Towards robust data-driven reduced-order modelling for turbulent flows: application to vortex-induced vibrations.

This work presents a robust method that minimises the impact of user-selected parameter on the identification of generic models to study the coherent dynamics in turbulent flows. The objective is to gain insight into the flow dynamics from a data-driven reduced order model (ROM) that is developed from measurement data of the respective flow. For an efficient separation of the coherent dynamics, spectral proper orthogonal decomposition (SPOD) is used, projecting the flow field onto a low-dimensional subspace, so that the dominating dynamics can be represented with a minimal number of modes. A function library is defined using polynomial combinations of the temporal modal coefficients to describe the flow dynamics with a system of nonlinear ordinary differential equations. The most important library functions are identified in a two-stage cross-validation procedure (conservative and restrictive sparsification) and combined in the final model. In the first stage, the process uses a simple approximation of the derivative to match the model with the data. This stage delivers a reduced set of possible library function candidates for the model. In the second, more complex stage, the model of the entire flow is integrated over a short time and compared with the progression of the measured data. This restrictive stage allows a robust identification of nonlinearities and modal interactions in the data and their representation in the model. The method is demonstrated using data from particle image velocimetry (PIV) measurements of a circular cylinder undergoing vortex-induced vibration (VIV) at Re = 4000 . It delivers a reduced order model that reproduces the average dynamics of the flow and reveals the interaction of coexisting flow dynamics by the model structure.

Orthotropic hydraulic permeability of arrays of parallel cylinders.

Approximate analytical methods are presented to calculate the overall orthotropic hydraulic permeability of a flow with low Reynolds number, passing through a bundle of parallel circular cylinders. Two particular distributions are considered: (i) arrays with ordered rectangular lattices and (ii) irregular nonrandom distributions for which the unit cell cross sections are elliptical. The standard unit cell models, originally developed by Happel and Kuwabara for a random distribution of cylinders, are adapted to the case of nonrandom distributions. The drag force on a representative cylinder in a direction perpendicular to its axis is obtained based on the standard unit cell model: the actual unit cell of rectangular or elliptical cross section is replaced with an "equivalent" cylindrical unit cell of diameter equal to the maximum width of the actual unit cell. Using the obtained drag forces and referring back to the original geometry of the unit cell, closed-form approximate expressions for the overall permeabilities in the perpendicular directions are obtained. Numerical comparisons with more sophisticated approaches confirm the good efficiency of the presented approach, especially in the range of low solid volume fraction, i.e., of high porosity. Previous studies have revealed that, for the parallel fluid flow, the variation of permeability with aspect ratio (or in general the lateral arrangement) of parallel cylinders is generally weak. These observations suggest that Happel's model for parallel permeability in a random distribution of cylinders could be a good approximation for parallel permeabilities in nonrandom distributions with the same volume fraction.

Nutrient media optimization for simultaneous enhancement of the laccase and peroxidases production by coculture of Dichomitus squalens and Ceriporiopsis subvermispora.

Coculturing of two white-rot fungi, Dichomitus squalens and Ceriporiopsis subvermispora, was explored for the optimization of cultivation media for simultaneous augmentation of laccase and peroxidase activities by response surface methodology (RSM). Nutrient parameters chosen from our previous studies with the monocultures of D. squalens and C. subvermispora were used to design the experiments for the cocultivation study. Glucose, arabinose, sodium nitrate, casein, copper sulfate (CuSO4 ), and manganese sulfate (MnSO4 ) were combined according to central composite design and used as the incubation medium for the cocultivation. The interaction of glucose and sodium nitrate resulted in laccase and peroxidase activities of approximately 800 U/g protein. The addition of either glucose or sodium nitrate to the medium also modifies the impact of other nutrients on the ligninolytic activity. Both enzyme activities were cross-regulated by arabinose, casein, CuSO4 , and MnSO4 as a function of concentrations. Based on RSM, the optimum nutrient levels are 1% glucose, 0.1% arabinose, 20 mM sodium nitrate, 0.27% casein, 0.31 mM CuSO4 , and 0.07 mM MnSO4 . Cocultivation resulted in the production of laccase of 1,378 U/g protein and peroxidase of 1,372 U/g protein. Lignin (16.9%) in wheat straw was degraded by the optimized enzyme mixture.

