Mixed uncertainty analysis on pumping by peristaltic hearts using Dempster-Shafer theory.

In this paper, we introduce the numerical strategy for mixed uncertainty propagation based on probability and Dempster-Shafer theories, and apply it to the computational model of peristalsis in a heart-pumping system. Specifically, the stochastic uncertainty in the system is represented with random variables while epistemic uncertainty is represented using non-probabilistic uncertain variables with belief functions. The mixed uncertainty is propagated through the system, resulting in the uncertainty in the chosen quantities of interest (QoI, such as flow volume, cost of transport and work). With the introduced numerical method, the uncertainty in the statistics of QoIs will be represented using belief functions. With three representative probability distributions consistent with the belief structure, global sensitivity analysis has also been implemented to identify important uncertain factors and the results have been compared between different peristalsis models. To reduce the computational cost, physics constrained generalized polynomial chaos method is adopted to construct cheaper surrogates as approximations for the full simulation.

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.

An Explicit-Correction-Force Scheme of IB-LBM Based on Interpolated Particle Distribution Function.

In order to obtain a better numerical simulation method for fluid-structure interaction (FSI), the IB-LBM combining the lattice Boltzmann method (LBM) and immersed boundary method (IBM) has been studied more than a decade. For this purpose, an explicit correction force scheme of IB-LBM was proposed in this paper. Different from the current IB-LBMs, this paper introduced the particle distribution function to the interpolation process from the fluid grids to the immersed boundary at the mesoscopic level and directly applied the LBM force models to obtain the interface force with a simple form and explicit process. Then, in order to ensure the mass conservation in the local area of the interface, this paper corrected the obtained interface force with the correction matrix, forming the total explicit-correction-force (ECP) scheme of IB-LBM. The results of four numerical tests were used to verify the order of accuracy and effectiveness of the present method. The streamline penetration is limited and the numerical simulation with certain application significance is successful for complex boundary conditions such as the movable rigid bodies (free oscillation of the flapping foil) and flexible deformable bodies (free deformation of cylinders). In summary, we obtained a simple and alternative simulation method that can achieve good simulation results for engineering reference models with complex boundary problems.

Thermal Lattice Boltzmann Flux Solver for Natural Convection of Nanofluid in a Square Enclosure.

In the present study, mathematical modeling was performed to simulate natural convection of a nanofluid in a square enclosure using the thermal lattice Boltzmann flux solver (TLBFS). Firstly, natural convection in a square enclosure, filled with pure fluid (air and water), was investigated to validate the accuracy and performance of the method. Then, influences of the Rayleigh number, of nanoparticle volume fraction on streamlines, isotherms and average Nusselt number were studied. The numerical results illustrated that heat transfer was enhanced with the augmentation of Rayleigh number and nanoparticle volume fraction. There was a linear relationship between the average Nusselt number and solid volume fraction. and there was an exponential relationship between the average Nusselt number and Ra. In view of the Cartesian grid used by the immersed boundary method and lattice model, the immersed boundary method was chosen to treat the no-slip boundary condition of the flow field, and the Dirichlet boundary condition of the temperature field, to facilitate natural convection around a bluff body in a square enclosure. The presented numerical algorithm and code implementation were validated by means of numerical examples of natural convection between a concentric circular cylinder and a square enclosure at different aspect ratios. Numerical simulations were conducted for natural convection around a cylinder and square in an enclosure. The results illustrated that nanoparticles enhance heat transfer in higher Rayleigh number, and the heat transfer of the inner cylinder is stronger than that of the square at the same perimeter.

A Simplified Linearized Lattice Boltzmann Method for Acoustic Propagation Simulation.

A simplified linearized lattice Boltzmann method (SLLBM) suitable for the simulation of acoustic waves propagation in fluids was proposed herein. Through Chapman-Enskog expansion analysis, the linearized lattice Boltzmann equation (LLBE) was first recovered to linearized macroscopic equations. Then, using the fractional-step calculation technique, the solution of these linearized equations was divided into two steps: a predictor step and corrector step. Next, the evolution of the perturbation distribution function was transformed into the evolution of the perturbation equilibrium distribution function using second-order interpolation approximation of the latter at other positions and times to represent the nonequilibrium part of the former; additionally, the calculation formulas of SLLBM were deduced. SLLBM inherits the advantages of the linearized lattice Boltzmann method (LLBM), calculating acoustic disturbance and the mean flow separately so that macroscopic variables of the mean flow do not affect the calculation of acoustic disturbance. At the same time, it has other advantages: the calculation process is simpler, and the cost of computing memory is reduced. In addition, to simulate the acoustic scattering problem caused by the acoustic waves encountering objects, the immersed boundary method (IBM) and SLLBM were further combined so that the method can simulate the influence of complex geometries. Several cases were used to validate the feasibility of SLLBM for simulation of acoustic wave propagation under the mean flow.

Digital transformation of droplet/aerosol infection risk assessment realized on "Fugaku" for the fight against COVID-19.

