An immersed boundary lattice Boltzmann approach to simulate deformable liquid capsules and its application to microscopic blood flows

Lattice Boltzmann simulation of deformable fluid-filled bodies: progress and perspectives

With the rapid development of studies involving droplet microfluidics, drug delivery, cell detection, and microparticle synthesis, among others, many scientists have invested significant efforts to model the flow of these fluid-filled bodies. Motivated by the intricate coupling between hydrodynamics and the interactions of fluid-filled bodies, several methods have been developed. The objective of this review is to present a compact foundation of the methods used in the literature in the context of lattice Boltzmann methods. For hydrodynamics, we focus on the lattice Boltzmann method due to its specific ability to treat time- and spatial-dependent boundary conditions and to incorporate new physical models in a computationally efficient way. We split the existing methods into two groups with regard to the interfacial boundary: fluid-structure and fluid-fluid methods. The fluid-structure methods are characterised by the coupling between fluid dynamics and mechanics of the flowing body, often used in applications involving membranes and similar flexible solid boundaries. We further divide fluid-structure-based methods into two subcategories, those which treat the fluid-structure boundary as a continuum medium and those that treat it as a discrete collection of individual springs and particles. Next, we discuss the fluid-fluid methods, particularly useful for the simulations of fluid-fluid interfaces. We focus on models for immiscible droplets and their interaction in a suspending fluid and describe benchmark tests to validate the models for fluid-filled bodies.

In silico modeling of patient-specific blood rheology in type 2 diabetes mellitus

Increased blood viscosity in type 2 diabetes mellitus (T2DM) is a risk factor for the development of insulin resistance and diabetes-related vascular complications; however, individuals with T2DM exhibit heterogeneous hemorheological properties, including cell deformation and aggregation. Using a multiscale red blood cell (RBC) model with key parameters derived from patient-specific data, we present a computational study of the rheological properties of blood from individual patients with T2DM. Specifically, one key model parameter, which determines the shear stiffness of the RBC membrane (μ) is informed by the high-shear-rate blood viscosity of patients with T2DM. At the same time, the other, which contributes to the strength of the RBC aggregation interaction (D0), is derived from the low-shear-rate blood viscosity of patients with T2DM. The T2DM RBC suspensions are simulated at different shear rates, and the predicted blood viscosity is compared with clinical laboratory-measured data. The results show that the blood viscosity obtained from clinical laboratories and computational simulations are in agreement at both low and high shear rates. These quantitative simulation results demonstrate that the patient-specific model has truly learned the rheological behavior of T2DM blood by unifying the mechanical and aggregation factors of the RBCs, which provides an effective way to extract quantitative predictions of the rheological properties of the blood of individual patients with T2DM.

Rheology and structure of elastic capsule suspensions within rectangular channels

Three-dimensional simulations of the pressure-driven flow dynamics of elastic capsule suspensions within both slit and rectangular cross-section channels are presented. The simulations utilize the Immersed Boundary Method and the Lattice-Boltzmann Method models. The capsule volume fraction is fixed at 0.1 (i.e., a semi-dilute suspension), while the channel Reynolds number (Re), the capillary number (Ca), and the cross-sectional channel dimensions are systematically varied. Comparing results for slit and rectangular channels, it is found that multi-directional confinement hinders inertial focusing due to the capsule-free layers that develop in the two transverse directions. Furthermore, the thicknesses of the capsule-free layers in the two transverse directions differ when the height and width of the channel are not equal. Both the size and aspect ratio of the channel impact the apparent viscosity. It is found that square channels exhibit maximal viscosity and that holding one dimension fixed while increasing or decreasing the other results in a decrease in viscosity. The results therefore represent an expansion of the Fahraeus-Lindqvist effect from 1D cylindrical channels to 2D rectangular channels.

Effect of constitutive law on the erythrocyte membrane response to large strains

Three constitutive laws, that is the Skalak, neo-Hookean and Yeoh laws, commonly employed for describing the erythrocyte membrane mechanics are theoretically analyzed and numerically investigated to assess their accuracy for capturing erythrocyte deformation characteristics and morphology. Particular emphasis is given to the nonlinear deformation regime, where it is known that the discrepancies between constitutive laws are most prominent. Hence, the experiments of optical tweezers and micropipette aspiration are considered here, for which relationships between the individual shear elastic moduli of the constitutive laws can also be established through analysis of the tension-deformation relationship. All constitutive laws were found to adequately predict the axial and transverse deformations of a red blood cell subjected to stretching with optical tweezers for a constant shear elastic modulus value. As opposed to Skalak law, the neo-Hookean and Yeoh laws replicated the erythrocyte membrane folding, that has been experimentally observed, with the trade-off of sustaining significant area variations. For the micropipette aspiration, the suction pressure-aspiration length relationship could be excellently predicted for a fixed shear elastic modulus value only when Yeoh law was considered. Importantly, the neo-Hookean and Yeoh laws reproduced the membrane wrinkling at suction pressures close to those experimentally measured. None of the constitutive laws suffered from membrane area compressibility in the micropipette aspiration case.

