Analysis of a swimmer's hand and arm in steady flow conditions using computational fluid dynamics

Propulsive forces generated by swimmers' hands and arms have, to date, been determined strictly through experimental testing. As an alternative to these complex and costly experiments, the present research has applied the numerical technique of computational fluid dynamics (CFD) to calculate the steady flow around a swimmer's hand and arm at various angles of attack. Force coefficients computed for the hand and arm compared well with steady-state coefficients determined experimentally. The simulations showed significant boundary layer separation from the arm and hand, suggesting that Bernoulli's equation should not be used to mathematically describe the lift generated by a swimmer. Additionally, "2D" lift was shown to be inaccurate for the arm at all angles of attack and for the hand near angles of attack of 90 degrees. Such simulations serve to validate the chosen CFD techniques, and are an important first step towards the use of CFD methods for determining swimming hydrodynamic forces in more complex unsteady flow conditions.     

Using computational fluid dynamics software to estimate circulation time distributions in bioreactors

Nonideal mixing in many fermentation processes can lead to concentration gradients in nutrients, oxygen, and pH, among others. These gradients are likely to influence cellular behavior, growth, or yield of the fermentation process. Frequency of exposure to these gradients can be defined by the circulation time distribution (CTD). There are few examples of CTDs in the literature, and experimental determination of CTD is at best a challenging task. The goal in this study was to determine whether computational fluid dynamics (CFD) software (FLUENT 4 and MixSim) could be used to characterize the CTD in a single-impeller mixing tank. To accomplish this, CFD software was used to simulate flow fields in three different mixing tanks by meshing the tanks with a grid of elements and solving the Navier-Stokes equations using the kappa-epsilon turbulence model. Tracer particles were released from a reference zone within the simulated flow fields, particle trajectories were simulated for 30 s, and the time taken for these tracer particles to return to the reference zone was calculated. CTDs determined by experimental measurement, which showed distinct features (log-normal, bimodal, and unimodal), were compared with CTDs determined using CFD simulation. Reproducing the signal processing procedures used in each of the experiments, CFD simulations captured the characteristic features of the experimentally measured CTDs. The CFD data suggests new signal processing procedures that predict unimodal CTDs for all three tanks.     

Using computational modeling to investigate sperm navigation and behavior in the female reproductive tract

The processes by which individual sperm cells navigate the length and complexity of the female reproductive tract and then reach and fertilize the oocyte is fascinating. Numerous complex processes potentially influence the transport of spermatozoa within the tract, resulting in a regulated supply of spermatozoa to the oocytes at the site of fertilization. Despite significant differences between species, breeds, and individuals, these processes converge to ensure that a sufficient number of high quality spermatozoa reach the oocytes, resulting in successful fertilization without a significant risk of polyspermy. Different factors, such as the physical complexity of the oviductal environment, changing swimming patterns, capacitation, chemotactic and thermotactic attraction, attachment and detachment from the oviductal epithelium, interactions with local oviductal secretions, individual variations in spermatozoa and subpopulations, peristaltic contractions, and the movement of fluid have all been theorized to influence the transport of spermatozoa to the site of fertilization. However, the predominance of each factor is not fully understood. Computational modeling provides a useful method for combining knowledge about the individual processes in complex systems to help understand the relative significance of each factor. The process of constructing and validating an agent-based computational model of sperm movement and transport within the oviductal environment is described in this report. Spermatozoa are modeled as individual cells with a set of behavioral rules defining how they interact with their local environment and regulate their internal state. The inclusion or potential exclusion of each factor is discussed, along with problems identifying parameters and defining behavioral rules from available literature. Finally, the benefits and limitations of the model are described.     

Stable small animal ventilation for dynamic lung imaging to support computational fluid dynamics models

Pulmonary computational fluid dynamics models require that three-dimensional images be acquired over multiple points in the dynamic breathing cycle without breath holds or changes in ventilatory mechanics. With small animals, these requirements can result in long imaging times (～90 minutes), over which lung mechanics, such as compliance, may gradually change if not carefully monitored and controlled. These changes, caused by derecruitment of parenchymal tissue, are manifested as an upward drift in peak inspiratory pressure (PIP) or by changes in the pressure waveform and/or lung volume over the course of the experiment. We demonstrate highly repeatable mechanical ventilation in anesthetized rats over a long duration for dynamic lung x-ray computed tomography (CT) imaging. We describe significant updates to a basic commercial ventilator that was acquired for these experiments. Key to achieving consistent results was the implementation of periodic deep breaths, or sighs, of extended duration to maintain lung recruitment. In addition, continuous monitoring of breath-to-breath pressure and volume waveforms and long-term trends in PIP and flow provide diagnostics of changes in breathing mechanics.     

