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Publication Metadata only ‘Anti-commutable’ local pre-Leibniz algebroids and admissible connections(Elsevier, 2023) Department of Physics; N/A; Dereli, Tekin; Doğan, Keremcan; Faculty Member; PhD Student; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; 201358; N/AThe concept of algebroid is convenient as a basis for constructions of geometrical frameworks. For example, metric-affine and generalized geometries can be written on Lie and Courant algebroids, respectively. Furthermore, string theories might make use of many other algebroids such as metric algebroids, higher Courant algebroids, or conformal Courant algebroids. Working on the possibly most general algebroid structure, which generalizes many of the algebroids used in the literature, is fruitful as it creates a chance to study all of them at once. Local pre-Leibniz algebroids are such general ones in which metric-connection geometries are possible to construct. On the other hand, the existence of the 'locality operator', which is present for the left-Leibniz rule for the bracket, necessitates the modification of torsion and curvature operators in order to achieve tensorial quantities. In this paper, this modification of torsion and curvature is explained from the point of view that the modification is applied to the bracket instead. This leads one to consider 'anti-commutable' local pre-Leibniz algebroids which satisfy an anti-commutativity-like property defined with respect to a choice of an equivalence class of connections. These 'admissible' connections are claimed to be the necessary ones while working on a geometry of algebroids. This claim is due to the fact that one can prove many desirable properties and relations if one uses only admissible connections. For instance, for admissible connections, we prove the first and second Bianchi identities, Cartan structure equations, Cartan magic formula, the construction of Levi-Civita connections, the decomposition of connection in terms of torsion and non-metricity. These all are possible because the modified bracket becomes anti-symmetric for an admissible connection so that one can apply the machinery of almost-or pre-Lie algebroids. We investigate various algebroid structures from the literature and show that they admit admissible connections which are metric-compatible in some generalized sense. Moreover, we prove that local pre-Leibniz algebroids that are not anti-commutable cannot be equipped with a torsion-free, and in particular Levi-Civita, connection.Publication Metadata only 10-NJ multipass-cavity femtosecond CR3+: LiCAF laser pumped by low-power single-mode diodes(Optical Society of America, 2009) Kärtner, Franz X.; Fujimoto, James G.; Demirbaş, Ümit; Department of Physics; Sennaroğlu, Alphan; Faculty Member; Department of Physics; College of Sciences; 23851We report on the generation of 9.9-nJ, 95-fs pulses at a repetition rate of 9.58 MHz from a multipass-cavity Cr3+:LiCAF laser pumped by single-mode diodes with a total absorbed pump power of only 540 mW.Publication Metadata only 1200 nm pumped Tm3+:Lu2O3 ceramic lasers(Optical Soc Amer, 2018) Özharar, Sarper; N/A; Department of Physics; Toker, Işınsu Baylam; Sennaroğlu, Alphan; PhD Student; Faculty Member; Department of Physics; N/A; College of Sciences; N/A; 23851We report on an experimental demonstration of a 1200-nm pumped Tm3+:Lu2O3 ceramic laser. By using a gain-switched, tunable Cr4+:forsterite laser, the excitation spectrum was measured, with optimum pumping bands centered near 1198 nm, 1204 nm, and 1211 nm. The highest slope efficiency of 21.5% was obtained at the pump wavelength of 1204 nm. Comparative energy efficiency measurements performed near 1200-nm and 800-nm pumping further showed that nearly 40% improvement was obtained in slope efficiency measured with respect to the incident pump energy for 1200-nm pumping. A transition was further observed from single-wavelength operation at 2066 nm to dual-wavelength operation near 2066 nm and 1967 nm for absorbed pump energies above 50 mu J. In this regime, two consecutive output pulses were observed in the time domain. The shortest temporal duration of the first pulse was 1.1 mu s at the incident pulse energy of 105 mu J. The duration and build-up time of the second pulse remained around 5.9 mu s and 18.5 mu s. We believe that the improved energy efficiency demonstrated for the 1.5% Tm3+:Lu2O3 ceramic with 1200-nm pumping can be used as an alternative scheme for the excitation of Tm3+:Lu2O3 ceramic lasers.Publication Metadata only 21 fs