Simulations of time harmonic blood flow in the Mesenteric artery: comparing finite element and lattice Boltzmann methods

<p>Abstract</p> <p>Background</p> <p>Systolic blood flow has been simulated in the abdominal aorta and the superior mesenteric artery. The simulations were carried out using two different computational hemodynamic methods: the finite element method to solve the Navier Stokes equations and the lattice Boltzmann method.</p> <p>Results</p> <p>We have validated the lattice Boltzmann method for systolic flows by comparing the velocity and pressure profiles of simulated blood flow between methods. We have also analyzed flow-specific characteristics such as the formation of a vortex at curvatures and traces of flow.</p> <p>Conclusion</p> <p>The lattice Boltzmann Method is as accurate as a Navier Stokes solver for computing complex blood flows. As such it is a good alternative for computational hemodynamics, certainly in situation where coupling to other models is required.</p

The use of the lattice Boltzmann method in thrombosis modelling.

The effects of thrombosis greatly contribute to the incidence of mortality in the Western World. Understanding thrombosis is therefore crucial in providing the correct treatment for the underlying pathologies. Numerical methods have previously been used to investigate various factors associated with thrombosis, usually starting from solutions of the Navier-Stokes equations. This thesis presents the development and implementation of models of thrombosis using the lattice Boltzmann method, which is a relatively new technique for simulating fluid dynamics. The advantages and disadvantages of this methodology are critically reviewed and two major pathologies, atherosclerosis and deep vein thrombosis have been chosen to demonstrate principles of the application. The first part of the work concentrates on the simulation of flow and clotting in idealised stenotic occlusions representative of the geometry and flow conditions in a diseased human femoral artery. Simulations of unsteady flow are reported and comparisons are made to previous flow visualisation studies. Stability issues regarding the diffusion algorithm are investigated in detail. In the first instance, clotting is simulated with the use of an aging model with extensions including proximity and shear stress. Comparisons are made with experimental results obtained using milk as a blood analogue. )'he second part of the work focuses on increasing the complexity of the models to incorporate the representations of the actions and distribution of the platelets, proteins and enzymes involved in the coagulation cascade. The models are tested in 2D geometries to demonstrate their functionality. As an example of this work, a model of deep vein thrombosis was developed, based on a hypothesis supported by the clinical literature. The foundations laid in this project allow for future developments, which will incorporate further details of thrombotic processes, in the hope that a valuable predictor of thrombosis can be developed

Computational Fluid Dynamics (CFD) Simulation for the Extraction of Blood Clot in Middle Cerebral Artery using ‘GP’ 2 Device

Stroke has become the number three killer disease in Malaysia following heart disease and cancer; with 110 of people dying from it every day. The effects of stroke often lead to life-changing, permanent impairment to the patients such as paralysis, speech and logic sequencing. Hence, recent studies are looking into stroke treatments with minimal after surgical effect to patients. One of the alternatives is using mechanical thrombectomy devices. In this project, the simulation for ‘GP’ 2 device which functions to extract the blood clot in the artery without damaging the arterial wall and causing downstream embolism is presented. The simulation will be carried out using computational fluid dynamics; applying the Volume of Fluid (VOF) model. In grid size selection, it is clear that finer grids results in higher accuracy calculations i.e. better results. However, this is achieved at the cost of prolonged computational time. From grid sensitivity study in identifying the optimum grid size that is fine enough to generate accurate calculations but large enough to avoid extra computational time; the grid size of 0.2mm is used. The design for ‘GP’ 2 Device has to be characterised to identify which of the two proposed designs is efficient for the suction of blood clot for 100% occlusion in the Middle Cerebral Artery. Design for ‘GP’ 2 Model 1 device is better at clot extraction than the Model 2 device because increase in surface area for suction favours same-suction principle rather than vortex creation to break the clot. Theoretically, higher pressure results in faster clot extraction. However, the value of pressure applied shall be observed closely so that no arterial damage is done and it can be applied for clinical tests. For both models, it can be shown that higher pressure extracts blood clot at lower time whereby the fastest clot extraction occurs at time 0.00498s for Model 1, and 0.01211s for Model 2 both at 60 kPa

Computational Fluid Dynamics (CFD) Simulation for the Extraction of Blood Clot in Middle Cerebral Artery using ‘GP’ 2 Device

