Scaling the tail beat frequency and swimming speed in underwater undulatory swimming.

Undulatory swimming is the predominant form of locomotion in aquatic vertebrates. A myriad of animals of different species and sizes oscillate their bodies to propel themselves in aquatic environments with swimming speed scaling as the product of the animal length by the oscillation frequency. Although frequency tuning is the primary means by which a swimmer selects its speed, there is no consensus on the mechanisms involved. In this article, we propose scaling laws for undulatory swimmers that relate oscillation frequency to length by taking into account both the biological characteristics of the muscles and the interaction of the moving swimmer with its environment. Results are supported by an extensive literature review including approximately 1200 individuals of different species, sizes and swimming environments. We highlight a crossover in size around 0.5-1 m. Below this value, the frequency can be tuned between 2-20 Hz due to biological constraints and the interplay between slow and fast muscles. Above this value, the fluid-swimmer interaction must be taken into account and the frequency is inversely proportional to the length of the animal. This approach predicts a maximum swimming speed around 5-10 m.s-1 for large swimmers, consistent with the threshold to prevent bubble cavitation.

Reinforcement learning approach to control an inverted pendulum: A general framework for educational purposes.

Machine learning is often cited as a new paradigm in control theory, but is also often viewed as empirical and less intuitive for students than classical model-based methods. This is particularly the case for reinforcement learning, an approach that does not require any mathematical model to drive a system inside an unknown environment. This lack of intuition can be an obstacle to design experiments and implement this approach. Reversely there is a need to gain experience and intuition from experiments. In this article, we propose a general framework to reproduce successful experiments and simulations based on the inverted pendulum, a classic problem often used as a benchmark to evaluate control strategies. Two algorithms (basic Q-Learning and Deep Q-Networks (DQN)) are introduced, both in experiments and in simulation with a virtual environment, to give a comprehensive understanding of the approach and discuss its implementation on real systems. In experiments, we show that learning over a few hours is enough to control the pendulum with high accuracy. Simulations provide insights about the effect of each physical parameter and tests the feasibility and robustness of the approach.

Three-dimensional liquid foam flow through a hopper resolved by fast X-ray microtomography.

We probe the complex rheological behaviour of liquid foams flowing through a conical constriction. With fast X-ray tomographic microscopy we measure in situ the displacement and deformation of up to fifty thousand bubbles at any single time instance while varying systematically the foam liquid fraction, the bubble size and the flow direction - convergent vs. divergent. The large statistics and high spatio-temporal resolution allows to observe and quantify the deviations from a purely viscous flow. We indeed reveal an asymmetry between the convergent and divergent flows associated to the emergence of elastic stresses in the latter case, and enhanced as the liquid fraction is reduced. Such effect is related to the reorientation of the deformed bubbles flowing out of the constriction, from a prolate to an oblate shape in average, while they pass through the hopper waist.

Intracellular pH Control by Membrane Transport in Mammalian Cells. Insights Into the Selective Advantages of Functional Redundancy.

Intracellular pH is a vital parameter that is maintained close to neutrality in all mammalian cells and tissues and acidic in most intracellular compartments. After presenting the main techniques used for intracellular an vesicular pH measurements we will briefly recall the main molecular mechanisms that affect and regulate intracellular pH. Following this we will discuss the large functional redundancy found in the transporters of H+ or acid-base equivalents. For this purpose, we will use mathematical modeling to simulate cellular response to persistent and/or transient acidification, in the presence of different transporters, single or in combination. We will also test the presence or absence of intracellular buffering. This latter section will highlight how modeling can yield fundamental insight into deep biological questions such as the utility of functional redundancy in natural selection.

Use of compliant actuators for throwing rigid projectiles.

Muscles and tendons, actuators in robotics, and various sports implements are examples that exploit elasticity to accelerate objects. Tuning the mechanical properties of elastic elements connecting objects can greatly enhance the transfer of mechanical energy between the objects. Here, we study experimentally the throw of rigid projectiles by an actuator, which has a soft elastic element added to the distal end. We vary the thickness of the elastic layer and suggest a simple mass-spring chain model to find the properties of the elastic layer, which will maximize the energy transfer from the actuator to the projectile. The insertion of a soft layer, impedance matched to the ejection frequency of the projectile mass, can increase the throwing efficiency by over 400%. Finally, we identify that very thick and very soft compliant layers could potentially lead to high efficiency and flexibility simultaneously.