Cr:LiSAF laser mode locked with a single-walled carbon nanotube saturable absorber(Optical Soc Amer, 2019) Bae, Ji Eun; Rotermund, Fabian; Demirbaş, Ümit; N/A; N/A; N/A; Department of Physics; Tanısalı, Gökhan; Toker, Işınsu Baylam; Taşçı, Mısra; Sennaroğlu, Alphan; PhD Student; PhD Student; Undergraduate Student; Faculty Member; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; School of Medicine; College of Sciences; N/A; N/A; N/A; 23851We report the shortest femtosecond pulses directly generated from a solid-state laser that is mode locked by using a single-walled carbon nanotube saturable absorber (SWCNT-SA). In the experiments, we used a 660 nm diode-pumped, low-threshold extended-cavity Cr:LiSAF laser operating around 850 nm with a repetition rate of 47.9 MHz. The SWCNT-SA mode-locked Cr:LiSAF laser produced 21 fs pulses with a time-bandwidth product of 0.56 by using only 210 mW of pump power. Pump-probe spectroscopy measurements showed that the SWCNT-SA exhibited saturable absorption with slow and fast decay times of 2.7 ps and 0.4 ps. The single-pass modulation depth and saturation fluence of the SWCNT-SA were further determined as 0.3% and 45 mu J/cm(2) at the pump wavelength of 850 nm.Publication Metadata only 5-nj Femtosecond Ti3+:sapphire laser pumped with a single 1 W green diode(Iop Publishing Ltd, 2018) N/A; N/A; Department of Physics; Department of Physics; Muti, Abdullah; Kocabaş, Aşkın; Sennaroğlu, Alphan; PhD Student; Faculty Member; Faculty Member; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; 227753; 23851We report a Kerr-lens mode-locked, extended-cavity femtosecond Ti3+:sapphire laser directly pumped at 520 nm with a 1 W AlInGaN green diode. To obtain energy scaling, the short x-cavity was extended with a q-preserving multi-pass cavity to reduce the pulse repetition rate to 5.78 MHz. With 880 mW of incident pump power, we obtained as high as 90 mW of continuous-wave output power from the short cavity by using a 3% output coupler. In the Kerr-lens mode-locked regime, the extended cavity produced nearly transform-limited 95 fs pulses at 776 nm. The resulting energy and peak power of the pulses were 5.1 nJ and 53 kW, respectively. To our knowledge, this represents the highest pulse energy directly obtained to date from a mode-locked, single-diode-pumped Ti3+:sapphire laser.Publication Metadata only 70 femtosecond Kerr-lens mode-locked multipass-cavity Alexandrite laser(Optical Soc Amer, 2018) Demirbaş, Umit; N/A; N/A; N/A; Department of Physics; Department of Physics; Cihan, Can; Muti, Abdullah; Toker, Işınsu Baylam; Kocabaş, Aşkın; Sennaroğlu, Alphan; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; N/A; 227753; 23851We report, to the best of our knowledge, the shortest femto-second pulses generated from a Kerr-lens mode-locked (KLM) Alexandrite laser operating near 750 nm. The Alexandrite gain medium was pumped with a continuous-wave (cw), 532 nm laser, and the performance of both the short and extended resonators was investigated. The use of an extended cavity eliminated the multi-wavelength spectral instabilities observed during the cw operation of the short cavity. Furthermore, since the repetition rate of the Alexandrite laser was reduced from 107 to 5.6 MHz, the resulting increase in the intracavity pulse energy provided enhanced Kerr nonlinearity and eliminated the Q-switching instabilities during mode- locked operation. The KLMMPC Alexandrite laser produced nearly transform-limited, 70 fs pulses at a pulse repetition rate of 5.6MHz with only 1 W of pump power. The time-bandwidth product was further measured to be 0.331. (C) 2018 Optical Society of AmericaPublication Metadata only 80-NJ multipass-cavity chirped-pulse Cr4+: forsterite laser(Optical Society of America, 2010) Fujimoto, James G.; Department of Physics; Sennaroğlu, Alphan; Çankaya, Hüseyin; Faculty Member; Researcher; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; 23851; N/ABy using 8.5 W of incident pump power, we obtained 80-nJ, 5.5-ps pulses at 1260 nm with a spectral width of 17 nm from a multipass-cavity, chirped-pulse Cr4+:forsterite laser operated at 4.9-MHz repetition rate. © 2010 Optical Society of America.Publication Metadata only A computational study of the reactivity of diethenylnaphthalenes towards anionic polymerization(Royal Soc Chemistry, 1999) Akın, Fatma Ahu; Erdem, Safiye Sağ; Nugay, Turgut; Aviyente, Viktorya; Department of Physics; Reşat, Haluk; Faculty Member; Department of Physics; College of Sciences; N/ADiethenyl, di(1-methylethenyl), and di(1-phenylethenyl) naphthalenes are known to