arXiv subjects

Thomas D. Montenegro-Johnson

Publications and source records attributed to Thomas D. Montenegro-Johnson.

At least 19 recordsLinked to original sources

arXiv2025

Surfing on chemical waves: a simple yet dynamically rich two-sphere responsive gel swimmer

Self-oscillating gels are chemically-responsive hydrogels coupled to an oscillating chemical reaction of a stimulus solute. In response to the oscillating solute concentration field, responsive gels periodically swell and deswell, expelling their adsorbed water as they transition to a drier state, and reswelling once they return to a hydrophilic state. This volume phase transition occurs when the local stimulus concentration crosses a critical value, about which the hydrophilicity of the polymer chains changes abruptly. These gels have been used to make surface crawlers or other pulsatile machines, but here we show that a very simple system comprising two oscillating gel spheres linked by a rigid rod can also swim in the inertialess Stokes regime - albeit rather slowly. Developing a full continuum-mechanical model for a gel that employs a reaction described by the Brusselator model to generate oscillating chemical concentrations that couple to gel and fluid dynamics, we quantify the rate of shrinkage and swelling and associated flows as the gels pump out or draw in water. Herein, we derive analytical results for the swimming velocity of these swimmers, and upon placing them in a solute bath, identify two modes of behaviour upon encountering propagating reaction-diffusion waves: 'bobbing' and 'surfing'. Though somewhat slower than flagellated swimmers, the relative simplicity of the system, with no hinges or moving components, lends itself well to large scale production.

physics.flu-dyn↗

arXiv2025

Oscillating chemical reactions enable communication between responsive hydrogels

Responsive hydrogels can sense environmental stimuli and respond as actuators by expelling water and changing shape. In this article, we develop theory to demonstrate that groups of responsive hydrogels can also communicate with each other, by utilising the effect of elastic deformation on chemical reaction dynamics. Specifically, we consider a system of two spatially-separated chemically responsive hydrogels suspended in a solution in which a Belousov-Zhabotinsky (BZ)-type reaction occurs. Solving for the gel dynamics with the transport of solvent through the poroelastic network and the chemical kinetics, we show how the periodic swelling-deswelling oscillations of each gel can become coupled, and how this coupling can be exploited to send signals from one gel to the other via mechanical manipulation of the sender that affect the local (and thus global) frequency of oscillation.

cond-mat.soft↗

arXiv2025

Poromechanical modelling of responsive hydrogel pumps

Thermo-responsive hydrogels are smart materials that rapidly switch between hydrophilic (swollen) and hydrophobic (shrunken) states when heated past a threshold temperature, resulting in order-of-magnitude changes in gel volume. Modelling the dynamics of this switch is notoriously difficult, and typically involves fitting a large number of microscopic material parameters to experimental data. In this paper, we present and validate an intuitive, macroscopic description of responsive gel dynamics and use it to explore the shrinking, swelling and pumping of responsive hydrogel displacement pumps for microfluidic devices. We finish with a discussion on how such tubular structures may be used to speed up the response times of larger hydrogel smart actuators and unlock new possibilities for dynamic shape change.

physics.flu-dyn↗

arXiv2024

Slender Phoretic Loops and Knots

We present an asymptotic theory for solving the dynamics of slender autophoretic loops and knots. Our formulation is valid for non-intersecting 3D centrelines, with arbitrary chemical patterning and varying (circular) cross-sectional radius, allowing a broad class of slender active loops and knots to be studied. The theory is amenable to closed-form solutions in simpler cases, allowing us to analytically derive the swimming speed of chemically patterned tori, and the pumping strength (stresslet) of a uniformly active slender torus. Using simple numerical solutions of our asymptotic equations, we then elucidate the behaviour of many exotic active particle geometries, such as a bumpy uniformly active torus that spins and a Janus trefoil knot, which rotates as it swims forwards.

physics.flu-dyn↗

arXiv2022

The swelling and shrinking of spherical thermo-responsive hydrogels

Thermo-responsive hydrogels are a promising material for creating controllable actuators for use in micro-scale devices, since they expand and contract significantly (absorbing or expelling fluid) in response to relatively small temperature changes. Understanding such systems can be difficult because of the spatially- and temporally-varying properties of the gel, and the complex relationships between the fluid dynamics, elastic deformation of the gel and chemical interaction between the polymer and fluid. We address this using a poro-elastic model, considering the dynamics of a thermo-responsive spherical hydrogel after a sudden change in the temperature that should result in substantial swelling or shrinking. We focus on two model examples, with equilibrium parameters extracted from data in the literature. We find a range of qualitatively different behaviours when swelling and shrinking, including cases where swelling and shrinking happen smoothly from the edge, and other situations which result in the formation of an inwards-travelling spherical front that separates a core and shell with markedly different degrees of swelling. We then characterise when each of these scenarios is expected to occur. An approximate analytical form for the front dynamics is developed, with two levels of constant porosity, that well-approximates the numerical solutions. This system can be evolved forward in time, and is simpler to solve than the full numerics, allowing for more efficient predictions to be made, such as when deciding dosing strategies for drug-laden hydrogels.