The repeated replacement method: a pure lagrangian meshfree method for computational fluid dynamics

In this paper we describe the repeated replacement method (RRM), a new meshfree method for computational fluid dynamics (CFD). RRM simulates fluid flow by modeling compressible fluids' tendency to evolve towards a state of constant density, velocity, and pressure. To evolve a fluid flow simulation forward in time, RRM repeatedly "chops out" fluid from active areas and replaces it with new "flattened" fluid cells with the same mass, momentum, and energy. We call the new cells "flattened" because we give them constant density, velocity, and pressure, even though the chopped-out fluid may have had gradients in these primitive variables. RRM adaptively chooses the sizes and locations of the areas it chops out and replaces. It creates more and smaller new cells in areas of high gradient, and fewer and larger new cells in areas of lower gradient. This naturally leads to an adaptive level of accuracy, where more computational effort is spent on active areas of the fluid, and less effort is spent on inactive areas. We show that for common test problems, RRM produces results similar to other high-resolution CFD methods, while using a very different mathematical framework. RRM does not use Riemann solvers, flux or slope limiters, a mesh, or a stencil, and it operates in a purely Lagrangian mode. RRM also does not evaluate numerical derivatives, does not integrate equations of motion, and does not solve systems of equations.     

CaATP as a substrate to investigate the myosin lever arm hypothesis of force generation

In an effort to test the lever arm model of force generation, the effects of replacing magnesium with calcium as the ATP-chelated divalent cation were determined for several myosin and actomyosin reactions. The isometric force produced by glycerinated muscle fibers when CaATP is the substrate is 20% of the value obtained with MgATP. For myosin subfragment 1 (S1), the degree of lever arm rotation, determined using transient electric birefringence to measure rates of rotational Brownian motion in solution, is not significantly changed when calcium replaces magnesium in an S1-ADP-vanadate complex. Actin activates S1 CaATPase activity, although less than it does MgATPase activity. The increase in actin affinity when S1. CaADP. P(i) is converted to S1. CaADP is somewhat greater than it is for the magnesium case. The ionic strength dependence of actin binding indicates that the change in apparent electrostatic charge at the acto-S1 interface for the S1. CaADP. P(i) to S1. CaADP step is similar to the change when magnesium is bound. In general, CaATP is an inferior substrate compared to MgATP, but all the data are consistent with force production by a lever arm mechanism for both substrates. Possible reasons for the reduced magnitude of force when CaATP is the substrate are discussed.     

Microscopy approaches to investigate protein dynamics and lipid organization

The structure of cell membranes has been intensively investigated and many models and concepts have been proposed for the lateral organization of the plasma membrane. While proteomics and lipidomics have identified many if not all membrane components, how lipids and proteins interactions are coordinated in a specific cell function remains poorly understood. It is generally accepted that the organization of the plasma membrane is likely to play a critical role in the regulation of cell function such as receptor signalling by governing molecular interactions and dynamics. In this review we present different plasma membrane models and discuss microscopy approaches used for investigating protein behaviour, distribution and lipid organization.     

Anatomically based three-dimensional model of airways to simulate flow and particle transport using computational fluid dynamics.

