Publications

Changes in the geometry and topology of self-assembled membranes underlie diverse processes across cellular biology and engineering. Similar to lipid bilayers, monolayer colloidal membranes have in-plane fluid-like dynamics and out-of-plane bending elasticity. Their open edges and micron length scale provide a tractable system to study the equilibrium energetics and dynamic pathways of membrane assembly and reconfiguration. Here, we find that doping colloidal membranes with short miscible rods transforms disk-shaped membranes into saddle-shaped surfaces with complex edge structures. The saddle-shaped membranes are well-approximated by Enneper's minimal surfaces. Theoretical modeling demonstrates that their formation is driven by increasing positive Gaussian modulus, which in turn is controlled by the fraction of short rods. Further coalescence of saddle-shaped surfaces leads to diverse topologically distinct structures, including catenoids, tri-noids, four-noids, and higher order structures. At long time scales, we observe the formation of a system-spanning, sponge-like phase. The unique features of colloidal membranes reveal the topological transformations that accompany coalescence pathways in real time. We enhance the functionality of these membranes by making their shape responsive to external stimuli. Our results demonstrate a novel pathway towards control of thin elastic sheets' shape and topology -- a pathway driven by the emergent elasticity induced by compositional heterogeneity.

We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a thermodynamically consistent, quasi-equilibrium approximation of the particle distribution function, the model closely captures important analytical properties of the kinetic theory, including its linear stability and the balance of entropy production and dissipation. Nonlinear simulations show the model reproduces the qualitative behavior and nonequilibrium statistics of the kinetic theory, unlike commonly used closure models. We use the closure model to simulate highly turbulent suspensions in both two and three dimensions in which we observe complex multiscale dynamics, including large concentration fluctuations and a proliferation of polar and nematic defects.

Despite their importance in tissue homeostasis and renewal, human pituitary stem cells (PSCs) are incompletely characterized. We describe a human single nucleus RNA-seq and ATAC-seq resource from pediatric, adult, and aged postmortem pituitaries (snpituitaryatlas.princeton.edu) and characterize cell-type-specific gene expression and chromatin accessibility programs for all major pituitary cell lineages. We identify uncommitted PSCs, committing progenitor cells, and sex differences. Pseudotime trajectory analysis indicates that early-life PSCs are distinct from the other age groups. Linear modeling of same-cell multiome data identifies regulatory domain accessibility sites and transcription factors that are significantly associated with gene expression in PSCs compared with other cell types and within PSCs. We identify distinct deterministic mechanisms that contribute to heterogeneous marker expression within PSCs. These findings characterize human stem cell lineages and reveal diverse mechanisms regulating key PSC genes and cell type identity.

A single flexible filament can be actuated to escape from the scallop theorem and generate net propulsion at low Reynolds number. In this work, we study the dynamics of a simple boundary-driven multi-filament swimmer, a two-arm clamshell actuated at the hinged point, using a nonlocal slender body approximation with full hydrodynamic interactions. We first consider an elastic clamshell consisted of flexible filaments with intrinsic curvature, and then build segmental models consisted of rigid segments connected by different mechanical joints with different forms of response torques. The simplicity of the system allows us to fully explore the effect of various parameters on the swimming performance. Optimal included angles and elastoviscous numbers are identified. The segmental models capture the characteristic dynamics of the elastic clamshell. We further demonstrate how the swimming performance can be significantly enhanced by the asymmetric beating patterns induced by biased torques.

It has long been known that FGF signaling contributes to mesoderm formation, a germ layer found in triploblasts that is composed of highly migratory cells that give rise to muscles and to the skeletal structures of vertebrates. FGF signaling activates several pathways in the developing mesoderm, including transient activation of the Erk pathway, which triggers mesodermal fate specification through the induction of the gene brachyury and activates morphogenetic programs that allow mesodermal cells to position themselves in the embryo. In this review, we discuss what is known about the generation and interpretation of transient Erk signaling in mesodermal tissues across species. We focus specifically on mechanisms that translate the level and duration of Erk signaling into cell fate and cell movement instructions and discuss strategies for further interrogating the role that Erk signaling dynamics play in mesodermal gastrulation and morphogenesis.

Cytoskeletal networks are the main actuators of cellular mechanics, and a foundational example for active matter physics. In cytoskeletal networks, motion is generated on small scales by filaments that push and pull on each other via molecular-scale motors. These local actuations give rise to large-scale stresses and motion. To understand how microscopic processes can give rise to self-organized behavior on larger scales it is important to consider what mechanisms mediate long-ranged mechanical interactions in the systems. Two scenarios have been considered in the recent literature. The first scenario is systems that are relatively sparse, in which most of the large-scale momentum transfer is mediated by the solvent in which cytoskeletal filaments are suspended. The second scenario is systems in which filaments are coupled via cross-link molecules throughout. Here, we review the differences and commonalities between the physics of these two regimes. We also survey the literature for the numbers that allow us to place a material within either of these two classes.

