During the 2022–23 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 1:00 pm – 2:00 pm (Boston time). The meetings will take place in Room G10 at the CMSA, 20 Garden Street, Cambridge MA 02138, and some meetings will take place virtually on Zoom or be held in hybrid formats. To learn how to attend, please fill out this form, or contact Farzan Vafa (fvafa@cmsa.fas.harvard.edu). The schedule will be updated as talks are confirmed.

CMSA COVID-19 Policies



  • November 17, 2022 01:00 PM
Speaker: Max Prigozhin
Title: Dynamic and multicolor electron microscopy
Venue: CMSA Room G10

Active Matter Seminar Speaker: Max Prigozhin (Harvard) Title: Dynamic and multicolor electron microscopy Abstract: My lab is developing biophysical methods to achieve multicolor and dynamic biological imaging at the molecular scale. Our approach to capturing the dynamics of cellular processes involves cryo-vitrifying samples after known time delays following stimulation using custom cryo- plunging and high-pressure freezing instruments. To achieve multicolor electron imaging, we are exploring the property of cathodoluminescence—optical emission induced by the electron beam. We are developing nanoprobes (“cathodophores”) that will be used as luminescent protein tags in electron microscopy. We are applying these new methods to study G-protein- coupled receptor signaling and to visualize the formation of biomolecular condensates.

  • November 03, 2022 01:00 PM
Speaker: Siavash Monfared
Title: Force transmission informs the collective behavior of active cell layers
Venue: CMSA Room G10

Active Matter Seminar Speaker: Siavash Monfared, Niels Bohr Institute, Copenhagen Title: Force transmission informs the collective behavior of active cell layers Abstract: Collective cell migration drives numerous physiological processes such as tissue morphogenesis, wound healing, tumor progression and cancer invasion. However, how the interplay of mechanical interactions and the modes of collective self-organization among cells informs such processes is yet to be established. In this talk, I will focus on the role of three-dimensional force transmission, from a theoretical and computational perspective, on two phenomena: (1) cell extrusion from a cellular monolayer and (2) density-independent solid-like to fluid-like transition of active cell layers. For the first topic, I will focus on how increasing cell-cell adhesion relative to cell-substrate adhesion…

  • October 20, 2022 12:00 PM
Speaker: Sharad Ramanathan
Title: Attempts at understanding human axial elongation and patterning
Venue: CMSA Room G10

Active Matter Seminar Speaker: Sharad Ramanathan, Harvard Title: Attempts at understanding human axial elongation and patterning Abstract: Some of the most dramatic events during human development is the axial elongation of the embryo with concomitant changes in the geometry and composition of the underlying tissues. The posterior part of the embryo gives rise to the spinal cord, vertebral column, ribcage, back muscles, and dermis.  In this talk, I will present our attempts at coaxing human embryonic stem cells to form these structures of the early human embryo that closely recapitulate the geometry, relative arrangements, composition, and dynamics of development of the early spinal cord flanked progenitors of the musculoskeletal system. Our goal was to do so, such that we could…

  • September 21, 2022 11:00 AM
Speaker: Shenshen Wang
Title: Limit and potential of adaptive immunity
Venue: CMSA Room G10

Active Matter Seminar Speaker: Shenshen Wang, UCLA Title:  Limit and potential of adaptive immunity Abstract: The adaptive immune system is able to learn from past experiences to better fit an unforeseen future. This is made possible by a diverse and dynamic repertoire of cells expressing unique antigen receptors and capable of rapid Darwinian evolution within an individual. However, naturally occurring immune responses exhibit limits in efficacy, speed and capacity to adapt to novel challenges. In this talk, I will discuss theoretical frameworks we developed to (1) explore functional impacts of non-equilibrium antigen recognition, and (2) identify conditions under which natural selection acting local in time can find adaptable solutions favorable in the long run, through exploiting environmental variations and functional constraints.

  • September 06, 2022 01:00 PM
Speaker: Josef Käs
Title: State Diagram of Cancer Cell Unjamming Predicts Metastatic Risk
Venue: CMSA, 20 Garden St, G10

Speaker: Josef Käs, Leipzig University Title: State Diagram of Cancer Cell Unjamming Predicts Metastatic Risk Abstract: Distant metastasis is probably the most lethal hallmark of cancer. Due to a lack of suitable markers, cancer cell motility only has a negligible impact on current diagnosis. Based on cell unjamming we derive a cell motility marker for static histological images. This enables us to sample huge numbers of breast cancer patient data to derive a comprehensive state diagram of unjamming as a collective transition in cell clusters of solid tumors. As recently discovered, cell unjamming transitions occur in embryonic development and as pathological changes in diseases such as cancer. No consensus has been achieved on the variables and the parameter…

  • April 28, 2022 01:00 PM
Speaker: Guillaume Duclos
Title: Building active nematic and active polar liquids out of biological machines
Venue: Lyman 425

Speaker: 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…

  • April 07, 2022 01:00 PM
Speaker: Ben Simons
Title: Theories of branching morphogenesis
Venue: Virtual

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…

  • March 24, 2022 01:00 PM
Speaker: Katherine Copenhagen
Title: Topological defects drive layer formation in gliding bacteria colonies
Venue: Virtual

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…

  • February 24, 2022 01:00 PM
Speaker: Amin Doostmohammadi
Title: Taming Active Matter: from ordered topological defects to autonomous shells
Venue: Virtual

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…

  • February 10, 2022 01:00 PM
Speaker: Margaret Gardel
Title: Active Matter Controlling Epithelial Dynamics
Venue: Virtual

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…

  • January 27, 2022 01:00 PM
Speaker: Petros Koumoutsakos
Title: Learning to School in the presence of hydrodynamic interactions
Venue: Virtual

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…

  • September 30, 2021 01:00 PM
Speaker: Daniel Needleman, Harvard
Title: Cytoskeletal Energetics and Energy Metabolism
Venue: Virtual

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…

  • December 02, 2021 01:15 PM
Speaker: Luca Giomi, Leiden University
Title: Hydrodynamics and multi-scale order in confluent epithelia
Venue: Virtual

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.

  • November 11, 2021 01:00 PM
Speaker: Nikta Fakhri, MIT
Title: Nonreciprocal matter: living chiral crystals
Venue: Virtual

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.

  • October 28, 2021 01:00 PM
Speaker: Luca Giomi, Leiden University
Title: Drivers of Morphological Complexity
Venue: Virtual

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…

  • October 14, 2021 01:00 PM
Speaker: Wai-Tong (Louis) Fan, Indiana University
Title: Stochastic PDE as scaling limits of interacting particle systems
Venue: Virtual

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…

  • September 23, 2021 01:00 PM
Speaker: Krishna Shrinivas, Harvard
Title: The many phases of a cell
Venue: Virtual

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…

  • September 02, 2021 01:00 PM
Speaker: Andreas Bausch, Technical University of Munich
Title: Eppur si muovono: rotations in active matter
Venue: Virtual

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.