Accurate modelling of unsteady flows in collapsible tubes

The context of this paper is the development of a general and efficient numerical haemodynamic tool to help clinicians and researchers in understanding of physiological flow phenomena. We propose an accurate one-dimensional Runge–Kutta discontinuous Galerkin (RK-DG) method coupled with lumped parameter models for the boundary conditions. The suggested model has already been successfully applied to haemodynamics in arteries and is now extended for the flow in collapsible tubes such as veins. The main difference with cardiovascular simulations is that the flow may become supercritical and elastic jumps may appear with the numerical consequence that scheme may not remain monotone if no limiting procedure is introduced. We show that our second-order RK-DG method equipped with an approximate Roe's Riemann solver and a slope-limiting procedure allows us to capture elastic jumps accurately. Moreover, this paper demonstrates that the complex physics associated with such flows is more accurately modelled than with traditional methods such as finite difference methods or finite volumes. We present various benchmark problems that show the flexibility and applicability of the numerical method. Our solutions are compared with analytical solutions when they are available and with solutions obtained using other numerical methods. Finally, to illustrate the clinical interest, we study the emptying process in a calf vein squeezed by contracting skeletal muscle in a normal and pathological subject. We compare our results with experimental simulations and discuss the sensitivity to parameters of our model.     

Strong convergence of integrators for nonequilibrium Langevin dynamics

Several numerical schemes are proposed for the solution of Nonequilibrium Langevin Dynamics (NELD), and the strong rate of convergence for each scheme is analyzed. The schemes considered here employ specialised periodic boundary conditions that deform with the flow, namely Lees-Edwards and Kraynik-Reinelt boundary conditions and their generalisations. We show that care must be taken when implementing standard stochastic integration schemes with these boundary conditions in order to avoid a breakdown in the strong order of convergence.     

Geometric and potential driving formation and evolution of biomolecular surfaces

This paper presents new geometrical flow equations for the theoretical modeling of biomolecular surfaces in the context of multiscale implicit solvent models. To account for the local variations near the biomolecular surfaces due to interactions between solvent molecules, and between solvent and solute molecules, we propose potential driven geometric flows, which balance the intrinsic geometric forces that would occur for a surface separating two homogeneous materials with the potential forces induced by the atomic interactions. Stochastic geometric flows are introduced to account for the random fluctuation and dissipation in density and pressure near the solvent–solute interface. Physical properties, such as free energy minimization (area decreasing) and incompressibility (volume preserving), are realized by some of our geometric flow equations. The proposed approach for geometric and potential forces driving the formation and evolution of biological surfaces is illustrated by extensive numerical experiments and compared with established minimal molecular surfaces and molecular surfaces. Local modification of biomolecular surfaces is demonstrated with potential driven geometric flows. High order geometric flows are also considered and tested in the present work for surface generation. Biomolecular surfaces generated by these approaches are typically free of geometric singularities. As the speed of surface generation is crucial to implicit solvent model based molecular dynamics, four numerical algorithms, a semi-implicit scheme, a Crank–Nicolson scheme, and two alternating direction implicit (ADI) schemes, are constructed and tested. Being either stable or conditionally stable but admitting a large critical time step size, these schemes overcome the stability constraint of the earlier forward Euler scheme. Aided with the Thomas algorithm, one of the ADI schemes is found to be very efficient as it balances the speed and accuracy.      

Numerical simulation of blood flow in the left ventricle and aortic sinus using magnetic resonance imaging and computational fluid dynamics

Understanding cardiac blood flow patterns has many applications in analysing haemodynamics and for the clinical assessment of heart function. In this study, numerical simulations of blood flow in a patient-specific anatomical model of the left ventricle (LV) and the aortic sinus are presented. The realistic 3D geometry of both LV and aortic sinus is extracted from the processing of magnetic resonance imaging (MRI). Furthermore, motion of inner walls of LV and aortic sinus is obtained from cine-MR image analysis and is used as a constraint to a numerical computational fluid dynamics (CFD) model based on the moving boundary approach. Arbitrary Lagrangian–Eulerian finite element method formulation is used for the numerical solution of the transient dynamic equations of the fluid domain. Simulation results include detailed flow characteristics such as velocity, pressure and wall shear stress for the whole domain. The aortic outflow is compared with data obtained by phase-contrast MRI. Good agreement was found between simulation results and these measurements.     

