Active Matter Seminar

2022-02-24 13:00 - 14:30

During the 2021–22 academic year, the CMSA will be hosting a seminar on Active Matter, organized by Farzan Vafa and David Nelson. This seminar will take place bi-weekly on Thursdays at 1:00pm – 2:30pm (Boston time). The meetings will take place virtually on Zoom. To learn how to attend, please fill out this form, or contact Farzan Vafa (

The schedule below will be updated as talks are confirmed.

Spring 2022

Date Speaker Title/Abstract
1/27/2022 Petros Koumoutsakos, Harvard Title: Learning to School in the presence of hydrodynamic interactions

Abstract: Fluids pervade complex systems, ranging from fish schools, to bacterial colonies and nanoparticles in drug delivery. Despite its importance, little is known about the role of fluid mechanics in such applications. Is schooling the result of vortex dynamics synthesized by individual fish wakes or the result of behavioral traits? Is fish schooling energetically favorable?  I will present multifidelity computational studies of collective swimming in 2D and 3D flows. Our studies demonstrate that classical models of collective swimming (like the Reynolds model) fail to maintain coherence in the presence of long-range hydrodynamic interactions. We demonstrate in turn that collective swimming can be achieved through reinforcement learning. We extend these studies to 2D and 3D viscous flows governed by the Navier Stokes equations. We examine various hydrodynamic benefits with a progressive increase of the school size and demonstrate the importance of controlling the vorticity field generated by up to 300 synchronized swimmers.

2/10/2022 Margaret Gardel, University of Chicago Title: Active Matter Controlling Epithelial Dynamics

Abstract: My lab is interested in the active and adaptive materials that underlie control of cell shape.  This has centered around understanding force transmission and sensing within the actin cytoskeleton.  I will first review our current understanding of the types of active matter that can be constructed by actin polymers.  I will then turn to our recent experiments to understand how Cell shape changes in epithelial tissue.  I will describe the two sources of active stresses within these tissues, one driven by the cell cycle and controlling cell-cell stresses and the other controlled by cell-matrix signaling controlling motility.  I will then briefly describe how we are using optogenetics to locally control active stresses to reveal adaptive and force-sensitive mechanics of the cytoskeletal machinery. Hopefully, I will convince you that recent experimental and theoretical advances make this a very promising time to study this quite complicated form of active matter.

2/24/2022 Amin Doostmohammadi, Niels Bohr Institute, University of Copenhagen Title: Taming Active Matter: from ordered topological defects to autonomous shells 

Abstract: The spontaneous emergence of collective flows is a generic property of active fluids and often leads to chaotic flow patterns characterized by swirls, jets, and topological
disclinations in their orientation field. I will first discuss two examples of these collective features helping us understand biological processes: (i) to explain the tortoise & hare story in bacterial competition: how motility of Pseudomonas aeruginosa bacteria leads to a slower invasion of bacteria colonies, which are individually faster, and
(ii) how self-propelled defects lead to finding an unanticipated mechanism for cell death.

I will then discuss various strategies to tame, otherwise chaotic, active flows, showing how hydrodynamic screening of active flows can act as a robust way of controlling and guiding active particles into dynamically ordered coherent structures. I will also explain how combining hydrodynamics with topological constraints can lead to further control of exotic morphologies of active shells.

3/24/22 Katherine Copenhagen, Princeton Title: Topological defects drive layer formation in gliding bacteria colonies

Abstract: The developmental cycle of Myxococcus xanthus involves the coordination of many hundreds of thousands of cells aggregating to form mounds known as fruiting bodies. This aggregation process begins with the sequential formation of more and more cell layers. Using three-dimensional confocal imaging we study this layer formation process by observing the formation of holes and second layers within a base monolayer of M xanthus cells. We find that cells align with each other over the majority of the monolayer forming an active nematic liquid crystal with defect point where cell alignment is undefined. We find that new layers and holes form at positive and negative topological defects respectively. We model the cell layer using hydrodynamic modeling and find that this layer and hole formation process is driven by active nematic forces through cell motility and anisotropic substrate friction.
4/7/2022 Ben Simons, Cambridge Title: Theories of branching morphogenesis

