AF: Small: Programmable Nanowalkers:Models and Simulations

AF：小型：可编程纳米行走者：模型和模拟

• 批准号: 1422840
• 负责人: Darko Stefanovic
• 金额: $ 40万
• 依托单位: University of New Mexico
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-01 至 2019-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1422840&HistoricalAwards=false
• 关键词: AF; Small; Programmable; Nanowalkers; Models

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.

所有的纳米器件都受到随机扩散力的影响，导致材料和信息的传输缓慢，无法控制。 为计算和自组装任务设计的合成纳米级系统需要更精确地控制携带能量和信息的分子。 这种系统包括目前正在开发的纳米级装置，用于将诊断逻辑电路递送到细胞，查询特定细胞或亚细胞结构的健康状态，以及治疗性货物分子的条件释放。理想情况下，这样的系统可以采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的方式运送信息和材料，类似于活细胞中的天然分子马达，从而实现在纯粹的扩散驱动环境中不可能实现的行为。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，以帮助合成化学家构建下一代纳米级步行者系统。在该项目中，各级学生（高中到博士后）将接受跨学科研究的培训。高中生将通过已经建立的、跟踪的科学参与计划参与该项目，这些计划强调传统上代表性不足的群体的参与。在该项目的背景下，将在生物医学工程学位课程中定期举办纳米技术，分子计算和分子机器人技术的研讨会，以教育未来的学生（本科生和研究生）在这个新兴的科学领域。以前的工作表明，简单的DNA-酶驱动的合成步行者可以超扩散沿着纳米轨道移动，并可以做机械工作。在这个项目中，更先进的步行者设计与大型，复杂的身体形状和异质性，在他们的相互作用与其他步行者和分子在他们的环境将被建模和模拟。 这类结构化的步行者支架将表现出在对称步行者中不可用的运动模式，例如，旋转持久性、方向感知排序、手性步行者-步行者和步行者-轨道交互。 这些特征将被用来打破步行者的局部环境中的对称性，从而导致更强的方向偏差和更有效的定向运输。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，以及如何将这些功能模块化地组合到具有可编程控制的更大的纳米级运输系统中，以实现定向运输，即使在布朗运动的随机化和迷失方向的影响下。开发的模型将使更复杂的纳米系统能够利用可编程的纳米级传输进行工程设计。步行者运动被视为一个连续时间马尔可夫过程，在抽象的水平，平衡物理细节和计算的易处理性。 将开发一个蒙特卡罗模拟层次，以适当的相对尺度近似物理和化学过程，同时保持计算的易处理性。