Oxygen transport across tank-treading red blood cell: Individual and joint roles of flow convection and oxygen-hemoglobin reaction

Gas, especially oxygen, transport in the microcirculation is a complex phenomenon, however, of critical importance for maintaining normal biological functions, and the cytoplasm fluid in red blood cells (RBCs) is the major vehicle for transporting oxygen from lungs to tissues via the circulatory system. Existing theoretical and numerical studies have neglected the cytoplasm convection effect by treating RBCs as rigid particles undergoing a constant translation velocity. As a consequence, the influence and mechanism of the cytoplasm flow on oxygen transport are still not clear in microcirculation research. In this study, we consider a tank-treading capsule in shear flow, which is generated with two parallel plates moving in opposite directions: the top plate of a higher oxygen pressure (P_O2) representing the RBC core in the central region of a microvessel and the bottom plate of a lower P_O2 representing the microvessel wall. Numerical simulations are conducted to investigate the individual and combined effects of cytoplasm convection and oxygen-hemoglobin (O₂-Hb) reaction on the oxygen transport efficiency across the tank-treading capsule, and different P_O2 situations and shear rates are also tested. Due to the lower oxygen diffusivity in cytoplasm, the presence of the capsule reduces the oxygen transfer flux across the gap by 7.34 % in the pure diffusion system where the flow convection and O₂-Hb reaction are both neglected. Including the flow convection or the O₂-Hb reaction has little influence on the oxygen flux; however, when they act together as in real microcirculation situations, the enhancement in oxygen transport could be significant, especially in the low P_O2 and high shear rate situations. In particular, with the respective P_O2 at 60 and 30 mmHg on the top and bottom plates and a 400 s^-1 shear rate, the oxygen flux reduction is only 0.02 %, suggesting that the cytoplasm convection can improve the oxygen transport across RBCs considerably. The simulation results are scrutinized to explore the underlying mechanism for the enhancement, and a new nondimensional parameter is introduced to characterize the importance of cytoplasm convection in oxygen transport. These simulation results, discussion and analysis could be helpful for a better understanding of the complex oxygen transport process and therefor valuable for relevant studies.

Tank-treading dynamics of red blood cells in shear flow: On the membrane viscosity rheology

In this article, extensive three-dimensional simulations are conducted for tank-treading (TT) red blood cells (RBCs) in shear flow with different cell viscous properties and flow conditions. Apart from recent numerical studies on TT RBCs, this research considers the uncertainty in cytoplasm viscosity, covers a more complete range of shear flow situations of available experiments, and examines the TT behaviors in more details. Key TT characteristics, including the rotation frequency, deformation index, and inclination angle, are compared with available experimental results of similar shear flow conditions. Fairly good simulation-experiment agreements for these parameters can be obtained by adjusting the membrane viscosity values; however, different rheological relationships between the membrane viscosity and the flow shear rate are noted for these comparisons: shear thinning from the TT frequency, Newtonian from the inclination angle, and shear thickening from the cell deformation. Previous studies claimed a shear-thinning membrane viscosity model based on the TT frequency results; however, such a conclusion seems premature from our results and more carefully designed and better controlled investigations are required for the RBC membrane rheology. In addition, our simulation results reveal complicate RBC TT features and such information could be helpful for a better understanding of in vivo and in vitro RBC dynamics.

Evidence for a HURP/EB free mixed-nucleotide zone in kinetochore-microtubules

Current models infer that the microtubule-based mitotic spindle is built from GDP-tubulin with small GTP caps at microtubule plus-ends, including those that attach to kinetochores, forming the kinetochore-fibres. Here we reveal that kinetochore-fibres additionally contain a dynamic mixed-nucleotide zone that reaches several microns in length. This zone becomes visible in cells expressing fluorescently labelled end-binding proteins, a known marker for GTP-tubulin, and endogenously-labelled HURP - a protein which we show to preferentially bind the GDP microtubule lattice in vitro and in vivo. We find that in mitotic cells HURP accumulates on the kinetochore-proximal region of depolymerising kinetochore-fibres, whilst avoiding recruitment to nascent polymerising K-fibres, giving rise to a growing "HURP-gap". The absence of end-binding proteins in the HURP-gaps leads us to postulate that they reflect a mixed-nucleotide zone. We generate a minimal quantitative model based on the preferential binding of HURP to GDP-tubulin to show that such a mixed-nucleotide zone is sufficient to recapitulate the observed in vivo dynamics of HURP-gaps.

Recent advances in blood rheology: a review

Due to the potential impact on the diagnosis and treatment of various cardiovascular diseases, work on the rheology of blood has significantly expanded in the last decade, both experimentally and theoretically. Experimentally, blood has been confirmed to demonstrate a variety of non-Newtonian rheological characteristics, including pseudoplasticity, viscoelasticity, and thixotropy. New rheological experiments and the development of more controlled experimental protocols on more extensive, broadly physiologically characterized, human blood samples demonstrate the sensitivity of aspects of hemorheology to several physiological factors. For example, at high shear rates the red blood cells elastically deform, imparting viscoelasticity, while at low shear rates, they form "rouleaux" structures that impart additional, thixotropic behavior. In addition to the advances in experimental methods and validated data sets, significant advances have also been made in both microscopic simulations and macroscopic, continuum, modeling, as well as novel, multiscale approaches. We outline and evaluate the most promising of these recent developments. Although we primarily focus on human blood rheology, we also discuss recent observations on variations observed across some animal species that provide some indication on evolutionary effects.

Numerical Simulations of Red-Blood Cells in Fluid Flow: A Discrete Multiphysics Study

In this paper, we present a methodological study of modelling red blood cells (RBCs) in shear-induced flows based on the discrete multiphysics (DMP) approach. The DMP is an alternative approach from traditional multiphysics based on meshless particle-based methods. The proposed technique has been successful in modelling multiphysics and multi-phase problems with large interfacial deformations such as those in biological systems. In this study, we present the proposed method and introduce an accurate geometrical representation of the RBC. The results were validated against available data in the literature. We further illustrate that the proposed method is capable of modelling the rupture of the RBC membrane with minimum computational difficulty.

