Publications with Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open 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; 179997We 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.Publication Open Access Optimal reduced dimensional representation of classical molecular dynamics(American Institute of Physics (AIP) Publishing, 2003) Dey, Bijoy K.; Rabitz, H.; Department of Mathematics; Aşkar, Attila; Faculty Member; Department of Mathematics; College of Sciences; 178822An optimal reduced space method for capturing the low-frequency motion in classical molecular dynamics calculations is presented. This technique provides a systematic means for carrying out reduced-dimensional calculations in an effective set of reduced coordinates. The method prescribes an optimal reduced subspace linear transformation for the low frequency motion. The method is illustrated with a dynamics calculation for a model potential, where the original six-dimensional space is reduced to two (three) dimensions, depending on the desired frequency cutoff value.Publication Open Access Solvation of carbonaceous molecules by para-H2 and ortho-D2clusters. II. Fullerenes(American Institute of Physics (AIP) Publishing, 2016) Calvo, F.; Department of Chemistry; Yurtsever, İsmail Ersin; Doctor; Department of Chemistry; College of Sciences; 7129The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D-2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C-60(+) and C-70(+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.Publication Open Access Solvation of carbonaceous molecules by para-H-2 and ortho-D-2 clusters. I. Polycyclic aromatic hydrocarbons(American Institute of Physics (AIP) Publishing, 2016) Calvo, F.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H-2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.Publication Open Access Lubricated friction and volume dilatancy are coupled(American Institute of Physics (AIP) Publishing, 2002) Granick, S.; Demirel, Adem Levent; Faculty Member; College of Sciences; 6568Dilation (expansion of film thickness) by similar to0.1 A, which is less than one-tenth of the width of confined fluid molecules, was observed when confined films crossed from the resting state ("static friction") to sliding ("kinetic friction"). These measurements were based on using piezoelectric bimorph sensors possessing extremely high resolution for detecting position changes, during the course of sliding molecularly thin films of squalane, a model lubricant fluid, between atomically smooth single crystals of mica. Detailed inspection of energy balance shows that the dilation data and the friction forces satisfied energy conservation of identifiable energies at the slip point, from static to kinetic friction. This shows experimentally, for the first time to the best of our knowledge, a direct coupling between friction forces and decrease in the mean density of the intervening molecularly thin fluid.Publication Open Access Correcting for electrostatic cutoffs in free energy simulations: toward consistency between simulations with different cutoffs(American Institute of Physics (AIP) Publishing, 1998) McCammon, J. Andrew; Department of Physics; Reşat, Haluk; Faculty Member; Department of Physics; College of SciencesThe use of electrostatic cutoffs in calculations of free energy differences by molecular simulations introduces errors. Even though both solute-solvent and solvent-solvent cutoffs are known to create discrepancies, past efforts have mostly been directed toward correcting for the solute-solvent cutoffs. In this work, an approach based on the generalized reaction field formalism is developed to correct for the solvent-solvent cutoff errors as well. It is shown using a series of simulations that when the cutoff lengths are significantly smaller than the half unit cell size, and the solute-solvent cutoff is not much larger than the solvent-solvent cutoff, the new algorithm is able to yield better agreement among simulations employing different truncation lengths.Publication Open Access Vibrational cooling of spin-stretched dimer states by He buffer gas: quantum calculations for Li(2)(a (3)Sigma(+)(u)) at ultralow energies(American Institute of Physics (AIP) Publishing, 2008) Bovino, S.; Bodo, E.; Gianturco, F. A.; Department of Chemistry; Yurtsever, İsmail Ersin; PhD Student; Department of Chemistry; College of Sciences; 7129The interaction between the triplet state of the lithium dimer, (7)Li(2), with (4)He is obtained from accurate ab initio calculations where the vibrational dependence of the potential is newly computed. Vibrational quenching dynamics within a coupled-channel quantum treatment is carried out at ultralow energies, and large differences in efficiency as a function of the initial vibrational state of the targets are found as one compares the triplet results with those of the singlet state of the same target.Publication Open Access Correcting for solvent-solvent electrostatic cutoffs considerably improves the ion-pair potential of mean force(American Institute of Physics (AIP) Publishing, 1999) Department of Physics; Reşat, Haluk; Faculty Member; Department of Physics; College of SciencesA recently developed algorithm based on the continuum treatment of the solvent molecules beyond the electrostatic cutoff sphere is applied to the potential of mean force results between sodium and chloride ions to study the effects of the solute-solvent and solvent-solvent cutoff errors. The results show that although the solute-solvent correction improves the thermodynamic results slightly, physically realistic results are obtained only when the solvent-solvent correction is applied. This further supports past findings that proper treatment of solvent-solvent interactions is as important as that of the solute interactions, and should not be ignored.Publication Open 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; 179997Statistical 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.Publication Open Access Ionic dimers in He droplets: interaction potentials for Li-2(+)-He,Na-2(+)-He, and K-2(+)-He and stability of the smaller clusters(American Institute of Physics (AIP) Publishing, 2006) Bodo, E.; Yurtsever, M.; Gianturco, F. A.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129We present post Hartree-Fock calculations of the potential energy surfaces (PESs) for the ground electronic states of the three alkali dimer ions Li-2(+), Na-2(+), and K-2(+) interacting with neutral helium. The calculations were carried out for the frozen molecular equilibrium geometries and for an extensive range of the remaining two Jacobi coordinates, R and theta, for which a total of about 1000 points is generated for each surface. The corresponding raw data were then fitted numerically to produce analytic expressions for the three PESs, which were in turn employed to evaluate the bound states of the three trimers for their J=0 configurations: The final spatial features of such bound states are also discussed in detail. The possible behavior of additional systems with more helium atoms surrounding the ionic dopants is gleaned from further calculations on the structural stability of aggregates with up to six He atoms. The validity of a sum-of-potential approximation to yield realistic total energies of the smaller cluster is briefly discussed vis-a-vis the results from many-body calculations.