Browsing by Subject "Molecular Dynamics"
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Item Atomic Scale Details of Defect-Boundary Interactions(2014-12-18) Chen, DiThe study is aimed to understand atomic scale details of defect-boundary interactions, which are critical to develop radiation tolerant fuel cladding materials for harsher neutron environments. By means of molecular dynamics simulations, we addressed the key questions of (1) how defects are trapped by a grain boundary, (2) how defect are annihilated at a grain boundary, and (3) what are upper limits of radiation tolerance of boundary-engineered metals. The modeling is performed by using large-scale atomic/molecular massively parallel simulator (LAMMPS) code and pure Fe is selected as the model material. For mechanism of defect tapping towards a grain boundary, we find that, instead of the general consensus that the trapping is caused by biased defect diffusions due to relatively lower defect formation energies at a grain boundary, long range defect migration is realized by creation of chain like defects. A chain is induced by the stress field around a defect, and is formed by pushing its immediate lattice atom neighbor into an interstitial site. This newly formed interstitial can induce formation of another vacancy-interstitial pair along the chain direction. The process is repeated or simultaneously occurs along the chain. Thus, a chain consists of alternately positioned interstitials and vacancies. The subsequent defect annihilation between neighboring defects on the chain leads to the defect transport. We identify three types of defect transport models which involve different chains. For mechanism of defect annihilation on a grain boundary, we find that both defect transport and interstitial-vacancy recombination are realized by formation of similar chain-like defects. The vacancy and interstitial along the chain correspond to the sites of their corresponding formation energy minima, thus the capability to form such chains is determined by the patterns of boundary defect formation energies. For a boundary of small misorientation angle, chain formation is allowed to occur in one direction only and all chains are parallel to each other. At large angles, however, chains are so close to each other that new allowable chain directions are created by linking patterns from different chains. This suggests that large angle boundaries are more efficient to move and recombine defects. The modeling further calculates the energy barriers for chain-mediated defect recombination under different boundary configurations. These findings lead to the conclusion that defect sink strengths of grain boundaries are determined by not only the efficiency to transport to boudnaries, but also the efficiency to recombine boundary defects. Otherwise, the difficulty to remove defects will quickly turn of the sink property. This is confirmed by comparing the width of defect denuded zone created around a boundary, in a cell randomly bombarded by Fe self-ions to different damage levels. A large angle boundary is more preferred to achieve maximum radiation tolerance.Item Dynamic Response Of Complex Materials Under Shock Loading(2012-10-19) Arman, BedriWe investigated dynamic response of Cu46Zr54 metallic glass under adiabatic planar shock wave loading (one-dimensional strain) with molecular dynamics simulations, including Hugoniot (shock) states, shock-induced plasticity, and spallation. The Hugoniot states are obtained up to 60 GPa along with the von Mises shear flow strengths, and the dynamic spall strengths, at different strain rates and temperatures. For the steady shock states, a clear elastic-plastic transition is identified. The local von Mises shear strain analysis is used to characterize local deformation, and the Voronoi tessellation analysis, the corresponding local structures at various stages of shock, release, tension and spallation. The plasticity in this glass, manifested as localized shear transformation zones, is of local structure rather than thermal origin, and void nucleation occurs preferentially at the highly shear-deformed regions. The Voronoi and shear strain analyses show that the atoms with different local structures are of different shear resistances that lead to shear localization. Additionally, we performed large-scale molecular dynamics simulations to investigate plasticity in Cu/Cu46Zr54 glass nanolaminates under uniaxial compression. Partial and full dislocations are observed in the Cu layers, and screw dislocations, near the amorphous?crystalline interfaces (ACIs). Shear bands are directly induced by the dislocations in the crystalline Cu layer through ACIs, and grow from the ACIs into the glass layers and absorb ambient shear transformation zones. Plasticity in the glass layers is realized via pronounced, stable shear banding. As the last part of the dissertation, we investigated with nonreactive molecular dynamics simulations, the dynamic response of phenolic resin and its carbon-nanotube (CNT) composites to shock wave compression. For phenolic resin, our simulations yielded shock states in agreement with experiments on similar polymers, except the "phase change" observed in experiments, indicating that such phase change is chemical in nature. The elastic?plastic transition is characterized by shear stress relaxation and atomic-level slip, and