DepositOnce Collection:
https://depositonce.tu-berlin.de/handle/11303/6864
2019-03-23T03:30:12ZDissipative systems with nonlocal delayed feedback control
https://depositonce.tu-berlin.de/handle/11303/8569
Main Title: Dissipative systems with nonlocal delayed feedback control
Author(s): Grawitter, Josua; van Buel, Reinier; Schaaf, Christian; Stark, Holger
Abstract: We present a linear model, which mimics the response of a spatially extended dissipative medium to a distant perturbation, and investigate its dynamics under delayed feedback control. The time a perturbation needs to propagate to a measurement point is captured by an inherent delay time (or latency). A detailed linear stability analysis demonstrates that a nonzero system delay acts to destabilize the otherwise stable fixed point for sufficiently large feedback strengths. The imaginary part of the dominant eigenvalue is bounded by twice the feedback strength. In the relevant parameter space it changes discontinuously along specific lines when switching between eigenvalues. When the feedback control force is bounded by a sigmoid function, a supercritical Hopf bifurcation occurs at the stability–instability transition. Perturbing the fixed point, the frequency and amplitude of the resulting limit cycles respond to parameter changes like the dominant eigenvalue. In particular, they show similar discontinuities along specific lines. These results are largely independent of the exact shape of the sigmoid function. Our findings match well with previously reported results on a feedback-induced instability of vortex diffusion in a rotationally driven Newtonian fluid (Zeitz et al 2015 Eur. Phys. J. E 38 22). Thus, our model captures the essential features of nonlocal delayed feedback control in spatially extended dissipative systems.2018-11-26T12:22:20ZSimulating the complex cell design of Trypanosoma brucei and its motility
https://depositonce.tu-berlin.de/handle/11303/7876
Main Title: Simulating the complex cell design of Trypanosoma brucei and its motility
Author(s): Alizadehrad, Davod; Krüger, Timothy; Engstler, Markus; Stark, Holger
Abstract: The flagellate Trypanosoma brucei, which causes the sleeping sickness when infecting a mammalian host, goes through an intricate life cycle. It has a rather complex propulsion mechanism and swims in diverse microenvironments. These continuously exert selective pressure, to which the trypanosome adjusts with its architecture and behavior. As a result, the trypanosome assumes a diversity of complex morphotypes during its life cycle. However, although cell biology has detailed form and function of most of them, experimental data on the dynamic behavior and development of most morphotypes is lacking. Here we show that simulation science can predict intermediate cell designs by conducting specific and controlled modifications of an accurate, nature-inspired cell model, which we developed using information from live cell analyses. The cell models account for several important characteristics of the real trypanosomal morphotypes, such as the geometry and elastic properties of the cell body, and their swimming mechanism using an eukaryotic flagellum. We introduce an elastic network model for the cell body, including bending rigidity and simulate swimming in a fluid environment, using the mesoscale simulation technique called multi-particle collision dynamics. The in silico trypanosome of the bloodstream form displays the characteristic in vivo rotational and translational motility pattern that is crucial for survival and virulence in the vertebrate host. Moreover, our model accurately simulates the trypanosome's tumbling and backward motion. We show that the distinctive course of the attached flagellum around the cell body is one important aspect to produce the observed swimming behavior in a viscous fluid, and also required to reach the maximal swimming velocity. Changing details of the flagellar attachment generates less efficient swimmers. We also simulate different morphotypes that occur during the parasite's development in the tsetse fly, and predict a flagellar course we have not been able to measure in experiments so far.2018-05-28T12:48:26ZGravity-induced dynamics of a squirmer microswimmer in wall proximity
https://depositonce.tu-berlin.de/handle/11303/7481
Main Title: Gravity-induced dynamics of a squirmer microswimmer in wall proximity
Author(s): Rühle, Felix; Blaschke, Johannes; Kuhr, Jan-Timm; Stark, Holger
Abstract: We perform hydrodynamic simulations using the method of multi-particle collision dynamics and a theoretical analysis to study a single squirmer microswimmer at high Péclet number, which moves in a low Reynolds number fluid and under gravity. The relevant parameters are the ratio α of swimming to bulk sedimentation velocity and the squirmer type β. The combination of self-propulsion, gravitational force, hydrodynamic interactions with the wall, and thermal noise leads to a surprisingly diverse behavior. At α > 1 we observe cruising states, while for α < 1 the squirmer resides close to the bottom wall with the motional state determined by stable fixed points in height and orientation. They strongly depend on the squirmer type β. While neutral squirmers permanently float above the wall with upright orientation, pullers float for α larger than a threshold value ath and are pinned to the wall below αth. In contrast, pushers slide along the wall at lower heights, from which thermal orientational fluctuations drive them into a recurrent floating state with upright orientation, where they remain on the timescale of orientational persistence.2018-03-01T10:23:55ZPhysical minimal models of amoeboid cell motility
https://depositonce.tu-berlin.de/handle/11303/7349
Main Title: Physical minimal models of amoeboid cell motility
Author(s): Kulawiak, Dirk Alexander
Abstract: Cell locomotion plays an important role in many biological processes such as the immune system, embryonic development, or cancer metastasis. In these examples, cells interact with their environments or coordinate their movements with other cells, creating collective behavior. In this thesis, we utilize minimal modeling to investigate single and collective cell motility in three different settings. The key question we strive to answer is whether cell locomotion is a physical process that can function without the biochemistry that controls it.
