A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes
Vamsi Spandan, Valentina Meschini, Rodolfo Ostilla-Monico, Detlef Lohse, Giorgio Querzoli, Marco D de Tullio, Roberto Verzicco
In this paper we show and discuss the use of a versatile interaction potential approach coupled with an immersed boundary method to simulate a variety of flows involving deformable bodies. In particular, we focus on two kinds of problems, namely (i) deformation of liquid-liquid interfaces and (ii) flow in the left ventricle of the heart with either a mechanical or a natural valve. Both examples have in common the two-way interaction of the flow with a deformable interface or a membrane. The interaction potential approach (de Tullio & Pascazio, Jou. Comp. Phys., 2016; Tanaka, Wada and Nakamura, Computational Biomechanics, 2016) with minor modifications can be used to capture the deformation dynamics in both classes of problems. We show that the approach can be used to replicate the deformation dynamics of liquid-liquid interfaces through the use of ad-hoc elastic constants. The results from our simulations agree very well with previous studies on the deformation of drops in standard flow configurations such as deforming drop in a shear flow or a cross flow. We show that the same potential approach can also be used to study the flow in the left ventricle of the heart. The flow imposed into the ventricle interacts dynamically with the mitral valve (mechanical or natural) and the ventricle which are simulated using the same model. Results from these simulations are compared with ad- hoc in-house experimental measurements. Finally, a parallelisation scheme is presented, as parallelisation is unavoidable when studying large scale problems involving several thousands of simultaneously deforming bodies on hundreds of distributed memory computing processors.
Microorganisms are rarely found in Nature swimming freely in an unbounded fluid. Instead, they typically encounter other organisms, hard walls, or deformable boundaries such as free interfaces or membranes. Hydrodynamic interactions between the swimmer and nearby objects lead to many interesting phenomena, such as changes in swimming speed, tendencies to accumulate or turn, and coordinated flagellar beating. Inspired by this class of problems, we investigate locomotion of microorganisms near deformable boundaries. We calculate the speed of an infinitely long swimmer close to a flexible surface…
Deformable elastic bodies in viscous and viscoelastic media constitute a large portion of synthetic and biological complex fluids. We present a parallelized 3D-simulation methodology which fully resolves the momentum balance in the solid and fluid domains. An immersed boundary algorithm is exploited known as the immersed finite element method (IFEM) which accurately determines the internal forces in the solid domain. The scheme utilized has the advantages of requiring no costly re-meshing, handling finite Reynold's number, as well as incorporating non-linear viscoelasticity in the fluid domain…
In this work, a dynamic-Immersed--Boundary method combined with a BGK-Lattice--Boltzmann technique is developed and critically discussed. The fluid evolution is obtained on a three-dimensional lattice with 19 reticular velocities (D3Q19 computational molecule) while the immersed body surface is modeled as a collection of Lagrangian points responding to an elastic potential and a bending resistance. A moving least squares reconstruction is used to accurately interpolate flow quantities and the forcing field needed to enforce the boundary condition on immersed bodies. The proposed model is widel…
Immersed boundary methods are extensively used for simulations of dynamic solid objects interacting with fluids due to their computational efficiency and modelling flexibility compared to body-fitted grid methods. However, thin geometries, such as shells and membranes, cause a violation of the boundary conditions across the surface for many immersed boundary projection algorithms. Using a one-dimensional analytical derivation and multi-dimensional numerical simulations, this manuscript shows that adjustment of the Poisson matrix itself is require to avoid large velocity, pressure, and force pr…
We perform a stability analysis for a fluid-structure interaction problem in which a spherical elastic shell or membrane is immersed in a 3D viscous, incompressible fluid. The shell is an idealised structure having zero thickness, and has the same fluid lying both inside and outside. The problem is formulated mathematically using the immersed boundary framework in which Dirac delta functions are employed to capture the two-way interaction between fluid and immersed structure. The elastic structure is driven parametrically via a time-periodic modulation of the elastic membrane stiffness. We per…