phenolic resin shows strong strain hardening. Shock loading of the CNT-resin composites was applied parallel or perpendicular to the CNT axis, and the composites demonstrated anisotropy in wave propagation, yield and CNT deformation. Our simulations suggested that the bulk shock response of the composites depends on the volume fraction, length ratio, impact cross-section, and geometry of the CNT components; the short CNTs in current simulations had insignificant effect on the bulk response of resin polymer.Item Elucidating Nucleation and Growth Behavior of Single-Walled Carbon Nanotubes obtained via Catalyzed Synthesis(2014-11-07) Burgos Beltran, Juan CarlosThe catalytic growth of single-walled carbon nanotubes (SWCNTs) is studied using reactive molecular dynamics (RMD) simulations and density functional theory (DFT) calculations. Computational calculations are performed in order to achieve a better understanding of the catalytic reaction mechanism at the initial stages of synthesis, where most of the structural characteristics are defined. Different process variables such as catalyst chemical composition and size, temperature, pressure, and the nature of catalyst support, can be optimized with the purpose of tuning the structure and physical properties of SWCNTs. Controlling the structure of SWCNTs during synthesis and avoiding additional purification and/or separation processes are critical for the direct use of SWCNTs in electronic devices. RMD simulations demonstrate that small catalyst particles favor the growth of lengthy nanotubes over catalyst encapsulation as a result of an increase of the curvature energies of the carbon capsule. Furthermore, simulations performed over deposited catalyst particles demonstrate that the catalyst-support adhesion must be controlled in order to grow nanotubes with high structural quality and avoid catalyst poisoning. Results herein reported suggest that growth conditions must be optimum to minimize the nucleation of topological defects in nanotubes. RMD trajectories prove the vital role played by the catalyst surface in healing defects via adsorption and diffusion. These results significantly impact the field of chirality control since the presence of defects introduce misorientation of hexagons, shifts the overall chiral angle, and therefore, modifies the physical properties of the nanotube. DFT calculations are employed to evaluate the interaction between SWCNTs and the ST-cut quartz substrate. The outstanding performance of CNT-based FET relies on the alignment of the horizontally grown nanotubes on silica substrates, as well as on the selective growth of semiconducting nanotubes. It is demonstrated that finite-length zigzag nanotubes are adsorbed stronger than armchair tubes on the quartz support. This suggests that the nanotube electronic band structure is a key factor on the preferential adsorption of zigzag tubes. DFT calculations suggest that patterns of unsaturated silicon atoms of silica surfaces define the crystallographic directions of preferential alignment. These patterns might be chemically altered in order to favor other directions of alignment.Item Investigation on Gas-phase Structures of Biomolecules Using Ion Mobility-mass Spectrometry(2011-08-08) Tao, LeiIM-MS is a 2-D technique which provides separations based on ion shape (ion-neutral collision cross-section, ?) and mass (m/z ratio). Ion structures can be deduced from the measured collision cross-section (?meas) by calculating the collision cross-sections (?calc) of candidates generated by molecular dynamics (MD) and compared with the experiment results. A database of ?s for singly-charged peptide ions is presented. Standard proteins are digested using different enzymes (trypsin, chymotrypsin and pepsin), resulting in peptides that differ in amino acid composition. The majority (63%) of the peptide ion correlates well with the globular structures, but some exhibit ?s that are significantly larger or smaller than the average correlation. Of the peptide ions having larger ?s, approximately 71% are derived from trypsin digestion and most of the peptide ions that have smaller ?s are derived from pepsin digestion (90%). We use computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH2-Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI and compare the structures of MIFAGIK derivatives to test the ?sensitivity? of the cluster analysis method. Cluster analysis suggests that [MIFAGIK + H]+ ions formed by MALDI have a predominantly turn structure even though the low energy ions prefer partial helical conformers. Although the ions formed by ESI have ?s that are different from those formed by MALDI, the results of cluster analysis indicate that the ions backbone structures are similar. Chemical modifications (N-acetyl, methylester, as well as addition of Boc or Fmoc groups) of MIFAGIK alter the distribution of various conformers, the most dramatic changes are observed for the [M + Na]+ ion, which show a strong preference for random coil conformers owing to the strong solvation by the backbone amide groups. ?meas of oligodeoxynucleotides in different length have been measured in both positive and negative modes. For a given molecular weight and charge state, ?meas of the oligodeoxynucleotide ions are smaller than those of the peptides, indicating their different packing efficiency. A novel generalized non-Boltzman