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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 Open Access 3D bioprinted organ?on?chips(Wiley, 2022) Mustafaoğlu, Nur; Zhang, Yu Shrike; Department of Mechanical Engineering; N/A; N/A; Dabbagh, Sajjad Rahmani; Sarabi, Misagh Rezapour; Birtek, Mehmet Tuğrul; Taşoğlu, Savaş; Faculty Member; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); College of Engineering; Graduate School of Social Sciences and Humanities; Graduate School of Sciences and Engineering; N/A; N/A; N/A; 291971Organ-on-a-chip (OOC) platforms recapitulate human in vivo-like conditions more realistically compared to many animal models and conventional two-dimensional cell cultures. OOC setups benefit from continuous perfusion of cell cultures through microfluidic channels, which promotes cell viability and activities. Moreover, microfluidic chips allow the integration of biosensors for real-time monitoring and analysis of cell interactions and responses to administered drugs. Three-dimensional (3D) bioprinting enables the fabrication of multicell OOC platforms with sophisticated 3D structures that more closely mimic human tissues. 3D-bioprinted OOC platforms are promising tools for understanding the functions of organs, disruptive influences of diseases on organ functionality, and screening the efficacy as well as toxicity of drugs on organs. Here, common 3D bioprinting techniques, advantages, and limitations of each method are reviewed. Additionally, recent advances, applications, and potentials of 3D-bioprinted OOC platforms for emulating various human organs are presented. Last, current challenges and future perspectives of OOC platforms are discussed.Publication Metadata only A coarse graining approach in molecular simulations: fuzzy potentials(Istanbul Technical University, 2003) Department of Chemistry; Department of Chemistry; Yurtsever, İsmail Ersin; Eşsiz, Şebnem; Faculty Member; Undergraduated Student; Department of Chemistry; College of Sciences; College of Sciences; 7129; 191615A new representation for interaction potential functions is presented. Unlike the orthodox approaches, the potential function is not a fixed function in terms of internuclear coordinates but a probabilistic one which contains information over a wide range of angular degrees of freedom. It is shown that such approaches can provide practical solutions for bulk systems of high density.Publication Open Access A near-infrared benzothiazole-based chemodosimeter for rapid and selective detection of hydrogen sulfide(Turkish Chemical Society / Türkiye Kimya Derneği, 2021) Department of Chemistry; Kölemen, Safacan; Faculty Member; 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); College of Sciences; 272051Hydrogen sulfide (H2S) is a biologically relevant gaseous molecule, which involves in a wide variety of physiological and pathological processes. Thus, detection of H2S is highly valuable in order to clarify its complex roles. In this study, a new benzothiazole-based donor-acceptor type H 2S selective chemodosimeter (HP-1) was synthesized and its H2S detection capabilities were investigated in aqueous solutions. HP-1 exhibited a red-shifted absorption signal at 530 nm and a near-infrared (NIR) fluorescence peak at 680 nm as a result of enhanced intramolecular charge transfer (ICT) in the presence of H2S, which enabled a selective and very rapid ratiometric fluorescent detection. HP-1 was also showed to be highly sensitive toward H2S with a very low limit of detection value.Publication Metadata only Acousto-optic mode-locking of a Cr2+: ZnSe laser(Optica Publishing Group, 2000) Carrig, Timothy J.; Wagner, Gregory J.; Jeong, Jay Y.; Pollock, Clifford R.; Department of Physics; Sennaroğlu, Alphan; Faculty Member; Department of Physics; College of Sciences; 23851Acousto-optic mode-locking of a Cr2+:ZnSe laser that produces 4.4 psec duration, transform-limited, Gaussian shaped pulses is described. The laser outputs 82 mW of output power at an 81 MHz pulse repetition frequency.Publication Metadata only AFM investigation of segmented, highly branched polyurethaneureas(American Chemical Society (ACS), 2006) Fornof, Ann R.; Long, Timothy E.; Sheth, Jignesh; Wilkes, Garth L.; Department of Chemistry; Department of Chemistry; Department of Chemistry; Yılgör, İskender; Yılgör, Emel; Ünal, Serkan; Faculty