Mass transfer enhancement in moving biofilm structures

Biofilms are layers of microbial cells growing on an interface and they can form highly complex structures adapted to a wide variety of environmental conditions. Biofilm streamers have a small immobile base attached to the support and a flexible tail elongated in the flow direction, which can vibrate in fast flows. Herein we report numerical results for the role of the periodical movement of biofilm streamers on the nutrient uptake and in general on the solute mass transfer enhancement due to flow-induced oscillations. We developed what to our knowledge is a novel two-dimensional fluid-structure interaction model coupled to unsteady solute mass transport and solved the model using the finite element method with a moving mesh. Results demonstrate that the oscillatory movement of the biofilm tail significantly increases the substrate uptake. The mass transfer coefficient is the highest in regions close to the streamer tip. The reason for substrate transfer enhancement is the increase in speed of tip movement relative to the surrounding liquid, thereby reducing the thickness of the mass transfer boundary layer. In addition, we show that the relative mass transfer enhancement in unsteady conditions compared with the rigid static structure is larger at higher flow velocities, and this relative increase favors a more flexible structure.     

The fish tail motion forms an attached leading edge vortex

The tail (caudal fin) is one of the most prominent characteristics of fishes, and the analysis of the flow pattern it creates is fundamental to understanding how its motion generates locomotor forces. A mechanism that is known to greatly enhance locomotor forces in insect and bird flight is the leading edge vortex (LEV) reattachment, i.e. a vortex (separation bubble) that stays attached at the leading edge of a wing. However, this mechanism has not been reported in fish-like swimming probably owing to the overemphasis on the trailing wake, and the fact that the flow does not separate along the body of undulating swimmers. We provide, to our knowledge, the first evidence of the vortex reattachment at the leading edge of the fish tail using three-dimensional high-resolution numerical simulations of self-propelled virtual swimmers with different tail shapes. We show that at Strouhal numbers (a measure of lateral velocity to the axial velocity) at which most fish swim in nature (approx. 0.25) an attached LEV is formed, whereas at a higher Strouhal number of approximately 0.6 the LEV does not reattach. We show that the evolution of the LEV drastically alters the pressure distribution on the tail and the force it generates. We also show that the tail''s delta shape is not necessary for the LEV reattachment and fish-like kinematics is capable of stabilising the LEV. Our results suggest the need for a paradigm shift in fish-like swimming research to turn the focus from the trailing edge to the leading edge of the tail.     

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.     

Computational fluid dynamics simulations on a Devonian spiriferid Paraspirifer bownockeri (Brachiopoda): Generating mechanism of passive feeding flows

A mechanism of generating passive feeding flow for the Devonian spiriferide brachiopod Paraspirifer bownockeri was theoretically elucidated through fluid dynamics simulations for flow around rigid shells. The RANS equations were used as a turbulence model, and the unsteady incompressible flow was solved using the finite volume method. Two directions of ventral and dorsal flows were investigated as typical cases where little exchange flow occurs inside the shells. The digital model of the shell was constructed using image processing of X-ray CT images of a shell replica made by molding a polycarbonate plate to a well-preserved fossil specimen of Paraspirifer. To examine the effect of flow velocity, three conditions of ambient flow velocity were adopted for both the ventral and dorsal flows. The pressure distribution along the gape showed that a relatively high pressure occurred around the sulcus in all simulated cases. This high pressure generated inflow from the sulcus and subsequent spiral internal flow, especially in fast ambient flows. This means that the sulcus generated the considerable pressure gradient around the gape passively and generated the stable intake of seawater and a spiral flow of water inside the shell for feeding. We conclude that the shell form of certain spiriferides could generate spiral flows so as to promote passive feeding, and the sulcus is interpreted as an important form for the passive intake of water.     

Biological Inspiration: From Carangiform Fish to Multi-Joint Robotic Fish

This paper presents a novel approach to modelling carangiform fish-like swimming motion for multi-joint robotic fish so that they can obtain fish-like behaviours and mimic the body motion of carangiform fish. A given body motion function of fish swimming is firstly converted to a tail motion function which describes the tail motion relative to the head. Then, the tail motion function is discretized into a series of tail postures over time. Thirdly, a digital approximation method calculates the taming angles of joints in the tail to approximate each tail posture; and finally, these angles are grouped into a look-up table, or re-gressed to a time-dependent function, for practically controlling the tail motors in a multi-joint robotic fish. The paper made three contributions: tail motion relative to the head, an error function for digital approximation and regressing a look-up table for online optimization. To prove the feasibility of the proposed methodology, two basic swimming motion patterns, cruise straight and C-shape sharp turning, are modelled and implemented in our robotic fish. The experimental results show that the relative tail motion and the approximation error function are good choices and the proposed method is feasible.     

