Browsing by Subject "Calculation"

Now showing 1 - 18 of 18

Open Access
Charged bosons in a quasi-one-dimensional system
(American Physical Society, 2000) Tanatar, Bilal; Davoudi, B.; Kohandel, M.
The ground-state properties of a system of charged bosons in a quasi-one-dimensional model with a neutralizing background are investigated within the hypernetted-chain approximation. Strong correlation effects drive the system from a homogeneous fluid phase toward a more ordered structure akin to Wigner crystallization in higher-dimensional charged quantum systems. The ordered phase of charged bosons is signaled by the development of a peak in the static structure factor, which is analyzed as a function of the density and the lateral width of the one-dimensional structure. We also calculate the pair-distribution function, the ground-state energy, and the local-field correction, and compare our results with other theoretical approaches.
Open Access
A comparative study of O2 adsorbed carbon nanotubes
(2003) Dag, S.; Gülseren, O.; Çıracı, Salim
First-principles, density functional calculations show that O2 adsorbed single-wall carbon nanotubes (SWNT) show dramatic differences depending on the type of the tube. Upon O2 physisorption, the zig-zag SWNT remains semiconducting, while the metallicity of the armchair is lifted for the spin-down bands. The spin-up bands continue to cross at the Fermi level, and make the system metallic only for one type of spin. The singlet bound state of O2 occurs at the bridge site of the (6,6) SWNT at small distance from the surface of the tube. However, for the hollow site, the molecule dissociates when it comes close to the surface. © 2003 Elsevier B.V. All rights reserved.
Open Access
Electronic excited states of the CP29 antenna complex of green plants: a model based on exciton calculations
(Springer / Kluwer Academic Publishers, 2000) İşerı, E. İ.; Albayrak, D.; Gülen, D.
We have suggested a model for the electronic excited states of the minor plant antenna, CP29, by incorporating a considerable part of the current information offered by structure determination, site-directed mutagenesis, and spectroscopy in the modeling. We have assumed that the electronic excited states of the complex have been decided by the chlorophyll-chlorophyll (Chl) and Chl-protein interactions and have modeled the Coulombic interaction between a pair of Chls in the point-dipole approximation and the Chl-protein interactions are treated as empirical fit parameters. We have suggested the Qy dipole moment orientations and the site energies for all the chlorophylls in the complex through a simultaneous simulation of the absorption and linear dichroism spectra. The assignments proposed have been discussed to yield a satisfactory reproduction of all prominent features of the absorption, linear and circular dichroism spectra as well as the key spectral and temporal characteristics of the energy transfer processes among the chlorophylls. The orientations and the spectral assignments obtained by relatively simple exciton calculations have been necessary to provide a good point of departure for more detailed treatments of structure-function relationship in CP29. Moreover, it has been discussed that the CP29 model suggested can guide the studies for a better understanding of the structure-function relationship in the major plant antenna, LHCII.
Open Access
Electronic structure of Te-and As-covered Si(211)
(American Physical Society, 2003) Sen, P.; Batra, I. P.; Sivananthan, S.; Grein, C. H.; Dhar, N.; Çıracı, Salim
Electronic and atomic structures of the clean and As- and Te-covered Si(211) surface are studied using pseudopotential density-functional method. The clean surface is found to have (2 x 1) and rebonded (1 x 1) reconstructions as stable surface structures, but no π-bonded chain reconstruction. Binding energies of As and Te adatoms at a number of symmetry sites on the ideal and (2 x 1) reconstructed surfaces have been calculated because of their importance in the epitaxial growth of CdTe and other materials on the Si(211) surface. The special symmetry sites on these surfaces having the highest binding energies for isolated As and Te adatoms are identified. But more significantly, several sites are found to be nearly degenerate in binding-energy values. This has important consequences for epitaxial growth processes. Optimal structures calculated for 0.5 monolayer of As and Te coverage reveal that the As adatoms dimerize on the surface while the Te adatoms do not. However, both As- and Te-covered surfaces are found to be metallic in nature.