Autism is a highly heritable neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in autism, with dozens of cross-sectional microbiome and other omic studies revealing autism-specific profiles along the GBA albeit with little agreement in composition or magnitude. To explore the functional architecture of autism, we developed an age and sex-matched Bayesian differential ranking algorithm that identified autism-specific profiles across 10 cross-sectional microbiome datasets and 15 other omic datasets, including dietary patterns, metabolomics, cytokine profiles, and human brain expression profiles. The analysis uncovered a highly significant, functional architecture along the GBA that encapsulated the overall heterogeneity of autism phenotypes. This architecture was determined by autism-specific amino acid, carbohydrate and lipid metabolism profiles predominantly encoded by microbial species in the genera Prevotella, Enterococcus, Bifidobacterium, and Desulfovibrio, and was mirrored in brain-associated gene expression profiles and restrictive dietary patterns in individuals with autism. Pro-inflammatory cytokine profiling and virome association analysis further supported the existence of an autism-specific architecture associated with particular microbial genera. Re-analysis of a longitudinal intervention study in autism recapitulated the cross-sectional profiles, and showed a strong association between temporal changes in microbiome composition and autism symptoms. Further elucidation of the functional architecture of autism, including of the role the microbiome plays in it, will require deep, multi-omic longitudinal intervention studies on well-defined stratified cohorts to support causal and mechanistic inference.

The large-scale organization of the genome inside the cell nucleus is critical for the cell’s function. Chromatin – the functional form of DNA in cells – serves as a substrate for active nuclear processes such as transcription, replication and DNA repair. Chromatin’s spatial organization directly affects its accessibility by ATP-powered enzymes, e.g., RNA polymerase II in the case of transcription. In differentiated cells, chromatin is spatially segregated into compartments – euchromatin and heterochromatin – the former being largely transcriptionally active and loosely packed, the latter containing mostly silent genes and densely compacted. The euchromatin/heterochromatin segregation is crucial for proper genomic function, yet the physical principles behind it are far from understood. Here, we model the nucleus as filled with hydrodynamically interacting active Zimm chains – chromosomes – and investigate how large heterochromatic regions form and segregate from euchromatin through their complex interactions. Each chromosome presents a block copolymer composed of heterochromatic blocks, capable of crosslinking that increases chromatin’s local compaction, and euchromatic blocks, subjected to stochastic force dipoles that capture the microscopic stresses exerted by nuclear ATPases. These active stresses lead to a dynamic self-organization of the genome, with its coherent motions driving the mixing of chromosome territories as well as large-scale heterochromatic segregation through crosslinking of distant genomic regions. We study the stresses and flows that arise in the nucleus during the heterochromatic segregation, and identify their signatures in Hi-C proximity maps. Our results reveal the fundamental role of active mechanical processes and hydrodynamic interactions in the kinetics of chromatin compartmentalization and in the emergent large-scale organization of the nucleus.

We characterize and remedy a failure mode that may arise from multi-scale dynamics with scale imbalances during training of deep neural networks, such as physics informed neural networks (PINNs). PINNs are popular machine-learning templates that allow for seamless integration of physical equation models with data. Their training amounts to solving an optimization problem over a weighted sum of data-fidelity and equation-fidelity objectives. Conflicts between objectives can arise from scale imbalances, heteroscedasticity in the data, stiffness of the physical equation, or from catastrophic interference during sequential training. We explain the training pathology arising from this and propose a simple yet effective inverse Dirichlet weighting strategy to alleviate the issue. We compare with Sobolev training of neural networks, providing the baseline of analytically ε-optimal training. We demonstrate the effectiveness of inverse Dirichlet weighting in various applications, including a multi-scale model of active turbulence, where we show orders of magnitude improvement in accuracy and convergence over conventional PINN training. For inverse modeling using sequential training, we find that inverse Dirichlet weighting protects a PINN against catastrophic forgetting.

The mammalian mitotic spindle segregates an equal number of chromosomes to daughter cells. Over the course of spindle assembly, many initially erroneous attachments between kinetochores and microtubules are fixed through a process called error correction. Despite the importance of chromosome segregation errors in many human health conditions, we lack quantitative methods to characterize the dynamic error correction process and how it is impaired in disease states. We have developed a novel experimental method and analysis framework to quantify chromosome segregation error correction in human tissue culture cells with live cell confocal imaging of spindle assembly, timed premature chromosome separation, and automated counting of kinetochores after cell division. Using our assay we targeted Aurora B kinase, a key regulator of kinetochore-microtubule attachments, with two small molecules that either inhibited Aurora B activity or perturbed its localization. While both inhibitors increased the steady state error baseline over 10-fold from control, they differed in their initial error states and times to reach steady state. Our results indicate that error correction dynamics, and not just endpoint segregation errors, are important for understanding the involvement of proteins in error correction. Future work will focus on distinguishing the functional roles of different proteins in error correction, characterizing how kinetochore-microtubule affinity and microtubule stability determine error correction dynamics, and constructing and testing a mathematical theory of error correction.