İSTANBUL TEKNİK ÜNİVERSİTESİ Ayazağa Kampüsü
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İSTANBUL TEKNİK ÜNİVERSİTESİ Ayazağa Kampüsü, İSTANBUL BİLİM KURULU Prof. Dr. Zehra AKDENİZ Piri Reis Üniversitesi Prof. Dr. Canan ATILGAN Sabancı Üniversitesi Prof. Dr. Nihat BERKER Sabancı Üniversitesi Prof. Dr. Can Fuat DELALE Mef Üniversitesi Prof. Dr. A. Levent DEMİREL Koç Üniversitesi Prof. Dr. Gülay DERELİ Koç Üniversitesi Prof. Dr. Sondan Durukanoğlu FEYİZ Sabancı Üniversitesi Doç. Dr. Zafer GEDİK Sabancı Üniversitesi Doç. Dr. Gül GÜLPINAR Dokuz Eylül Üniversitesi Prof. Dr. Avadis HACINLIYAN Yeditepe Üniversitesi Doç. Dr. Alkan KABAKÇIOĞLU Koç Üniversitesi Prof. Dr. Mustafa KESKİN Erciyes Üniversitesi Doç. Dr. Muhittin MUNGAN Boğaziçi Üniversitesi Prof. Dr. Özgür MÜSTECAPLIOĞLU Koç Üniversitesi Doç. Dr. Sevtap Yıldız ÖZBEK İstanbul Teknik Üniversitesi Doç. Dr. A.Levent SUBAŞI İstanbul Teknik Üniversitesi Prof. Dr. Bilal TANATAR Bilkent Üniversitesi Prof. Dr. Uğur TIRNAKLI Ege Üniversitesi Prof. Dr. Cemal YALABIK Bilkent Üniversitesi Prof. Dr. Ayşe ERZAN İstanbul Teknik Üniversitesi Prof. Dr. Mehmet ERBUDAK University of Zurih DANIŞMA KURULU 2 DÜZENLEME KOMİTESİ Doç. Dr. Sevtap Yıldız Özbek İstanbul Teknik Üniversitesi Doç. Dr. Ahmet Levent Subaşı İstanbul Teknik Üniversitesi Araş. Gör Mehmet Can Çetinkaya İstanbul Teknik Üniversitesi Şenay Üstünel İstanbul Teknik Üniversitesi Seda Kol İstanbul Teknik Üniversitesi Sevtap Yıldız Özbek İstanbul Teknik Üniversitesi PROGRAM YÜRÜTÜCÜSÜ Doç. Dr. DESTEKLEYEN KURULUŞLAR İSTANBUL TEKNİK ÜNİVERSİTESİ TÜBA – Türkiye Bilimler Akademisi SABANCI ÜNİVERSİTESİ 3 22. İSTATİKSEL FİZİK GÜNLERİ 25-27 HAZİRAN 2015 İSTANBUL TEKNİK ÜNİVERSİTESİ Ayazağa Kampüsü Elektrik Elektronik Fakültesi – İdris Yamantürk Konferans Salonu PROGRAM 25 HAZİRAN PERŞEMBE 08:30-09:00 Karşılama ve Kayıt 09:00-10:00 Anna Minguzzi (Université Grenoble-Alpes and CNRS) ‘’Persistent current flows and macroscopic superpositions of current states for interacting bosons on a ring with a gauge field’’ 10:00-10:30 Tonguç Rador (Boğaziçi Üniversitesi) ‘’2 Agent games on Graphs’’ 10:30-10:50 Ara 10:50-11:20 Miguel Navascues (Bilkent Universitesi) ‘’Non-thermal operations as a quantum thermodynamical resource’’ 11:20-11:50 R.Onur Umucalılar (Koç Universitesi) ‘’Artificial magnetic field effects in photonic systems’’ 11:50 – 12:50 Kısa Konuşmalar (A1 – A6) 12:50-14:00 Öğle Yemeği 14:00-14.30 Öznur Taştan (Bilkent Üniversitesi) ‘’ Active Learning by Statistical Leverage Samplingi’’ 14:30 – 16:10 Kısa Konuşmalar (B1 – B10) 4 26 HAZİRAN CUMA 09:00-10:00 Anna Minguzzi (Université Grenoble-Alpes and CNRS) ‘’Excitons-polaritons : properties of an out-of-equilibrium quantum gas’’ 10:00-10:30 Cem Celebi (İzmir Yüksek Teknoloji Üniversitesi) ‘’Epitaxial Graphene Transparent Electrode for Silicon Carbide Based Ultraviolet Photodetector’’ 10:30-10:50 Ara 10:50-11:20 Deniz Eroglu (Humboldt University) ‘’Connectivity-Driven Coherence of Heterogeneous Oscillators on Complex Networks’’ 11:20-11:50 Cetin Kılıc (Gebze Teknik Üniversitesi) ‘’ Computational studies of doped ZnO nanowires’’ 11:50 – 12:50 Kısa Konuşmalar (C1 – C6) 12:50-14:00 Öğle Yemeği 14:00-14:30 Aslı Tuncer (Istanbul Teknik Üniversitesi) ‘’Spectral Renormalization Group and Critical Exponents on Cayley and Diamond Lattices’’ 14:30-15:00 Ethem Aktürk (Adnan Menderes Üniversitesi) ‘’The Hallmark of Two and One dimensional Hexagonal Structures’’ 15:00 – 16:00 Kısa Konuşmalar (D1 – D6) 16:00-16:30 Mine Konuk (Piri Reis Üniversitesi) ‘’ Molecular and Atomic Mechanisms on Metal Nanostructures’’ 16:30-17:00 Efe İlker (Sabancı Üniversitesi) ‘’ Controlling Frustration, Chaos, and Novel Ordering in Spin-Glasses’’ 5 27 HAZİRAN CUMARTESİ 09:30-10:00 Umut Gursoy (Utrecht University) ‘’(Non)-renormalization of anomalous conductivities and holography’’ OTURUMLAR 10:00-11:00 Prof. Dr. Nazmi Postacıoğlu 11:00-12:00 Doç. Dr. M. Sinan Özeren 6 KISA KONUŞMA OTURUMLARI – Yazarlar (Konuşmacı) ve Başlıklar A Oturumu- 25 Haziran Perşembe (11:50 – 12:50) A1. Sofia Piepoli (Sabancı Üniversitesi) , Batu Erman, Canan Atılgan “Analysis on Target specific Transcription Activator-like Effectors by Free Energy Perturbation Calculations and Perturbation-Response Scanning” A2. Uğur Tırnaklı (Ege Üniversitesi), Ernesto P. Borges “Düşük-boyutlu korunumlu mapler: Boltzmann-Gibbs istatistiğinden Tsallis istatistiğine” A3. Selcuk Cakmak (On Dokuz Mayıs Üniversitesi),Ozgur E. Mustecaplioglu “Investigation of Lipkin-Meshkov-Glick Model As a Working Substance In Quantum Otto Cycle” A4. Sibel Gökçe (Celal Bayar Üniversitesi) “Study on bi-directional pedestrian movement using ant algorithm” A5. Gülşen Akın Evingür (Piri Reis Üniversitesi), Hakan Kaygusuz, F. Bedia Erim, Önder Pekcan “Slow Release Kinetics of Alginate Beads” A6. Gökhan Bilir (İstanbul Teknik Üniversitesi), Gönül Eryürek “Doped and Un-doped Metal Oxide Nano-powders as a Source of Incandescent Lamp-like Emission” 7 B Oturumu 25 Haziran Perşembe (14:30 – 16:10) B1. Buğra Tüzemen (İstanbul Teknik Üniversitesi) “Spin Momentum Bağlı Fermiyon Sistemlerinde Richardson Modeli'nin Uygulanması” B2. Enes Doko (Koç Üniversitesi) “Dönen iki boyutlu spin-orbit bağlı fermi gazlar” B3. Can F. Delale (MEF Üniversitesi), Şenay Pasinlioğlu “Reduced Order Gas Pressure Law for the Thermal Behaviour of Gas Bubbles” B4. Ayşe Ferhan Yeşil (Bilkent Üniversitesi), M. Cemal Yalabik “Analysis of resonance-like response of a memoryless system under periodic boundary conditions” B5. Bilal Tanatar (Bilkent Üniversitesi), V. Moldoveanu, I. V. Dinu “Tek-Molekül Mıknatıslarında Zamana Bağlı Taşınım” B6. Gökhan Şahin (Yeditepe Üniversitesi) “Derlem Dışı Parametrizasyon ile Dillerde ki Uzun Dönemli Korelasyonların Bulunması” B7. Tolga Kostak , Can Ertugay , Aslı Gençaslan, M. Özgür Güler , Deniz Kaya (Akdeniz Üniversitesi) “Video Mikroskop ve Koloit Parçacıklar kullanılarak Yumuşak Maddelerin Mikro-Reolojik Özelliklerinin Ölçülmesi” B8. Haled Abdizadeh (Sabancı Üniversitesi) “Detailed Molecular Dynamics Simulations of Human Transferrin Provide Insights on Iron Release Dynamics at Serum and Endosomal pH” B9. Engin Kandiran (Yeditepe Üniversitesi), Avadis Hacinliyan “Smoothing discontinuities in Predator Prey Models” B10. Birses Debir (Boğaziçi Üniversitesi) “BEC in curved backround” 8 C Oturumu 26 Haziran Cuma (11:50 – 12:50) C1.Efe Ilker (Sabancı Üniversitesi), Sondan Durukanoğlu “Growth Modes of Nano Size Cu-Ni alloys” C2.Deniz Türkpençe (Koç Üniversitesi) “Thermodynamic properties of photonic quantum engines” C3.Fatma Nur Ünal (Bilkent Üniversitesi) “Impurity coupled to an artificial magnetic field in a Fermi gas in a ring trap” C4.Numan Şarlı (Erciyes Üniversitesi) “The end of the paramagnetism at Tan” C5.İskender Yalçınkaya (Sabancı Üniversitesi), Zafer Gedik “Kesikli zaman kuantum yürüyüşleri ile kubit hali aktarımı” C6.Ahmet Çelikoğlu (Ege Üniversitesi), Uğur Tırnaklı “Gaussiyen olmayan dağılımlar için çarpıklık ve basıklık analizi” 9 D Oturumu 26 Haziran Cuma (15:00 – 16:00) D1. Kıvanç Çetin (Ege Üniversitesi), Özgür Afşar, Uğur Tırnaklı “Düşük-Boyutlu Dinamik Sistemlerin Kaos Geçiş Eşiği Civarında Davranışları ve Bunların Sağlamlık Analizi” D2. Gizem Özbaykal (Sabancı Üniversitesi), Canan Atılgan, and Ali Rana Atılgan “Motifs resolve how random the protein structures are” D3. Gökşin Liu (Sabancı Üniversitesi), Eren Yalçın, Ali Rana Atılgan, Canan Atılgan, Ali Koşar, Alpay Taralp “Monitoring iron release/binding mechanism with a microfluidic stopped flow device” D4. Batuhan Kav (Koç Üniversitesi), Murat Öztürk, Alkan Kabakçıoğlu “GR Protein Ailesinde Gerçekleşen İşlev Değiştiren Mutasyonlar ve Mod Etkileşimindeki Rolleri” D5. Ibrahim Ozken (Ege Üniversitesi), Deniz Eroglu, Thomas Stemler, Norbert Marwan, Baris Bagci, and Jürgen Kurths “Eşit Zaman Aralığına Sahip Olmayan Verilerin Analizi için Dönüşüm Maliyet Zaman Serisi (Transformation Cost Time Series - TACTS) Yöntemi” D6. Ceren B. Dağ (Istanbul Teknik Üniversitesi), A. Levent Subaşı, Özgür E. Müstecaplıoğlu “Tek modlu oyukların 3-atomlu rezervuarlarla termalleşmesi” 10 KONUŞMA ÖZETLERİ 11 Persistent current flows and macroscopic superpositions of current states for interacting bosons on a ring with a gauge field A. Minguzzi E-mail: [email protected] We study interacting one-dimensional bosons on a ring lattice, subjected to a rotating barrier potential, which induces an artificial U(1) gauge field and a persistent current flow on the ring. We show that, at intermediate interactions, the persistent current response is maximal, due to a subtle interplay of effects due to the barrier, interactions and quantum fluctuations [1]. We then study how the persistent current amplitude scales with system size finding that the also scaling is optimal, i.e. the current amplitude decreases slower with the system size at intermediate interactions [2]. Finally, we study the gap and the visibility of the macroscopic superposition state of current states realized with this setup. We find that a mesoscopic ring lattice with intermediate-tostrong interactions and weak barrier depth is a favourable candidate for setting up, manipulating and probing a qubit in the next generation of experiments with ultracold atoms [3]. References [1] M. Cominotti, D. Rossini, M. Rizzi, F.W.J. Hekking and A. Minguzzi, Phys. Rev. Lett. 113, 025301 (2014) [2] M. Cominotti, D. Rossini, M. Rizzi, D. Aghamalayan, L. Amico, L.