The induced phenomena caused by rolling or sliding action of a nano-particle on the work were considered in this study. The analysis was done by the molecular dynamics method.The effects on the removals of work, the roughness induced by nano-particle and the thickness of the damage layer caused by the depth of indentation, the shape of particle and the adhesive strength btween the particle and the work will also be discussed. The result shows that the particle in rolling process removed atoms easier than in sliding process. The removals of work in the process of rolling depend on the adhesive strength between the nano-particle and the work. More powerful of the adhesive strength will increase the amount of removal. But, the adhesive strength was not the only factor in the process of sliding. The rake angle between the nano-particle and the work was the important factor, too. In order to remove the atoms during sliding process, not only the adhesive strength must be strong enough but also the rake angle must be small enough. The increase of the strength between the particle in the shape of ball and the work will cause more amorphous atoms in both rolling and sliding process. The thickness of the damage layer of the work surface was also affected by the rake angle. But the roughness was little affected by the adhesive strength between the nano-particle and the work.

In order to better understand the interfacial peptide–water interaction, molecular dynamics simulations were made for both water, and an amphipathic peptide, LKα14, adsorbed at hy- drophobic and hydrophilic surfaces. Structural and orientational analyses were performed on both systems. Vibrational mode frequency and oscillator coupling were analyzed for the interfacial water. When looking at the peptide, DFT (density functional theory) ab initio calculations were performed to obtain the non linear vibrational information of the different side chains conformers. Non linear vibrational spectra derived from these results were simulated for both interfacial water and adsorbed peptide. The sum frequency vibrational spectra obtained were correlated to the orientation analysis results. Comparison with literature results were made for both spectral and orientational analysis. The results obtained of water at hydrophilic surfaces lead us to conclude that the absence of signal in the 3700 cm−1 region is due to a cancellation of strongly opposite oriented water layers rather than the absence of O–H oscillators at this vibrational frequency region. The hydrophobic and water-air simulation resulted in surprisingly strong similarity but with difference in the depth of those features. When analyzing the structure of LKα14, results showed that it retained an α helix conformation preference in bulk and adsorbed on surfaces. The hydrophobic surface results lead us to conclude a strong orientation of the leucine side chain towards the interface. Results from the adsorption of LKα14 at the hydrophilic surface proved that the adsorption process takes longer than for the hydrophobic surface. Due to results of water and peptide adsorption, we propose that the time scale of the adsorption process for peptide interaction with hydrophilic surface is partially due to the multiple, strongly orientated, water layers. / Graduate

Nanocrystalline materials could exhibit high mechanical yield strength. Nevertheless, with a high volume fraction in nanocrystalline material, grain boundaries and triple junctions which store a relatively high free energy, are thermally instable which potentially contribute to grain growth. On the other hand, since both grain boundaries and triple junctions are prior sites of impurity enrichment which could in return reduce the triple junction energy, alloys with impurity enriched in grain boundaries and triple junctions are widely applied to stabilize the nanostructures. However, past studies mainly focused on grain boundaries and the kinetic properties of triple junctions and their influences on the thermal stability of nanocrystalline metals is less studied. In this work, triple junction mobility and impurity diffusivity in triple junction are studied by molecular dynamics simulations. Specifically, interface random walk method due to thermal fluctuation which has been widely applied to extract grain boundary mobility is extended to study triple junction motion.

We use molecular dynamics to simulate the rapid directional solidification of binary alloy solid-liquid interface in the non-equilibrium state. In the pulling fixed velocities, we report the temperature, density, and diffusion coefficient of the interface. In cooling fast, controlling the velocities of solidification for the important parameter of this text¡Ait produces different changes that velocity value will be affected by atom potential energy and system temperature and density¡Athough the system is pulling a fixed velocities, that the speed of every atom of the system is all not constant .The velocity will be changed into the driving force that the solute will be separated and trapped. In the segregation regime, we recover the exponential form of the concentration profile within the liquid phase. Solute trapping is shown to settle in progressively as V is increased or reduction and our results are in good agreement with the theoretical predictions of Aziz.

