Browsing by Author "Erman, Burak."
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Item Effects of alkali-carbonate rock reactions on performance of concrete(Thesis (M.S.) - Robert College. Faculty of Graduate School of Engineering, 1969., 1969.) Erman, Burak.; Tümay, Mehmet.Item Efficient computational models and methods for investigating local polymer dynamics(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1996., 1996.) Baysal, Canan.; Bahar, Ivet.; Erman, Burak.Local Phenomena related to the isomerization of torsional angles in polymers are studied using computational tools with emphasis on the problem of efficiency. Molecular and Brownian Dynamics, Dynamic Rotational Isomeric States Model, Cooperative Kinematics methods are utilized to study various aspects of local dynamics. The results provide a clear picture of local phenomena: Disturbances along the chain are accommodated by local motion confined to a segment of ten bonds approximately. Mainly, large and small amplitude torsions in the neighboring bonds, spatial reorientation of bonds, and translational motion of chain atoms occur. The exact mechanism of relaxation behavior is dictated by the geometry of the backbone bonds. All of the mentioned mechanisms are composed of the combined effect of rotameric jumps and librational motions. Coupling between the two is particularly enhanced during the passage over the rotation barrier. It is now known that librational motion which are generally assumed to be decoupled from the slow relaxation processes in polymer chains in many studies in literature are not random. On the contrary, they are highly correlated so that local chain direction is preserved and the reorientations induced by isomeric jumps are accommodated without significant distortion of chain conformation on a large scale.Item Phase transition in homogeneous flow of nematic fluids(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1983., 1983.) Bahar, İvet.; Erman, Burak.; Dinçer, Salih.Possibility of fonnation of a highly concentrated anisotropic phase in a dilute soluticn of rodlike molecules is investigated. The free energy expression for quiescent solutions of rodlike particles, introduced by Flory, is extended to the case where the molecules are subject to homogeneous velocity field. An additional term accounting for the contribution of the flow field to phase transition is incorporated into the free energy expression. The contribution of stressinduced diffusion is considered too. It is concluded that there will be a highly concentrated liquid crystalline phase deposition on the stagnant regions of the conduit, provided that the solvent-solute interaction is sufficiently high. The application of the theory to the aggregation of cholesterol molecules, in blood vessels, is discussed.Item Segmental orientation and conformational dynamics of polymer chains(Thesis (Ph.D)- Bogazici University. Institute for Graduate Studies in Science and Engineering, 1992., 1992.) Haliloğlu, Türkan.; Bahar, Ivet.; Erman, Burak.Various remarkable features of polymers, as compared with metallic and inorganic materials, arise from the fact that macromolecules can take up various conformations. The study of macromolecular conformations and dynamics is undoubtedly important in polymer science and technology from both basic and practical viewpoints. Comprehension of the configurational statistics of chain molecules leads to a rational interpretation and understanding of their physical properties. In previous studies, much effort have been devoted to dilute solutions. Though, recently there is a clear trend towards studying molecular properties in condensed systems, studies in the area of dilute solutions still remain a cornerstone of polymer characterization. Orientational motions of segments in polymer chains depend sensitively on both intra- and intermolecular configurational characteristics of the chains, and thus are of special interest for the understanding of polymer behavior. This thesis is mainly composed of two parts. In the first part, segmental orientation of polymers related to the chemical structure and resulting configurational characteristics of the chains are investigated using polyetylene (PE) and polyoxyethylene (POE) networjr of the angle that m makes with a laboratory-fixed axis is formulated for a chain with fixed end-to-end vector r. A series expression including terms up to fifth inverse power of n, where n is the number of bonds in the network chain, is obtained for r. Next, the corresponding averages over all chains of a network and the associated orientation function S, which is macroscopically observed are found in terms of (i) unperturbed chain moments readily obtainable by the rotational isomeric state scheme(RIS) (ii) the extension ratio A. for uniaxially deformed networks. Such a rigorous expression for S is particularly useful for relatively short chains and for moderate to large deformations that can not satisfactorily be accounted for by the existing simpler formulations. Thus, we estimate ranges of extension ratios A. to which the conventional first order approximation may be confidently applied. Calculations are performed for PE and POE chains of n = 21, 51 and 101 bonds which are generated by Monte Carlo simulation. The results are compared with those obtained by previous theoretical approaches. These comparisons demonstrate the importance of the adoption of higher order terms in the serial expansion of the orientation function for . In the second part, static and dynamic correlations between bond conformations and reorientations are examined by Brownian dynamics simulations for polymer chains with fixed ends. Polyethylenelike model chains are considered. Rates of rotational isomeric transitions and time evolution of orientational correlations are analyzed for various extensions of the chain. The