-C. Kwek, F.W.J. Hekking and A. Minguzzi, arXiv:1409.1835 [3] D. Aghamalyan, M. Cominotti, M. Rizzi, D. Rossini, F.W.J. Hekking, A. Minguzzi, L.-C. Kwek and L. Amico, arXiv:1411.4812 12 2 Agent games on Graphs Tonguc Rador Let us assign agent on the nodes of a graph and endow them with integerpoints. Now let us randomly pick an edge on the graph, thisunambiguously defines two agents with points say L and S. We increasethe point of one and only one of them as follows: If L>S we have (L,S)to (L+1,S) with probability p, if L<S we have (L,S) to (L,S+1) withprobability q=1-p, and if L=S only one receives the point equallylikely.We study the infinite time behavior of the point distribution -providedan initial condition is given- on various graphs. The model can bemapped to a type of altered coloring model on regular graphs whereason irregular graphs there are also various interesting aspects dependingon the local geometry of the graph.In particular we study the model on n-dimensional tori and find criticalbehavior in n=2. 13 Non-thermal operations as a quantum thermodynamical resource Miguel Navascues Quantum thermodynamics studies the emergence of thermodynamical laws inquantum microscopic systems. An important input from quantum informationscience has been to reformulate quantum thermodynamics as a resourcetheory, whereby thermal states are free and the only allowed operationsare unitary transformations commuting with the total Hamiltonian of thesystem. This approach to quantum thermodynamics has allowed us, forinstance, to re-interpret quantum free energy as the asymptotic conversion rate between different states, or the amount of work which can beextracted on average out of a resource quantum state. Previous literatureon quantum thermodynamics has just focused on transformations betweendifferent state resources, forgetting that quantum operations which do notcommute with the total energy also constitute a nonfree resource. In thiswork, given a number of non-thermal quantum channels, we study the problemof how to integrate them in a thermal engine so as to generate the maximum amount of work W_max. We find that W_max is an additive function of theconsidered channels, computable for both finite dimensional quantumoperations and bosonic channels. We apply these insights to bound theamount of extractable work due to the natural non-thermal processespostulated in the Ghirardi-Rimini-Weber (GRW) theory. We find that,although GRW theory (and, for the matter, any proposed collapse model) predicts the possibility to extract work from the vacuum at no cost, inthe best of the cases the rate of extraction would be ridiculously low. 14 Artificial magnetic field effects in photonic systems R. O. Umucalılar Department of Physics, Koç University, Rumelifeneri Yolu, 34450 Sarıyer, İstanbul, Turkey In this talk, I will present some of the outcomes of my theoretical work on photonic systems experiencing an artificial magnetic field. After a brief introduction to quantum fluids of light where the quasiparticles of light-matter interaction, namely polaritons, behave collectively in a nonequilibrium setting, I will continue with the problem of simulating a magnetic field for photons (and polaritons) which are neutral particles. I will discuss various phenomena predicted to appear in these systems ranging from the integer quantum Hall effect in a coupled cavity array to the nonequilibrium fractional quantum Hall physics where photons can be driven into strongly-correlated states resembling the Laughlin state in the presence of strong optical nonlinearity. 15 Active Learning by Statistical Leverage Sampling Oznur Tastan Active learning aims to obtain a classifier of high accuracy by using fewer label requests in comparison to passive learning by selecting effective queries. Many active learning methods have been developed in the past two decades, which sample queries based on informativeness or representativeness of unlabeled data points. In this work, we explore a novel querying criterion based on statistical leverage scores. The statistical leverage scores of a row in a matrix are the squared row-norms of the matrix containing its (top) left singular vectors and is a measure of influence of the row on the matrix. Leverage scores have been used for detecting high influential points in regression diagnostics and have been recently shown to be useful for data analysis and randomized low-rank matrix approximation algorithms. We explore how sampling data instances with high statistical leverage scores perform in active learning. Our empirical comparison on several binary classification datasets indicate that querying high leverage points is an effective strategy. This is joint work with Cem Orhan, (Bilkent University, Department of Computer Engineering) 16 Excitons-polaritons : properties of an out-of-equilibrium quantum gas A. Minguzzi Laboratoire de Physique et Modélisation des Milieux Condensés, Université GrenobleAlpes and CNRS, Grenoble, France E-mail: [email protected] Exciton polaritons are out-of-equilibrium quantum fluids, obtained under drivendissipative conditions in reduced dimensionality (quasi-one-dimension, two-dimension). The first-order correlation function is accessible experimentally *1+. I will present first a mean-field model which allows to take into account both the driven-dissipative nature of the fluid and the effect of a smooth disorder, yielding a very good agreement with the experiment *1+. Then, I will use a quantum Langevin approach combined with a Luttinger-liquid description of the fluid to determine the large-distance behaviour of the first-order correlation function at arbitrary interaction strength in the clean case, showing how beyond-mean-field interactions yield a reduction of coherence at large distances *2+. Finally, I will present an application of the out-of-equilibrium polariton gas as refrigerant, capable of absorbing low-energy phonons in a solid *3+. References [4] Aurélien Trichet, Emilien Durupt, François Médard, Sanjoy Datta, Anna Minguzzi, Maxime Richard, Phys. Rev. B 88, 121407(R) (2013) [5] S. Datta, M. Wouters and A. Minguzzi, in preparation [6] Sebastian Klembt, Emilien Durupt, Sanjoy Datta,Thorsten Klein, Augustin Baas, Yoan Léger, Carsten Kruse, Detlef Hommel, Anna Minguzzi, and Maxime Richard, in preparation 17 Epitaxial Graphene Transparent Electrode for Silicon Carbide Based Ultraviolet Photodetector Cem Çelebi İzmir Institute of Technology, Department of Physics, Nanophysics Research Group 35430 Urla / İzmir Graphene is considered to be used as transparent conductive electrode for next generation photodetectors and solar cells due to its excellent optical transparency, high electrical conductivity and mechanical flexibility. During the last decade, conventional transparent conductors out of Ni/Au, Ti, Ti/W, and ITO have been widely employed to collect photo-generated charge carriers in those optoelectronic and photovoltaic devices. However, most of these materials inherently have very low optical transmittance (< 80%) especially in the ultraviolet (UV) regime below 400 nm due to high surface reflection and absorption. Unlike those above mentioned contact materials, graphene is capable of transmitting more than 90% of