Researcher:
Kocabaş, Aşkın

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Aşkın

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Kocabaş

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Kocabaş, Aşkın

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2017 - 201952020 - 20235

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    Polar solvent-free room temperature synthesis of CsPbX3 (X = Br, Cl) perovskite nanocubes
    (Royal Society of Chemistry, 2023) Güvenç, C. Meriç; Balcı, Sinan; Department of Physics; Kocabaş, Aşkın; Faculty Member; Department of Physics; College of Sciences; 227753
    Conventionally, colloidal lead halide perovskite nanocubes have been synthesized by the hot-injection or ligand-assisted reprecipitation (LARP) methods. We herein demonstrate a polar solvent-free room temperature method for the synthesis of CsPbX3 (X = Br, Cl) nanocubes. In addition to the commonly used ligand pair of oleylamine and oleic acid, guanidinium (GA) has been used to passivate the surface of the nanocrystals. Our study demonstrates that GA inhibits the formation of low dimensional structures such as nanowires and nanoplatelets and further supports the formation of perovskite nanocubes. In fact, GA diminishes the restricted monomer-addition effect of long-chain oleylammonium (OLAM) ions to the nanocrystal. We show that above a critical GA/OLAM molar ratio, the synthesis yields homogeneous CsPbX3 (X = Br, Cl) nanocubes. Importantly, we observe the nucleation and growth kinetics of the GA-assisted CsPbBr3 nanocube formation by using in situ absorption and photoluminescence (PL) measurements. Small nanocrystals with an excitonic absorption peak at around 435 nm and photoluminescence (PL) maxima at 447 nm were nucleated and continuously shifted to longer wavelengths during the growth period. Crucially, our method allows the synthesis of CsPbCl3 nanocubes at room temperature without using polar organic solvents. The synthesized CsPbBr3, CsPb(Cl0.5Br0.5)3, and CsPbCl3 nanocubes have PL peaks at 508 nm, 443 nm, and 405 nm, photoluminescence quantum yields (PLQY) of 85%, 58% and 5%, and lifetimes of 18.98 ns, 18.97 ns, and 14.74 ns, respectively.
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    Localized X-ray photoelectron impedance spectroscopy (LoXPIS) for capturing charge dynamics of an ionic liquid electrolyte within an energy storage device
    (2022) Öz, Erdinç; Ergöktaş, Said; Kocabaş, Coşkun; Ulgut, Burak; Süzer, Şefik; N/A; Department of Physics; Başaran, Mustafa; Kocabaş, Aşkın; Master Student; Faculty Member; Department of Physics; N/A; College of Sciences; N/A; 227753
    Many electrochemical devices are based on the fundamental process of ion migration and accumulation on surfaces. Complex interplay of molecular properties of ions and device dimensions control the entire process and define the overall dynamics of the system. Particularly, for ionic liquid-based electrolytes it is often not clear which property, and to what extent, contributes to the overall performance of the device. Herein we use X-ray photoelectron spectroscopy (XPS) while the device is under electrical bias. Such a procedure reveals localized electrical potential developments, through binding energy shifts of the atomic core levels, in a chemically specific fashion. Combining it with square-wave AC modulation, the information can also be extended to time domain, and we investigate devices configured as a coplanar capacitor, with an ionic liquid as the electrolyte, in macro-dimensions. Our analysis reveals that a nonlinear voltage profile across the device emerges from spatially non-uniform electrical double layer formation on electrode surfaces. Interestingly the coplanar capacitor has an extremely slow time response which is particularly controlled by IL film thickness. XPS measurements can capture the ion dynamics in the tens of seconds to microseconds range, and reveal that ionic motion is all over the device, including on metallic electrode regions. This behavior can only be attributed to motion in more than one dimension. The ion dynamics can also be faithfully simulated by using a modified PNP equation, taking into account steric effects, and device dimensions. XPS measurements on two devices with different dimensions corroborated and validated the simulation results. The present results propose a new experimental approach and provide new insights into the dynamics of ions across electrochemical devices.
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    Large-scale orientational order in bacterial colonies during inward growth
    (Elife Sciences Publ Ltd, 2022) Vetter, Roman; Department of Physics; Department of Electrical and Electronics Engineering; Department of Physics; N/A; Yaman, Yusuf İlker; Yüce, Tevfik Can; Kocabaş, Aşkın; Başaran, Mustafa; Other; Undergraduate Student; Faculty Member; Master Student; Department of Electrical and Electronics Engineering; Department of Physics; College of Sciences; College of Engineering; College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; 227753; N/A
