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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 Open Access A compressed sensing framework for efficient dissection of neural circuits(Nature Publishing Group (NPG), 2019) Lee, Jeffrey B.; Yonar, Abdullah; Hallacy, Timothy; Shen, Ching-Han; Milloz, Josselin; Srinivasan, Jagan; Ramanathan, Sharad; Department of Physics; Kocabaş, Aşkın; Department of Physics; College of Sciences; 227753A fundamental question in neuroscience is how neural networks generate behavior. The lack of genetic tools and unique promoters to functionally manipulate specific neuronal subtypes makes it challenging to determine the roles of individual subtypes in behavior. We describe a compressed sensing-based framework in combination with non-specific genetic tools to infer candidate neurons controlling behaviors with fewer measurements than previously thought possible. We tested this framework by inferring interneuron subtypes regulating the speed of locomotion of the nematode Caenorhabditis elegans. We developed a real-time stabilization microscope for accurate long-term, high-magnification imaging and targeted perturbation of neural activity in freely moving animals to validate our inferences. We show that a circuit of three interconnected interneuron subtypes, RMG, AVB and SIA control different aspects of locomotion speed as the animal navigates its environment. Our work suggests that compressed sensing approaches can be used to identify key nodes in complex biological networks.Publication Open Access A hybrid broadband metalens operating at ultraviolet frequencies(Nature Publishing Group (NPG), 2021) Department of Physics; Ali, Farhan; Ramazanoğlu, Serap Aksu; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 243745The investigation on metalenses have been rapidly developing, aiming to bring compact optical devices with superior properties to the market. Realizing miniature optics at the UV frequency range in particular has been challenging as the available transparent materials have limited range of dielectric constants. In this work we introduce a low absorption loss and low refractive index dielectric material magnesium oxide, MgO, as an ideal candidate for metalenses operating at UV frequencies. We theoretically investigate metalens designs capable of efficient focusing over a broad UV frequency range (200–400 nm). The presented metalenses are composed of sub-wavelength MgO nanoblocks, and characterized according to the geometric Pancharatnam–Berry phase method using FDTD method. The presented broadband metalenses can focus the incident UV light on tight focal spots (182 nm) with high numerical aperture (NA ≈ 0.8). The polarization conversion efficiency of the metalens unit cell and focusing efficiency of the total metalens are calculated to be as high as 94%, the best value reported in UV range so far. In addition, the metalens unit cell can be hybridized to enable lensing at multiple polarization states. The presented highly efficient MgO metalenses can play a vital role in the development of UV nanophotonic systems and could pave the way towards the world of miniaturization.Publication Metadata only A micropillar-based microfluidic viscometer for newtonian and non-newtonian fluids(Elsevier, 2020) Tanyeri, Melikhan; Erten, Ahmet; Department of Physics; N/A; N/A; N/A; N/A; Kiraz, Alper; Yalçın, Özlem; Mustafa, Adil; Aksu, Ali Cenk; Eser, Ayşenur; Faculty Member; Faculty Member; PHD Student; PHD Student; Master Student; Department of Physics; College of Sciences; School of Medicine; Graduate School of Sciences and Engineering; School of Medicine; Graduate School of Sciences and Engineering; 22542; 218440; N/A; N/A; N/AIn this study, a novel viscosity measurement technique based on measuring the deflection of flexible (poly) dimethylsiloxane (PDMS) micropillars is presented. The experimental results show a nonlinear relationship between fluid viscosity and the deflection of micropillars due to viscoelastic properties of PDMS. A calibration curve, demonstrating this nonlinear relationship, is generated, and used to determine the viscosity of an unknown fluid. Using our method, viscosity measurements for Newtonian fluids (glycerol/water solutions) can be performed within 2-100 cP at shear rates gamma = 60.5-398.4 s(-1). We also measured viscosity of human whole blood samples (non-Newtonian fluid) yielding 2.7-5.1 cP at shear rates gamma = 120-345.1 s(-1), which compares well with measurements using conventional rotational vis-cometers (3.6-5.7 cP). With a sensitivity better than 0.5 cP, this method has the potential to be used as a portable microfluidic viscometer for real-time rheological studies. (C) 2020 Elsevier B.V. All rights reserved.Publication Open Access A narrow-band multi-resonant metamaterial in near-ir(Multidisciplinary Digital Publishing Institute (MDPI), 2020) Ali, Farhan; Department of Physics; Ramazanoğlu, Serap Aksu; Faculty Member; Department of Physics; College of Sciences; 243745We theoretically investigate a multi-resonant plasmonic metamaterial perfect absorber operating between 600 and 950 nm wavelengths. The presented device generates 100% absorption at two resonance wavelengths and delivers an ultra-narrow band (sub-20 nm) and high quality factor (Q = 44) resonance. The studied perfect absorber is a metal–insulator–metal configuration where a