light in the wavelength range between 200 and 400 nm. As a consequence of its relatively high UV transmission level and zero band gap, graphene has become a promising candidate as transparent and conductive electrode for UV sensitive photodetectors. In my talk, I will present our preliminary experimental results on the fabrication and characterization of graphene-semiconductor-graphene (GSG) ultraviolet photodetector based on the rectifying character of Schottky junction at the interface between epitaxial graphene and Silicon Carbide SiC semiconductor. As-grown single layer epitaxial graphene is interdigitated as transparent conductive electrode to probe photogenerated charge carriers in a semi-insulating 4H-SiC substrate. The fabricated device exhibits the typical current-voltage characteristics of a conventional metalsemiconductor-metal type photodetector with low leakage current. Our measurements based on time-resolved photocurrent measurements suggest an excellent photocurrent reversibility and high response speed of the device. The measurements performed for different illumination wavelengths showed that the sample reveals higher responsivity values when it is exposed to the light with 254 nm wavelength. The obtained results imply that epitaxial graphene can be used readily as transparent conductor for SiC based optoelectronic device applications. 18 Connectivity-Driven Coherence of Heterogeneous Oscillators on Complex Networks Deniz Eroglu 1,2 , T. Pereira3, G. B. Bagci4, U. Tirnakli4, and H.J. Jensen3 1 Potsdam Institute for Climate Impact Research (PIK), 14473 Potsdam, Germany 2 Department of Physics, Humboldt University, 12489 Berlin, Germany 3 Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK 4 Department of Physics, Faculty of Science, Ege University, 35100 Izmir, Turkey October 20, 2014 In the nature, there is a tendency towards to collective motion. Collective behaviour of coupled elements is one of the observed and proved phenomena on dynamical systems. Moreover, we see this behaviour on different structures of connected elements which are named complex networks. During the past decades, our understanding of collective behaviour on complex networks has increased significantly. So far, in general, researchers have focused on synchronization of coupled periodic elements with different frequencies such as Kuramoto model [1, 2] or identical periodic/chaotic oscillators [3, 4] via interaction akin to diffusion. We study the emergence of coherence in complex networks of mutually coupled nonidentical ele-ments [5]. We uncover the precise dependence of the dynamical coherence on the network connectivity, the isolated dynamics of the elements, and the coupling function. These findings predict that in random graphs the enhancement of coherence is proportional to the mean degree. In locally connected networks, coherence is no longer controlled by the mean degree but rather by how the mean degree scales with the network size. In these networks, even when the coherence is absent, adding a fraction s of random con-nections leads to an enhancement of coherence proportional to s. Our results provide a way to control the emergent properties by the manipulation of the dynamics of the elements and the network connectivity. References [1] [2] [3] [4] [5] K. Wiesenfeld, P. Colet, and S.H. Strogatz„ Phys. Rev. Lett. 76, 404 (1996). S. H. Strogatz, Physica (Amsterdam) 143D, 1 (2000). M. Barahona and L. Pecora, Phys. Rev. Lett. 89, 054101 (2002). C. W. Wu, Phys. Lett. A 319, 495 (2003). T. Pereira, D. Eroglu, G.B. Bagci, U. Tirnakli and H.J. Jensen, Phys. Rev. Lett. 110, 234103 (2013) 19 Computational studies of doped ZnO nanowires Çetin Kılıç Department of Physics, Gebze Technical University, Gebze, Kocaeli 41400, Turkey At the beginning of this century, the technological interest has been shifted from bulk ZnO, which is one of the most studied semiconductors in the second half of the last century[1], to ZnO nanorods, nanowires and other nanostructures, especially in terms of sensors and optoelectronic applications[2,3]. Some recent studies have shown that the doping characteristics of ZnO nanowires could be qualitatively different in comparison to bulk samples[4], which might prove advantageous for the applications in semiconductor devices. On the other hand, first-principles calculations have increasingly been used to gain microscopic understanding of the semiconductor doping. Thus, this presentation concerns itself with a variety of properties of doped ZnO nanowires studied by means of computational modeling within the framework of the density functional theory. It will be demonstrated that the latter enables one to compare various (bulk or surface) doping configurations in regard to structure and stability, and to perform characterization of their electronic levels. It will be articulated that surface doping ultrathin nanowires with a heavy non-magnetic element such as bismuth might lead to the spin-orbit induced effects as well as the spin-dependent modification of the band structure where exchange and/or Rashba-type splitting could occur depending on a particular configuration. [1] e.g., Ü.Özgür et al., J. Appl. Phys. 98, 041301 (2005). [2] C. Klingshirn et al., Superlattices and Microstructures 38, 209 (2005). [3] J. Gomez and O. Tigli, J. Mater. Sci. 48, 612 (2013). [4] e.g., J. S. Lee et al., Adv. Mater. 23, 4183 (2011). Acknowledgements Part of this presentation is based on the results of calculations performed by Mehmet Aras and Dr. Sümeyra Güler-Kılıç. This work is supported by TÜBİTAK under Grant No. 114F155. 20 Spectral Renormalization Group and Critical Exponents on Cayley and Diamond Lattices Aslı Tuncer and Ayşe Erzan Department of Physics, Istanbul Technical University, Maslak 34469, Istanbul, Turkey (Dated: December 14, 2014) In a previous paper, we proposed a spectral renormalization group scheme as a general approach to the study of fluctuations on arbitrary networks. [1] This approach is modeled on the “field theoretic” renormalization group a là Wilson [2, 3]. In the spectral renormalization group approach, the fluctuations of the order parameter are expanded in terms of the eigenvectors of the graph Laplacian[4], on arbitrary undirected networks. Elimination of the large eigenvalue fluctuations and rescaling of the effective hamiltonian are expected to yield, in the same spirit as in the Wilson renormalization group, the rescaling factors for the coupling constants, which can then be related to the critical exponents. We implemented the spectral renormalization group theory for the Gaussian model [5–7] on two deterministic networks, namely the Cayley tree and the diamond lattice [9] as well as the square and cubic periodic lattices. [8]. The nearest neighbor interaction is diagonalized by using the eigenvectors of the graph Laplacian, giving rise to a Gaussian theory for continuous fields. The scaling dimensions of the fields and of the “mass” term are determined numerically as well as analytically, in terms of β, the scaling exponent of the spectral density for small eigenvalues. We compute the specific heat and magnetic field exponents, α and δ, defined respectively as ch ∼ t−α, and h ∼ mδ on the critical isotherm; t = (T − Tc)/Tc is the reduced temperature and m the magnetization per spin. We obtain theGaussian model values, which go over to the mean field results if one heuristically takes into account the dangerousirrelevant fourth order term in the Landau expansion [7].We have since then extended our results to ψ4 theory, which, on periodic lattices, exhibits critical behavior in the same universality class as the Ising model. The ψ4 interaction terms are treated perturbatively, using the usual Feynman graph expansion [2, 3, 7]. We find, as in the Euclidean case, that to first order in the ψ4 coupling 21 constant, the Gaussian fixed point is stable. Higher order calculations are possible using a perturbation expansion in both thecoupling constant and βc − β = s, where βc = 1.On the Cayley tree, which has an effective graph spectral dimension d˜ = 2 (or β ≡ (d˜/2) − 1 = 0), we find thatthe second order calculation does not yield a non-Gaussian fixed point, as should indeed be expected for the Isingmodel on a Bethe lattice. Explicit solutions for the eigenvectors of the graph Laplacian