Computational models of cancer cell transport through the microcirculation

The transport of cancerous cells through the microcirculation during metastatic spread encompasses several interdependent steps that are not fully understood. Computational models which resolve the cellular-scale dynamics of complex microcirculatory flows offer considerable potential to yield needed insights into the spread of cancer as a result of the level of detail that can be captured. In recent years, in silico methods have been developed that can accurately and efficiently model the circulatory flows of cancer and other biological cells. These computational methods are capable of resolving detailed fluid flow fields which transport cells through tortuous physiological geometries, as well as the deformation and interactions between cells, cell-to-endothelium interactions, and tumor cell aggregates, all of which play important roles in metastatic spread. Such models can provide a powerful complement to experimental works, and a promising approach to recapitulating the endogenous setting while maintaining control over parameters such as shear rate, cell deformability, and the strength of adhesive binding to better understand tumor cell transport. In this review, we present an overview of computational models that have been developed for modeling cancer cells in the microcirculation, including insights they have provided into cell transport phenomena.

Numerical simulations of capsule deformation using a dual time-stepping lattice Boltzmann method

In this work a quasisteady, dual time-stepping lattice Boltzmann method is proposed for simulation of capsule deformation. At each time step the steady-state lattice Boltzmann equation is solved using the full approximation storage multigrid scheme for nonlinear equations. The capsule membrane is modeled as an infinitely thin shell suspended in an ambient fluid domain with the fluid structure interaction computed using the immersed boundary method. A finite element method is used to compute the elastic forces exerted by the capsule membrane. Results for a wide range of parameters and initial configurations are presented. The proposed method is found to reduce the computational time by a factor of ten.

Modeling ternary fluids in contact with elastic membranes

We present a thermodynamically consistent model of a ternary fluid interacting with elastic membranes. Following a free-energy modeling approach for the fluid phases, we derive the governing equations for the dynamics of the ternary fluid flow and membranes. We also provide the numerical framework for simulating such fluid-structure interaction problems. It is based on the lattice Boltzmann method for the ternary fluid (Eulerian description) and a finite difference representation of the membrane (Lagrangian description). The ternary fluid and membrane solvers are coupled through the immersed boundary method. For validation purposes, we consider the relaxation dynamics of a two-dimensional elastic capsule placed at a fluid-fluid interface. The capsule shapes, resulting from the balance of surface tension and elastic forces, are compared with equilibrium numerical solutions obtained by surface evolver. Furthermore, the Galilean invariance of the proposed model is proven. The proposed approach is versatile, allowing for the simulation of a wide range of geometries. To demonstrate this, we address the problem of a capillary bridge formed between two deformable capsules.

Dynamic characteristics of a deformable capsule in a simple shear flow

The dynamic characteristics of a two-dimensional deformable capsule in a simple shear flow are studied with an immersed boundary-lattice Boltzmann method. Simulations are conducted by varying the Reynolds number (Re) from 0.0125 to 2000 and the dimensionless shear rate (G) from 0.001 to 0.5. The G-Re plane can be divided into four regions according to the deformation dependence on the parameters considered: viscous dominant, inertia dominant, transitional, and anomalous regions. There are four typical dynamic behaviors over the G-Re plane: steady deformation, prerupture state, quasisteady deformation, and continuous elongation. Analysis indicates that the pressure distribution and its variations due to the interplay of the fluid inertia force, the viscous shear stress, and the membrane elastic force determines the complex behaviors of the capsule. The effects of the bending rigidity and the internal-to-external viscosity ratio on the dynamics of the capsule are further studied. It is found that the capsule experiences smaller deformation when the higher bending rigidity is included, and the low bending rigidity does not have a remarkable influence on the capsule deformation. The capsule normally experiences smaller deformation due to the increase of the internal-to-external viscosity ratio.

Shear stress in the microvasculature: influence of red blood cell morphology and endothelial wall undulation

The effect of red blood cells and the undulation of the endothelium on the shear stress in the microvasculature is studied numerically using the lattice Boltzmann-immersed boundary method. The results demonstrate a significant effect of both the undulation of the endothelium and red blood cells on wall shear stress. Our results also reveal that morphological alterations of red blood cells, as occur in certain pathologies, can significantly affect the values of wall shear stress. The resulting fluctuations in wall shear stress greatly exceed the nominal values, emphasizing the importance of the particulate nature of blood as well as a more realistic description of vessel wall geometry in the study of hemodynamic forces. We find that within the channel widths investigated, which correspond to those found in the microvasculature, the inverse minimum distance normalized to the channel width between the red blood cell and the wall is predictive of the maximum wall shear stress observed in straight channels with a flowing red blood cell. We find that the maximum wall shear stress varies several factors more over a range of capillary numbers (dimensionless number relating strength of flow to membrane elasticity) and reduced areas (measure of deflation of the red blood cell) than the minimum wall shear stress. We see that waviness reduces variation in minimum and maximum shear stresses among different capillary and reduced areas.

Transport mechanism of deformable micro-gel particle through micropores with mechanical properties characterized by AFM

Deformable micro-gel particles (DMP) have been used to enhanced oil recovery (EOR) in reservoirs with unfavourable conditions. Direct pore-scale understanding of the DMP transport mechanism is important for further improvements of its EOR performance. To consider the interaction between soft particle and fluid in complex pore-throat geometries, we perform an Immersed Boundary-Lattice Boltzmann (IB-LB) simulation of DMP passing through a throat. A spring-network model is used to capture the deformation of DMP. In order to obtain appropriate simulation parameters that represent the real mechanical properties of DMP, we propose a procedure via fitting the DMP elastic modulus data measured by the nano-indentation experiments using Atomic Force Microscope (AFM). The pore-scale modelling obtains the critical pressure of the DMP for different particle-throat diameter ratios and elastic modulus. It is found that two-clog particle transport mode is observed in a contracted throat, the relationship between the critical pressure and the elastic modulus/particle-throat diameter ratio follows a power law. The particle-throat diameter ratio shows a greater impact on the critical pressure difference than the elastic modulus of particles.