Abstract: The morphogenesis of branched tissues has been a subject of long-standing debate. Although much is known about the molecular pathways that control cell fate decisions, it remains unclear how macroscopic features of branched organs, including their size, network topology and spatial pattern are encoded. Based on large-scale reconstructions of the mouse mammary gland and kidney, we begin by showing that statistical features of the developing branched epithelium can be explained quantitatively by a local self-organizing principle based on a branching and annihilating random walk (BARW). In this model, renewing tip-localized progenitors drive a serial process of ductal elongation and stochastic tip bifurcation that terminates when active tips encounter maturing ducts. Then, based on reconstructions of the developing mouse salivary gland, we propose a generalisation of BARW model in which tips arrested through steric interaction with proximate ducts reactivate their branching programme as constraints become alleviated through the expansion of the underlying mesenchyme. This inflationary branching-arresting random walk model offers a more general paradigm for branching morphogenesis when the ductal epithelium grows cooperatively with the tissue into which it expands/

4/28/2022 Guillaume Duclos (Brandeis) Title: Building active nematic and active polar liquids out of biological machines

Abstract: Active matter describes out-of-equilibrium materials composed of motile building blocks that convert free energy into mechanical work. The continuous input of energy at the particle scale liberates these systems from the constraints of thermodynamic equilibrium, leading to emergent collective behaviors not found in passive materials. In this talk, I will describe our recent efforts to build simple active systems composed of purified proteins and identify generic emergent behaviors in active systems. I will first discuss two distinct activity-driven instabilities in suspensions of microtubules and molecular motors. Second, I will describe a new model system for polar fluid whose collective dynamics are driven by the non-equilibrium turnover of actin filaments. Our results illustrate how biomimetic materials can serve as a platform for studying non-equilibrium statistical mechanics, as well as shine light on the physical mechanisms that regulate self-organization in living matter.

Fall 2021

Date Speaker Title/Abstract
9/2/2021 Andreas Bausch, Technical University of Munich Title: Eppur si muovono: rotations in active matter

Abstract: Living matter relies on the self organization of its components into higher order structures, on the molecular as well as on the cellular, organ or even organism scale. Collective motion due to active transport processes has been shown to be a promising route for attributing fascinating order formation processes on these different length scales. Here I will present recent results on structure formation on actively transported actin filaments on lipid membranes and vesicles, as well as the cell migration induced structure formation in the developmental phase of mammary gland organoids. For both systems spherical structures with persistent collective rotations are observed.

9/23/2021 Krishna Shrinivas, Harvard Title: The many phases of a cell

Abstract: I will begin by introducing an emerging paradigm of cellular organization – the dynamic compartmentalization of biochemical pathways and molecules by phase separation into distinct and multi-phase condensates. Motivated by this, I will discuss two largely orthogonal problems, united by the theme of phase separation in multi-component and chemically active fluid mixtures.

1. I will propose a theoretical model based on Random-Matrix Theory, validated by phase-field simulations, to characterizes the rich emergent dynamics, compositions, and steady-state properties that underlie multi-phase coexistence in fluid mixtures with many randomly interacting components.

2. Motivated by puzzles in gene-regulation and nuclear organization, I will propose a role for how liquid-like nuclear condensates can be organized and regulated by the active process of RNA synthesis (transcription) and RNA-protein coacervation. Here, I will describe theory and simulations based on a Landau formalism and recent experimental results from collaborators.

9/30/2021 Daniel Needleman, Harvard Title: Cytoskeletal Energetics and Energy Metabolism

Abstract: Life is a nonequilibrium phenomenon. Metabolism provides a continuous flux of energy that dictates the form and function of many subcellular structures. These subcellular structures are active materials, composed of molecules which use chemical energy to perform mechanical work and locally violate detailed balance. One of the most dramatic examples of such a self-organizing structure is the spindle, the cytoskeletal based assembly which segregates chromosomes during cell division. Despite its central role, very little is known about the nonequilibrium thermodynamics of active subcellular matter, such as the spindle. In this talk, I will describe ongoing work from my lab aimed at understanding the flows of energy which drive the nonequilibrium behaviors of the cytoskeleton in vitro and in vivo.

