Numerical simulation of aneurysmal haemodynamics with calibrated porous-medium models of flow-diverting stents

Modelling flow-diverting (FD) stents as porous media (PM) markedly improves the efficiency of computational fluid dynamics (CFD) simulations in the study of intracranial aneurysm treatment. Nonetheless, the parameters of PM models adopted for simulations up until now were rarely calibrated to match the represented FD structure. We therefore sought to evaluate the PM parameters for a representative variety of commercially available stents, so characterising the flow-diversion behaviours of different FD devices on the market.We generated fully-resolved geometries for treatments using PED, Silk+, FRED, and dual PED stents. We then correspondingly derived the calibrated PM parameters—permeability (k) and inertial resistance factor (C₂)—for each stent design from CFD simulations, to ensure the calibrated PM model has identical flow resistance to the FD stent it represents. With each of the calibrated PM models respectively deployed in two aneurysms, we studied the flow-diversion effects of these stent configurations.This work for the first time reported several sets of parameters for PM models, which is vital to address the current knowledge gap and rectify the errors in PM model simulations, thereby setting right the modelling protocol for future studies using PM models. The flow resistance parameters were strongly affected by porosity and effective thickness of the commercial stents, and thus accounted for in the PM models. Flow simulations using the PM stent models revealed differences in aneurysmal mass flowrate (MFR) and energy loss (EL) between various stent designs.This study improves the practicability of FD simulation by using calibrated PM models, providing an individualised method with improved simulation efficiency and accuracy.     

CFD predicted pH gradients in lactic acid bacteria cultivations

The formation of pH gradients in a 700 L batch fermentation of Streptococcus thermophilus was studied using multi-position pH measurements and computational fluid dynamics (CFD) modeling. To this end, a dynamic, kinetic model of S. thermophilus and a pH correlation were integrated into a validated one-phase CFD model, and a dynamic CFD simulation was performed. First, the fluid dynamics of the CFD model were validated with NaOH tracer pulse mixing experiments. Mixing experiments and simulations were performed whereas multiple pH sensors, which were placed vertically at different locations in the bioreactor, captured the response. A mixing time of about 46 s to reach 95% homogeneity was measured and predicted at an impeller speed of 242 rpm. The CFD simulation of the S. thermophilus fermentation captured the experimentally observed pH gradients between a pH of 5.9 and 6.3, which occurred during the exponential growth phase. A pH higher than 7 was predicted in the vicinity of the base solution inlet. Biomass growth, lactic acid production, and substrate consumption matched the experimental observations. Moreover, the biokinetic results obtained from the CFD simulation were similar to a single-compartment simulation, for which a homogeneous distribution of the pH was assumed. This indicates no influence of pH gradients on growth in the studied bioreactor. This study verified that the pH gradients during a fermentation in the pilot-scale bioreactor could be accurately predicted using a coupled simulation of a biokinetic and a CFD model. To support the understanding and optimization of industrial-scale processes, future biokinetic CFD studies need to assess multiple types of environmental gradients, like pH, substrate, and dissolved oxygen, especially at industrial scale.     

Simulated and experimental estimates of hydrodynamic drag from bio-logging tags

Drag force acting on swimming marine mammals is difficult to measure directly. Researchers often use simple modeling and kinematic measurements from animals, or computational fluid dynamics (CFD) simulations to estimate drag. However, studies that compare these methods are lacking. Here, computational simulation and physical experiments were used to estimate drag forces on gliding bottlenose dolphins (Tursiops truncatus). To facilitate comparison, variable drag loading (no-tag, tag, tag + 4, tag + 8) was used to increase force in both simulations and experiments. During the experiments, two dolphins were trained to perform controlled glides with variable loading. CFD simulations of dolphin/tag geometry in steady flow (1–6 m/s) were used to model drag forces. We expect both techniques will capture relative changes created by experimental conditions, but absolute forces predicted by the methods will differ. CFD estimates were within a calculated 90% confidence interval of the experimental results for all but the tag condition. Relative drag increase predicted by the simulation vs. experiment, respectively, differed by between 21% and 31%: tag, 4% vs. 33%; tag + 4, 47% vs. 68%; and tag + 8, 108% vs. 77%. The results from this work provide a direct comparison of computational and experimental estimates of drag, and provide a framework to quantify uncertainty.     