A monolithic fluid-structure interaction framework applied to red blood cells

A parallel fully coupled (monolithic) fluid-structure interaction (FSI) algorithm has been applied to the deformation of red blood cells (RBCs) in capillaries, where cell deformability has significant effects on blood rheology. In the present FSI algorithm, fluid domain is discretized using the side-centered unstructured finite volume method based on the Arbitrary Lagrangian-Eulerian (ALE) formulation; meanwhile, solid domain is discretized with the classical Galerkin finite element formulation for the Saint Venant-Kirchhoff material in a Lagrangian frame. In addition, the compatible kinematic boundary condition is enforced at the fluid-solid interface in order to conserve the mass of cytoplasmic fluid within the red cell at machine precision. In order to solve the resulting large-scale algebraic linear systems in a fully coupled manner, a new matrix factorization is introduced similar to that of the projection method, and the parallel algebraic multigrid solver BoomerAMG is used for the scaled discrete Laplacian provided by the HYPRE library, which we access through the PETSc library. Three important physical parameters for the blood flow are simulated and analyzed: (1) the effect of capillary diameter, (2) the effect of red cell membrane thickness, and (3) the effect of red cell spacing (hematocrit). The numerical calculations initially indicate a shape deformation in which biconcave discoid shape changes to a parachute-like shape. Furthermore, the parachute-like cell shape in small capillaries undergoes a cupcake-shaped buckling instability, which has not been observed in the literature. The instability forms thin riblike features, and the red cell deformation is not axisymmetric but three-dimensional.

Numerical Investigation of the Effects of Red Blood Cell Cytoplasmic Viscosity Contrasts on Single Cell and Bulk Transport Behaviour

In-silico cellular models of blood are invaluable to gain understanding about the many interesting properties that blood exhibits. However, numerical investigations that focus on the effects of cytoplasmic viscosity in these models are not very prevalent. We present a parallelised method to implement cytoplasmic viscosity for HemoCell, an open-source cellular model based on immersed boundary lattice Boltzmann methods, using an efficient ray-casting algorithm. The effects of the implementation are investigated with single-cell simulations focusing on the deformation in shear flow, the migration due to wall induced lift forces, the characteristic response time in periodic stretching and pair collisions between red blood cells and platelets. Collective transport phenomena are also investigated in many-cell simulations in a pressure driven channel flow. The simulations indicate that the addition of a viscosity contrast between internal and external fluids significantly affects the deformability of a red blood cell, which is most pronounced during very short time-scale events. Therefore, modelling the cytoplasmic viscosity contrast is important in scenarios with high velocity deformation, typically high shear rate flows.

Extended photoacoustic transport model for characterization of red blood cell morphology in microchannel flow

The dynamic response behavior of red blood cells holds the key to understanding red blood cell related diseases. In this regard, an understanding of the physiological functions of erythrocytes is significant before focusing on red blood cell aggregation in the microcirculatory system. In this work, we present a theoretical model for a photoacoustic signal that occurs when deformed red blood cells pass through a microfluidic channel. Using a Green's function approach, the photoacoustic pressure wave is obtained analytically by solving a combined Navier-Stokes and photoacoustic equation system. The photoacoustic wave expression includes determinant parameters for the cell deformability such as plasma viscosity, density, and red blood cell aggregation, as well as involving laser parameters such as beamwidth, pulse duration, and repetition rate. The effects of aggregation on blood rheology are also investigated. The results presented by this study show good agreements with the experimental ones in the literature. The comprehensive analytical solution of the extended photoacoustic transport model including a modified Morse type potential function sheds light on the dynamics of aggregate formation and demonstrates that the profile of a photoacoustic pressure wave has the potential for detecting and characterizing red blood cell aggregation.

Numerical Simulations of the Motion and Deformation of Three RBCs during Poiseuille Flow through a Constricted Vessel Using IB-LBM

The immersed boundary-lattice Boltzmann method (IB-LBM) was used to examine the motion and deformation of three elastic red blood cells (RBCs) during Poiseuille flow through constricted microchannels. The objective was to determine the effects of the degree of constriction and the Reynolds (Re) number of the flow on the physical characteristics of the RBCs. It was found that, with decreasing constriction ratio, the RBCs experienced greater forced deformation as they squeezed through the constriction area compared to at other parts of the microchannel. It was also observed that a longer time was required for the RBCs to squeeze through a narrower constriction. The RBCs subsequently regained a stable shape and gradually migrated toward the centerline of the flow beyond the constriction area. However, a sick RBC was observed to be incapable of passing through a constricted vessel with a constriction ratio ≤1/3 for Re numbers below 0.40.

Flow-Driven Assembly of Microcapsules into Three-Dimensional Towers

By harnessing biochemical signaling and chemotaxis, unicellular slime molds can aggregate on a surface to form a long, vertical stalk. Few synthetic systems can self-organize into analogous structures that emerge out of the plane. Through computational modeling, we devise a mechanism for assembling tower-like structures using microcapsules in solution as building blocks. In the simulations, chemicals diffusing from a central patch on a surface produce a concentration gradient, which generates a radially directed diffusioosmotic flow along the surface toward the center. This toroidal roll of a fluid pulls the microcapsules along the surface and lifts them above the patch. As more capsules are drawn toward the patch, some units are pushed off the surface but remain attached to the central microcapsule cluster. The upward-directed flow then draws out the cluster into a tower-like shape. The final three-dimensional (3D) structure depends on the flow field, the attractive capsule-capsule and capsule-surface interaction strengths, and the sedimentation force on the capsules. By tuning these factors, we can change the height of the structures that are produced. Moreover, by patterning the areas of the wall that are attractive to the capsules, we can form multiple vertical strands instead of a single tower. Our approach for flow-directed assembly can permit the growth of reconfigurable, 3D structures from simple subunits.

