Session A43: Biological Fluid Dynamics

Invited Talk: Agnese SeminaraPhysics-informed reinforcement learning for animal navigation: strategies to navigate turbulence

I will introduce turbulent navigation by discussing a set of behavioral experiments with sea robins, fishes with sensory appendages akin to legs that they use to dig prey from sand. Data suggest these animals sense chemicals both from the water column as well as on sand, an "alternating" behavior well documented in rodents and dogs, suggesting that animals integrate both fluid-borne and substrate cues into a multi-modal navigation strategy. I will then discuss an algorithm showing animals may alternate tasting surfaces and smelling fluids to improve search efficiency. Far from the target, the searcher is most likely to rely on bulk odors as the search is information limited. Agents explore cross wind to search for odor and then surge upwind when cast and surge provide the same benefits, a decision boundary that can be understood theoretically. In this model, agents guess where the source is and use odor to refine their guess -- but can animals respond solely to odor, without relying on a map of space? I will propose a second algorithm for turbulent navigation, where agents use temporal memory to measure salient features of odor time series. I will show that using the physics of odor cues, memory can be adjusted based on experience with no need of prior information. I will then discuss how agents can recognize and correct mistakes based on odor alone, suggesting accurate predictions can overcome intermittency, and enable navigation in the presence of turbulence.   

Invited Talk: Getting in shape—unraveling the morphodynamics of microbial collectives

In nature, microorganisms often collectively self-organize into spatially structured communities, with distinct groups of cells occupying distinct spatial domains. This spatial structure plays a pivotal role in influencing diverse biological functions, such as community growth, stability, resilience, and diversity; and yet, how exactly spatial structure emerges in a multicellular microbial community remains poorly understood. In this talk, I will describe my group's use of both experiments and theory to address this gap in knowledge. First, I will describe our studies of proliferating bacteria, in which the competition by different cells for space and resources shapes the structure of the different domains they inhabit. Next, I will describe our studies of motile bacteria, in which the coupling between cellular motility, metabolism, and nutrient transport gives rise to the formation of dense, immotile phases that coexist with less dense, highly motile phases in a manner reminiscent of Motility-Induced Phase Separation (MIPS). Finally, I will describe our studies of how the phenomenology of MIPS itself is dramatically altered by directed motion along chemical gradients as well as by non-reciprocal predator-prey interactions, two features of many natural microbial communities. Taken altogether, our work helps to provide a biophysical basis for understanding the morphodynamics of microbial communities, as well as other forms of active matter, in complex environments.   

Flow-driven biofilm assembly and dynamics in fluids

Biofilms are aggregates of microorganisms in which cells are embedded in a self-secreted matrix of polymeric substances, which protects the microbial community from chemical and mechanical insults, thus favoring its survival and evolutionary success. As a result, biofilms have a crucial impact in environmental, industrial, and medical settings. Despite this, a mechanistic understanding of how the fluid environment shapes properties is lacking.

We investigate how fluid dynamics conditions drive biofilm assembly and the emergence of distinctive morphological and mechanical properties. Flow can influence several stages of biofilm formation, starting from surface colonization. On curved surfaces, flow can promote the formation of colonization hotspots, which lately impact biofilm formation. Surface geometry, flow shear, fluid rheology, and bacterial phenotype are the parameters controlling surface colonization. During biofilm maturation, the interplay between biological functions and flow controls biofilm morphology and rheology, ultimately affecting biofilms' physiological protective function. By shedding light on this interplay, we can control biofilm development, showing the prominent role that physics can play in developing novel antifouling strategies.        

Invited Talk: Squeeze confinement-induced changes in flow fields of ciliated marine larvae

Ciliated marine invertebrate larvae swim and feed in a viscous low Reynolds number (< 1) environment in the ocean. Larvae swim in three-dimensions (3D) using ciliary beating, resulting in complex flow fields that are challenging to quantify in experimental studies. The conventional microscopic imaging configuration of trapping larvae in between a glass slide and cover slip induces a quasi-two-dimensional (2D) confinement. We systematically quantify the fluid dynamical effects of 2D squeeze-confinement on flows generated by ciliated larvae at low Reynolds numbers (< 1). We explore both spherical and non-spherical larval morphologies in our study. Spherical morphologies include coral larvae and non-spherical morphologies include sea star and sea urchin larvae. We vary the confinement parameter – the gap between the glass slide and cover slip (h) – and observe changes in the number of vortices, vortex size, and intensity. Across both morphologies, increasing confinement (smaller h) increases the number of vortices that form and decreasing confinement (larger h) gives rise to a pair of counter rotating vortices. We compare our experimental results with low Reynolds number theoretical predictions and find a very good agreement. Our results are broadly applicable for quantification of the fluid dynamical effects of 2D squeeze confinement for ciliated larvae with a variety of morphologies.   

Collective functionalities emerging in active matter

Organisms often cooperate to achieve functionalities that they cannot accomplish alone. However, this puzzle of how biological self-organization emerges from the collective dynamics of individual constituents remains unsolved. In this talk, I will discuss some of these collective functionalities, including non-reciprocal communication, coordinated navigation, and cooperative nutrient transport. First, we focus on ultra-fast communication through "hydrodynamic trigger waves", signals between cells that propagate hundreds of times faster than their swimming speed [1]. Second, we will explore how bacteria can reorient against flows and contaminate reservoirs upstream [2]. Third, we consider how bacteria generate their own flows to transport nutrients [3], and how "active carpets" like biofilms can lead to enhanced non-equilibrium diffusion [4]. Together, these ideas help us understand emergent self-organization in biological systems, but they also teach us about the design space of active and adaptive materials.