involve much reduced cyclic and acyclic permutation symmetries, in comparison to the much larger translational and rotational symmetry present in the case of periodic latices. The coupling term that is fourth order in the fields does not scale with a power of s, leading to the stability of the Gaussian fixed point at second order.We have also applied the spectral renormalization group to a scalar ψ4 model on the diamond lattice, which we have found numerically to have a spectral dimension of d˜ = 1.70. However, here again we found no non-Gaussian fixed point of the RG transformations up to second order, due to the same mechanism. This, however is problematic, since it is known that the Ising model on the diamond lattice exhibits a phase transition with ergodicity breaking at a finite temperature in the thermodynamic limit [11], with non-classical exponents [9]. The diamond lattice, as well as its Laplace eigenvectors have a further reduced symmetry consisting of just the “right/left” and “up/down” permutations [10], which apparently leads to this result. This may imply that the correct critical behavior on lattices without translational symmetry are not accessible within a perturbative approach via the spectral RG. [1] E. Aygün, A. Erzan, J. Phys. Conf. Ser. 319, 012007 (2011). [2] KG Wilson, Phys. Rev. (1971) [3] K.G. Wilson and J. Kogut J Phys. Rep. 83, 75 (1974) [4] F.R.K. Chung, Spectral graph theory, (American Mathematical Society, Washington DC, 1997) [5] T.H. Berlin and M. Kac, Phys. Rev.86, 821 (1952). [6] K. Huang, Statistical Mechanics (John Wiley and Sons, N.Y., 1987) [7] N. Goldenfeld, Lectures on phase transitions and the renormalization group (Perseus Books, Reading Mass., 1992) [8] A. Tuncer and A. Erzan, “Spectral Renormalization Group and Critical Exponents on Cayley and Diamond Lattices,” arXiv:1312.2885. [9] A.N. Berker and S. Ostlund, J. Phys. C 12, 4961 1979. [10] R.B. Griffiths and M. Kaufman, Phys. Rev. B 26, 5022 (1982). [11] Bleher, P.M., Zalys, E., Commun. Math. Phys. 67, 17-42 (1979) 22 The Hallmark of Two and One dimensional Hexagonal Structures Ethem Aktürk The synthesis of a single atomic layer of graphite, i.e. graphene, with covalently bonded honeycomb lattice in 2004 has been a breakthrough in basic and applied science. Two dimensional honeycomb structures derived from other Group IV elements and Group IIIV compounds are generating significant current interest because of unusual electronic and magnetic properties. Based recent studies published, the properties of silicene, hBN, h-MoS2 appear to be complementary to graphene and hence provide new physical and chemical properties. Therefore, the main object of my talk is to present exceptional electronic properties of two dimensional hexagonal structures. To understand how these properties are affected by adatoms and defects, the effects of foreign atoms and vacancies on the electronic structure will be also discussed. We found that adatoms and defects can induce important changes in the electronic and magnetic properties of two dimensional structures. For example, the semimetallic graphene with carriers behaving as massless Dirac fermions can be metallized as a result of adsorption of Li or Ca atoms and hence Li or Ca covered graphene can serve as a high-capacity hydrogen storage medium with each adsorbed Li or Ca absorbing up to four hydrogen molecules. Functionalization of two dimensional structures through adatom adsorption and vacancy creation appears to be a promising way to extend the application of monolayer hexagonal structures. 23 Molecular and Atomic Mechanisms on Metal Nanostructures Mine Konuka,b, Sondan Durukanoğluc, d a Department of Physics, Istanbul Technical University, 34469 Istanbul, Turkey b Department of Physics, Pîrî Reis University, 34940 Istanbul, Turkey c Faculty of Engineering and Natural Sciences, Sabancı University, 34950 Istanbul, Turkey d Nanotechnology Research and Application Center, Sabancı University, 34950 Istanbul, Turkey We investigated the mechanisms underlying the controlled motion of adatoms and molecules on metal surfaces at atomic scale. The role of reaction conditions in the growth of cubic Ag nano-clusters is determined using molecular dynamic simulations based on the potential extracted from the embedded atom method. In the simulations, we successfully reproduced the experimentally observed growth modes and our results interestingly show that the growth modes of Ag nano-cubes can readily be controlled through fine-tuning of diffusion rates with respect to the single atom mobility on the respective facets. We performed further simulations to understand the nature of the atomic-scale motions of molecular motors on metal surfaces using density functional theory calculations and also molecular static calculations based on the charge optimized many body potential. We will discuss atomistic nature of the observed translational and rotational motion of triptycene molecules (C20H14) on Cu surface. 24 Controlling Frustration, Chaos, and Novel Ordering in Spin-Glasses Efe Ilker, Sabancı University, Tuzla, Istanbul 34956 Turkey Spin-glass phases and phase transitions for q-state clock models and their q→∞ limit the XY model, in spatial dimension d= 3, are studied by a detailed renormalization-group study that is exact for the d = 3 hierarchical lattice and approximate for the cubic lattice. For even q [1], in addition to the now well established chaotic rescaling behavior of the spin-glass phase, each of the two types of spin-glass phase boundaries displays, under renormalization-group trajectories, their own distinctive chaotic behavior. These chaotic renormalization-group trajectories subdivide into two categories, namely as strong coupling chaos (in the spin-glass phase and, distinctly, on the spinglass–ferromagnetic phase boundary) and as intermediate-coupling chaos (on the spin-glass–paramagnetic phase boundary). We thus characterize each different phase and phase boundary exhibiting chaos by its distinct Lyapunov exponent, which we calculate. We show that, under renormalization group, chaotic trajectories and fixed distributions are mechanistically and quantitatively equivalent. The phase diagrams for arbitrary even q, for all non-infinite q, have a finite-temperature spin-glass phase. Furthermore, the spin-glass phases exhibit a universal ordering behavior, independent of q. The spin-glass phases and the spinglass–paramagnetic phase boundaries exhibit universal fixed distributions, chaotic trajectories and Lyapunov exponents. In the XY model limit, our calculations indicate a zero-temperature spin-glass phase. Very distinctive orderings and phase diagram structures are found for odd q.[3] These models exhibit asymmetric phase diagrams, as is also the case for quantum Heisenberg spin-glass models. No finite-temperature spin-glass phase occurs. For all odd q > 5, algebraically ordered antiferromagnetic phases occur. One such phase is dominant and occurs for all q > 5. Other such phases occupy small lowtemperature portions of the phase diagrams and occur for 5 ≤ q ≤ 15. All algebraically ordered phases have the same structure, determined by an attractive finite-temperature sink fixed point where a dominant and a subdominant pair states have the only non-zero Boltzmann weights. The phase transition critical exponents quickly saturate to the high q value. Furthermore, we realized that in spinglass systems, frustration can be adjusted continuously and considerably,[2] without changing the antiferromagnetic bond probability p, by using locally correlated quenched randomness, as we demonstrate on hypercubic lattices and hierarchical lattices. Such overfrustrated and underfrustrated Ising systems on hierarchical lattices in d = 3 and 2 are studied. With the removal of just 51% of frustration, a spin-glass phase occurs in d = 2. With the addition of just 33% frustration, the spin-glass phase disappears in d = 3. Sequences of 18 different phase diagrams for different levels of frustration 25 are calculated in both dimensions. In general, frustration lowers the spin glass ordering temperature. At low temperatures, increased frustration favors the spin-glass phase (before it disappears) over the ferromagnetic phase and symmetrically the antiferromagnetic phase. When any amount, including infinitesimal, frustration is introduced, the chaotic rescaling of local interactions occurs in the spin-glass phase. Chaos increases with increasing frustration, as can be seen from the increased positive value of the calculated Lyapunov exponent λ, starting from λ = 0 when frustration is absent. The calculated runaway exponent y_R of the renormalization-group flows decreases with increasing frustration to y_R = 0 when the spin-glass phase disappears. From our calculations of entropy and specific-heat curves in d = 3, it is shown that frustration lowers in temperature the onset of both long- and short-range order in spin-glass phases, but is more effective on the former. From calculations of the entropy as a function of antiferromagnetic bond concentration p, it is shown that the ground-state and low-temperature entropy already mostly sets in within the ferromagnetic and antiferromagnetic phases, before the spin-glass phase is reached. [1] E. Ilker and A.N. Berker, Phys. Rev. E 87, 032124 (2013). [2] E. Ilker and A.N. Berker, Phys. Rev. E 89, 042139 (2014). [3] E. Ilker and A.N. Berker, Phys. Rev. E 90, 062112 (2014). 