Stroke has become the number three killer disease in Malaysia following heart disease and cancer; with 110 of people dying from it every day. The effects of stroke often lead to life-changing, permanent impairment to the patients such as paralysis, speech and logic sequencing. Hence, recent studies are looking into stroke treatments with minimal after surgical effect to patients. One of the alternatives is using mechanical thrombectomy devices. In this project, the simulation for ‘GP’ 2 device which functions to extract the blood clot in the artery without damaging the arterial wall and causing downstream embolism is presented. The simulation will be carried out using computational fluid dynamics; applying the Volume of Fluid (VOF) model. In grid size selection, it is clear that finer grids results in higher accuracy calculations i.e. better results. However, this is achieved at the cost of prolonged computational time. From grid sensitivity study in identifying the optimum grid size that is fine enough to generate accurate calculations but large enough to avoid extra computational time; the grid size of 0.2mm is used. The design for ‘GP’ 2 Device has to be characterised to identify which of the two proposed designs is efficient for the suction of blood clot for 100% occlusion in the Middle Cerebral Artery. Design for ‘GP’ 2 Model 1 device is better at clot extraction than the Model 2 device because increase in surface area for suction favours same-suction principle rather than vortex creation to break the clot. Theoretically, higher pressure results in faster clot extraction. However, the value of pressure applied shall be observed closely so that no arterial damage is done and it can be applied for clinical tests. For both models, it can be shown that higher pressure extracts blood clot at lower time whereby the fastest clot extraction occurs at time 0.00498s for Model 1, and 0.01211s for Model 2 both at 60 kPa

3-Dimensional Blood Clot Simulation On Plastic Arterial Catheter using GAMBIT & FLUENT

The Volume Of Fluid (VOF) model is a surface-tracking technique applied to a fixed Eulerian mesh. It is designed for two or more immiscible fluids where the position of the interface between the fluids is of interest. The fluids share a single set of momentum equations, and the volume fraction of each of the fluids in each computational cell is tracked throughout the domain. As such, VOF is an advection scheme that acts as a numerical recipe that allows the programmer to track the shape and position of the interface, but it is not a standalone flow-solving algorithm. The Navier Stokes equations describing the motion of the flow have to be solved separately. The movement of one fluid with regards to its interface is studied to help the researchers and engineers in deciding certain parameters such as pressure and velocity in plastic arterial catheter in order to reduce error, computational cost, and save simulation time. Good resemblance between CFD predictions with the experimental data in certain locations was obtained with the factor of species (blood clot) transport and pressure profile, where dependence of VOF models and grid sizes were discussed in details. The results show us that, the demand in grid study is vital to obtain accurate results with minimal computational cost. On the other hand, wall adhesion is solved in an iterative way, modifying holdups at the wall until the specified wall contact angle had been satisfied. Since the VOF method is a Direct Numerical Simulation (DNS) approach, the time and length scales on which the equations are being solved should be sufficiently small to directly take fluctuating fluid motion due to turbulence into account. Therefore, VOF simulations do not incorporate any other turbulence models, thus only applicable to laminar models

Design and fabrication of novel microfluidic systems for microsphere generation

In this thesis, a study of the rational design and fabrication of microfluidic systems for microsphere generation is presented. The required function of microfluidic systems is to produce microspheres with the following attributes: (i) the microsphere size being around one micron or less, (ii) the size uniformity (in particular coefficient of variation (CV)) being less than 5%, and (iii) the size range being adjustable as widely as possible. Micro-electro-mechanical system (MEMS) technology, largely referring to various micro-fabrication techniques in the context of this thesis, has been applied for decades to develop microfluidic systems that can fulfill the foregoing required function of microsphere generation; however, this goal has yet to be achieved. To change this situation was a motivation of the study presented in this thesis. The philosophy behind this study stands on combining an effective design theory and methodology called Axiomatic Design Theory (ADT) with advanced micro-fabrication techniques for the microfluidic systems development. Both theoretical developments and experimental validations were carried out in this study. Consequently, the study has led to the following conclusions: (i) Existing micro-fluidic systems are coupled designs according to ADT, which is responsible for a limited achievement of the required function; (ii) Existing micro-fabrication techniques, especially for pattern transfer, have difficulty in producing a typical feature of micro-fluidic systems - that is, a large overall size (~ mm) of the device but a small channel size (~nm); and (iii) Contemporary micro-fabrication techniques to the silicon-based microfluidic system may have reached a size limit for microspheres, i.e., ~1 micron. Through this study, the following contributions to the field of the microfluidic system technology have been made: (i) Producing three rational designs of microfluidic systems, device 1 (perforated silicon membrane), device 2 (integration of hydrodynamic flow focusing and crossflow principles), and device 3 (liquid chopper using a piezoelectric actuator), with each having a distinct advantage over the others and together having achieved the requirements, size uniformity (CV ≤ 5%) and size controllability (1-186 µm); (ii) Proposing a new pattern transfer technique which combines a photolithography process with a direct writing lithography process (e.g., focused ion beam process); (iii) Proposing a decoupled design principle for micro-fluidic systems, which is effective in improving microfluidic systems for microsphere generation and is likely applicable to microfluidic systems for other applications; and (iv) Developing the mathematical models for the foregoing three devices, which can be used to further optimize the design and the microsphere generation process

