The degenerate Cahn–Hilliard equation is a standard model to describe living tissues. It takes into account cell populations undergoing short-range attraction and long-range repulsion effects. In this framework, we consider the usual Cahn–Hilliard equation with a singular single-well potential and degenerate mobility. These degeneracy and singularity induce numerous difficulties, in particular for its numerical simulation. To overcome these issues, we propose a relaxation system formed of two second-order equations which can be solved with standard packages. This system is endowed with an energy and an entropy structure compatible with the limiting equation. Here, we study the theoretical properties of this system: global existence and convergence of the relaxed system to the degenerate Cahn–Hilliard equation. We also study the long-time asymptotics which interest relies on the numerous possible steady states with given mass.

We present a model for the force acting to fragment a biofilm-seeded microbial aggregate in shear flow, which we derive by coupling an existing model for the shape and orientation of a deforming ellipsoid with one for the surface force density on a solid ellipsoid. The model can be used to simulate the motion, shape, surface force density, and breakage of colloidal aggregates in shear flow. We apply the model to the case of exhaustive fragmentation of microbial aggregates in order to compute a post-fragmentation density function, indicating the likelihood of a fragmenting aggregate yielding daughter aggregates of a certain size.

We present a moving-least-square immersed boundary method for solving viscous incompressible flow involving deformable and rigid boundaries on a uniform Cartesian grid. For rigid boundaries, noslip conditions at the rigid interfaces are enforced using the immersed-boundary direct-forcing method. We propose a reconstruction approach that utilizes moving least squares (MLS) method to reconstruct the velocity at the forcing points in the vicinity of the rigid boundaries. For deformable boundaries, MLS method is employed to construct the interpolation and distribution operators for the immersed boundary points in the vicinity of the rigid boundaries instead of using discrete delta functions. The MLS approach allows us to avoid distributing the Lagrangian forces into the solid domains as well as to avoid using the velocity of points inside the solid domains to compute the velocity of the deformable boundaries. The present numerical technique has been validated by several examples including a Poiseuille flow in a tube, deformations of elastic capsules in shear flow and dynamics of red-blood cell in microfluidic devices.

Many biological settings involve complex fluids that have non-Newtonian mechanical responses that arise from suspended microstructures. In contrast, Newtonian fluids are liquids or mixtures of a simple molecular structure that exhibit a linear relationship between the shear stress and the rate of deformation. In modeling complex fluids, the extra stress from the non-Newtonian contribution must be included in the governing equations.

In this study we compare Lagrangian mesh and Oldroyd-B formulations of fluid-structure interaction in an immersed boundary framework. The start-up phase of planar Poiseuille flow between two parallel plates is used as a test case for the fluid models. For Newtonian and Oldroyd-B fluids there exist analytical solutions which are used in the comparison of simulation and theoretical results. The Lagrangian mesh results are compared with Oldroyd-B using comparable parameters. A regridding algorithm is introduced for the Lagrangian mesh model. We show that the Lagrangian mesh model simulations with regridding produce results in close agreement with the Oldfoyd-B model.

Mast cells (MCs) play an important role in the immune system. Through connective tissues, mechanical stimuli activate intracellular calcium signaling pathways, induce a variety of mediators including leukotriene C4 (LTC4) release, and affect MCs’ microenvironment. This paper focuses on MCs’ intracellular calcium dynamics and LTC4 release responding to mechanical stimuli, explores signaling pathways in MCs and the effect of interstitial fluid flow on the transport of biological messengers and feedback in the MCs network. We use a mathematical model to show that (i) mechanical stimuli including shear stress induced by interstitial fluid flow can activate mechano-sensitive (MS) ion channels on MCs’ membrane and allow Ca2+ entry, which increases intracellular Ca2+ concentration and leads to LTC4 release; (ii) LTC4 in the extracellular space (ECS) acts on surface cysteinyl leukotriene receptors (LTC4R) on adjacent cells, leading to Ca2+ influx through Ca2+ release-activated Ca2+ (CRAC) channels. An elevated intracellular Ca2+ concentration further stimulates LTC4 release and creates a positive feedback in the MCs network. The findings of this study may facilitate our understanding of the mechanotransduction process in MCs induced by mechanical stimuli, contribute to understanding of interstitial flow-related mechanobiology in MCs network, and provide a methodology for quantitatively analyzing physical treatment methods including acupuncture and massage in traditional Chinese medicine (TCM).

