Wednesday, 25 October 2023
I will give an overview over several simple models of a single active particle. In particular, I will derive in a pedagogical way the propagator in the Fourier domain, also known as intermediate scattering function.
The term colloid stems from the Greek word ‘Kolla’ for glue, combined with the ending ‘oid’ for forming and describes a mixture consisting of one non-crystalline substance dispersed in a second substance. Colloids include for example gels, sols, smoke and emulsions and a number of techniques have been established to produce and characterize this fascinating state of matter. In this first class we will look at different techniques to produce particles and droplets and learn how to manipulate them.
Extreme confinement of microorganisms between rigid boundaries often arises in their habitat, yet measurements of swimming mechanics in this regime are absent. We show that strongly confining the microalga Chlamydomonas between two parallel plates not only inhibits its motility through contact friction with the walls but also leads, for purely mechanical reasons, to inversion of the surrounding vortex flows. Our experimental data naturally leads to a simplified theoretical description of flow fields based on a quasi-2D Brinkman approximation to the Stokes equation rather than the usual method of images. We find that the vortex flow inversion provides advantage of enhanced fluid mixing despite higher friction. Overall, our results offer a comprehensive framework for analyzing the collective flows of strongly confined swimmers
Thursday, 26 October 2023
I will extend the active Brownian particle model to a circle swimmer and provide a complete characterization of its dynamics in terms of the intermediate scattering function. I will show that circle swimmers exposed to an external field, e.g. gravity, display a resonance close to an underlying classical bifurcation
... or to enable them to convert energy from one form to another in order to move or exert force, we need to push them out of equilibrium. While this broad definition encompasses all living systems, artificial 'out-of-equilibrium' systems have become the focus of interdisciplinary research over the last two decades. In this talk we will explore different ways to create 'artificial active matter' and the different properties that result from the different motion mechanisms.
Friday, 27 October 2023
I will discuss the motion of passive and active needles in a crowded environment of other needles. In particular, I will elucidate the Doi-Edwards prediction for the exact solution in the highly entangled regime. We show that for active needles crowding accelerates the dynamics. Futher I introduce a complex landscape consisting of fixed obstacle and discuss percolative transport both for active and passive particles. If time permits, I will discuss the meandering transition of circle swimmers in such an environment.
While the behaviour of biological microswimmers is undoubtedly influenced by physics, it is often controlled and manipulated by active sensing processes. Understanding the respective influences of the environment can help to engineer the desired response in artificial swimmers. In most cases, the achievement of biomimetic behaviour requires an understanding of the swimming mechanisms of both biological and artificial microswimmers and the parameters that induce mechanosensory responses. Using different examples of tactic behaviour, I will show how active matter can be tuned to mimic bacteria or other microorganisms.
Monday, 30 October 2023
While the motion and collective behavior of cells are well-studied on flat surfaces or in unconfined liquid media, in most natural settings, cells thrive in complex 3D environments. Bioprinting processes are capable of structuring cells in 3D and conventional bioprinting approaches address this challenge by embedding cells in bio-degradable polymer networks. However, heterogeneity in network structure and biodegradation often preclude quantitative studies of cell behavior in specified 3D architectures. Here, I will present a new approach to 3D bioprinting of cellular communities that utilizes jammed, granular polyelectrolyte microgels as a support medium. The self-healing nature of this medium allows the creation
of highly precise cellular communities and tissue-like structures by direct injection of cells inside the 3D medium. Further, the transparent nature of this medium enables precise characterization of cellular behavior. I will describe two examples of my work using this platform to study the behavior of two different classes of cells in 3D. First, I will describe how we interrogate the growth, viability, and migration of mammalian cells—ranging from epithelial cells, cancer cells, and T cells—in the 3D pore space. Second, I will describe how we interrogate the migration of E. coli bacteria through the 3D pore space. Direct visualization enables us to reveal a new mode of motility exhibited by individual cells, in stark contrast to the paradigm of run-and-tumble motility, in which cells are intermittently and transiently trapped as they navigate the pore space; further, analysis of these dynamics enables prediction of single-cell transport over large length and time scales. Moreover, we show that concentrated populations of E. coli can collectively migrate through a porous medium—despite being strongly confined—by chemotactically “surfing” a self-generated nutrient gradient. Together, these studies highlight how the jammed microgel medium provides a powerful platform to design and interrogate complex cellular communities in 3D— with implications for tissue engineering, microtissue mechanics, studies of cellular interactions, and biophysical studies of active matter.