    During colony growth, complex interactions regulate the bacterial orientation, leading to the formation of large-scale ordered structures, including topological defects, microdomains, and branches. These structures may benefit bacterial strains, providing invasive advantages during colonization. Active matter dynamics of growing colonies drives the emergence of these ordered structures. However, additional biomechanical factors also play a significant role during this process. Here, we show that the velocity profile of growing colonies creates strong radial orientation during inward growth when crowded populations invade a closed area. During this process, growth geometry sets virtual confinement and dictates the velocity profile. Herein, flow-induced alignment and torque balance on the rod-shaped bacteria result in a new stable orientational equilibrium in the radial direction. Our analysis revealed that the dynamics of these radially oriented structures, also known as aster defects, depend on bacterial length and can promote the survival of the longest bacteria around localized nutritional hotspots. The present results indicate a new mechanism underlying structural order and provide mechanistic insights into the dynamics of bacterial growth on complex surfaces.
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    Investigation of oxygen-dependent motility and swarming behavior in nematode Nematode Caenorhabditis Elegans
    (Atatürk Üniversitesi, 2022) N/A; Department of Physics; Kocabaş, Aşkın; Faculty Member; Department of Physics; College of Sciences; 227753
    Model organism Caenorhabditis elegans can perform swarming behavior in nature. This behavior is intricately linked to the presence of bacteria and oxygen levels in the environment. The complex interplay of all these factors drives the emergence of a self-organized swarming response. The collective motility of this behavior is particularly controlled by the oxygen-dependent velocity profile of the animals which triggers phase separation into dense and dilute clusters. However, the exact velocity profile leading to this transition has not been determined yet. In this study, we experimentally identified this missing information by using a liquid environment. The main difference in this measurement is to use liquid culture to be able to stimulate both head and tail neurons with the same oxygen level. We utilized fiber optic-based sensors to precisely measure oxygen levels that correlated with the animal’s velocity. Finally, based on these experimental results, we modeled swarming behavior using phase separation principles. / Nematod Caenorhabditis elegans (C. elegans) doğada sürü davranışı gösterebilen bir model Model organism Caenorhabditis elegans can perform swarming behavior in nature. This behavior is intricately linked to the presence of bacteria and oxygen levels in the environment. The com- plex interplay of all these factors drives the emergence of a self-organized swarming response. The collective motility of this behavior is particularly controlled by the oxygen-dependent velocity profile of the animals which triggers phase separation into dense and dilute clusters. However, the exact velocity profile leading to this transition has not been determined yet. In this study, we experimentally identified this missing information by using a liquid environment. The main difference in this measurement is to use liquid culture to be able to stimulate both head and tail neurons with the same oxygen level. We utilized fiber optic-based sensors to precisely mea- sure oxygen levels that correlated with the animal’s velocity. Finally, based on these experimental results, we modeled swarming behavior using phase separation principles. / Nematod Caenorhabditis elegans (C. elegans) doğada sürü davranışı gösterebilen bir model orga- nizmadır. C. elegans sürü oluşturma özellikleri, bulunduğu ortamdaki oksijen ve bakteri seviyesi ile direk ilişkilidir. Bu etkilerin karmaşık bir sonucu olarak C. elegans kendiliğinden organize olabilen kalabalık gruplar oluşturmaktadır. Bu grupların kolektif hareketleri canlının hız profilinin oksijen seviyesine bağlılığı tarafından kontrol edilmekte ve yoğunluğa göre farklı faz geçişleri göstermek- tedir. Bu grup oluşturma davranışlarını kontrol eden, gerçek hız profili tam olarak tespit edile- memektedir. Bu çalışmada C. elegans’ın hareket hızının, bulunduğu ortamın oksijen seviyesine bağlılığı tespit edilmiştir. Bu çalışmanın ayırıcı özelliği, canlının hem kuyruk hem de kafa sinir- leri aynı ortamı algılayacak şekilde, bir sıvı ortam ölçümü ile yapılmasıdır. Oksijen seviyeleri fiber optik oksijen sensörü ile belirlenmiş ve hareket hızı ile bağlantısı tespit edilmiştir. Tespit edilen deneysel hız profili, faz ayrımı prensibi kullanılarak sürü oluşturma davranışı matematiksel olarak modellenmiştir. organism Caenorhabditis elegans can perform swarming behavior in nature. This behavior is intricately linked to the presence of bacteria and oxygen levels in the environment. The com- plex interplay of all these factors drives the emergence of a self-organized swarming response. The collective motility of this behavior is particularly controlled by the oxygen-dependent velocity profile of the animals which triggers phase separation into dense and dilute clusters. However, the exact velocity profile leading to this transition has not been determined yet. In this study, we experimentally identified this missing information by using a liquid environment. The main difference in this measurement is to use liquid culture to be able