AF: Small: Programmable Nanowalkers:Models and Simulations

所有纳米级的设备都会受到随机扩散力的影响，导致材料和信息的缓慢、不可控的传输。设计用于计算和自组装任务的合成纳米级系统需要对携带能量和信息的分子进行更精确的控制。这种系统包括目前正在开发的纳米级设备，用于向细胞提供诊断逻辑电路，查询特定细胞或亚细胞结构的健康状态，以及有条件地释放治疗货物分子。理想情况下，这样的系统可以使用可编程的合成分子马达，在复杂的轨道网络上以定向运动运送信息和材料，类似于活细胞中的自然分子马达，从而实现在纯粹扩散驱动的环境中原本不可能实现的行为。在这个项目中，将开发计算模型、模拟算法和数据可视化工具，帮助合成化学家建立下一代纳米级步行者系统。在该项目中，所有级别的学生(从高中到博士后)将接受跨学科研究方面的培训。高中生将通过已经建立的、跟踪的科学参与计划参与到这个项目中，这些计划强调传统上代表不足的群体的参与。在该项目的背景下，将在生物医学工程学位课程中开发一个关于纳米技术、分子计算和分子机器人的定期研讨会，以教育下一代学生(本科生和研究生)这一新兴科学领域。以前的工作表明，简单的DNA酶驱动的合成步行器可以沿纳米级轨迹超扩散移动，并可以进行机械工作。在这个项目中，将对更先进的步行器设计进行建模和模拟，这些设计具有大型、复杂的体型，并且在它们与环境中的其他步行器和分子的相互作用中具有异质性。这类结构化的步行器支架将展示对称步行器所不具备的运动模式，例如旋转持久性、方向感知分类、手性步行器-步行器以及步行器-轨道相互作用。这些特征将被用来打破步行者局部环境中的对称性，导致更强的方向偏差和更高效的定向运输。该项目的目标是了解步行者的形状和结构如何影响其运动的算法基础，以及如何将这些特征模块化地组合到具有可编程控制的更大纳米级运输系统中，以实现定向运输，即使在布朗运动的随机和迷失方向的影响下也是如此。所开发的模型将使更复杂的纳米系统能够被设计成利用可编程纳米级传输的优势。该项目所采用的方法是计算性的。Walker运动被视为一个连续时间的马尔可夫过程，处于平衡物理细节和计算可操纵性的抽象水平。将开发一系列蒙特卡罗模拟，以在适当的相对尺度上近似物理和化学过程，同时保持计算的易操作性。

All nanoscale devices are subject to random diffusive forces that lead to slow, uncontrollable transport of materials and information. Synthetic nanoscale systems designed for computational and self-assembly tasks, require more precise control over energy- and information-carrying molecules. Such systems include nanoscale devices currently being developed for delivery of diagnostic logic circuits to cells, querying the state of health of specific cells or subcellular structures, and conditional release of therapeutic cargo molecules. Ideally, such systems could employ programmable synthetic molecular motors to ferry information and materials in directed motion over a complex network of tracks, analogous to natural molecular motors in living cells, thus enabling behaviors otherwise not possible in a purely diffusion-driven environment. In this project computational models, simulation algorithms, and data visualization tools will be developed that will help synthetic chemists build the next generation of nanoscale walker systems. In the project, students at all levels (high-school to postdoctoral) will be trained in interdisciplinary research. High-school students will be engaged on the project through already established, tracked science involvement programs that emphasize participation of traditionally underrepresented groups. In the context of the project, a regular seminar will be developed on nanoscale technology, molecular computing, and molecular robotics within the biomedical engineering degree program, to educate future generations of students (undergraduate and graduate) in this emerging field of science.Previous work has shown that simple DNA-enzyme driven synthetic walkers can move superdiffusively along nanoscale tracks, and can do mechanical work. In this project more advanced walker designs with large, complex body shapes and heterogeneity in their interactions with other walkers and molecules in their environment will be modeled and simulated. This class of structured walker scaffolds will exhibit modes of motion not available in symmetrical walkers, e.g., rotational persistence, orientation-aware sorting, chiral walker-walker and walker-track interactions. These features will be used to break symmetries in the walker's local environment, leading to stronger directional biases and more efficient directional transport. The goal of the project is to understand the algorithmic basis of how a walker's shape and structure affect its motion, and how these features can be composed, modularly, into larger nanoscale transportation systems with programmable control, to achieve directed transport even under the randomizing and disorienting influence of Brownian motion. The models developed will enable more complex nano systems to be engineered to take advantage of programmable nanoscale transport.The approach taken in the project is computational. Walker motion is treated as a continuous-time Markov process, at a level of abstraction that balances physical detail and computational tractability. A hierarchy of Monte Carlo simulations will be developed to approximate physical and chemical processes at the appropriate relative scales, while maintaining computational tractability.