Open Access
Experimental results for 2D magnetic resonance electrical impedance tomography (MR-EIT) using magnetic flux density in one direction
(Institute of Physics Publishing, 2003) Birgül, Ö.; Eyüboğlu, B. M.; İder, Y. Z.
Magnetic resonance electrical impedance tomography (MR-EIT) is an emerging imaging technique that reconstructs conductivity images using magnetic flux density measurements acquired employing MRI together with conventional EIT measurements. In this study, experimental MR-EIT images from phantoms with conducting and insulator objects are presented. The technique is implemented using the 0.15 T Middle East Technical University MRI system. The dc current method used in magnetic resonance current density imaging is adopted. A reconstruction algorithm based on the sensitivity matrix relation between conductivity and only one component of magnetic flux distribution is used. Therefore, the requirement for object rotation is eliminated. Once the relative conductivity distribution is found, it is scaled using the peripheral voltage measurements to obtain the absolute conductivity distribution. Images of several insulator and conductor objects in saline filled phantoms are reconstructed. The L2 norm of relative error in conductivity values is found to be 13%, 17% and 14% for three different conductivity distributions.
Open Access
Formation of quantum structures on a single nanotube by modulating hydrogen adsorption
(American Physical Society, 2003) Gülseren, O.; Yildirim, T.; Çıracı, Salim
Using first-principles density functional calculations we showed that quantum structures can be generated on a single carbon nanotube by modulating the adsorption of hydrogen atoms. The band gap of the hydrogen-free zone of the tube widens in the adjacent hydrogen covered zone. The sudden variation of the band gap leads to band offsets at the conduction- and valence-band edges. At the end, the band gap of the whole system is modulated along the axis of the tube, which generates quantum wells or quantum dots. Specific electronic states are confined in these quantum wells. The type and radius of the nanotube and the extent and sequence of hydrogen-free and hydrogen-covered zones can provide several options to design a desired optoelectronic nanodevice.
Open Access
Initial stages of Pt growth on Ge (001) studied by scanning tunneling microscopy and density functional theory
(American Physical Society, 2004) Gurlu, O.; Zandvliet, H. J. W.; Poelsema, B.; Dag, S.; Çıracı, Salim
We have studied the initial stages of submonolayer Pt growth on the Ge(001). We have observed several stable and meta-stable adsorption configurations of Pt atoms at various temperatures. Calculations indicate relatively high binding energies of Pt atoms onto the Ge lattice, at different adsorption sites. Our results show that through-the-substrate bonding (concerted bonding) of two Pt atoms is more favored on Ge(001) surface then a direct Pt-Pt bond. Both our experiments and calculations indicate the breaking of Ge-Ge bonds on the surface in the vicinity of Pt adsorbates. We have also observed the spontaneous generation of 2 + 1 dimer vacancy defects at room temperature that cause the ejection of Ge atoms onto the surface. Finally we have studied the diffusion of Pt atoms into the bulk as a result of annealing and found out that they get trapped at subsurface sites.
Open Access
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications
(Oxford University Press, 2014) Hach, F.; Sarrafi, I.; Hormozdiari, F.; Alkan C.; Eichler, E. E.; Sahinalp, S. C.
High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net. © 2014 The Author(s).
Open Access
Point normal metal-superconductor (NS) contact in nonballistic regime
(World Scientific Publishing, 2003) Askerzade, İ. N.; Kulik, Igor Orestovich
We analyze the point NS contact conductivity taking into account the depression of superconductivity at high-injection current density and Andreev reflection at the adaptive NS boundary. The dependence of the excess current on the voltage, as well as conductivity of contact at arbitrary voltage is obtained.
Open Access
A portable microfluidic system for rapid measurement of the erythrocyte sedimentation rate
(Royal Society of Chemistry, 2016) Isiksacan, Z.; Erel, O.; Elbuken, C.
