25 GB of memory, which we propose to purchase. A multi-processor server computer is more suited to a small group of independent users than is a large number of client workstations because of the speed deriving from fast processors and from coarse parallelization, because memory and software can be shared among several users, and because of the savings in support and maintenance. The use of a locally located multi-processor computer is also more appropriate than the use of national supercomputer centers because of the faster and more flexible networking, sustained availability of computing power, smaller backlog, and access to local consultants. In comparison with the current equipment, the new server computer will provide a four-fold increase in computation speed and will allow effective execution of very large jobs by avoiding swapping to hard disks. The server will also free the current client workstations for their original purpose, interactive and graphical work, both of which are impeded by the large jobs running in the background. As a result, current computational bottlenecks in protein structure refinement in X-ray crystallography, NMR, and electron microscopy will be eliminated. The server will thus help in the structural determination of eukaryotic RNA polymerase system, DNA polymerase complex, E. coli RNA polymerase, voltage-gated potassium channel, Abl SH(32) dual domain, and other proteins. It will also allow many simulations that are currently out of reach. For example, NMR and molecular dynamics will be used to determine motions of protein domains and large loops on the nanosecond time scale; proteins will be identified rapidly by mass spectrometry and database searching, which will be useful in the analysis of sequences produced by genome projects; protein structure modeling by homology will be improved by simultaneous optimization of the model and the alignment, which will allow a significantly larger fraction of protein sequences determined by genome projects to be modeled with useful accuracy; molecular orbital calculations of retinal and its environment will elucidate the opsin shift mechanism in visual pigments; the experimental data on the condensation of eukaryotic chromosomes will be analyzed statistically and the models for this process will be proposed; and more realistic neural models will be solved that may result in better understanding of the function of the brain. The server will also provide graduate students and postdoctoral fellows at The Rockefeller University an opportunity to program and exploit the latest generation of mini supercomputers. This will be made easier and encouraged by the existing infrastructure for networking and consulting. In addition, the new server computer will facilitate planned recruitment of new faculty in the areas of structural biology and computational physics. And finally, it will stimulate the growing interest of all the faculty in structure-function studies in biology and in the problems at the interface between physics and biology.
项目概述这项提案寻求为洛克菲勒大学的结构生物学和计算物理的新的多处理器计算机提供资金。结构生物学家需要速度越来越快、内存超过256MB的计算机,因为来自X射线结晶学、核磁共振光谱和电子显微镜的数据集的规模需要通过复杂的模型进行处理和拟合。此外,结构生物学的主要学科,了解结构和功能之间的关系,经常依赖于大型计算机模拟,如分子动力学和蛋白质结构建模。同样,计算物理中的计算也需要比目前可用的更多的计算能力和内存,以便以更高的分辨率模拟更大的系统,并探索更大的参数空间。11个主要用户的项目包括结晶学、核磁共振和电子显微镜对蛋白质的结构、动力学和功能的研究。研究中的蛋白质涉及信号转导、染色体复制、转录和通过细胞膜传递信号。主要用户的其他工作包括通过质谱学进行蛋白质鉴定和表征,模拟蛋白质、DNA和染色体的结构和动力学,以及对神经元功能和视觉皮质结构进行建模。研究人员目前使用的是小型工作站,其中许多已有三年多的历史,内存不到MB。这些工作站的速度和内存越来越受到限制。现有和未来的需求最能满足多处理器计算机,如我们建议购买的配备12个R10000处理器和1.25 GB内存的Silicon Graphics Power ChallengeXL系统。多处理器服务器计算机比大量客户端工作站更适合于一小群独立用户,这是因为快速处理器和粗略并行所产生的速度,因为存储器和软件可以在几个用户之间共享,并且因为节省了支持和维护。使用当地的多处理器计算机也比使用国家超级计算机中心更合适,因为它的联网速度更快、更灵活,计算能力持续可用,积压的计算机更少,而且可以联系到当地的顾问。与目前的设备相比,新的服务器计算机的计算速度将提高四倍,并将通过避免更换硬盘而有效地执行非常大的任务。服务器还将释放当前的客户端工作站,用于其原始目的、交互和图形工作,这两项工作都受到后台运行的大型作业的阻碍。因此,目前在X射线结晶学、核磁共振和电子显微镜中蛋白质结构精细化的计算瓶颈将被消除。该服务器将有助于真核RNA聚合酶系统、DNA聚合酶复合体、大肠杆菌RNA聚合酶、电压门控钾通道、Abl SH(32)双域和其他蛋白质的结构测定。它还将允许许多目前无法实现的模拟。例如,核磁共振和分子动力学将被用来确定蛋白质结构域和大环在纳秒时间尺度上的运动;蛋白质将通过质谱学和数据库搜索得到快速鉴定,这将有助于基因组计划产生的序列的分析;同源性的蛋白质结构建模将通过模型和比对的同时优化得到改进,这将允许以有用的精度对由基因组计划确定的更大比例的蛋白质序列进行建模;视网膜及其环境的分子轨道计算将阐明视觉色素中的视蛋白移动机制;将对真核细胞染色体凝聚的实验数据进行统计分析,并提出这一过程的模型;并将解决更现实的神经模型,这可能会导致更好地理解大脑的功能。该服务器还将为洛克菲勒大学的研究生和博士后研究员提供一个编程和利用最新一代迷你超级计算机的机会。现有的网络和咨询基础设施将使这一点变得更容易,并得到鼓励。此外,新的服务器计算机将促进按计划征聘结构生物学和计算物理领域的新教员。最后,它将激发所有教职员工对生物学结构功能研究和物理学与生物学交界处的问题日益增长的兴趣。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Andrej Sali其他文献
Filamentous phage assembly: variation on a protein export theme.
