Learning deterministic hydrodynamic equations from stochastic active particle dynamics
Technische Universität Dresden（德累斯顿工业大学）；Max Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）；Center for Systems Biology Dresden（德累斯顿系统生物学中心）；Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI（可扩展数据分析与人工智能中心 ScaDS.AI）；Cluster of Excellence Physics of Life, TU Dresden（德累斯顿工业大学生命物理卓越集群）；Max Planck Institute for the Physics of Complex Systems（马克斯·普朗克复杂系统物理研究所）；University of Geneva（日内瓦大学）
Suryanarayana Maddu, Quentin Vagne, Ivo F. Sbalzarini
We present a principled data-driven strategy for learning deterministic hydrodynamic models directly from stochastic non-equilibrium active particle trajectories. We apply our method to learning a hydrodynamic model for the propagating density lanes observed in self-propelled particle systems and to learning a continuum description of cell dynamics in epithelial tissues. We also infer from stochastic particle trajectories the latent phoretic fields driving chemotaxis. This demonstrates that statistical learning theory combined with physical priors can enable discovery of multi-scale models of non-equilibrium stochastic processes characteristic of collective movement in living systems.
Kyushu Institute of Technology（九州工业大学）；The Institute of Statistical Mathematics（统计数学研究所）；RIKEN AIP（理化学研究所人工智能研究中心）
Active learning is a framework in which the learning machine can select the samples to be used for training. This technique is promising, particularly when the cost of data acquisition and labeling is high. In active learning, determining the timing at which learning should be stopped is a critical issue. In this study, we propose a criterion for automatically stopping active learning. The proposed stopping criterion is based on the difference in the expected generalization errors and hypothesis testing. We derive a novel upper bound for the difference in expected generalization errors before …
Self-propelled phoretic colloids have recently emerged as a promising avenue for the design of artificial swimmers. These swimmers combine purely phoretic interactions with intricate hydrodynamics which critically depend on the swimmer shape. Thermophobic dimer shaped colloids are here investigated by means of hydrodynamic simulations, from the single particle motion to their collective behavior. The combination of phoretic repulsion with hydrodynamic lateral attraction favors the formation of planar moving clusters. The resulting hydrodynamic assembly in flattened swarms is therefore very spe…
We simulate with hydrodynamics a suspension of active disks squirming through a Newtonian fluid. We explore numerically the full range of squirmer area fractions from dilute to close packed and show that "motility induced phase separation" (MIPS), which was recently proposed to arise generically in active matter, and which has been seen in simulations of active Brownian disks, is strongly suppressed by hydrodynamic interactions. We give an argument for why this should be the case and support it with counterpart simulations of active Brownian disks in a parameter regime that provides a closer c…
The lack of detailed balance in active colloidal suspensions allows dissipation to determine stationary states. Here we show that slow viscous flow produced by polar or apolar active colloids near plane walls mediates attractive hydrodynamic forces that drive crystallization. Hydrodynamically mediated torques tend to destabilize the crystal but stability can be regained through critical amounts of bottom-heaviness or chiral activity. Numerical simulations show that crystallization is not nucleational, as in equilibrium, but is preceded by a spinodal-like instability. Harmonic excitations of th…
The equations of hydrodynamics including mass, linear momentum, angular momentum, and energy are derived by coarse-graining the microscopic equations of motion for systems consisting of rotary dumbbells driven by internal torques.
