Nonequilibrium responses of complex fluids and proteins to nano-mechanical perturbation

We use optical trapping experiments as well as Stokesian Dynamics and Steered Molecular Dynamics simulations to study the nonequilibrium responses of complex fluids and proteins to mechanical perturbation. We study the coupling of an optically driven colloid particle to a monodisperse quasi-two-dimensional (q2d) colloid bath to elucidate the structure and dynamics of excitations created. In response to constant velocity motion, stress propagation occurs via anisotropic displacement chains which, when averaged over all configurations, beget a leading density wave and a trailing wake. The displacement chain protrusion direction depends on the projection of the perturbation onto the local colloid packing. An oscillatory displacement perturbation allows capturing dipolar displacement fields of the bath colloid particles. Stokesian Dynamics (SD) simulations of a q2d colloid fluid corroborate these excitations and allow separating direct colloid-colloid and hydrodynamic interactions. A radial displacement perturbation is used to form large areas of disordered, low density colloid and to study the relaxation into ordered states. Dynamics in equilibrium and nonequilibrium steady state (NESS) is studied by characterizing temporal fluctuations of order parameters that define the system properties in the immediate proximity to and away from the trapped colloid. In addition, the force exerted on the trapped colloid during the perturbation is modeled in the sparse and high density colloid cases. Finally, the remainder of thesis is transition from statistical mechanics of mesoscopic colloidal fluids to that of complex molecular systems. Photoactive Yellow Protein (PYP) is used as a model system to study anisotropic protein response to mechanical unfolding along two different protein axes. A reconstruction of Potential of Mean Force (PMF) is obtainedusing the Jarzynski Equality and the Fluctuation Theorem. Finally we discuss the application of the Extended Jarzynski Equality to calculate the PMF along different reaction coordinates.