Analysis of fluid flow and wall shear stress patterns inside partially filled agitated culture well plates.

The appearance of highly resistant bacterial biofilms in both community and hospitals environments is a major challenge in modern clinical medicine. The biofilm structural morphology, believed to be an important factor affecting the behavioral properties of these "super bugs", is strongly influenced by the local hydrodynamics over the microcolonies. Despite the common use of agitated well plates in the biology community, they have been used rather blindly without knowing the flow characteristics and influence of the rotational speed and fluid volume in these containers. The main purpose of this study is to characterize the flow in these high-throughput devices to link local hydrodynamics to observed behavior in cell cultures. In this work, the flow and wall shear stress distribution in six-well culture plates under planar orbital translation is simulated using Computational Fluid Dynamics (CFD). Free surface, flow pattern and wall shear stress for two shaker speeds (100 and 200 rpm) and two volumes of fluid (2 and 4 mL) were investigated. Measurements with a non-intrusive optical shear stress sensor and High Frame-rate Particle Imaging Velocimetry (HFPIV) are used to validate CFD predictions. An analytical model to predict the free surface shape is proposed. Results show a complex three-dimensional flow pattern, varying in both time and space. The distribution of wall shear stress in these culture plates has been related to the topology of flow. This understanding helps explain observed endothelial cell orientation and bacterial biofilm distributions observed in culture dishes. The results suggest that the mean surface stress field is insufficient to capture the underlying dynamics mitigating biological processes.

Methicillin resistant Staphylococcus aureus adhesion to human umbilical vein endothelial cells demonstrates wall shear stress dependent behaviour.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is an increasingly prevalent pathogen capable of causing severe vascular infections. The goal of this work was to investigate the role of shear stress in early adhesion events. METHODS: Human umbilical vein endothelial cells (HUVEC) were exposed to MRSA for 15-60 minutes and shear stresses of 0-1.2 Pa in a parallel plate flow chamber system. Confocal microscopy stacks were captured and analyzed to assess the number of MRSA. Flow chamber parameters were validated using micro-particle image velocimetry (PIV) and computational fluid dynamics modelling (CFD). RESULTS: Under static conditions, MRSA adhered to, and were internalized by, more than 80% of HUVEC at 15 minutes, and almost 100% of the cells at 1 hour. At 30 minutes, there was no change in the percent HUVEC infected between static and low flow (0.24 Pa), but a 15% decrease was seen at 1.2 Pa. The average number of MRSA per HUVEC decreased 22% between static and 0.24 Pa, and 37% between 0.24 Pa and 1.2 Pa. However, when corrected for changes in bacterial concentration near the surface due to flow, bacteria per area was shown to increase at 0.24 Pa compared to static, with a subsequent decline at 1.2 Pa. CONCLUSIONS: This study demonstrates that MRSA adhesion to endothelial cells is strongly influenced by flow conditions and time, and that MSRA adhere in greater numbers to regions of low shear stress. These areas are common in arterial bifurcations, locations also susceptible to generation of atherosclerosis.

Impact of silver-containing wound dressings on bacterial biofilm viability and susceptibility to antibiotics during prolonged treatment.

