Acquisition of a Computer System for Biophysical and Computational Chemistry

获取生物物理和计算化学计算机系统

基本信息

  • 批准号:
    9601851
  • 负责人:
  • 金额:
    $ 23.78万
  • 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:
    1996-08-01 至 2001-06-30
  • 项目状态:
    已结题

项目摘要

Funding is requested to purchase a multi-processor computer based on the RISC architecture to replace the Convex C220. The projects for which the requested equipment will be used include: Computer Simulations of Solvated Proteins and Liquids (R.M. Levy), Computer Simulations of Double Helical DNA (W.K. Olson), Biomolecular Structure and Interactions (H. M. Berman), Potential Surfaces for Internal Rotation in Conjugated Molecules (L. Goodman), Medium Effects in Electronic Structure Calculations (K. Krogh-Jespersen), NMR Structure Determination and Protein Folding (J. Baum), and Structure and Interactions of Macromolecular Complexes (M. Georgiadis). The need for the RISC based multi-processor is based on the computationally intensive nature of these projects, and the need for the visualization of the computed results concerning complex biomolecular systems. Rutgers University is internationally recognized for the strength of its research program in Biophysical Chemistry. A central theme connecting the investigators participating in this proposal is that of "Biomolecular Structure and Dynamics". The complexity and sheer size of biological macromolecules makes the analysis of the structural and dynamic features in these systems computationally intensive. This is true for the theoretical studies including molecular modeling using computer graphics, computer simulations of biomolecules in solution and quantum chemical calculations of electronic properties of biomolecules and conjugated molecules. This is also true of the experimental techniques that are represented in the proposal: macromolecular x-ray crystallography and NMR spectroscopy. The individual projects carried out by the coinvestigators all involve very large scale computations. The shared computational facilities for molecular biophysics and computational chemistry are housed primarily within the chemistry department. The backbone of the computational resources for biophysical chemistry is the Convex C220 dual processor. In 1986 a Convex Cl uniprocessor was purchased with funding from a National Institutes of Health Shared Instrumentation Grant. In 1989, with funding provided by an instrumentation grant from the National Science Foundation and by Rutgers University, the Convex was upgraded to a dual processor C220. At the time of its purchase, the vector architecture of the Convex was quite remarkable, providing 10-50 times the performance gains over the DEC VAX 780 hardware which it replaced. In the context of today's computing environment, with the availability of RISC computer workstations, the performance of the Convex is much less impressive. At present, perhaps the only remaining remarkable attributes of the Convex are its sheer physical size, its power requirements, and exhorbitant maintenance costs. We propose to replace the Convex C220 with a multi-processor RISC computer system. A final choice of vendor will be made after competitive evaluations of alternative RISC systems is carried out after the grant award. Possible vendors include Silicon Graphics, Hewlett Packard, IBM and DEC. At this time, we are seriously considering the Silicon Graphics Power Onyx primarily because of its cost effective floating point performance, but also because of its graphics features. Our proposed budget is based on the purchase of an SGI Power Onyx system with eight R8000 90 Mhz processors, 2 GByte high density memory, Reality Engine graphics hardware, and 64 GBytes of magnetic disk storage.
要求提供资金以购买一台基于RISC结构的多处理器计算机,以取代Convex C220。 将使用所要求的设备的项目包括:溶剂化蛋白质和液体的计算机模拟(R.M. Levy),Computer Simulations of Double Helical DNA(W.K. Olson),Biomolecular Structure and Interactions(H. M. Berman),Potential Surfaces for Internal Rotation in Conjugated Molecules(L. 电子结构计算中的介质效应(K. Krogh-Jespersen)、NMR结构测定和蛋白质折叠(J. Baum)以及大分子复合物的结构和相互作用 (M. Georgiadis)。 的必要性 RISC 基于多处理器是基于这些项目的计算密集型的性质,以及对有关复杂生物分子系统的计算结果的可视化的需要。 罗格斯大学因其生物物理化学研究项目的实力而受到国际认可。 一个中心主题连接参与这项建议的研究人员是“生物分子结构和动力学”。 生物大分子的复杂性和庞大的规模使得分析这些系统中的结构和动力学特征的计算密集型。 这是真实的理论研究,包括分子建模,使用计算机图形学,计算机模拟的生物分子在溶液中和量子化学计算的电子性质的生物分子和共轭分子。这也是真实的实验技术,是代表在建议:大分子x射线 晶体学和NMR光谱学。 由共同研究者进行的各个项目都涉及非常大规模的计算。 分子生物物理学和计算化学的共享计算设施主要位于 化学系。生物物理化学计算资源的支柱是Convex C220双处理器。 1986年,在美国国立卫生研究院共享仪器赠款的资助下购买了一台Convex Cl单处理器。 1989年,在美国国家科学基金会和罗格斯大学的仪器资助下,Convex升级为双处理器C220。在购买时,Convex的矢量架构非常出色,与它所取代的DEC VAX 780硬件相比,性能提高了10-50倍。在当今的计算环境中,随着RISC计算机工作站的可用性,Convex的性能大大提高。 不那么令人印象深刻。 目前,也许凸形的唯一剩下的显着属性是它纯粹的物理尺寸,它的功率要求,以及令人信服的维护成本。 我们建议用多处理器RISC计算机系统取代Convex C220。供应商的最终选择将在赠款授予后对替代RISC系统进行竞争性评估后作出。可能的供应商包括Silicon Graphics、Hewlett Packard、IBM和DEC。目前,我们正在认真考虑Silicon Graphics Power Onyx,主要是因为其具有成本效益的浮点性能,但也因为其图形功能。我们提出的预算是基于购买一个SGI Power Onyx系统,该系统配备8个R8000 90 Mhz处理器、2 GB高密度内存、Reality Engine图形硬件和64 Gbit磁盘存储。