Turbulence model choice for the calculation of drag forces when using the CFD method

The aim of this work is to specify which model of turbulence is the most adapted in order to predict the drag forces that a swimmer encounters during his movement in the fluid environment. For this, a Computational Fluid Dynamics (CFD) analysis has been undertaken with a commercial CFD code (Fluent^®). The problem was modelled as 3D and in steady hydrodynamic state. The 3D geometry of the swimmer was created by means of a complete laser scanning of the swimmer’s body contour. Two turbulence models were tested, namely the standard k–ε model with a specific treatment of the fluid flow area near the swimmer’s body contour, and the standard k–ω model. The comparison of numerical results with experimental measurements of drag forces shows that the standard k–ω model accurately predicts the drag forces while the standard k–ε model underestimates their values. The standard k–ω model also enabled to capture the vortex structures developing at the swimmer’s back and buttocks in underwater swimming; the same vortices had been visualized by flow visualization experiments carried out at the INSEP (National Institute for Sport and Physical Education in Paris) with the French national swimming team.     

Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea

Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an ‘extinct’ avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O''Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.     

Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids

Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4–386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset reveals that the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6–6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.     

Airflow behavior changes in upper airway caused by different head and neck positions: Comparison by computational fluid dynamics

The feasibility of computational fluid dynamics (CFD) to evaluate airflow characteristics in different head and neck positions has not been established. This study compared the changes in volume and airflow behavior of the upper airway by CFD simulation to predict the influence of anatomical and physiological airway changes due to different head–neck positions on mechanical ventilation. One awake volunteer with no risk of difficult airway underwent computed tomography in neutral position, extension position (both head and neck extended), and sniffing position (head extended and neck flexed). Three-dimensional airway models of the upper airway were reconstructed. The total volume (V) and narrowest area (A_min) of the airway models were measured. CFD simulation with an Spalart–Allmaras model was performed to characterize airflow behavior in neutral, extension, and sniffing positions of closed-mouth and open-mouth ventilation. The comparison result for V was neutral <extension≈sniffing, and for A_min was neutral<extension<sniffing. A_min in sniffing position was nearly 3.0 times that in neutral position and 1.7 times that in extension position. The pressure drop and velocity increasing were more obvious in neutral than sniffing or extension position at the same airflow rate. In sniffing position, pressure differences decreased and velocity remained almost constant. Recirculation airflow was generated near the subglottic region in neutral and extension positions. Sniffing position improves airway patency by increasing airway volume and decreasing airway resistance, suggesting that sniffing position may be the optimal choice for mask ventilation.     

Computational fluid dynamics analysis of cyclist aerodynamics: Performance of different turbulence-modelling and boundary-layer modelling approaches

This study aims at assessing the accuracy of computational fluid dynamics (CFD) for applications in sports aerodynamics, for example for drag predictions of swimmers, cyclists or skiers, by evaluating the applied numerical modelling techniques by means of detailed validation experiments. In this study, a wind-tunnel experiment on a scale model of a cyclist (scale 1:2) is presented. Apart from three-component forces and moments, also high-resolution surface pressure measurements on the scale model’s surface, i.e. at 115 locations, are performed to provide detailed information on the flow field. These data are used to compare the performance of different turbulence-modelling techniques, such as steady Reynolds-averaged Navier–Stokes (RANS), with several k–ε and k–ω turbulence models, and unsteady large-eddy simulation (LES), and also boundary-layer modelling techniques, namely wall functions and low-Reynolds number modelling (LRNM). The commercial CFD code Fluent 6.3 is used for the simulations. The RANS shear-stress transport (SST) k–ω model shows the best overall performance, followed by the more computationally expensive LES. Furthermore, LRNM is clearly preferred over wall functions to model the boundary layer. This study showed that there are more accurate alternatives for evaluating flow around bluff bodies with CFD than the standard k–ε model combined with wall functions, which is often used in CFD studies in sports.     