We have studied gas flow and particle deposition in a realistic three-dimensional (3D) model of the bronchial tree, extending from the trachea to the segmental bronchi (7th airway generation for the most distal ones) using computational fluid dynamics. The model is based on the morphometrical data of Horsfield et al. (Horsfield K, Dart G, Olson DE, Filley GF, and Cumming G. J Appl Physiol 31: 207-217, 1971) and on bronchoscopic and computerized tomography images, which give the spatial 3D orientation of the curved ducts. It incorporates realistic angles of successive branching planes. Steady inspiratory flow varying between 50 and 500 cm(3)/s was simulated, as well as deposition of spherical aerosol particles (1-7 microm diameter, 1 g/cm(3) density). Flow simulations indicated nonfully developed flows in the branches due to their relative short lengths. Velocity flow profiles in the segmental bronchi, taken one diameter downstream of the bifurcation, were distorted compared with the flow in a simple curved tube, and wide patterns of secondary flow fields were observed. Both were due to the asymmetrical 3D configuration of the bifurcating network. Viscous pressure drop in the model was compared with results obtained by Pedley et al. (Pedley TJ, Schroter RC, and Sudlow MF. Respir Physiol 9: 387-405, 1970), which are shown to be a good first approximation. Particle deposition increased with particle size and was minimal for approximately 200 cm(3)/s inspiratory flow, but it was highly heterogeneous for branches of the same generation.     

Using biofeedback to reduce left arm extensor EMG of string players during musical performance

Electromyographic (EMG) feedback offers a mechanism for helping musicians reduce specific muscle tension during performance. Nine intermediate to advanced level string players participated in a four-session, pretest/posttest design study to determine (1) if left forearm extensor EMG could be reduced using biofeedback, (2) if reductions in EMG would generalize to a no-feedback condition, and (3) if reductions in EMG would generalize from extensors to flexors. Results indicate that biofeedback did facilitate significant decreases in EMG, that the reductions in EMG did generalize to a no-feedback condition, and that generalization from extensors to flexors did not occur.     

Neural mass models as a tool to investigate neural dynamics during seizures

Epilepsy is one of the most common neurological disorders and is characterized by recurrent seizures. We use theoretical neuroscience tools to study brain dynamics during seizures. We derive and simulate a computational model of a network of hippocampal neuronal populations. Each population within the network is based on a model that has been shown to replicate the electrophysiological dynamics observed during seizures. The results provide insights into possible mechanisms for seizure spread. We observe that epileptiform activity remains localized to a pathological region when a global connectivity parameter is less than a critical value. After establishing the critical value for seizure spread, we explored how to correct the effect by altering particular synaptic gains. The spreading of seizures is quantified using numerical methods for seizure detection. The results from this study provide a new avenue of exploration for seizure control.     

The transport of wear particles in the prosthetic hip joint: a computational fluid dynamics investigation

The joint fluid mechanics and transport of wear particles in the prosthetic hip joint were analyzed for subluxation and flexion motion using computational fluid dynamics (CFD). The entire joint space including a moving capsule boundary was considered. It was found that particles suspended in the joint space are drawn into the joint gap between prosthesis cup and head during subluxation, which was also documented by Lundberg et al. (2007; Journal of Biomechanics 40, 1676-1685), however, wear particles remain in the joint gap. Wear particles leave the joint gap during flexion and can finally migrate to the proximal boundaries including the acetabular bone, where the particle deposition can cause osteolysis according to the established literature. Thus, the present study supports the theory of polyethylene wear particle induced osteolysis of the acetabular bone as a major factor in the loosening of hip prosthesis cups.     

Measurement of hemodynamics in human carotid artery using ultrasound and computational fluid dynamics.

The objective of the study was to investigate the feasibility of using computational fluid dynamic modeling (CFD) with noninvasive ultrasound measurements to determine time-variant three-dimensional (3D) carotid arterial hemodynamics in humans in vivo. The effects of hyperoxia and hypoxic hypercapnia on carotid artery local hemodynamics were examined by use of this approach. Six normotensive volunteers followed a double-blind randomized crossover design. Blood pressure, heart rate, and carotid blood flow were measured while subjects breathed normal air, a mixture of 5% CO(2) and 15% O(2) (hypoxic hypercapnia), and 100% O(2) (hyperoxia). Carotid artery geometry was reconstructed on the basis of B-mode ultrasound images by using purpose-built image processing software. Time-variant 3D carotid hemodynamics were estimated by using finite volume-based CFD. Systemic blood pressure was not significantly affected by hyperoxia or hypoxic hypercapnia, but heart rate decreased significantly with hyperoxia. There was an increase in diastolic flow velocity in the external carotid artery after hypoxic hypercapnia, but otherwise carotid blood flow velocities did not change significantly. Compared with normal air, hyperoxic conditions were associated with a decrease in the width of the region of flow separation in the external carotid artery. During hyperoxia, there was also an increase in the minimum and a decrease in maximum shear stress in the bifurcation and hence a reduction in cyclic variation in shear stress. Hypoxic hypercapnia was associated with a reduced duration of flow separation in the external carotid artery and an increase in the minimum shear stress without affecting the cyclic variation in shear stress. This study demonstrates the feasibility of using noninvasive ultrasound techniques in conjunction with CFD to describe time-variant 3D hemodynamics in the human carotid arterial bifurcation in vivo.     