be difunctional initiators used in the synthesis of thermoplastic elastomers. Semiempirical (AM1, PM3) and ab initio calculations (HF/6-31G, HF/6-31G*) have been carried out to determine the reactivity of these compounds towards anionic polymerization. For this purpose, geometrical parameters, electrostatic potentials, and frontier orbitals have been analyzed. Reaction paths starting from the diethenylnaphthalenes and reaching the proposed products have been studied, and transition structures along the paths have been located. The minimum energy conformers were determined through a conformational search around single bonds for a series of diethenylnaphthalenes. We have attempted to predict how the location of the vinyl groups affects the reactivity of diethenylnaphthalenes. Our results have revealed that the most suitable difunctional initiators for anionic polymerization are the compounds where the substituents lie away from the naphthalene bridge. We have also found that in some cases the substituents are conjugated with each other and di(1-phenylethenyl)naphthalenes are more reactive th an diethenylnaphthalenes which in turn are more reactive than di(1-methylethenyl)naphthalenes towards anionic polymerization.Publication Metadata only A deep learning model for automated segmentation of fluorescence cell images(IOP Publishing Ltd, 2022) Aydın, Musa; Kiraz, Berna; Eren, Furkan; N/A; Department of Physics; N/A; N/A; N/A; Ayhan, Ceyda Açılan; Kiraz, Alper; Uysallı, Yiğit; Morova, Berna; Özcan, Selahattin Can; Faculty Member; Faculty Member; PhD Student; Researcher; Researcher; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; 219658; 22542; N/A; N/A; N/ADeep learning techniques bring together key advantages in biomedical image segmentation. They speed up the process, increase the reproducibility, and reduce the workload in segmentation and classifcation. Deep learning techniques can be used for analysing cell concentration, cell viability, as well as the size and form of each cell. In this study, we develop a deep learning model for automated segmentation of fuorescence cell images, and apply it to fuorescence images recorded with a home-built epi-fuorescence microscope. A deep neural network model based on U-Net architecture was built using a publicly available dataset of cell nuclei images [1]. A model accuracy of 97.3% was reached at the end of model training. Fluorescence cell images acquired with our home-built microscope were then segmented using the developed model. 141 of 151 cells in 5 images were successfully segmented, revealing a segmentation success rate of 93.4%. This deep learning model can be extended to the analysis of diferent cell types and cell viability. © 2021 Published under licence by IOP Publishing Ltd.Publication Metadata only A leucine aminopeptidase activatable photosensitizer for cancer cell selective photodynamic therapy action(Elsevier Sci Ltd, 2021) N/A; N/A; N/A; Department of Chemistry; N/A; Department of Physics; Department of Chemistry; Department of Chemistry; Arslan, Büşra; Bilici, Kübra; Demirci, Gözde; Almammadov, Toghrul; Khan, Minahil; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; Kölemen, Safacan; Master Student; PhD Student; Master Student; Researcher; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; N/A; N/A; N/A; 23851; 178902; 272051Activity based photosensitizers (PS) continue to attract great attention as they enable selective photodynamic therapy action on cancer cells while sparing normal cells even under light irradiation. Sensitivity to specific enzymes that are differentially overexpressed in cancer cells is crucial in the design of activatable PSs. In this direction, we report here, for the first time, a leucine aminopeptidase (LAP) activatable PDT agent (HCL), which is a red-shifted, water soluble and photostable brominated hemicyanine derivative. HCL was activated by endogenous LAP enzyme selectively in A549 (lung) and HCT116 (colon) cancer cells containing high LAP levels and induced effective photocytotoxicity with negligible dark toxicity. Furthermore, the fluorescence of the parent bromo-hemicyanine core was restored upon LAP-based activation in cancer cells. On the other side, no remarkable phototoxicity or fluorescence turn-on was detected in healthy L929 cells. Thus, HCL serves as an effective and tumour associated LAP-sensitive phototheranostic agent. We believe different cancer-associated analytes can be utilized in combination with near-IR absorbing scaffolds in the scope of activatable PDT designs to enrich the tumour-selective PS arsenal.