Cytochrome c oxidase (CcO), the terminal enzyme in the electron transport chain, couples proton pumping to the reduction of dioxygen into water. The coupling mechanism remains to be elucidated. Previous studies have identified several mutations within CcO's primary proton uptake pathway (the D-channel) that decouple proton pumping from redox activity. Here, I examine the molecular basis for decoupling in single and double mutants of highly conserved residues, D132 and N139, in order to gain insight into the coupling mechanism. In particular, I use molecular dynamics and free energy simulations of a new, unconstrained model of bacterial CcO embedded in a solvated lipid bilayer to investigate how such mutants affect functional hydration and ionic selectivity in the D-channel. Results support earlier mechanistic insights obtained in our laboratory from simplified molecular models and predict a new, testable hypothesis by which cations such as K+ may inhibit proton pumping in charged mutants of N139.

Cytochrome c oxidase (CcO), the terminal enzyme in the electron transport chain, couples proton pumping to the reduction of dioxygen into water. The coupling mechanism remains to be elucidated. Previous studies have identified several mutations within CcO's primary proton uptake pathway (the D-channel) that decouple proton pumping from redox activity. Here, I examine the molecular basis for decoupling in single and double mutants of highly conserved residues, D132 and N139, in order to gain insight into the coupling mechanism. In particular, I use molecular dynamics and free energy simulations of a new, unconstrained model of bacterial CcO embedded in a solvated lipid bilayer to investigate how such mutants affect functional hydration and ionic selectivity in the D-channel. Results support earlier mechanistic insights obtained in our laboratory from simplified molecular models and predict a new, testable hypothesis by which cations such as K+ may inhibit proton pumping in charged mutants of N139.

In the last few decades, an increasing number of physicists specialized in soft matter, including polymers, have turned their attention to biologically relevant materials. The properties of various molecules and fibres, such as DNA, RNA, proteins, and filaments of all sorts, are studied to better understand their behaviours and functions. Self-assembled biological membranes, or lipid bilayers, are also the focus of much attention as many life processes depend on these. Small lipid bilayers vesicles dubbed liposomes are also frequently used in the pharmaceutical and cosmetic industries. In this thesis, work is presented on both the elastic properties of polymers and the response of lipid bilayer vesicles to extrusion in narrow-channels. These two areas of research may seem disconnected but they both concern deformed soft materials. The thesis contains four articles: the first presenting a fundamental study of the entropic elasticity of circular chains; the second, a simple universal description of the effect of sequence on the elasticity of linear polymers such as DNA; the third, a model of the symmetric thermophoretic stretch of a nano-confined polymer; the fourth, a model that predicts the final sizes of vesicles obtained by pressure extrusion. These articles are preceded by an extensive introduction that covers all of the essential concepts and theories necessary to understand the work that has been done.

Metal-organic frameworks (MOFs), a new class of porous solids comprised of metal-containing nodes linked by organic ligands, have become promising materials for gas separations. In particular, their flexible chemistry makes them attractive for CO2 capture from flue gas streams in post-combustion plants. Although numerous efforts have been exerted on the investigation of MOFs for CO2 capture, the exploration of the effects from coexisting components present in very dilute proportions in flue gases is limited because of the experimental difficulty to determine the coadsorption of CO2 with trace components. In this regard, molecular simulations show superiority. In this study, molecular simulations are used to estimate the influence of impurities: water, O2, and SO2 on post-combustion CO2 capture in MOFs. Firstly, two MOFs with coordinatively unsaturated metal sites (CUMs), HKUST-1 and Mg-MOF-74 are explored. Increase of CO2 adsorption is observed for hydrated HKUST-1; on the contrary, the opposite water adsorption behavior is observed in hydrated Mg-MOF-74, leading to decrease of CO2 adsorption. Further, water effects on CO2 capture in M-HKUST1 (M = Mg, Zn, Co, Ni) are evaluated to test whether comparing the binding energy could be a general method to evaluate water effects in MOFs with CUMs. It is found that the method works well for Zn-, Co-, and Ni-HKUST1 but partially for Mg-HKUST1. In addition, the effects of O2 and SO2 on CO2 capture in MOFs are also investigated for the first time, showing that the effects of O2 may be negligible but SO2 has negative effects in the CO2 capture process in HKUST-1 systems. Secondly, the influences of water on CO2 capture in three UiO-66 MOFs with functional groups, –NH2, –OH and –Br are explored, respectively. For UiO-66-NH2 and -OH, the presence of water lowers CO2 adsorption significantly; in contrast, water shows much smaller effects in UiO-66-Br. Moreover, the presence of SO2 decreases water adsorption but enhances CO2 uptakes slightly in both UiO-66-NH2 and -Br. Finally, the effects of impurities on CO2 capture in a MOF with suitable pore size (PCN-200) are analyzed. The adsorption of both CO2 and N2 decrease substantially even with 1% water present in the mixture. In addition, the presence of low SO2 does not show obvious effect in PCN-200. However, a lower CO2 adsorption is observed for a mixture with a high SO2 content. In collaboration with experimental groups, the performances of three new MOFs in CO2 capture are evaluated using molecular simulations. The computational results demonstrate the feasibility of precisely designing single-molecule traps (SMT) for CO2 capture. Also, a multi-functional MOF with micro-porosity, open Cu2+ sites and amine groups has also proved computationally the selective adsorption of CO2 over CH4 and N2. Last, we demonstrate that charge separation is an effective strategy for improving CO2 capture in MOFs.

