Browsing by Subject "molecular dynamics"
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Item A Molecular Mechanics Knowledge Base Applied to Template Based Structure Prediction(2011-02-22) Qu, XiaotaoPredicting protein structure using its primary sequence has always been a challenging topic in biochemistry. Although it seems as simple as finding the minimal energy conformation, it has been quite difficult to provide an accurate yet reliable solution for the problem. On the one hand, the lack of understanding of the hydrophobic effect as well as the relationship between different stabilizing forces, such as hydrophobic interaction, hydrogen bonding and electronic static interaction prevent the scientist from developing potential functions to estimate free energy. On the other hand, structure databases are limited with redundant structures, which represent a noncontinuous, sparsely-sampled conformational space, and preventing the development of a method suitable for high-resolution, high-accuracy structure prediction that can be applied for functional annotation of an unknown protein sequence. Thus, in this study, we use molecular dynamics simulation as a tool to sample conformational space. Structures were generated with physically realistic conformations that represented the properties of ensembles of native structures. First, we focused our study on the relationship among different factors that stabilize protein structure. Using a wellcharacterized mutation system of the B-hairpin, a fundamental building block of protein, we were able to identify the effect of terminal ion-pairs (salt-bridges) on the stability of the beta-hairpin, and its relationship with hydrophobic interactions and hydrogen bonds. In the same study, we also correlated our theoretical simulations qualitatively with experimental results. Such analysis provides us a better understanding of beta-hairpin stability and helps us to improve the protein engineering method to design more stable hairpins. Second, with large-scale simulations of different representative protein folds, we were able to conduct a fine-grained analysis by sampling the continuous conformational space to characterize the relationship among backbone conformation, side-chain conformation and side-chain packing. Such information is valuable for improving high-resolution structure prediction. Last, with this information, we developed a new prediction algorithm using packing information derived from the conserved relative packing groups. Based on its performance in CASP7, we were able to draw the conclusion that our simulated dataset as well as our packing-oriented prediction method are useful for template based structure prediction.Item An Atomistic Study of the Mechanical Behavior of Carbon Nanotubes and Nanocomposite Interfaces(2011-02-22) Awasthi, Amnaya P.The research presented in this dissertation pertains to the evaluation of stiffness of carbon nanotubes (CNTs) in a multiscale framework and modeling of the interfacial mechanical behavior in CNT-polymer nanocomposites. The goal is to study the mechanical behavior of CNTs and CNT-polymer interfaces at the atomic level, and utilize this information to develop predictive capabilities of material behavior at the macroscale. Stiffness of CNTs is analyzed through quantum mechanical (QM) calculations while the CNT-polymer interface is examined using molecular dynamics (MD) simulations. CNT-polymer-matrix composites exhibit promising properties as structural materials and constitutive models are sought to predict their macroscale behavior. The reliability of determining the homogenized response of such materials depends upon the ability to accurately capture the interfacial behavior between the nanotubes and the polymer matrix. In the proposed work, atomistic methods are be used to investigate the behavior of the interface by utilizing appropriately chosen atomistic representative volume elements (RVEs). Atomistic simulations are conducted on the RVEs to study mechanical separation with and without covalent functionalization between the polymeric matrix and two filler materials, namely graphite and a (12,0) Single Wall zig zag CNT. The information obtained from atomistic studies of separation is applicable for higher level length scale models as cohesive zone properties. The results of the present research have been correlated with available experimental data from characterization efforts.Item Environmetally Assisted Cracking in Metals under Extreme Conditions(2012-10-19) Pham, HieuEnvironmentally Assisted cracking (EAC) is a very critical materials science problem that concerns many technological areas such as petrochemical engineering, aerospace operations and nuclear power generation, in which cracking or sudden failure of materials may happen at stress far below the tensile strength. This type of corrosion is initiated at the microscopic level and is complicated due to the combination of chemistry (reaction caused by corrosive agents) and mechanics (varying load). As EAC is generally related to the segregation of impurity elements to defects (mainly grain boundaries), the symptoms of risk may not be apparent from the exterior of the metal components: hence EAC remains latent and gives no sign of warning until the failure occurs. Due to its intricate nature, conducting experiments on this phenomenon involves difficulties and requires much effort. In this work, we employed advanced molecular simulation techniques to study EAC in order to give insight into its atomistic behavior. First, Density-Functional Theory (DFT) method was used to investigate the fundamental processes and mechanism of EAC-related issues at the nanoscale level, with two case studies concerning the stress corrosion in iron and hydrogen embrittlement in palladium. When