26 (Non)-renormalization of anomalous conductivities and holography Umut Gürsoy The chiral magnetic and the chiral vortical effects are recently discovered phenomena arising from chiral gauge and gravitational anomalies that lead to generation of electric currents in presence of magnetic field or vorticity. The magnitude of these effects is determined by the anomalous conductivities. In most of the cases these conductivities are on-loop exact. I will discuss the issue of renormalization of these conductivities both from the field theory and from the holographic point of view. In particular I will identify the holographic counterpart to the radiative corrections that arise from the dynamical gluon fields as the axionic degrees of freedom in the bulk. It turns out that the effects of the gluonic contribution to the anomalous conductivities of order N_f/N_c hence detectable only in the Veneziano limit in holography. 27 A1 Analysis on Target specific Transcription Activator-like Effectors by Free Energy Perturbation Calculations and Perturbation-Response Scanning Sofia Piepoli*, Batu Erman, Canan Atılgan Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul [email protected] Bacterial plant pathogens belonging to Xanthomonasgenus infect cells by injecting Transcription Activator-Like effector(TALE) proteins to modify plant gene expression1. DNA binding TALE proteins have been modified to generate site specific engineered TALENs (transcription activator-like nucleases)2. Crystal structure of the PthXo1 TALE protein bound to its DNA target reveals specificity of interactions between the two molecules at the sequence level3. TALE DNA binding domains consist of ~17 repeats, each consisting of 33-34 conserved amino acids. Alignment of the sequence of the repeats shows perfect homology except for the amino acids at positions 12-13 (repeat variable diresidues-RVDs) which specifically bind to DNA bases4according to the code: HD→C, NG→T, NI→A and NN→G in most cases, while there are some exceptions. Not all repeats have to perfectly contact DNA to bind and it is unclear how TALE pairs up with a target DNA sequence while avoiding off-target sites. To address this problem, we apply molecular dynamics-based tools to quantify specific binding stability, mimicking cellular conditions. We analyze selected point mutations introduced into the RVD region of the protein sequence and predict resulting free energy differences using detailed freeenergy perturbation calculation5. Identification of key residues for stability of binding at specific positions will allow computational design of TALEs that can be experimentally tested for binding affinity and off-target specificity. By systematically applying this method, we interpret the role of local interactions in contributing to the overall stability of the system. Additionally, we investigate the role of other residues along the repeat and their allosteric effect on the stability of the RVD by using the Perturbation-Response Scanning (PRS)6statistical method.While directed forces are applied on a single target residue, the resulting relative changes in next residues coordinates are recorded in magnitude and directionality. The analysis is aimed to contribute to the study of TALE-DNA binding mechanism regulation. 1) Kay S., Bonas U. How Xanthomonas type III effectors manipulate the host plant, Current Opinion in Microbiology, 2009, 12, 1. 2) Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res.2011, 39, 359. 3) Mak A. N., Bradley P., Cernadas R. A., Bogdanove A. J., Stoddard B. L. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science.2012, 335, 6069. 4) Moscou M. J., Bogdanove A. J. A simple cipher governs DNA recognition by TAL effectors. Science, 2009, 326, 5959 5) Pohorille A., Jarzynski C., Chipot C. Good practices in free-energy calculations. J PhysChem, 2010, 114, 32. 6) Atilgan C., Atilgan A. R. Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein.PLoS Comput. Biol., 2009, 5, e1000544 28 A2 Düşük-boyutlu korunumlu mapler: Boltzmann-Gibbs istatistiğinden Tsallis istatistiğine Uğur Tırnaklı1 ve Ernesto P. Borges2 1Fizik Bölümü, Fen Fakültesi, Ege Üniversitesi 35100 İzmir-Türkiye 2Fizik Enstitüsü, Bahia Federal Üniversitesi, Rua Barao de Jeremoabo, 40170-115 Salvador-BA, Brezilya İyi bilindiği gibi Boltzmann-Gibbs istatistiği ergodik sistemlere termoistatisitik olarak yaklaşmanın doğru yoludur. Öte yandan, ergodikliğin bozulması ve kuvvetli korelasyonlar sistemi, Boltzmann-Gibbs istatistiğinin çalışmadığı denge dışı durumlara sürükler. Bu tip sistemlerin büyük bir sınıfı için, doğru yaklaşımın Tsallis istatistiği olduğu son yıllarda gösterilmiştir. Burada, son derece açık bir biçimde, paradigmatik korunumlu sistemlerden standard mapin dinamiğin bir istatistikten diğerine nasıl geçiş sergilediğini gösteriyoruz. Sonuçlarımız açıkça Boltzmann-Gibbs ve Tsallis istatistiğinin geçerlilik alanlarını tanımlar. Birçok önemli fiziksel sistem düşük-boyutlu korunumlu maplere indirgenebildiğinden sonuçlarımızın çeşitli deneysel ve gözlemsel sonuçların daha gelişmiş yorumlarına ışık tutacağı beklenmektedir. 29 A3 30 A4 Study on bi-directional pedestrian movement using ant algorithm Sibel Gokcea, Ozhan Kayacanb Department of Physics, Faculty of Arts and Sciences, Celal Bayar University, 45140, Muradiye, Manisa-TURKEY a,b Abstract A cellular automata model is proposed to simulate the bi-directional pedestrian flow. Apart from the study in literature, pedestrian movement is investigated by using ant algorithms. Ants communicate each other by dropping a chemical, called pheromone, on the substrate while they crawl forward. Similarly, it is considered that oppositely moving pedestrians drop a ‘visual pheromone’ on their way and it might cause attractive or repulsive interactions. This phenomena is introduced to modelling the pedestrians’ walking preference. By this way, decision-making process of pedestrians will be based on ‘the instinct of following’. At some values of densities, the relationships of velocity-density and flux-density will be analyzed for different evoporation rates of ‘visual pheromone’. The most interesting result is that lane formation and phase transitions are observed for certain evaporation rate for visual pheromones. Keywords: Pedestrian movement, Cellular automata, Computer simulation 31 A5 32 A6 Doped and Un-doped Metal Oxide Nano-powders as a Source of Incandescent Lamplike Emission Gökhan Bilir*, Gönül Eryürek Department of Physics, Istanbul Technical University, 34469 Istanbul, TURKEY [email protected] In the last decade, a good deal of research has been devoted to the synthesis and characterization of materials with nano-sizes because of their unusual properties. This interest in nano–materials has been intensified by the development of new, cheap and efficient synthesis techniques of these materials. It has been proven by most researchers in the literature that some thermal, optical and mechanical properties of nano-materials are enhanced with respect to those of their bulk counterparts [1]. Especially, nano–systems have revealed some extraordinary properties with decreasing size that do not appear in their bulk counterparts because they are small enough