Genotypically similar cells of tissues show phenotypic heterogeneity dictated by differential protein expression patterns. In epithelia, this biochemical heterogeneity is further complexed by a physical heterogeneity, dictated by cellular contractility and matrix stiffness. However, for epithelial tissues, such inherent bio-physical heterogeneity in space and time remains uncharacterized, and its relevance to tissue function remains unknown. In this presentation, I will discuss our work on how biochemical and physical stochasticity in epithelial cells dictate tissue function. I will focus on tissue remodelling during wound healing, and on mutant cell extrusion during epithelial defence against cancer, and demonstrate how both these functions require bio-physical heterogeneity. I will also discuss how spatial heterogeneity is regulated in time, and how deregulated biological oscillators might influence tissue heterogeneity and subsequently its function.
Tuesday, 31 October 2023
Microtubule filaments are an important example of active polymer where the motor protein (kinesin) make use of chemical energy derived from the hydrolysis of adenosine triphosphate (ATP) to induce the conformational changes, which then leads to its motion on microtuble. In our work, we are interested in studying such active polymer that exhibits various interesting dynamics like self-propulsion, swelling, shrinkage, loop formation, spontaneous oscillation, spiral formations, enhanced diffusion etc.
Microtubule filaments are an important example of active polymer where the motor protein (kinesin) make use of chemical energy derived from the hydrolysis of adenosine triphosphate (ATP) to induce the conformational changes, which then leads to its motion on microtuble. In our work, we are interested in studying such active polymer that exhibits various interesting dynamics like self-propulsion, swelling, shrinkage, loop formation, spontaneous oscillation, spiral formations, enhanced diffusion etc.
Active turbulence — the spatio-temporally complex motion of a dense suspension of microorganisms such as bacteria — has gathered great traction recently as an intriguing class of emergent, complex flows, occurring in several living systems at the mesoscale, whose understanding lies at the interface of non-equilibrium physics and biology. However, are these low Reynolds number living flows really turbulent or just chaotic with structural, or even superficial, similarities with high Reynolds number (classical) inanimate turbulence? This is a vital question as the fingerprints of classical turbulence —-- universality, intermittency and chaos —-- makes it unique amongst the many different driven-dissipative systems. In this talk we address these questions with a focus on the issues of (approximate) scale-invariance, intermittency and maximally chaotic states and how they lead to anomalous diffusion in bacterial suspensions. In particular, we show the existing of a critical level of activity beyond which the physics of bacterial flows become universal, accompanied by maximally chaotic states which allow for efficient, Levy-walk mediated foraging strategies.
In assemblies of passive particles, increasing the packing fraction can drive the system to a glassy or jammed state. Epithelial cell monolayers, however, can jam, unjam, and reveal many aspects of glassy-slowing down, often seen in passive systems while remaining confluent, i.e., the packing fraction remains unity. This remarkable feature of cell monolayers is largely due to the ability of the individual cells to change shape and thereby surmount the constraining effects of crowding. Living cell collectives, however, are complex, and besides cell shape changes, many other mechanisms that cause fluidization, such as cell division, apoptosis, and cell size changes, operate independently or together. It is impossible to suppress these processes completely, and there is no consensus on whether cell shape changes alone can drive jamming/unjamming. In my talk, I will describe a synthetic model system that allowed us to directly confront the question of whether shape changes alone can lead to jamming/unjamming.
Friday, 03 November 2023
Unraveling the motion of microorganisms in dilute and porous media is important for our understanding of both the molecular basis of their swim gait and their survival strategies in microbial habitats. First, I will show that by using renewal processes to analyze experimental measurements of wild-type {\it E. Coli}, we can provide a quantitative spatiotemporal characterization of their run-and-tumble dynamics in bulk. We further demonstrate quantitatively how the persistence length of an engineered strain can be controlled by a chemical inducer and characterize a transition from perpetual tumbling to smooth swimming. Second, I will address how this run-and-tumble gait evolves towards a hop-and-trap motility pattern of agents moving in a porous environment. Using computer simulations, we discover a geometric criterion for their optimal spreading, which emerges when their persistence lengths are comparable to the longest straight path available in the porous medium. Our criterion provides a fundamental principle for optimal transport in densely-packed environments, which could be tested experimentally by using engineered cells and may provide insights into microbial adaption mechanisms.
Saturday, 04 November 2023
A general lecture giving an up-to-date overview of what we know about the Vicsek model and the continuous theories describing it
A more specialized talk focused on the effects of (spatial) quenched disorder on the collective dynamics of the VM