segregating to the grain boundary (GB) of iron, different impurity elements such as sulfur, phosphorus and nitrogen raise corrosion failures in a variety of ways. Hydrogen atoms, due to their mobility and small atomic size, are able to form high occupation at crystal defects, but show different interactions to vacancy and GB. Then, we used the classical Molecular Dynamics (MD) method to gain an understanding of the dynamic response of materials to mechanical load and the effects of temperature, strain and extreme conditions (high pressure shock compression) on structural properties. The MD simulations show that hydrogen maintains the highest localization at grain boundaries in the vicinity of ambient temperatures, and grain boundaries are the preferred nucleation sites for dislocations and voids. This computational work, using DFT and MD techniques, is expected to contribute to the better understanding on chemistry and mechanisms of complex environment-assisted cracking phenomenon at a fundamental level in order to beneficially complement conventional laboratory approaches.Item Fundamental Properties and Processes of Energetic Materials(2012-10-19) Ojeda Mota, Oscar UlisesEnergetic materials comprise a set of systems of tremendous technological importance. Besides helping shape landscapes to establish communications, they have been used to reach fuel reservoirs, deploy safety bags and prevent heart strokes. Understanding its behavior can help in attaining strategic and tactical superiority, and importantly, preserve lives of people who handle these materials. The large discrepancy in length and time scales at which characteristic processes of energetic materials are of relevance pose a major challenge for current simulation techniques. We present a systematic study of crystalline energetic materials of different sensitivity and analyze their properties at different theoretical levels. Equilibrium structures, vibrational frequencies, conformational rearrangement and mechanical properties can be calculated within the density functional theory and molecular dynamics at finite temperatures. We have found marked differences in the calculated properties in systems with ranging sensitivities. Reactions at elevated temperatures have been studied using ab initio molecular dynamics method for crystals of nitroethane. Furthermore, while presenting the state of the art of energetic materials modeling, the limitations of each methodology are also discussed. Prospective systems and an elasticity driven approach that can be applied to other type of materials is also presented.Item Gas-phase and Solution-phase Peptide Conformations Studied by Ion Mobility-mass Spectrometry and Molecular Dynamics Simulations(2012-10-19) Chen, LiuxiIon mobility spectrometry (IMS) separates ions on the basis of ion-neutral collision cross-sections (CCS, [omega]), which are determined by the geometry or conformation of the ions. The size-based IM separation can be extended to distinguish conformers that have different shapes in cases where shape differences influence the accessible surface area of the molecule. In recent years, IM has rapidly evolved as a structural characterization technique, which has applied on various structural biology problems. In this work, IMS is combined with molecular dynamics simulation (MDS), specially the integrated tempering sampling molecular dynamics simulation (ITS-MDS) to explore the gas-phase conformation space of two molecular systems (i) protonated tryptophan zipper 1 (trpzip1) ions and its six derivatives (ii) alkali metal ion (Na, K and Cs) adducts of gramicidin A (GA). The structural distributions obtained from ITS-MDS are compared well with results obtained from matrix-assisted laser desorption ionization-ion mobility-mass spectrometry (MALDI-IM-MS) for trpzip 1 series and electrospray ionization-ion mobility-mass spectrometry (ESI-IM-MS) for alkali metal ion adducts of GA. Furthermore, the solvent dependence on conformational preferences of the GA dimer is investigated using a combination of mass spectrometry techniques, viz. ESI-IM-MS and hydrogen/deuterium exchange (HDX)-MS, and MDS. The IM experiments reveal three distinct gramicidin A species, detected as the sodium ion adduct ions, [2GA + 2Na]??, and the equilibrium abundances of the dimer ions varies with solvent polarity. The solution phase conformations are assigned as the parallel and anti-parallel [beta]-helix dimer, and the anti-parallel dimer is the preferred conformation in non-polar organic solvent. The calculated CCS profiles by ITS-MDS agree very well with the experimentally measured CCS profiles, which underscore the utility of the method for determining candidate structures as well as the relative abundances of the candidate structures. The benefit of combining ion mobility measurements with solution-phase H/D exchange is allowing identifications and detail analysis of the solution-phase subgroup conformations, which cannot be uncovered by one method alone.Item Geometric Nanoconfinement Effects on the Electronic and Mechanical Properties of Self-Assembled Molecular Systems(2014-08-20) Ewers, Bradley WilliamWith the ongoing research and development of nanoscale technologies and materials, it becomes increasingly important to understand how local environment influences molecular and material properties. An important factor in this regard is geometric nanoconfinement, for example, the restriction of molecules to nanostructure surfaces. The bulk or average characteristics of materials and molecules do not appropriately define their behavior in these circumstances, and highly localized measurement techniques developed to specifically identify the influence of confinement on their properties is essential to understanding their characteristics and behavior. In this