A recently developed chemical vapor deposition (CVD) synthesis process called CoMoCAT yields single-wall carbon nanotubes (SWCNT)s of controlled diameter and chirality, making them extremely attractive for technological applications. In this dissertation, we use molecular dynamics simulations and density functional theory to study the selective growth mechanisms. In the CoMoCAT process, growth of SWCNTs happens on Co clusters with diameters of about 1 �. Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes and the reactive empirical bond order Brenner potential for C-C interactions are modified to describe interactions in such system. Classical molecular dynamics (MD) simulations using this force field are carried out to study the growth of SWCNT on floating and supported metal clusters. The effect of metal-cluster interactions on the growth process is discussed. The energy of forming one more ring at the open end of one-end-closed nanotubes with different chiralities, which is believed to be the basic step of nanotube elongation, are studied as a function of tube length. The energy and shape of the frontier highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of armchair nanotubes are studied and used to explain the change of reaction energy with tube length. Another property, the aromaticity of the rings forming a tube is also studied using Nucleus Independent Chemical Shift (NICS) as probe. NICS of rings in one-end-closed nanotubes with different chirality are studied as a function of tube length. NICS behavior of one-end-closed nanotube is compared with that of two-ends-open nanotube with the same chirality for nanotubes (6, 5) and (9, 1). Also (8, 3) nanotubes with one end open and the other end bonded to three different kinds of cap structures are compared. Since from both experimental observation and from our MD simulation results, the growth process of SWCNT can be affected by the interaction between Co clusters and their substrate, the performance of a series of CoN Clusters (N=1-4, 7, 10, 14, 15) adsorbed on MoC surface are studied with density functional theory.

The aim of DNA sequencing is to obtain the order of DNA composition comprising the base pairs A (adenine) T (thymine), and C (cytosine) G (guanine). The fast development of DNA sequencing technology allows us to better understand the relationships among diseases, inheritance, and individuality. Solid state nanopores have been recommended as the next generation platform for DNA sequencing due to its low-cost and high-throughput. In particular, nanopores fabricated from graphene sheets are extremely thin and structurally robust and have been extensively used in DNA detection in recent years. In DNA sequencing, the translocation of a DNA molecule through a nanopore is known to be a very complicated issue and is affected by many factors, such as ion concentration, thickness of the nanopore, and the nanopore diameter. The technique of molecular dynamic simulations has been a complementary tool to study DNA translocation through nanopores.       In this thesis, I summarize my work of computational studies of DNA sequencing using graphene nanopores. These studies include: DNA translocation through single-layer graphene nanopores of different diameters under conditions of various ion concentrations and applied voltages; DNA translocation through multilayer graphene nanopores varied from a single to a few layers; pulling out single strand DNA molecules from small graphene nanopores of different geometries. The major contributions of this work include: 1. Effects of bias voltage on DNA translocation time were investigated leading to the insight that lower applied voltages can extend the time of DNA translocation through monolayer graphene nanopores. The effect of salt concentration on the corresponding ionic current was studied. At a low ionic concentration (&lt; 0.3M), the current increases as DNA translocates through a nanopore. However, at a high ionic concentration (&gt;0.5M), the current decreases as DNA translocates through the nanopore. A theoretical model was proposed to explore the relationship between the current and the occupied nanopore area. We demonstrated that the DNA translocation time can be prolonged by narrowing the diameter of a nanopore properly and the reduction of the blockade current depends on the ratio of the unoccupied nanopore area to the total nanopore area. 2.  DNA translocation through multilayer graphene nanopores was studied by molecular dynamics simulations with the aim to achieve single-base resolution. We show that the DNA translocation time can be extended by increasing the graphene layers up to a moderate number (7) and that the current in DNA translocation undergoes a stepwise change upon DNA going through an multi-layer graphene (MLG) nanopore. A model was built to account for the relationship between the current change and the unoccupied volume of the MLG nanopore. We demonstrate that the blockade current is closely related to the unoccupied volume. The dynamics of DNA translocation depends specifically on the interaction of nucleotides with the graphene sheet. Thus, our study indicates that the resolution of DNA detection can be improved by increasing the number of graphene layers in a certain range and by modifying the surface of graphene nanopores. 3. The effect of graphene nanopore geometry on DNA sequencing has been assessed by steered molecular dynamics simulations. DNA fragments including A, T, C, G and 5-methylcytosine (MC) were pulled through graphene nanopores of different geometries with diameters down to ~1nm by steered molecular dynamics simulations. We demonstrated that the bases (A, T, C, G, and MC) can be indentified in single-base resolution by the characteristic force peak values in a circular graphene nanopore but not in graphene nanopores of other geometries. Symmetric nanopores are thus better suited to DNA sequence detection via force curves than asymmetric nanopores. This implies that the graphene nanopore surface should be modified as symmetric as possible to sequence DNA by an atomic force microscope or optical tweezers. This helps us to understand low-cost and time-efficient DNA sequencing in narrow nanopores. 4. The translocation time for different nucleotides to pass through graphene nanopores with certain diameters was investigated. It was found that the translocation times are different for different bases under a low electric field. The results indicate that DNA can be sequenced by the translocation time to pass through a graphene nanopore. 5. Inspired by the structure of K+ channel proteins, a series of oxygen doped graphene nanopores of different size were designed to discriminate the transport of K+ and Na+ ions. The results indicate that the ion selectivity of such biomimetic graphene nanopores can be simply controlled by the size of the nanopore.  Compared to K+, the smaller radius of Na+ leads to a much higher free energy barrier in the nanopore of a certain size. / <p>QC 20141212</p>

