Researcher:
Demir, Esin

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PhD Student

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Esin

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Demir

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Demir, Esin

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2019 - 20202

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Researcher Of Publications: search.filters.isAuthorOfPublication.a1c7d561-7abb-49b1-a0f1-8e14ad345dfc

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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
    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.