cond-mat.soft↗

arXiv2021

Local drag of a slender rod parallel to a plane wall in a viscous fluid

The viscous drag on a slender rod by a wall is important to many biological and industrial systems. This drag critically depends on the separation between the rod and the wall and can be approximated asymptotically in specific regimes, namely far from, or very close to, the wall, but is typically determined numerically for general separations. In this note we determine an asymptotic representation of the local drag for a slender rod parallel to a wall which is valid for all separations. This is possible through matching the behaviour of a rod close to the wall and a rod far from the wall. We show that the leading order drag in both these regimes has been known since 1981 and that they can used to produce a composite representation of the drag which is valid for all separations. This is in contrast to a sphere above a wall, where no simple uniformly valid representation exists. We estimate the error on this composite representation as the separation increases, discuss how the results could be used as resistive-force theory and demonstrate their use on a two-hinged swimmer above a wall.

physics.flu-dyn↗

arXiv2020

Slender Phoretic Theory of chemically active filaments

Artificial microswimmers, or "microbots" have the potential to revolutionise non-invasive medicine and microfluidics. Microbots that are powered by self-phoretic mechanisms, such as Janus particles, often harness a solute fuel in their environment. Traditionally, self-phoretic particles are point-like, but slender phoretic rods have become an increasingly prevalent design. While there has been substantial interest in creating efficient asymptotic theories for slender phoretic rods, hitherto such theories have been restricted to straight rods with axisymmetric patterning. However, modern manufacturing methods will soon allow fabrication of slender phoretic filaments with complex three-dimensional shape. In this paper, we develop a slender body theory for the solute of self-diffusiophoretic filaments of arbitrary three-dimensional shape and patterning. We demonstrate analytically that, unlike other slender body theories, first-order azimuthal variations arising from curvature and confinement can have a leading order contribution to the swimming kinematics.

physics.flu-dyn↗

arXiv2019

Efficient Implementation of Elastohydrodynamics via Integral Operators

The dynamics of geometrically non-linear flexible filaments play an important role in a host of biological processes, from flagella-driven cell transport to the polymeric structure of complex fluids. Such problems have historically been computationally expensive due to numerical stiffness associated with the inextensibility constraint, as well as the often non-trivial boundary conditions on the governing high-order PDEs. Formulating the problem for the evolving shape of a filament via an integral equation in the tangent angle has recently been found to greatly alleviate this numerical stiffness. The contribution of the present manuscript is to enable the simulation of non-local interactions of multiple filaments in a computationally efficient manner using the method of regularized stokeslets within this framework. The proposed method is benchmarked against a non-local bead and link model, and recent code utilizing a local drag velocity law. Systems of multiple filaments (1) in a background fluid flow, (2) under a constant body force, and (3) undergoing active self-motility are modeled efficiently. Buckling instabilities are analyzed by examining the evolving filament curvature, as well as by coarse-graining the body frame tangent angles using a Chebyshev approximation for various choices of the relevant non-dimensional parameters. From these experiments, insight is gained into how filament-filament interactions can promote buckling, and further reveal the complex fluid dynamics resulting from arrays of these interacting fibers. By examining active moment-driven filaments, we investigate the speed of worm- and sperm-like swimmers for different governing parameters. The MATLAB(R) implementation is made available as an open-source library, enabling flexible extension for alternate discretizations and different surrounding flows.

physics.flu-dyn↗

arXiv2019

Simulations of particle tracking in the oligociliated mouse node and implications for left-right symmetry breaking mechanics