Impact dynamics of composite elastorigid projectiles onto solid surfaces.

We investigate the impact of composite objects. They consist of a soft layer on top of a rigid part with a hemispherical impacting end. The coefficient of restitution (e) of such objects is studied systematically as a function of the mass ratio and of the nature of the materials. For rather elastic materials, the coefficient of restitution is a nonmonotonic function of the mass ratio and exhibits important variations. The dynamics of the impact can be characterized by several bounces depending on the ratios between the four timescales at play. These include the duration of contact of the rigid part with the substrate and the time for the elastic waves to travel back and forth in the soft layer. In that sense, describing these projectiles requires one to take into account both the Hertzian theory of contact and the elastic waves described by Saint-Venant's approach.

Equilibrium and dynamics of strained islands.

We focus in this work on the effect of the surface energy anisotropy on an elastically strained semiconductor film and in particular on its role on the coarsening dynamics of elastically strained islands. To study the dynamics of a strained film, we establish a one-dimensional nonlinear and nonlocal partial differential equation which takes into account the elastic, capillary, wetting, and anisotropic effects. We first construct an approximate stationary solution of our model using a variational method and an appropriate ansatz. This stationary solution is used to compute the chemical potential dependence on the island height. In particular, we find that the surface energy anisotropy increases the convexity of the chemical potential and this is shown to have an effect on the driving force for the coarsening. Second, we study the coarsening dynamics of an islands pair by means of numerical simulations. We find that the presence of the surface energy anisotropy may increase or decrease the coarsening time of the system. We show that this phenomenon depends on the initial heights of island pairs. We thus highlight that the driving force for the coarsening is due to the variation of the chemical potential with respect to the islands height and that two different regimes are possible.

Shape and coarsening dynamics of strained islands.

We investigate the formation and the coarsening dynamics of islands in a strained epitaxial semiconductor film. These islands are commonly observed in thin films undergoing a morphological instability due to the presence of the elastocapillary effect. We first describe both analytically and numerically the formation of an equilibrium island using a two-dimensional continuous model. We have found that these equilibrium island-like solutions have a maximum height h_{0} and they sit on top of a flat wetting layer with a thickness h_{w}. We then consider two islands, and we report that they undergo a noninterrupted coarsening that follows a two stage dynamics. The first stage may be depicted by a quasistatic dynamics, where the mass transfers are proportional to the chemical potential difference of the islands. It is associated with a time scale t_{c} that is a function of the distance d between the islands and leads to the shrinkage of the smallest island. Once its height becomes smaller than a minimal equilibrium height h_{0}^{*}, its mass spreads over the entire system. Our results pave the way for a future analysis of coarsening of an assembly of islands.

Bubble dynamics inside an outgassing hydrogel confined in a Hele-Shaw cell.

We report an experimental study of bubble dynamics in a non-Newtonian fluid subjected to a pressure decrease. The fluid is a hydrogel, composed of water and a synthetic clay, prepared and sandwiched between two glass plates in a Hele-Shaw geometry. The rheological properties of the material can be tuned by the clay concentration. As the imposed pressure decreases, the gas initially dissolved in the hydrogel triggers bubble formation. Different stages of the process are observed: bubble nucleation, growth, interaction, and creation of domains by bubble contact or coalescence. Initially bubble behave independently. They are trapped and advected by the mean deformation of the hydrogel, and the bubble growth is mainly driven by the diffusion of the dissolved gas through the hydrogel and its outgassing at the reactive-advected hydrogel-bubble interface. In this regime, the rheology of the fluid does not play a significant role on the bubble growth. A model is proposed and gives a simple scaling that relates the bubble growth rate and the imposed pressure. Carbon dioxide is shown to be the gas at play, and the hydrogel is degassing at the millimeter scale as a water solution does at a smaller scale. Later, bubbles are not independent anymore. The growth rate decreases, and the morphology becomes more anisotropic as bubbles interact because they are separated by a distance smaller than the individual stress field extension. Our measurements show that the interaction distance scales with the bubbles' size.