The complete set of Kubo conductivity tensors are computed for two- and three-dimensional linear magnetic null systems using collisionless single-particle simulations. Chaos regions are constructed for each case, along with the complete Lyapunov spectrum. It is found that stochastic frequency mixing of particle bounce motion, as well as gyromotion, contribute significantly to the conductivity. For many cases, the conductivity curve is well approximated by power-laws, resulting in a divergent value of the direct-current conductivity, while others can be described by a sum of Maxwellian curves. The energy dissipation of these systems is also briefly discussed.

Heterogeneity of surfaces is often included in mathematical treatments of colloid transport and deposition as an afterthought, if at all. Most previous models of colloid transport and deposition have employed idealizations and simplifications such as assuming smooth collector surfaces with uniform chemical properties. This research proposes a new heterogeneous interaction model (HIM) to account for colloidal forces between particles and heterogeneous substrates. Extending the approach employed with the HIM, the inclusion of convection and diffusion in the model leads to a Lagrangian particle tracking model (PTM) for predicting colloid transport and deposition on a planar substrate containing one or more protruding asperities in the presence of shear flow. An important part of the PTM is an accurate rendering of the fluid flow field around the model substrate, which is obtained from a numerical solution of the Stokes equations. A simple approximation of the particle-substrate hydrodynamic interactions was developed for the PTM based on the universal hydrodynamic correction functions. This model was employed to quantitatively predict how presence of asperities on a collector can influence the deposition of particles on the substrate in shear flow. Flow field modifications due to the substrate's physical heterogeneity -- coupled with hydrodynamic interactions -- and the lateral migration (colloidal) forces near chemically heterogeneous substrates yield remarkably diverse deposition probabilities and deposit morphologies. The general approach of this research, which involves the use of the HIM in conjunction with the Brownian PTM, results in the first simulation tool of its kind to attempt to quantify deposition on heterogeneous substrates.

Knowledge about the structure, conformation and dynamics of carbohydrates is important in our understanding of the way carbohydrates function in biological systems, for example in intermolecular signaling and recognition. This thesis is a summary of five papers studying these properties in carbohydrate-containing molecules with NMR spectroscopy and molecular dynamics simulations. In paper I, the ring-conformations of the six-membered rings of two carbaiduronic analogs were investigated. These carbasugars could potentially be used as hydrolytically stable mimics of iduronic acid in drugs. The study showed that the equilibrium is entirely shifted towards the 4C1 conformation. Paper II is an investigation of the conformational flexibility and dynamics of two (1→6)-linked disaccharides related to an oligosaccharide epitope expressed on malignant tumor cells. In paper III, the conformational space of the glycosidic linkage of an alfa-(1→2) linked mannose disaccharide present in N- and O-linked glycoproteins, was studied. A maximum entropy analysis using different priors as background information was used and four new Karplus equations for 3JC,C and 3JC,H coupling constants, related to the glycosidic linkage, were presented. Paper IV describes a structural elucidation of the exopolysaccharide (EPS) produced by Streptococcus thermophilus ST1, a major dairy starter used in yoghurt and cheese production. The EPS contains a hexasaccharide repeating unit of d-galactose and d-glucose residues, which is a new EPS structure of the S. thermophilus species. In paper V, the dynamics of three generations of glycodendrimers were investigated by NMR diffusion and 13C NMR relaxation studies. Three different correlations times were identified, one global correlation time describing the rotation of the dendrimer as a whole, one local correlation time describing the reorientation of the C-H vectors, and one correlation time describing the pulsation of a dendrimer branch.