The concept of internal anatomical asymmetry is familiar; usually in humans the heart is on the left and the liver is on the right, however how does the developing embryo know to produce this consistent laterality? Symmetry breaking initiates with left-right asymmetric cilia-driven fluid mechanics in a small fluid-filled structure called the ventral node in mice. However the question of what converts this flow into left-right asymmetric development remains unanswered. A leading hypotheses is that flow transports morphogen containing vesicles within the node, the absorption of which results in asymmetrical gene expression. To investigate how vesicle transport might result in the situs patterns observed in wildtype and mutant experiments, we extend the open source Stokes flow package, NEAREST, to consider the hydrodynamic and Brownian motion of particles in a mouse model with flow driven by one, two, and 112 beating cilia. Three models for morphogen-containing particle released are simulated to assess their compatibility with observed results in oligociliated and wildtype mouse embryos: uniformly random release, localised cilium stress induced release, and localised release from motile cilia themselves. Only the uniformly random release model appears consistent with the data, with neither localised-release model resulting in significant transport in the oligociliated embryo.

q-bio.TO↗

arXiv2018

Thrifty swimming with shear-thinning

Microscale propulsion is integral to numerous biomedical systems, for example biofilm formation and human reproduction, where the surrounding fluids comprise suspensions of polymers. These polymers endow the fluid with non-Newtonian rheological properties, such as shear-thinning and viscoelasticity. Thus, the complex dynamics of non-Newtonian fluids presents numerous modelling challenges, strongly motivating experimental study. Here, we demonstrate that failing to account for "out-of-plane" effects when analysing experimental data of undulatory swimming through a shear-thinning fluid results in a significant overestimate of fluid viscosity around the model swimmer C. elegans. This miscalculation of viscosity corresponds with an overestimate of the power the swimmer expends, a key biophysical quantity important for understanding the internal mechanics of the swimmer. As experimental flow tracking techniques improve, accurate experimental estimates of power consumption using this technique will arise in similar undulatory systems, such as the planar beating of human sperm through cervical mucus, will be required to probe the interaction between internal power generation, fluid rheology, and the resulting waveform.

physics.flu-dyn↗

arXiv2018

Clustering-induced self-propulsion of isotropic autophoretic particles

Self-diffusiophoretic particles exploit local concentration gradients of a solute species in order to self-propel at the micron scale. While an isolated chemically- and geometrically-isotropic particle cannot swim, we show that it can achieve self-propulsion through interactions with other individually-non-motile particles by forming geometrically-anisotropic clusters via phoretic and hydrodynamic interactions. This result identifies a new route to symmetry-breaking for the concentration field and to self-propulsion, that is not based on an anisotropic design, but on the collective dynamics of identical and homogeneous active particles. Using full numerical simulations as well as theoretical modelling of the clustering process, the statistics of the propulsion properties are obtained for arbitrary initial arrangement of the particles. The robustness of these results to thermal noise, and more generally the effect of Brownian motion of the particles, is also discussed.

cond-mat.soft↗

arXiv2018

Microtransformers: controlled microscale navigation with flexible robots

Artificial microswimmers are a new technology with promising microfluidics and biomedical applications, such as directed cargo transport, microscale assembly, and targeted drug delivery. A fundamental barrier to realising this potential is the ability to control the trajectories of multiple individuals within a large group. A promising navigation mechanism for "fuel-based" microswimmers, for example autophoretic Janus particles, entails modulating the local environment to guide the swimmer, for instance by etching grooves in microchannels. However, such techniques are currently limited to bulk guidance. This paper will argue that by manufacturing microswimmers from phoretic filaments of flexible shape-memory polymer, elastic transformations can modulate swimming behaviour, allowing precision navigation of selected individuals within a group through complex environments.

physics.flu-dyn↗

arXiv2017

Fake $μ$s: A cautionary tail of shear-thinning locomotion

Propulsion through fluids is a key component in the life cycle of many microbes, be it in development, infection, or simply finding nutrients. In systems of biomedical relevance, this propulsion is often through polymer suspensions that endow the fluid with complex non-Newtonian properties, such as shear-thinning and viscoelastic behaviour. Due to the complexity of 3D non-Newtonian modelling, 2D undulatory propulsion has recently been extensively-studied as a means of garnering physical intuition for these systems. However, while streamlines, swimming speeds, and swimmer trajectories are strikingly similar in 2D and 3D Newtonian calculations, behaviour in non-Newtonian fluids depends upon flow derivatives, such as the shear rate, which are radically different. Taking shear-thinning as an example rheology, prevalent in biological fluids such as physiological mucus, this communication demonstrates how failing to account for this difference can misguide our understanding of 3D non-Newtonian swimming.