Volumetric imaging of shark tail hydrodynamics reveals a three-dimensional dual-ring vortex wake structure

Understanding how moving organisms generate locomotor forces is fundamental to the analysis of aerodynamic and hydrodynamic flow patterns that are generated during body and appendage oscillation. In the past, this has been accomplished using two-dimensional planar techniques that require reconstruction of three-dimensional flow patterns. We have applied a new, fully three-dimensional, volumetric imaging technique that allows instantaneous capture of wake flow patterns, to a classic problem in functional vertebrate biology: the function of the asymmetrical (heterocercal) tail of swimming sharks to capture the vorticity field within the volume swept by the tail. These data were used to test a previous three-dimensional reconstruction of the shark vortex wake estimated from two-dimensional flow analyses, and show that the volumetric approach reveals a different vortex wake not previously reconstructed from two-dimensional slices. The hydrodynamic wake consists of one set of dual-linked vortex rings produced per half tail beat. In addition, we use a simple passive shark-tail model under robotic control to show that the three-dimensional wake flows of the robotic tail differ from the active tail motion of a live shark, suggesting that active control of kinematics and tail stiffness plays a substantial role in the production of wake vortical patterns.     

A continuous dynamic beam model for swimming fish

When a fish swims in water, muscle contraction, controlled by the nervous system, interacts with the body tissues and the surrounding fluid to yield the observed movement pattern of the body. A continuous dynamic beam model describing the bending moment balance on the body for such an interaction during swimming has been established. In the model a linear visco-elastic assumption is made for the passive behaviour of internal tissues, skin and backbone, and the unsteady fluid force acting on the swimming body is calculated by the 3D waving plate theory. The body bending moment distribution due to the various components, in isolation and acting together, is analysed. The analysis is based on the saithe (Pollachius virens), a carangiform swimmer. The fluid reaction needs a bending moment of increasing amplitude towards the tail and near-standing wave behaviour on the rear-half of the body. The inertial movement of the fish results from a wave of bending moment with increasing amplitude along the body and a higher propagation speed than that of body bending. In particular, the fluid reaction, mainly designed for propulsion, can provide a considerable force to balance the local momentum change of the body and thereby reduce the power required from the muscle. The wave of passive visco-elastic bending moment, with an amplitude distribution peaking a little before the mid-point of the fish, travels with a speed close to that of body bending. The calculated muscle bending moment from the whole dynamic system has a wave speed almost the same as that observed for EMG-onset and a starting instant close to that of muscle activation, suggesting a consistent matching between the muscle activation pattern and the dynamic response of the system in steady swimming. A faster wave of muscle activation, with a variable phase relation between the strain and activation cycle, appears to be designed to fit the fluid reaction and, to a lesser extent, the body inertia, and is limited by the passive internal tissues. Higher active stress is required from caudal muscle, as predicted from experimental studies on fish muscle. In general, the active force development by muscle does not coincide with the propulsive force generation on the tail. The stiffer backbone may play a role in transmitting force and deformation to maintain and adjust the movement of the body and tail in water.     

Computational hydrodynamics of animal swimming: boundary element method and three-dimensional vortex wake structure.

The slender body theory, lifting surface theories, and more recently panel methods and Navier-Stokes solvers have been used to study the hydrodynamics of fish swimming. This paper presents progress on swimming hydrodynamics using a boundary integral equation method (or boundary element method) based on potential flow model. The unsteady three-dimensional BEM code 3DynaFS that we developed and used is able to model realistic body geometries, arbitrary movements, and resulting wake evolution. Pressure distribution over the body surface, vorticity in the wake, and the velocity field around the body can be computed. The structure and dynamic behavior of the vortex wakes generated by the swimming body are responsible for the underlying fluid dynamic mechanisms to realize the high-efficiency propulsion and high-agility maneuvering. Three-dimensional vortex wake structures are not well known, although two-dimensional structures termed 'reverse Karman Vortex Street' have been observed and studied. In this paper, simulations about a swimming saithe (Pollachius virens) using our BEM code have demonstrated that undulatory swimming reduces three-dimensional effects due to substantially weakened tail tip vortex, resulting in a reverse Karman Vortex Street as the major flow pattern in the three-dimensional wake of an undulating swimming fish.     

