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Understanding and optimizing the design of helical micro-swimmers is crucial for advancing their application in various fields. This study presents an innovative approach combining Free-Form Deformation with Bayesian Optimization to enhance the shape of these swimmers. Our method facilitates the computation of generic swimmer shapes that achieve optimal average speed and efficiency. Applied to both monoflagellated and biflagellated swimmers, our optimization framework has led to the identification of new optimal shapes. These shapes are compared with biological counterparts, highlighting a diverse range of swimmers, including both pushers and pullers.

The self-organization of active particles on a two-dimensional single-occupancy lattice is investigated, with an emphasis on the effects of boundary confinement and the influence of an external mean fluid flow. The study examines collective behaviors, particularly the transition from a disordered phase to the formation of orientationally ordered patterns, and their impact on particle transport and flux. In the absence of fluid flow, confinement causes particles to accumulate near the walls, leading to clogs or obstructions that hinder movement, or to the formation of bands aligned with the channel. Although these bands limit the particles ability to freely self-propel, they still result in a net flux along the channel. The introduction of an external Poiseuille fluid flow induces vorticity, shifts the phase transition to higher alignment sensitivities, and promotes particle clustering at the channel center, significantly enhancing overall flux.

Swimming involves a body's capability to navigate through a fluid by undergoing self-deformations. Typically, fluid dynamics are described by the Navier-Stokes equations, and when integrated with a swimming body, it results in a highly intricate model. This paper introduces a computational framework for simulating the movement of multiple swimmers with various geometries immersed in a Navier-Stokes fluid. The approach relies on the finite element method with an Arbitrary Lagrangian-Eulerian (ALE) framework to handle swimmer displacements. Numerous numerical experiments demonstrate the adaptability of the computational framework across various scenarios.All the implementations are made using the Feel++ finite element library.

We studied numerically the dynamics of colliding rigid bodies in a Newtonian fluid. The finite element method is used to solve the fluid-body interaction and the fluid motion is described in the Arbitrary-Lagrangian-Eulerian framework. To model the interactions between bodies, we consider a repulsive collision-avoidance model, defined by R. Glowinski. The main emphasis in this work is the generalization of this collision model to multiple rigid bodies of arbitrary shape. Our model first uses a narrow-band fast marching method to detect the set of colliding bodies. Then, collision forces and torques are computed for these bodies via a general expression, which does not depend on their shape. Numerical experiments examining the performance of the narrow-band fast marching method and the parallel execution of the collision algorithm are discussed. We validate our model with literature results and show various applications of colliding bodies in two and three dimensions. In these applications, the bodies move due to forces such as gravity, a fluid flow, or their own actuation. Finally, we present a tool to create arbitrarily shaped bodies in discretized fluid domains, enabling conforming body-fluid interface and allowing to perform simulations of fluid-body interactions with collision treatment in these realistic environments. All simulations are conducted with the Feel++ open source library.

This work aims at finding optimal navigation policies for thin, deformable microswimmers that progress in a viscous fluid by propagating a sinusoidal undulation along their slender body. These active filaments are embedded in a prescribed, non-homogeneous flow, in which their swimming undulations have to compete with the drifts, strains, and deformations inflicted by the outer velocity field. Such an intricate situation, where swimming and navigation are tightly bonded, is addressed using various methods of reinforcement learning. Each swimmer has only access to restricted information on its configuration and has to select accordingly an action among a limited set. The optimisation problem then consists in finding the policy leading to the most efficient displacement in a given direction. It is found that usual methods do not converge and this pitfall is interpreted as a combined consequence of the non-Markovianity of the decision process, together with the highly chaotic nature of the dynamics, which is responsible for high variability in learning efficiencies. Still, we provide an alternative method to construct efficient policies, which is based on running several independent realisations of Q-learning. This allows the construction of a set of admissible policies whose properties can be studied in detail and compared to assess their efficiency and robustness., Comment: 18 pages, 14 figures

In this paper we are interested in optimizing the shape of multi-flagellated helical microswimmers. Mimicking the propagation of helical waves along the flagella, they self-propel by rotating their tails. The swimmer's dynamics is computed using the Boundary Element Method, implemented in the open source Matlab library $Gypsilab$. We exploit a Bayesian optimization algorithm to maximize the swimmer's speeds through their shape optimization. Our results show that the optimal tail shapes are helices with large wavelength, such that the shape periodicity is disregarded. Moreover, the best propulsion speed is achieved for elongated heads when the swimmer has one or two flagella. Surprisingly, a round head is obtained when more flagella are considered. Our results indicate that the position and number of flagella modify the propulsion pattern and play a significant role in the optimal design of the head. It appears that Bayesian optimization is a promising method for performance improvement in microswimming., Comment: 19 pages, 10 figures

We address the swimming problem at low Reynolds number. This regime, which is typically used for micro-swimmers, is described by Stokes equations. We couple a PDE solver of Stokes equations, derived from the Feel++ finite elements library, to a quaternion-based rigid-body solver. We validate our numerical results both on a 2D exact solution and on an exact solution for a rotating rigid body respectively. Finally, we apply them to simulate the motion of a one-hinged swimmer, which obeys to the scallop theorem.

