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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Few-qubit quantum refrigerator for cooling a multi-qubit system(Nature Publishing Group (NPG), 2021) Arısoy, Onat; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674We propose to use a few-qubit system as a compact quantum refrigerator for cooling an interacting multi-qubit system. We specifically consider a central qubit coupled to N ancilla qubits in a so-called spin-star model to be used as refrigerant by means of short interactions with a many-qubit system to be cooled. We first show that if the interaction between the qubits is of the longitudinal and ferromagnetic Ising model form, the central qubit is colder than the environment. We summarize how preparing the refrigerant qubits using the spin-star model paves the way for the cooling of a many-qubit system by means of a collisional route to thermalization. We discuss a simple refrigeration cycle, considering the operation cost and cooling efficiency, which can be controlled by N and the qubit–qubit interaction strength. Besides, bounds on the achievable temperature are established. Such few-qubit compact quantum refrigerators can be significant to reduce dimensions of quantum technology applications, can be easy to integrate into all-qubit systems, and can increase the speed and power of quantum computing and thermal devices.Publication Open Access Exciton recycling via InP quantum dot funnels for luminescent solar concentrators(Tsinghua University, 2021) Ow-Yang, Cleva W.; N/A; N/A; Department of Physics; Department of Electrical and Electronics Engineering; Jalali, Houman Bahmani; Sadeghi, Sadra; Toker, Işınsu Baylam; Han, Mertcan; Sennaroğlu, Alphan; Nizamoğlu, Sedat; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; N/A; 23851; 130295Luminescent solar concentrators (LSC) absorb large-area solar radiation and guide down-converted emission to solar cells for electricity production. Quantum dots (QDs) have been widely engineered at device and quantum dot levels for LSCs. Here, we demonstrate cascaded energy transfer and exciton recycling at nanoassembly level for LSCs. The graded structure composed of different sized toxic-heavy-metal-free InP/ZnS core/shell QDs incorporated on copper doped InP QDs, facilitating exciton routing toward narrow band gap QDs at a high nonradiative energy transfer efficiency of 66%. At the final stage of non-radiative energy transfer, the photogenerated holes make ultrafast electronic transitions to copper-induced mid-gap states for radiative recombination in the near-infrared. The exciton recycling facilitates a photoluminescence quantum yield increase of 34% and 61% in comparison with semi-graded and ungraded energy profiles, respectively. Thanks to the suppressed reabsorption and enhanced photoluminescence quantum yield, the graded LSC achieved an optical quantum efficiency of 22.2%. Hence, engineering at nanoassembly level combined with nonradiative energy transfer and exciton funneling offer promise for efficient solar energy harvesting.Publication Open Access Emergence of active nematics in chaining bacterial biofilms(Nature Publishing Group (NPG), 2019) Vetter, Roman; Department of Physics; N/A; Kocabaş, Aşkın; Yaman, Yusuf İlker; Demir, Esin; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; 227753; N/A; N/AGrowing tissue and bacterial colonies are active matter systems where cell divisions and cellular motion generate active stress. Although they operate in the non-equilibrium regime, these biological systems can form large-scale ordered structures. How mechanical instabilities drive the dynamics of active matter systems and form ordered structures are not well understood. Here, we use chaining Bacillus subtilis, also known as a biofilm, to study the relation between mechanical instabilities and nematic ordering. We find that bacterial biofilms have intrinsic length scales above which a series of mechanical instabilities occur. Localized stress and friction drive buckling and edge instabilities which further create nematically aligned structures and topological defects. We also observe that topological defects control stress distribution and initiate the formation of sporulation sites by creating three-dimensional structures. In this study we propose an alternative active matter platform to study the essential roles of mechanics in growing biological tissue.Publication Open Access Emergence of correlated proton tunnelling in water ice(The Royal Society, 2019) Farrow, Tristan; Deliduman, Cemsinan; Vedral, Vlatko; Department of Physics; Pusuluk, Onur; Department of Physics; Graduate School of Sciences and EngineeringSeveral experimental and theoretical studies report instances of concerted or correlated multiple proton tunnelling in solid phases of water. Here, we construct a pseudo-spin model for the quantum motion of protons in a hexameric H2O ring and extend it to open system dynamics that takes environmental effects into account in the form of O-H stretch vibrations. We approach the problem of correlations in