Simulation of Morphogen and Tissue Dynamics

Morphogenesis, the process by which an adult organism emerges from a single cell, has fascinated humans for a long time. Modeling this process can provide novel insights into development and the principles that orchestrate the developmental processes. This chapter focuses on the mathematical description and numerical simulation of developmental processes. In particular, we discuss the mathematical representation of morphogen and tissue dynamics on static and growing domains, as well as the corresponding tissue mechanics. In addition, we give an overview of numerical methods that are routinely used to solve the resulting systems of partial differential equations. These include the finite element method and the Lattice Boltzmann method for the discretization as well as the arbitrary Lagrangian-Eulerian method and the Diffuse-Domain method to numerically treat deforming domains.

Computational Biomechanics of Human Red Blood Cells in Hematological Disorders

We review recent advances in multiscale modeling of the biomechanical characteristics of red blood cells (RBCs) in hematological diseases, and their relevance to the structure and dynamics of defective RBCs. We highlight examples of successful simulations of blood disorders including malaria and other hereditary disorders, such as sickle-cell anemia, spherocytosis, and elliptocytosis.

Numerical simulation of the red blood cell aggregation and deformation behaviors in ultrasonic field

The objective of this paper is to propose an immersed boundary lattice Boltzmann method (IB-LBM) considering the ultrasonic effect to simulate red blood cell (RBC) aggregation and deformation in ultrasonic field. Numerical examples involving the typical streamline, normalized out-of-plane vorticity contours and vector fields in pure plasma under three different ultrasound intensities are presented. Meanwhile, the corresponding transient aggregation behavior of RBCs, with special emphasis on the detailed process of RBC deformation, is shown. The numerical results reveal that the ultrasound wave acted on the pure plasma can lead to recirculation flow, which contributes to the RBCs aggregation and deformation in microvessel. Furthermore, increasing the intensity of the ultrasound wave can significantly enhance the aggregation and deformation of the RBCs. And the formation of the RBCs aggregation leads to the fluctuated and dropped vorticity value of plasma in return.

Numerical investigation on red blood cell dynamics in microflow: Effect of cell deformability

The radial dispersion of red blood cells (RBCs) near the vessel wall can significantly affect the transport dynamics in small vessels. The radial dispersion of RBCs is mainly caused by collisions between RBCs and this can be enhanced by aggregation. The objective of this study is to numerically investigate on the effect of RBC deformability on the radial motion of individual RBCs in a range of flow rates. Immersed Boundary - Lattice Boltzmann Method was utilized to study the radial motion of RBCs in a two-dimensional flow domain. The RBC flow simulations were performed at 40% hematocrit in a microvessel with diameter of 25μm and length of 100μm. The dispersion of less deformable RBCs was notably greater than that of normal RBCs at all flow rates and this effect seemed to be more pronounced when the flow rate was increased. The cell dispersion was higher near the vessel wall than the flow center regardless of flow rate and RBCs deformability. Thus, the dispersion of RBCs could be enhanced with flow rate and RBC rigidity. Our findings would be especially useful in investigating blood flows in arterioles and venules.

Numerical Simulation of Real-Time Deformability Cytometry To Extract Cell Mechanical Properties

The measurement of cell stiffness is an important part of biological research with diverse applications in biology, biotechnology and medicine. Real-time deformability cytometry (RT-DC) is a new method to probe cell stiffness at high throughput by flushing cells through a microfluidic channel where cell deformation provides an indicator for cell stiffness (Otto et al. Real-time deformability cytometry: on-the-fly cell 725 mechanical phenotyping. Nat. Methods 2015, 12, 199-202). Here, we propose a full numerical model for single cells in a flow channel to quantitatively relate cell deformation to mechanical parameters. Thereby the cell is modeled as a viscoelastic material surrounded by a thin shell cortex, subject to bending stiffness and cortical surface tension. For small deformations our results show good agreement with a previously developed analytical model that neglects the influence of cell deformation on the fluid flow (Mietke et al. Extracting Cell Stiffness from Real-Time Deformability Cytometry: 728 Theory and Experiment. Biophys. J. 2015, 109, 2023-2036). Including linear elasticity as well as neo-Hookean hyperelasticity, our model is valid in a wide range of cell deformations and allows to extract cell stiffness for largely deformed cells. We introduce a new measure for cell deformation that is capable to distinguish between deformation effects stemming from cell cortex and cell bulk elasticity. Finally, we demonstrate the potential of the method to simultaneously quantify multiple mechanical cell parameters by RT-DC.

Deformation of a Capsule in a Power-Law Shear Flow

An immersed boundary-lattice Boltzmann method is developed for fluid-structure interactions involving non-Newtonian fluids (e.g., power-law fluid). In this method, the flexible structure (e.g., capsule) dynamics and the fluid dynamics are coupled by using the immersed boundary method. The incompressible viscous power-law fluid motion is obtained by solving the lattice Boltzmann equation. The non-Newtonian rheology is achieved by using a shear rate-dependant relaxation time in the lattice Boltzmann method. The non-Newtonian flow solver is then validated by considering a power-law flow in a straight channel which is one of the benchmark problems to validate an in-house solver. The numerical results present a good agreement with the analytical solutions for various values of power-law index. Finally, we apply this method to study the deformation of a capsule in a power-law shear flow by varying the Reynolds number from 0.025 to 0.1, dimensionless shear rate from 0.004 to 0.1, and power-law index from 0.2 to 1.8. It is found that the deformation of the capsule increases with the power-law index for different Reynolds numbers and nondimensional shear rates. In addition, the Reynolds number does not have significant effect on the capsule deformation in the flow regime considered. Moreover, the power-law index effect is stronger for larger dimensionless shear rate compared to smaller values.