The long-term antimicrobial efficacy of silver dressings against bacterial biofilms was investigated in a 7-day treatment in vitro model where the protein-rich medium was refreshed daily in order to mimic the conditions found in a wound bed. The use of plate-to-plate transfer assays demonstrated measurable differences in the effectiveness of several silver dressings on the viability of biofilm bacteria and their susceptibility to antibiotics. Whereas after the first day of treatment, all dressings used resulted in a significant reduction in the number of viable cells in the biofilms and disruption of the biofilm colonies, during prolonged treatment, the efficacy of dressings with hydrophilic base materials diminished with daily transfers, and bacterial populations recovered. For dressings with hydrophobic base materials, the level of efficacy correlated with the silver species loaded. Biofilm bacteria, which survived the initial silver treatment, were susceptible to tobramycin, ciprofloxacin, and trimethoprim-sulfamethoxazole, in contrast to untreated biofilms, which were highly tolerant to the same antibiotics. This acquired susceptibility was unaffected by the longevity of pretreatment with the silver dressings but depended on the dressing used. The antimicrobial efficacy of the dressings correlated with the type of the dressing base material and silver species loaded.

Relation between the activity of anaerobic microbial populations in oil sands tailings ponds and the sedimentation of tailings.

Oil sands tailings ponds contain a variety of anaerobic microbes, including methanogens, sulfate- and nitrate-reducing bacteria. Methanogenic activity in samples from a tailings pond and its input streams was higher with trimethylamine (TMA) than with acetate. Methanogens closely affiliated to Methanomethylovorans hollandica were found in the TMA enrichments. Tailings sedimentation increased with methanogenic activity, irrespective whether TMA or acetate was used to stimulate methanogenesis. Increased sedimentation of autoclaved tailings was observed with added pure cultures under methanogenic, as well as under nitrate-reducing conditions, but not under sulfate-reducing conditions. Scanning electron microscopy and energy-dispersive X-ray spectroscopy indicated the presence of microbes and of extracellular polymeric substances in tailings particle aggregates, especially under methanogenic and nitrate-reducing conditions. Hence different classes of microorganisms growing in tailings ponds contribute to increased tailings aggregation and sedimentation. Because addition of nitrate is known to lower methane production by methanogenic consortia, these observations offer the potential to combine lower methane emissions with improved microbially-induced tailings sedimentation.

Staphylococcus aureus biofilm formation and tolerance to antibiotics in response to oscillatory shear stresses of physiological levels.

Bacterial infections in the blood system are usually associated with blood flow oscillation generated by some cardiovascular pathologies and insertion of indwelling devices. The influence of hydrodynamically induced shear stress fluctuations on the Staphylococcus aureus biofilm morphology and tolerance to antibiotics was investigated. Fluctuating shear stresses of physiologically relevant levels were generated in wells of a six-well microdish agitated by an orbital shaker. Numerical simulations were performed to determine the spatial distribution and local fluctuation levels of the shear stress field on the well bottom. It is found that the local biofilm deposition and morphology correlate strongly with shear stress fluctuations and maximum magnitude levels. Tolerance to killing by antibiotics correlates with morphotype and is generally higher in high shear regions.

Use of quorum sensing antagonists to deter the formation of crystalline Proteus mirabilis biofilms.

Proteus mirabilis biofilms are a major cause of urinary catheter blockage. Antibiotic-impregnated catheters used to prevent catheter blockage have achieved limited success. Research has examined the efficacy of quorum sensing inhibitors against Pseudomonas aeruginosa biofilms, but there are few reports of the effects of these compounds against crystalline P. mirabilis biofilms. This study examined the effect of two quorum sensing antagonists, p-nitrophenyl glycerol (PNPG) and tannic acid, against crystalline P. mirabilis biofilms. Tannic acid and PNPG were observed to inhibit the quorum sensing system and the formation of P. mirabilis biofilms grown in artificial urine. The success of these compounds provides a possible means of preventing urinary catheter encrustation.

Poroelastic evaluation of fluid movement through the lacunocanalicular system.