In active nematic liquid crystals activity is able to drive chaotic spatiotemporal flows referred to as active turbulence. Active turbulence has been characterized through theoretical and experimental work as a low Reynolds number phenomenon. We show that, in two-dimensions, the active forcing alone is able to trigger hydrodynamic turbulence leading to the coexistence of active and inertial turbulence. This type of flows develops for sufficiently active and extensile flow-aligning nematics. We observe that the combined effect of an extensile nematic and large values of the flow-aligning parame…
Estimation of spatial and time scales of collective behaviors of active matters through learning hydrodynamic equations from particle dynamics
Future University Hakodate（函馆未来大学）；AIST（产业技术综合研究所）；Mathematics for Advanced Materials-OIL (MathAM-OIL), AIST（产业技术综合研究所 先进材料数学-OIL）；WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University（东北大学 WPI-材料研究高级研究所）
This is a series of four lectures presented at the 2015 Enrico Fermi summer school in Varenna. The aim of the lectures is to give an introduction to the hydrodynamics of active matter concentrating on low Reynolds number examples such as cells and molecular motors. Lecture 1 introduces the hydrodynamics of single active particles, covering the Stokes equation and the Scallop Theorem, and stressing the link between autonomous activity and the dipolar symmetry of the far flow field. In lecture 2 I discuss applications of this mathematics to the behaviour of microswimmers at surfaces and in exter…
Spontaneously flowing liquids have been successfully engineered from a variety of biological and synthetic self-propelled units. Together with their orientational order, wave propagation in such active fluids have remained a subject of intense theoretical studies. However, the experimental observation of this phenomenon has remained elusive. Here, we establish and exploit the propagation of sound waves in colloidal active materials with broken rotational symmetry. We demonstrate that two mixed modes coupling density and velocity fluctuations propagate along all directions in colloidal-roller f…
We derive the hydrodynamic equations of motion for a fluid of active particles described by under- damped Langevin equations that reduce to the Active-Brownian-Particle model, in the overdamped limit. The contraction into the hydrodynamic description is performed by locally averaging the par- ticle dynamics with the non-equilibrium many-particle probability density, whose formal expression is found in the physically relevant limit of high-friction through a multiple-time-scale analysis. This approach permits to identify the conditions under which self-propulsion can be subsumed into the fluid …
Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium fluctuating flows collectively generated by the enzymes, mixing in the solution and diffusion of passive particles within it are expected to get enhanced. Here, we investigate the intensity and statistical properties of such force dipoles in the minimal active dimer model of a mechanochemical enzyme. In the framework of this model, novel estimates for hydrodynamic co…
We utilize a generalized Irving-Kirkwood procedure to derive the hydrodynamic equations of an active matter suspension with internal structure and driven by internal torque. The internal structure and torque of the active Brownian particles give rise to a balance law for internal angular momentum density, making the hydrodynamic description a polar theory of continuum mechanics. We derive exact microscopic expressions for the stress tensor, couple stress tensor, internal energy density, and heat flux vector. Unlike passive matter, the symmetry of the stress tensor is broken explicitly due to a…
In dense colloids it is commonly assumed that hydrodynamic interactions do not play a role. However, a found theoretical quantification is often missing. We present computer simulations that are motivated by experiments where a large colloidal particle is dragged through a colloidal crystal. To qualify the influence of long-ranged hydrodynamics, we model the setup by conventional Langevin dynamics simulations and by an improved scheme with limited hydrodynamic interactions. This scheme significantly improves our results and allows to show that hydrodynamics strongly impacts on the development …
We develop a general hydrodynamic theory describing a system of interacting actively propelling particles of arbitrary shape suspended in a viscous fluid. We model the active part of the particle motion using a slip velocity prescribed on the otherwise rigid particle surfaces. We introduce the general framework for particle rotations and translations by applying the Lorentz reciprocal theorem for a collection of mobile particles with arbitrary surface slip. We then develop an approximate theory applicable to widely separated spheres, including hydrodynamic interactions up to the level of force…
We study the collective motion of confined spherical microswimmers such as active colloids which we model by so-called squirmers. To simulate hydrodynamic flow fields including thermal noise, we use the method of multi-particle collision dynamics. We demonstrate that hydrodynamic near fields acting between squirmers as well as squirmers and bounding walls crucially determine their collective motion. In particular, with increasing density we observe a clear phase separation into a gas-like and cluster phase for neutral squirmers whereas strong pushers and pullers more gradually approach the hex…
We study numerically the role of hydrodynamics in the liquid-hexatic transition of active colloids at intermediate activity, where motility induced phase separation (MIPS) does not occur. We show that in the case of active Brownian particles (ABP), the critical density of the transition decreases upon increasing the particle's mass, enhancing ordering, while self-propulsion has the opposite effect in the activity regime considered. Active hydrodynamic particles (AHP), instead, undergo the liquid-hexatic transition at higher values of packing fraction $ϕ$ than the corresponding ABP, suggesting …
The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We analyze the effects that hydrodynamic flows induced by active proteins have on other passive molecules in solution or membranes. We show that the diffusion constants of passive particles are enhanced substantially. Furthermore, when gradients of active proteins are present, a chemotaxis-like drift of passive particles takes place. In lipid bilayers, the effects ar…
Quasi-one-dimensional motion of an active MXene sheet driven by chemo-hydrodynamic waves
China University of Mining and Technology, College of Chemical Engineering（中国矿业大学化学工程学院）；Brandeis University,Department of Chemistry and Volen Center for Complex Systems（布兰迪斯大学化学系与沃尔恩复杂系统中心）