First, we examine contact inhibition of locomotion (CIL), which is one of the ways that cells interact. In experiments, cell migration can be restricted to quasi-one-dimensional stripes. In these stripes, head-on collisions of two cells occur frequently with only a few outcomes, such as cells reversing their directions, sticking to one another, or walking past each other. By utilizing a phase field model that includes the mechanics of cell shape and a minimal chemical model for CIL, we are able to reproduce all cases seen in these collisions. In addition, we found qualitative agreements such as the occurrence of ``cell trains''.
Next, we investigate cells migrating on substrates with heterogeneous rigidity. By utilizing substrate configurations where cells with varying propulsion strength and membrane stiffness behave differently, we demonstrate that heterogeneous substrates are able to sort and distinguish those cells. Further, we investigate collective interactions and reproduce collective phenomena such as persistent rotational motion.
We then study flow-driven amoeboid motility that is exhibited by microplasmodia of physarum. This motion is caused by a feedback loop between a chemical regulator, active mechanical deformations, and induced flows that give rise to spatio-temporal contraction patterns. We develop a poroelastic model consisting of two phases: (1) an active viscoelastic gel representing the cytoskeleton, that is permeated by (2) a fluid depicting the cytosol. Our model incorporates active contractions of the gel that are controlled by calcium. In turn, the calcium is advected with the fluid. By using free boundary conditions, nonlinear substrate friction and a nonlinear reaction kinetic for the calcium regulator, we reproduce the oscillatory motion of these microplasmodia with a net motion in each cycle.
We demonstrate in all three cases that we can reproduce experimental behavior with these minimal models. This substantiates our assumption that some aspects of cell motility can be thought of as a ``physical machine'' that is controlled by the cell's biochemistry but can operate without it.; Zellbewegung ist die Grundlage vieler biologischer Vorgänge. Beispiele sind das Immunsystem, die Entwicklung von Embryonen und metastasierender Krebs. In diesen Beispielen wechselwirken Zellen mit ihrer Umgebung oder kooperieren untereinander, wodurch kollektive Bewegung entsteht. Mit Hilfe von Minimalmodellen versuchen wir zu beantworten, ob Zellbewegung durch physikalische Prozesse erklärbar ist, welche durch die Biochemie der Zelle gesteuert werden, aber auch ohne sie funktionieren können.
Zuerst analysieren wir die Interaktion von Zellen über contact inhibition of locomotion (CIL). In Experimenten kann Zellbewegung auf quasi-eindimensionale Streifen beschränkt werden. Dadurch kommt es zu frontalen Zell-Zell-Kollisionen, bei denen es nur wenige mögliche Ergebnisse gibt: Beide Zellen drehen um oder die Zellen haften aneinander bzw. quetschen sich aneinander vorbei. Zur Modellierung dieser Kollisionen benutzen wir ein Phasenfeld-Modell, welches die Zellform berücksichtigt und einen minimalen Ansatz für CIL beinhaltet. Damit können wir alle Kollisionsergebnisse reproduzieren.
Als nächstes untersuchen wir Zellbewegung auf Substraten mit heterogener Steifheit. Wir identifizieren Heterogenitäten, bei denen sich Zellen mit unterschiedlicher Membransteifigkeit oder Vortriebsstärke unterschiedlich verhalten und nutzen dies, um Zellen zu sortieren. Zusätzlich untersuchen wir kollektive Zellbewegung und reproduzieren einige kooperative Phänomene, z.B. persistente Rotation und stabile Zellpaare, deren Bewegung von einer der Zellen gesteuert wird.
Im letzten Kapitel betrachten wir die Bewegung von Mikroplasmodien (MP). Deren Bewegung entsteht durch eine Rückkopplungsschleife zwischen einem chemischen Regulator und aktiver mechanischer Kontraktion, welche zur Ausbildung von raum-zeitlichen Mustern führt. Wir entwickeln ein poroelastisches Zweiphasen-Modell, dessen erste Phase das aktive viskoelastische Cytoskelett beschreibt. Dieses ist vom Cytosol, die zweite viskose Phase im Modell, durchdrungen. Unser Modell beinhaltet aktive Kontraktionen des Gels, welche von Kalzium reguliert werden. Kalzium wird wiederum mit dem Fluid advektiert. Mit freien Randbedingungen, nichtlinearer Substratreibung und Reaktionskinetik für Kalzium können wir die oszillatorische Bewegung von MP reproduzieren. Im Besonderen identifizieren wir die nötigen Voraussetzungen für gerichtete Netto-Bewegung.
