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Multi-Scale Modeling Of Biophysical Phenomena: Ionic Transport, Biomineralization, And Force Spectroscopy

Biophysics is the study of the complex physical processes occurring in biological systems that are responsible for life. This dissertation addresses three important topics in biophysics: ionic transport, biomineralization, and force spectroscopy. Ionic transport involves the passage of ions through a special class of hollow, transmembrane proteins called ion channels which regulate the movement of charged species across nearly all biological membranes with varying degrees of specificity. Despite the fundamental importance of these channels to many physiological processes little is known about how channel structure and composition couple to determine its function. Deriving inspiration from these systems, a simple computational platform is developed to study the salient features of these channels in order to better understand the fundamental physics of these systems. The results of this work indicate that a converging-diverging region formed within the pore to create a single constriction is the most effective method to regulate the passage of ions through the pore. By controlling the geometry of the constriction the local potential and chemical gradients can be manipulated to tailor the channel for specific applications. The process of selective extraction and incorporation of local elements from the surrounding environment into functional structures under strict biological control is known as biomineralization. As an initial step to gain a more fundamental understanding of directed crystallization of zinc oxide molecular dynamics simulations were performed to study the conformational behavior of two experimentally derived biomimetic peptides in a precursor solution. Substantial differences in the conformational properties and affinity for zinc and hydroxide ions in solution were observed. These findings are in qualitative agreement with experimental observations. The mechanical response of biopolymers such as RNA and DNA to externally applied forces is a topic that has received wide interest both experimentally and theoretically. In the first of two separate force spectroscopy studies, the mechanical response of linear uncharged polymer chains of variable molecular weight subjected to repeated pulling-retraction cycles in poor solvent was investigated. It was found that the observed hysteresis in this system is highly dependent on the speed at which the chain is perturbed. In the second study, the force-induced globule-coil transition of a linear polyelectrolyte chain in poor solvent was examined. It was observed that the magnitude of the change in the degree of ionization of the chain at the transition is a strong function of counterion size and Coulombic strength.
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