Facilitating the Clinical Integration of Nanomedicines: The Roles of Theoretical and Computational Scientists

Since the launch of multiple research initiatives on nanotechnology applied to medicine in the early 2000s, a plethora of nanomedicines have been developed that exhibit great therapeutic efficacy in preclinical models but yet minimal impact in daily clinical practice. The successful and complete clinical fruition of nanomedicines requires addressing three major technical challenges: improving loading efficacy and on-command release, modulating recognition and sequestration by immune cells, and maximizing accumulation at biological targets. In this Perspective, I describe how theoretical and computational models can help address each of these challenges. This armamentarium represents an ideal tool for maximizing the therapeutic efficacy of nanomedicines, thus facilitating their integration into daily clinical operations.

Local membrane length conservation in two-dimensional vesicle simulation using a multicomponent lattice Boltzmann equation method

We present a method for applying a class of velocity-dependent forces within a multicomponent lattice Boltzmann equation simulation that is designed to recover continuum regime incompressible hydrodynamics. This method is applied to the problem, in two dimensions, of constraining to uniformity the tangential velocity of a vesicle membrane implemented within a recent multicomponent lattice Boltzmann simulation method, which avoids the use of Lagrangian boundary tracers. The constraint of uniform tangential velocity is carried by an additional contribution to an immersed boundary force, which we derive here from physical arguments. The result of this enhanced immersed boundary force is to apply a physically appropriate boundary condition at the interface between separated lattice fluids, defined as that region over which the phase-field varies most rapidly. Data from this enhanced vesicle boundary method are in agreement with other data obtained using related methods [e.g., T. Krüger, S. Frijters, F. Günther, B. Kaoui, and J. Harting, Eur. Phys. J. 222, 177 (2013)10.1140/epjst/e2013-01834-y] and underscore the importance of a correct vesicle membrane condition.

Computational fluid dynamics in the microcirculation and microfluidics: what role can the lattice Boltzmann method play?

Patient-specific simulations, efficient parametric analyses, and the study of complex processes that are otherwise experimentally intractable are facilitated through the use of Computational Fluid Dynamics (CFD) to study biological flows. This review discusses various CFD methodologies that have been applied across different biological scales, from cell to organ level. Through this discussion the lattice Boltzmann method (LBM) is highlighted as an emerging technique capable of efficiently simulating fluid problems across the midrange of scales; providing a practical analytical tool compared to methods more attuned to the extremities of scale. Furthermore, the merits of the LBM are highlighted through examples of previous applications and suggestions for future research are made. The review focusses on applications in the midrange bracket, such as cell-cell interactions, the microcirculation, and microfluidic devices; wherein the inherent mesoscale nature of the LBM renders it well suited to the incorporation of fluid-structure interaction effects, molecular/particle interactions and interfacial dynamics. The review demonstrates that the LBM has the potential to become a valuable tool across a range of emerging areas in bio-CFD, such as understanding and predicting disease, designing lab-on-a-chip devices, and elucidating complex biological processes.

Inversion of hematocrit partition at microfluidic bifurcations

Partitioning of red blood cells (RBCs) at the level of bifurcations in the microcirculatory system affects many physiological functions yet it remains poorly understood. We address this problem by using T-shaped microfluidic bifurcations as a model. Our computer simulations and in vitro experiments reveal that the hematocrit (ϕ0) partition depends strongly on RBC deformability, as long as ϕ0<20% (within the normal range in microcirculation), and can even lead to complete deprivation of RBCs in a child branch. Furthermore, we discover a deviation from the Zweifach-Fung effect which states that the child branch with lower flow rate recruits less RBCs than the higher flow rate child branch. At small enough ϕ0, we get the inverse scenario, and the hematocrit in the lower flow rate child branch is even higher than in the parent vessel. We explain this result by an intricate up-stream RBC organization and we highlight the extreme dependence of RBC transport on geometrical and cell mechanical properties. These parameters can lead to unexpected behaviors with consequences on the microcirculatory function and oxygen delivery in healthy and pathological conditions.

Temporal and spatial variations of wall shear stress in the entrance region of microvessels

Using a simplified two-dimensional divider-channel setup, we simulate the development process of red blood cell (RBC) flows in the entrance region of microvessels to study the wall shear stress (WSS) behaviors. Significant temporal and spatial variation in WSS is noticed. The maximum WSS magnitude and the strongest variation are observed at the channel inlet due to the close cell-wall contact. From the channel inlet, both the mean WSS and variation magnitude decrease, with a abrupt drop in the close vicinity near the inlet and then a slow relaxation over a relatively long distance; and a relative stable state with approximately constant mean and variation is established when the flow is well developed. The correlations between the WSS variation features and the cell free layer (CFL) structure are explored, and the effects of several hemodynamic parameters on the WSS variation are examined. In spite of the model limitations, the qualitative information revealed in this study could be useful for better understanding relevant processes and phenomena in the microcirculation.

LBIBCell: a cell-based simulation environment for morphogenetic problems

MOTIVATION

The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell-cell interactions and spatially restricted signalling events. A tightly coupled cell-based mechano-regulatory simulation tool is therefore required.

