Design rules for controlling active topological defects.

Topological defects play a central role in the physics of many materials, including magnets, superconductors, and liquid crystals. In active fluids, defects become autonomous particles that spontaneously propel from internal active stresses and drive chaotic flows stirring the fluid. The intimate connection between defect textures and active flow suggests that properties of active materials can be engineered by controlling defects, but design principles for their spatiotemporal control remain elusive. Here, we propose a symmetry-based additive strategy for using elementary activity patterns, as active topological tweezers, to create, move, and braid such defects. By combining theory and simulations, we demonstrate how, at the collective level, spatial activity gradients act like electric fields which, when strong enough, induce an inverted topological polarization of defects, akin to a negative susceptibility dielectric. We harness this feature in a dynamic setting to collectively pattern and transport interacting active defects. Our work establishes an additive framework to sculpt flows and manipulate active defects in both space and time, paving the way to design programmable active and living materials for transport, memory, and logic.

Pathogenic variants in autism gene KATNAL2 cause hydrocephalus and disrupt neuronal connectivity by impairing ciliary microtubule dynamics.

Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (cerebral ventriculomegaly), the cardinal feature of congenital hydrocephalus (CH), is increasingly recognized among patients with autism spectrum disorders (ASD). KATNAL2, a member of Katanin family microtubule-severing ATPases, is a known ASD risk gene, but its roles in human brain development remain unclear. Here, we show that nonsense truncation of Katnal2 (Katnal2Δ17) in mice results in classic ciliopathy phenotypes, including impaired spermatogenesis and cerebral ventriculomegaly. In both humans and mice, KATNAL2 is highly expressed in ciliated radial glia of the fetal ventricular-subventricular zone as well as in their postnatal ependymal and neuronal progeny. The ventriculomegaly observed in Katnal2Δ17 mice is associated with disrupted primary cilia and ependymal planar cell polarity that results in impaired cilia-generated CSF flow. Further, prefrontal pyramidal neurons in ventriculomegalic Katnal2Δ17 mice exhibit decreased excitatory drive and reduced high-frequency firing. Consistent with these findings in mice, we identified rare, damaging heterozygous germline variants in KATNAL2 in five unrelated patients with neurosurgically treated CH and comorbid ASD or other neurodevelopmental disorders. Mice engineered with the orthologous ASD-associated KATNAL2 F244L missense variant recapitulated the ventriculomegaly found in human patients. Together, these data suggest KATNAL2 pathogenic variants alter intraventricular CSF homeostasis and parenchymal neuronal connectivity by disrupting microtubule dynamics in fetal radial glia and their postnatal ependymal and neuronal descendants. The results identify a molecular mechanism underlying the development of ventriculomegaly in a genetic subset of patients with ASD and may explain persistence of neurodevelopmental phenotypes in some patients with CH despite neurosurgical CSF shunting.

Harnessing elastic instabilities for enhanced mixing and reaction kinetics in porous media.

Turbulent flows have been used for millennia to mix solutes; a familiar example is stirring cream into coffee. However, many energy, environmental, and industrial processes rely on the mixing of solutes in porous media where confinement suppresses inertial turbulence. As a result, mixing is drastically hindered, requiring fluid to permeate long distances for appreciable mixing and introducing additional steps to drive mixing that can be expensive and environmentally harmful. Here, we demonstrate that this limitation can be overcome just by adding dilute amounts of flexible polymers to the fluid. Flow-driven stretching of the polymers generates an elastic instability, driving turbulent-like chaotic flow fluctuations, despite the pore-scale confinement that prohibits typical inertial turbulence. Using in situ imaging, we show that these fluctuations stretch and fold the fluid within the pores along thin layers ("lamellae") characterized by sharp solute concentration gradients, driving mixing by diffusion in the pores. This process results in a [Formula: see text] reduction in the required mixing length, a [Formula: see text] increase in solute transverse dispersivity, and can be harnessed to increase the rate at which chemical compounds react by [Formula: see text]-enhancements that we rationalize using turbulence-inspired modeling of the underlying transport processes. Our work thereby establishes a simple, robust, versatile, and predictive way to mix solutes in porous media, with potential applications ranging from large-scale chemical production to environmental remediation.

Densitaxis: Active particle motion in density gradients.