A poroelastic lacunocanalicular model was developed for the quantification of physiologically relevant parameters related to bone fluid flow. The canalicular and lacunar microstructures were explicitly represented by a dual-continuum poroelastic model. Effective material properties were calculated using the theory of composite materials. Porosity and permeability values were determined using capillaric and spherical-shell models for the canalicular and lacunar microstructures, respectively. Pore fluid pressure and fluid shear stress were calculated in response to simulated mechanical loading applied over a range of frequencies. Species transport was simulated with convective and diffusive flow, and osteocyte consumption of nutrients was incorporated. With the calculated parameter values, realistic pore fluid pressure and fluid shear stress responses were predicted and shown to be consistent with previous experimental and theoretical studies. Stress-induced fluid flow was highlighted as a potent means of species transport, and the importance of high-magnitude low-frequency loading on osteocyte nutrition was demonstrated. This new model can serve as the foundation for future hierarchical modeling efforts that may provide insight into the underlying mechanisms of mechanotransduction and functional adaptation of bone.

The influence of flow cell geometry related shear stresses on the distribution, structure and susceptibility of Pseudomonas aeruginosa 01 biofilms.

The effects of non-uniform hydrodynamic conditions resulting from flow cell geometry (square and rectangular cross-section) on Pseudomonas aeruginosa 01 (PAO1) biofilm formation, location, and structure were investigated for nominally similar flow conditions using a combination of confocal scanning laser microscope (CSLM) and computational fluid dynamics (CFD). The thickness and surface coverage of PAO1 biofilms were observed to vary depending on the location in the flow cell and thus also the local wall shear stress. The biofilm structure in a 5:1 (width to height) aspect ratio rectangular flow cell was observed to consist mainly of a layer of bacterial cells with thicker biofilm formation observed in the flow cell corners. For square cross-section (1:1 aspect ratio) flow cells, generally thicker and more uniform surface coverage biofilms were observed. Mushroom shaped structures with hollow centers and wall breaks, indicative of 'seeding' dispersal structures, were found exclusively in the square cross-section tubes. Exposure of PAO1 biofilms grown in the flow cells to gentamicin revealed a difference in susceptibility. Biofilms grown in the rectangular flow cell overall exhibited a greater susceptibility to gentamicin compared to those grown in square flow cells. However, even within a given flow cell, differences in susceptibility were observed depending on location. This study demonstrates that the spanwise shear stress distribution within the flow cells has an important impact on the location of colonization and structure of the resultant biofilm. These differences in biofilm structure have a significant impact on the susceptibility of the biofilms grown within flow channels. The impact of flow modification due to flow cell geometry should be considered when designing flow cells for laboratory investigation of bacterial biofilms.

Biofilm structure differentiation based on multi-resolution analysis.

Quantitative parameters for describing the morphology of biofilms are crucial towards establishing the influence of growing conditions on biofilm structure. Parameters used in earlier studies generally fail to differentiate complex three-dimensional structures. This article presents a novel approach of defining a parameter vector based on the energy signature of multi-resolution analysis, which was applied to differentiating biofilm structures from confocal laser scanning microscopy (CLSM) biofilm images. The parameter vector distinguished differences in the spatial arrangements of synthetic images. For real CLSM images, this parameter vector detected subtle differences in biofilm structure for three sample cases: (1) two adjacent images of a CLSM stack; (2) two partial stacks from the same CLSM stack with equal numbers of images but spatially offset by one image; and (3) three complete CLSM stacks from different bacterial strains. It was also observed that filtering the noise in CLSM images enhanced the sensitivity of the differentiation using our parameter vector.

Influence of vascular porosity on fluid flow and nutrient transport in loaded cortical bone.

Load-induced fluid flow is a key factor in triggering bone modeling and remodeling processes that maintain bone mass and architecture. To provide an enhanced understanding of fluid flow in bone, unique computational models of a tibial section were developed. The purpose of the study was to examine the effects of incorporating vascular porosity on pore fluid pressure and resulting lacunocanalicular flow and to determine the role of load-induced fluid flow in tracer transport. Simulations revealed large local pressure gradients surrounding the vascular canals that were dependent on the magnitude and state (i.e., compressive or tensile) of the stress. Fluid velocity magnitudes were increased by over an order of magnitude in the dual-porosity model, relative to the single-porosity model. Fluid flow had a marked effect on tracer perfusion within the cortex. After 10 loading cycles, a 9-fold increase in tracer concentration, relative to diffusion alone, was observed in the compressive region where fluid exchange was greatest between the lacunocanalicular porosity and the vascular canals. Agreement was achieved between computational results and experimental investigations of electrokinetic phenomenon, tracer transport, cellular stimulation, and functional adaptation. The models produced substantial improvements in bone fluid flow simulation and underscored the significance of incorporating vascular porosity in models designed to quantify fluid pressure and flow characteristics within mechanically loaded cortical bone.

