| Application of force to individual rod-like macromolecules can cause structural transformations. We address the occurrence of such transformations in a class of molecules called coiled-coils, and in DNA. These transitions are characterized by a distinctive force-extension curve, and by the existence of two or more metastable structural states. We propose that the structural transition occurs via the motion of a folded/unfolded interface or phase boundary along the length of the molecule. The interface separates these two metastable states and its mechanics are governed by the Abeyaratne-Knowles theory of phase transitions. The mobility of the phase boundary is determined using a kinetic relation and the second law of thermodynamics. We replicate, using relevant parameters, several different boundary conditions and solution conditions used in single molecule experiments. We derive an expression for the thermodynamic driving force across the interface and also show that the process is reversible in the chosen regime. We use a finite difference computational scheme that is capable of tracking moving phase boundaries.;We show how a variety of experimentally observed force-extension behaviors can be reproduced within a common theoretical framework. By choosing an appropriate kinetic relation for the unfolding conditions and the macromolecule under consideration, we have been able to model unfolding processes in a number of molecules. Connections are made with several existing theories, experiments and simulation studies, thus demonstrating the effectiveness of the phase transitions-based approach in a biological setup.;Finally, we study the consequences of molecular unfolding on the networks of rod-like macromolecules. We focus on the evolution of the angular distribution of fibers under the application of varying force. We present a method that is capable of tracking the motion and properties of individual fibers while they are undergoing unfolding. We discuss a modification to the affine deformation assumption and also show that experimental results for evolution of network order parameter can be recreated using a simple excluded volume formulation, thereby demonstrating the effective coupling of constitutive laws for individual molecules and empirical constraints on the entire volume under consideration. |