Use of computational fluid dynamics as a tool for establishing process design space for mixing in a bioreactor

The concept of "design space" plays an integral part in implementation of quality by design for pharmaceutical products. ICH Q8 defines design space as "the multidimensional combination and interaction of input variables (e.g., material attributes) and process parameters that have been demonstrated to provide assurance of quality. Working within the design space is not considered as a change. Movement out of the design space is considered to be a change and would normally initiate a regulatory post-approval change process. Design space is proposed by the applicant and is subject to regulatory assessment and approval." Computational fluid dynamics (CFD) is increasingly being used as a tool for modeling of hydrodynamics and mass transfer. In this study, a laboratory-scale aerated bioreactor is modeled using CFD. Eulerian-Eulerian multiphase model is used along with dispersed k-ε turbulent model. Population balance model is incorporated to account for bubble breakage and coalescence. Multiple reference frame model is used for the rotating region. We demonstrate the usefulness of CFD modeling for evaluating the effects of typical process parameters like impeller speed, gas flow rate, and liquid height on the mass transfer coefficient (k(L)a). Design of experiments is utilized to establish a design space for the above mentioned parameters for a given permissible range of k(L)a.     

Functional imaging using computational fluid dynamics to predict treatment success of mandibular advancement devices in sleep-disordered breathing

Mandibular advancement devices (MADs) have emerged as a popular alternative for the treatment of sleep-disordered breathing. These devices bring the mandibula forward in order to increase upper airway (UA) volume and prevent total UA collapse during sleep. However, the precise mechanism of action appears to be quite complex and is not yet completely understood; this might explain interindividual variation in treatment success. We examined whether an UA model, that combines imaging techniques and computational fluid dynamics (CFD), allows for a prediction of the treatment outcome with MADs. Ten patients that were treated with a custom-made mandibular advancement device (MAD), underwent split-night polysomnography. The morning after the sleep study, a low radiation dose CT scan was scheduled with and without the MAD. The CT examinations allowed for a comparison between the change in UA volume and the anatomical characteristics through the conversion to three-dimensional computer models. Furthermore, the change in UA resistance could be calculated through flow simulations with CFD. Boundary conditions for the model such as mass flow rate and pressure distributions were obtained during the split-night polysomnography. Therefore, the flow modeling was based on a patient specific geometry and patient specific boundary conditions. The results indicated that a decrease in UA resistance and an increase in UA volume correlate with both a clinical and an objective improvement. The results of this pilot study suggest that the outcome of MAD treatment can be predicted using the described UA model.     

Analysis of thoracic aorta hemodynamics using 3D particle tracking velocimetry and computational fluid dynamics

Parallel to the massive use of image-based computational hemodynamics to study the complex flow establishing in the human aorta, the need for suitable experimental techniques and ad hoc cases for the validation and benchmarking of numerical codes has grown more and more.     

Computational fluid dynamics modeling of steady-state momentum and mass transport in a bioreactor for cartilage tissue engineering

Computational fluid dynamics (CFD) models to quantify momentum and mass transport under conditions of tissue growth will aid bioreactor design for development of tissue-engineered cartilage constructs. Fluent CFD models are used to calculate flow fields, shear stresses, and oxygen profiles around nonporous constructs simulating cartilage development in our concentric cylinder bioreactor. The shear stress distribution ranges from 1.5 to 12 dyn/cm(2) across the construct surfaces exposed to fluid flow and varies little with the relative number or placement of constructs in the bioreactor. Approximately 80% of the construct surface exposed to flow experiences shear stresses between 1.5 and 4 dyn/cm(2), validating the assumption that the concentric cylinder bioreactor provides a relatively homogeneous hydrodynamic environment for construct growth. Species mass transport modeling for oxygen demonstrates that fluid-phase oxygen transport to constructs is uniform. Some O(2) depletion near the down stream edge of constructs is noted with minimum pO(2) values near the constructs of 35 mmHg (23% O(2) saturation). These values are above oxygen concentrations in cartilage in vivo, suggesting that bioreactor oxygen concentrations likely do not affect chondrocyte growth. Scale-up studies demonstrate the utility and flexibility of CFD models to design and characterize bioreactors for growth of tissue-engineered cartilage.     

