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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6

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Department: search.filters.department.Department of Chemical and Biological EngineeringSubject: search.filters.subject.Physical chemistry

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Now showing 1 - 3 of 3
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    PublicationOpen Access
    Optimum folding pathways of proteins: their determination and properties
    (American Institute of Physics (AIP) Publishing, 2006) Department of Chemical and Biological Engineering; Güner, Pınar Tatar; Arkun, Yaman; Erman, Burak; Teaching Faculty; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 188227; 108526; 179997
    We develop a dynamic optimization technique for determining optimum folding pathways of proteins starting from different initial configurations. A coarse-grained Go model is used. Forces acting on each bead are (i) the friction force, (ii) forces from bond length constraints, (iii) excluded volume constraints, and (iv) attractive forces between residue pairs that are in contact in the native state. An objective function is defined as the total attractive energy between nonbonded residues, which are neighbors in the native state. The objective function is minimized over all feasible paths, satisfying bond length and excluded volume constraints. The optimization problem is nonconvex and contains a large number of constraints. An augmented Lagrangian method with a penalty barrier function was used to solve the problem. The method is applied to a 36-residue protein, chicken villin headpiece. Sequences of events during folding of the protein are determined for various pathways and analyzed. The relative time scales are compared and scaled according to experimentally measured events. Formation times of the helices, turn, and the loop agree with experimental data. We obtain the overall folding time of the protein in the range of 600 ns-1.2 mu s that is smaller than the experimental result of 4-5 mu s, showing that the optimal folding times that we obtain may be possible lower bounds. Time dependent variables during folding and energies associated with short- and long-range interactions between secondary structures are analyzed in modal space using Karhunen-Loeve expansion.
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    PublicationOpen Access
    Composites of porous materials with ionic liquids: synthesis, characterization, applications, and beyond
    (Elsevier, 2022) Department of Chemical and Biological Engineering; Durak, Özce; Zeeshan, Muhammad; Habib, Nitasha; Gülbalkan, Hasan Can; Alsuhile, Ala Abdulalem Abdo Moqbel; Çağlayan, Hatice Pelin; Öztulum, Samira Fatma Kurtoğlu; Zhao, Yuxin; Haşlak, Zeynep Pınar; Uzun, Alper; Keskin, Seda; PhD Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 59917; 40548
    Modification of the physicochemical properties of porous materials by using ionic liquids (ILs) has been widely studied for various applications. The combined advantages of ILs and porous materials provide great potential in gas adsorption and separation, catalysis, liquid-phase adsorption and separation, and ionic conductivity owing to the superior performances of the hybrid composites. In this review, we aimed to provide a perspective on the evolution of IL/porous material composites as a research field by discussing several different types of porous materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), zeolites, and carbonaceous-materials. The main challenges and opportunities in synthesis methods, characterization techniques, applications, and future opportunities of IL/porous materials are discussed in detail to create a road map for the area. Future advances of the field addressed in this review will provide in-depth insights into the design and development of these novel hybrid materials and their replacement with conventional materials.
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    PublicationOpen Access
    Statistical thermodynamics of residue fluctuations in native proteins
    (American Institute of Physics (AIP) Publishing, 2009) Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Yoğurtçu, Osman Nuri; Gür, Mert; Erman, Burak; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; 179997
    Statistical thermodynamics of residue fluctuations of native proteins in a temperature, pressure, and force reservoir is formulated. The general theory is discussed in terms of harmonic and anharmonic fluctuations of residues. The two elastic network models based on the harmonic approximation, the anisotropic network and the Gaussian network models are discussed as the limiting cases of the general theory. The heat capacity and the correlations between the energy fluctuations and residue fluctuations are obtained for the harmonic approximation. The formulation is extended to large fluctuations of residues in order to account for effects of anharmonicity. The fluctuation probability function is constructed for this purpose as a tensorial Hermite series expansion with higher order moments of fluctuations as coefficients. Evaluation of the higher order moments using the proposed statistical thermodynamics model is explained. The formulation is applied to a hexapeptide and the fluctuations of residues obtained by molecular dynamics simulations are characterized in the framework of the model developed. In particular, coupling of two different modes in the nonlinear model is discussed in detail.