Boundary Conditions for Heat Transfer and Evaporative Cooling in the Trachea and Air Sac System of the Domestic Fowl: A Two-Dimensional CFD Analysis

Various parts of the respiratory system play an important role in temperature control in birds. We create a simplified computational fluid dynamics (CFD) model of heat exchange in the trachea and air sacs of the domestic fowl (Gallus domesticus) in order to investigate the boundary conditions for the convective and evaporative cooling in these parts of the respiratory system. The model is based upon published values for respiratory times, pressures and volumes and upon anatomical data for this species, and the calculated heat exchange is compared with experimentally determined values for the domestic fowl and a closely related, wild species. In addition, we studied the trachea histologically to estimate the thickness of the heat transfer barrier and determine the structure and function of moisture-producing glands. In the transient CFD simulation, the airflow in the trachea of a 2-dimensional model is evoked by changing the volume of the simplified air sac. The heat exchange between the respiratory system and the environment is simulated for different ambient temperatures and humidities, and using two different models of evaporation: constant water vapour concentration model and the droplet injection model. According to the histological results, small mucous glands are numerous but discrete serous glands are lacking on the tracheal surface. The amount of water and heat loss in the simulation is comparable with measured respiratory values previously reported. Tracheal temperature control in the avian respiratory system may be used as a model for extinct or rare animals and could have high relevance for explaining how gigantic, long-necked dinosaurs such as sauropoda might have maintained a high metabolic rate.     

An integrated physical and biological model for anaerobic lagoons

A computational fluid dynamics (CFD) model that integrates physical and biological processes for anaerobic lagoons is presented. In the model development, turbulence is represented using a transition k-ω model, heat conduction and solar radiation are included in the thermal model, biological oxygen demand (BOD) reduction is characterized by first-order kinetics, and methane yield rate is expressed as a linear function of temperature. A test of the model applicability is conducted in a covered lagoon digester operated under tropical climate conditions. The commercial CFD software, ANSYS-Fluent, is employed to solve the integrated model. The simulation procedures include solving fluid flow and heat transfer, predicting local resident time based on the converged flow fields, and calculating the BOD reduction and methane production. The simulated results show that monthly methane production varies insignificantly, but the time to achieve a 99% BOD reduction in January is much longer than that in July.     

Ancient life and moving fluids

Over 3.7 billion years of Earth history, life has evolved complex adaptations to help navigate and interact with the fluid environment. Consequently, fluid dynamics has become a powerful tool for studying ancient fossils, providing insights into the palaeobiology and palaeoecology of extinct organisms from across the tree of life. In recent years, this approach has been extended to the Ediacara biota, an enigmatic assemblage of Neoproterozoic soft-bodied organisms that represent the first major radiation of macroscopic eukaryotes. Reconstructing the ways in which Ediacaran organisms interacted with the fluids provides new insights into how these organisms fed, moved, and interacted within communities. Here, we provide an in-depth review of fluid physics aimed at palaeobiologists, in which we dispel misconceptions related to the Reynolds number and associated flow conditions, and specify the governing equations of fluid dynamics. We then review recent advances in Ediacaran palaeobiology resulting from the application of computational fluid dynamics (CFD). We provide a worked example and account of best practice in CFD analyses of fossils, including the first large eddy simulation (LES) experiment performed on extinct organisms. Lastly, we identify key questions, barriers, and emerging techniques in fluid dynamics, which will not only allow us to understand the earliest animal ecosystems better, but will also help to develop new palaeobiological tools for studying ancient life.     

Virtual Reconstruction and Prey Size Preference in the Mid Cenozoic Thylacinid,Nimbacinus dicksoni (Thylacinidae,Marsupialia)

Thylacinidae is an extinct family of Australian and New Guinean marsupial carnivores, comprizing 12 known species, the oldest of which are late Oligocene (∼24 Ma) in age. Except for the recently extinct thylacine (Thylacinus cynocephalus), most are known from fragmentary craniodental material only, limiting the scope of biomechanical and ecological studies. However, a particularly well-preserved skull of the fossil species Nimbacinus dicksoni, has been recovered from middle Miocene (∼16-11.6 Ma) deposits in the Riversleigh World Heritage Area, northwestern Queensland. Here, we ask whether N. dicksoni was more similar to its recently extinct relative or to several large living marsupials in a key aspect of feeding ecology, i.e., was N. dicksoni a relatively small or large prey specialist. To address this question we have digitally reconstructed its skull and applied three-dimensional Finite Element Analysis to compare its mechanical performance with that of three extant marsupial carnivores and T. cynocephalus. Under loadings adjusted for differences in size that simulated forces generated by both jaw closing musculature and struggling prey, we found that stress distributions and magnitudes in the skull of N. dicksoni were more similar to those of the living spotted-tailed quoll (Dasyurus maculatus) than to its recently extinct relative. Considering the Finite Element Analysis results and dental morphology, we predict that N. dicksoni likely occupied a broadly similar ecological niche to that of D. maculatus, and was likely capable of hunting vertebrate prey that may have exceeded its own body mass.     