RESULTS

We developed an open-source software framework for morphogenetic problems. The environment offers core functionalities for the tissue and signalling models. In addition, the software offers great flexibility to add custom extensions and biologically motivated processes. Cells are represented as highly resolved, massless elastic polygons; the viscous properties of the tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used to model the interaction between the viscous and elastic properties of the cells, thus extending on the IBCell model. The fluid and signalling processes are solved using the Lattice Boltzmann method. As application examples we simulate signalling-dependent tissue dynamics.

AVAILABILITY AND IMPLEMENTATION

The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html

Synergy between shear-induced migration and secondary flows on red blood cells transport in arteries: considerations on oxygen transport

Shear-induced migration of red blood cells (RBCs) is a well-known phenomenon characterizing blood flow in the small vessels (micrometre to millimetre size) of the cardiovascular system. In large vessels, like the abdominal aorta and the carotid artery (millimetre to centimetre size), the extent of this migration and its interaction with secondary flows has not been fully elucidated. RBC migration exerts its influence primarily on platelet concentration, oxygen transport and oxygen availability at the luminal surface, which could influence vessel wall disease processes in and adjacent to the intima. Phillips' shear-induced particle migration model, coupled to the Quemada viscosity model, was employed to simulate the macroscopic behaviour of RBCs in four patient-specific geometries: a normal abdominal aorta, an abdominal aortic aneurysm (AAA), a normal carotid bifurcation and a stenotic carotid bifurcation. Simulations show a migration of RBCs from the near-wall region with a lowering of wall haematocrit (volume fraction of RBCs) on the posterior side of the normal aorta and on the lateral-external side of the iliac arteries. A marked migration is observed on the outer wall of the carotid sinus, along the common carotid artery and in the carotid stenosis. No significant migration is observed in the AAA. The spatial and temporal patterns of wall haematocrit are correlated with the near-wall shear layer and with the secondary flows induced by the vessel curvature. In particular, secondary flows accentuate the initial lowering in RBC near-wall concentration by convecting RBCs from the inner curvature side to the outer curvature side. The results reinforce data in literature showing a decrease in oxygen partial pressure on the inner curvature wall of the carotid sinus induced by the presence of secondary flows. The lowering of wall haematocrit is postulated to induce a decrease in oxygen availability at the luminal surface through a diminished concentration of oxyhaemoglobin, hence contributing, with the reported lowered oxygen partial pressure, to local hypoxia.

Cell-free layer development process in the entrance region of microvessels

We simulated red blood cell flows through a finite length channel with a two-dimensional immersed boundary lattice Boltzmann model. The local instantaneous variation in wall-cell distance has been examined in details, and a nominal cell-free layer (CFL) thickness has been proposed. The CFL development process along the channel has been then analyzed, showing that the CFL thickness profile can be basically split into two regimes: the initial rapid increase due to cell migration and the later gradual growth due to cell reorganization. Effects of various hemorheological factors, such as rigidity, aggregation, hematocrit, and channel width, have also been investigated. The development length of the CFL to 90% of its final width ranges from 150 to 300 μm, and the development length is sensitive to changes in hemorheological conditions. The correlation between the CFL features and hemorheological parameters has also been explored. The simulation results have been compared to available experimental studies, and qualitative agreement has been noticed. In spite of the model limitations, this study reveals the complexity of CFL development process, and it could be useful for better understanding relevant processes and phenomena in the microcirculation.

Numerical simulation of red blood cell distributions in three-dimensional microvascular bifurcations

We constructed three-dimensional microvascular bifurcation models using a parent vessel of diameter 10μm and investigated the flow behavior of the red blood cells (RBCs) through bifurcations. We considered symmetric and asymmetric model types. Two cases of equal daughter vessel diameter were employed for the asymmetric models, where the first was 10μm, which is the same as the parent vessel and the second was 7.94μm, which satisfies Murray's law. Simulated blood flow was computed using the lattice Boltzmann method in conjunction with the immersed boundary method for incorporating fluid-membrane interactions between the flow field and deformable RBCs. First, we investigated the flow behavior of a single RBC through microvascular bifurcations. In the case of the symmetric bifurcation, the turning point of the fractional plasma flow wherein the RBC flow changed from one daughter vessel to the other was 0.50. This turning point was however different for asymmetric bifurcations. Additionally, we varied the initial offset of RBCs from the centerline of the parent vessel. The simulation results indicated that the RBCs preferentially flow through the branch of a larger flow ratio. Next, we investigated the distribution characteristics of multiple RBCs. Simulations indicated that the results of the symmetric model were similar to those predicted by a previously published empirical model. On the other hand, results of asymmetric models deviated from those of the symmetric and empirical models. These results suggest that the distribution of RBCs varies according to the bifurcation angle and daughter vessel diameter in a microvascular bifurcation of the size considered.

Rheology of red blood cells under flow in highly confined microchannels: I. effect of elasticity

We analyze the rheology of dilute red blood cell suspensions in pressure driven flows at low Reynolds number, in terms of the morphologies and elasticity of the cells. We focus on narrow channels of width similar to the cell diameter, when the interactions with the walls dominate the cell dynamics. The suspension presents a shear-thinning behaviour, with a Newtonian-behaviour at low shear rates, an intermediate region of strong decay of the suspension viscosity, and an asymptotic regime at high shear rates in which the effective viscosity converges to that of the solvent. We identify the relevant aspects of cell elasticity that contribute to the rheological response of blood at high confinement. In a second paper, we will explore the focusing of red blood cells while flowing at high shear rates and how this effect is controlled by the geometry of the channel.

