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 Collective excitations of a laser driven atomic condensate in an optical cavity(Maik Nauka/Interperiodica Publishing, 2013) Öztop, B.; Türeci, H. E.; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674We theoretically examine collective excitations of an optically driven atomic Bose-Einstein condensate, coupled to a high-finesse optical cavity. This open system has been recently used for the experimental demonstration of the Dicke superradiance of cavity photons, which is simultaneously and mutually triggered by spontaneous breaking of translational symmetry of the condensate into a crystalline order. We first develop a Hartree-Fock mean field dynamical model of the physical system. Using this model, we compute the dynamics of the cavity photons, the condensate density profile and the Dicke phase transition diagram. Both the imaginary-time and real-time evolution methods are used in the calculations. Collective excitations are determined by the solving Bogoliubov-de Gennes equations. The spectrum, softening of the modes and energetic hierarchy of excitations are determined.Publication Open Access Top-down technique for scaling to nano in silicon MEMS(American Vacuum Society (AVS), 2017) Wollschlaeger, Nicole; Oesterle, Werner; Leblebici, Yusuf; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Nadar, Gökhan; Yılmaz, Mustafa Akın; Kılınç, Yasin; Taşdemir, Zuhal; Faculty Member; PhD Student; PhD Student; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; 115108; N/A; N/A; N/A; N/ANanoscale building blocks impart added functionalities to microelectromechanical systems (MEMS). The integration of silicon nanowires with MEMS-based sensors leading to miniaturization with improved sensitivity and higher noise immunity is one example highlighting the advantages of this multiscale approach. The accelerated pace of research in this area gives rise to an urgent need for batch-compatible solutions for scaling to nano. To address this challenge, a monolithic fabrication approach of silicon nanowires with 10-mu m-thick silicon-on-insulator (SOI) MEMS is developed in this work. A two-step Si etching approach is adopted, where the first step creates a shallow surface protrusion and the second step releases it in the form of a nanowire. It is during this second deep etching step that MEMS-with at least a 2-order-of-magnitude scale difference-is formed as well. The technique provides a pathway for preserving the lithographic resolution and transforming it into a very high mechanical precision in the assembly of micro-and nanoscales with an extreme topography. Validation of the success of integration is carried out via in situ actuation of MEMS inside an electron microscope loading the nanowire up to its fracture. The technique yields nanowires on the top surface of MEMS, thereby providing ease of access for the purposes of carrying out surface processes such as doping and contact formation as well as in situ observation. As the first study demonstrating such monolithic integration in thick SOI, the work presents a pathway for scaling down to nano for future MEMS combining multiple scales.Publication Open Access Self-Q-Switched Cr:LiCAF laser near 800 nm(Society of Photo-optical Instrumentation Engineers (SPIE), 2013) Department of Physics; Beyatlı, Ersen; Sennaroğlu, Alphan; Demirbaş, Ümit; PhD Student; Faculty Member; Master Student; Department of Physics; College of Sciences; N/A; 23851; N/ASelf-Q-switching (SQS) of lasers enable the generation of Q-switched pulses from simple laser cavities without using any additional saturable absorbers or active modulators. Earlier studies have reported SQS in ruby, Nd:YAG, and Cr:LiSAF lasers. However, these systems were mostly flashlamp pumped and required cooling of the crystal and/or misalignment of the laser cavity for the observation of SQS. In this presentation, for the first time to our knowledge, we report SQS operation of a Cr:LiCAF laser. SQS was achieved in an astigmatically compensated x-cavity containing only a Cr:LiCAF crystal that was end-pumped with a 130-mW continuous-wave (cw) diode at 660 nm. During regular cw operation, the laser produced a diffraction-limited beam with 50 mW of output power and had a spectral width of 0.5 nm near 795 nm. SQS operation of the Cr:LiCAF laser could be initiated by fine adjustment of the separation between the curved mirrors of the cavity and was observed at several mirror separations within the stability range of the resonator. During SQS operation, the laser generated pulses with about 5 