Pleistocene and Holocene rhinocerotids (Mammalia,Perissodactyla) from the Indochinese Peninsula

Rhinocerotids were abundant and diverse in southern Asia during the Pleistocene and the Holocene epochs, as shown by palaeontological and archaeological discoveries published throughout the last century, whereas the only living rhinoceros in the Indochinese Peninsula is Rhinoceros sondaicus (Cat Loc Reserve, Vietnam). The Pleistocene-Holocene Indochinese rhinocerotid record consists of the extinct species Dicerorhinus gwebinensis (Early Pleistocene, Myanmar) and representatives of the Recent Asian Species Rhinoceros unicornis (Middle-Late Pleistocene), R. sondaicus (Middle Pleistocene-Recent), and Dicerorhinus sumatrensis (Middle Pleistocene-Holocene). This fossil record is synthesized, mapped for Early/Middle/Late Pleistocene and Holocene/Recent times, and then compared with coeval rhinocerotid assemblages from the adjacent areas (South China), subregions (Indian, Sundaic, Philippine, and Wallacean), and region (Palearctic), from a biochronological and biogeographical perspective.     

Modeling methodology for defining a priori the hydrodynamics of a dynamic suspension bioreactor. Application to human induced pluripotent stem cell culture

Three-dimensional dynamic suspension is becoming an effective cell culture method for a wide range of bioprocesses, with an increasing number of bioreactors proposed for this purpose. The complex hydrodynamics establishing within these devices affects bioprocess outcomes and efficiency, and usually expensive in vitro trial-and-error experiments are needed to properly set the working parameters.Here we propose a methodology to define a priori the hydrodynamic working parameters of a dynamic suspension bioreactor, selected as a test case because of the complex hydrodynamics characterizing its operating condition. A combination of computational and analytical approaches was applied to generate operational guideline graphs for defining a priori specific working parameters. In detail, 43 simulations were performed under pulsed flow regime to characterize advective transport within the device depending on different operative conditions, i.e., culture medium flow rate and its duty cycle, cultured particle diameter, and initial particle suspension volume. The operational guideline graphs were then used to set specific hydrodynamic working parameters for an in vitro proof-of-principle test, where human induced pluripotent stem cell (hiPSC) aggregates were cultured for 24 h within the bioreactor. The in vitro findings showed that, under the selected pulsed flow regime, sedimentation was avoided, hiPSC aggregate circularity and viability were preserved, and culture heterogeneity was reduced, thus confirming the appropriateness of the a priori method. This methodology has the potential to be adaptable to other dynamic suspension devices to support experimental studies by providing in silico-based a priori knowledge, useful to limit costs and to optimize culture bioprocesses.     

Molecular modeling studies of atorvastatin analogues as HMGR inhibitors using 3D-QSAR,molecular docking and molecular dynamics simulations

3-Hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR) is generally regarded as targets for the treatment of hypercholesterolemia. HMGR inhibitors (more commonly known as statins) are discovered as plasma cholesterol lowering molecules. In this work, 120 atorvastatin analogues were studied using a combination of molecular modeling techniques including three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulation. The results show that the best CoMFA (comparative molecular field analysis) model has q² = 0.558 and r² = 0.977, and the best CoMSIA (comparative molecular similarity indices analysis) model has q² = 0.582 and r² = 0.919. Molecular docking and MD simulation explored the binding relationship of the ligand and the receptor protein. The calculation results indicated that the hydrophobic and electrostatic fields play key roles in QSAR model. After MD simulation, we found four vital residues (Lys735, Arg590, Asp690 and Asn686) and three hydrophobic regions in HMGR binding site. The calculation results show that atorvastatin analogues obtained by introduction of F atoms or gem-difluoro groups could obviously improve the inhibitory activity. The new HMGR inhibitor analogues design in this Letter had been submitted which is being currently synthesized by our laboratories.     