We present an automated procedure for the design of optimal actuation for flagellar magnetic microswimmers based on numerical optimization. Using this method, a new magnetic actuation method is provided which allows these devices to swim significantly faster compared to the usual sinusoidal actuation. This leads to a novel swimming strategy which makes the swimmer perform a 3D figure-8 trajectory. This shows that a faster propulsion is obtained when the swimmer is allowed to go out-of-plane. This approach is experimentally validated on a scaled-up flexible swimmer.

We consider affine control systems with two scalar controls, such that one control vector field vanishes at an equilibrium state. We state two necessary conditions of local controllability around this equilibrium, involving the iterated Lie brackets of the system vector fields, with controls that are either bounded, small in L $\infty$ or small in W 1,$\infty$. These results are illustrated with several examples.

Micron-scale swimmers move in the realm of negligible inertia, dominated by viscous drag forces. In this paper, we formulate the leading-order dynamics of a slender multi-link (N-link) microswimmer assuming small-amplitude undulations about its straight configuration. The energy-optimal stroke to achieve a given prescribed displacement in a given time period is obtained as the largest eigenvalue solution of a constrained optimal control problem. Remarkably, the optimal stroke is an ellipse lying within a two-dimensional plane in the (N-1)-dimensional space of joint angles, where N can be arbitrarily large. For large N, the optimal stroke is a traveling wave of bending, modulo edge effects. If the number of shape variables is small, we can consider the same problem when the prescribed displacement in one time period is large, and not attainable with small variations of the joint angles. The fully nonlinear optimal control problem is solved numerically for the cases N=3 (Purcell's three-link swimmer) and N=5 showing that, as the prescribed displacement becomes small, the optimal solutions obtained using the small-amplitude assumption are recovered. We also show that, when the prescribed displacements become large, the picture is different. For N=3 we recover the non-convex planar loops already known from previous studies. For N=5 we obtain non-planar loops, raising the question of characterizing the geometry of complex high-dimensional loops.

The inertialess fluid-structure interactions of active and passive inextensible filaments and slender- rods are ubiquitous in nature, from the dynamics of semi-flexible polymers and cytoskeletal filaments to cellular mechanics and flagella. The coupling between the geometry of deformation and the phys- ical interaction governing the dynamics of bio-filaments is complex. Governing equations negotiate elastohydrodynamical interactions with non-holonomic constraints arising from the filament inex- tensibility. Such elastohydrodynamic systems are structurally convoluted, prone to numerical erros, thus requiring penalization methods and high-order spatiotemporal propagators. The asymptotic coarse-graining formulation presented here exploits the momentum balance in the asymptotic limit of small rod-like elements which are integrated semi-analytically. This greatly simplifies the elas- tohydrodynamic interactions and overcomes previous numerical instability. The resulting matricial system is straightforward and intuitive to implement, and allows for a fast and efficient computation, over than a hundred times faster than previous schemes. Only basic knowledge of systems of linear equations is required, and implementation achieved with any solver of choice. Generalisations for complex interaction of multiple rods, Brownian polymer dynamics, active filaments and non-local hydrodynamics are also straightforward. We demonstrate these in four examples commonly found in biological systems, including the dynamics of filaments and flagella. Three of these systems are novel in the literature. We additionally provide a Matlab code that can be used as a basis for further generalisations., Comment: 16 pages, 7 figures

In the above mentioned note (, , published in IEEE Trans. Autom. Cont., 2017), the first and fourth authors proved a local controllability result around the straight configuration for a class of magneto-elastic micro-swimmers.That result is weaker than the usual small-time local controllability (STLC), and the authors left the STLC question open. The present addendum closes it by showing that these systems cannot be STLC.

