Interface Focus最新文献

We discuss connections between different types of models of gene-regulatory network dynamics that include Boolean, finite multilevel and monotone Boolean models. We recast the methodology of describing attractors of Boolean and finite multilevel dynamics using motifs of the expanded network $eRN$ in terms of Petri net dynamics on $eRN$ . We show that the Petri net can be used to recover dynamics of the finite multilevel dynamics on the state transition graph. We conclude with new insights that the expanded network viewpoint offers for the robustness of equilibria and complex attractors.

Mechanistic ordinary differential equation models of gene regulatory networks are a valuable tool for understanding biological processes that occur inside a cell, and they allow for the formulation of novel hypotheses on the mechanisms underlying these processes. Although data-driven methods for inferring these mechanistic models are becoming more prevalent, it is often unclear how recent advances in machine learning can be used effectively without jeopardi zing the interpretability of the resulting models. In this work, we present a framework to leverage neural networks for the identification of data-driven models for time-dependent intracellular processes, such as cell differentiation. In particular, we use a graph autoencoder model to suggest novel connections in a gene regulatory network. We show how the improvement of the graph suggested using this neural network leads to the generation of hypotheses on the dynamics of the resulting identified dynamical system.

Growing experimental evidence highlights the relevant role of mechanics in the physiology of solid tumours, even in their early stages. While most of the mathematical models describe tumour growth as a volumetric increase in mass in the bulk, in vitro experiments on tumour spheroids have demonstrated that cell proliferation occurs in a thin layer at the boundary of the cellular aggregate. In this work, we investigate how elasticity and surface tension interact during the development of tumour spheroids. We model the spheroid as a hyperelastic material undergoing boundary accretion, where the newly created cells are deformed by the action of surface tension. This growth leads to a frustrated reference configuration, resulting in the appearance of residual stress. Our theoretical framework is validated using experimental results from the literature. Like fully developed tumours, spheroids open when subjected to radial cuts. Remarkably, this behaviour is observed even in newly formed spheroids, which lack residual stress. Through both analytical solutions and numerical simulations, we show that this phenomenon is driven by elastocapillary interactions, where the residual stress developed in grown spheroids amplifies the tumour opening. Our model's outcomes align with experimental observations and allow us to estimate the surface tension acting on tumour spheroids.

Aquatic animals like fishes and larval amphibians have flexible gills with a large surface area for gas exchange. When exposed to air, gills typically collapse and coalesce due to the elastocapillary effect, reducing gas exchange and potentially causing death. To resist these effects, some amphibians are hypothesized to have evolved stiffened gills, but these elastocapillarity effects have not been investigated empirically or theoretically. Here, we examine the deformations of artificial elastomeric gill lamellae under quasi-static and dynamic liquid crossing scenarios, inspired by conditions faced by amphibious animals when leaving water. First, we discovered multiple equilibrium states when the liquid interface is pinned to the lamellae tips, where lamellae either coalesce or remain separated depending on the liquid volume constraints. Moreover, we observe a unidirectional collapse pattern, termed the 'dominos pattern', under spatially variant drainage rate. A reduced-order dynamic model provides quantitative insights into these equilibria based on the lamellae properties, liquid volumes and drainage conditions leading to dominos patterns. These results inspire novel hypotheses about how elastocapillary may influence the evolution of gill structure in amphibious species, and also provide bioinspiration for engineering applications such as polymorphic display devices using flexible lamellae.

The California blackworm, Lumbriculus variegatus, lives underwater and latches its tail to the water surface for respiration and stability. Little is known about the upward force generated by this posture. In this combined experimental and theoretical study, we visualize the menisci shape for blackworms and blackworm mimics, composed of smooth and corrugated epoxy rods. We apply previous theoretical models for floating cylinders to predict the upward force and safety factor of blackworms as well as other organisms such as mosquito larvae, leeches and aquatic snails. Understanding the upward forces of organisms that latch onto the water surface may help to understand the evolution of interfacial attachment and inspire biomimetic robots.