Hydrodynamic equations for an isotropic solution of active polar filaments are derived from a microscopic mean-field model of the forces exchanged between motors and filaments. We find that a spatial dependence of the motor stepping rate along the filament is essential to drive bundle formation. A number of differences arise as compared to hydrodynamics derived (earlier) from a mesoscopic model where relative filament velocities were obtained on the basis of symmetry considerations. Due to the anisotropy of filament diffusion, motors are capable of generating net filament motion relative to th…
The conformational and dynamical properties of active self-propelled filaments/polymers are investigated in the presence of hydrodynamic interactions by both, Brownian dynamics simulations and analytical theory. Numerically, a discrete linear chain composed of active Brownian particles is considered, analytically, a continuous linear semiflexible polymer with active velocities changing diffusively. The force-free nature of active monomers is accounted for - no Stokeslet fluid flow induced by active forces - and higher order hydrodynamic multipole moments are neglected. The nonequilibrium chara…
Using a simple model of self-propelled particle, the effective shear viscosity of a dilute, spatially homogeneous suspension of active particles is studied. We use formulation of non-linear Fokker-Planck equation to drive a kinetic description, including the effect of external flow field, rotary diffusion, and particle-particle hydrodynamic interactions in two dimensions. Analytical expressions are obtained for the stress tensor at small Peclet numbers, in a simple shear flow, up to second order of volume fraction of the swimmers, which shows the explicit dependence of shear viscosity on the d…
The success of spectroscopy to characterise equilibrium fluids, for example the heat capacity ratio, suggests a parallel approach for active fluids. Here, we start from a hydrodynamic description of chiral active fluids composed of spinning constituents and derive their low-frequency, long-wavelength response functions using the Kadanoff-Martin formalism. We find that the presence of odd (equivalently, Hall) viscosity leads to mixed density-vorticity response even at linear order. Such response, prohibited in time-reversal-invariant fluids, is a large-scale manifestation of the microscopic bre…
We propose a simple deterministic dynamic equation and reveal the mechanism of large-scale endless evolvement of spatial density inhomogeneity in active nematic. We determine the phase regions analytically. The interplay of density, magnitude of nematic order, and nematic director is crucial for the long-wave-length instability and the emergence of seemingly fluctuated collective motions. Ordered nematic domains can absorb particles, grow and divide endlessly. The present finding extends our understanding of the large-scale and seemingly fluctuated organization in active fluids.
Collective motion is often modeled within the framework of active fluids, where the constituent active particles, when interactions with other particles are switched off, perform normal diffusion at long times. However, in biology, single-particle superdiffusion and fat-tailed displacement statistics are also widespread. The collective properties of interacting systems exhibiting such anomalous diffusive dynamics, which we call active Lévy matter, cannot be captured by current active fluid theories. Here, we formulate a hydrodynamic theory of active Lévy matter by coarse-graining a microscopic…
We investigate the motion of active semiflexible filament with shape kinematics and hydrodynamic interaction including. Three types of filament motion are found: Translation, snaking and rotation. Change of flexibility will induce instability of shape kinematics and further result in asymmetry of shape kinematics respect to the motion of mass center, which are responsible to a continuous-like transition from translation to snaking and a first-order-like transition from snaking to rotation, respectively. Of particular interest, we find that long-range hydrodynamic interaction is not necessary f…
Topological defects play a prominent role in the physics of two-dimensional materials. When driven out of equilibrium in active nematics, disclinations can acquire spontaneous self-propulsion and drive self-sustained flows upon proliferation. Here we construct a general hydrodynamic theory for a two-dimensional active nematic interrupted by a large number of such defects. Our equations describe the flows and spatio-temporal defect chaos characterizing active turbulence, even close to the defect unbinding transition. At high activity, nonequilibrium torques combined with many-body screening cau…
We study the role of hydrodynamic interactions in the collective behaviour of collections of microscopic active particles suspended in a fluid. We introduce a novel calculational framework that allows us to separate the different contributions to their collective dynamics from hydrodynamic interactions on different length scales. Hence we are able to systematically show that lubrication forces when the particles are very close to each other play as important a role as long-range hydrodynamic interactions in determining their many-body behaviour. We find that motility-induced phase separation i…
We examine the scaling with activity of the emergent length scales that control the nonequilibrium dynamics of an active nematic liquid crystal, using two popular hydrodynamic models that have been employed in previous studies. In both models we find that the chaotic spatio-temporal dynamics in the regime of fully developed active turbulence is controlled by a single active scale determined by the balance of active and elastic stresses, regardless of whether the active stress is extensile or contractile in nature. The observed scaling of the kinetic energy and enstropy with activity is consist…
Active bodies in viscous fluids interact hydrodynamically through self-generated flows. Here we study spontaneous aggregation induced by hydrodynamic flow in a suspension of stiff, apolar, active filaments. Lateral hydrodynamic attractions in extensile filaments lead, independent of volume fraction, to anisotropic aggregates which translate and rotate ballistically. Lateral hydrodynamic repulsion in contractile filaments lead, with increasing volume fractions, to microstructured states of asters, clusters, and incipient gels where, in each case, filament motion is diffusive. Our results demons…
A system of active colloidal particles driven by harmonic potentials to oscillate about the vertices of a regular polygon, with hydrodynamic coupling between all particles, is described by a piece-wise linear model which exhibits various patterns of synchronization. Analytical solutions are obtained for this class of dynamical systems. Depending only on the number of particles, the synchronization occurs into states in which nearest neighbors oscillate either in-phase, or anti-phase, or in phase-locked (time-shifted) trajectories.
