Activated and nonlinear kinetics in biomolecules and interfaces

Activated and nonlinear kinetics in biomolecules and interfaces Activated and nonlinear kinetics in biomolecules and interfaces This is a proposal for a theoretical study of activated glassy dynamics of proteins and polarization of water interfaces. The main fundamental focus is on mechanisms of catalysis by enzymes and its connection to the interface of proteins with water. We propose that significantly lower barriers for catalyzed reactions are achieved through the separation between the effective configurational temperature of the active site and the kinetic temperature of the thermal bath. Equilibration to the bath temperature, or aging, eventually limits the time on which enzymetic cycle has to be finished. We propose a broad program to connect enzymetic efficiency with the interfacial structure and glassy aging dynamics of collective variables linked to the activated barrier crossing. The proposed research will address some of most fundamental problems of water polarization at interfaces and its influence on protein-catalyzed reactions. We will address the following questions: (a) Characterization of configurational temperature of redox proteins and the dynamics of equilibration with the thermal bath. Coarse-grained models of the protein will be numerically simulated and the relation between the linear response and the correlation function of the collective coordinates established. (b) An analytical theory for the effective susceptibility of water in the interface developed. The susceptibility of the interface is very different from the bulk and the new theory will incorporate the interfacial structure into the equations for interfacial electrostatics. This concept will be applied to develop a new theory of depolarized light scattering by aqueous solutions and used to consistently interpret THz absorption, depolarized light scattering, and dielectric measurements for the same solution as a part of an international collaboration with experimentalists. As a low-frequency application of this theoretical framework, a theory of dielectrophoresis of proteins will be developed and tested on experiments through a collaboration with experimental colleagues at ASU. (c) A theory of non-linear dielectric response of solutions will be developed. Its main goal is to provide a new approach to interrogate structural crossovers in the interface. The nonlinear susceptibility is predicted to strongly increase for solutions undergoing changes in the interfacial structure. This novel approach provides theoretical underpinning for a potentially new interface-sensitive technique. (d) Non-linear dielectric effect in low-temperature liquids close to the glass transition. We are interested in extending theories of thermodynamics of low-temperature liquids to non-linear dielectric polarization of glass-formers. This project is also a theory-experiment collaboration. The problems addressed by the proposal will connect to significant current challenges with broad technological and societal outcomes: (a) efficiency of enzymes and biological electron transport chains in producing energy and food, (b) properties of interfaces between man-made and biological materials, (c) interrogating nano-scale and meso-scale dimensions to develop new products and technologies, and (d) water and interfaces in biology. The proposal suggest a number of specific activities to improve STEM education and to increase public scientific literacy and preparation of high school students to future carriers in STEM related fields. We have established a functioning program to channel local high school students through research activities organized by the PI's group. We plan on continuing this program largely through summer schools educating talented high school students from the valley, but also through regular meetings with the students, for education on relevant theoretical topics, coaching on scientific programming, and monitoring and facilitating overall student progress. These activities will be supported by the computer lab that we have helped to establish at Arete preparatory academy (Gilbert, AZ) and in conjunction with the physics group at Arete established by PI's former student who is now a science teacher. The students are admitted to summer schools based on recommendation by their teachers. We provide the materials from our training back to them thus helping in professional development of K-12 mathematics and science teachers. The graduate students from the PIs group are highly involved with tutoring and will continue to participate in this important exposure to outreach. The PI's group will continue disseminating research results through publications, conferences, and by making their codes available to the research community. Strong connection of the proposed activities to experimental effort will help in educating young scientists with a broad understanding of the field and the ability to establish collaborative programs on their own.