Dissipation in the mechanics of soft molecules

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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.