A microfluidic device is constructed from PDMS with a single channel having a short section that is a thin flexible membrane, in order to investigate the complex fluid-structure interaction that arises between a flowing fluid and a deformable wall. Experimental measurements of membrane deformation and pressure drop are compared with predictions of two-dimensional and three-dimensional computational models which numerically solve the equations governing the elasticity of the membrane coupled with the equations of motion for the fluid. It is shown that the two-dimensional model, which assumes a …
Active gel theory has recently been very successful in describing biologically active materials such as actin filaments or moving bacteria in temporally fixed and simple geometries such as cubes or spheres. Here we develop a computational algorithm to compute the dynamic evolution of an arbitrarily shaped, deformable thin membrane of active material embedded in a 3D flowing liquid. For this, our algorithm combines active gel theory with the classical theory of thin elastic shells. To compute the actual forces resulting from active stresses, we apply a parabolic fitting procedure to the triangu…
The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable so…
The emerging field of deformable microfluidics widely employed in the Lab-on-a-Chip and MEMS communities offers an opportunity to study a relatively under-examined physics. The main objective of this work is to provide a deeper insight into the underlying coupled fluid-solid interactions of a low-Reynolds-number fluid flow through a shallow deformable microchannel with ultra-low height-to-width ratios. The fabricated deformable microchannels of several microns in height and few millimeters in width, whose aspect ratio is about two orders of magnitude smaller than that of the previous reports, …
A computational study of capsule ejection from a narrow channel into a reservoir is undertaken for a combination of varying deformable capsule sizes and channel dimensions. A mass spring membrane model is coupled to an Immersed Boundary Lattice Boltzmann model solver. The aim of the present work is the description of the capsules motion, deformation and the response of the fluid due to the complex particle dynamics. The interactions between the capsules affect the local velocity field significantly and are responsible for the dynamics observed. Capsule membrane deformability is also seen to af…
The steady flow of three viscoelastic fluids (Oldroyd-B, FENE-P, and Owens model for blood) in a two-dimensional channel, partly bound by a deformable, finite thickness neo-Hookean solid, is computed. The limiting Weissenberg number beyond which computations fail to converge is found to increase with increasing dimensionless solid elasticity parameter Γ, following the trend Owens > FENE- P > Oldroyd-B. The highly shear thinning nature of Owens model leads to the elastic solid always collapsing into the channel, for the wide range of values of Γ considered here. In the case of the FENE-P and Ol…
Modeling the transport of deformable capsules under different flow regimens is crucial in a variety of fields, including oil rheology, blood flow and the dispersion of pollutants. The aim of this study is twofold. Firstly, a combined Lattice Boltzmann-Immersed Boundary (LBM-IB) approach is developed for predicting the transport of inertial deformable capsules. A Moving Least Squares (MLS) scheme has been implemented to correlate the pressure, velocity and force fields of the fluid domain with the capsule dynamics. This computational strategy has been named LBM Dynamic IB. Secondly, this strate…
We study the instability of a thin membrane (of zero bending rigidity) to out-of-plane deflections, when the membrane is immersed in an inviscid fluid flow and sheds a trailing vortex-sheet wake. We solve the nonlinear eigenvalue problem iteratively with large ensembles of initial guesses, for three canonical boundary conditions---both ends fixed, one end fixed and one free, and both free. Over several orders of magnitude of membrane mass density, we find instability by divergence or flutter (particularly at large mass density, or with one or both ends free). The most unstable eigenmodes gener…
We present an open-source adaptive front-tracking solver for biological capsules in viscous flows. The membrane elastic and bending forces are solved on a Lagrangian triangulation using a linear Finite Element Method and a paraboloid fitting method. The fluid flow is solved on an octree adaptive grid using the open-source platform Basilisk. The Lagrangian and Eulerian grids communicate using an Immersed Boundary Method by means of Peskin-like regularized Dirac delta functions. We demonstrate the accuracy of our solver with extensive validations: in Stokes conditions against the Boundary Integr…
In this paper, the dynamic of inertial capsules into microfluidic bifurcations is studied. The fluid evolution is based on the solution of the BGK -- lattice Boltzmann scheme including a forcing term accounting for immersed geometries. The dynamic-Immersed Boundary forcing strategy is adopted for imposing no-slip boundary conditions on moving deformable or rigid structures, while, on fixed immersed geometries the Bouzidi-Firdaouss-Lallemand second-order bounce back technique is implemented. The proposed computational framework is employed to detail dynamics and deformation of rigid and deforma…