dissertation, two forms of geometric confinement are considered in the context of different molecular properties. First, the role of radial confinement on the tribological properties of self-assembled monolayers (SAMs) is considered. SAMs are an excellent model lubricant for experimental studies of boundary lubrication, and they have been employed as boundary lubricant additives and surface coatings. The lubricated contacts of technologically relevant surfaces, however, consist of asperity interactions, and the summit curvature of these asperities can impact the critical cohesive forces from which the properties of the SAM are derived. Molecular dynamics simulation was employed to understand the influence of nanoscopic surface curvature, as well as surface coverage density, two factors which together contribute to the cohesive forces of SAMs, on their tribological properties. In particular their dissipative potential and effective surface protection were examined, as well as the influence of these factors on the contact mechanics of functionalized nanoasperity contacts. Another mode of geometric confinement studiedin this work is two-dimensional nanoconfinement of molecules and its influence on the mechanism of charge transport in molecular systems. Effective control of charge transport in molecules is essential for molecular modification of CMOS technologies, and is critical in controlling charge carrier dynamics in dye-sensitized photovoltaics. In this work, the size dependence of the electronic properties of thiol-tethered zinc porphyrin aggregateson the Au(111) surface was investigated. AFM nanolithography was used to confine these molecules within an alkanethiol matrix on the Au(111) surface, forming molecular islands of specific dimensions to investigate the relationship between island size and charge transport, demonstrating a shift from tunneling based charge transport to the more tunable and efficient charge hopping based transport.Item Laser cooling and sympathetic cooling in a linear quadrupole rf trap(Texas A&M University, 2005-02-17) Ryjkov, Vladimir LeonidovichAn investigation of the sympathetic cooling method for the studies of large ultra-cold molecular ions in a quadrupole ion trap has been conducted.Molecular dynamics simulations are performed to study the rf heating mechanisms in the ion trap. The dependence of rf heating rates on the ion temperature, trapping parameters, and the number of ions is obtained. New rf heating mechanism affecting ultra-cold ion clouds exposed to laser radiation is described.The saturation spectroscopy setup of the hyperfine spectra of the molecular iodine has been built to provide an accurate frequency reference for the laser wavelength. This reference is used to obtain the fluorescence lineshapes of the laser cooled Mg$^+$ ions under different trapping conditions.The ion temperatures are deduced from the measurements, and the influence of the rf heating rates on the fluorescence lineshapes is also discussed. Cooling of the heavy ($m=720$a.u.) fullerene ions to under 10K by the means of the sympathetic cooling by the Mg$^+$ ions($m=24$a.u.) is demonstrated. The single-photon imaging system has been developed and used to obtain the images of the Mg$^+$ ion crystal structures at mK temperatures.Item Surface Oxidation and Dissolution of Metal Nanocatalysts in Acid Medium(2012-10-19) Callejas-Tovar, JuanOne of the most important challenges in low-temperature fuel cell technology is improving the catalytic efficiency at the electrode-catalyst where the oxygen reduction reaction (ORR) occurs. Platinum is the best pure catalyst for this reaction but its high cost and scarcity hinder the commercial implementation of fuel cells in automobiles. Pt-based alloys are promising alternatives to substitute platinum while maintaining the efficiency and life-time of the pure catalyst. However, the acid medium and the oxidation of the surface reduce the activity and durability of the alloy catalyst through changes in its local composition and structure. Molecular simulation techniques are applied to characterize the thermodynamics and dynamic evolution of the surface of platinum-based alloy catalysts under reaction conditions.1-10 A simulation scheme of the surface oxidation is proposed which combines classical molecular dynamics (MD) and density functional theory (DFT). This approach is able to reproduce the main features of the oxidation phenomena observed experimentally, it is concluded that the dissolution mechanism of metal atoms involves: 1) Surface segregation of alloy atoms, 2) oxygen absorption into the subsurface of the catalyst, and 3) metal detachment through the interaction with ions in the solvent. Therefore, to improve the durability of platinum-based alloy catalysts, the steps of the dissolution mechanism must be prevented. A versatile 3-D kinetic Monte Carlo (KMC) code is developed to study the degradation and dealloying in nanocatalysts. The results on the degradation of Pt nanoparticles under different potential regimes demonstrate that the dissolution depends on the potential path to which the nanocatalyst is exposed. Metal atoms detach from the boundaries of (111) facets expecting a reduction in the activity of the nanoparticle. Also, the formation of Pt hollow nanoparticles by the Kirkendall effect is addressed, the role of vacancies is crucial in the removal of the non-noble core that yields to hollow nanoparticles. To investigate the reasons for the experimentally found enhanced ORR activity in porous/hollow nanoparticles, the effect of subsurface vacancies on the main ORR activity descriptors is studied with DFT. It is found that an optimum amount of vacancies may enhance the ORR activity of Pt-monolayer catalysts over certain alloy cores by changing the binding energies of O and OH.