in size to create quantum confinement effects [1]. In particular, these properties of nanomaterials are due to the increasing surface area to volume ratio with decreasing crystalline sizes. We are reporting the white light (WL) emission from metal oxide nano-powders under laser diode excitation, which is one of these unexpected behavior of nano-particles. We have obtained white light emission with high efficiency and color rendering index (CRI) approaching the theoretical limit. The production of a broad band (ranging from 400 to 900 nm) white light following the monochromatic infrared laser light (803.5 and 975 nm) excitation was achieved from both nominally un-doped and rare earth and transition metal ions-doped oxide nano-powders. Experimental results indicate that such an emission feature is a nano-scale phenomenon, cannot be ascribed to an overlap of sharp emission bands in the un-doped case and, even if assisted by the dopant presence, is a host matrix-related process. The spectral distribution of the detected WL resembles very closely that of an incandescent lamp, which in turn is the most comfortable light to human eyes. Our experimental results make our WL emission very interesting at both the fundamental and the applicative level and may open the way to an alternative route with respect to incandescent lamps. 33 B1 34 B2 Dönen iki boyutlu spin-orbit bağlı fermi gazlar Enes Doko İki boyutlu dönen spin-orbit bağlı (SOB) fermi gazlar yerel yoğunluk yaklaşımı altında ve hiç girdap oluşmayacağı varsayımı ile incelenecektir. Önce etkileşmeyen iki boyutlu SOB fermi gazlar incenecek yüksek dönme veya yüksek SOB gazın tuzağın merkezini boşaltacağı gösterilecektir. Daha sonra ortalama alan yaklaşımı altında etkileşim de eklenip, SOB paçacık çiftlerinin kopma durumu incelenecektir. 35 B3 Reduced Order Gas Pressure Law for the Thermal Behaviour of Gas Bubbles Can F Delale1and Şenay Pasinlioğlu2 of Engineering, MEF University, Ayazağa Caddesi No 4, 34980 Maslak, Sarıyer, Istanbul, Turkey 2Department of Mathematics, Istanbul Technical University, Büyükdere Caddesi, 34465 Maslak, Sarıyer, Istanbul,Turkey E-mail: [email protected] ; [email protected] 1Faculty The thermal behaviour of a spherical gas bubble in a liquid driven by an acoustic pressure is investigated in the uniform pressure approximation by considering the energy balance between the gas bubble and the surrounding liquid. An iterative method of solution is constructed [1] to solve the temporal evolution of the coupled equations for the temperature distribution and the pressure inside the bubble. It is shown that the first iterative solution leads to the first order law of the gas pressure as a polytropic power law of the bubble wall temperature and of the bubble radius, with the polytropic index given as an explicit function of the isentropic exponent of the gas. The resulting first order law of the gas pressure reduces to the classical isothermal and adiabatic laws in the appropriate limits. The bubble wall temperature is obtained from the PlessetZwick solution [2,3] of the energy equation from the liquid side coupled to the equation of spherical bubble dynamics. The first order gas pressure law is then applied to an acoustically driven cavitation bubble coupled to the Rayleigh-Plesset equation of spherical bubble dynamics. Results obtained for a typical acoustic signal show that the bubble wall temperature pulses during collapse and rebound can become an order of magnitude higher than the liquid temperature, which agree with the recent results of molecular dynamics simulations [4]. [1] Delale C F and Pasinlioglu S 2015 Ninth International Symposium on Cavitation, Lausanne,Switzerland, Dec. 6-10, 2015. [2] Plesset M S and Zwick S A 1952 J. Appl. Phys. 23 95 [3] Brennen C E 1995 Cavitation and Bubble Dynamics (Oxford University Press, Oxford) 47-67 [4] Schanz D, Metten B, Kurz T and Lauterborn W 2012 New J. Phys 14 113019 36 B4 37 B5 Tek-Molekül Mıknatıslarında Zamana Bağlı Taşınım B. Tanatar1*, V. Moldoveanu2, I. V. Dinu2 *Department of Physics, Bilkent University, Bilkent, 06800 Ankara, Turkey1 National Institute of Materials Physics, PO Box MG-7, Bucharest-Magurele, Romania2 [email protected] Ferromanyetik uçlara bağlı tek-molekül mıknatısları kuantum bilgi-işlem protokollerinin katı-hal ortamlarında uygulamaları açısından ümit vaad eden sistemler olmuştur *1+. Boş moleküler orbital ve lokalize molekül spini S arasındaki degiş-tokuş etkileşmesi, lokalize molekulün elektriksel anahtar olarak kullanılmasını sağlar. Buradaki temel özelliklerden biri D ve E parametreleri ile karakterize edilen eksendeki anizotropi (yönbağlılık) terimi D(S2z) ve dik yöndeki anizotropi terimi E(S2x-S2y) manyetik anizotropilerdir. Tekmolekül mıknatıslarında zamana bağlı taşınım için Genelleştirilmis Master Denklemi çerçevesinde teorik çalışmalarımızı sunuyoruz *2+. Dik yöndeki anizotropinin tranziyent akımlar ve moleküler spin dinamiği üzerindeki etkilerini analiz ediyor ve daha önce elde edilmiş bazı sonuçları genelleştiriyoruz *3+. Moleküler spin dinamiğini tranziyent akımdan okuma olasılığı ve dik yöndeki manyetik alan etkilerini inceliyoruz. Son olarak, molekül ve parçacık rezervuarları arasındaki uçlara zamana bağlı sinyaller uygulandığında ve moleküler spinleri manipüle etmenin bir yolu olarak önerdiğimiz kuantum turnikesi koşullarında *4,5+ ortaya çıkan etkileri inceliyoruz. Anti-paralel spin polarizasyonlarında ferromanyetik uçlar için turnike protokolünün moleküler seviyelerin spinlerini basamak şeklinde yazma ve okumaya olanak sağladığını gösteriyoruz. References [1] L. Bogani and W. Wernsdorfer, Nature Mater. 7, 179 (2008). [2] V. Moldoveanu, A. Manolescu, C-S Tang, and V. Gudmundsson, Phys. Rev. B 81, 155442 (2010). [3] F. Elste and C. Timm, Phys. Rev. B 71, 155403 (2005). [4] T. Fujisawa, T. Hayashi, S. Sasaki, Reports on Progress in Physics 69, 759 (2006). [5] W-T Lai, D. M. T. Kuo, P-W Li, Physica E 41, 886 (2009). 38 B6 Derlem Dışı Parametrizasyon ile Dillerde ki Uzun Dönemli Korelasyonların Bulunması (Gökhan Şahin a) a Bil. Sis. Tek. Bölümü, Yeditepe Universitesi , İstanbul 34755 , Türkiye Doğal dillerin yazılı metinleri karmaşık ve yüksek boyutlu olguları bir boyutlu semantik anlamlı sembollere projeksiyonudurlar . Bu projeksiyonun anlamlı olabilmesi için bilginin yapısal örüntülere sahip olması ve uzun vadeli korelasyonları içermesi gerekmektedir *1, 2+. Genelde bu korelasyonların belirlenmesi ve diğer istatistiksel analizler derlem (korpus) adı verilen kelime ve/veya metin veri bankaları kullanılarak yapılmakta ve yapılan analizlerin çoğu da derleme bağlı olmakta ve genelleme ve karşılaştırma yapmaya zorlaştırmaktadırlar [3-5+. Hata bazı diller için bu pratik olarak imkansız hale getirmektedir. Bu çalışma da derlemden bağımsız bir yöntem önerilmekte ve bu yöntem kullanarak dillerin ( farklı dil aile gruplarından 12 dil) uzun dönemli büyüklük olarak kendine has ama bütün diller için aynı örgüyü tekrar eden karakteristik korelasyonlara sahip olduğu iki farklı yöntem Diffusion Entropy analysis *6+ ( Difuzyon entropisi analizi) ve Detrended Fluctuation analysis *7+( Trendden arındırılmış dalgalanma analizi) kullanarak gösterilmiştir. [1] Schenkel A, Zhang J, Zhang Y (1993) Long range correlation in human writings. Fractals 1:4755. [2] Alvarez-Lacalle E, Dorow B, Eckmann JP, Moses E, (2006) Hierarchical structures induce longrange dynamical correlations in written texts. Proc Natl Acad Sci USA 103:7956- 7961. *3+ Montemurro MA, Pury PA. ”Long-range fractal correlations in literary corpora.” (2002). Available from cond-mat/0201139. *4+ Bhan,J, S. Kim, J. Kim, Y. Kwon, ”Long-range correlations in Korean literary corpora”, Chaos, Solitons and Fractals, 29, 69- 81, (2006). *5+ P. Allegrini, P. Grigolinib and L. Palatella, ”Intermittency and scale-free networks: a dynamical model for human language complexity”, Chaos, Solitons and Fractals, 20, 95-105, (2004). *6+ N. Scafetta, V. Latora and P. Grigolini, ”L´evy scaling: The diffusion entropy analysis applied to DNA sequences”, Phys. Rev. E, 66, 031906, (2002). [7]Peng C-K, Havlin S, Stanley HE, Goldberger AL .Quantification of scaling exponents and crossover phenomena in nonstationary heartbeat time series,5:82-87, Chaos,(1995). 