TY - GEN A1 - Weber, Ariane A1 - Bahrs, Marco A1 - Alirezaeizanjani, Zahra A1 - Zhang, Xingyu A1 - Beta, Carsten A1 - Zaburdaev, Vasily T1 - Rectification of Bacterial Diffusion in Microfluidic Labyrinths T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - In nature as well as in the context of infection and medical applications, bacteria often have to move in highly complex environments such as soil or tissues. Previous studies have shown that bacteria strongly interact with their surroundings and are often guided by confinements. Here, we investigate theoretically how the dispersal of swimming bacteria can be augmented by microfluidic environments and validate our theoretical predictions experimentally. We consider a system of bacteria performing the prototypical run-and-tumble motion inside a labyrinth with square lattice geometry. Narrow channels between the square obstacles limit the possibility of bacteria to reorient during tumbling events to an area where channels cross. Thus, by varying the geometry of the lattice it might be possible to control the dispersal of cells. We present a theoretical model quantifying diffusive spreading of a run-and-tumble random walker in a square lattice. Numerical simulations validate our theoretical predictions for the dependence of the diffusion coefficient on the lattice geometry. We show that bacteria moving in square labyrinths exhibit enhanced dispersal as compared to unconfined cells. Importantly, confinement significantly extends the duration of the phase with strongly non-Gaussian diffusion, when the geometry of channels is imprinted in the density profiles of spreading cells. Finally, in good agreement with our theoretical findings, we observe the predicted behaviors in experiments with E. coli bacteria swimming in a square lattice labyrinth created in amicrofluidic device. Altogether, our comprehensive understanding of bacterial dispersal in a simple two-dimensional labyrinth makes the first step toward the analysis of more complex geometries relevant for real world applications. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 801 KW - diffusion KW - rectification KW - random walk KW - bacteria KW - confinement Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441222 SN - 1866-8372 IS - 801 ER - TY - JOUR A1 - Weber, Ariane A1 - Bahrs, Marco A1 - Alirezaeizanjani, Zahra A1 - Zhang, Xingyu A1 - Beta, Carsten A1 - Zaburdaev, Vasily T1 - Rectification of Bacterial Diffusion in Microfluidic Labyrinths JF - Frontiers in Physics N2 - In nature as well as in the context of infection and medical applications, bacteria often have to move in highly complex environments such as soil or tissues. Previous studies have shown that bacteria strongly interact with their surroundings and are often guided by confinements. Here, we investigate theoretically how the dispersal of swimming bacteria can be augmented by microfluidic environments and validate our theoretical predictions experimentally. We consider a system of bacteria performing the prototypical run-and-tumble motion inside a labyrinth with square lattice geometry. Narrow channels between the square obstacles limit the possibility of bacteria to reorient during tumbling events to an area where channels cross. Thus, by varying the geometry of the lattice it might be possible to control the dispersal of cells. We present a theoretical model quantifying diffusive spreading of a run-and-tumble random walker in a square lattice. Numerical simulations validate our theoretical predictions for the dependence of the diffusion coefficient on the lattice geometry. We show that bacteria moving in square labyrinths exhibit enhanced dispersal as compared to unconfined cells. Importantly, confinement significantly extends the duration of the phase with strongly non-Gaussian diffusion, when the geometry of channels is imprinted in the density profiles of spreading cells. Finally, in good agreement with our theoretical findings, we observe the predicted behaviors in experiments with E. coli bacteria swimming in a square lattice labyrinth created in amicrofluidic device. Altogether, our comprehensive understanding of bacterial dispersal in a simple two-dimensional labyrinth makes the first step toward the analysis of more complex geometries relevant for real world applications. KW - diffusion KW - rectification KW - random walk KW - bacteria KW - confinement Y1 - 2019 U6 - https://doi.org/10.3389/fphy.2019.00148 SN - 2296-424X SN - 0429-7725 VL - 7 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf T1 - Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects JF - New journal of physics : the open-access journal for physics N2 - During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the dynamics and statistical behavior of two flexible ring polymers in the presence of cylindrical confinement