Organisms often swim through density-stratified fluids. Here, we investigate the dynamics of active particles swimming in fluid density gradients and report theoretical evidence of taxis as a result of these gradients (densitaxis). Specifically, we calculate the effect of density stratification on the dynamics of a force- and torque-free spherical squirmer and show that density gradients induce reorientation that tends to align swimming either parallel or normal to the gradient depending on the swimming gait. In particular, swimmers that propel by generating thrust in the front (pullers) rotate to swim parallel to gradients and hence display (positive or negative) densitaxis, while swimmers that propel by generating thrust in the back (pushers) rotate to swim normal to the gradients. This work could be useful to understand the motion of marine organisms in ocean or be leveraged to sort or organize a suspension of active particles by modulating density gradients.

Asymmetric fluid flow in helical pipes inspired by shark intestines.

Unlike human intestines, which are long, hollow tubes, the intestines of sharks and rays contain interior helical structures surrounding a cylindrical hole. One function of these structures may be to create asymmetric flow, favoring passage of fluid down the digestive tract, from anterior to posterior. Here, we design and 3D print biomimetic models of shark intestines, in both rigid and deformable materials. We use the rigid models to test which physical parameters of the interior helices (the pitch, the hole radius, the tilt angle, and the number of turns) yield the largest flow asymmetries. These asymmetries exceed those of traditional Tesla valves, structures specifically designed to create flow asymmetry without any moving parts. When we print the biomimetic models in elastomeric materials so that flow can couple to the structure's shape, flow asymmetry is significantly amplified; it is sevenfold larger in deformable structures than in rigid structures. Last, we 3D-print deformable versions of the intestine of a dogfish shark, based on a tomogram of a biological sample. This biomimic produces flow asymmetry comparable to traditional Tesla valves. The ability to influence the direction of a flow through a structure has applications in biological tissues and artificial devices across many scales, from large industrial pipelines to small microfluidic devices.

Designing turbulence with entangled vortices.

Matter entanglement is a common chaotic structure found in both quantum and classical systems. For classical turbulence, viscous vortices are like sinews in fluid flows, storing and dissipating energy and accommodating strain and stress throughout a complex vortex network. However, to explain how the statistical properties of turbulence arise from elemental vortical structures remains challenging. Here, we use the quantum vortex tangle as a skeleton to generate an instantaneous classical turbulent field with intertwined vortex tubes. Combining the quantum skeleton and tunable vortex thickness makes the synthetic turbulence satisfy key statistical laws, offering valuable insights for elucidating energy cascade and extreme events. By manipulating the elemental structures, we customize turbulence with desired statistical features. This bottom-up approach of designing turbulence provides a testbed for analyzing and modeling turbulence.

Forecasting small-scale dynamics of fluid turbulence using deep neural networks.

Turbulence in fluid flows is characterized by a wide range of interacting scales. Since the scale range increases as some power of the flow Reynolds number, a faithful simulation of the entire scale range is prohibitively expensive at high Reynolds numbers. The most expensive aspect concerns the small-scale motions; thus, major emphasis is placed on understanding and modeling them, taking advantage of their putative universality. In this work, using physics-informed deep learning methods, we present a modeling framework to capture and predict the small-scale dynamics of turbulence, via the velocity gradient tensor. The model is based on obtaining functional closures for the pressure Hessian and viscous Laplacian contributions as functions of velocity gradient tensor. This task is accomplished using deep neural networks that are consistent with physical constraints and explicitly incorporate Reynolds number dependence to account for small-scale intermittency. We then utilize a massive direct numerical simulation database, spanning two orders of magnitude in the large-scale Reynolds number, for training and validation. The model learns from low to moderate Reynolds numbers and successfully predicts velocity gradient statistics at both seen and higher (unseen) Reynolds numbers. The success of our present approach demonstrates the viability of deep learning over traditional modeling approaches in capturing and predicting small-scale features of turbulence.

Proprioceptive feedback amplification restores effective locomotion in a neuromechanical model of lampreys with spinal injuries.

Spinal injuries in many vertebrates can result in partial or complete loss of locomotor ability. While mammals often experience permanent loss, some nonmammals, such as lampreys, can regain swimming function, though the exact mechanism is not well understood. One hypothesis is that amplified proprioceptive (body-sensing) feedback can allow an injured lamprey to regain functional swimming even if the descending signal is lost. This study employs a multiscale, integrative, computational model of an anguilliform swimmer fully coupled to a viscous, incompressible fluid and examines the effects of amplified feedback on swimming behavior. This represents a model that analyzes spinal injury recovery by combining a closed-loop neuromechanical model with sensory feedback coupled to a full Navier-Stokes model. Our results show that in some cases, feedback amplification below a spinal lesion is sufficient to partially or entirely restore effective swimming behavior.

