The synthesis of four homologous anthraquinones (AQ I-IV) bearing increasing lengths of polyethylene glycol (PEG) side chains and their binding to AT- and GC-rich DNA hairpins are reported. The molecules were designed such that the cationic charge is at a constant position and the ethylene glycol units chosen to allow significant increases in size with minimal changes in hydrophobicity. The mode and affinity of binding were assessed using circular dichroism (CD), nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). The binding affinity decreased as the AQ chain length increased along the series with both AT- and GC-rich DNA. ITC measurements showed that the thermodynamic parameters of AQ I-IV binding to DNA exhibited significant enthalpy-entropy compensation. The enthalpy became more favorable while the entropy became less favorable. The correlation between enthalpy and entropy may involve not only the side chains, but also changes in the binding of water and associated counterions and hydrogen bonding. The interactions of AQ I-IV with GC-rich DNA have been studied via molecular dynamics (MD) simulations. The geometry, conformation, interactions, and hydration of the complexes were examined. As the side chain lengthened, binding to DNA reduced the conformational space, resulting in an increase in unfavorable entropy. Increased localization of the PEG side chain in the DNA groove, indicating some interaction of the side chain with DNA, also contributed unfavorably to the entropy. The changes in free energy of binding due to entropic considerations (-3.9 to -6.3 kcal/mol) of AQ I-IV were significant. The kinetics of a homologous series of anthraquinone threading intercalators, AQT I-IV with calf thymus DNA was studied using the stopped-flow. The threading mechanisms of the anthraquinones binding to DNA showed sensitivity to their side chain length. Fitting of the kinetic data led to our proposal of a two step mechanism for binding of AQT I, bearing the shortest side chain, and a three step mechanism for binding of the three longer homologs. Binding involves formation of an externally bound anthraquinone-DNA complex, followed by intercalation of the anthraquinone for AQT I-IV, then isomerization to another complex with similar thermodynamic stability for AQT II-IV.

We apply a molecular dynamics (MD) simulation technique to complex molecules at interfaces. Partitioning of dendritic surfactants into clay gallery and Ab protein behavior near hydrated lipids are chosen for the purpose. Using a full atomistic model of dendritic surfactants, the confinement force profiles featuring oscillatory fashion at moderate layer separation of 10 to 25 Å were observed. Integration of the confinement forces led to free energy profiles, which, in turn, were used to determine the final morphology of the nanocomposite. From the free energy profiles, smaller and linear surfactants (G1 and G2L) are expected to intercalate into the clay comfortably, while larger surfactants (G2 and G3) are expected to form frustrated intercalated structures due to the location and depth of the free energy minima. This would agree with the previous observations. As primary steps to understand the Ab protein behavior under biological conditions, simulations of bulk water and hydrated lipids were performed and the results were compared with the literature. Hydrated lipids were simulated using a full atomistic model of lipids (dipalmitoylphosphatidylcholine) and water with a cvff force-field and it was found that structural properties such as the molecular head group area and membrane thickness were accurately produced with MD simulation. Systems of the protein Ab(1-42) in bulk water were simulated and some secondary structural change, with loss of part of the a-helical structure, occurred during the 1 ns of simulation time at 323K. The fragment Ab(31-42) with b-sheet conformation was also simulated in bulk water, and the extended b-sheet structure became a bent structure. Simulations of Ab(1- 42) or Ab(31-42) near lipid bilayers have been performed to investigate the structural property changes under biological conditions. The different nature of structural change was observed from the simulations of the protein or fragment in water and near lipid bilayers due to the different solvent environment. The protein has close contacts with the membrane surface. It was impossible to observe the conformational change to b-sheet and protein entrance into the lipid bilayer within 1 ns simulations.