We present a fully Eulerian hybrid immersed-boundary/phase-field model to simulate wetting and contact line motion over any arbitrary geometry. The solid wall is described with a volume-penalisation ghost-cell immersed boundary whereas the interface between the two fluids by a diffuse-interface method. The contact line motion on the complex wall is prescribed via slip velocity in the momentum equation and static/dynamic contact angle condition for the order parameter of the Cahn-Hilliard model. This combination requires accurate computations of the normal and tangential gradients of the scalar…
Strongly coupled immersed boundary (IB) methods solve the nonlinear fluid and structural equations of motion simultaneously for strongly enforcing the no-slip constraint on the body. Handling this constraint requires solving several large dimensional systems that scale by the number of grid points in the flow domain even though the nonlinear constraints scale only by the small number of points used to represent the fluid-structure interface. These costly large scale operations for determining only a small number of unknowns at the interface creates a bottleneck to efficiently time-advancing st…
We study the motion of a solid particle immersed in a Newtonian fluid and confined between two parallel elastic membranes possessing shear and bending rigidity. The hydrodynamic mobility depends on the frequency of the particle motion due to the elastic energy stored in the membrane. Unlike the single-membrane case, a coupling between shearing and bending exists. The commonly used approximation of superposing two single-membrane contributions is found to give reasonable results only for motions in the parallel, but not in the perpendicular direction. We also compute analytically the membrane d…
IB-Flows: an open-source multi-GPU immersed boundary code for fluid-structure interaction
Gran Sasso Science Institute (GSSI)（格兰萨索科学研究所）；INFN–Laboratori Nazionali del Gran Sasso（意大利国家核物理研究所-格兰萨索国家实验室）；Department of Physics and INFN, University of Rome, Tor Vergata（罗马托尔维加塔大学物理系及意大利国家核物理研究所）；NVIDIA Corporation（英伟达公司）；Physics of Fluids Group, University of Twente（特温特大学流体力学组）
Fluid-structure interaction (FSI) of thin flexible fins coupled with convective heat transfer has applications in energy harvesting and in understanding functioning of several biological systems. We numerically investigate FSI of the thin flexible fins involving large-scale flow-induced deformation as a potential heat transfer enhancement technique. An in-house, strongly-coupled fluid-structure interaction (FSI) solver is employed in which flow and structure solvers are based on sharp-interface immersed boundary and finite element method, respectively. We consider twin flexible fins in a heate…
In this paper we consider the effects of the interaction between droplets or other deformable objects in an emulsion under random stirring of the host fluid. Our main interest is to obtain autocorrelation functions of the shape fluctuations in such randomly stirred host fluids, beyond the dilute limit regime. Thus, a system of deformable objects immersed in a host liquid that is randomly stirred is considered, where the objects interact with each other via the host liquid. Keeping expressions in the first order in the density of objects and in deviation of objects shapes from spherical, the sh…
The non-linear interaction between air and a water droplet just prior to high-speed impingement on a surface is a phenomenon that has been researched extensively and occurs in a number of industrial settings. The role that surface deformation plays in an air cushioned impact of a liquid droplet is considered here. In a two-dimensional framework, assuming small density and viscosity ratios between the air and the liquid, a reduced system of integro-differential equations is derived governing the liquid droplet free-surface shape, the pressure in the thin air film and the deformation of the surf…
We present a thermodynamically consistent model of a ternary fluid interacting with elastic membranes. Following a free-energy modelling approach and taking into account the thermodynamics laws, we derive the equations governing the ternary fluid flow and dynamics of the membranes. We also provide the numerical framework for simulating such fluid-structure interaction problems. It is based on the lattice Boltzmann method, employed for resolving the evolution equations of the ternary fluid in an Eulerian description, coupled to the immersed boundary method, allowing for the membrane equations o…
A three-dimensional numerical model of vesicle electrohydrodynamics in the presence of DC electric fields is presented. The vesicle membrane is modeled as a thin capacitive interface through the use of a semi-implicit level set Jet scheme. The enclosed volume and surface area are conserved both locally and globally by a new Navier-Stokes projection method. The electric field calculations explicitly take into account the capacitive interface by an implicit Immersed Interface Method formulation, which calculates the electric potential field and the trans-membrane potential simultaneously. The re…