A fast strong coupling algorithm for the partitioned fluid–structure interaction simulation of BMHVs

The numerical simulation of Bileaflet Mechanical Heart Valves (BMHVs) has gained strong interest in the last years, as a design and optimisation tool. In this paper, a strong coupling algorithm for the partitioned fluid–structure interaction simulation of a BMHV is presented. The convergence of the coupling iterations between the flow solver and the leaflet motion solver is accelerated by using the Jacobian with the derivatives of the pressure and viscous moments acting on the leaflets with respect to the leaflet accelerations. This Jacobian is numerically calculated from the coupling iterations. An error analysis is done to derive a criterion for the selection of useable coupling iterations. The algorithm is successfully tested for two 3D cases of a BMHV and a comparison is made with existing coupling schemes. It is observed that the developed coupling scheme outperforms these existing schemes in needed coupling iterations per time step and CPU time.     

Direct numerical simulation of a 2D-stented aortic heart valve at physiological flow rates

We study the nonlinear interaction of an aortic heart valve, composed of hyperelastic corrugated leaflets of finite density attached to a stented vessel under physiological flow conditions. In our numerical simulations, we use a 2D idealised representation of this arrangement. Blood flow is caused by a time-varying pressure gradient that mimics that of the aortic valve and corresponds to a peak Reynolds number equal to 4050. Here, we fully account for the shear-thinning behaviour of the blood and large deformations and contact between the leaflets by solving the momentum and mass balances for blood and leaflets. The mixed finite element/Galerkin method along with linear discontinuous Lagrange multipliers for coupling the fluid and elastic domains is adopted. Moreover, a series of challenging numerical issues such as the finite length of the computational domain and the conditions that should be imposed on its inflow/outflow boundaries, the accurate time integration of the parabolic and hyperbolic momentum equations, the contact between the leaflets and the non-conforming mesh refinement in part of the domain are successfully resolved. Calculations for the velocity and the shear stress fields of the blood reveal that boundary layers appear on both sides of a leaflet. The one along the ventricular side transfers blood with high momentum from the core region of the vessel to the annulus or the sinusoidal expansion, causing the continuous development of flow instabilities. At peak systole, vortices are convected in the flow direction along the annulus of the vessel, whereas during the closure stage of the valve, an extremely large vortex develops in each half of the flow domain.     

Effect of viscoelastic relaxation on moisture transport in foods. Part I: Solution of general transport equation

Within the framework of continuum mechanics, Singh et al. [1] developed an integro-differential equation, which applies to both Darcian (Fickian) and non-Darcian (non-Fickian) modes of fluid transport in swelling biological systems. A dimensionless form of the equation was obtained and transformed from moving Eulerian to the stationary Lagrangian coordinates. Here a solution scheme for the transport equation is developed to predict moisture transport and viscoelastic stresses in spheroidal biopolymeric materials. The equation was solved numerically and results used for predicting drying and sorption curves, moisture profiles, and viscoelastic stresses in soybeans. The Lagrangian solution was obtained by assembling together several schemes: the finite element method was used to discretize the equation in space; non-linearity was addressed using the Newton-Raphson method; the Volterra term was handled via a time integration scheme of Patlashenko et al. [2] and the Galerkin rule was used to solve the time-differential term. The solution obtained in Lagrangian coordinates was transformed back to the Eulerian coordinates. In part II of this sequence we present the numerical results.Revised version: 5 October 2003     

Mechanical action of the blood onto atheromatous plaques: influence of the stenosis shape and morphology

The vulnerability of atheromatous plaques in the carotid artery may be related to several factors, the most important being the degree of severity of the endoluminal stenosis and the thickness of the fibrous cap. It has recently been shown that the plaque length can also affect the mechanical response significantly. However, in their study on the effect of the plaque length, the authors did not consider the variations of the plaque morphology and the shape irregularities that may exist independently of the plaque length. These aspects are developed in this paper. The mechanical interactions between the blood flow and an atheromatous plaque are studied through a numerical model considering fluid–structure interaction. The simulation is achieved using the arbitrary Lagrangian–Eulerian scheme in the COMSOL TM commercial finite element package. The stenosis severity and the plaque length are, respectively, set to 45% and 15 mm. Different shapes of the stenosis are modelled, considering irregularities made of several bumps over the plaque. The resulting flow patterns, wall shear stresses, plaque deformations and stresses in the fibrous cap reveal that the effects of the blood flow are amplified if the slope upstream stenosis is steep or if the plaque morphology is irregular with bumps. More specifically, the maximum stress in the fibrous cap is 50% larger for a steep slope than for a gentle slope. These results offer new perspectives for considering the shape of plaques in the evaluation of the vulnerability.     