Dependence of leukocyte capture on instantaneous pulsatile flow

Atherosclerosis, an artery disease, is currently the leading cause of death in the United States in both men and women. The first step in the development of atherosclerosis involves leukocyte adhesion to the arterial endothelium. It is broadly accepted that blood flow, more specifically wall shear stress (WSS), plays an important role in leukocyte capture and subsequent development of an atherosclerotic plaque. What is less known is how instantaneous WSS, which can vary by up to 5 Pa over one cardiac cycle, influences leukocyte capture. In this paper we use direct numerical simulations (DNS), performed using an in-house code, to illustrate that leukocyte capture is different whether as a function of instantaneous or time-averaged blood flow. Specifically, a stenotic plaque is modeled using a computational fluid dynamics (CFD) solver through fully three-dimensional Navier-Stokes equations and the immersed boundary method. Pulsatile triphasic inflow is used to simulate the cardiac cycle. The CFD is coupled with an agent-based leukocyte capture model to assess the impact of instantaneous hemodynamics on stenosis growth. The computed wall shear stress agrees well with the results obtained with a commercial software, as well as with theoretical results in the healthy region of the artery. The analysis emphasizes the importance of the instantaneous flow conditions in evaluating the leukocyte rate of capture. That is, the capture rate computed from mean flow field is generally underpredicted compared to the actual rate of capture. Thus, in order to obtain a reliable estimate, the flow unsteadiness during a cardiac cycle should be taken into account.     

Can indicator species predict restoration outcomes early in the monitoring process? a case study with peatlands

Success in ecological restoration is rarely assessed rigorously due to insufficient planning for post-restoration monitoring programs, limited funding and, especially, lack of scientifically validated evaluation criteria and protocols. In this article, we propose the use of the Indicator Value Index technique (IndVal), which statistically determines the association of species to one or several particular site types, to obtain indicators of success at the early stages of the recovery process in restoration projects. Peat bogs extracted by the vacuum method, subsequently restored by a moss-transfer technique and regularly monitored for ~10 years were used as a model system to test this approach. We first identified 34 restored sectors of ~10 ha from 4 to 11 years old in twelve eastern-Canadian bogs. These sectors were then classified according to their degree of success in recovering a typical sphagnum moss carpet (restoration goal). Then, we retrospectively reviewed vegetation communities recorded at the third year after restoration to identify indicator species of different categories of restoration success, using the IndVal methodology. By identifying early indicator species, our method provides a tool that guides intervention soon after restoration if a site is not on a desired successional trajectory. Typical bog species, namely the bryophytes S. rubellum and Mylia anomala and the tree Picea mariana, were indicative of successful restoration; while bare peat, lichens and one species of ericaceous shrubs (Empetrum nigrum), which cope better under drier conditions, indicated sites where restoration failed. A surprising finding was that the moss Polytrichum strictum, which is known to facilitate the colonization of sphagnum in disturbed peatlands, is an early indicator of unsuccessful restoration. This finding made us question the nursing role of P. strictum at a cover threshold above ca. 30%, when P. strictum could be outcompeting sphagnum and become dominant. We conclude that the IndVal method is an effective tool to identify early indicators of restoration success when combined with a thoughtful examination of species frequency and cover within each site type.     

3D external restorations of stegocephalian skulls using ZBrush: The renaissance of fossil amphibians

Cranial soft tissues (eyes, dermis, muscles, etc.) have never been preserved in fossil stegocephalians, and few specific studies have been done on their related osteological features (such as dermosensory canals, dermal bone ornamentation and microstructure). Consequently, the most useful tool to reconstruct stegocephalians remains the actualistic comparison with analogous living ecomorphotypes. Coupled with numerical sculpturing technologies available with the software ZBrush, it is now possible to appreciate the cranial soft tissues in 3D and to better reconstruct the external skull structures. Examples are given of the early tetrapod Acanthostega gunnari from the Devonian of Greenland and the Triassic temnospondyls Edingerella madagascariensis from Madagascar and Parotosuchus sp. from Antarctica. This palaeontological application of ZBrush is one of its first scientific uses. The obtained reconstructions are useful for scientific publication and in return they allow palaeontologists to better understand the palaeobiology of extinct organisms.     

Optimization and scale‐up of oligonucleotide synthesis in packed bed reactors using computational fluid dynamics modeling

A computational fluid dynamics (CFD) model for the analysis of oligonucleotide synthesis in packed bed reactors was developed and used to optimize the scale up of the process. The model includes reaction kinetics data obtained under well defined conditions comparable to the situation in the packed bed. The model was validated in terms of flow conditions and reaction kinetics by comparison with experimental data. Experimental validation and the following model parameter studies by simulation were performed on the basis of a column with 0.3 g oligonucleotide capacity. The scale‐up studies based on CFD modelling were calculated on a 440 g scale (oligonucleotide capacity). © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1048–1056, 2014