In allen behandelten Beispielen können wir experimentelles Verhalten mit minimalen Modellen reproduziert. Dies untermauert unsere Annahme, dass einige Aspekte von Zellbewegung durch physikalische Prozesse erklärbar sind, welche von der Biochemie der Zelle gesteuert werden, aber auch ohne sie funktionieren.2018-01-22T10:12:35ZDynamics of a bacterial flagellum under reverse rotation
https://depositonce.tu-berlin.de/handle/11303/6900
Main Title: Dynamics of a bacterial flagellum under reverse rotation
Author(s): Adhyapak, Tapan Chandra; Stark, Holger
Abstract: To initiate tumbling of an E. coli, one of the helical flagella reverses its sense of rotation. It then transforms from its normal form first to the transient semicoiled state and subsequently to the curly-I state. The dynamics of polymorphism is effectively modeled by describing flagellar elasticity through an extended Kirchhoff free energy. However, the complete landscape of the free energy remains undetermined because the ground state energies of the polymorphic forms are not known. We investigate how variations in these ground state energies affect the dynamics of a reversely rotated flagellum of a swimming bacterium. We find that the flagellum exhibits a number of distinct dynamical states and comprehensively summarize them in a state diagram. As a result, we conclude that tuning the landscape of the extended Kirchhoff free energy alone cannot generate the intermediate full-length semicoiled state. However, our model suggests an ad hoc method to realize the sequence of polymorphic states as observed for a real bacterium. Since the elastic properties of bacterial flagella are similar, our findings can easily be extended to other peritrichous bacteria.
Notes: Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.; This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.2017-10-24T07:15:26ZPhase separation and coexistence of hydrodynamically interacting microswimmers
https://depositonce.tu-berlin.de/handle/11303/6886
Main Title: Phase separation and coexistence of hydrodynamically interacting microswimmers
Author(s): Blaschke, Johannes; Maurer, Maurice; Menon, Karthik; Zöttl, Andreas; Stark, Holger
Abstract: A striking feature of the collective behavior of spherical microswimmers is that for sufficiently strong self-propulsion they phase-separate into a dense cluster coexisting with a low-density disordered surrounding. Extending our previous work, we use the squirmer as a model swimmer and the particle-based simulation method of multi-particle collision dynamics to explore the influence of hydrodynamics on their phase behavior in a quasi-two-dimensional geometry. The coarsening dynamics towards the phase-separated state is diffusive in an intermediate time regime followed by a final ballistic compactification of the dense cluster. We determine the binodal lines in a phase diagram of Peclet number versus density. Interestingly, the gas binodals are shifted to smaller densities for increasing mean density or dense-cluster size, which we explain using a recently introduced pressure balance [S. C. Takatori, et al., Phys. Rev. Lett. 2014, 113, 028103] extended by a hydrodynamic contribution. Furthermore, we find that for pushers and pullers the binodal line is shifted to larger Peclet numbers compared to neutral squirmers. Finally, when lowering the Peclet number, the dense phase transforms from a hexagonal "solid'' to a disordered "fluid'' state.2017-10-24T06:17:26ZTaylor line swimming in microchannels and cubic lattices of obstacles
https://depositonce.tu-berlin.de/handle/11303/6874
Main Title: Taylor line swimming in microchannels and cubic lattices of obstacles
Author(s): Münch, Jan L.; Alizadehrad, Davod; Babu, Sujin B.; Stark, Holger
Abstract: Microorganisms naturally move in microstructured fluids. Using the simulation method of multi-particle collision dynamics, we study in two dimensions an undulatory Taylor line swimming in a microchannel and in a cubic lattice of obstacles, which represent simple forms of a microstructured environment. In the microchannel the Taylor line swims at an acute angle along a channel wall with a clearly enhanced swimming speed due to hydrodynamic interactions with the bounding wall. While in a dilute obstacle lattice swimming speed is also enhanced, a dense obstacle lattice gives rise to geometric swimming. This new type of swimming is characterized by a drastically increased swimming speed. Since the Taylor line has to fit into the free space of the obstacle lattice, the swimming speed is close to the phase velocity of the bending wave traveling along the Taylor line. While adjusting its swimming motion within the lattice, the Taylor line chooses a specific swimming direction, which we classify by a lattice vector. When plotting the swimming velocity versus the magnitude of the lattice vector, all our data collapse on a single master curve. Finally, we also report more complex trajectories within the obstacle lattice.2017-10-24T06:17:01Z