Acquisition of Unix Computer Cluster for Molecular Dynamics Simulation Calculations

购置 Unix 计算机集群用于分子动力学模拟计算

基本信息

批准号：
10799081
负责人：
Bernard MONTGOMERY PETTITT
金额：
$ 5万
依托单位：
UNIVERSITY OF TEXAS MED BR GALVESTON
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-06-01 至 2025-05-31
项目状态：
未结题

项目摘要

PROJECT SUMMARY In response to NOT-GM-22-017, Notice of Special Interest: Administrative Supplements for Equipment Purchases for Select NIGMS-Funded Awards, we request funds to upgrade our local Unix compute cluster, which was purchased in 2012, with GPU nodes that are needed for the calculations described on the parent grant. Our parent grant aims to understand the formation of non-enveloped organelles and condensates. Many calculations of smaller size arise and are hampered by writing supercomputing proposals. The current nodes are nearly impossible to maintain due to changes in hardware compatibility. Our calculations focus on deciphering the thermodynamic manifold, enthalpic versus entropic driving forces, underlying the solubility limit and consequent phase transition associated with the formation of condensates.1 We also investigate the role of compositional/sequence dependencies and protein disorder2 on the formation and stability of these assemblies. Design of therapeutic targets that promote or inhibit formation of component proteins or nucleic acids in biomolecular condensates requires a detailed understanding of the molecular forces that drive their formation or dissolution. We will consider model mixtures relevant to cell signaling consisting of pentapeptides GGXGG, GGpXGG, and GXGXG systems, where X is serine, threonine, and tyrosine, to model the compositional dependency on condensate formation. We will also study the mitochondrial Cox17 protein where the level of disorder is controlled by physiological conditions.3 This 60 aa protein is an ideal system to test our insights from the small pentapeptide model studies.

项目摘要为了响应非GM-22-017，特别关注通知：购买精选NIGMS资助的奖项的设备购买，我们要求资金升级本地UNIX 计算群集于2012年购买，并带有计算所需的GPU节点在父母赠款中描述。我们的父母赠款旨在了解非共同的形成细胞器和冷凝物。出现了许多较小尺寸的计算，并通过写作受到阻碍超级计算提案。由于变化的变化，当前的节点几乎无法维护硬件兼容性。我们的计算重点是解密热力学歧管相对于熵驱动力，溶解度极限和随之而来的相变与冷凝水的形成相关。1我们还研究了组成/序列依赖性和蛋白质障碍2对这些形成和稳定性集会。设计促进或抑制成分蛋白质形成或生物分子冷凝物中的核酸需要对分子力的详细理解这推动了他们的形成或解散。我们将考虑与细胞信号相关的模型混合物由五肽GGXGG，GGPXGG和GXGXG系统组成，其中x是丝氨酸，苏氨酸，和酪氨酸，以建模对凝结物形成的组成依赖性。我们还将学习线粒体COX17蛋白，其中疾病水平受生理状况控制。3 该60 AA蛋白是从小型五肽模型研究中测试我们的见解的理想系统。

项目成果

期刊论文数量（90）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace.

DOI：
10.1080/08927022.2015.1110583
发表时间：
2016
期刊：
Molecular simulation
影响因子：
2.1
作者：
Zhang C;Lai CL;Pettitt BM
通讯作者：
Pettitt BM

Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide.

亲水水合和分子内相互作用在十丙氨酸肽螺旋-螺旋转变和螺旋-螺旋组装的热力学中的重要性。

DOI：
10.1021/acs.jpcb.5b09881
发表时间：
2016
期刊：
The journal of physical chemistry. B
影响因子：
0
作者：
Tomar,DheerajS;Weber,Valéry;Pettitt,BMontgomery;Asthagiri,D
通讯作者：
Asthagiri,D

Mobility of Histidine Side Chains Analyzed with 15N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions.

使用 15N NMR 弛豫和互相关数据分析组氨酸侧链的迁移率：深入了解锌指-DNA 相互作用。

DOI：
10.1021/acs.jpcb.9b03132
发表时间：
2019
期刊：
The journal of physical chemistry. B
影响因子：
0
作者：
Kemme,CatherineA;Luu,RossH;Chen,Chuanying;Pletka,ChanningC;Pettitt,BMontgomery;Iwahara,Junji
通讯作者：
Iwahara,Junji

Examining the assumptions underlying continuum-solvent models.