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Department: search.filters.department.Department of Chemical and Biological EngineeringSubject: search.filters.subject.Molecular dynamics

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Now showing 1 - 4 of 4
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    Computational screening of ZIFs for CO2 separations
    (Taylor & Francis Ltd, 2015) N/A; N/A; Department of Chemical and Biological Engineering; Yılmaz, Gamze; Özcan, Aydın; Keskin, Seda; Master Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 40548
    Using molecular simulations, we studied a diverse collection of zeolite-imidazolate frameworks (ZIFs) to evaluate their performances in adsorption- and membrane-based gas separations. Molecular simulations were performed for both single-component gases (CH4, CO2, H-2 and N-2) and binary gas mixtures (CO2/CH4, CO2/N-2, CO2/H-2 and CH4/H-2) to predict the intrinsic and mixture selectivities of ZIFs. These two selectivities were compared to discuss the importance of multi-component mixture effects on making predictions about the separation performance of a material. Gas separation performances of ZIFs were compared with other nanoporous materials and our results showed that several ZIFs can outperform well-known zeolites and metal-organic frameworks in CO2 separations. Several other properties of ZIFs such as gas permeability, working capacity and sorbent selection parameter were computed to identify the most promising materials in adsorption- and membrane-based separation of CO2/CH4, CO2/N-2, CO2/H-2 and CH4/H-2.
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    Conformational similarities in isomerization dynamics of clusters
    (Amer Chemical Soc, 2003) Department of Chemistry; N/A; Department of Chemical and Biological Engineering; Yurtsever, İsmail Ersin; Palazoğlu, Ahmet; Arkun, Yaman; Faculty Member; N/A; Faculty Member; Department of Chemistry; Department of Chemical and Biological Engineering; College of Sciences; N/A; College of Engineering; 7129; N/A; 108526
    A method for characterization of the isomerization dynamics from classical trajectories is presented. A measure function describing the topological distance between two clusters of atoms is first developed. Next, this measure is used to identify the regions of the potential energy surface visited by the trajectories. Unlike the commonly used techniques such as simulated annealing or quenching, the proposed method does not require repeated treatment of the trajectory and can be safely used to study the isomerization dynamics of large systems, especially those of monatomic clusters.
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    Migration of single iridium atoms and tri-iridium clusters on MgO surfaces: aberration-corrected STEM imaging and ab initio calculations
    (American Chemical Society (ACS), 2015) Han, Chang Wan; Iddir, Hakim; Curtiss, Larry A.; Browning, Nigel D.; Gates, Bruce C.; Ortalan, Volkan; Department of Chemical and Biological Engineering; Uzun, Alper; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 59917
    To address the challenge of fast, direct atomic-scale visualization of the migration of atoms and clusters on surfaces, we used aberration-corrected scanning transmission electron microscopy (STEM) with high scan speeds (as little as similar to 0.1 s per frame) to visualize the migration of (1) a heavy atom (Ir) on the surface of a support consisting of light atoms, MgO(100), and (2) an Ir-3 cluster on MgO(110). Sequential Z-contrast images elucidate the surface transport mechanisms. Density functional theory (DFT) calculations provided estimates of the migration energy barriers and binding energies of the iridium species to the surfaces. The results show how the combination of fast-scan STEM and DFT calculations allow visualization and fundamental understanding of surface migration phenomena pertaining to supported catalysts and other materials.
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    Quantum mechanical calculations of tryptophan and comparison with conformations in native proteins
    (amer Chemical Soc, 2006) Department of Chemistry; Department of Computer Engineering; Department of Chemical and Biological Engineering; Yurtsever, İsmail Ersin; Yüret, Deniz; Erman, Burak; Faculty Member; Faculty Member; Faculty Member; Department of Chemistry; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; College of Engineering; 7129; 179996; 179997
    We report a detailed analysis of the potential energy surface of N-acetyl-L-tryptophan-N-methylamide, (NaTMa) both in the gas phase and in solution. the minima are identified using the density-functional-theory (DFT) with the 6-31g(d) basis set. the full potential energy surface in terms of torsional angles is spanned starting from various initial configurations. We were able to locate 77 distinct L-minima. the calculated energy maps correspond to the intrinsic conformational propensities of the individual NaTMa molecule. We show that these conformations are essentially similar to the conformations of tryptophan in native proteins. for this reason, we compare the results of DFT calculations in the gas and solution phases with native state conformations of tryptophan obtained from a protein library. in native proteins, tryptophan conformations have strong preferences for the, sheet, right-handed helix, tight turn, and bridge structures. the conformations calculated by DFT, the solution-phase results in particular, for the single tryptophan residue are in agreement with native state values obtained from the Protein Data Bank.