Zigbee is a relatively new wireless mesh networking standard with emphasis on low cost and energy conservation. It is intended to be used in wireless monitoring and control applications such as sensors and remotely operated switches where the end devices are battery powered. Because it is a recent technology there is not sufficient understanding on how network architecture and configuration affect power consumption of the battery powered devices. This research investigates the power consumption and delivery ratio of Zigbee wireless mesh and star networks for a single sink real time monitoring system at varying traffic rates and the beacon and non beacon mode operation of its underlying standard IEEE 802.15.4 in the star network architecture. To evaluate the performance of Zigbee, the network operation was simulated using the simulation tool NS-2. NS-2 is capable of simulating the entire network operation including traffic generation and energy consumption of each node in the network. After first running the simulation it was obvious that there were problems in the configuration of the simulator as well as some unexpected behaviour. After performing several modifications to the simulator the results improved significantly. To validate the operation of the simulator and to give insight on the operation of Zigbee, a real Zigbee wireless network was constructed and the same experiments that were conducted on the simulator were repeated on the Zigbee network. The research showed that the modified simulator produced good results that were close to the experimental results. It was found that the non beacon mode of operation had the lowest power consumption and best delivery ratio at all tested traffic rates. The operation of Zigbee mesh and star networks were compared to the results for IEEE 802.15.4 star networks in non beacon mode which revealed that the extra routing traffic sent by the Zigbee networking layers does contribute significantly to the power consumption, however even with the extra routing traffic, power consumption is still so low that it the battery life of the device would be limited by the shelf life of the battery, not by the energy consumption of the device. This research has successfully achieved its objectives and identified areas for future development. The simulator model for NS-2 could be improved to further increase the accuracy of the results as well as include the Zigbee routing layers and the experimental results could be improved by a more accurate power consumption data acquisition method.

Asymmetrical dispersal is when dispersal rates differ in opposite directions. This is expected to be common in natural populations. This work aims to study the symmetrical and asymmetrical dispersal through the use of a simulation program, simuPOP. The main questions were (i) "what are the differences between asymmetrical and symmetrical dispersal in relation to genetic differentiation and equilibrium?" and (ii) "Is it possible to identify asymmetrical dispersal structure from observed patterns of genetic differentiation between populations, and variation within populations?". To address these questions, simulations were conducted with two and three subpopulations subject by three different dispersal rate contrasts and several spatial patterns of dispersal. Variables were estimated at drift-dispersal equilibrium included genetic differentiation between subpopulations (θ) and heterozygosity. With pairwise θ for three subpopulations it was possible to determine whether the metapopulations were subject to symmetrical or asymmetrical dispersal and sometimes to identify the structure of dispersal. Equilibrium heterozygosities did not aid diagnosis of asymmetrical dispersal patterns. I also checked the applicability of two predictions originally made for symmetrical dispersal: Wright's expectations for θ at equilibrium, and Whitlock's expectations fro time to half of equilibrium θ. In most cases these expectations were not applicable. Study of asymmetrical dispersal on living organisms is strongly encouraged.

Zigbee is a relatively new wireless mesh networking standard with emphasis on low cost and energy conservation. It is intended to be used in wireless monitoring and control applications such as sensors and remotely operated switches where the end devices are battery powered. Because it is a recent technology there is not sufficient understanding on how network architecture and configuration affect power consumption of the battery powered devices. This research investigates the power consumption and delivery ratio of Zigbee wireless mesh and star networks for a single sink real time monitoring system at varying traffic rates and the beacon and non beacon mode operation of its underlying standard IEEE 802.15.4 in the star network architecture. To evaluate the performance of Zigbee, the network operation was simulated using the simulation tool NS-2. NS-2 is capable of simulating the entire network operation including traffic generation and energy consumption of each node in the network. After first running the simulation it was obvious that there were problems in the configuration of the simulator as well as some unexpected behaviour. After performing several modifications to the simulator the results improved significantly. To validate the operation of the simulator and to give insight on the operation of Zigbee, a real Zigbee wireless network was constructed and the same experiments that were conducted on the simulator were repeated on the Zigbee network. The research showed that the modified simulator produced good results that were close to the experimental results. It was found that the non beacon mode of operation had the lowest power consumption and best delivery ratio at all tested traffic rates. The operation of Zigbee mesh and star networks were compared to the results for IEEE 802.15.4 star networks in non beacon mode which revealed that the extra routing traffic sent by the Zigbee networking layers does contribute significantly to the power consumption, however even with the extra routing traffic, power consumption is still so low that it the battery life of the device would be limited by the shelf life of the battery, not by the energy consumption of the device. This research has successfully achieved its objectives and identified areas for future development. The simulator model for NS-2 could be improved to further increase the accuracy of the results as well as include the Zigbee routing layers and the experimental results could be improved by a more accurate power consumption data acquisition method.