Granular circulation in a cylindrical pan: simulations of reversing radial and tangential flows.

Granular flows due to simultaneous vertical and horizontal excitations of a flat-bottomed cylindrical pan are investigated using event-driven molecular dynamics simulations. In agreement with recent experimental results, we observe a transition from a solidlike state to a fluidized state in which circulatory flow occurs simultaneously in the radial and tangential directions. By going beyond the range of conditions explored experimentally, we find that each of these circulations reverses its direction as a function of the control parameters of the motion. We numerically evaluate the dynamical phase diagram for this system and show, using a simple model, that the solid-fluid transition can be understood in terms of a critical value of the radial acceleration of the pan bottom and that the circulation reversals are controlled by the phase shift relating the horizontal and vertical components of the vibrations. We also discuss the crucial role played by the geometry of the boundary conditions and point out a relationship of the circulation observed here and the flows generated in vibratory conveyors.

Increased tolerance of Staphylococcus aureus to vancomycin in viscous media.

The increased viscosity observed in biofilms, adherent communities of bacterial cells embedded in a polymeric matrix, was hypothesized to induce increased tolerance of bacteria to antibiotics. To test this concept, planktonic Staphylococcus aureus cells were grown and exposed to vancomycin in media brought to specific viscosities in order to mimic the biofilm extracellular polymeric matrix. A viscous environment was observed to decrease the vancomycin susceptibility of planktonic S. aureus to levels seen for biofilms. Both planktonic S. aureus at a viscosity of 100 mPa s and staphylococcal biofilms were able to survive at >500 times the levels of the antibiotic effective against planktonic populations in standard medium. Time-dependent and dose-dependent viability curves revealed that more than one mechanism was involved in high S. aureus tolerance to vancomycin in viscous media. Increased viscosity affects antibiotic susceptibility by reducing diffusion and the mass transfer rate; this mechanism alone, however, cannot explain the increased tolerance demonstrated by S. aureus in viscous media, suggesting that viscosity may also alter the phenotype of the planktonic bacteria to one more resistant to antimicrobials, as seen in biofilms. However, these latter changes are not yet understood and will require further study.

A two-step procedure for automatic and accurate segmentation of volumetric CLSM biofilm images.

This paper presents a robust two-step segmentation procedure for the study of biofilm structure. Without user intervention, the procedure segments volumetric biofilm images generated by a confocal laser scanning microscopy (CLSM). This automated procedure implements an anisotropic diffusion filter as a preprocessing step and a 3D extension of the Otsu method for thresholding. Applying the anisotropic diffusion filter to even low-contrast CLSM images significantly improves the segmentation obtained with the 3D Otsu method. A comparison of the results for several CLSM data sets demonstrated that the accuracy of this procedure, unlike that of the objective threshold selection algorithm (OTS), is not affected by biofilm coverage levels and thus fills an important gap in developing a robust and objective segmenting procedure. The effectiveness of the present segmentation procedure is shown for CLSM images containing different bacterial strains. The image saturation handling capability of this procedure relaxes the constraints on user-selected gain and intensity settings of a CLSM. Therefore, this two-step procedure provides an automatic and accurate segmentation of biofilms that is independent of biofilm coverage levels and, in turn, lays a solid foundation for achieving objective analysis of biofilm structural parameters.

Metal ions may suppress or enhance cellular differentiation in Candida albicans and Candida tropicalis biofilms.