项目成果

期刊论文数量(0)
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Ronald Levy其他文献

Co-Occurrence of Clonally Related Follicular Lymphoma and Histiocytic Sarcoma
  • DOI:
    10.1182/blood-2023-189712
  • 发表时间:
    2023-11-02
  • 期刊:
  • 影响因子:
  • 作者:
    Sarah Haebe;Debra K. Czerwinski;Anuja Sathe;Susan Grimes;Tianqi Chen;Brock Martin;Hanlee Ji;Ronald Levy;Tanaya Shree
  • 通讯作者:
    Tanaya Shree
The immediate post-exercise ventriculogram: A scintigraphic tool for the pre-operative assessment of reversible myocardial asynergy
  • DOI:
    10.1016/0002-9149(81)90769-4
  • 发表时间:
    1981-02-01
  • 期刊:
  • 影响因子:
  • 作者:
    Alan Rozanski;Daniel Berman;Ronald Levy;Richard Gray;Marjorie Raymond;Jamshid Maddahi;James Forrester;Alan Waxman;H.J.C. Swan;Jack Matloff
  • 通讯作者:
    Jack Matloff
Monoclonal Immunoglobulin Rescue From a Patient With Chronic Lymphocytic Leukemia and Autoimmune Hemolytic Anemia
  • DOI:
    10.1182/blood.v54.2.513.513
  • 发表时间:
    1979-08-01
  • 期刊:
  • 影响因子:
  • 作者:
    Karol Sikora;John Krikorian;Ronald Levy
  • 通讯作者:
    Ronald Levy
One minute multiple gated equilibrium scintigraphy for assessment of left ventricular ejection fraction and segmental wall motion: Validation with state of the art instrumentation and optimized space-time smoothing
  • DOI:
    10.1016/0002-9149(81)90891-2
  • 发表时间:
    1981-02-01
  • 期刊:
  • 影响因子:
  • 作者:
    Ronald Levy;Alan Rozanski;David Brown;Ken Van Train;Ernest Garcia;Nancy Pantaleo;Jamshid Maddahi;Alan Waxman;Daniel Berman
  • 通讯作者:
    Daniel Berman
Activating Immune Effectors and Dampening Immune Suppressors Generates Successful Therapeutic Cancer Vaccination in Patients with Lymphoma
  • DOI:
    10.1182/blood-2022-167469
  • 发表时间:
    2022-11-15
  • 期刊:
  • 影响因子:
  • 作者:
    Tanaya Shree;Sarah Haebe;Debra K. Czerwinski;Erik Eckhert;Grady Day;Anuja Sathe;Susan M. Grimes;Matthew J Frank;Lauren S. Maeda;Ash A. Alizadeh;Ranjana H. Advani;Richard Hoppe;Steven R. Long;Brock Martin;Michael G. Ozawa;Michael S. Khodadoust;Hanlee P. Ji;Ronald Levy
  • 通讯作者:
    Ronald Levy

Ronald Levy的其他文献

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{{ truncateString('Ronald Levy', 18)}}的其他基金

CDS&E: Adaptive Biomolecular Free Energy Simulations on Massive Computational Grids
CDS
  • 批准号:
    1665032
  • 财政年份:
    2017
  • 资助金额:
    $ 23.78万
  • 项目类别:
    Continuing Grant
U.S.-Japan Cooperative Science: Theoretical and Experimental Studies of Aqueous Solutions Under Extreme Conditions
美日合作科学:极端条件下水溶液的理论与实验研究
  • 批准号:
    9815256
  • 财政年份:
    1999
  • 资助金额:
    $ 23.78万
  • 项目类别:
    Standard Grant
Computer System for Biophysical Chemistry
生物物理化学计算机系统
  • 批准号:
    8820760
  • 财政年份:
    1989
  • 资助金额:
    $ 23.78万
  • 项目类别:
    Standard Grant
Dynamics of Peptides and Proteins
肽和蛋白质的动力学
  • 批准号:
    8519866
  • 财政年份:
    1985
  • 资助金额:
    $ 23.78万
  • 项目类别:
    Standard Grant
Acquisition of a Computer System for Biophysical and Quantum Chemistry
获取生物物理和量子化学计算机系统
  • 批准号:
    8306023
  • 财政年份:
    1983
  • 资助金额:
    $ 23.78万
  • 项目类别:
    Standard Grant

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