Small-scale fluid motion mediates growth and nutrient uptake of Selenastrum capricornutum

1. A fluid‐flow reactor using submersible speakers was constructed to generate small‐scale fluid motion similar to conditions measured in open water environments; flow was quantified by particle image velocimetry. Additionally a Couette‐type rotating cylinder was used to generate shear flows; flow was quantified using an optical hotwire probe and torque measurements. Growth rates of the green alga Selenastrum capricornutum were determined from changes in cell counts and viability was tested using the fluorogenic probe fluoresceine diacetate. 2. Evidence that fluid motion directly affects growth rates was obtained as a significant difference between growth in a moving versus non‐moving fluid. A near 2‐fold increase in growth rate was achieved for an energy dissipation rate of ? = 10^?7 m² s^?3; a rate common in lakes and oceans. The onset of the viability equilibrium, identified as the day of the test period when the number of active cells equalled non‐active cells, was delayed by 2 days for moving fluid conditions as compared with a non‐moving fluid. 3. Nutrient uptake was determined by a decrease in the bulk fluid concentration and cellular phosphorus concentration was also estimated. The thickness of the diffusive sublayer surrounding a cell, a zone dominated by molecular diffusion, was estimated. Increasing fluid motion was found to decrease the thickness of this layer. The Sherwood number (ratio of total mass flux to molecular mass flux) showed that advective flux surrounding cells dominated molecular diffusion flux with regard to Péclet numbers (ratio of advective transport to molecular diffusion transport). Fluid motion facilitated uptake rates and resulted in increased growth rates, compared with no‐flow conditions. The rate‐of‐rotation and the rate‐of‐strain in a moving fluid equally mediated the diffusive sublayer thickness surrounding the cells. Our study demonstrates that small‐scale fluid motion mediates algal growth kinetics and therefore should be included in predictive models for algal blooms.     

Cyclic loading on the red cell membrane in a shear flow: a possible cause of hemolysis

The fluid force acting on single human red cells in a high shear flow was analyzed. A two-dimensional elliptical microcapsule as a model of the deformed red cells was adopted to numerically calculate the distributions of the shear forces on both sides of the cell membrane. It is theoretically shown that the cell membrane undergoes an unsteady cyclic loading under the rotational motion around the interior. The mechanism leading to blood cell trauma is examined by repeatedly loading the continuously moving cell membrane.     

Motion of nonaxisymmetric red blood cells in cylindrical capillaries

We analyze theoretically the single-file flow of asymmetric red blood cells along cylindrical capillaries. Red cells in narrow capillaries are typically nonaxisymmetric, with the cell membrane moving continuously around the cell. In our analysis, cell shape and streamlines of membrane motion are prescribed. Lubrication theory is used to compute velocities and pressures in the fluid surrounding the cell. Conditions of zero lift, zero torque, zero drag, and energy conservation in the cell are imposed. Predicted tank-treading frequency, cell inclination and transverse displacement are small. Cell asymmetry and tank-treading are found to have little effect on the apparent viscosity of blood in capillaries with diameters up to 7 microns.     

Numerical simulation of local blood flow in the carotid and cerebral arteries under altered gravity

A computational fluid dynamics (CFD) approach was presented to model the blood flows in the carotid bifurcation and the brain arteries under altered gravity. Physical models required for CFD simulation were introduced including a model for arterial wall motion due to fluid-wall interactions, a shear thinning fluid model of blood, a vascular bed model for outflow boundary conditions, and a model for autoregulation mechanism. The three-dimensional unsteady incompressible Navier-Stokes equations coupled with these models were solved iteratively using the pseudocompressibility method and dual time stepping. Gravity source terms were added to the Navier-Stokes equations to take the effect of gravity into account. For the treatment of complex geometry, a chimera overset grid technique was adopted to obtain connectivity between arterial branches. For code validation, computed results were compared with experimental data for both steady-state and time-dependent flows. This computational approach was then applied to blood flows through a realistic carotid bifurcation and two Circle of Willis models, one using an idealized geometry and the other using an anatomical data set. A three-dimensional Circle of Willis configuration was reconstructed from subject-specific magnetic resonance images using an image segmentation method. Through the numerical simulation of blood flow in two model problems, namely, the carotid bifurcation and the brain arteries, it was observed that the altered gravity has considerable effects on arterial contraction/dilatation and consequent changes in flow conditions.     

Machine Vision Based Measurement of Dynamic Contact Angles in Microchannel Flows

When characterizing flows in miniaturized channels, the determination of the dynamic contact angle is important. By measuring the dynamic contact angle, the flow properties of the flowing liquid and the effect of material properties on the flow can be characterized. A machine vision based system to measure the contact angle of front or rear menisci of a moving liquid plug is described in this article. In this research, transparent flow channels fabricated on thermoplastic polymer and sealed with an adhesive tape are used. The transparency of the channels enables image based monitoring and measurement of flow variables, including the dynamic contact angle. It is shown that the dynamic angle can be measured from a liquid flow in a channel using the image based measurement system. An image processing algorithm has been developed in a MATLAB environment. Images are taken using a CCD camera and the channels are illuminated using a custom made ring light. Two fitting methods, a circle and two parabolas, are experimented and the results are compared in the measurement of the dynamic contact angles.     