and crowding molecules. From extensive computer simulations we determine the degree of ring-ring overlap and the number of inter-monomer contacts for varying volume fractions phi of crowders. We also examine the entropic demixing of polymer rings in the presence of mobile crowders and determine the characteristic times of the internal polymer dynamics. Effects of the ring length on ring-ring overlap are also analyzed. In particular, on systematic variation of the fraction of crowding molecules, a (1 - phi)-scaling is found for the ring-ring overlap length along the cylinder axis, and a non-monotonic dependence of the 3D ring-ring contact number with a maximum at phi approximate to 0.2 is obtained. Our results demonstrate that polymer rings are demixed and separated by particular entropy-favourable partitioning of crowders along the axis of the cylindrical simulation box. These findings help to rationalize the implications of macromolecular crowding for circular DNA molecules in confined spaces inside bacteria as well as in localized cellular compartments inside eukaryotic cells. KW - polymers KW - confinement KW - crowding Y1 - 2014 U6 - https://doi.org/10.1088/1367-2630/16/5/053047 SN - 1367-2630 VL - 16 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Cherstvy, Andrey G. T1 - Critical polyelectrolyte adsorption under confinement Planar slit, cylindrical pore, and spherical cavity JF - Biopolymers N2 - We explore the properties of adsorption of flexible polyelectrolyte chains in confined spaces between the oppositely charged surfaces in three basic geometries. A method of approximate uniformly valid solutions for the Green function equation for the eigenfunctions of polymer density distributions is developed to rationalize the critical adsorption conditions. The same approach was implemented in our recent study for the inverse problem of polyelectrolyte adsorption onto a planar surface, and on the outer surface of rod-like and spherical obstacles. For the three adsorption geometries investigated, the theory yields simple scaling relations for the minimal surface charge density that triggers the chain adsorption, as a function of the Debye screening length and surface curvature. The encapsulation of polyelectrolytes is governed by interplay of the electrostatic attraction energy toward the adsorbing surface and entropic repulsion of the chain squeezed into a thin slit or small cavities. Under the conditions of surface-mediated confinement, substantially larger polymer linear charge densities are required to adsorb a polyelectrolyte inside a charged spherical cavity, relative to a cylindrical pore and to a planar slit (at the same interfacial surface charge density). Possible biological implications are discussed briefly in the end. KW - polymers KW - adsorption KW - electrostatics KW - confinement Y1 - 2012 U6 - https://doi.org/10.1002/bip.22023 SN - 0006-3525 VL - 97 IS - 5 SP - 311 EP - 317 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Fischer, Anna T1 - "Reactive hard templating" : from carbon nitrides to metal nitrides T1 - Synthese von Metallnitrid Nanostrukturen durch "Reaktives Hardtemplating" N2 - Nanostructured inorganic materials are routinely synthesized by the use of templates. Depending on the synthesis conditions of the product material, either “soft” or “hard” templates can be applied. For sol-gel processes, usually “soft” templating techniques are employed, while “hard” templates are used for high temperature synthesis pathways. In classical templating approaches, the template has the unique role of structure directing agent, in the sense that it is not participating to the chemical formation of the resulting material. This work investigates a new templating pathway to nanostructured materials, where the template is also a reagent in the formation of the final material. This concept is described as “reactive templating” and opens a synthetic path toward materials which cannot be synthesised on a nanometre scale by classical templating approaches. Metal nitrides are such kind of materials. They are usually produced by the conversion of metals or metal oxides in ammonia flow at high temperature (T > 1000°C), which make the application of classical templating techniques difficult. Graphitic carbon nitride, g-C3N4, despite its fundamental and theoretical importance, is probably one of the most promising materials to complement carbon in material science and many efforts are put in the synthesis of this material. A simple polyaddition/elimination reaction path at high temperature (T = 550°C) allows the polymerisation of cyanamide toward graphitic carbon nitride solids. By hard templating, using nanostructured silica or aluminium oxide as nanotemplates, a variety of nanostructured graphitic carbon nitrides such as nanorods, nanotubes, meso- and macroporous