sampling MD has been utilized to investigate the gas-phase ion conformations of dGGATC based on the free energy values. Theory predicts only one low-energy conformer for the zwitterionic form of dGGATC- while dGGATC+ ions have several stable conformers in both canonical and zwitterionic form in the gas phase, in good agreement with the experiment.Item Molecular Dynamics Simulation of Damage Cascade Formation in Ion Bombarded Solids(2012-10-19) Chen, DiPresented in this thesis are the results from an integrated experimental and modeling study on damage cascade formation in ion bombarded solids. The molecular dynamics (MD) simulations were performed by using LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). In one subtask, we studied damage cascade interactions caused by two 2 keV Si atoms simultaneously bombarding a crystalline Si substrate. We found that the enhanced displacement creation appears primarily in the thermal spike stage with all atoms at energies less than the displacement threshold. The study lead to the conclusion that the cascade interactions increased local melting by increasing energy deposition density, thus promoting defect creation. In another subtask, we studied radiation damage in Si0.8Ge2 layer caused by Agn clusters with number of atoms in a cluster, n, taking values from 1 to 4. It showed that strained SiGe, a material known to have poor radiation tolerance, still follows the overlap model, rather than the direct amorphization model. In the third subtask, MD simulation has shown that crowdion defects formed in bcc Fe are propagating along <111> directions. Crowdion defect starts to form when damage cascade reaches the maximum volume and contributes a second peak in defect buildups with increasing times. Upon defect recombination, crowdion defects shrink and form <111> oriented dumbbell defects at the crowdion end. In subsequent structural relaxation, <111> dumbbell defects rotate and finally align themselves with <110> directions. The surviving dumbbell defects represent a significant contribution to the final defect distribution after thermal spike formation. The overall research reveals atomic scale details of damage buildups at early stages of defect developments. Although the target systems cover both semiconductor materials and metal, these results show that MD simulation is a powerful tool to show the details at a spatial and time scale beyond experiments. These details are very important to develop understanding the precursor formation in defect clustering in such a case.Item Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films(2010-07-14) Kim, Bo HungMolecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface. In order to properly simulate the flow and heat transfer in nano-scale channels, an interactive thermal wall model is developed. Using this model, the Fourier?s law of heat conduction is verified in a 3.24 nm height channel, where linear temperature profiles with constant thermal conductivity is obtained. The thermal conductivity is verified using the predictions of Green-Kubo theory. MD simulations at different wall wettability ( ??f /? ) and crystal bonding stiffness values (K) have shown temperature jumps at the liquid/solid interface, corresponding to the well known Kapitza resistance. Using systematic studies, the thermal resistance length at the interface is characterized as a function of the surface wettability, thermal oscillation frequency, wall temperature and thermal gradient. An empirical model for the thermal resistance length, which could be used as the jump-coefficient of a Navier boundary condition, is developed. Temperature distributions in the nano-channels are predicted using analytical solution of the continuum heat conduction equation subjected to the new temperature jump condition, and validated using the MD results. Momentum and heat transfer in shear driven nanochannel flows are also investigated. Work done by the viscous stresses heats the fluid, which is dissipated through the channel walls, maintained at isothermal conditions. Spatial variations in the fluid density, kinematic viscosity, shear- and energy dissipation rates are presented. The energy dissipation rate is almost a constant for ??f /? < 0.6, which results in parabolic temperature profiles in the domain with temperature jumps due to the Kapitza resistance at the liquid/solid interfaces. Using the energy dissipation rates predicted by MD simulations and the continuum energy equation subjected to the temperature jump boundary conditions developed in this study, the analytical solutions are obtained for the temperature profiles, which agree well with the MD results.Item Multiscale analysis of nanocomposite and nanofibrous structures(2009-05-15) Unnikrishnan, Vinu UnnithanThe overall goal of the present research is to provide a computationally based methodology to realize the projected extraordinary properties of Carbon Nanotube (CNT)- reinforced composites and polymeric nanofibers for engineering applications. The discovery of carbon nanotubes (CNT) and its derivatives has led to considerable study both experimentally and computationally as carbon based materials are ideally suited for molecular level building blocks for nanoscale systems. Research in nanomechanics is currently focused on the utilization of CNTs as reinforcements in polymer matrices as CNTs have a very high modulus and