The erythrocyte sedimentation rate (ESR) is a frequently used 30 min or 60 min clinical test for screening of several inflammatory conditions, infections, trauma, and malignant diseases, as well as non-inflammatory conditions including prostate cancer and stroke. Erythrocyte aggregation (EA) is a physiological process where erythrocytes form face-to-face linear structures, called rouleaux, at stasis or low shear rates. In this work, we proposed a method for ESR measurement from EA. We developed a microfluidic opto-electro-mechanical system, using which we experimentally showed a significant correlation (R2 = 0.86) between ESR and EA. The microfluidic system was shown to measure ESR from EA using fingerprick blood in 2 min. 40 μl of whole blood is filled in a disposable polycarbonate cartridge which is illuminated with a near infrared emitting diode. Erythrocytes were disaggregated under the effect of a mechanical shear force using a solenoid pinch valve. Following complete disaggregation, transmitted light through the cartridge was measured using a photodetector for 1.5 min. The intensity level is at its lowest at complete disaggregation and highest at complete aggregation. We calculated ESR from the transmitted signal profile. We also developed another microfluidic cartridge specifically for monitoring the EA process in real-time during ESR measurement. The presented system is suitable for ultrafast, low-cost, and low-sample volume measurement of ESR at the point-of-care.
Open Access
Reduced density matrix approach to phononic dissipation in friction
(2000) Özpineci, A.; Leitner, D. M.; Çıracı, Salim
Understanding mechanisms for energy dissipation from nanoparticles in contact with large samples is a central problem in describing friction microscopically. Calculation of the reduced density matrix appears to be the most suitable method to study such systems that are coupled to a large environment. In this paper, the time evolution of the reduced density matrix has been evaluated for an arbitrary system coupled to a heat reservoir. The formalism is then applied to study the vibrational relaxation following the stick-slip motion of an asperity on a surface. The frequency and temperature dependence of the relaxation time is also determined. Predictions of the reduced density matrix are compared with those obtained by using the Golden Rule approach.
Open Access
Role of the environmental spectrum in the decoherence and dephasing of multilevel quantum systems
(The American Physical Society, 2005) Hakioǧlu T.; Savran, K.
We examine the effect of multilevels on decoherence and dephasing properties of a quantum system consisting of a nonideal two level subspace, identified as the qubit, and a finite set of higher energy levels above this qubit subspace. The whole system is under interaction with an environmental bath through a Caldeira-Leggett type coupling. The model that we use is an rf-SQUID under macroscopic quantum coherence and coupled inductively to a flux noise characterized by an environmental spectrum. The model interaction can generate dipole couplings which can be appreciable between the qubit and the high levels. The decoherence properties of the qubit subspace is examined numerically using the master equation formalism of the system's reduced density matrix. We calculate the relaxation and dephasing times as the spectral parameters of the environment are varied. We observe that, these calculated time scales receive contribution from all available frequencies in the noise spectrum (even well above the system's resonant frequency scales) stressing the dominant role played by the nonresonant transitions. The relaxation and dephasing and the leakage times thus calculated, strongly depend on the appreciably interacting levels determined by the strength of the dipole coupling. Under the influence of these nonresonant and multilevel effects, the validity of the two level approximation is dictated not by the low temperature as conveniently believed, but by these multilevel dipole couplings as well as the availability of the environmental modes.
Open Access
Spin-dependent analysis of two-dimensional electron liquids
(The American Physical Society, 2002) Bulutay, C.; Tanatar, Bilal
Two-dimensional electron liquid (2D EL) at full Fermi degeneracy is revisited, giving special attention to the spin-polarization effects. First, we extend the recently proposed classical-map hypernetted-chain (CHNC) technique to the 2D EL, while preserving the simplicity of the original proposal. An efficient implementation of CHNC is given utilizing Lado's quadrature expressions for the isotropic Fourier transforms. Our results indicate that the paramagnetic phase stays to be the ground state until the Wigner crystallization density, even though the energy separation with the ferromagnetic and other partially polarized states become minute. We analyze compressibility and spin stiffness variations with respect to density and spin polarization, the latter being overlooked until now. Spin-dependent static structure factor and pair-distribution functions are computed; agreement with the available quantum Monte Carlo data persists even in the strong-coupling regime of the 2D EL.