powders could be obtained by nanocasting or nanocoating. Due to the special semi-conducting properties of the graphitic carbon nitride matrix, the nanostructured graphitic carbon nitrides show unexpected catalytic activity for the activation of benzene in Friedel-Crafts type reactions, making this material an interesting metal free catalyst. Furthermore, due to the chemical composition of g-C3N4 and the fact that it is totally decomposed at temperatures between 600°C and 800°C even under inert atmosphere, g-C3N4 was shown to be a good nitrogen donor for the synthesis of early transition metal nitrides at high temperatures. Thus using the nanostructured carbon nitrides as “reactive templates” or “nanoreactors”, various metal nitride nanostructures, such as nanoparticles and porous frameworks could be obtained at high temperature. In this approach the carbon nitride nanostructure played both the role of the nitrogen source and of the exotemplate, imprinting its size and shape to the resulting metal nitride nanostructure. N2 - Die Nanostrukturierung anorganischer Materialien, d.h. die Kontrolle ihrer Form und Größe auf der Nanometerebene durch unterschiedliche Herstellungsverfahren, ist ein sich immer noch erweiterndes Forschungsgebiet. Eine solche Nanostrukturierung wird oft über sogenannte Templatierungsverfahren erreicht: Hier werden Formgeber (Template) mit definierter Morphologie und Größe verwendet und deren Struktur in ein neues Material abgebildet. Templatierungsverfahren können, je nach der Beschaffenheit des Templats, zwischen „weich“ und „hart“ unterschieden werden. Die Begriffe beziehen sich dabei vor allem auf die mechanische und thermische Stabilität der Template, d.h. weiche Template sind vornehmlich organischer, harte Template anorganischer Natur. Wo weiche Template in milden chemischen Verfahren eingesetzt werden, werden harte Template zur Herstellung von Materialien bei Hochtemperaturverfahren verwendet (z. B. poröse Kohlenstoffe). Allgemein dienen Template ausschließlich als Strukturgeber und gehen in keiner Weise in Form einer chemischen Reaktion in die Synthese des gewünschten Materials mit ein. Gegenstand dieser Arbeit ist ein neues Templatierungsverfahren: Die „reaktive Templatierung“. Hierbei wird das Templat - neben seiner Funktion als Strukturgeber – auch als Reagenz für die Synthese des Produktes verwendet. Dieser Synthese-Ansatz öffnet damit neue Wege für die Synthese von nanostrukturierten Materialien, die durch klassische Templatierungsansätze schwer zugänglich sind. Hierzu zählen zum Beispiel die Metallnitride. Üblicherweise werden Metallnitride über die Umsetzung von Metallen oder Metalloxiden in einem Ammoniakstrom bei Mindesttemperaturen von 1000°C gewonnen, was die Anwendung klassischer Templatierungsverfahren beinahe unmöglich macht. Darüber hinaus sind konzentrierte Lauge oder Flusssäure, welche zur Entfernung klassischer harter Template benötigt werden auch Aufschlussmittel für Metallnitride. Graphitisches Kohlenstoffnitrid, g-C3N4, ist wohl eines der meistversprechendsten Materialien um Kohlenstoff in der Materialwissenschaft zu ergänzen. Es wurden bereits viele potentielle Syntheseansätze beschrieben. Eine durch Groenewolt M. erstellte Route ist die thermisch induzierte Polykondensation von Cyanamid (NCNH2) bei 550°C. Da g-C3N4 sich zwischen 600°C und 800°C vollständig in NH3 und CxNyH-Gase zersetzt, ist es eine geeignete Festkörper-Stickstoffquelle für die Herstellung von Metalnitriden. Daher boten sich nanostrukturierte graphitische Kohlenstoffnitride als geeignete reaktive Template oder Nanoreaktoren zur Herstellung von nano-strukturierten Metalnitriden an. Die Templatierung der g-C3N4-Matrix wurde über klassische Harttemplatierungsverfahren erreicht. So konnte eine Vielzahl nano-strukturierter g-C3N4 Materialien synthetisiert werden wie zum Beispiel Nanostäbchen, Nanoröhren, mesoporöse oder makroporöse graphitische Kohlenstoffnitride. Diese haben sich interessanterweise, als metalfreie Katalysatoren für die Aktivierung von Benzol in Friedel-Crafts-Acylierung und -Alkylierung erwiesen. Durch die Infiltrierung der nano-strukturierten g-C3N4-Materialien mit diversen Metal-Präkursoren und nachfolgendem Tempern bei 800°C unter Schutzgas, konnten entsprechende nano-strukturierte Metalnitride, als Nanoabdrücke der vorgegebenen Kohlenstoffnitrid Nanostrukturen hergestellt werden. So konnten TiN, VN, GaN, AlGaN und TiVN Nanopartikel synthetisiert werden, macroporöse TiN/Kohlenstoff Komposite sowie TiN Hohlkugeln. Die so hergestellten Materialien erwiesen sich als effektive basische Katalysatoren für Aldol-Kondensations Reaktionen. KW - Kohlenstoffnitride KW - Metallnitride KW - nano KW - Templatierung KW - Carbonitrides KW - metal nitrides KW - reactive templating KW - confinement KW - nano Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-19777 ER -