10/14/2021 Wai-Tong (Louis) Fan, Indiana University Title: Stochastic PDE as scaling limits of interacting particle systems

Abstract: Interacting particle models are often employed to gain understanding of the emergence of macroscopic phenomena from microscopic laws of nature. These individual-based models capture fine details, including randomness and discreteness of individuals, that are not considered in continuum models such as partial differential equations (PDE) and integral-differential equations. The challenge is how to simultaneously retain key information in microscopic models as well as efficiency and robustness of macroscopic models. In this talk, I will illustrate how this challenge can be overcome by elucidating the probabilistic connections between models of different levels of detail. These connections explain how stochastic partial differential equations (SPDE) arise naturally from particle models.

I will also present some novel scaling limits including SPDE on graphs and coupled SPDE. These SPDE not only interpolate between particle models and PDE, but also quantify the source and the order of magnitude of stochasticity. Scaling limit theorems and duality formulas are obtained for these SPDE, which connect phenomena across scales and offer insights about the genealogies and the time-asymptotic properties of the underlying population dynamics.

10/28/2021 Aissam Ikmi, EMBL Title: Drivers of Morphological Complexity

Abstract: During development, organisms interact with their natural habitats while undergoing morphological changes, yet we know little about how the interplay between developing systems and their environments impacts animal morphogenesis. Cnidaria, a basal animal lineage that includes sea anemones, corals, hydras, and jellyfish, offers unique insight into the development and evolution of morphological complexity.  In my talk, I will introduce our research on “ethology of morphogenesis,” a novel concept that links the behavior of organisms to the development of their size and shape at both cellular and biophysical levels, opening new perspectives about the design principle of soft-bodied animals. In addition, I will discuss a fascinating feature of cnidarian biology. For humans, our genetic code determines that we will grow two arms and two legs. The same fate is true for all mammals. Similarly, the number of fins of a fish or legs and wings of an insect is embedded in their genetic code. I will describe how sea anemones defy this rule.

Anniek Stokkermans, Aditi Chakrabarti, Ling Wang, Prachiti Moghe, Kaushikaram Subramanian, Petrus Steenbergen, Gregor Mönke, Takashi Hiiragi, Robert Prevedel, L. Mahadevan, and Aissam Ikmi. Ethology of morphogenesis reveals the design principles of cnidarian size and shape development. bioRxiv 2021.08.19.456976

Ikmi A, Steenbergen P, Anzo M, McMullen M, Stokkermans M, Ellington L, and Gibson M (2020). Feeding-dependent tentacle development in the sea anemone Nematostella vectensisNature communications, Sept 02; 11:4399

He S, Del Viso F, Chen C, Ikmi A, Kroesen A, Gibson MC (2018). An axial Hox code controls tissue segmentation and body patterning in Nematostella vectensisScience, Vol. 361, Issue 6409, pp. 1377-1380.
Ikmi A, McKinney SA, Delventhal KM, Gibson MC (2014). TALEN and CRISPR/Cas9 mediated genome editing in the early-branching metazoan Nematostella vectensisNature communications. Nov 24; 5:5486.

11/11/21 Nikta Fakhri, MIT Title: Nonreciprocal matter: living chiral crystals

Abstract: Active crystals are highly ordered structures that emerge from the nonequilibrium self-organization of motile objects, and have been widely studied in synthetic and bacterial active matter. In this talk, I will describe how swimming sea star embryos spontaneously assemble into chiral crystals that span thousands of spinning organisms and persist for tens of hours. Combining experiment, hydrodynamic theory, and simulations, we demonstrate that the formation, dynamics, and dissolution of these living crystals are controlled by the natural development of the embryos. Remarkably, due to nonreciprocal force and torque exchange between the embryos, the living chiral crystals exhibit self-sustained oscillations with dynamic signatures recently predicted to emerge in materials with odd elasticity.

12/2/21 Luca Giomi, Leiden University Title: Hydrodynamics and multi-scale order in confluent epithelia

Abstract: In this talk I will review our ongoing theoretical and experimental efforts toward deciphering the hydrodynamic behavior of confluent epithelia. The ability of epithelial cells to collectively flow lies at the heart of a myriad of processes that are instrumental for life, such as embryonic morphogenesis and wound healing, but also of life-threatening conditions, such as metastatic cancer. Understanding the physical origin of these mechanisms requires going beyond the current hydrodynamic theories of complex fluids and introducing a new theoretical framework, able to account for biomechanical activity as well as for scale-dependent liquid crystalline order.