The fastest supercomputer in 2020, Fugaku, has not only achieved digital transformation of epidemiology in allowing end-to-end, detailed quantitative modeling of COVID-19 transmissions for the first time but also transformed the behavior of the entire Japanese public through its detailed analysis of transmission risks in multitudes of societal situations entailing heavy risks. A novel aerosol simulation methodology was synthesized out of a combination of a new CFD methods meeting industrial demands in the solver, CUBE (Jansson et al., 2019), which not only allowed the simulations to scale massively with high resolution required for micrometer virus-containing aerosol particles but also enabled extremely rapid time-to-solution due to its ability to generate the digital twins representing multitudes of societal situations in a matter of minutes, attaining true overall application high performance; such simulations have been running for the past 1.5°years on Fugaku, cumulatively consuming top supercomputer-class resources and the communicated by the media as well as becoming the basis for official public policies.

Lattice Boltzmann simulations on the tumbling to tank-treading transition: effects of membrane viscosity.

The tumbling to tank-treading (TB-TT) transition for red blood cells (RBCs) has been widely investigated, with a main focus on the effects of the viscosity ratio [Formula: see text] (i.e., the ratio between the viscosities of the fluids inside and outside the membrane) and the shear rate [Formula: see text] applied to the RBC. However, the membrane viscosity [Formula: see text] plays a major role in a realistic description of RBC dynamics, and only a few works have systematically focused on its effects on the TB-TT transition. In this work, we provide a parametric investigation on the effect of membrane viscosity [Formula: see text] on the TB-TT transition for a single RBC. It is found that, at fixed viscosity ratios [Formula: see text], larger values of [Formula: see text] lead to an increased range of values of capillary number at which the TB-TT transition occurs; moreover, we found that increasing [Formula: see text] or increasing [Formula: see text] results in a qualitatively but not quantitatively similar behaviour. All results are obtained by means of mesoscale numerical simulations based on the lattice Boltzmann models. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.

Electrodiffusion with Calcium-Activated Potassium Channels in Dendritic Spine.

We investigate calcium signaling feedback through calcium-activated potassium channels of a dendritic spine by applying the immersed boundary method with electrodiffusion. We simulate the stochastic gating of such ion channels and the resulting spatial distribution of concentration, current, and membrane voltage within the dendritic spine. In this simulation, the permeability to ionic flow across the membrane is regulated by the amplitude of chemical potential barriers. With spatially localized ion channels, chemical potential barriers are locally and stochastically regulated. This regulation represents the ion channel gating with multiple subunits, the open and closed states governed by a continuous-time Markov process. The model simulation recapitulates an inhibitory action on voltage-sensitive calcium channels by the calcium-activated potassium channels in a stochastic manner as a non-local feedback loop. The model predicts amplified calcium influx with more closely placed channel complexes, proposing a potential mechanism of differential calcium handling by channel distributions. This work provides a foundation for future computer simulation studies of dendritic spine motility and structural plasticity.

Exploring the sensitivity in jellyfish locomotion under variations in scale, frequency, and duty cycle.

Jellyfish have been called one of the most energy-efficient animals in the world due to the ease in which they move through their fluid environment, by product of their bell kinematics coupled with their morphological, muscular, material properties. We investigated jellyfish locomotion by conducting in silico comparative studies and explored swimming performance across different fluid scales (i.e., Reynolds Number), bell contraction frequencies, and contraction phase kinematics (duty cycle) for a jellyfish with a fineness ratio of 1 (ratio of bell height to bell diameter). To study these relationships, an open source implementation of the immersed boundary method was used (IB2d) to solve the fully coupled fluid-structure interaction problem of a flexible jellyfish bell in a viscous fluid. Thorough 2D parameter subspace explorations illustrated optimal parameter combinations in which give rise to enhanced swimming performance. All performance metrics indicated a higher sensitivity to bell actuation frequency than fluid scale or duty cycle, via Sobol sensitivity analysis, on a higher performance parameter subspace. Moreover, Pareto-like fronts were identified in the overall performance space involving the cost of transport and forward swimming speed. Patterns emerged within these performance spaces when highlighting different parameter regions, which complemented the global sensitivity results. Lastly, an open source computational model for jellyfish locomotion is offered to the science community that can be used as a starting place for future numerical experimentation.

Pumping Patterns and Work Done During Peristalsis in Finite-Length Elastic Tubes.

Balloon dilation catheters are often used to quantify the physiological state of peristaltic activity in tubular organs and comment on their ability to propel fluid which is important for healthy human function. To fully understand this system's behavior, we analyzed the effect of a solitary peristaltic wave on a fluid-filled elastic tube with closed ends. A reduced order model that predicts the resulting tube wall deformations, flow velocities, and pressure variations is presented. This simplified model is compared with detailed fluid-structure three-dimensional (3D) immersed boundary (IB) simulations of peristaltic pumping in tube walls made of hyperelastic material. The major dynamics observed in the 3D simulations were also displayed by our one-dimensional (1D) model under laminar flow conditions. Using the 1D model, several pumping regimes were investigated and presented in the form of a regime map that summarizes the system's response for a range of physiological conditions. Finally, the amount of work done during a peristaltic event in this configuration was defined and quantified. The variation of elastic energy and work done during pumping was found to have a unique signature for each regime. An extension of the 1D model is applied to enhance patient data collected by the device and find the work done for a typical esophageal peristaltic wave. This detailed characterization of the system's behavior aids in better interpreting the clinical data obtained from dilation catheters. Additionally, the pumping capacity of the esophagus can be quantified for comparative studies between disease groups.