Polymer Derived Ceramics are a promising class of Materials that allow for higher levels of tunability and shaping that traditional sintering methods do not allow for. Polysiloxanes are commonly used as a precursor for these types of material because of their highly tunable microstructures by adjusting the side groups on the initial polymer. These Polymers are generally cross linked and pyrolyzed in inert atmospheres to form the final polymer. The microstructures of Polymer Derived Ceramics is complex and hard to observe due to the size of each microstructure region and the proximity in the periodic table that the elements present have. The process of forming phases such as Graphitic Carbon, Amorphous Carbon, Silicon Carbide. Silicon Oxide, and SiliconOxycarbide are not well understood. Simulation provides a route to understanding the phenomenon behind these phase formations. Specifically, Molecular dynamics simulation paired with the Reaxff forcefield provides a framework to simulate the complex processes involved in pyrolysis such as chemical reactions and a combination of thermodynamic and kinetic interactions. This Thesis examines firstly the size effect that a system can have on phase separation and the change in composition. Showing that size plays a major role in how the system develops and limits the occurrence of specific reactions. Secondly, this thesis shows that using polymer precursors with different initial polymer components leads to vastly different microstructures and yield. This provides insights into how the transition from polymer to ceramic takes place on a molecular level. / Master of Science / Ceramics and Polymers are seen all around the world. Polymers are used in many things from grocery bags to high performance panels on airplanes. Polymers are generally cheap to produce and can be molded into a variety of shapes. Ceramics are generally hard materials and are also used in a wide variety of situations from the concrete in buildings to coatings that protect turbine blades. Ceramics tend to be harder to form specific shapes and more costly to machine. Polymer derived polysiloxanes address this problem by being formed in the polymer state and then transformed into a ceramic by being heated in inert atmospheres. The process of the heating is very complex and the effect that different polymers have on the atomic level is not well understood. This thesis works to address this by using simulation to see what cannot be seen through experimentation alone.