to stimulate both head and tail neurons with the same oxygen level. We utilized fiber optic-based sensors to precisely mea- sure oxygen levels that correlated with the animal’s velocity. Finally, based on these experimental results, we modeled swarming behavior using phase separation principles. / Nematod Caenorhabditis elegans (C. elegans) doğada sürü davranışı gösterebilen bir model orga- nizmadır. C. elegans sürü oluşturma özellikleri, bulunduğu ortamdaki oksijen ve bakteri seviyesi ile direk ilişkilidir. Bu etkilerin karmaşık bir sonucu olarak C. elegans kendiliğinden organize olabilen kalabalık gruplar oluşturmaktadır. Bu grupların kolektif hareketleri canlının hız profilinin oksijen seviyesine bağlılığı tarafından kontrol edilmekte ve yoğunluğa göre farklı faz geçişleri göstermek- tedir. Bu grup oluşturma davranışlarını kontrol eden, gerçek hız profili tam olarak tespit edile- memektedir. Bu çalışmada C. elegans’ın hareket hızının, bulunduğu ortamın oksijen seviyesine bağlılığı tespit edilmiştir. Bu çalışmanın ayırıcı özelliği, canlının hem kuyruk hem de kafa sinir- leri aynı ortamı algılayacak şekilde, bir sıvı ortam ölçümü ile yapılmasıdır. Oksijen seviyeleri fiber optik oksijen sensörü ile belirlenmiş ve hareket hızı ile bağlantısı tespit edilmiştir. Tespit edilen deneysel hız profili, faz ayrımı prensibi kullanılarak sürü oluşturma davranışı matematiksel olarak modellenmiştir.nizmadır. C. elegans sürü oluşturma özellikleri, bulunduğu ortamdaki oksijen ve bakteri seviyesi ile direk ilişkilidir. Bu etkilerin karmaşık bir sonucu olarak C. elegans kendiliğinden organize olabilen kalabalık gruplar oluşturmaktadır. Bu grupların kolektif hareketleri canlının hız profilinin oksijen seviyesine bağlılığı tarafından kontrol edilmekte ve yoğunluğa göre farklı faz geçişleri göstermektedir. Bu grup oluşturma davranışlarını kontrol eden, gerçek hız profili tam olarak tespit edilememektedir. Bu çalışmada C. elegans’ın hareket hızının, bulunduğu ortamın oksijen seviyesine bağlılığı tespit edilmiştir. Bu çalışmanın ayırıcı özelliği, canlının hem kuyruk hem de kafa sinirleri aynı ortamı algılayacak şekilde, bir sıvı ortam ölçümü ile yapılmasıdır. Oksijen seviyeleri fiber optik oksijen sensörü ile belirlenmiş ve hareket hızı ile bağlantısı tespit edilmiştir. Tespit edilen deneysel hız profili, faz ayrımı prensibi kullanılarak sürü oluşturma davranışı matematiksel olarak modellenmiştir.
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    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; 23851
    We 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 America
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    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; 23851
    We 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.
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    PublicationOpen 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/A
    Growing 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.
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    PublicationOpen Access
    Generation of 4-nJ pulses from a diode-pumped femtosecond Ti3+: sapphire laser
    (Optical Society of America (OSA), 2017) Department of Physics; Department of Electrical and Electronics Engineering; Muti, Abdullah; Kocabaş, Aşkın; Sennaroğlu, Alphan; PhD Student; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; N/A; 227753; 23851
    We generated 106-fs, 4.1-nJ pulses at 778 nm from a single green diode-pumped multipass-cavity Kerr-lens mode-locked Ti3+:sapphire laser. To our knowledge, these represent the highest pulse energies generated directly with a diode-pumped Ti3+:sapphire laser.
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    PublicationOpen Access
    Dynamics of pattern formation and emergence of swarming in Caenorhabditis elegans
    (eLife Sciences Publications, 2020) N/A; Department of Physics; Demir, Esin; Başaran, Mustafa; Yaman, Yusuf İlker; Kocabaş, Aşkın; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 227753
    Many animals collectively form complex patterns to tackle environmental difficulties. Several biological and physical factors, such as animal motility, population densities, and chemical cues, play significant roles in this process. However, very little is known about how sensory information interplays with these factors and controls the dynamics of pattern formation. Here, we study the direct relation between oxygen sensing, pattern formation, and emergence of swarming in active Caenorhabditis elegans aggregates. We find that when thousands of animals gather on food, bacteria-mediated decrease in oxygen level slows down the animals and triggers motility-induced phase separation. Three coupled factors-bacterial accumulation, aerotaxis, and population density-act together and control the entire dynamics. Furthermore, we find that biofilm-forming bacterial lawns including Bacillus subtilis and Pseudomonas aeruginosa strongly alter the collective dynamics due to the limited diffusibility of bacteria. Additionally, our theoretical model captures behavioral differences resulting from genetic variations and oxygen sensitivity.
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    PublicationOpen 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; 227753
    A 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.