tunnelling using quantum information theory in a departure from previous studies. Our formalism enables us to quantify the coherent proton mobility around the hexagonal ring by one of the principal measures of coherence, the l(1) norm of coherence. The nature of the pairwise pseudo-spin correlations underlying the overall mobility is further investigated within this formalism. We show that the classical correlations of the individual quantum tunnelling events in long-time limit is sufficient to capture the behaviour of coherent proton mobility observed in low-temperature experiments. We conclude that long-range intra-ring interactions do not appear to be a necessary condition for correlated proton tunnelling in water ice.Publication Open Access An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction(Public Library of Science, 2022) Aydın, Musa; Doğan, Buket; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Kiraz, Alper; Karalar, Elif Nur Fırat; Morova, Berna; Uysallı, Yiğit; Özgönül, Ekin; Faculty Member; Researcher; PhD Student; PhD Student; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; 22542; 206349; N/A; N/A; N/AWhen combined with computational approaches, fluorescence imaging becomes one of the most powerful tools in biomedical research. It is possible to achieve resolution figures beyond the diffraction limit, and improve the performance and flexibility of high-resolution imaging systems with techniques such as structured illumination microscopy (SIM) reconstruction. In this study, the hardware and software implementation of an LED-based superresolution imaging system using SIM employing GPU accelerated parallel image reconstruction is presented. The sample is illuminated with two-dimensional sinusoidal patterns with various orientations and lateral phase shifts generated using a digital micromirror device (DMD). SIM reconstruction is carried out in frequency space using parallel CUDA kernel functions. Furthermore, a general purpose toolbox for the parallel image reconstruction algorithm and an infrastructure that allows all users to perform parallel operations on images without developing any CUDA kernel code is presented. The developed image reconstruction algorithm was run separately on a CPU and a GPU. Two different SIM reconstruction algorithms have been developed for the CPU as mono-thread CPU algorithm and multi-thread OpenMP CPU algorithm. SIM reconstruction of 1024 × 1024 px images was achieved in 1.49 s using GPU computation, indicating an enhancement by*28 and*20 in computation time when compared with mono-thread CPU computation and multi-thread OpenMP CPU computation, respectively.Publication Open Access A new type of microphotoreactor with integrated optofluidic waveguide based on solid-air nanoporous aerogels(Royal Society of Chemistry (RSC), 2018) Jonas, Alexandr; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; College of Engineering; College of Sciences; N/A; 29633; 22542In this study, we developed a new type of microphotoreactor based on an optofluidic waveguide with aqueous liquid core fabricated inside a nanoporous aerogel. To this end, we synthesized a hydrophobic silica aerogel monolith with a density of 0.22 g cm(-3) and a low refractive index of 1.06 that-from the optical point of view-effectively behaves like solid air. Subsequently, we drilled an L-shaped channel within the monolith that confined both the aqueous core liquid and the guided light, the latter property arising due to total internal reflection of light from the liquid-aerogel interface. We characterized the efficiency of light guiding in liquid-filled channel and-using the light delivered by waveguiding-we carried out photochemical reactions in the channel filled with aqueous solutions of methylene blue dye. We demonstrated that methylene blue could be efficiently degraded in the optofluidic photoreactor, with conversion increasing with increasing power of the incident light. The presented optofluidic microphotoreactor represents a versatile platform employing light guiding concept of conventional optical fibres for performing photochemical reactions.Publication Open Access Evidence for broken ergodicity due to chemical alloying from the dissociation kinetics of binary clusters(American Institute of Physics (AIP) Publishing, 2014) Calvo, Florent; Department of Physics; Yurtsever, İsmail Ersin; Faculty Member; Department of Physics; College of Sciences; 7129The interplay between thermal relaxation and statistical dissociation in binary Morse clusters (AB)N has been investigated using numerical simulations and simple statistical approaches, for a variety of interaction parameters covering miscible and non-miscible regimes. While all clusters exhibit a core/shell phase separation pattern in their most stable, T = 0 structure, different melting mechanisms are identified depending on the ranges and their mismatch, including two-step melting of the surface and the core or premelting as alloying. The preference for emitting A or B particles upon evaporation has been evaluated assuming that the cluster is either thermally