Open Access
Structure of aluminum atomic chains
(American Physical Society, 2001) Sen, P.; Çıracı, Salim; Buldum, A.; Batra, I. P.
First-principles density-functional calculations reveal that aluminum can form planar chains in zigzag and ladder structures. The most stable one has equilateral triangular geometry with four nearest neighbors; the other stable zigzag structure has wide bond angle and allows for two nearest neighbors. An intermediary structure has the ladder geometry and is formed by two strands. While all these planar geometries are more favored energetically than the linear chain, the binding becomes even stronger in nonplanar geometries. We found that by going from bulk to a chain the character of bonding changes and acquires directionality. The conductance of zigzag and linear chains is 4e2/h under ideal ballistic conditions.
Open Access
A switching synchronization scheme for a class of chaotic systems
(Elsevier, 2002) Morgül, Ö.; Akgül, M.
In this Letter, we propose an observer-based synchronization scheme for a class of chaotic systems. This class of systems are given by piecewise-linear dynamics. By using some properties of such systems, we give a procedure to construct the gain of the observer. We prove various stability results and comment on the robustness of the proposed scheme. We also present some simulation results. © 2002 Elsevier Science B.V. All rights reserved.
Open Access
Te covered Si(001): a variable surface reconstruction
(American Physical Society, 2001) Sen, P.; Çıracı, Salim; Batra, I. P.; Grein, C. H.
At a given temperature, clean and adatom covered silicon surfaces usually exhibit well-defined reconstruction patterns. Our finite temperature ab initio molecular dynamics calculations show that the tellurium covered Si(001) surface is an exception. Soft longitudinal modes of surface phonons due to the strongly anharmonic potential of the bridged tellurium atoms prevent the reconstruction structure from attaining any permanent, two-dimensional periodic geometry. This explains why experiments attempting to find a definite model for the reconstruction have reached conflicting conclusions.
Open Access
Theoretical study of crossed and parallel carbon nanotube junctions and three-dimensional grid structures
(American Physical Society, 2004) Dag, S.; Senger, R. T.; Çıracı, Salim
This work presents a first-principles study of parallel and crossed junctions of single-wall carbon nanotubes (SWNT). The crossed junctions are modeled by two-dimensional grids of zigzag SWNTs. The atomic and electronic structure, stability, and energetics of the junctions are studied for different magnitudes of contact forces pressing the tubes towards each other and hence inducing radial deformations. Under relatively weak contact forces the tubes are linked with intertube bonds which allow a significant conductance through the junction. These interlinking bonds survive even after the contact forces are released and whole structure is fully relaxed. Upon increasing contact force and radial deformation the tube surfaces are flattened but the interlinking bonds are broken to lead to a relatively wider intertube spacing. The intertube conductance through such a junction diminish because of finite potential barrier intervening between the tubes. The linkage of crossing tubes to form stable junctions is enhanced by a vacancy created at the contact. The three-dimensional grid structure formed by SWNTs is also investigated as a possible framework in device integration.
Open Access
Theoretical study of Ga-based nanowires and the interaction of Ga with single-wall carbon nanotubes
(American Physical Society, 2004) Durgun, Engin; Dag, S.; Çıracı, Salim
Gallium displays physical properties which can make it a potential element to produce metallic nanowires and high-conducting interconnects in nanoelectronics. Using first-principles pseudopotential plane method we showed that Ga can form stable metallic linear and zigzag monatomic chain structures. The interaction between individual Ga atom and single-wall carbon nanotube (SWNT) leads to a chemisorption bond involving charge transfer. Doping of SWNT with Ga atom gives rise to donor states. Owing to a significant interaction between individual Ga atom and SWNT, continuous Ga coverage of the tube can be achieved. Ga nanowires produced by the coating of carbon nanotube templates are found to be stable and high conducting.