relatively more extended chain exhibits the higher mobility in the short-time scale but possesses lower effective rate of rotational isomerization. This follows from a hazard analysis covering ranges up to 10 ns. The time decays of bond orientational correlations are reproducible by stretch--exponential functions with exponent almost independent of chain extension. The imposition of deformation by fixing chain ends, affects the orientational mobility of the chain down to the scale of individual bonds which may be observed from the biased evolution of time-dependent distribution functions for bond spatial reorientations. The analysis is also extended to the study of local orientational motions as seen by a laboratory fixed-observer. Time-dependent joint probability distribution functions for orientations of a vector affixed to a polymer chain are expressed in terms of double spherical harmonics. An expansion of the distribution function up to the second order harmonics accurately reproduces the results of Brownian dynamics simulations for a 49 bond polyethylene chain whose end-to-end separation is fixed at different extensions. Various functions related to the anisotropy of segmental dynamics such as the mobility, orientation-mobility correlation, directivity of mobility and the sense of mobility are examined and observed to be strongly dependent on the degree of chain extension.Item Simulation of protein structure by a simplified model: |application to the rop dimer(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1996., 1996.) Akten, E. Demet.; Bahar, Ivet.; Erman, Burak.In this thesis, the estimation of the native three-dimensional structure of a dimeric protein, Rop, from its amino-acid sequence is performed. Rop is a small RNA-binding protein that is coded by certain plasmids and is involved in plasmid replication. This is a four-helix bundle dimer, the monomers being identical oppositely oriented helical hairpins of 63 residues, each. The native state is considered to be the most thermodynamically stable state corresponding to the lowest energy conformation. Here, a molecular model which significantly decreases the number of variables required for describing a given configuration is introduced. This is the so-called coarse-grained or low-resolution approach which is based on the idea that each residue is composed of two heterogeneous interaction sites, one on the backbone atom and the other on the side group selected atoms. A framework model of rigid building blocks is adopted in the computational approach to the protein folding problem. The blocks are the secondary structural units which possess sufficient internal stability so as to form at early stages of folding and maintain their integrity during the large-scale structural reorganization of the protein. Within the approximation of the model, the problem reduces to determination of the optimal organization of the already predicted secondary structural elements in space. The lowest energy conformation of the Rop dimer is generated by considering all the possible threedimensional rearrangements that can exist between the two monomers. The potential energies between the interaction sites of the protein are extracted from a database of known protein structures, using the Brookhaven Protein Data Bank (PDB). These potential energies are referred to as knowledge-based potentials. The predicted lowest energy conformation obtained by the knowledge-based potentials is in reasonable agreement with the native structure of Rop dimer. It is concluded that the simplified knowledge-based potentials can be satisfactorily used for a low-resolution estimation of the native state of globular proteins. Computations are repeated by using the effective interresidue contact energies which replace the knowledge-based potentials. The effective interresidue contact energies are defined for two distance ranges, 2 A... and 4.4 A... , only for a given pair of amino acid side chains i and j separated by a distance rij· Accordingly, they provide a relatively simplified basis for evaluating the conformations, as opposed to the knowledge-based potentials which are determined at 0.4 A throughout the ranges 2.0 A ...A. In fact, it is found that the lowest energy conformation obtained with the effective interresidue contact energies conform with the native structure of the protein and it is concluded that the contact energies are sufficient for estimating the three-dimensional structure of globular proteins. Hovewer, PDB extracted knowedge-based potentials are shown to yield a more satisfactory account of the native state behaviour.Item The solution of nonhomogeneous state of stress strain and swelling problem in amorphous polymer networks(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1984., 1984.) Kahramanoğlu, Cengiz Ömer.; Tezel, Akın.; Erman, Burak.The total free energy a swollen and deformed amorphous cross-linked polymer network is given as ... where .. is the free energy of mixing of polymer and solvent; ... indicates the first part of elastic energy by representing ideal conditions called as "Phantom Case; ... covers the local constraints and completes the total free energy as a second part of elastic free energy. The explicit form of all free energies are obtained from molecular theory of rubber elasticity by including their recent developments. Expressions for stress in terms of strain and swelling ratio are obtained from free energy. Bending of a cross-linked amorphous cuboid is formulated as a boundary value problem and the distribution of solvent and stresses are numerically calculated for six distinct solvents. The magnitude of bending moments are found for different degrees of flexures up to 180. Results are compared with each other and also with their linear solutions. As swelling increases a decrease in elasticity modulus is observed.