thin MgF2 spacer is sandwiched between an optically thick gold layer and uniformly patterned gold circular nanodisc antennas. The localized and propagating nature of the plasmonic resonances are characterized and confirmed theoretically. The origin of the perfect absorption is investigated using the impedance matching and critical coupling phenomenon. We calculate the effective impedance of the perfect absorber and confirm the matching with the free space impedance. We also investigate the scattering properties of the top antenna layer and confirm the minimized reflection at resonance wavelengths by calculating the absorption and scattering cross sections. The excitation of plasmonic resonances boost the near-field intensity by three orders of magnitude which enhances the interaction between the metamaterial surface and the incident energy. The refractive index sensitivity of the perfect absorber could go as high as S = 500 nm/RIU. The presented optical characteristics make the proposed narrow-band multi-resonant perfect absorber a favorable platform for biosensing and contrast agent based bioimaging.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 Algorithmic quantum heat engines(American Physical Society (APS), 2019) Çakmak, Selçuk; Gençten, Azmi; Kominis, Iannis K.; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; 1674; N/AWe suggest alternative quantum Otto engines, using heat bath algorithmic cooling with a partner pairing algorithm instead of isochoric cooling and using quantum SWAP operations instead of quantum adiabatic processes. Liquid state nuclear magnetic resonance systems in a single entropy sink are treated as working fluids. The extractable work and thermal efficiency are analyzed in detail for four-stroke and two-stroke types of alternative quantum Otto engines. The role of the heat bath algorithmic cooling in these cycles is to use a single entropy sink instead of two so that a single incoherent energy resource can be harvested and processed using an algorithmic quantum heat engine. Our results indicate a path to programmable quantum heat engines as analogs of quantum computers beyond traditional heat engine cycles. We find that for our NMR system example implementation of quantum algorithmic heat engine stages yields more power due to increased cycle speeds.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.Publication Open Access An easy-to-fabricate microfluidic shallow trench induced three-dimensional cell culturing and imaging (STICI3D) platform(American Chemical Society (ACS), 2022) Coşkun, Umut Can; Rehman, Ateeq Ur; Gülle, Merve; Erten, Ahmet; N/A; Department of Physics; Department of Electrical and Electronics Engineering; N/A; Başer, Hatice Nur; Baysal, Kemal; Kiraz, Alper; Kul, Demet; Kuş, Funda; Morova, Berna; Faculty Member; Faculty Member; Researcher; Department of Physics; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; School of Medicine; College of Sciences; College of Engineering; N/A; 119184; 22542; N/A; N/A; N/ACompared to the established monolayer approach of two-dimensional cell cultures, three-dimensional (3D) cultures more closely resemble in vivo models; that is, the cells interact and form clusters mimicking their organization in native tissue. Therefore, the cellular microenvironment of these 3D cultures proves to be more clinically relevant. In this study, we present a novel easy-to-fabricate microfluidic shallow trench induced 3D cell culturing and imaging (STICI3D) platform, suitable for rapid fabrication as well as mass manufacturing. Our design consists of a shallow trench, within which various hydrogels can be formed in situ via capillary action, between and fully in contact with two side channels that allow cell seeding and media replenishment, as well as forming concentration gradients of various molecules. Compared to a micropillar-based burst valve design, which requires sophisticated microfabrication facilities, our capillary-based STICI3D can be fabricated using molds prepared with simple adhesive tapes and razors alone. The simple design supports the easy applicability of mass-production methods such as hot embossing and injection molding as well. To optimize the STICI3D design, we investigated the effect of individual design parameters such as corner radii, trench height, and surface wettability under various inlet pressures on the confinement of a hydrogel solution within the shallow trench using Computational Fluid Dynamics simulations supported with experimental validation. We identified ideal design values that improved the robustness of hydrogel confinement and reduced the effect of end-user dependent factors such as hydrogel solution loading pressure. Finally, we demonstrated cultures of human mesenchymal stem cells and human umbilical cord endothelial cells in the STICI3D to show that it supports 3D cell cultures and enables precise control of cellular microenvironment and real-time microscopic imaging. The easy-to-fabricate and highly adaptable nature of the STICI3D platform makes it suitable for researchers interested in fabricating custom polydimethylsiloxane devices as well as those who are in need of ready-to-use plastic platforms. As such, STICI3Ds can be used in imaging cell-cell interactions, angiogenesis, semiquantitative analysis of drug response in cells, and measurement of transport through cell sheet barriers.