In the beginning of this study, Molecular dynamics simulation is utilized to investigate the behavior of water molecules confined between two Au plates of (001) planes separated by gaps of 24.48, 16.32, 12.24, 11.22, and 10.20 . The simulation results indicate that the arrangements of the water molecules are dependent on the gap size. An inspection of the variation of the self-diffusion coefficients with the gap size suggests that the difference between the dynamic properties of the water molecules in the z-direction and the x-y plane decreases as the distance between the two Au plates increases. Moreover, we discuss the effects of different lattice structures, (100), (110) and (111)¡Aon the water molecules. The simulation results indicate that the arrangements of the water molecules are dependent on Au plate surface structures. The adsorption of the plate creates flat water layers in the proximity of each plate surface for (100) and (111) cases, but wave-like water layer for Au (110) plate. The absorbed water layer is the most close to plate surface for (110) lattice structure. Moreover, the self-diffusion coefficient in the z-direction for (110) case is the largest, meanwhile, the water molecules have a greater ability to diffuse in the x-y plane for (100) case. Finally¡Athe density distribution, velocity profile, and diffusion coefficients of the water film in a Couette flow are studied. Shear viscosity and its dependence on the shear rate of the water film are also examined in the present research. The diffusion of the whole film increases dramatically as the shear rate greater than a critical value. The shear viscosity decreases as the shear rate increases, especially for the water film with a small thickness, which implies the shear-thinning behavior for viscosity of the nanoconfined film. Moreover, increase in shear viscosity with a decrease in the film thickness can also be found in the present study.

This thesis proposes algorithms to construct various nanosystems such as nanotori, nanogear and nanojunctions based on graphite type structures, exploiting the observed pentagonal and heptagonal defects. These produced systems are then simulated to test for their thermal stability and for their electronic properties. A brief review of the methods used is also included.

A central goal of computational biophysics and biochemistry is to understand the behavior, interactions, and reactions of molecules, and to interpret and facilitate experimental design. The objective of this thesis research is to use the molecular modeling and simulation techniques to advance our understanding of principles in molecular structure properties, recognition and interaction at the atomic level. First, a physical molecular mechanics model is built to study the conformational properties of depsipeptide, which shows potential for engineered protein mimetics with controllable structure and function. We explore the possible kinase-substrate binding modes and the likelihood of an [alpha]-helix docking interaction within a kinase active site. Finally, efficient physical models based on a polarizable potential function are developed to describe the structural properties and calculate protein-ligand binding affinities accurately for both trypsin and matrix metalloproteinase. / text

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The practical applications of surfactant solutions in confined geometries require a thorough understanding of the system properties. Coarse-grained simulation techniques are useful for studying the qualitative behaviour of these systems, whereas the atomistic molecular dynamics (MD) technique can be used to obtain a molecular-level description. In this work, canonical MD simulations were performed using GROMACS version 4.0 to investigate the self-assembling behaviour of sodium octanoate (SO) confined between two parallel walls. In particular, the effects of gap size, wall type, and surfactant concentrations on the morphology of the surfactant aggregates were studied to gain in-depth knowledge of the system. The simulation results reveal that the morphology of the micelles formed between two parallel walls are affected not only by the gap size and surfactant concentration, but also by the nature and characteristics of the confining walls. With the graphite walls, most octanoate molecules are adsorbed at lower concentrations, but they form micellar aggregates as the surfactant concentration increases. Spherical micelles were found in the larger gaps (4 nm and 5 nm) but not in the smaller gap (3 nm), and the micellar shape also changes with increasing surfactant concentration. SO forms bilayer structures instead of spherical micelles between two silica walls. Interestingly, in the hydrophilic silica confinement, the orientation of these bilayers changes with gap sizes, whereas in the hydrophobic silica confinement, these bilayers remain perpendicular to the wall in all cases. Potentials of mean force between different molecules and atomic groups were determined under different conditions in order to develop a better understanding of the simulation results. It reveals, the presence of the confinement can alter the intermolecular interactions among the surfactant molecules, which, in turn, directly affects the self-assembling process, particularly the size and shape of the aggregates. Indeed, the formation of bilayers in silica wall confinement, as opposed to spherical micelles in graphite confinement, is caused by the enhanced electrostatic interactions between the charged atoms in the solution. The results of this study are expected to provide further insight into the self-assembling behaviour of confined surfactant systems, and may ultimately lead to the development of novel nanomaterials.