physics.flu-dyn↗

arXiv2017

The autophoretic torus

Phoretic swimmers provide new avenues to study non-equilibrium statistical physics and are also hailed as a promising technology for bioengineering at the cellular scale. Exact solutions for the locomotion of such swimmers have been restricted so far to spheroidal shapes. In this paper we solve for the flow induced by the canonical non-simply connected shape, namely an axisymmetric phoretic torus. The analytical solution takes the form of an infinite series solution, which we validate against boundary element computations. For a torus of uniform chemical activity, confinement effects in the hole allow the torus to act as a pump, which we optimize subject to fixed particle surface area. Under the same constraint, we next characterize the fastest swimming Janus torus for a variety of assumptions on the surface chemistry. Perhaps surprisingly, none of the optimal tori occur in the limit where the central hole vanishes.

physics.flu-dyn↗

arXiv2016

Microscale Flow Dynamics of Ribbons and Sheets

Numerical study of the hydrodynamics of thin sheets and ribbons presents difficulties associated with resolving multiple length scales. To circumvent these difficulties, asymptotic methods have been developed to describe the dynamics of slender fibres and ribbons. However, such theories entail restrictions on the shapes that can be studied, and often break down in regions where standard boundary element methods are still impractical. In this paper we develop a regularised stokeslet method for ribbons and sheets in order to bridge the gap between asymptotic and boundary element methods. The method is validated against the analytical solution for plate ellipsoids, as well as the dynamics of ribbon helices and an experimental microswimmer. We then demonstrate the versatility of this method by calculating the flow around a double helix, and the swimming dynamics of a microscale "magic carpet".

physics.flu-dyn↗

arXiv2016

Flow analysis of the low-Reynolds number swimmer C. elegans

Swimming cells and microorganisms are a critical component of many biological processes. In order to better interpret experimental studies of low Reynolds number swimming, we combine experimental and numerical methods to perform an analysis of the flow-field around the swimming nematode Caenorhabditis elegans. We first use image processing and particle tracking velocimetry to extract the body shape, kinematics, and flow-fields around the nematode. We then construct a three-dimensional model using the experimental swimming kinematics and employ a boundary element method to simulate flow-fields, obtaining very good quantitative agreement with experiment. We use this numerical model to show that calculation of flow shear rates using purely planar data results in significant underestimates of the true three-dimensional value. Applying symmetry arguments, validated against numerics, we demonstrate that the out-of-plane contribution can be accounted for via incompressibility and therefore simply calculated from particle tracking velocimetry. Our results show how fundamental fluid mechanics considerations may be used to improve the accuracy of measurements in biofluiddynamics.

physics.flu-dyn↗

arXiv2016

Three-dimensional flow in Kupffer's Vesicle

Whilst many vertebrates appear externally left-right symmetric, the arrangement of internal organs is asymmetric. In zebrafish, the breaking of left-right symmetry is organised by Kupffer's Vesicle (KV): an approximately spherical, fluid-filled structure that begins to form in the embryo 10 hours post fertilisation. A crucial component of zebrafish symmetry breaking is the establishment of a cilia-driven fluid flow within KV. However, it is still unclear (a) how dorsal, ventral and equatorial cilia contribute to the global vortical flow, and (b) if this flow breaks left-right symmetry through mechanical transduction or morphogen transport. Fully answering these questions requires knowledge of the three-dimensional flow patterns within KV, which have not been quantified in previous work. In this study, we calculate and analyse the three-dimensional flow in KV. We consider flow from both individual and groups of cilia, and (a) find anticlockwise flow can arise purely from excess of cilia on the dorsal roof over the ventral floor, showing how this vortical flow is stabilised by dorsal tilt of equatorial cilia, and (b) show that anterior clustering of dorsal cilia leads to around 40% faster flow in the anterior over the posterior corner. We argue that these flow features are supportive of symmetry breaking through mechano-sensory cilia, and suggest a novel experiment to test this hypothesis. From our new understanding of the flow, we propose a further experiment to reverse the flow within KV to potentially induce situs inversus.

physics.flu-dyn↗

arXiv2015

A regularised singularity approach to phoretic problems

An efficient, accurate, and flexible numerical method is proposed for the solution of the swimming problem of one or more autophoretic particles in the purely-diffusive limit. The method relies on successive boundary element solutions of the Laplacian and the Stokes flow equations using regularised Green's functions for swift, simple implementations, an extension of the well-known method of "regularised stokeslets" for Stokes flow problems. The boundary element method is particularly suitable for phoretic problems, since no quantities in the domain bulk are required to compute the swimming velocity. For time-dependent problems, the method requires no re-meshing and simple boundaries such as a plane wall may be added at no increase to the size of the linear system through the method of images. The method is validated against two classical examples for which an analytical or semi-analytical solution is known, a two-sphere system and a Janus particle, and provides a rigorous computational pipeline to address further problems with complex geometry and multiple bodies.

physics.flu-dyn↗