Manu jumping, a popular water diving style among M $\overline{\text{a}}$ ori people in New Zealand, focuses on creating large splashes. Divers perform aerial manoeuvres such as the 'utkatasana' pose, entering the water in a V-shape, and executing underwater manoeuvres to enhance the splash size. Our study explores the underlying fluid dynamics of Manu jumping and demonstrates how two key parameters, the V-angle and the timing of body opening, can enhance Worthington jet formation. To accurately replicate human Manu jumping, we studied water entry of both passive solid objects with varying V-angles and an active body opening robot (Manubot). The analysis revealed that a 45° V-angle enhances Worthington jet formation, consistent with human diving data. This angle balances a large cavity size and a deep pinch-off depth. The body opening within a timing window of ${\hat{t}}_r=1.1-1.5$ synchronizes the robot's potential energies to be timely transferred to the cavity formation, producing the strongest and most vertical, i.e. ideal, Worthington jets. Based on our experimental findings, we propose a range of parameters for generating the large Manu splashes. These insights offer engineering perspectives on how to modulate underwater cavity dynamics using both passive and active body formations.

The nucleation and/or spreading of bubbles in water under tension (due to water evaporation) can be problematic for most plants along the ascending sap network-from roots to leaves-called xylem. Due to global warming, trees facing drought conditions are particularly threatened by the formation of such embolisms, which hinders sap flow and can ultimately be fatal. Polydimethylsiloxane (PDMS)-based biomimetic leaves simulating evapotranspiration have demonstrated that, in a linear configuration, the existence of a slender constriction in the channel allows for the creation of intermittent embolism propagation (as an interaction between the elasticity of the biomimetic leaf and the capillary forces at the air/water interfaces) (Keiser et al. 2022 J. Fluid Mech. 948, A52 (doi:10.1017/jfm.2022.733); Keiser et al. 2024 J. R. Soc. Interface 21, 20240103 (doi:10.1098/rsif.2024.0103)). Here, we use analogue PDMS-based biomimetic leaves in one dimension and two dimensions. To better explore the embolism spreading mechanism, we add to the setup an additional technique, allowing to measure directly the microchannel's ceiling deformation versus time, which corresponds to the pressure variations. We present here such a method that allows one to have quantitative insights into the dynamics of embolism spreading. The coupling between channel deformations and the Laplace pressure threshold explains the observed elastocapillary dynamics.

Aquatic animals that live in water often leap out to catch prey in the air, while terrestrial and aerial animals dive into water to hunt aquatic animals. Some animals locomote on the water surface or lap water by repeated slamming and water-exiting motions. These dynamic interactions with the water-air interface have similarities in engineering, where water entry and exit problems play crucial roles in an object crossing the interface in industrial and physical systems. This review examines the physics of water entry and exit in biological systems through fluid mechanics principles originally developed for engineering applications. By identifying common governing forces, we aim to establish connections between biological strategies and engineering solutions, potentially leading innovations in bio-inspired technology.

Surface instability and elastocapillarity represent critical phenomena in biological and engineered systems. In this study, we investigate capillarity-induced fold localization in film-substrate systems through experiments and finite element simulations. Upon water droplet deposition, globally ordered wrinkles transform into localized folds. The fold morphology and dimensions depend on the aspect ratio of initial wrinkles. Our results demonstrate that high-aspect-ratio wrinkles facilitate spontaneous formation of closed channels beneath the surface upon fold emergence. Additionally, the morphological transition between wrinkles and folds exhibits reversible control through applied strain adjustment. These findings enable technological applications such as the creation of fold nanochannels and graphene oxide folding. This work establishes a fundamental framework for understanding the interplay between surface instability and elastocapillarity, which represents a crucial mechanism in biological and engineered systems while providing design principles for functional surfaces and devices.