DNA scaffolds self-assembled by short-stranded synthetic DNA can be tailored to build thermally reversible hydrogels with target binding sites. These hydrogels exhibit highly selective binding properties due to the specificity of DNA and also provide an aqueous environment for various reactions to happen within the network constraints. Hence, a careful study on the assembly mechanism and other physical aspects of DNA hydrogels is required to facilitate the future design and construction of such materials at the precise control. In this thesis, I present the work on well-designed DNA nano-stars as scaffolds for functional bulk materials with potential applications in bio-sensing. Chapter 1 starts with introducing the fundamental properties of DNA molecules, focusing on the advantages of utilising short-stranded DNA to programme and engineer micro- and macro- materials. Then it briefly reviews the field of rheology and micro-rheology, with the diffusing wave spectroscopy (DWS) technique illustrated explicitly as an example passive micro-rheology tool. Afterwards, a critical literature review on computational modelling of DNA systems is present, followed by the thesis outline at the end. Chapter 2 describes a simple DNA dendrimer system self-assembled from three-armed DNA nano-stars. The characterisation tools such as UV-vis spectroscopy, gel electrophoresis and dynamic light scattering (DLS) are introduced to verify the final production of the complex DNA structures. From this practice, we develop a routine for designing DNA scaffolds that yield optimal productivity. Chapter 3 investigates the mechanical properties of DNA hydrogels made of three-armed DNA nano-stars and how they change upon cooling and heating empolying DWS micro-rheology. The resulting viscoelastic moduli over a broad range of frequencies reveal a clear, temperature-reversible percolation transition coinciding with the melting temperature of the system's sticky ends. This indicates that we can achieve precise control in mechanical properties of DNA hydrogels, which is beneficial for designing more sensitive molecular sensing tools and controlled release systems. Chapter 4 develops a coarse-graining computational model of DNA hydrogels that resembles the system in Chapter 3 using LAMMPS, a classical molecular dynamics code. Thermodynamics, structural analysis and rheology tests were taken, qualitatively reproducing the physical phenomena of DNA assembly of the hydrogel network. Chapter 5 studies the internal behaviours of three-armed DNA complexes using oxDNA model also implemented in LAMMPS, with particular focus on the effect of the inert bases in the core and between double-stranded branches and single-stranded sticky ends. A deep insight into sequence-dependent behaviour of such complex structures can guide the parameter optimisation of the individual building blocks for the model described in Chapter 4. Chapter 6 concludes the thesis and presents an outlook for the future work that emerged out of my experimental and numerical studies.

Modeling of single-walled carbon nanotubes, multi-walled nanotubes and nanotube reinforced polymer composites using both the Finite Element method and the Molecular Dynamic simulation technique is presented. Nanotubes subjected to mechanical loading have been analyzed. Elastic moduli and thermal coefficient of expansion are calculated and their variation with diameter and length is investigated. In particular, the nanotubes are modeled using 3D elastic beam finite elements with six degrees of freedom at each node. The difficulty in modeling multi walled nanotubes is the van der Waal's forces between adjacent layers which are geometrically non linear in nature. These forces are modeled using truss elements. The nanotube-polymer interface in a nano-composite is modeled on a similar basis. While performing the molecular dynamic simulations, the geometric optimization is performed initially to obtain the minimized configuration and then the desired temperature is attained by rescaling the velocities of carbon atoms in the nanotube. Results show that the Young's modulus increases with tube diameter in molecular mechanics whereas decreases in molecular dynamics since the inter-atomic potential due to chemical reactions between the atoms is taken into consideration in molecular dynamics unlike in molecular mechanics.

The zinc metalloprotease neprilysin (NEP) has been shown to degrade small bioactive peptides. Crystal structures of seven NEP-inhibitor complexes and biochemical characterization of NEP activity have highlighted amino acid interactions that are crucial to ligand binding. Studies also indicate that NEP is one of a select group of metalloenzymes that degrade the amyloid-beta peptide (Aß) in vivo and in situ. Accumulation of neurotoxic Aß aggregates in the brain appears to be a causative agent in the pathophysiology of Alzheimer's Disease (AD). For this reason the enzymatic degradation of Aß has been studied extensively, but little is known about specific binding interactions underlying NEP degradation of Aß. Using known crystal structures of NEP, we have conducted comparative computational studies of ligand binding that predict NEP residues Arg 102 and 110 form binding interactions specific to Aß. These interactions may provide insight for using NEP degradation of Aß in AD therapy. / Bayer School of Natural and Environmental Sciences; / Chemistry and Biochemistry; / MS; / Thesis;