Acupuncture has been in clinical practice in China for thousands of years and its analgesia effect is worldwide accepted. However, the mechanism of acupuncture effect is not well understood. The study focus on signaling pathways induced by acupuncture, analyzes the cooperative action of the acupoints’ structure and the associated chemical mediators during acupuncture, establishes a mathematical model clarifying the roadmap of electroneurographic signal startup and transmission mechanism induced by acupuncture, quantitatively analyzing the response in acupoints to acupuncture. These work contribute to reveal the activation and transmission mechanism of neural signals induced by acupuncture from systems biology perspective, lay the foundation for the integration of acupuncture theory and modern science and further guide the clinical treatment and experimental research of acupuncture.

(Aims) Acupuncture was employed since 2 millenaries, but the underlying mechanisms are not globally handled. The present study is aimed at proposing an explanation by pointing out involved processes and a convincing modeling to demonstrate its efficiency when carried out by trained practitioners.

(Method) In the absence of global knowledge of any mechanism explaining the acupuncture process, a biological model is first developed, based on stimulation in a given domain around the needle tip of a proper mastocyte population by a mechanical stress, electrical, electromagnetic, or heat field. Whatever the type of mechanical or physical stimuli, mastocytes degranulate. Released messengers either facilitate the transfer of main mediators, or target their cognate receptors of local nerve terminals or after being conveyed by blood their receptors on cerebral cells. Signaling to the brain is fast by nervous impulses and delayed by circulating messengers that nevertheless distribute preferentially in the brain region of interest due to hyperemia. The process is self-sustained due to mastocyte chemotaxis from the nearby dense microcirculatory circuit and surrounding mastocyte pools, which are inadequate for acupuncture, but serve as a signal relay. A simple mathematical model is solved analytically. Numerical simulations are also carried out using the finite element method with mesh adaptivity.

(Results) The analytical solution of the simple mathematical model demonstrates the conditions filled by a mastocyte population to operate efficiently. A theorem gives the blow-up condition. This analytical solution serves for validation of numerical experiments. Numerical simulations show that when the needle is positioned in the periphery of the acupoint or outside it, the response is too weak. This explains why a long training is necessary as the needle implantation requires a precision with a magnitude of the order of 1mm.

(Conclusion) The acupoint must contain a highly concentrated population of mastocytes (e.g., very-high–amplitude, small-width Gaussian distribution) to get an initial proper response. Permanent signaling is provided by chemotaxis and continuous recruitment of mastocytes. Therefore, the density and distribution of mastocytes are crucial factors for efficient acupuncture as well as availability of circulating and neighboring pools of mastocytes.

Red blood cells (RBCs) are very important due to their role of oxygen transport from lungs. As the malaria parasite grows in the malaria-infected red blood cells (IRBCs), the properties of the cells change. In the present work, the oxygen uptake by RBCs and IRBCs at the pulmonary capillaries is simulated using a numerical technique based on the two-dimensional immersed interface method. The results for the oxygen uptake by a stationary single RBC have fair agreements with the previously reported results. The numerical results show that the malaria infection could significantly cause deterioration on the oxygen uptake by red blood cells. The results also suggest that the oxygen uptake by individual stationary RBC/IRBC would not be significantly affected by the neighboring cells provided the separation distance is about the dimension of the cell. Furthermore, it appears that the oxygen uptake by both RBCs and IRBCs is dominated by mass diffusion over the convection although the Peclet number is of the order of unity.

Experimental observations show that a strong magnetic field has a dramatic influence on the sedimentation of RBCs, which motivates us to model the sedimentation of red blood cell (RBC) under strong external magnetic body force. To model the sedimentation of a RBC in a square duct and a circular pipe, a recently developed technique derived from the lattice Boltzmann and the distributed Lagrange multiplier/fictitious domain methods (LBM-DLM/FD) is extended to employ the mesoscopic network model for simulations of the sedimentation of a RBC in flow. The flow is simulated by the LBM with a strong magnetic body force, while the network model is used for modeling RBC deformation. The fluid-RBC interactions are enforced by the Lagrange multiplier. The sedimentation of RBC in a square duct and a circular pipe is simulated, which demonstrates the developed method's capability to model the sedimentation of RBCs in various flows. Numerical results illustrate that the terminal settling velocity increases incrementally with the exerted body force. The deformation of RBC has a significant effect on the terminal settling velocity due to the change in the frontal area. The larger the exerted force, the smaller the frontal area and the larger the RBC deformation become. Additionally, the wall effect on the motion and deformation of RBC is also investigated.