We study the hydrodynamic behavior of three dimensional (3D) incompressible collections of self-propelled entities in contact with a momentum sink in a state with non-zero average velocity, hereafter called 3D easy-plane incompressible polar active fluids. We show that the hydrodynamic model for this system belongs to the same universality class as that of an equilibrium system, namely a special 3D anisotropic magnet. The latter can be further mapped onto yet another equilibrium system, a DNA-lipid mixture in the sliding columnar phase. Through these connections we find a divergent renormaliza…
We simulate clustering, phase separation and hexatic ordering in a monolayered suspension of active squirming disks subject to an attractive Lennard-Jones-like pairwise interaction potential, taking hydrodynamic interactions between the particles fully into account. By comparing the hydrodynamic case with counterpart simulations for passive and active Brownian particles, we elucidate the relative roles of self-propulsion, interparticle attraction, and hydrodynamic interactions in determining clustering and phase behaviour. Even in the presence of an attractive potential, we find that hydrodyna…
We describe the basic properties and consequences of introducing active stresses, with principal direction along the local director, in cholesteric liquid crystals. The helical ground state is found to be linearly unstable to extensile stresses, without threshold in the limit of infinite system size, whereas contractile stresses are hydrodynamically screened by the cholesteric elasticity to give a finite threshold. This is confirmed numerically and the non-linear consequences of instability, in both extensile and contractile cases, are studied. We also consider the stresses associated to defec…
We derive hydrodynamic equations from Vicsek-style dry active matter models in three dimensions (3D), building on our experience on the 2D case using the Boltzmann-Ginzburg-Landau approach. The hydrodynamic equations are obtained from a Boltzmann equation expressed in terms of an expansion in spherical harmonics. All their transport coefficients are given with explicit dependences on particle-level parameters. The linear stability analysis of their spatially-homogeneous solutions is presented. While the equations derived for the polar case (original Vicsek model with ferromagnetic alignment) a…
Microswimmers often exhibit surprising patterns due to the nonequilibrium nature of their dynamics. Collectively, suspensions of microswimmers appear as a liquid whose properties set it apart from its passive counterpart. To understand the impact of hydrodynamic interactions on the basic statistical features of a microswimmer's liquid, we investigate its structure by means of the pair distribution function. We perform particle-based simulations of microswimmers that include steric effects, shape anisotropy, and hydrodynamic interactions. We find that hydrodynamic interactions considerably alte…
A plethora of active matter models exist that describe the behavior of self-propelled particles (or swimmers), both with and without hydrodynamics. However, there are few studies that consider shape-anisotropic swimmers and include hydrodynamic interactions. Here, we introduce a simple method to simulate self-propelled colloids interacting hydrodynamically in a viscous medium using the lattice-Boltzmann technique. Our model is based on raspberry-type viscous coupling and a force/counter-force formalism which ensures that the system is force free. We consider several anisotropic shapes and char…
Active fluids comprise a variety of systems composed of elements immersed in a fluid environment which can convert some form of energy into directed motion; as such they are intrinsically out-of-equilibrium in the absence of any external forcing. A fundamental problem in the physics of active matter concerns the understanding of how the characteristics of the autonomous propulsion and agent-agent interactions determine the collective dynamics of the system. We study numerically suspensions of self-propelled diffusiophoretic colloids, in (quasi)-2d configurations, accounting for both dynamicall…
Self-propelled particles with hydrodynamic interactions (microswimmers) have previously been shown to produce long-range ordering phenomena. Many theoretical explanations for these collective phenomena are connected to instabilities in the hydrodynamic or kinetic equations. By incorporating stochastic fluxes into the mean field kinetic equation, we quantify the dynamics of a suspension of microswimmers in the parameter regime where the deterministic equation is stable. We can thereby compute nontrivial collective phenomena concerning spatial correlations of orientation and stress as well as th…