Progress in particle-based multiscale and hybrid methods for flow applications

This work focuses on the review of particle-based multiscale and hybrid methods that have surfaced in the field of fluid mechanics over the last 20 years. We consider five established particle methods: molecular dynamics, direct simulation Monte Carlo, lattice Boltzmann method, dissipative particle dynamics and smoothed-particle hydrodynamics. A general description is given on each particle method in conjunction with multiscale and hybrid applications. An analysis on the length scale separation revealed that current multiscale methods only bridge across scales which are of the order of O(102)−O(103) and that further work on complex geometries and parallel code optimisation is needed to increase the separation. Similarities between methods are highlighted and combinations discussed. Advantages, disadvantages and applications of each particle method have been tabulated as a reference

The effect of stochastic nano-scale surface roughness on microfluidic flow in computational microchannels

Microfluidics is a promising technology that is used extensively in biomedical devices, so called lab-on-a-chip devices. These devices harness a network of microchannels to mix, react, and conduct fluid flow. Most microchannel fabrication methods produce a stochastic surface roughness with heights ranging in the micro- to nano- scale. This inherent, stochastic roughness can potentially be harnessed to enhance microfluidic operations. Previous research on rough surfaces in microfluidics has focused on periodic, micro-scale obstructions, not of any stochastic nature. The purpose of this research is to characterize the effect of stochastic nano-scale surface roughness on microfluidic flow using very large-scale direct numerical simulations (DNS) and micro- particle image velocimetry (micro-PIV). The two studies are focused on a microchannel with one of the walls, the bottom surface, which has a manufactured surface roughness using a hydrofluoric-acid (HF) etching process. The rough surface is scanned by an optical profilometer, and the exact topography is imported as the bottom surface of the computational microchannel. HF-acid etched glass and un-etched glass surfaces are directly compared to each other. In the first study, the DNS simulations are compared to micro-PIV experiments for a Newtonian fluid (water). The flow regime was laminar, diffusion dominated and limited to Re \u3c 10. The second study used a longer microchannel relative to the first study that was made possible by stitching together consecutive profilometer surface scans. This study only used simulations to study the effect of nano-scale roughness on microfluidic flow (with the previous study forming a basis for model validation). In the future, the study will be extended to Newtonian as well as non-Newtonian (shear-thinning) fluids in the same flow regime as the first study. Overall, we have shown that an experimentally validated and experimentally driven three-dimensional computational study for microfluidic stochastic surface roughness is possible. Additionally, we have shown that the stochastic nature of the surface roughness and its effect on fluid flow can be characterized with numerous tools including velocity-perturbation contours, autocorrelation length (ACL), and energy spectra analysis. The different analyses illustrated the effect of the rough surface in different ways. Velocity-perturbation contours showed that both the etched and un-etched rough surfaces produced very small velocity structures (eddies) very near the rough surface that merge to form larger structures as the height above the rough surface increases. The velocity-perturbation contours revealed an increase in the magnitude of the velocity perturbations by an order of magnitude by using the etched glass, which was directly caused by the increase in roughness height from HF etching. The ACL analyses also showed how the surface roughness produces small perturbation structures that merge and persist well into the midplane of the microchannel. Energy spectra analyses revealed a transfer of energy caused by the structures of the rough surfaces. Notably for the same Reynolds number, the etched surface produced velocity-perturbation structures that contained more energy and persisted higher into the microchannel compared to the un-etched surface. This research has shown that a chemical etching surface treatment and other stochastic rough surfaces, even at the nano-scale, have an effect on microfluidic flow that can be characterized and potentially be harnessed across a range of fluid flow rates. Devices that use microchannels such as lab-on-a-chip medical devices can therefore be tuned and optimized for their respective applications such as reagent mixing, bubble creation and transport, fluid transport, and cell manipulation using stochastic surface roughness