This paper presents a modified Loop’s subdivision algorithm for studying the deformation of a single capsule, the hydrodynamic interaction between two capsules and the hydrodynamic diffusion of a suspension of capsules in bounded shear flow. A subdivision thin-shell model is employed to compute the forces generated on the surface of the elastic capsule during deformation. The capsule surface is approximated using the modified Loop’s subdivision scheme which guarantees bounded curvature and C1 continuity everywhere on the limit surface. The present numerical technique has been validated by studying the deformation of a spherical capsule in shear flow. Computations are also performed for a biconcave capsule over a wide range of shear rates and viscosity ratios to investigate its dynamics. In addition, the hydrodynamic interaction between two elastic capsules in bounded shear flow is studied. Depending on the wall separation distance, the trajectory-bifurcation points that separate reversing and crossing motions for both spherical and biconcave capsules can be found. Compared to the spherical capsules, the biconcave capsules exhibit additional types of interaction such as rotation and head-on collision. The head-on collision results in a large trajectory shift which contribute to the hydrodynamic diffusion of a suspension. A suspension of a large number of biconcave capsules in shear flow is also simulated to show the ability of the modified scheme in running a large-scale simulation over a long period of time.

Understanding blood flow in human body’s cerebral arterial system is of both fundamental and practical significance for prevention and treatment of vascular diseases. The mechanism and treatment for the growth of daughter aneurysm on its mother aneurysm are not yet fully understood. Themain purpose of the present paper is to elucidate the relationships between hemodynamics and the genesis, growth, subsequent rupture of the mother and daughter aneurysm on the cerebral vascular. The intensified stents with different porosities and structures are investigated to reduce the wall shear stress and pressure of mother and daughter aneurysm. The simulation is based on a lattice Boltzmann modeling of non-Newtonian blood flow. A novel stent structurewith “dense in front and sparse in rear” is proposed,which is verified to have good potential to reduce the wall shear stress of both mother and daughter aneurysm. The simulation is based on a lattice Boltzmann modeling of non-Newtonian blood flow. A novel stent structurewith “dense in front and sparse in rear” is proposed,which is verified to have good potential to reduce the wall shear stress of both mother and daughter aneurysm.

The shapes of vesicles formed by lipid bilayers with phase separation are governed by a bending energy with phase dependent material parameters together with a line energy associated with the phase interfaces. We present a numerical method to approximate solutions to the Euler-Lagrange equations featuring triangulated surfaces, isoparametric quadratic surface finite elements and the phase field approach for the phase separation. Furthermore, the method involves an iterative solution scheme that is based on a relaxation dynamics coupling a geometric evolution equation for the membrane surface with a surface Allen-Cahn equation. Remeshing and grid adaptivity are discussed, and in various simulations the influence of several physical parameters is investigated.

In studying biomechanical deformation in articular cartilage, the presence of cells (chondrocytes) necessitates the consideration of inhomogeneous elasticity problems in which cells are idealized as soft inclusions within a stiff extracellular matrix. An analytical solution of a soft inclusion problem is derived and used to evaluate iterative numerical solutions of the associated linear algebraic system based on discretization via the finite element method, and use of an iterative conjugate gradient method with algebraic multigrid preconditioning (AMG-PCG). Accuracy and efficiency of the AMG-PCG algorithm is compared to two other conjugate gradient algorithms with diagonal preconditioning (DS-PCG) or a modified incomplete LU decomposition (Euclid-PCG) based on comparison to the analytical solution. While all three algorithms are shown to be accurate, the AMG-PCG algorithm is demonstrated to provide significant savings in CPU time as the number of nodal unknowns is increased. In contrast to the other two algorithms, the AMG-PCG algorithm also exhibits little sensitivity of CPU time and number of iterations to variations in material properties that are known to significantly affect model variables. Results demonstrate the benefits of algebraic multigrid preconditioners for the iterative solution of assembled linear systems based on finite element modeling of soft elastic inclusion problems and may be particularly advantageous for large scale problems with many nodal unknowns.

In this paper, a numerical method employing a finite difference technique is used for an investigation of viscous, incompressible fluid flow in a tube with absorbing wall and slowly varying cross-section. The effect of fluid absorption through permeable wall is accounted by prescribing flux as a function of axial distance. The method is not restricted by the parameters in the problem such as wave number, permeability parameter, amplitude ratio and Reynolds number. The effects of these parameters on the radial velocity and mean pressure drop is studied and the results are presented graphically. Comparison is also made between the results obtained by perturbation method of solution and present approach.

This paper provides a detailed stochastic analysis of leucocyte cell movement based on the dynamics of a rigid body. The cell's behavior is studied in two relevant anisotropic environments displaying adhesion mediated movement (haptotaxis) and stimulus mediated movement (chemotaxis). This behavior is modeled by diffusion processes on three successively longer time scales, termed locomotion, translocation, and migration.