The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed active noise. Essential elements of this circuitry are enzymes, catalysts that speed up the rate of metabolic reactions by orders of magnitude, thereby making life possible. Here, we examine the possibility that active noise in the cell, or in vitro, affects enzymatic catalytic rate by accelerating or decelerating the crossing rate of energy barriers during the reaction. Considering hydrodynamic perturbations induced by biochemical activity as a source o…
We derive the Hydrodynamics for a system of N active, spherical, underdamped particles, interacting through conservative forces. At the microscopic level, we represent the evolution of the particles in terms of the Kramers equation for the probability density distribution of their positions, velocities, and orientations, while at a mesoscopic level we switch to a coarse-grained description introducing an appropriate set of hydrodynamic fields given by the lower-order moments of the distribution. In addition to the usual density and polarization fields, the Hydrodynamics developed in this paper…
We present a hydrodynamic theory of polar active smectics, for systems both with and without number conservation. For the latter, we find quasi long-ranged smectic order in d=2 and long-ranged smectic order in d=3. In d=2 there is a Kosterlitz-Thouless type phase transition from the smectic phase to the ordered fluid phase driven by increasing the noise strength. For the number conserving case, we find that giant number fluctuations are greatly suppressed by the smectic order; that smectic order is long-ranged in d=3; and that nonlinear effects become important in d=2.
We perform a coarse-graining analysis of the paradigmatic active matter model, Active Brownian Particles, yielding a continuum description in terms of balance laws for mass, linear and angular momentum, and energy. The derivation of the balance of linear momentum reveals that the active force manifests itself directly as a continuum-level body force proportional to an order parameter-like director field, which therefore requires its own evolution equation to complete the continuum description of the system. We derive this equation, demonstrating in the process that bulk currents may be sustain…
We analyze the conformational dynamics and statistical properties of an active polymer model. The polymer is described as a freely-jointed bead-rod chain subject to stochastic active force dipoles that act on the suspending solvent where they drive long-ranged fluid flows. Using Langevin simulations of isolated chains in unconfined domains, we show how the coupling of active flows with polymer conformations leads to emergent dynamics. Systems with contractile dipoles behave similarly to passive Brownian chains with enhanced fluctuations due to dipolar flows. In systems with extensile dipoles, …
We theoretically describe the dynamics of swimmer populations confined in thin liquid films. We first demonstrate that hydrodynamic interactions between confined swimmers only depend on their shape and are independent of their specific swimming mechanism. We also show that due to friction with the walls, confined swimmers do not reorient due to flow gradients but the flow field itself. We then quantify the consequences of these microscopic interaction rules on the large-scale hydrodynamics of isotropic populations. We investigate in details their stability and the resulting phase behavior, hig…
Strongly confined active liquids are subject to unique hydrodynamic interactions due to momentum screening and lubricated friction by the confining walls. Using numerical simulations, we demonstrate that 2D dilute suspensions of fore-aft asymmetric polar swimmers in a Hele-Shaw geometry can exhibit a rich variety of novel phase behaviors depending on particle shape, including: coherent polarized density waves with global alignment, stationary asters, persistent counter-rotating vortices, density shocks and rarefaction waves. We also explain these phenomena using a linear stability analysis and…
Using lattice Boltzmann simulations we study the hydrodynamics of an active spherical particle near a no-slip wall. We develop a computational model for an active Janus particle, by considering different and independent mobilities on the two hemispheres and compare the behaviour to a standard squirmer model.We show that the topology of the far-field hydrodynamic nature of the active Janus particle is similar to the standard squirmer model, but in the near-field the hydrodynamics differ. In order to study how the near-field effects affect the interaction between the particle and a flat wall, we…
Active colloids self-organise to a variety of collective states, ranging from highly motile 'molecules' to complex 3D structures. Using large-scale simulations, we show that hydrodynamic interactions, together with a gravity-like aligning field, lead to tunable self-assembly of active colloidal spheres near a surface. The observed structures depend on the hydrodynamic characteristics: particles driven at the front, pullers, form small chiral spinners consisting of two or three particles, whereas those driven at the rear, pushers, assemble to large dynamic aggregates. The rotational motion of t…