39 B7 Video Mikroskop ve Koloit Parçacıklar kullanılarak Yumuşak Maddelerin MikroReolojik Özelliklerinin Ölçülmesi Tolga Kostak a, Can Ertugay a, Aslı Gençaslan a, M. Özgür Güler b, Deniz Kaya a a Fizik Bölümü, Akdeniz Üniversitesi, Antalya, 07053, Türkiye b UNAM, Bilkent Üniversitesi, Ankara, 06800 , Türkiye Polimerler, koloitler ve benzeri yumuşak malzemeler bulundukları şartlara bağlı olarak hem katıların elastik (esneklik) özelliklerini, hem de sıvıların viskozite (akmazlık) özelliklerini gösterirler. Viskoelastik madde olarak da adlandırılan yumuşak maddelerin karakterizasyonu için, yapısının, denge ve denge-dışı dinamiğinin ve reolojik (akış-bilim) özelliklerinin bilinmesi gerekmektedir. Yumuşak bir malzemeye kuvvet uygulayarak, yapısı ve dinamiği hakkında bilgi alınabilir. Bu prensipte üretilmiş ticari reometrelerde, belirli bir geometrik tanımda malzemeye gerinim (shear) uygulanarak, malzemedeki elastik (esneklik) ve gerinim (shear) modülüsü elde edilir. Reolojik deneylerin amacı, viskoelastik özellikleri olabildiğince geniş bir zaman ve deformasyon ölçüsüne yaymak doğrultusundadır, böylelikle malzemenin viskoelastisitesi, mezo ve makro yapısıyla ilişkilendirilir. Ticari bir reometre ile ölçülemeyen ve lokal etkileşimlere karşı hassas olan mikro-reoloji tekniği, yüksek magnifikasyonlu bir mikroskop ve yumuşak malzemeye gömülmüş koloit parçacıkların Brownian hareketlerinin görüntü analizi metodları ile ölçülmesi prensibine dayanır. Bu teknik hemen her üniversite kolaylıkla bulunabilen bir mikroskobu, bilgisayar ve görüntü analiz metodları yardımıyla, uyarımsız, yani dış bir kuvvet uygulamayan bir reometre olarak kullanmayı mümkün kılar. Bu çalışmada, mikro-reoloji metodu için kullandığımız deney düzeneği ve görüntü analiz metodlarının temel noktaları açıklanacak ve örnek sıvı ve jel sistemlerin akmazlık ve esneklik katsayı ölçümleri karşılaştırmalı olarak sunulacaktır. Bir sonraki adımımız olan Nano-Jel yapıların mikroreolojik özelliklerinin elde edilmesi konusundaki deneysel planımız aktarılacaktır. * Bu çalışma TÜBİTAK-3001 Programı 114M143 Nolu projesi ile desteklenmiştir. 40 B8 Detailed Molecular Dynamics Simulations of Human Transferrin Provide Insights on Iron Release Dynamics at Serum and Endosomal pH Haled Abdizadeh Human serum transferrin (hTf) transports ferric ions in the blood stream and delivers them to cells via receptor mediated endocytosis. hTf is folded into two homologous lobes; we utilize three of the available crystal structures delineating large conformational changes involved in iron binding/dissociation. We address the problems of whether the release process follows the same trend at serum (~7.4) and endosomal (~5.6) pH, and if there is communication between the lobes. In the absence of the transferrin-receptor, we study the dynamics of the full structure as well as the separate lobes in different closed, partially open, and open conformations under neutral and endosomal pH conditions. Results corroborate those experimental observations underscoring the distinguishing effect of pH on the dynamics of hTf. Furthermore, in a total of 2 μs molecular dynamics simulations, residue fluctuations elucidate the crosstalk between the lobes correlated by the peptide linker bridging them at serum pH, while their correlations are lost under endosomal conditions. At serum pH, interplay between relative mobility of the lobes is correlated with iron release rates, rendering the initial conformational change an important contributor to the dynamics under these conditions. Interestingly, C-lobe opening lags behind that of the N-lobe as long as there is at least one iron bound, making the more stable C-lobe an attractive target for recognition by receptors. At endosomal pH, both lobes readily open, making irons available for delivery. 41 B9 Smoothing discontinuities in Predator Prey Models Engin Kandiran Department of Information Systems and Technologies, Yeditepe University, Ataşehir, Istanbul, Turkey and The Institute for Graduate Studies in Sciences and Engineering, Boğaziçi University, İstanbul Turkey. E-mail: [email protected] Avadis Hacinliyan Department of Physics and Department of Information Systems and Technologies, Yeditepe University, Ataşehir, Istanbul, Turkey E-mail: [email protected] Abstract: Many modern predator prey systems and their generalizations such as the HANDY model used in ecological systems or systems with general functional response involve discontinuous functions. This causes difficulties in simulating such systems in order to obtain characteristics such as stationary points, local and structural stability, Lyapunov Exponents or limit cycles. These parameters are very important in understanding the models. The distinction between differential equations and discretized maps is also of interest, particularly in two dimensional systems. In this work, we propose to replace discontinuous functions by continuous functions that approximate them in order to facilitate the analysis. For example, the step function can be replaced by an inverse tangent or inverse hyperbolic tangent. Keywords: Predator-Prey models, Discontinuous functions, Local and Structural Stability, Simulation of Chaotic Syetems and Lyapunov Exponents.. 42 B10 BEC in curved backround Birses Debir First, we will introduce the basics of a Bose-Einstein condensate on the flat space. Necessity of the Heat kernel expansion for a curved space- time will be pointed out. Then to calculate the non-relativistic Schroedinger equation, we will interfere the metric and obtain an analogue optical metric. Therefore we will satisfy the pure laplacian that the kernel expasion required. Afterwards we are going to use the laplacian in the Heat kernel expansion and Mellin transformation. As a result of these techniques certain coefficients are going to come occur, and we will need area and volume of the container to find them. So after handling geometrical calculations , finally we will be left to find results for the thermodynamical variables in question and the horizon divergences. 43 C1 44 C2 45 C3 46 C4 47 C5 Kesikli zaman kuantum yürüyüşleri ile kubit hali aktarımı İskender Yalçınkaya, Zafer Gedik Sabancı Üniversitesi Bir kuantum iletişim ağında hal aktarımının esası, sözkonusu halin ne olduğundan bağımsız olarak onu ağın iki noktası arasında aktarabilmektir. Bu nedenle oluşturulacak aktarım protokolü, tüm haller için aynı davranışı göstermeli ve ideal olarak hepsini mükemmel bir şekilde aktarılabilmelidir. Çalışmamızda, kesikli zaman kuantum yürüyüşleri ile tüm kubit hallerinin mükemmel bir şekilde aktarılmasını sağlayan bir yöntem geliştirdik. Bu yöntem, ilk para halini elde edebilmek; kubit hali aktarımını gerçekleştirebilmek için, yürüyüş öncesinde belirlenebilen, “kurtarma işleci” adını verdiğimiz bir tane daha para işlecinin yürüyüş sonunda uygulanmasını içermektedir. Yöntemimiz, yansıyan ve periyodik sınır koşulları altında bir boyutlu kuantum ağları üzerinden, eğilimli veya eğilimsiz bazı para işleçleri ile tüm kubit hallerinin mükemmel aktarımını mümkün kılmaktadır. Çalışmamızda mükemmel hal aktarımının, eğilimsiz para işleçleri ile ancak sınırlı mesafeler üzerinden gerçekleşirken, aksine birim veya çevirme para işleçleri ile herhangi rastgele bir mesafe boyunca gerçekleştirilebileceğini gösterdik *1+. *1+ İ. Yalçınkaya, Z. Gedik, J. Phys. A 48, 22 (2015). 48 C6 49 D1 Düşük-Boyutlu Dinamik Sistemlerin Kaos Geçiş Eşiği Civarında Davranışları ve Bunların Sağlamlık Analizi Kıvanç Çetin, Özgür Afşar, Uğur Tırnaklı Fizik Bölümü, Fen Fakültesi, Ege Üniversitesi İzmir Ergodik sistemler için geçerli olan merkezsel limit teoremi, sistemin limit dağılımının bir Gausyen’e yakınsayacağını söyler. Ancak ergodikliğin bozulduğu ve kuvvetli korelasyonların ortaya çıktığı durumlarda elde edilen limit dağılımın Gausyen’den farklı olacağı ve merkezsel limit teoreminin bir genelleştirilmesinin varlığı gösterilmiştir. Bu çalışmada bir-boyutlu yitimli dinamik sistemlerden lojistik mapin, mapin iterasyonları arasında kuvvetli korelasyonların bulunduğu ve sistemin artık ergodik olmadığı kaos geçiş eşiğine yaklaşırken elde edilen dağılımların, uygun şartlar altında toplanabilir olmayan Tsallis entropisini maksimum yapan qGausyen dağılıma yakınsadığını gösterip, bu davranışın iki farklı gürültü ile sağlamlık testini yapıyoruz. Kaos eşiğine yaklaşırken, q-Gausyen dağılımların ortaya çıkış mekanizmasını anlamak için; elde edilen dağılım genişlikleri ile korelasyon boyutu, fraktal boyut, Lyapunov üsteli arasındaki ölçeklenme ilişkileri analiz edilmektedir. 