Deformable bodies in a 3-dimensional viscous flow: Vorticity-Stream vector formulation
Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, Inserm, Université PSL（跨学科生物研究中心，法兰西学院，法国国家科学研究中心，法国国家健康与医学研究院，巴黎文理研究大学）；Facultat de Física, Universitat de Barcelona（巴塞罗那大学物理学院）；Instituto de Investigación Tecnológica (IIT) and Grupo Interdisciplinar de Sistemas Complejos (GISC), Universidad Pontificia Comillas（技术研究所和复杂系统跨学科小组，科米利亚斯宗座大学）；Institute of Nanoscience and Nanotechnology (IN2UB)（纳米科学与技术研究所）
ETH Zurich（苏黎世联邦理工学院）；ETH AI Center（苏黎世联邦理工学院人工智能中心）；Institute of Neuroinformatics, ETH Zurich（苏黎世联邦理工学院神经信息学研究所）
Aquatic locomotion is a classic fluid-structure interaction (FSI) problem of interest to biologists and engineers. Solving the fully coupled FSI equations for incompressible Navier-Stokes and finite elasticity is computationally expensive. Optimizing robotic swimmer design within such a system generally involves cumbersome, gradient-free procedures on top of the already costly simulation. To address this challenge we present a novel, fully differentiable hybrid approach to FSI that combines a 2D direct numerical simulation for the deformable solid structure of the swimmer and a physics-constra…
The dynamics of a spherical elastic capsule, containing a Newtonian fluid bounded by an elastic membrane and immersed in another Newtonian fluid, in a uniform DC electric field is investigated. Discontinuity of electrical properties such as conductivities of the internal and external fluid media as well as capacitance and conductance of the membrane lead to a net interfacial Maxwell stress which can cause the deformation of such an elastic capsule. We investigate this problem considering well established membrane laws for a thin elastic membrane, with fully resolved hydrodynamics in the Stokes…
The shear-induced deformation of a capsule with a stiff nucleus, a model of eukaryotic cells, is studied numerically. The membrane of the cell and of its nucleus are modelled as a thin and impermeable elastic material obeying a Neo-Hookean constitutive law. The membranes are discretised by a Lagrangian mesh and their governing equations are solved in spectral space using spherical harmonics, while the fluid equations are solved on a staggered grid using a second-order finite differences scheme. The fluid-structure coupling is obtained using an immersed boundary method. The numerical approach i…
An algorithm is proposed to implement unsteady jump boundary conditions, presenting discontinuity in physical quantities, within the lattice Boltzmann method (LBM). This is useful to tackle problems involving mass or heat transfer through interfaces or membranes that exhibit resistance to transport. The algorithm is simple to implement within an existing LBM based code that computes diffusion and advection of a scalar field, either temperature or solute concentration. Analytical solutions are recovered numerically with acceptable accuracy for the limiting case of a planar membrane. The algorit…
Using a fully analytical theory, we compute the leading order corrections to the translational, rotational and translation-rotation coupling mobilities of an arbitrary axisymmetric particle immersed in a Newtonian fluid moving near an elastic cell membrane that exhibits resistance towards stretching and bending. The frequency-dependent mobility corrections are expressed as general relations involving separately the particle's shape-dependent bulk mobility and the shape-independent parameters such as the membrane-particle distance, the particle orientation and the characteristic frequencies ass…
A three-dimensional deformable capsule convected through a square duct with a corner is studied via numerical simulations. We develop an accelerated boundary integral implementation adapted to general geometries and boundary conditions. A global spectral method is adopted to resolve the dynamics of the capsule membrane developing elastic tension according to the neo-Hookean constitutive law and bending moments in an inertialess flow. The simulations show that the trajectory of the capsule closely follows the underlying streamlines independently of the capillary number. The membrane deformabili…
Understanding the flow of deformable particles such as liquid drops, synthetic capsules and vesicles, and biological cells confined in a small channel is essential to a wide range of potential chemical and biomedical engineering applications. Computer simulations of this kind of fluid-structure (membrane) interaction in low-Reynolds-number flows raise significant challenges faced by an intricate interplay between flow stresses, complex particles' interfacial mechanical properties, and fluidic confinement. Here, we present an isogeometric computational framework by combining the finite-element …
