CAREER: Experimental and Computational Studies of Biomolecular Topology

我们制造的一切都是由原子或分子构成的。我们对原子和简单分子的行为有很好的理解，但要理解更复杂的分子就更难了。一些更复杂的分子以更简单的分子没有的方式连接在一起。简单的分子可能像乐高积木一样连接起来，而更复杂的分子可能像链上的链环一样连接起来。挑战在于分子非常小，小到无法用显微镜看到，又快到无法用相机记录。我们通过两种方式来克服这一挑战。一种是使用更大的分子。DNA以包含我们的遗传密码而闻名，但它也是一个非常大的分子，我们可以在显微镜下研究。我们可以用DNA做实验来了解分子的行为，并将这些经验应用到更小的分子上。例如，我们测量单个DNA分子的弹性，并利用这些信息来了解构成橡胶的分子是如何变得有弹性的。另一种方法是使用计算机模拟，它可以向我们展示分子的行为，如果我们能看到它们。在这个项目中研究的主要分子被称为动质体，它就像中世纪的链甲，由成千上万个相连的DNA环组成。我们用显微镜和计算机模拟来研究这些分子，以了解化学家们正在学习制造的小得多的链甲状分子的行为。在未来，如果我们首先了解DNA链甲，我们对化学链甲分子的理解将允许原子一个原子地制造出更新、更新奇的材料和纳米机器。我们还会教新一代的学生学习分子，让他们拍摄充满分子的液滴蒸发时的微观视频。由于之前没有人观察到这些特定的分子以这种方式蒸发，学生们除了学习如何做实验外，还将学习发现新事物的感觉。作为这项资助的教育方面的一部分，在少数民族服务的主要本科院校的学生将开展原创性研究，作为基于课程的本科研究经验的一部分。新发现的经历将在科学界建立一种归属感，并支持他们作为科学家而不仅仅是理科生的身份。本项目的目标是通过单分子实验和粗粒度模拟来了解复杂生物聚合物的分子拓扑结构与材料特性之间的关系。生物聚合物作为一种微米尺度的介观体系，类似于纳米尺度的合成聚合物。实验将主要集中在单分子荧光显微镜上。着丝体是拓扑连接DNA的平面网络，将作为合成聚连环烷和热化石墨烯的模型系统进行研究。我们特别感兴趣的是，该网络的拓扑结构如何通过酶的作用来调节，从而影响微流体剪切流动中对着丝体的弹性响应。我们还将开发使用基因组长度的DNA作为活性流体中的示踪聚合物的检测方法，这些活性流体通过化学能的转换驱动它们自己的内部复杂流动。分子的波动和构象将被用来确定类生命系统如何接近和避免最大熵状态，建立有助于我们理解生命物理学的规则。此外，我们将探索使用部分变性（线性DNA的拓扑变化）来改进纳米孔基因组图谱技术。模拟将使用朗之万动力学和梯度优化来研究分子链甲的拓扑结构与它们形成的片的大规模结构之间的关系，以及研究变性转变与结分子拓扑结构之间的关系。作为这项资助的更广泛影响的一部分，在少数民族服务的主要本科院校的学生将进行原创性研究，作为基于课程的本科研究经验的一部分，最初研究马兰戈尼流中的向列液晶。新发现的经历将在科学界建立一种归属感，并支持他们作为科学家而不仅仅是理科生的身份。该奖项反映了美国国家科学基金会的法定使命，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。

NON TECHNICAL SUMMARYEverything we make, we make out of atoms or molecules. We have a good understanding of how atoms and simple molecules behave, but it is harder to understand more complicated molecules. Some of the more complicated molecules are connected in ways that simpler molecules aren’t. Where simple molecules might connect like Lego bricks, more complicated molecules might connect like links on a chain. The challenge is that molecules are very small, too small to see with a microscope, and too fast to record with a camera. We overcome this challenge in two ways. One is by using bigger molecules. DNA is best known for containing our genetic code, but it’s also just an extremely large molecule that we can study in a microscope. We can do experiments with DNA to learn about how molecules behave, and apply those lessons to smaller molecules. For example, we measure how stretchy a single DNA molecule is, and use that information to understand how the molecules that make up rubber become stretchy. The other way is to use computer simulations, which can show us how molecules would behave if we could see them. The main molecules studied in this project are called kinetoplasts, which are like medieval chainmail armor made of thousands of connected loops of DNA. We study these with a microscope, and with computer simulations, to understand how much smaller chainmail-like molecules, which chemists are now learning to make, would behave. In the future, our understanding of chemical chainmail molecules could allow newer, fancier materials and nanomachines created atom by atom, if we first understand DNA chainmail. We will also teach a new generation of students to study molecules, by having them take microscopic videos of droplets full of molecules as they evaporate. Since nobody has observed those specific molecules evaporating in that way before, the students will learn what it’s like to discover something new, in addition to learning how to do the experiments. As part of the educational aspects of this grant, students at a minority-serving primarily-undergraduate institution will carry out original research as part of a course-based undergraduate research experience. The experience of a new discovery will build a sense of belonging in the scientific community and support their identities as scientists rather than just science students.TECHNICAL SUMMARYThe goal of this project is to understand the relationship between molecule topology and material properties of complex biopolymers through single-molecule experiments and coarse-grained simulations. Biopolymers serve as a mesoscopic system on the micron scale analogous to synthetic polymers on the nanometer scale. The experiments will largely focus on single-molecule fluorescence microscopy. Kinetoplasts, which are planar networks of topologically linked DNA, will be studied as a model system for synthetic polycatenanes and thermalized graphene. In particular, we are interested in how the topology of then network, which can be tuned by the action of enzymes, effects the elastic response to kinetoplasts in microfluidic shear flow. We will also develop assays to use genomic-length DNA as a tracer polymer in active fluids, which drive their own internal complex flows through the conversion of chemical energy. The fluctuations and conformations of the molecule will be used to determine how life-like systems approach and avoid maximum-entropy states, establishing rules that help us understand the physics of life. Additionally, we will explore the use of partial denaturation (a topological change in linear DNA) to improve nanopore genomic mapping technology. Simulations will use Langevin dynamics and gradient optimization to study the relationship between the topology of molecular chainmail and the large-scale structure of the sheets that they form, as well as to investigate the relationship between denaturation transitions and knotted molecular topologies. As part of the broader impacts of this grant, students at a minority-serving primarily-undergraduate institution will carry out original research as part of a course-based undergraduate research experience, initially studying nematic liquid crystals in Marangoni flow. The experience of a new discovery will build a sense of belonging in the scientific community and support their identities as scientists rather than just science students.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.