Researcher:
Başaran, Mustafa

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Master Student

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Mustafa

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Başaran

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Başaran, Mustafa

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2020 - 20223

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Researcher Of Publications: search.filters.isAuthorOfPublication.5227313c-f549-4375-9d7a-3a68e00ce771

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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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    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.