Vortex shedding as a mechanism for free emboli formation in mechanical heart valves

The high incidence of thromboembolic complications of mechanical heart valves (MHV) limits their success as permanent implants. The thrombogenicity of all MHV is primarily due to platelet activation by contact with foreign surfaces and by nonphysiological flow patterns. The latter include elevated flow stresses and regions of recirculation of blood that are induced by valve design characteristics. A numerical simulation of unsteady turbulent flow through a bileaflet MHV was conducted, using the Wilcox k-omega turbulence model for internal low-Reynolds-number flows, and compared to quantitative flow visualization performed in a pulse duplicator system using Digital Particle Image Velocimetry (DPIV). The wake of the valve leaflet during the deceleration phase revealed an intricate pattern of interacting shed vortices. Particle paths showed that platelets that were exposed to the highest flow stresses around the leaflets were entrapped within the shed vortices. Potentially activated, such platelets may tend to aggregate and form free emboli. Once formed, such free emboli would be convected downstream by the shed vortices, increasing the risk of systemic emboli.     

Unsteady flow of Casson fluids through the eccentric circular tube.

As a model of the flow through the false lumen of the dissecting aortic aneurysm, the starting and stopping flows of the Casson fluid through the eccentric circular tube are studied numerically. The calculations are performed by using the one-direction fully developed unsteady flow model. The calculation results show that the non-Newtonian property of the Casson fluid has the following two effects. One is the decrease in the flow rate through the false lumen, the other is the effect to strengthen the non-uniformity of the velocity distribution in the false lumen. Moreover, the calculations based on a triphasic waveform measured by McDonald are performed and the development of the dissecting aortic aneurysm is discussed on the basis of the calculated wall shear stress.     

Waveform dependence of pulsatile flow in a stenosed channel

Bloodflow in arteries often shows a rich variety of vortical flows, which are dominated by the complex geometry of blood vessels, the dynamic pulsation of blood flow, and the complicated boundary conditions. With a two-dimensional model of unsteady flow in a stenosed channel, the pulsatile influence on such vortical fluid dynamics has been numerically studied in terms of waveform dependence on physiological pulsation. Results are presented for unsteady flows downstream of the stenosed portion with variation in the wavefiorms of systole and diastole. Overall, a train of propagating vortex waves is observed for all the cases, but it shows great sensitivity to the waveforms. The generation and development of the vortex waves may be linked to the presence of an adverse pressure gradient within a specific interval between two points of inflection of the systolic waveform. The adverse pressure gradient consists of a global pressure gradient that is found to be closely related to the dynamnics of' the pulsation, and a local pressure gradient, which is obsented to be dominated by the nonlinear vortex dynamics.     

Time-accurate,parallel, multi-zone,multi-block solver to study the human cardio-vascular system

A parallel, time-accurate flow solver is devised to study the human cardio-vascular system. The solver is capable of dealing with moving boundaries and moving grids. It is designed to handle complex, three-dimensional vascular systems. The computational domain is divided into multiple block subdomains. At each cross section the plane is divided into twelve sub-zones to allow flexibility for handling complex geometries and, if needed, appropriate parallel data partitioning. The unsteady, three-dimensional, incompressible Navier-Stokes equations are solved numerically. A second-order in time and third-order upwind finite volume method for solving time-accurate incompressible flows based on pseudo-compressibility and dual time-stepping technique is used. For parallel execution, the flow domain is partitioned. Communication between the subdomains of the flow on Riken's VPP/700E supercomputer is implemented using MPI message-passing library. A series of numerical simulations of biologically relevant flows is used to validate this code.     

Blood flow downstream of a two-dimensional bifurcation

Many cardiovascular lesions such as aneurysms, intimal cushions, and atherosclerotic plaques tend to occur near bifurcations. This suggests that hemodynamic factors may be involved. Since measuring devices (such as anemometers) are still too large to allow local measurements of flow disturbances, we have attempted to predict the nature of these factors mathematically. Biological variables include pulsatile flow of a nonNewtonian fluid in distensible branching vessels with different angles and flow rates. Our initial analysis considers the flow in a two-dimensional bifurcation with a symmetrical flow divider perfused with steady flow at variable Reynolds numbers. At all flows, high shear forces develop on either side of the flow divider (i.e. at the apex of the bifurcation). With high flows, regions of sluggish or reverse flow develop near the outer walls of the bifurcation. The analysis confirms that the flow at the apex is quite different from that at the outer angles and that the latter varies more with flow rate than the former.