Dissipation in the mechanics of soft molecules

软分子力学中的耗散

• 批准号: 1809381
• 负责人: Giovanni Zocchi
• 金额: $ 51.3万
• 依托单位: University of California-Los Angeles
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-01 至 2023-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1809381&HistoricalAwards=false
• 关键词: Dissipation; mechanics; soft; molecules

Nontechnical. Dissipation, or friction, relates to the Second Law of thermodynamics, thus the arrow of time, and everything living. A world without friction is a world of Kepler orbits and pendulums, time reversible, and unconscious. But matter is made of atoms, and individual atoms are non-dissipative systems. At what scale, then, does "the arrow of time" start to form? Previous NSF funded research in the PI's group opened a new experimental window on dissipative processes occurring in the deformation of big molecules. Building on this expertise, the PI and his group characterize the dissipation involved in the working of enzymes. They measure friction at the scale of molecules and look for new phenomena such as light emission from the dissipative dynamics discovered in their system. A small group of young people, comprising two graduate students and two undergrads, is thus set on a path of scientific discovery, while acquiring state-of-the-art technical skills in the field of nanoscience. The primary goal of this project is the creation of knowledge. More specifically, this research focuses on developing a new materials science of biomolecules, introduced in the PI's forthcoming book "Molecular Machines". Technical. Microscopic mechanisms of friction, the relation between dissipation and nonlinearity, non-equilibrium processes in nanoscale systems, are all incompletely understood, fundamental, interconnected problems in nanoscience. These topics appear with experimental immediacy when probing enzyme mechanics by nano-rheology. Using the unique capability of measuring directly dissipation occurring in the driven deformation of folded enzyme molecules, the PI and his group investigate the origin of this molecular scale friction, specifically the contribution of the surface of the molecule, which includes the hydration layer. Hydration layer dynamics, explored by nano-rheology, is also the starting point of a new, dynamic understanding of kosmotropic (order inducing) and chaotropic agents, a physical chemistry topic which this research develops. Finally, the project explores the possibility of light emission from dynamically stressed molecules, with the aim of developing a new spectroscopy to characterize dissipation at the molecular scale. Nano-rheology, invented in the PI's lab, allows the measurement of the stress - strain relations for a folded, native enzyme with sub-Angstrom resolution and at different frequencies. Through recent improvements, the method now allows accurate measurements of the phase of the mechanical response, as well as the amplitude, and thus gives direct access to the dissipation. This project focuses on the dissipative part of the dynamics, which is the nonlinear (but reversible) mechanical regime of large amplitude deformations for these molecules.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.

非技术性的耗散，或摩擦力，与热力学第二定律有关，因此是时间之箭，也是一切生物的箭头。一个没有摩擦力的世界是一个开普勒轨道和时间轴、时间可逆和无意识的世界。 但物质是由原子组成的，单个原子是非耗散系统。 那么，“时间之箭”在多大的尺度上开始形成呢？ 先前NSF资助的PI小组的研究为大分子变形中发生的耗散过程打开了一个新的实验窗口。 基于这种专业知识，PI和他的团队描述了酶工作中涉及的耗散。 他们在分子尺度上测量摩擦，并寻找新的现象，如在他们的系统中发现的耗散动力学的光发射。 因此，一小群年轻人，包括两名研究生和两名本科生，走上了科学发现的道路，同时获得了纳米科学领域最先进的技术技能。 这个项目的主要目标是创造知识。更具体地说，这项研究的重点是开发生物分子的新材料科学，在PI即将出版的书“分子机器”中介绍。技术.摩擦的微观机制，耗散和非线性之间的关系，纳米尺度系统中的非平衡过程，都是纳米科学中尚未完全理解的，基本的，相互关联的问题。 这些主题出现与实验的直接性时，探测酶力学纳米流变学。 利用直接测量折叠酶分子驱动变形中发生的耗散的独特能力，PI和他的团队研究了这种分子尺度摩擦的起源，特别是分子表面的贡献，其中包括水合层。 水化层动力学，探索纳米流变学，也是一个新的，动态的理解kosmotropic（秩序诱导）和离液剂，本研究开发的物理化学课题的起点。 最后，该项目探讨了动态应力分子发光的可能性，目的是开发一种新的光谱学来表征分子尺度上的耗散。 PI实验室发明的纳米流变学允许在不同频率下测量折叠的天然酶的应力-应变关系，具有亚埃分辨率。通过最近的改进，该方法现在允许精确测量机械响应的相位以及振幅，从而直接获得耗散。 该项目的重点是动力学的耗散部分，这是这些分子大幅度变形的非线性（但可逆）力学机制。该奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

Critical behavior in the artificial axon

• DOI: 10.1088/2399-6528/ac43d0
• 发表时间: 2021-12-01
• 期刊: JOURNAL OF PHYSICS COMMUNICATIONS
• 影响因子: 1.2
• 作者: Pi，Ziqi;Zocchi，Giovanni
• 通讯作者: Zocchi，Giovanni

Enzyme-DNA chimeras: Construction, allostery, applications

酶-DNA 嵌合体：构建、变构、应用

• DOI: 10.1016/bs.mie.2020.09.010
• 发表时间: 2021
• 期刊: Methods in enzymology
• 作者: Tseng, Chiao-Yu;Wang, Yong;Zocchi, Giovanni
• 通讯作者: Zocchi, Giovanni

Kink propagation in the Artificial Axon

人工轴突中的扭结传播

• DOI: 10.1209/0295-5075/ac44e2
• 发表时间: 2022
• 期刊: Europhysics Letters
• 作者: Qi, Xinyi;Zocchi, Giovanni
• 通讯作者: Zocchi, Giovanni

Opportunities for materials science: From molecules to neural networks

材料科学的机遇：从分子到神经网络

• DOI: 10.1557/mrs.2019.23
• 发表时间: 2019
• 期刊: MRS Bulletin
• 影响因子: 5
• 作者: Zocchi, Giovanni

Analog control with two Artificial Axons

使用两个人工轴突进行模拟控制

• DOI: 10.1088/1748-3190/aaf123
• 发表时间: 2019
• 期刊: Bioinspiration & Biomimetics
• 影响因子: 3.4
• 作者: Vasquez, Hector G;Zocchi, Giovanni
• 通讯作者: Zocchi, Giovanni