Browsing by Subject "molecular modeling"

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    Documenting and harnessing the biological potential of molecules in Distributed Drug Discovery (D3) virtual catalogs
    (Wiley, 2017-11) Abraham, Milata M.; Denton, Ryan E.; Harper, Richard W.; Scott, William L.; O'Donnell, Martin J.; Durrant, Jacob D.; Chemistry and Chemical Biology, School of Science
    Virtual molecular catalogs have limited utility if member compounds are (i) difficult to synthesize or (ii) unlikely to have biological activity. The Distributed Drug Discovery (D3) program addresses the synthesis challenge by providing scientists with a free virtual D3 catalog of 73,024 easy-to-synthesize N-acyl unnatural α-amino acids, their methyl esters, and primary amides. The remaining challenge is to document and exploit the bioactivity potential of these compounds. In the current work, a search process is described that retrospectively identifies all virtual D3 compounds classified as bioactive hits in PubChem-cataloged experimental assays. The results provide insight into the broad range of drug-target classes amenable to inhibition and/or agonism by D3-accessible molecules. To encourage computer-aided drug discovery centered on these compounds, a publicly available virtual database of D3 molecules prepared for use with popular computer docking programs is also presented.
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    Molecular Dynamics Simulations of the Mechanical Deformation Behavior of Face-Centered Cubic Metallic Nanowires
    (2010-05-05T14:41:16Z) Heidenreich, Joseph David; Wang, Guofeng; Chen, Jie; Jones, Alan
    Nanoscale materials have become an active area of research due to the enhanced mechanical properties of the nanomaterials in comparison to their respective bulk materials. The effect that the size and shape of a nanomaterial has on its mechanical properties is important to understand if these materials are to be used in engineering applications. This thesis presents the results of molecular dynamics (MD) simulations on copper, gold, nickel, palladium, platinum, and silver nanowires of three cross-sectional shapes and four diameters. The cross-sectional shapes investigated were square, circular, and octagonal while the diameters varied from one to eight nanometers. Due to a high surface area to volume ratio, nanowires do not have the same atomic spacing as bulk materials. To account for this difference, prior to tensile loading, a minimization procedure was applied to find the equilibrium strain for each structure size and shape. Through visualization of the atomic energy before and after minimization, it was found that there are more than two energetically distinct areas within the nanowires. In addition, a correlation between the anisotropy of a material and its equilibrium strain was found. The wires were then subjected to a uniaxial tensile load in the [100] direction at a strain rate of 108 s-1 with a simulation temperature of 300 K. The embedded-atom method (EAM) was employed using the Foiles potential to simulate the stretching of the wires. The wires were stretched to failure, and the corresponding stress-strain curves were produced. From these curves, mechanical properties including the elastic modulus, yield stress and strain, and ultimate strain were calculated. In addition to the MD approach, an energy method was applied to calculate the elastic modulus of each nanowire through exponential fitting of an energy function. Both methods used to calculate Young’s modulus qualitatively gave similar results indicating that as diameter decreases, Young’s modulus decreases. The MD simulations were also visualized to investigate the deformation and yield behavior of each nanowire. Through the visualization, most nanowires were found to yield and fail through partial dislocation nucleation and propagation leading to {111} slip. However, the 5 nm diameter octagonal platinum nanowire was found to yield through reconstruction of the {011} surfaces into the more energetically favorable {021} surfaces.