Fluid dynamics alters liquid-liquid phase separation in confined aqueous two-phase systems.

Liquid-liquid phase separation is key to understanding aqueous two-phase systems (ATPS) arising throughout cell biology, medical science, and the pharmaceutical industry. Controlling the detailed morphology of phase-separating compound droplets leads to new technologies for efficient single-cell analysis, targeted drug delivery, and effective cell scaffolds for wound healing. We present a computational model of liquid-liquid phase separation relevant to recent laboratory experiments with gelatin-polyethylene glycol mixtures. We include buoyancy and surface-tension-driven finite viscosity fluid dynamics with thermally induced phase separation. We show that the fluid dynamics greatly alters the evolution and equilibria of the phase separation problem. Notably, buoyancy plays a critical role in driving the ATPS to energy-minimizing crescent-shaped morphologies, and shear flows can generate a tenfold speedup in particle formation. Neglecting fluid dynamics produces incorrect minimum-energy droplet shapes. The model allows for optimization of current manufacturing procedures for structured microparticles and improves understanding of ATPS evolution in confined and flowing settings important in biology and biotechnology.

Hybrid quantum algorithms for flow problems.

For quantum computing (QC) to emerge as a practically indispensable computational tool, there is a need for quantum protocols with end-to-end practical applications-in this instance, fluid dynamics. We debut here a high-performance quantum simulator which we term QFlowS (Quantum Flow Simulator), designed for fluid flow simulations using QC. Solving nonlinear flows by QC generally proceeds by solving an equivalent infinite dimensional linear system as a result of linear embedding. Thus, we first choose to simulate two well-known flows using QFlowS and demonstrate a previously unseen, full gate-level implementation of a hybrid and high precision Quantum Linear Systems Algorithms (QLSA) for simulating such flows at low Reynolds numbers. The utility of this simulator is demonstrated by extracting error estimates and power law scaling that relates [Formula: see text] (a parameter crucial to Hamiltonian simulations) to the condition number [Formula: see text] of the simulation matrix and allows the prediction of an optimal scaling parameter for accurate eigenvalue estimation. Further, we include two speedup preserving algorithms for a) the functional form or sparse quantum state preparation and b) in situ quantum postprocessing tool for computing nonlinear functions of the velocity field. We choose the viscous dissipation rate as an example, for which the end-to-end complexity is shown to be [Formula: see text], where [Formula: see text] is the size of the linear system of equations, [Formula: see text] is the solution error, and [Formula: see text] is the error in postprocessing. This work suggests a path toward quantum simulation of fluid flows and highlights the special considerations needed at the gate-level implementation of QC.

Fluctuating hydrodynamics and the Rayleigh-Plateau instability.

The Rayleigh-Plateau instability occurs when surface tension makes a fluid column become unstable to small perturbations. At nanometer scales, thermal fluctuations are comparable to interfacial energy densities. Consequently, at these scales, thermal fluctuations play a significant role in the dynamics of the instability. These microscopic effects have previously been investigated numerically using particle-based simulations, such as molecular dynamics (MD), and stochastic partial differential equation-based hydrodynamic models, such as stochastic lubrication theory. In this paper, we present an incompressible fluctuating hydrodynamics model with a diffuse-interface formulation for binary fluid mixtures designed for the study of stochastic interfacial phenomena. An efficient numerical algorithm is outlined and validated in numerical simulations of stable equilibrium interfaces. We present results from simulations of the Rayleigh-Plateau instability for long cylinders pinching into droplets for Ohnesorge numbers of Oh = 0.5 and 5.0. Both stochastic and perturbed deterministic simulations are analyzed and ensemble results show significant differences in the temporal evolution of the minimum radius near pinching. Short cylinders, with lengths less than their circumference, were also investigated. As previously observed in MD simulations, we find that thermal fluctuations cause these to pinch in cases where a perturbed cylinder would be stable deterministically. Finally, we show that the fluctuating hydrodynamics model can be applied to study a broader range of surface tension-driven phenomena.

Two-fluid dynamics and micron-thin boundary layers shape cytoplasmic flows in early Drosophila embryos.