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Ag nanoparticle (NP) paste was fabricated and used to bond Cu wire to Cu foil at low temperatures down to 433 K. The relatively low bonding temperature promotes this method to be used in polymer-based flexible electronics, which cannot withstand high bonding temperatures due the possible melting of the polymer substrate. Unlike low-temperature soldering techniquies, bonds formed by this method was proved to withstand temperatures higher than the bonding temperature, which also promotes it to be used in electronics that operate at high temperatures. The Ag NP paste was developed by increasing the concentration of 50 nm Ag NP sol from 0.001 vol.% to 0.1 vol.% by centrifugation. The 0.001 vol.% Ag NP sol was fabricated in water by reducing silver nitrate (AgNO3) using sodium citrate dihydrate (Na3C6H5O7.2H2O). The bond was formed by solid state sintering among the individual Ag NPs and solid state bonding of these Ag NPs onto both Cu wire and foil. Metallurgical bonds between Ag NPs and Cu were confirmed by transmission electron microscopy (TEM). The Ag NPs were coated with an organic shell to prevent sintering at room temperature. It was found that the organic shell decomposed at 433 K, defining the lowest temperature at which a bond could be formed. Shear tests showed that the joint strength increased as the bonding temperature increased due to enhanced sintering of Ag NPs at higher temperatures. For better understanding of the melting and the sintering kinetics of Ag NPs, a molecular dynamics (MD) simulation based on the embedded atom method (EAM) was conducted to different sizes of Ag NPs with diameters between 4 nm and 20 nm. Programmed heating of an equal rate was applied to all sizes of NPs to find the complete melting and surface premelting points and sintering kinetics of the Ag NPs. The initial structural configuration of the Ag NPs was FCC truncated octahedral, which found to be stable for this size range of NPs. As a first step toward drawing a phase map of stable solid phases of Ag NPs at different temperatures and sizes of Ag NPs, the stability of the FCC truncated octahedral was studied for Ag NPs in size range of 1 nm to 4 nm. The smallest Ag NPs at which this configuration is stable was determined as 1.8 nm. Unlike the previous theoretical models, this MD model predicted both complete melting and surface premelting points for a wider size range of NPs. Melting kinetics showed three different trends that are, respectively, associated with NPs in the size ranges of 4 nm to 7 nm, 8 nm to 10 nm, and 12 nm to 20 nm. Ag NPs in the first range melted at a single temperature without passing through a surface premelting stage. Melting of the second range started by forming a quasi-liquid layer that expanded to the core, followed by the formation of a liquid layer of 1.8 nm thickness that also subsequently expanded to the core with increasing temperature, completing the melting process. For particles in the third range, the 1.8 nm liquid layer was formed once the thickness of the quasi-liquid layer reached 5 nm. The liquid layer expanded to the core and formed thicker stable liquid layers as the temperature increased toward the complete melting point. The ratio of the quasi-liquid layer thickness to the NP radius showed a linear relationship with temperature. Sintering kinetics of two Ag NPs in the size range of 4 nm to 20 nm, and sintering of three and four Ag NPs of 4 nm diameter was also studied by MD simulation. The sintering process passed through three main stages. The first was the neck formation followed by a rapid increase of the neck radius to particle radius ratio at 50 K for 20 nm particles and at 10 K for smaller NPs. The second was characterized by a gradual linear increase of the neck radius to particle radius ratio as the temperature of the sintered structure was increased to the surface premelting point. A twin boundary was formed during the second stage that relaxed the sintered structure and decreased the average potential energy (PE) of all atoms. The third stage of sintering was a rapid shrinkage during surface premelting of the sintered structure. Based on pore geometry, densification occurred during the first stage for three 4 nm particles and during the second stage for four 4 nm particles. Sintering rates obtained here were higher than those obtained by theoretical models generally used for predicting sintering rates of micro-particles.