are extremely light weight. The nanometer dimension of a CNT and its interaction with a polymer chain requires a study involving the coupling of the length scales. This length scale coupling requires analysis in the molecular and higher order levels. The atomistic interactions of the nanotube are studied using molecular dynamic simulations. The elastic properties of neat nanotube as well as doped nanotube are estimated first. The stability of the nanotube under various conditions is also dealt with in this dissertation. The changes in the elastic stiffness of a nanotube when it is embedded in a composite system are also considered. This type of a study is very unique as it gives information on the effect of surrounding materials on the core nanotube. Various configurations of nanotubes and nanocomposites are analyzed in this dissertation. Polymeric nanofibers are an important component in tissue engineering; however, these nanofibers are found to have a complex internal structure. A computational strategy is developed for the first time in this work, where a combined multiscale approach for the estimation of the elastic properties of nanofibers was carried out. This was achieved by using information from the molecular simulations, micromechanical analysis, and subsequently the continuum chain model, which was developed for rope systems. The continuum chain model is modified using properties of the constituent materials in the mesoscale. The results are found to show excellent correlation with experimental measurements. Finally, the entire atomistic to mesoscale analysis was coupled into the macroscale by mathematical homogenization techniques. Two-scale mathematical homogenization, called asymptotic expansion homogenization (AEH), was used for the estimation of the overall effective properties of the systems being analyzed. This work is unique for the formulation of spectral/hp based higher-order finite element methods with AEH. Various nanocomposite and nanofibrous structures are analyzed using this formulation. In summary, in this dissertation the mechanical characteristics of nanotube based composite systems and polymeric nanofibrous systems are analyzed by a seamless integration of processes at different scales.Item Theoretical Investigation of Self-Assembled Peptide Nanostructures for Biotechnological and Biomedical Applications(2012-07-16) Carvajal Diaz, Jennifer AndreaIn this dissertation, molecular simulation techniques are used for the theoretical prediction of nanoscale properties for peptide-based materials. This work is focused on two particular systems: peptide nanotubes formed by cyclic-D,L peptide units and peptide nanotubes formed by phenylalanine dipeptides [-Phe-Phe-]. Mechanical characterization of cyclic peptide nanotubes is a challenging problem due the anisotropy resulting from the nature of their molecular interactions. To address rigorously the thermo-mechanical stability of cyclic peptide nanotubes (CPNTs), a homogeneous deformation method combined with the generalized elasticity theory and molecular dynamics simulations (MD) were used for the calculation of second order anisotropic elastic constants. The results for anisotropic elastic constants, yield behavior and engineering Young?s modulus show remarkable mechanical stability for these materials supporting experiments for the development of their applications. Furthermore, the heat capacity, thermal expansion coefficient and isothermal compressibility were predicted using numerical difference methods and molecular dynamics. In order to understand the transport properties of confined water in cyclic peptide nanotubes, the influence of nanotube diameter was studied and self-diffusion coefficient, dipole correlation functions and hydrogen bond probabilities were calculated via molecular dynamics and statistical mechanics. Enhanced transport and higher diffusion rates for water were obtained in cyclic peptide nanotubes (CPNTs) compared with commonly used biomedical channels like carbon nanotubes (CNTs). The greater transport efficiency in CPNTs is attributed to the hydrophilic character and high hydrogen bonding presence along their tubular structure, versus the hydrophobic core of CNTs. One of the most important opportunities for cyclic peptide nanotubes is their utilization as artificial ion channels in antibacterial applications. Here, molecular dynamics methods were used to investigate the effect of confinement on the transport properties of Na+ and K+ ions under the influence of electric field; the ion mobility, selectivity, radial distribution function, coordination number and effect of temperature were studied and results from simulations proved their ability to transport ions. Additionally, the molecular organization of phenylalanine dipeptides into ordered peptide nanotubes was investigated, a model for the molecular structure of these nanotubes was proposed and optimized through molecular simulations; a helical pattern was found and characterized. Thermal stability results show that phenylalanine dipeptide nanotubes are stable up to about 400K; above this temperature, a significant decrease in hydrogen bonding was observed and the perfect pattern was altered. Findings from this work open new opportunities for research in the area of peptide based materials and provide tools and methods to study these systems efficiently at nanoscale.