Prediction of cell growth rate over scaffold strands inside a perfusion bioreactor

Mathematical and computational modeling of the dynamic process where tissue scaffolds are cultured in perfusion bioreactors is able to provide insight into the cell and tissue growth which can facilitate the design of tissue scaffolds and selection of optimal operating conditions. To date, a resolved-scale simulation of cell growth in the culture process, by taking account of the influences of the supply of nutrients and fluid shear stress on the cells, is not yet available in the literature. This paper presents such a simulation study specifically on cartilage tissue regeneration by numerically solving the momentum, scalar transport and cell growth equations, simultaneously, based on the lattice Boltzmann method. The simulation uses a simplified scaffold that consists of two circular strands placed in tandem inside a microchannel, with the object of identifying the effect of one strand on the other. The results indicate that the presence of the front strand can reduce the cell growth rate on the surface of the rear strand, depending on the distance between them. As such, the present study allows for investigation into the influence of the scaffold geometry on the cell growth rate within scaffolds, thus providing a means to improve the scaffold design and the culture process.

Rheology of dense suspensions of elastic capsules: normal stresses, yield stress, jamming and confinement effects

We study the shearing rheology of dense suspensions of elastic capsules, taking aggregation-free red blood cells as a physiologically relevant example. Particles are non-Brownian and interact only via hydrodynamics and short-range repulsive forces. An analysis of the different stress mechanisms in the suspension shows that the viscosity is governed by the shear elasticity of the capsules, whereas the repulsive forces are subdominant. Evidence for a dynamic yield stress above a critical volume fraction is provided and related to the elastic properties of the capsules. The shear stress is found to follow a critical jamming scenario and is rather insensitive to the tumbling-to-tank-treading transition. The particle pressure and normal stress differences display some sensitivity to the dynamical state of the cells and exhibit a characteristic scaling, following the behavior of a single particle, in the tank-treading regime. The behavior of the viscosity in the fluid phase is rationalized in terms of effective medium models. Furthermore, the role of confinement effects, which increase the overall magnitude and enhance the shear-thinning of the viscosity, is discussed.

Two-dimensional strain-hardening membrane model for large deformation behavior of multiple red blood cells in high shear conditions

Background

Computational modeling of Red Blood Cell (RBC) flow contributes to the fundamental understanding of microhemodynamics and microcirculation. In order to construct theoretical RBC models, experimental studies on single RBC mechanics have presented a material description for RBC membranes based on their membrane shear, bending and area moduli. These properties have been directly employed in 3D continuum models of RBCs but practical flow analysis with 3D models have been limited by their computationally expensive nature. As such, various researchers have employed 2D models to efficiently and qualitatively study microvessel flows. Currently, the representation of RBC dynamics using 2D models is a limited methodology that breaks down at high shear rates due to excessive and unrealistic stretching.

Methods

We propose a localized scaling of the 2D elastic moduli such that it increases with RBC local membrane strain, thereby accounting for effects such as the Poisson effect and membrane local area incompressibility lost in the 2D simplification. Validation of our 2D Large Deformation (2D-LD) RBC model was achieved by comparing the predicted RBC deformation against the 3D model from literature for the case of a single RBC in simple shear flow under various shear rates (dimensionless shear rate G = 0.05, 0.1, 0.2, 0.5). The multi-cell flow of RBCs (38% Hematocrit) in a 20 μm width microchannel under varying shear rates (50, 150, 150 s^-1) was then simulated with our proposed model and the popularly-employed 2D neo-Hookean model in order to evaluate the efficacy of our proposed 2D-LD model.

Results

The validation set indicated similar RBC deformation for both the 2D-LD and the 3D models across the studied shear rates, highlighting the robustness of our model. The multi-cell simulation indicated that the 2D neo-Hookean model predicts noodle-like RBC shapes at high shear rates (G = 0.5) whereas our 2D-LD model maintains sensible RBC deformations.

Conclusion

The ability of the 2D-LD model to limit RBC strain even at high shear rates enables this proposed model to be employed in practical simulations of high shear rate microfluidic flows such as blood separation channels.

Choice of boundary condition for lattice-Boltzmann simulation of moderate-Reynolds-number flow in complex domains

Modeling blood flow in larger vessels using lattice-Boltzmann methods comes with a challenging set of constraints: a complex geometry with walls and inlets and outlets at arbitrary orientations with respect to the lattice, intermediate Reynolds (Re) number, and unsteady flow. Simple bounce-back is one of the most commonly used, simplest, and most computationally efficient boundary conditions, but many others have been proposed. We implement three other methods applicable to complex geometries [Guo, Zheng, and Shi, Phys. Fluids 14, 2007 (2002); Bouzidi, Firdaouss, and Lallemand, Phys. Fluids 13, 3452 (2001); Junk and Yang, Phys. Rev. E 72, 066701 (2005)] in our open-source application hemelb. We use these to simulate Poiseuille and Womersley flows in a cylindrical pipe with an arbitrary orientation at physiologically relevant Re number (1-300) and Womersley (4-12) numbers and steady flow in a curved pipe at relevant Dean number (100-200) and compare the accuracy to analytical solutions. We find that both the Bouzidi-Firdaouss-Lallemand (BFL) and Guo-Zheng-Shi (GZS) methods give second-order convergence in space while simple bounce-back degrades to first order. The BFL method appears to perform better than GZS in unsteady flows and is significantly less computationally expensive. The Junk-Yang method shows poor stability at larger Re number and so cannot be recommended here. The choice of collision operator (lattice Bhatnagar-Gross-Krook vs multiple relaxation time) and velocity set (D3Q15 vs D3Q19 vs D3Q27) does not significantly affect the accuracy in the problems studied.

Inertia- and deformation-driven migration of a soft particle in confined shear and Poiseuille flow

Non-linear soft particle lift caused by inertia- and deformation-driven lateral migration, leading to a migration-free zone in shear flow.