丝状噬菌体组装:蛋白质输出主题的变体。
- DOI:
10.1016/s0378-1119(96)00801-3 - 发表时间:
1997 - 期刊:
- 影响因子:3.5
- 作者:
Marjorie Russel;N. Linderoth;Andrej Sali - 通讯作者:
Andrej Sali
The structural basis of prostaglandin efflux by MRP4
- DOI:
10.1016/j.bpj.2023.11.2429 - 发表时间:
2024-02-08 - 期刊:
- 影响因子:
- 作者:
Robert M. Stroud;Sergei Pourmal;Evan Green;Ruchika Bajaj;Ilan E. Chemmama;Giselle Knudsen;Meghna Gupta;Andrej Sali;Yifan Cheng;Charles S. Craik;Deanna Kroetz - 通讯作者:
Deanna Kroetz
Rigid-body assignment in integrative determination of protein complex structures
- DOI:
10.1016/j.bpj.2021.11.2556 - 发表时间:
2022-02-11 - 期刊:
- 影响因子:
- 作者:
Tanmoy Sanyal;Andrej Sali - 通讯作者:
Andrej Sali
Structural heterogeneity of nuclear pores in yeast
- DOI:
10.1016/j.bpj.2022.11.507 - 发表时间:
2023-02-10 - 期刊:
- 影响因子:
- 作者:
Digvijay Singh;Neelesh Soni;Ignacia Echeverria;Farhaz Shaikh;Sergey Suslov;Javier Fernandez-Martinez;Paula Upla;Steven Ludtke;Christopher W. Akey;Andrej Sali;Michael P. Rout;Elizabeth Villa - 通讯作者:
Elizabeth Villa
In-situ molecular architecture dynamism of the nuclear pore complex
- DOI:
10.1016/j.bpj.2021.11.1880 - 发表时间:
2022-02-11 - 期刊:
- 影响因子:
- 作者:
Digvijay Singh;Christopher W. Akey;Christna Ouch;Ignacia Echeverria;Ilona Nudelman;Joseph M. Varberg;Zulin Yu;James C. Gumbart;Sue L. Jaspersen;Brian T. Chait;Andrej Sali;Javier Fernandez-Martinez;Steven Ludtke;Michael P. Rout;Elizabeth Villa - 通讯作者:
Elizabeth Villa
Andrej Sali的其他文献
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{{ truncateString('Andrej Sali', 18)}}的其他基金
Collaborative Research: Creating mechanisms to make integrative structures of large macromolecular assemblies available from the Protein Data Bank
合作研究:创建机制,使蛋白质数据库中的大分子组装体的整合结构可用
- 批准号:
2112967 - 财政年份:2021
- 资助金额:
$ 31.3万 - 项目类别:
Continuing Grant
Collaborative Research: ABI Development: Building a Pipeline for Validation, Curation and Archiving of Integrative/Hybrid Models
合作研究:ABI 开发:构建集成/混合模型的验证、管理和归档管道
- 批准号:
1756250 - 财政年份:2018
- 资助金额:
$ 31.3万 - 项目类别:
Continuing Grant
Integrated modeling of biological nanomachines
生物纳米机器的集成建模
- 批准号:
0705196 - 财政年份:2007
- 资助金额:
$ 31.3万 - 项目类别:
Standard Grant
ITR: Subnanometer Structure Based Fold Determination of Biological Complex
ITR:基于亚纳米结构的生物复合物折叠测定
- 批准号:
0324645 - 财政年份:2003
- 资助金额:
$ 31.3万 - 项目类别:
Continuing Grant
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适用于混合多核/众核处理器集群的自动调整并行算法
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可重构多核处理器硬件架构和软件系统
- 批准号:
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