We formulate and solve the equations governing the dynamics of a microscopic artificial swimmer composed of a head and of a tail made of a thin film of permanent magnetic material. This is a variant of the model swimmer proposed by Dreyfus et al. in 2005, whose tail is a filament obtained from the assembly of super-paramagnetic beads. The swimmer is actuated by an oscillating magnetic field, and its geometry is inspired by that of sperm cells. Using values for the geometric and material parameters that are realistic for a magnetic multilayer, we show that the model swimmer can reach swimming speeds exceeding one body length per second, under reasonable values of the driving magnetic field. This provides a proof of principle for the viability of the concept. In addition, we discuss the possibility to steer the system along curved paths. Finally, we compare the propulsion mechanism (swimming `gait') of our swimmer with that of sperm cells. The main difference between the two is that, contrary to its biological template, our artificial system does not rely on the propagation of bending waves along the tail, at least for the range of material and geometric parameters explored in this article.

This paper focuses on the mechanism of propulsion of a Purcell swimmer whose segments are magnetized and react to an external magnetic field applied into the fluid. By an asymptotic analysis, we prove that it is possible to steer the swimmer along a chosen direction when the control functions are prescribed as an oscillating field. Moreover, we discuss what are the main obstructions to overcome in order to get classical controllability result for this system.

- In this paper, we focus on a variant of a 3-link magnetic microswimmer which consists of three rigid magnetized segments connected by two torsional springs. In particular, we assume that one of the springs is twisted so that the swimmer is not aligned at rest. By acting on it with an external magnetic field, the swimmer twists and moves through the surrounding fluid. By considering the external magnetic field as a control function, we state a local partial controllability result around the equilibrium states. Then, we propose a constructive method to find the magnetic field that allows the swimmer to move along a prescribed trajectory. Finally, we show numerical simulations in which the swimmer moves along a prescribed path.

A recent promising technique for robotic micro-swimmers is to endow them with a magnetization and apply an external magnetic field to provoke their deformation. In this note we consider a simple planar micro-swimmer model made of two magnetized segments connected by an elastic joint, controlled via a magnetic field. After recalling the analytical model, we establish a local controllability result around the straight position of the swimmer.

In this paper, we analyse a model for the growth of three-dimensional walled cells. In this model the biomechanical expansion of the cell is coupled with the geometry of its wall. We consider that the density of building material depends on the curvature of the cell wall, thus yield-ing possible anisotropic growth. The dynamics of the axisymmetric cell wall is described by a system of nonlinear PDE including a nonlin-ear convection-diffusion equation coupled with a Poisson equation. We develop the linear stability analysis of the spherical symmetric config-uration in expansion. We identify three critical parameters that play a role in the possible instability of the radially symmetric shape, namely the degree of nonlinearity of the coupling, the effective diffusion of the building material, and the Poisson's ratio of the cell wall. We also investigate numerically pattern selection in the nonlinear regime. All the results are also obtained for a simpler, but similar, two-dimensional model.

In this paper we address the question of the optimal design for the Purcell 3-link swim-mer. More precisely we investigate the best link length ratio which maximizes its displace-ment. The dynamics of the swimmer is expressed as an ODE, using the Resistive Force Theory [13]. Among a set of optimal strategies of deformation (strokes), we provide an asymptotic estimate of the displacement for small deformations, from which we derive the optimal link ratio. Numerical simulations are in good agreement with this theoretical esti-mate, and also cover larger amplitudes of deformation. Compared with the classical design of the Purcell swimmer, we observe a gain in displacement of roughly 60%.

Swimming consists by definition in propelling through a fluid by means of bodily movements. Thus, from a mathematical point of view, swimming turns into a control problem for which the controls are the deformations of the swimmer. The aim of this paper is to present a unified geometric approach for the optimization of the body deformations of so-called driftless swimmers. The class of driftless swimmers includes, among other, swimmers in a 3D Stokes flow (case of micro-swimmers in viscous fluids) or swimmers in a 2D or 3D potential flow. A general framework is introduced, allowing the complete analysis of five usual nonlinear optimization problems to be carried out. The results are illustrated with examples coming from the literature and with an in-depth study of a swimmer in a 2D potential flow. Numerical tests are also provided.

We study the effect of a rough wall on the controllability of micro-swimmers made of several balls linked by thin jacks: the so-called 3-sphere and 4-sphere swimmers. We show that a controllable swimmer (the 4-sphere swimmer) is not impacted by the roughness. On the contrary, we show that the roughness changes the dynamics of the 3-sphere swimmer, so that it can reach any direction almost everywhere.

Swimming, i.e., being able to advance in the absence of external forces by performing cyclic shape changes, is particularly demanding at low Reynolds numbers which is the regime of interest for micro-organisms and micro-robots. We focus on self-propelled stokesian robots composed of assemblies of balls and we prove that the presence of a wall has an effect on their motility. More precisely, we demonstrate that a controllable swimmer remains controllable in a half space whereas the reachable set of a non fully controllable one is affected by the presence of a wall.