Publications with Fulltext

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

Browse

Filters

2006 - 200932010 - 20151

Advanced Search

Filter by

Settings

Department: search.filters.department.Department of Chemical and Biological EngineeringSubject: search.filters.subject.Applied physics

Search Results

Now showing 1 - 4 of 4
  • Thumbnail Image
    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.
  • Thumbnail Image
    PublicationOpen Access
    Optofluidic waveguides written in hydrophobic silica aerogels with a femtosecond laser
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2015) Yalızay, B.; Morova, Y.; Jonas, A.; Aktürk, S.; Department of Physics; Department of Chemical and Biological Engineering; Kiraz, Alper; Erkey, Can; Özbakır, Yaprak; Faculty Member; Faculty Member; Department of Physics; Department of Chemical and Biological Engineering; College of Sciences; 22542; 29633; N/A
    We present a new method to form liquid-core optofluidic waveguides inside hydrophobic silica aerogels. Due to their unique material properties, aerogels are very attractive for a wide variety of applications; however, it is very challenging to process them with traditional methods such as milling, drilling, or cutting because of their fragile structure. Therefore, there is a need to develop alternative processes for formation of complex structures within the aerogels without damaging the material. In our study, we used focused femtosecond laser pulses for high-precision ablation of hydrophobic silica aerogels. During the ablation, we directed the laser beam with a galvo-mirror system and, subsequently, focused the beam through a scanning lens on the surface of bulk aerogel which was placed on a three-axis translation stage. We succeeded in obtaining high-quality linear microchannels inside aerogel monoliths by synchronizing the motion of the galvo-mirror scanner and the translation stage. Upon ablation, we created multimode liquid-core optical waveguides by filling the empty channels inside low-refractive index aerogel blocks with high-refractive index ethylene glycol. In order to demonstrate light guiding and measure optical attenuation of these waveguides, we coupled light into the waveguides with an optical fiber and measured the intensity of transmitted light as a function of the propagation distance inside the channel. The measured propagation losses of 9.9 dB/cm demonstrate the potential of aerogel-based waveguides for efficient routing of light in optofluidic lightwave circuits.
  • Thumbnail Image
    PublicationOpen Access
    Dielectric response and tunability of a dielectric-paraelectric composite
    (American Institute of Physics (AIP) Publishing, 2008) Zhou, K.; Boggs, S. A.; Ramprasad, R.; Aindow, M.; Alpay, S. P.; Department of Chemical and Biological Engineering; Erkey, Can; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 29633
    A theoretical study was carried out to determine the dielectric response and tunability of a composite consisting of a linear, low-loss dielectric matrix with uniformly sized, randomly distributed paraelectric Ba0.60Sr0.40TiO3 (BST 60/40) particles as functions of the volume fraction and size of the particles. The field dependence of the polarization and the dielectric response of the inclusions are specified through a nonlinear thermodynamic model and then incorporated into a two-dimensional finite element analysis. Near the percolation threshold for BST particles (similar to 27% to 45% depending on the particle size), high dielectric tunabilities with a lower effective permittivity than monolithic BST can be realized. (C) 2008 American Institute of Physics. American Institute of Physics.
  • Thumbnail Image
    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.