microsecond duration in the 780-800 nm wavelength range, at repetition rates between 10 and 30 kHz. SQS operation was further accompanied with a decrease in the output power to the 30-45 mW range. In this regime, the output beam became multimode and spectral broadening up to 12.5 nm (FWHM) was observed.Publication Open Access Droplet resonator based optofluidic microlasers(Society of Photo-optical Instrumentation Engineers (SPIE), 2014) Brzobohaty, Oto; Jezek, Jan; Pilat, Zdenek; Zemanek, Pavel; Anand, Suman; McGloin, David; Department of Physics; Kiraz, Alper; Aas, Mehdi; Karadağ, Yasin; Jonas, Alexandr; Faculty Member; PhD Student; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; 22542; N/A; N/A; N/AAn SU-8 polymer microdisk resonator coated with a palladium (Pd) layer and coupled to a single-mode optical waveguide is used to as a hydrogen (H-2) gas sensor. In the presence of H2 a red shift is observed in the spectral positions of the microdisk whispering gallery modes (WGMs) due to the expansion in the Pd lattice. H-2 concentrations below the flammable limit (4%) down to 0.3% could be detected in nitrogen atmosphere at room temperature. For H-2 concentrations between 0.3 1%, WGM spectral positions shifted linearly with H-2 concentration at a rate of 32 pm/%H-2. Average response time of the devices was measured to be 50 s for 1% H-2. The proposed device concept can also be used to detect different chemical gases by using appropriate sensing layers.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 Time-resolved local strain tracking microscopy for cell mechanics(American Institute of Physics (AIP) Publishing, 2016) Aydın, O.; Aksoy, B.; Akalın, O. B.; Department of Chemistry; Department of Mechanical Engineering; Bayraktar, Halil; Alaca, Burhanettin Erdem; Faculty Member; Department of Chemistry; Department of Mechanical Engineering; College of Sciences; College of EngineeringA uniaxial cell stretching technique to measure time-resolved local substrate strain while simultaneously imaging adherent cells is presented. The experimental setup comprises a uniaxial stretcher platform compatible with inverted microscopy and transparent elastomer samples with embedded fluorescent beads. This integration enables the acquisition of real-time spatiotemporal data, which is then processed using a single-particle tracking algorithm to track the positions of fluorescent beads for the subsequent computation of local strain. The present local strain tracking method is demonstrated using polydimethylsiloxane (PDMS) samples of rectangular and dogbone geometries. The comparison of experimental results and finite element simulations for the two sample geometries illustrates the capability of the present system to accurately quantify local deformation even when the strain distribution is non-uniform over the sample. For a regular dogbone sample, the experimentally obtained value of local strain at the center of the sample is 77%, while the average strain calculated using the applied cross-head displacement is 48%. This observation indicates that considerable errors may arise when cross-head measurement is utilized to estimate strain in the case of non-uniform sample geometry. Finally, the compatibility of the proposed platform with biological samples is tested using a unibody PDMS sample with a well to contain cells and culture media. HeLa S3 cells are plated on collagen-coated samples and cell adhesion and proliferation are observed. Samples with adherent cells are then stretched to demonstrate simultaneous cell imaging and tracking of embedded fluorescent beads.Publication Open Access Temperature dependence of photoluminescence in non-crystalline silicon(Society of Photo-optical Instrumentation Engineers (SPIE), 2004) Bilici, T; İnanç, I; Carey, J; Mazur, E.; Department of Physics; Serpengüzel, Ali; Kurt, Adnan; Faculty Member; Teaching Faculty; Department of Physics; College of Sciences; 27855; 194455Crystalline silicon being ubiquitous throughout the microelectronics industry has an indirect bandgap, and therefore is incapable of light emission. However, strong room temperature visible and near-IR luminescence from non-crystalline silicon, e.g., amorphous silicon, porous silicon, and black silicon, has been observed. These silicon based materials are morphologically similar to each other, and have similar luminescence properties. We have studied the temperature dependence of the photoluminescence from these non-crystalline silicons to fully characterize and optimize these materials in the pursuit of obtaining novel optoelectronic devices.