Candida albicans and Candida tropicalis are polymorphic fungi that develop antimicrobial-resistant biofilm communities that are characterized by multiple cell morphotypes. This study investigated cell type interconversion and drug and metal resistance as well as community organization in biofilms of these microorganisms that were exposed to metal ions. To study this, Candida biofilms were grown either in microtiter plates containing gradient arrays of metal ions or in the Calgary Biofilm Device for high-throughput susceptibility testing. Biofilm formation and antifungal resistance were evaluated by viable cell counts, tetrazolium salt reduction, light microscopy, and confocal laser scanning microscopy in conjunction with three-dimensional visualization. We discovered that subinhibitory concentrations of certain metal ions (CrO(4)(2-), Co(2+), Cu(2+), Ag(+), Zn(2+), Cd(2+), Hg(2+), Pb(2+), AsO(2)(-), and SeO(3)(2-)) caused changes in biofilm structure by blocking or eliciting the transition between yeast and hyphal cell types. Four distinct biofilm community structure types were discerned from these data, which were designated "domed," "layer cake," "flat," and "mycelial." This study suggests that Candida biofilm populations may respond to metal ions to form cell-cell and solid-surface-attached assemblages with distinct patterns of cellular differentiation.

Structure of Proteus mirabilis biofilms grown in artificial urine and standard laboratory media.

Proteus mirabilis is a urinary pathogen that can differentiate from a swimmer cell into a swarmer cell morphotype and can form biofilms on the surfaces of urinary catheters. These biofilms block these catheters due to crystals trapped within these structures. The effect of encrustation on biofilm formation and structure has not been studied using confocal scanning laser microscopy (CSLM). Therefore, a comparison of biofilm structure in artificial urine (AU) and laboratory media was undertaken. We compared the structure of P. mirabilis biofilms in AU and Luria-Bertani broth using CSLM and 3D imaging. Biofilms grown in Luria-Bertani broth formed mushroom structures at 24 h and contained nutrient channels. AU biofilms were observed to form a different structure at 24 h. AU biofilm structure was observed to be a flat layer, almost devoid of nutrient channels. Swarmer cells were observed protruding out of the biofilm into the bulk fluid. This could be due to nutrient depravation within the biofilm or a means of further colonizing the surface. This study has demonstrated that two markedly different biofilm structures are formed, depending on the growth media utilized.

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the Calgary Biofilm Device.

Microbes frequently live within multicellular, solid surface-attached assemblages termed biofilms. These microbial communities have architectural features that contribute to population heterogeneity and consequently to emergent cell functions. Therefore, three-dimensional (3D) features of biofilm structure are important for understanding the physiology and ecology of these microbial systems. This paper details several protocols for scanning electron microscopy and confocal laser scanning microscopy (CLSM) of biofilms grown on polystyrene pegs in the Calgary Biofilm Device (CBD). Furthermore, a procedure is described for image processing of CLSM data stacks using amira, a virtual reality tool, to create surface and/or volume rendered 3D visualizations of biofilm microorganisms. The combination of microscopy with microbial cultivation in the CBD - an apparatus that was designed for high-throughput susceptibility testing - allows for structure-function analysis of biofilms under multivariate growth and exposure conditions.

Bulk motion of granular matter in an agitated cylindrical bed.

Experimental results are reported for the bulk motion induced in a bed of granular matter contained in a cylindrical pan with a flat bottom subjected to simultaneous vertical and horizontal vibrations. The motion in space of the moving pan is quantified. A number of distinct bulk dynamical modes are observed in which the particle bed adopts different shapes and motions. At the lowest pan excitation frequency omega , the bed forms a "heap," and rotates about the cylinder axis. As omega is increased, a more complex "toroidal" mode appears in which the bed takes the shape of a torus; in this mode, circulation occurs both about the cylinder axis, and also radially, with particles moving from the outer edge of the pan to the center on the top surface of the bed, and back to the outer edge along the pan bottom. At the highest omega , surface modulations ("surface waves" and "sectors") of the toroidal mode occur. The origin of this family of behavior in terms of the pan motion is discussed.