equilibrated or vibrationally excited in its ground state structure, and compared to the predictions of theWeisskopf theory. The variations of the dissociation rate constants with increasing energy and the branching ratio between the two channels show significant differences in both cases, especially when the clusters are miscible and bound by short-range forces, which indicates that the time scale for evaporation is much shorter than the equilibration time. Our results suggest that dissociation properties could be used to test the ergodic hypothesis in such compounds. © 2014 AIP Publishing LLC.Publication Open Access Cetuximab-Ag2S quantum dots for fluorescence imaging and highly effective combination of ALA-based photodynamic/chemo-therapy of colorectal cancer cells(Royal Society of Chemistry (RSC), 2021) Mohammad Hadi, Layla; Yaghini, Elnaz; Loizidou, Marilena; MacRobert, Alexander J.; Department of Chemistry; N/A; Department of Physics; Acar, Havva Funda Yağcı; Bayır, Ali; Hashemkhani, Mahshid; Demirci, Gözde; Muti, Abdullah; Sennaroğlu, Alphan; Researcher; PhD Student; Master Student; PhD Student; Faculty Member; Department of Chemistry; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; Graduate School of Sciences and Engineering; 178902; N/A; N/A; N/A; N/A; 23851Colorectal cancer (CRC) has a poor prognosis and urgently needs better therapeutic approaches. 5-Aminolevulinic acid (ALA) induced protoporphyrin IX (PpIX) based photodynamic therapy (PDT) is already used in the clinic for several cancers but not yet well investigated for CRC. Currently, systemic administration of ALA offers a limited degree of tumour selectivity, except for intracranial tumours, limiting its wider use in the clinic. The combination of effective ALA-PDT and chemotherapy may provide a promising alternative approach for CRC treatment. Herein, theranostic Ag2S quantum dots (AS-2MPA) optically trackable in near-infrared (NIR), conjugated with endothelial growth factor receptor (EGFR) targeting Cetuximab (Cet) and loaded with ALA for PDT monotherapy or ALA/5-fluorouracil (5FU) for the combination therapy are proposed for enhanced treatment of EGFR(+) CRC. AS-2MPA-Cet exhibited excellent targeting of the high EGFR expressing cells and showed a strong intracellular signal for NIR optical detection in a comparative study performed on SW480, HCT116, and HT29 cells, which exhibit high, medium and low EGFR expression, respectively. Targeting provided enhanced uptake of the ALA loaded nanoparticles by strong EGFR expressing cells and formation of higher levels of PpIX. Cells also differ in their efficiency to convert ALA to PpIX, and SW480 was the best, followed by HT29, while HCT116 was determined as unsuitable for ALA-PDT. The therapeutic efficacy was evaluated in 2D cell cultures and 3D spheroids of SW480 and HT29 cells using AS-2MPA with either electrostatically loaded, hydrazone or amide linked ALA to achieve different levels of pH or enzyme sensitive release. Most effective phototoxicity was observed in SW480 cells using AS-2MPA-ALA-electrostatic-Cet due to enhanced uptake of the particles, fast ALA release and effective ALA-to-PpIX conversion. Targeted delivery reduced the effective ALA concentration significantly which was further reduced with codelivery of 5FU. Delivery of ALA via covalent linkages was also effective for PDT, but required a longer incubation time for the release of ALA in therapeutic doses. Phototoxicity was correlated with high levels of reactive oxygen species (ROS) and apoptotic/necrotic cell death. Hence, both AS-2MPA-ALA-Cet based PDT and AS-2MPA-ALA-Cet-5FU based chemo/PDT combination therapy coupled with strong NIR tracking of the nanoparticles demonstrate an exceptional therapeutic effect on CRC cells and excellent potential for synergistic multistage tumour targeting therapy.Publication Open Access All optical control of magnetization in quantum confined ultrathin magnetic metals(Nature Publishing Group (NPG), 2021) Department of Physics; Department of Electrical and Electronics Engineering; N/A; Müstecaplıoğlu, Özgür Esat; Onbaşlı, Mehmet Cengiz; Naseem, Muhammad Tahir; Zanjani, Saeedeh Mokarian; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; 1674; 258783; N/A; N/AAll-optical control dynamics of magnetization in sub-10 nm metallic thin films are investigated, as these films with quantum confinement undergo unique interactions with femtosecond laser pulses. Our theoretical analysis based on the free electron model shows that the density of states at Fermi level (DOSF) and electron-phonon coupling coefficients (G(ep)) in ultrathin metals have very high sensitivity to film thickness within a few angstroms. We show that completely different magnetization dynamics characteristics emerge if DOSF and G(ep) depend on thickness compared with bulk metals. Our model suggests highly efficient energy transfer from femtosecond laser photons to spin waves due to minimal energy absorption by phonons. This sensitivity to the thickness and efficient energy transfer offers an opportunity to obtain ultrafast on-chip magnetization dynamics.