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.

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.

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.

A new method is proposed for correctly modeling the long range interaction between a fluid and a bounding wall in atomistic simulations. This method incorporates the molecular structure of the solid substrate while allowing for a finite interaction cutoff by making a proper estimation of long range correction for the fluid-wall interaction. The method is then applied to a molecular dynamic simulation of a spreading droplet. Conparison to simulations using several other previously used methods shows that the long range correction can be significant in some circumstances. / Singapore-MIT Alliance (SMA)

For decades, epitaxy is used in nanotechnologies and semiconductor fabrications. So far, it's the only affordable method of high quality crystal growth for many semiconductor materials. Heterostructures developed from these make it possible to solve the considerably more general problem of controlling the fundamental parameters inside the semiconductor crystals and devices. Moreover, as one newly arising study and application branch of epitaxy, selective area growth (SAG) is widely used to fabricate materials of different thicknesses and composition on different regions of a single wafer. All of these new and promising fields have caught the interests and attentions of all the researchers around the world. In this work, we will study the stress and strain analysis of epitaxy in nano-scale materials, in which we seek a methodology to bridge the gap between continuum mechanical models and incorporate surface excess energy effects, which can be obtained by molecular dynamical simulations. We will make a brief description of the elastic behavior of the bulk material, covering the concepts of stress, strain, elastic energy and especially, the elastic constants. After that, we explained in details about the definitions of surface/interface excess energy and their characteristic property tensors. For both elastic constants and surface excess energy, we will use molecular dynamic simulations to calculate them out, which is mainly about curve-fitting the parabola function between the total strain energy density and the strain. After this, we analyzed the stress and strain state in nanoisland during the selective area growth of epitaxy. When the nanoisland is relaxed, the lattice structure becomes equilibrated, which means the total strain energy of system need to be minimized. Compared to other researcher's work, our model is based on continuum mechanics but also adopts the outcome from MD simulations. By combining these microscopic informations and those macroscopic observable properties, such as bulk elastic constants, we can provide a novel way of analyzing the stress and strain profile in epitaxy. The most important idea behind this approach is that, whenever we can obtain the elastic constants and surface property tensors from MD simulations, we can follow the same methodology to analyse the stress and strain in any epitaxy process. This is the power of combining atomistic simulations and continuum method, which can take considerations of both the microscopic and macroscopic factors.

Medium chain fatty acids (MCFAs) are essential molecules for a wide range of pharmaceutical, biotechnological, and industrial applications. These are naturally occurring saturated or unsaturated fatty acids containing 6-12 carbons with complex and pH sensitive aggregation. Medium chain fatty acids such as capric acid (C10) or lauric acid (C12) have additionally been shown to exhibit antibacterial activity. A number of studies have observed the aggregation behavior of long chain fatty acid using the titration curves by molecular dynamic (MD) simulations.  In this study, we performed constant-pH coarse-grained MD simulations to determine pKa values and titration behavior using a two-states model for C10 and C12. In the simulations, pH was varied between 2 to 8 and pKa values were determined using the Hill equation. The pKa for C10 (capric acid) was found to be 4.8 and for C12 (lauric acid) 5.4, in good agreement with the literature values (4.9 and 5.3, respectively).