Allometric scaling of wall shear stress from mice to humans: quantification using cine phase-contrast MRI and computational fluid dynamics

Allometric scaling laws relate structure or function between species of vastly different sizes. They have rarely been derived for hemodynamic parameters known to affect the cardiovascular system, e.g., wall shear stress (WSS). This work describes noninvasive methods to quantify and determine a scaling law for WSS. Geometry and blood flow velocities in the infrarenal aorta of mice and rats under isoflurane anesthesia were quantified using two-dimensional magnetic resonance angiography and phase-contrast magnetic resonance imaging at 4.7 tesla. Three-dimensional models constructed from anatomic data were discretized and used for computational fluid dynamic simulations using phase-contrast velocity imaging data as inlet boundary conditions. WSS was calculated along the infrarenal aorta and compared between species to formulate an allometric equation for WSS. Mean WSS along the infrarenal aorta was significantly greater in mice and rats compared with humans (87.6, 70.5, and 4.8 dyn/cm(2), P < 0.01), and a scaling exponent of -0.38 (R(2) = 0.92) was determined. Manipulation of the murine genome has made small animal models standard surrogates for better understanding the healthy and diseased human cardiovascular system. It has therefore become increasingly important to understand how results scale from mouse to human. This noninvasive methodology provides the opportunity to serially quantify changes in WSS during disease progression and/or therapeutic intervention.     

Verification of energy dissipation rate scalability in pilot and production scale bioreactors using computational fluid dynamics

Suspension mammalian cell cultures in aerated stirred tank bioreactors are widely used in the production of monoclonal antibodies. Given that production scale cell culture operations are typically performed in very large bioreactors (≥ 10,000 L), bioreactor scale‐down and scale‐up become crucial in the development of robust cell‐culture processes. For successful scale‐up and scale‐down of cell culture operations, it is important to understand the scale‐dependence of the distribution of the energy dissipation rates in a bioreactor. Computational fluid dynamics (CFD) simulations can provide an additional layer of depth to bioreactor scalability analysis. In this communication, we use CFD analyses of five bioreactor configurations to evaluate energy dissipation rates and Kolmogorov length scale distributions at various scales. The results show that hydrodynamic scalability is achievable as long as major design features (# of baffles, impellers) remain consistent across the scales. Finally, in all configurations, the mean Kolmogorov length scale is substantially higher than the average cell size, indicating that catastrophic cell damage due to mechanical agitation is highly unlikely at all scales. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:760–764, 2014     

The active and passive ciliary motion in the embryo node: A computational fluid dynamics model

The breaking of left–right symmetry in the mammalian embryo is believed to occur in a transient embryonic structure, the node, when cilia create a leftward flow of liquid. The two-cilia hypothesis proposes that the node contains two kinds of primary cilia: motile cilia that rotate autonomously to generate the leftward fluid flow and passive cilia that act as mechano-sensors, responding to flow. While studies support this hypothesis, the mechanism by which the sensory cilia respond to the fluid flow is still unclear. In this paper, we present a computational model of two cilia, one active and one passive. By employing computational fluid dynamics, deformable mesh computational techniques and fluid–structure interaction analysis, and solving the three-dimensional unsteady transport equations, we study the flow pattern produced by the movement of the active cilium and the response of the passive cilium to this flow. Our results reveal that clockwise rotation of the active cilium can generate a counter-clockwise elliptical rotation and overall lateral displacement for its neighboring passive one, of measurable magnitude and consistent pattern. This supports the plausibility of the two-cilia hypothesis and helps quantify the motion pattern for the passive cilium induced by this regional flow.