Publications

Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak–Keller–Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.

This paper continues the analysis of the scattering problem for a network of open wave-guides started in [arXiv:2302.04353, arXiv:2310.05816]. In this part we present explicit, physically motivated radiation conditions that ensure uniqueness of the solution to the scattering problem. These conditions stem from a 2000 paper of A. Vasy on 3-body Schrodinger operators; we discuss closely related conditions from a 1994 paper of H. Isozaki. Vasy's paper also proves the existence of the limiting absorption resolvents, and that the limiting solutions satisfy the radiation conditions. The statements of these results require a calculus of pseudodifferential operators, called the 3-body scattering calculus, which is briefly introduced here. We show that the solutions to the model problem obtained in arXiv:2302.04353 satisfy these radiation conditions, which makes it possible to prove uniqueness, and therefore existence, for the system of Fredholm integral equations introduced in that paper.

In recent years, growth in our understanding of the computations performed in both biological and artificial neural networks has largely been driven by either low-level mechanistic studies or global normative approaches. However, concrete methodologies for bridging the gap between these levels of abstraction remain elusive. In this work, we investigate the internal mechanisms of neural networks through the lens of neural population geometry, aiming to provide understanding at an intermediate level of abstraction, as a way to bridge that gap. Utilizing manifold capacity theory (MCT) from statistical physics and manifold alignment analysis (MAA) from high-dimensional statistics, we probe the underlying organization of task-dependent manifolds in deep neural networks and neural recordings from the macaque visual cortex. Specifically, we quantitatively characterize how different learning objectives lead to differences in the organizational strategies of these models and demonstrate how these geometric analyses are connected to the decodability of task-relevant information. Furthermore, these metrics show that macaque visual cortex data are more similar to unsupervised DNNs in terms of geometrical properties such as manifold position and manifold alignment. These analyses present a strong direction for bridging mechanistic and normative theories in neural networks through neural population geometry, potentially opening up many future research avenues in both machine learning and neuroscience.

Collective behaviors require coordination of individuals. Thus, a population must adjust its phenotypic distribution to adapt to changing environments. How can a population regulate its phenotypic distribution? One strategy is to utilize specialized networks for gene regulation and maintaining distinct phenotypic subsets. Another involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse across diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. Surprisingly, we found that during collective migration, the distributions of swimming phenotypes adapt to the environment without mutations or gene regulation. Instead, adaptation is caused by the dynamic and reversible enrichment of high-performing swimming phenotypes within each environment. This adaptation mechanism is supported by a recent theoretical study, which proposed that the phenotypic composition of a migrating population results from a balance between cell growth generating diversity and collective migration eliminating the phenotypes that are unable to keep up with the migrating group. Furthermore, by examining chemoreceptor abundance distributions during migration towards different attractants, we found that this mechanism acts on multiple chemotaxis-related traits simultaneously. Our findings reveal that collective migration itself can enable cell populations with continuous, multi-dimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.

Few techniques are available for studying the nature of forces that drive subcellular dynamics. Here we develop two complementary ones. The first is femtosecond stereotactic laser ablation, which rapidly creates complex cuts of subcellular structures and enables precise dissection of when, where and in what direction forces are generated. The second is an assessment of subcellular fluid flows by comparison of direct flow measurements using microinjected fluorescent nanodiamonds with large-scale fluid-structure simulations of different force transduction models. We apply these techniques to study spindle and centrosome positioning in early Caenorhabditis elegans embryos and to probe the contributions of microtubule pushing, cytoplasmic pulling and cortical pulling upon centrosomal microtubules. Based on our results, we construct a biophysical model to explain the dynamics of centrosomes. We demonstrate that cortical pulling forces provide a general explanation for many behaviours mediated by centrosomes, including pronuclear migration and centration, rotation, metaphase spindle positioning, asymmetric spindle elongation and spindle oscillations. This work establishes methodologies for disentangling the forces responsible for cell biological phenomena.

We propose a practical finite volume method on cut cells using state redistribution. Our algorithm is provably monotone, total variation diminishing, and GKS (Gustafsson, Kreiss, Sundström) stable in many situations, and shuts off continuously as the cut cell size approaches a target value. Our analysis reveals why original state redistribution works so well: it results in a monotone scheme for most configurations, though at times subject to a slightly smaller CFL condition. Our analysis also explains why a premerging step is beneficial. We show computational experiments in two and three dimensions.

The high efficiency of a recently proposed method for computing with Gaussian processes relies on expanding a (translationally invariant) covariance kernel into complex exponentials, with frequencies lying on a Cartesian equispaced grid. Here we provide rigorous error bounds for this approximation for two popular kernels—Matérn and squared exponential—in terms of the grid spacing and size. The kernel error bounds are uniform over a hypercube centered at the origin. Our tools include a split into aliasing and truncation errors, and bounds on sums of Gaussians or modified Bessel functions over various lattices. For the Matérn case, motivated by numerical study, we conjecture a stronger Frobenius-norm bound on the covariance matrix error for randomly-distributed data points. Lastly, we prove bounds on, and study numerically, the ill-conditioning of the linear systems arising in such regression problems.

We numerically investigate the hydrodynamics and membrane dynamics of a multicomponent vesicle in two strongly confined geometries. This serves as a simplified model for red blood cells undergoing large deformations while traversing narrow constrictions. We propose a new parameterization for the bending modulus that remains positive for all lipid phase parameter values. For a multicomponent vesicle passing through a stenosis, we establish connections between various properties: lipid phase coarsening, size and flow profile of the lubrication layers, excess pressure, and the tank-treading velocity of the membrane. For a multicomponent vesicle passing through a contracting channel, we find that the lipid always phase separates so that the vesicle is stiffer in the front as it passes through the constriction. For both cases of confinement we find that lipid coarsening is arrested under strong confinement, and resumes at a high rate upon relief from extreme confinement. The results may be useful for efficient sorting lipid domains using microfluidic flows by controlled release of vesicles passing through strong confinement.

Substantial efforts have exploited reinforcement learning (RL) in the development of micro-robotic locomotion. These RL-powered micro-robots are capable of learning a locomotory policy based on their experience interacting with the surroundings, without requiring prior knowledge on the physics of locomotion in that environment. However, in their applications, micro-robots often encounter changes in the environment and need to adapt their locomotory gaits like living organisms in order to achieve robust locomotion performance. In standard RL methods, such a non-stationary environment can cause the micro-robots to continuously relearn the policy from scratch, degrading their locomotion performance. In this work, we explore a first use of a recently developed context detection method combined with deep RL to facilitate micro-robotic locomotion in a dynamically changing environment. As a proof-of-principle, we consider a simple micro-robot immersed in non-stationary environments switching between a viscous fluid environment and a dry frictional environment. We show that the RL with context detection approach enables the micro-robot to effectively detect changes in the environment and deploy specialized locomotory gaits for different environments accordingly to achieve significantly improved locomotion. Our results suggest the integration of deep RL with context detection as a potential tool for robust micro-robotic locomotion across different environments.

We introduce an electron-photon exchange-correlation functional for quantum electrodynamical density-functional theory (QEDFT). The approach, photon MBD (pMBD), is inspired by the many-body dispersion (MBD) method for weak intermolecular interactions, which is generalized to include both electronic and photonic (electromagnetic) degrees of freedom on the same footing. We demonstrate that pMBD accurately captures effects that arise in the context of strong light-matter interactions, such as anisotropic electron-photon interactions, beyond single-photon effects, and cavity modulated van der Waals interactions. Moreover, we show that pMBD is computationally efficient and allows simulations of large complex systems coupled to optical cavities.