CAREER: Programmable Assembly of Glycine-Rich Peptides on a Graphitic Surface

职业：在石墨表面上可编程组装富含甘氨酸的肽

• 批准号: 1945589
• 负责人: Jeffrey Comer
• 金额: $ 56.59万
• 依托单位: Kansas State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-04-15 至 2025-03-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1945589&HistoricalAwards=false
• 关键词: CAREER; Programmable; Assembly; Glycine; Rich

NONTECHNICAL SUMMARYThis CAREER award supports theoretical research, computer simulations, and validating experiments to design molecules that can be programmed to arrange themselves into complex devices. A modern smartphone that fits in a pocket has more computing power than a hefty laptop of 20 years ago, while also including a digital camera, GPS, and the ability to make wireless calls. The miniaturization of devices has been so successful that the size of some components is growing close to the size of molecules and atoms, requiring big changes in how devices are built. It is as if building sandcastles has given way to building tiny castles out of individual grains of sand. While making devices from individual molecules may be difficult, it can be done; living things make thousands of different proteins with single-atom precision, each performing a different function while often arranging themselves into larger, more complex structures.The goal of this project is to design protein-like molecules that are similarly able to arrange themselves, but in a way that can be easily programmed by a human engineer. To make imaging and design of the devices easier, the project is focused on molecules that arrange themselves on top of an atomically flat graphene surface. The research team will use computer simulations to optimize control over the arrangement, checking the computer predictions against experiments. This research should reveal new theoretical principles for designing future devices from single molecules. Also, the biological nature of the molecules means that they might be applied in medical applications. Undergraduate and graduate students, including those from minority groups underrepresented in scientific research, will participate, learning cutting-edge computational techniques.The research team also seeks to develop computer simulations of molecules for use in college classrooms and in K-12 outreach, letting students see how molecules move and giving them a feel for how the world works at this tiny level. The interactive simulations will include those aimed at helping students understand how medicines work and how new medicines can be designed. The educational modules and simulation programs will be made freely available to educators and the public, and will include English- and Spanish-language versions.TECHNICAL SUMMARYThis CAREER award supports research to address a fundamental problem in engineering self-assembled structures: how to design molecular elements that possess both the flexibility to adopt arbitrary useful structures and the selectivity to adopt a unique programmed structure with high fidelity. The goal of the project is to develop a theoretical framework and computational tools for designing building blocks for programmable assembly. The project is focused on glycine-rich peptides that fold into unique conformations on graphitic surfaces and self-assemble in predictable ways. This peptide-graphene system seems optimal for creation of programmable materials because the effectively two-dimensional architecture simplifies imaging and reduces the peptides' conformational and configurational freedom, favoring ordered structures and facilitating analysis by theory and molecular dynamics simulation.The research team will use molecular dynamics simulations and state-of-the-art free-energy calculation techniques to screen large numbers of peptide sequences to find sets of elements suitable for programmable assembly. The computational predictions will be experimentally validated using atomic force and electron microscopy. The results of this project are anticipated to advance the field of molecular self-assembly by establishing theoretical and computational tools to find sets of molecular motifs with optimal interaction thermodynamics for programmable assembly of nanodevices. The project will involve the development of new algorithms and freely available software for enhanced sampling, free-energy calculation, and interactive molecular design, likely advancing the field of molecular simulation.This CAREER award also supports education activities related to the research area. The team will also create interactive educational modules leveraging easy-to-use browser-based simulations, which will be tailored to a graduate course on drug design, undergraduate courses on thermodynamics, and K-12 outreach activities. These modules will include English- and Spanish-language versions. Graduate and undergraduate students participating in the research, including some from populations historically underrepresented in science and technology fields, will gain exposure to nanoscience and advanced computational techniques.This project is jointly funded by the Condensed-Matter-and-Materials-Theory program in the Division of Materials Research and by the Established Program to Stimulate Competitive Research (EPSCoR).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