Cytoplasmic flows are widely emerging as key functional players in development. In early Drosophila embryos, flows drive the spreading of nuclei across the embryo. Here, we combine hydrodynamic modeling with quantitative imaging to develop a two-fluid model that features an active actomyosin gel and a passive viscous cytosol. Gel contractility is controlled by the cell cycle oscillator, the two fluids being coupled by friction. In addition to recapitulating experimental flow patterns, our model explains observations that remained elusive and makes a series of predictions. First, the model captures the vorticity of cytosolic flows, which highlights deviations from Stokes' flow that were observed experimentally but remained unexplained. Second, the model reveals strong differences in the gel and cytosol motion. In particular, a micron-sized boundary layer is predicted close to the cortex, where the gel slides tangentially while the cytosolic flow cannot slip. Third, the model unveils a mechanism that stabilizes the spreading of nuclei with respect to perturbations of their initial positions. This self-correcting mechanism is argued to be functionally important for proper nuclear spreading. Fourth, we use our model to analyze the effects of flows on the transport of the morphogen Bicoid and the establishment of its gradients. Finally, the model predicts that the flow strength should be reduced if the shape of the domain is more round, which is experimentally confirmed in Drosophila mutants. Thus, our two-fluid model explains flows and nuclear positioning in early Drosophila, while making predictions that suggest novel future experiments.

Dynamics of plosive consonants via imaging, computations, and soft electronics.

A quantitative understanding of the coupled dynamics of flow and particles in aerosol and droplet transmission associated with speech remains elusive. Here, we summarize an effort that integrates insights into flow-particle dynamics induced by the production plosive sounds during speech with skin-integrated electronic systems for monitoring the production of these sounds. In particular, we uncover diffusive and ballistic regimes separated by a threshold particle size and characterize the Lagrangian acceleration and pair dispersion. Lagrangian dynamics of the particles in the diffusive regime exhibit features of isotropic turbulence. These fundamental findings highlight the value in skin-interfaced wireless sensors for continuously measuring critical speech patterns in clinical settings, work environments, and the home, based on unique neck biomechanics associated with the generation of plosive sounds. We introduce a wireless, soft device that captures these motions to enable detection of plosive sounds in multiple languages through a convolutional neural network approach. This work spans fundamental flow-particle physics to soft electronic technology, with implications in monitoring and studying critical speech patterns associated with aerosol and droplet transmissions relevant to the spread of infectious diseases.

Computational framework for the generation of one-dimensional vascular models accounting for uncertainty in networks extracted from medical images.

One-dimensional (1D) cardiovascular models offer a non-invasive method to answer medical questions, including predictions of wave-reflection, shear stress, functional flow reserve, vascular resistance and compliance. This model type can predict patient-specific outcomes by solving 1D fluid dynamics equations in geometric networks extracted from medical images. However, the inherent uncertainty in in vivo imaging introduces variability in network size and vessel dimensions, affecting haemodynamic predictions. Understanding the influence of variation in image-derived properties is essential to assess the fidelity of model predictions. Numerous programs exist to render three-dimensional surfaces and construct vessel centrelines. Still, there is no exact way to generate vascular trees from the centrelines while accounting for uncertainty in data. This study introduces an innovative framework employing statistical change point analysis to generate labelled trees that encode vessel dimensions and their associated uncertainty from medical images. To test this framework, we explore the impact of uncertainty in 1D haemodynamic predictions in a systemic and pulmonary arterial network. Simulations explore haemodynamic variations resulting from changes in vessel dimensions and segmentation; the latter is achieved by analysing multiple segmentations of the same images. Results demonstrate the importance of accurately defining vessel radii and lengths when generating high-fidelity patient-specific haemodynamics models. KEY POINTS: This study introduces novel algorithms for generating labelled directed trees from medical images, focusing on accurate junction node placement and radius extraction using change points to provide haemodynamic predictions with uncertainty within expected measurement error. Geometric features, such as vessel dimension (length and radius) and network size, significantly impact pressure and flow predictions in both pulmonary and aortic arterial networks. Standardizing networks to a consistent number of vessels is crucial for meaningful comparisons and decreases haemodynamic uncertainty. Change points are valuable to understanding structural transitions in vascular data, providing an automated and efficient way to detect shifts in vessel characteristics and ensure reliable extraction of representative vessel radii.