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Department: search.filters.department.Department of Computer EngineeringSubject: search.filters.subject.Chemical engineering

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Now showing 1 - 3 of 3
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    Inhibitor peptide design for NF- KB: Markov model and genetic algorithm
    (IEEE, 2010) N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Ünal, Evrim Besray; Gürsoy, Attila; Erman, Burak; PhD Student; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 8745; 179997
    Two peptide design approaches are proposed to block activities of disease related proteins. First approach employs a probabilistic method; the problem is set as Markov chain. The possible binding site of target protein and a path on this binding site are determined. 20 natural amino acids and 400 dipeptides are docked to the selected path using the AutoDock software. The statistical weight matrices for the binding energies are derived from AutoDock results; matrices are used to determine top 100 peptide sequences with affinity to target protein. Second approach utilizes a heuristic method for peptide sequence determination; genetic algorithm (GA) with tournament selection. The amino acids are the genes; the peptide sequences are the chromosomes of GA. Initial random population of 100 chromosomes leads to determination of 100 possible binding peptides, after 8-10 generations of GA. Thermodynamic properties of the peptides are analyzed by a method that we proposed previously. NF-κB protein is selected as case-study.
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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.
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    The rational design of a graphitic carbon nitride-based dual S-scheme heterojunction with energy storage ability as a day/night photocatalyst for formic acid dehydrogenation
    (Elsevier Science Sa, 2022) Department of Physics; Department of Computer Engineering; N/A; Department of Chemistry; Altan, Orhan; Altıntaş, Elvin; Alemdar, Sıla; Metin, Önder; Other; Researcher; Master Student; Faculty Member; Department of Physics; Department of Computer Engineering; Department of Chemistry; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 46962
    Photocatalytic formic acid dehydrogenation (FAD) has been regarded as one of the most promising methods of producing H2 in a sustainable manner. In the photocatalytic FAD reaction, photogenerated holes play an important role in the reaction mechanism and thus in the efficiency of photocatalysts. However, the design of photocatalytic systems capable of generating high hole potential without compromising the reducing ability of the photocatalyst is extremely rare for the FAD reaction. In this respect, we report herein a novel and highly efficient heterojunction photocatalyst composed of 2D graphitic carbon nitride, 2D MnO2, 1D MnOOH, and 0D PdAg alloy nanoparticles, denoted as GCN/MnO2/MnOOH-PdAg, that can create high reduction and oxidation potentials via a dual S-scheme heterojunction. The photocatalysts exhibited a superb photocatalytic activity in the FAD with a record turnover frequency (TOF) of 3919 h-1 under visible light irradiation, which was 6-, 5.2and 24-times greater than those of GCN-PdAg, GCN/MnO2-PdAg, and MnO2/MnOOH-PdAg heterojunctions, respectively. The structure and dual S-scheme mechanism of the photocatalyst have been clearly demonstrated by extensive instrumental analysis, radical trapping tests, and scavenger experiments. More importantly, it was discovered that the presented photocatalyst continued to function with comparable activity in dark for a prolonged time using the same photocatalytic mechanism. The activity of the photocatalyst in dark was attributed to the utilization of electrons stored on Mn2O3, which was detected as a 4-5 nm thick layer on the surface of MnOOH nanorods. This study, in addition to being the first example of both a "day/night photocatalyst" for FAD with an S-scheme mechanism, also demonstrates for the first time the boosting of FAD via a dual S-scheme heterojunction photocatalyst.