非技术总结这个职业奖支持理论研究，计算机模拟和验证实验，以设计可以编程的分子，以安排自己进入复杂的设备。一部可以放在口袋里的现代智能手机比20年前的笔记本电脑拥有更强的计算能力，同时还包括数码相机、GPS和无线通话功能。设备的小型化已经如此成功，以至于一些组件的大小正在接近分子和原子的大小，这要求设备的构建方式发生重大变化。这就好像建造沙堡已经让位于用单个沙粒建造微型城堡。虽然从单个分子制造设备可能很困难，但这是可以做到的;生物以单原子的精度制造数千种不同的蛋白质，每种蛋白质都有不同的功能，同时经常将自己排列成更大，更复杂的结构。这个项目的目标是设计类似蛋白质的分子，这些分子同样能够排列自己，但以一种人类工程师可以轻松编程的方式。为了使设备的成像和设计更容易，该项目的重点是在原子级平坦的石墨烯表面上排列自己的分子。研究小组将使用计算机模拟来优化对这种安排的控制，并将计算机预测与实验进行比较。这项研究应该揭示新的理论原则，设计未来的设备从单分子。此外，分子的生物学性质意味着它们可能应用于医学应用。本科生和研究生，包括那些在科学研究中代表性不足的少数群体的学生，将参加，学习尖端的计算技术。研究团队还寻求开发用于大学课堂和K-12推广的分子计算机模拟，让学生看到分子如何移动，并让他们感受到世界是如何在这个微小的水平上运作的。交互式模拟将包括那些旨在帮助学生了解药物如何工作以及如何设计新药的模拟。教育模块和模拟程序将免费提供给教育工作者和公众，并将包括英语和西班牙语版本。技术总结这个职业奖支持研究，以解决工程自组装结构的一个基本问题：如何设计分子元素，既具有灵活性，采用任意有用的结构和选择性，采用一个独特的编程结构与高保真度。该项目的目标是开发一个理论框架和计算工具，用于设计可编程组件的构建模块。该项目的重点是富含甘氨酸的肽，这些肽在石墨表面折叠成独特的构象，并以可预测的方式自组装。这种肽-石墨烯系统似乎是创建可编程材料的最佳选择，因为有效的二维结构简化了成像并降低了肽的构象和构型自由度，有利于有序结构，便于理论和分子动力学模拟分析。研究小组将使用分子动力学模拟和最先进的免费，能量计算技术来筛选大量肽序列，以找到适合于可编程组装的元件组。计算预测将使用原子力和电子显微镜进行实验验证。该项目的结果预计将通过建立理论和计算工具来推进分子自组装领域，以找到具有最佳相互作用热力学的分子基序集，用于纳米器件的可编程组装。该项目将涉及新的算法和免费软件的开发，用于增强采样，自由能计算和交互式分子设计，可能会推进分子模拟领域。该CAREER奖还支持与研究领域相关的教育活动。该团队还将利用易于使用的基于浏览器的模拟创建交互式教育模块，这些模块将针对药物设计研究生课程，热力学本科课程和K-12外展活动进行量身定制。这些单元将包括英文和西班牙文版本。参与研究的研究生和本科生，包括一些历史上在科学和技术领域代表性不足的人口，将获得接触纳米科学和先进的计算技术。该项目由材料研究部的凝聚态物质和材料理论计划和刺激竞争力研究的既定计划（EPSCoR）共同资助该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Simulation Files for Organic Contaminants and Atmospheric Nitrogen at the Graphene–Water Interface

石墨烯与水界面处有机污染物和大气氮的模拟文件

• DOI: 10.5281/zenodo.6050816
• 发表时间: 2022
• 期刊: Zenodo
• 作者: Thakkar, Ravindra;Sandun, Gajaweera;Comer, Jeffrey
• 通讯作者: Comer, Jeffrey

Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

石墨上折叠和自组装肽设计的模拟数据

• DOI: 10.5281/zenodo.6426152
• 发表时间: 2022
• 期刊: Zenodo
• 作者: Comer, Jeffrey;Thakkar, Ravindra;Velásquez-Silva, Astrid;Miranda-Carvajal, Ingrid
• 通讯作者: Miranda-Carvajal, Ingrid

Interfacial layering of hydrocarbons on pristine graphite surfaces immersed in water

• DOI: 10.1039/d2nr04161h
• 发表时间: 2022-09-20
• 期刊: NANOSCALE
• 影响因子: 6.7
• 作者: Arvelo, Diana M.;Uhlig, Manuel R.;Garcia, Ricardo
• 通讯作者: Garcia, Ricardo

Atomically resolved interfacial water structures on crystalline hydrophilic and hydrophobic surfaces

• DOI: 10.1039/d1nr00351h
• 发表时间: 2021-03-14
• 期刊: NANOSCALE
• 影响因子: 6.7
• 作者: Uhlig, Manuel R.;Benaglia, Simone;Garcia, Ricardo
• 通讯作者: Garcia, Ricardo

Urea-Modified Self-Assembling Peptide Amphiphiles That Form Well-Defined Nanostructures and Hydrogels for Biomedical Applications

• DOI: 10.1021/acsabm.2c00158
• 发表时间: 2022-06-02
• 期刊: ACS APPLIED BIO MATERIALS
• 影响因子: 4.7
• 作者: Xing，Huihua;Rodger，Alison;Conda-Sheridan，Martin
• 通讯作者: Conda-Sheridan，Martin