Validation of a fluid–structure interaction numerical model for predicting flow transients in arteries

Fluid–structure interaction (FSI) numerical models are now widely used in predicting blood flow transients. This is because of the importance of the interaction between the flowing blood and the deforming arterial wall to blood flow behaviour. Unfortunately, most of these FSI models lack rigorous validation and, thus, cannot guarantee the accuracy of their predictions. This paper presents the comprehensive validation of a two-way coupled FSI numerical model, developed to predict flow transients in compliant conduits such as arteries. The model is validated using analytical solutions and experiments conducted on polyurethane mock artery. Flow parameters such as pressure and axial stress (and precursor) wave speeds, wall deformations and oscillating frequency, fluid velocity and Poisson coupling effects, were used as the basis of this validation. Results show very good comparison between numerical predictions, analytical solutions and experimental data. The agreement between the three approaches is generally over 95%. The model also shows accurate prediction of Poisson coupling effects in unsteady flows through flexible pipes, which up to this stage have only being predicted analytically. Therefore, this numerical model can accurately predict flow transients in compliant vessels such as arteries.     

Effect of macroscale formation of intraluminal thrombus on blood flow in abdominal aortic aneurysms

A mathematical approach of blood flow within an abdominal aortic aneurysm (AAA) with intraluminal thrombus (ILT) is presented. The macroscale formation of ILT is modeled as a growing porous medium with variable porosity and permeability according to values proposed in the literature. The model outlines the effect of a porous ILT on blood flow in AAAs. The numerical solution is obtained by employing a structured computational mesh of an idealized fusiform AAA geometry and applying the Galerkin weighted residual method in generalized curvilinear coordinates. Results on velocity and pressure fields of independent cases with and without ILT are presented and discussed. The vortices that develop within the aneurysmal cavity are studied and visualized as ILT becomes more condensed. From a mechanistic point of view, the reduction of bulge pressure, as ILT is thickening, supports the observation that ILT could protect the AAA from a possible rupture. The model also predicts a relocation of the maximum pressure region toward the zone proximal to the neck of the aneurysm. However, other mechanisms, such as the gradual wall weakening that usually accompany AAA and ILT formation, which are not included in this study, may offset this effect.     

Design and comparison of gene-pyramiding schemes in animals

Marker-assisted gene pyramiding provides a promising way to develop new animal breeds or lines, in which genes responsible for certain favorable characters identified in different breeds or lines are incorporated. In consideration of features of animal populations, we proposed five schemes for pyramiding three genes, denoted Scheme A-E, and five schemes for pyramiding four genes, denoted Scheme F-J. These schemes are representative of the possible alternatives. We also provided an algorithm to compute the population sizes needed in each generation. We compared these schemes with respect to the total population size and the number of generations required under different situations. The results show that there is no scheme that is optimal in all cases. Among the schemes for pyramiding three genes from three lines (L1, L2 and L3), Scheme D (a three-way cross between the three lines are first performed, followed by a backcross to L1 and a subsequent intercross to obtain the desired genotype) has a significant advantage over the other schemes when the recombination rate between adjacent genes ranges from 0.1 to 0.4, while Scheme A (a two-way cross between L1 and L2 and a subsequent intercross are performed, followed by a cross with L3 and a subsequent intercross to obtain the desired genotype) is optimal when recombination rate is 0.5. Among schemes for pyramiding four genes from four lines (L1, L2, L3 and L4), Scheme I (seperately, a two-way cross between L1 and L2 (L3 and L4) followed by a backcross to L1 (L3) and a subsequent intercross are performed, then the offspring from the two sides are crossed and followed by a backcross to L1 and a subsequent intercross to obtain the desired genotype) is optimal when the recombination rate ranges from 0.1 to 0.4, while Scheme F (cross and subsequent intercross between the four lines are performed successively) is the optimal when the recombination rate is 0.5. We also disscuss how the animals' reproductive capacity, the probabilities of obtaining the desired genotypes and genetic distance between adjacent genes would affect the design of an optimal scheme.     

Coupled fluid–structure interaction hemodynamics in a zero-pressure state corrected arterial geometry

Hemodynamic conditions in large arteries are significantly affected by the interaction of the pulsatile blood flow with the distensible arterial wall. A numerical procedure for solving the fluid–structure interaction problem encountered in cardiovascular flows is presented. We consider a patient-specific carotid bifurcation geometry, obtained from 3D reconstruction of in vivo acquired tomography images, which yields a geometrical representation of the artery corresponding to its pressurized state. To recover the geometry of the artery in its zero-pressure state which is required for a fluid–structure interaction simulation we utilize inverse finite elastostatics. Time-dependent flow simulations with in vivo measured inflow volume flow rate in the 3D undeformed artery are performed through the finite element method. The coupled-momentum method for fluid–structure interaction is adopted to incorporate the influence of wall compliance in the numerical computation of the time varying flow domain. To demonstrate the importance in recovering the zero-pressure state of the artery in hemodynamic simulations we compute the time varying flow field with compliant walls for the original and the zero-pressure state corrected geometric configurations of the carotid bifurcation. The most important resulting effects in the hemodynamic environment are evaluated. Our results show a significant change in the wall shear stress distribution and the spatiotemporal extent of the recirculation regions.     