50 D2 Motifs resolve how random the protein structures are GizemOzbaykal*, CananAtilgan, and Ali RanaAtilgan Sabanci University, Istanbul [email protected] We create randomized protein structures to compare the change in the frequency and type of motifs appearing in the subgraphs obtained from proteins.A protein amino acid network is constructed by utilizing the spatial information of residues in the three dimensional structure provided in the Protein Data Bank(1). We use a set of 553 single chain proteins with sequence homology less than 25% and sizes between 54 and 1021(2). Each residue is considered as a point located at its Cβ atom (Cα for glycine) and two residues are considered interacting if the Euclidean distance between them is less than a cutoff, chosen as 7 A in this study(3). We randomizethe native structure by switching links between randomly selected nodes while keeping the total number of edges constant(4). We compare the probabilities of finding motifsin networks from three different classes: (i) proteins, (ii) crystal lattices, and (iii) randomly generated graphs with the given Poisson degree distribution andthe given average clustering coefficient (3). Crystal lattices are examples of perfect order and regularity while random networks are in the extreme opposite. We place the native and the randomized protein structures onthis randomness scale. For crystals, some lattice specific motifs (for example, diamonds in simple cubic) are observed with a probability of ~1, while other motifs with four nodes are very rare. In contrast, random networks display low probability of having any motif and the fully connected four-node-motif is the rarest.Proteins are found to inherit all types of possible four-node motifs except the diamond motif with a missing link. The probabilities of all other motifs lie in the interval [0.7, 1]. By using this approach, it is possible todistinguish proteins from lattices and randomly generated networks using motif probability of occurrences. Perhaps more important, we find that proteins are more similar to random networks with given degree distribution and average clustering coefficient than networks of crystal lattices. References 1. Berman HM, et al. (2000) The protein data bank. Nucleic acids research 28(1):235-242. 2. Atilgan AR, Turgut D, & Atilgan C (2007) Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophys J 92(9):3052-3062. 3. Atilgan AR, Akan P, & Baysal C (2004) Small-world communication of residues and significance for protein dynamics. Biophys J 86(1):85-91. 4. Milo R, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298(5594):824-827. 51 D3 MONITORING IRON RELEASE/BINDING MECHANISM WITH A MICROFLUIDIC STOPPED FLOW DEVICE Gökşin Liu*, Eren Yalçın, Ali Rana Atılgan, Canan Atılgan, Ali Koşar, Alpay Taralp Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul [email protected] Stopped flow technology is a recent technique used to study kinetics of the protein interactions. Miniaturization of systems down to micro scale enables to observe fast reactions within small volumes. The purpose of this study is to build a micro-fluidic stopped-flow device in order to be able to monitor the iron release and binding dynamics of Ferric Binding Proteins under different environmental conditions in milliseconds. The experimental data will be compared with MD (Molecular Dynamics) simulations of the same process. A micro-fluidic chip housing compartments of mixing chamber and detection cell is designed and connected to a high-pressure syringe pump controlled by solenoid valves. Diamond shape fins are placed in the mixing chamber to achieve an effective mixing, which provides better kinetic results within smaller volumes. The detection cell is extended to the mixing chamber so as to capture the entire mixing process. The reaction is monitored with a high-speed camera, from which spectroscopic properties of the reaction can also be extracted. The advantage of this system over similar systems lies in its compactness, small scale, low cost and disposability [1]. [1]R.Bleul,M.Ritzi--‐Lehnert,J.Hoth,N.Scharpfenecker,I.Frese,D.Duchs,etal.,"Compact,cost--‐efficient microfluidics--‐based stopped--‐flow device," Anal Bioanal Chem, vol.399,pp.1117--‐25,Jan 2011. 52 D4 GR Protein Ailesinde Gerçekleşen İşlev Değiştiren Mutasyonlar ve Mod Etkileşimindeki Rolleri Batuhan Kav1*, Murat Öztürk2, Alkan Kabakçıoğlu1 1Koç Üniversitesi Fizik Bölümü 2Koç Üniversitesi Malzeme Bilimi ve Mühendisliği Programı Rumelifeneri Yolu, Sarıyer, İstanbul, Türkiye 34450 Proteinlerdeki allosterik mekanizmanın açıklanması için mod etkileşimlerini de dikkate alan bir analiz yöntemi yakın zamanda grubumuz tarafından oluştulmuştu *1+ . İlk yapılan çalışmalar miyosin motor proteininde denenmiş ve protein işlevselliğinde önemli olan amino asitlerin aynı zamanda mod etkileşiminde de önemli rol oynadığı gösterilmişti *2+. Bu çalışmada, glukokortikoid almaçlardaki (reseptör) kortizol seçiciliğinin evrimsel olarak gelişmesinde rol oynayan amino asitlerin allosterik mekanizmadaki rolünü araştırdık *3-5+. Farklı evrimsel dönemlere ait dört farklı glukokortikoid almaç üzerinde yapılan moleküler benzetim çalışmaları ve mod etkileşim analizi yardımıyla, evrimsel olarak işlev değişikliğine yol açan ve almaçı sadece kortizole bağlanır hale getiren amino asit mutasyonlarının aynı zamanda farklı salınım modları arasındaki etkileşimlerde de önemli rol oynadığını, öte yandan aynı süreçte gerçekleşen ve işlev değişimine yol açmayan mutasyonların mod etkileşimi açısından da öne çıkmadığını gözledik. Özellikle, evrimsel süreçte işlev değişiminde en önemli rolü oynayan S106P mutasyonunun, mod etkileşiminde de en baskın konumda olduğunu gördük. En güçlü şekilde etkileşen salınım modlarının almaçlardaki ligand bağlanma bölgesini oluşturan sarmal bölgelerini birbirine bağlayan farklı döngüleri (loop) içermesi, global ve yerel (lokal) salınım modları arasındaki etkileşimin allosterik mekanizmada önemli rol oynadığı düşüncesini desteklerniteliktedir. Glukokortikoid almaçlardan elde edilen sonuçlar, mod etkileşimi analizinin proteinlerin yüzeyindeki işlevsel bölgeleri belirlemede önemli bir yardımcı araç olabileceğini göstermektedir. Kaynaklar: *1+ A. Kabakçıoğlu, M. Gur, D. Yuret, and B. Erman, Physical Biology, 7, 046005 (2010) *2+ O. Varol, D. Yuret, B. Erman, and A. Kabakçıoğlu, Proteins: Structure, Function, and Bioinformatics, 82(9), 1777 (2014) [3] E. A. Ortlund, J. T. Bridgham, M. R. Redinbo, and J. W. Thornton, Science, 317(5844):1544– 1548,(2007) [4] M. J. Harms and J. W. Thornton. Nature, 512(7513):203–207 (2014) [5] J. T. Bridgham, E. A. Ortlund, J. W. Thornton. Nature, 461(7263):515–519 (2009) 53 D5 54 D6 Tek modlu oyukların 3-atomlu rezervuarlarla termalleşmesi Ceren B. Dağ, A. Levent Subaşı, Istanbul Teknik Üniversitesi Özgür E. Müstecaplıoğlu Koç Üniversitesi Kuantum termalleşme, kuantum termodinamik döngülerin önemli bir sürecidir. Kuantum Carnot döngüsü ilk defa Scully ve diğerleri tarafından incelenmiştir *1+. Özellikle kuantum termalleşme ise tek ve iki atomlu sistemlerle mikromazer modeli baz alınarak çalışılmıştır *2-3+. Yine bu çalışmalarda eşfazlılık (coherence) ve dolanıklık (entanglement) etkisi incelenmiştir. Biz de mikromazer modelinde W and GHZ durumları gibi üç atomlu rezervuarların etkisini inceledik. W rezervuarının oyuğu termalleştirebildiğini ve oyuk kayıpsız farz edildiğinde ortalama foton sayısının 3 olduğunu bulduk. GHZ rezervuarının ise oyuğu termalleştiremediğini gözlemledik. Ayrıca tek ve çift foton süreçlerinin etkisini de çalıştık. Önceki çalışmaları ve kendi çalışma sonuçlarımızı da kapsayan bazı termalleşme kurallarını ifade ettik. [1] Marlan O. Scully, M. Suhail Zubairy, Girish S. Agarwal, and Herbert Walther. Extracting work from a single heat bath via vanishing quantum coherence. Science, 299(5608):862-864, 2003. [2] Jie-Qiao Liao, H. Dong, and C. P. Sun. Single-particle machine for quantum thermalization. Phys. Rev. A, 81:052121, May 2010. [3] Hai Li, Jian Zou, Wen-Li Yu, Bao-Ming Xu, Jun-Gang Li, and Bin Shao. Quantum coherence rather than quantum correlations reflect the effects of a reservoir on a system's work capability. Phys. Rev. E, 89:052132, May 2014. 55
