Looping Dynamics of Semiflexible Polymers

ID: MPS/DMR/BMAT(7623) 1006485 PI：托德，布莱恩ORG：普渡大学标题：半柔性聚合物的环动力学知识优点：分子内环可以形成每当一个聚合物链包含一个以上的反应位点。这一过程的物理基础是两个远端聚合物段扩散传输到一个共同的位置（“环”）。大多数聚合物理论预测聚合物环反应不遵循传统的动力学模型，但这些预测尚未得到充分的实验验证。提出的研究目标是表征半柔性聚合物环动力学，使用DNA作为模型实验系统。特别是，PI将测试最近的一个理论预测，即半柔性聚合物环适用于基于克莱默斯速率理论的简单描述。这种简单的描述将极大地促进在实际生物聚合物设计应用中的环动力学预测，例如用于非病毒基因治疗的DNA纳米颗粒的动力学决定处理。提出了两种独立的测量聚合物环速率的方法。在第一种方法中，将荧光团连接到聚合物的一端，并将猝灭剂连接到另一端。然后可以通过荧光相关光谱（FCS）测量环介导的荧光团猝灭来确定环动力学。第二种方法利用环反应和二级盖顶反应之间的动力学竞争。提出的研究将表征半柔性聚合物的环，最终建立一个详细描述聚合物结构对环速率影响的模型。这加深了我们对半柔性聚合物中节段运动的理解，并将广泛使用的生物聚合物模型扩展到涉及环的应用中。更广泛的影响：该项目的一个主要目标是训练学生思考如何将聚合物物理学应用于跨学科应用，如生物材料设计和分子生物学。PI已经招募了两名有才华的研究生进入实验室，预计实验室将很快包含不同层次的学生。他是普渡大学“视野项目”（Horizons Program）的导师，该项目针对的是处境危险的学生，他希望能吸引一些学生到他的实验室来。他还将继续通过指导、实验室参观和普渡大学科学学院支持的项目，招募和留住代表性不足的少数族裔。过去，PI是俄亥俄州东克利夫兰一所100%是少数族裔的公立中学的指导项目主任。他计划继续向印第安纳州西拉斐特的中学生伸出援手。PI目前正在开发一个外联实验室，旨在向中学生介绍“自下而上”的材料设计概念。这个想法是挑战学生们从宏观的磁性和非磁性“单体”中设计出“共聚物序列”，这些“单体”能够自组装成诸如环、结和立方体等结构。预算中包括少量资金，用于购买制作这些示范工具包的材料。不使用时，示范材料将通过该部门的物理外展资源室提供给K-12教师。

ID: MPS/DMR/BMAT(7623) 1006485 PI: Todd, Brian ORG: Purdue UniversityTitle: Looping Dynamics of Semiflexible PolymersINTELLECTUAL MERIT: Intramolecular loops can form whenever a polymer chain contains more than one reactive site. The physics underlying this process is the diffusive transport of two distal polymer segments to a common location ("looping"). Most polymer theories predict that polymer looping reactions do not follow traditional kinetic models, but these predictions have not been fully tested experimentally. The goal of the proposed research is to characterize semiflexible polymer looping dynamics, using DNA as a model experimental system. In particular, the PI will test a recent theoretical prediction that semiflexible polymer looping is amenable to a simple description based on Kramers rate theory. This simple description would greatly facilitate predictions of looping kinetics in practical biopolymer design applications, such as the kinetically-determined processing of DNA nanoparticles for non-viral gene therapy. Two independent methods of measuring polymer looping rates are proposed. In the first, a fluorophore will be attached to one end of the polymer and a quencher to the other. Looping kinetics can then be determined from loop-mediated fluorophore quenching, measured via fluorescence correlation spectroscopy (FCS). The second method uses kinetic competition between looping and a second-order capping reaction. The proposed research will characterize semiflexible polymer looping, culminating in a model that details the influence of polymer structure on the looping rate. This deepens our understanding of segmental motion in semiflexible polymers and extends a widely used biopolymer model into applications involving looping.BROADER IMPACTS: A major goal of this project is to train students to think about how polymer physics can be used in interdisciplinary applications such as biomaterials design and molecular biology. The PI has recruited two talented graduate students into the laboratory, and it is expected that the laboratory will soon contain a mix of students at different levels. The PI is a mentor in the "Horizons Program" for at-risk students at Purdue and hopes to attract some of his mentees into his lab. He will also continue to recruit and retain underrepresented minorities through mentoring, lab tours, and programs supported by the College of Sciences at Purdue University. In the past, the PI was a director of a mentoring program in a 100% minority public middle school in East Cleveland, Ohio. He plans to continue outreach with middle school-aged students in West Lafayette, Indiana. The PI is currently developing an outreach laboratory designed to introduce concepts of "bottom-up" materials design to middle school-aged students. The idea is to challenge the students to design "co-polymer sequences" out of macroscopic magnetic and non-magnetic "monomers" that are capable of self-assembling into structures, such as loops, knots, and cubes. Modest funding is included in the budget to purchase the materials to make these demonstration kits. When not in use, the demonstration materials will be made available to K-12 teachers through the department's Physics Outreach Resource Room.