Effects of transients on pulsatile flow in arteries

Analytical solutions to the model problem of unsteady Newtonian fluid flow in straight, elastic-walled vessels can provide: theoretical insights into the flow of blood in arteries; a theoretical basis for clinical measurements in diagnoses of arterial flow rates; and guidance for boundary conditions in numerical simulations of flow in finite computational domains. However, while Womersley's analyses of blood flow assume solution forms that treat the flow as periodic and continuously unsteady, many flow variables in the smaller arteries are not continuously unsteady at all. They are characterized more accurately as rapid transient motions followed by a period of recovery to a stationary state, repeated in successive cycles. These flows are not continually unsteady ones described by Womersley's solutions but unsteady flows restarted from rest in each cycle, characterized as initial-boundary value problems. In this paper, we compare the Womersley and initial-boundary value solutions for model transients that stop then restart, explain these previously unreported limitations of Womersley's solutions, and demonstrate how the initial-boundary value solutions provide excellent agreement with measurements of blood flow in the anterior tibial and popliteal arteries of patients. Some consequences of these findings for understanding and interpreting measurements of blood flow, and for prescribing boundary conditions in computer simulations of arterial blood flow are discussed.     

Examination of nanoflow in rectangular slits

This paper presents simulations of 3D nanoscale flow in rectangular channel with molecular dynamics simulation method. Rectangular cross section is a frequently encountered geometric shape for nanoscale flow problems. For a given cross sectional height h, we change the width w of the rectangular cross section and analyze the influence of w/h on the flow characteristics. The distributions of density, temperature, boundary slip and flow velocity inside the rectangular cross section are investigated in detail. Liquid argon material and Lennard-Jones potential are used in the simulations. The simulation results are also compared with Navier–Stokes solutions for rectangular channel flows.     

Finite element simulation of pulsatile flow through arterial stenosis.

The problem of blood flow through a stenosis is solved using the incompressible Navier-Stokes equations in a rigid circular tube presenting a partial occlusion. Calculations are based on a Galerkin finite element method. The time marching scheme employs a predictor-corrector technique using a variable time step. Results are obtained for steady and physiological pulsatile flows. Computational experiments analyse the effect of varying the degree of stenosis, the stricture length, the Reynolds number and Womersley number. The method gives results which agree well with previous computations for steady flows and experimental findings for steady and pulsatile flows.     

Computing flow pipe of embedded hybrid systems using deep group preserving scheme

In this paper, we propose a novel methodology of numerical approximation to analyze flow of a nonlinear embedded hybrid system. For proving that all trajectories of a hybrid system do not enter an unsafe region, many classic numerical approaches such as Euler, Runge–Kutta methods for ordinary differential equations (ODEs) are applied, whereas, there exist several defects, including so-called spurious solutions and ghost fixed points. Moreover, to approximate the proper solution as much as possible, step size selection becomes especially important. In comparison, integrating group preserving scheme (GPS) which calculates true circumstance getting rid of spurious solutions and ghost fixed points, with neural network model which reduces numerical errors, deep GPS (DGPS) eliminates aforementioned adverse factors and gains better numerical approximation using a large time step size. The experimental results show that the proposed method makes safety verification for an embedded hybrid system well.

     

Numerical schemes for unsteady fluid flow through collapsible tubes

The study of fluid flow through compliant tubes is a fluid-structure type problem, in which a dynamic equilibrium is maintained between the fluid and the tube wall. The analogy between this flow and gas dynamics initiated the use of a number of numerical methods which were originally developed to solve compressible flow in rigid ducts. In this study we investigate the solutions obtained by applying the Lax-Wendroff and MacCormack schemes to one-dimensional incompressible flow through a straight collapsible tube. The time-evolving numerical results were compared with exact steady-state solutions. For boundary conditions which were held fixed after a prescribed rise time, the unsteady numerical solution converges to the exact steady-state solution with very good accuracy. The stability and accuracy of all the methods depend on the amount of viscous pressure loss dictated by wall friction. Flows with undamped oscillations cannot, however, be solved with these techniques.