Thesis (Ph. D.)--Syracuse University, 2009. / "Publication number: AAT 3385846 ."

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.

Electron transport is a fundamental mechanism in a variety of biological systems such as photosynthesis and aerobic respiration. However, the transport has long been considered to occur only over short distances (< 1 μm), primary by metalloproteins. Recently, the conduction of electrons over large distances (> 10 μm) along networks of microbial pilin filaments known as microbial nanowires has been invoked to explain a wide range of important redox phenomena that influence carbon and mineral cycling in soils and sediments, bioremediation, corrosion, interspecies electron transfer and anaerobic conversion of organic wastes to methane or electricity. However, there has never been any direct experimental demonstration of this long-distance electron transport. In fact, previous measurements of microbial biofilms have noted just the opposite: that biofilms act as insulators, not conductors. In this thesis, we reconcile these confounding observations with the demonstration that biofilms of several species of commonly studied microorganisms do function as insulators, whereas biofilms of Geobacter sulfurreducens , common in soils and sediments can form a conductive matrix, with a conductivity comparable to synthetic conductive polymers. We show that biofilms are capable of conducting electrons over 1.25 cm, many thousands of times the size of a cell. Biofilm conductivity was found to be proportional to the abundance of pilin filaments and the conductivity of sheared pilins was comparable to biofilms. We also found that biofilm conductivity regulates fuel cell current density. We demonstrate that electron transport in the biofilms does not occur via localized charge carriers known as cytochromes, as almost universally predicted, but rather through delocalized electronic states. Moreover, we report a quantum mechanical interference phenomenon of weak localization in pilin nanowires. Additionally, we demonstrate that cytochromes can be used to store electrons with capacitance comparable to commercial supercapacitors. Furthermore, the degree of conductivity and capacitance within the films can be tuned via changes in gene expression or gate bias. This study demonstrates that pilin-associated long-distance electron transport through a microbial matrix is feasible, establishes approaches that could be used for evaluating the possibility of electron flow through natural microbial communities, and demonstrates the potential for developing novel bioelectronic materials.

<p> Interactions between particles and their environment can alter the dynamics of biological systems. In crowded media like the cell, interactions with obstacles can introduce anomalous subdiffusion. Active matter systems, <i>e.g. </i>, bacterial swarms, are nonequilibrium fluids where interparticle interactions and activity cause collective motion and dynamical phases. In this thesis, I discuss my advances in the fields of crowded media and active matter. For crowded media, I studied the effects of soft obstacles and bound mobility on tracer diffusion using a lattice Monte Carlo model. I characterized how bound motion can minimize the effects of hindered anomalous diffusion and obstacle percolation, which has implications for protein movement and interactions in cells. I extended the analysis of binding and bound motion to study the effects of transport across biofilters like the nuclear pore complex (NPC). Using a minimal model, I made predictions on the selectivity of the NPC in terms of physical parameters. Finally, I looked at active matter systems. Using dynamical density functional theory, I studied the temporal evolution of a self-propelled needle system. I mapped out a dynamical phase diagram and discuss the connection between a banding instability and microscopic interactions.</p><p>

Complexation found in nature was the inspiration and motivation to study three model systems to gain understanding into the underlying parameters that govern these events. Static and dynamic light scattering was predominately used to understand the complexation in three model systems: complexation of antimicrobial polymers with biomimetic vesicles, the complexation of protein to a semi-flexible polyelectrolyte and with a flexible polyelectrolyte. Characterization of antimicrobial polymers in solution and their interactions with biomimetic vesicles were investigated in order to understand how antimicrobial polymers interacted with and killed bacteria. These studies observed that an aggregation of the vesicles correlated with antimicrobial activity. For these synthetic polymer systems, aggregation appeared to be a necessary component for antimicrobial activity,but was not indicative of activity. Inspired by complexation found in nature between DNA and RNA and proteins model polyelectrolyte-protein systems were also investigated. The focus of this section was to understand how polymer flexibility, concentration, protein concentration, and ionic strength affected the phase behavior and presence of soluble aggregates in solution. Construction of phase diagrams for both semi-flexible and flexible polyelectrolye systems dsDNA and hyaluronic acid showed different phase diagrams,yet amazingly both systems showed a spontaneous selection of size of ∼230nm away from any phase boundary and was irrespective of salt concentration, polymer concentration, persistence length or protein concentration. It was possible to gain insight into the internal packing of these two polyelectrolyte-protein complexes through static light scattering and fractal dimension analysis. Comparisons of the fractal dimension analysis of the DNA-lysozyme and HA-lysozyme was not affected by salt concentration and from analysis of the fractal dimension it was observed DNA-lysozyme aggregates, had a denser aggregate structure than the HA-lysozyme aggregate. It was also observed that away from the phase boundaries in each system the aggregate sizes and fractal dimensions were irrespective of polymer, salt, persistence length or protein concentration.

Small devices capable of self-propulsion have potential application in areas of nanoscience where autonomous locomotion and programmability are needed. The specific base-pairing interactions that arise from DNA hybridisation permit the programmed assembly of matter and also the creation of controllable dynamical systems. The aim of this thesis is to use the tools of DNA nanotechnology to design synthetic active matter at the micro and nano scales. In the first section, DNA was used as an active medium capable of transporting information faster than diffusion in the form of chemical waves. DNA waves were generated experimentally using a DNA autocatalytic reaction in a microfluidic channel. The propagation velocity of DNA chemical waves was slowed down by creating concentration gradients that changed the reaction kinetics in space. The second section details the synthesis of chemically-propelled particles and the use of DNA as a 'programmable glue' to mediate their interactions. Janus micromotors were fabricated by physical vapour deposition and a wet-chemical approach was demonstrated to synthesise asymmetrical catalytic Pt-Au nanoparticles that function as nanomotors. Dynamic light scattering measurements showed nanomotor activity that depends on H₂O₂ concentration, consistent with chemical propulsion. Gold nanoparticles/Origami hybrids were assembled in 2D lattices of different symmetries arranged by DNA linkers. The third section details the design process and synthesis of nanomotors using DNA as a structural scaffold. 3D DNA Origami rectangular prisms were functionalised site-specifically with bioconjugated catalysts, i.e. Pt nanoparticles and catalase. Enzymatic nanomotors were also conjugated to various cargoes and their motor activity was demonstrated by Fluorescence Correlation Spectroscopy. In the final section, control mechanisms for autonomous nanomotors are studied, which includes the conformational change of DNA aptamers in response to chemical signals, as well as a design for an adaptive dynamical system based on DNA/enzyme reaction networks.