Gait and speed selection in slender inertial swimmers.

Inertial swimmers use flexural movements to push water and generate thrust. We quantify this dynamical process for a slender body in a fluid by accounting for passive elasticity and hydrodynamics and active muscular force generation and proprioception. Our coupled elastohydrodynamic model takes the form of a nonlinear eigenvalue problem for the swimming speed and locomotion gait. The solution of this problem shows that swimmers use quantized resonant interactions with the fluid environment to enhance speed and efficiency. Thus, a fish is like an optimized diode that converts a prescribed alternating transverse motion to forward motion. Our results also allow for a broad comparative view of swimming locomotion and provide a mechanistic basis for the empirical relation linking the swimmer's speed U, length L, and tail beat frequency f, given by U/L ~ f [Bainbridge R (1958) J Exp Biol 35:109-133]. Furthermore, we show that a simple form of proprioceptive sensory feedback, wherein local muscle activation is function of body curvature, suffices to drive elastic instabilities associated with thrust production and leads to a spontaneous swimming gait without the need for a central pattern generator. Taken together, our results provide a simple mechanistic view of swimming consistent with natural observations and suggest ways to engineer artificial swimmers for optimal performance.

Capturing intracellular pH dynamics by coupling its molecular mechanisms within a fully tractable mathematical model.

We describe the construction of a fully tractable mathematical model for intracellular pH. This work is based on coupling the kinetic equations depicting the molecular mechanisms for pumps, transporters and chemical reactions, which determine this parameter in eukaryotic cells. Thus, our system also calculates the membrane potential and the cytosolic ionic composition. Such a model required the development of a novel algebraic method that couples differential equations for slow relaxation processes to steady-state equations for fast chemical reactions. Compared to classical heuristic approaches based on fitted curves and ad hoc constants, this yields significant improvements. This model is mathematically self-consistent and allows for the first time to establish analytical solutions for steady-state pH and a reduced differential equation for pH regulation. Because of its modular structure, it can integrate any additional mechanism that will directly or indirectly affect pH. In addition, it provides mathematical clarifications for widely observed biological phenomena such as overshooting in regulatory loops. Finally, instead of including a limited set of experimental results to fit our model, we show examples of numerical calculations that are extremely consistent with the wide body of intracellular pH experimental measurements gathered by different groups in many different cellular systems.

A dynamical model for the Utricularia trap.

We propose a model that captures the dynamics of a carnivorous plant, Utricularia inflata. This plant possesses tiny traps for capturing small aquatic animals. Glands pump water out of the trap, yielding a negative pressure difference between the plant and its surroundings. The trap door is set into a meta-stable state and opens quickly as an extra pressure is generated by the displacement of a potential prey. As the door opens, the pressure difference sucks the animal into the trap. We write an ODE model that captures all the physics at play. We show that the dynamics of the plant is quite similar to neuronal dynamics and we analyse the effect of a white noise on the dynamics of the trap.

Wave-train-induced termination of weakly anchored vortices in excitable media.

A free vortex in excitable media can be displaced and removed by a wave train. However, simple physical arguments suggest that vortices anchored to large inexcitable obstacles cannot be removed similarly. We show that unpinning of vortices attached to obstacles smaller than the core radius of the free vortex is possible through pacing. The wave-train frequency necessary for unpinning increases with the obstacle size and we present a geometric explanation of this dependence. Our model-independent results suggest that decreasing excitability of the medium can facilitate pacing-induced removal of vortices in cardiac tissue.

Fluid-flow-induced flutter of a flag.

We give an explanation for the onset of fluid-flow-induced flutter in a flag. Our theory accounts for the various physical mechanisms at work: the finite length and the small but finite bending stiffness of the flag, the unsteadiness of the flow, the added mass effect, and vortex shedding from the trailing edge. Our analysis allows us to predict a critical speed for the onset of flapping as well as the frequency of flapping. We find that in a particular limit corresponding to a low-density fluid flowing over a soft high-density flag, the flapping instability is akin to a resonance between the mode of oscillation of a rigid pivoted airfoil in a flow and a hinged-free elastic plate vibrating in its lowest mode.