SGER: A Mechanics Framework for the Analysis and Design of Protein Based Nano Machines

该奖项的研究目标是应用机械学和机器人领域的运动分析方法来预测蛋白质在外部刺激存在时三维结构的变化。这项工作的基本前提是蛋白质分子是纳米级的基本机械装置，因此可以被认为是功能纳米机器的构建块。具体地说，我们提出了一种新的方法，绕过了传统的分子动力学模拟，因为传统的分子动力学模拟的计算成本高得令人望而却步。我们的方法，被称为“连续动静顺应性”，是预测在外力作用下分子结构的顺应性。表征和预测变形蛋白质的力学性质的能力将为基于功能蛋白质的纳米机器的合成和分析提供基础。如果成功，该项目的结果将是朝着发展基于蛋白质的纳米机器设计和分析的算法框架迈出的重要一步。这些能力在任何试图使工程设计和纳米级制造正规化的尝试中都是至关重要的。该项目的影响范围更广，从蛋白质组学、医学和合理的药物设计到生物计算机、生物机器人和生物传感器。通过将传统工程教育与生物学和生物化学知识以及计算技能相结合，该计划将有助于培养新一代专业人员，他们将有助于推动纳米技术的研究、开发和商业应用。

The research objective of this award is to apply motion analysis methods from the fields of mechanisms and robotics to predict the changes in the three dimensional structure of proteins in the presence of external stimuli. The underlying premise of this work is that protein molecules are elementary mechanical devices at nanoscales, and therefore can be considered the building blocks of functional nano machines. Specifically, we propose a novel methodology that bypasses the traditional molecular dynamic simulations, which are known to have prohibitively high computational cost. Our methodology, referred to as "Successive Kineto-Static Compliance", is predicting the compliance of the molecule structure under applied external forces. The ability to characterize and predict the mechanical properties of the deforming proteins will provide the foundations for the synthesis and analysis of nano-machines that are based on functional proteins.If successful, the results of this project will represent a first major step toward the development of an algorithmic framework for the design and analysis of protein based nano machines. These capabilities are paramount in any attempts to formalize the engineering design and manufacturing at nanoscales. The broader impacts of this project range from proteomics, medicine, and rational drug design to bio-computers, bio-robots, and biosensors. By combining traditional engineering education with knowledge from biology and biochemistry, as well as computational skills, this program will help develop a new generation of professionals that will be instrumental in helping the advance of research, development and commercial applications of nanotechnologies.