Member; Researcher; Undergraduate Student; Department of Chemistry; College of Sciences; College of Sciences; College of Sciences; 24181; 40527; 241611N/APublication Open Access An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser(International Union of Crystallography, 2020) Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A.; Department of Molecular Biology and Genetics; Demirci, Hasan; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 307350An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.Publication Metadata only An easily available lysosomal-targeted ratiometric fluorescent probe with aggregation induced emission characteristics for hydrogen polysulfide visualization in acute ulcerative colitis(Royal Society of Chemistry (RSC), 2021) Xiang, Chunbai; Li, Chunbin; Xiang, Jingjing; Luo, Yuan; Peng, Jiaofeng; Deng, Guanjun; Wang, Jianguo; Li, Hongchun; Zhang, Pengfei; Gong, Ping; Cai, Lintao; Department of Chemistry; Kölemen, Safacan; Faculty Member; Department of Chemistry; College of Sciences; 272051Hydrogen polysulfide (H2Sn, n >1), as a direct oxidizing form of hydrogen sulfide, is closely associated with intestinal diseases such as ulcerative colitis (UC). A probe that can selectively detect H2Sn in the pathological environment of UC is in urgent demand. Ratiometric probes are powerful in the quantitative detection of H2Sn in living organisms. Herein, we developed a ratiometric fluorescent probe TCFPB-H2Sn for selective detection of H(2)S(n)in vitro and in vivo. Significantly, TCFPB-H2Sn demonstrated a fast, sensitive and specific detection performance for H2Sn, and has excellent lysosomal targeting ability and aggregation-induced emission (AIE) characteristics. More importantly, TCFPB-H2Sn was the first probe to achieve endogenous H2Sn imaging in acute ulcerative colitis successfully.Publication Metadata only An experimental study on heat transfer performance of iron oxide based ferrofluids(ASME, 2012) Kaya, Alihan; Kurtoglu, Evrim; Kosar, Ali; Department of Chemistry; Acar, Havva Funda Yağcı; Faculty Member; Department of Chemistry; College of Sciences; 178902Nanofluids are colloidal compounds, where the solid phase material is composed of nano sized particles, and the liquid phase can potentially be any fluid but aqueous media are common. As a common nanofluid type, ferrofluids are formed by holding solid nanoparticles in suspension by weak intermolecular forces and may be produced from materials with different magnetic properties. Magnetite is one of the materials used for its natural ferromagnetic properties. Heat transfer performance of ferrofluids is one of the crucial properties among many others that should be analyzed and considered for their wide range of applications. For this purpose, experiments were conducted in order to characterize heat transfer properties of ironoxide based ferrofluids flowing through a microchannel. Promising results were obtained from this study, which are suggesting the use of ferrofluids for heat transfer applications can be advantageous.Publication Metadata only Antitumor efficacy of ceranib-2 with nano-formulation of PEG and rosin esters(Humana Press Inc, 2021) Ben Taleb, Ali; Karakus, Selcan; Tan, Ezgi; Ilgar, Merve; Kutlu, Ozlem; Kutlu, Hatice Mehtap; Kilislioglu, Ayben; N/A; Gözüaçık, Devrim; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; 40248Ceranib-2 is a recently discovered, poorly water-soluble potent ceramidase inhibitor, with the ability to suppress cancer cell proliferation and delay tumor growth. However, its poor water solubility and weak cellular bioavailability hinder its use as a therapeutic agent for cancer. PEGylated rosin esters are an excellent platform as a natural polymer for drug delivery applications, especially for controlling drug release due to their degradability, biocompatibility, capability to improve solubility, and pharmacokinetics of potent drugs. In this study, stable aqueous amphiphilic submicron-sized PEG400-rosin ester-ceranib-2 (PREC-2) particles, ranging between 100 and 350 nm in a 1:1 mixture, were successfully synthesized by solvent evaporation mediated by sonication. Conclusion: Stable aqueous PEGylated rosin ester nanocarriers might present a significant solution to improve solubility, pharmacokinetic, and bioavailability of ceranib-2, and hold promises for use as an anticancer adjacent drug after further investigations.