Immiscible Rayleigh-Taylor turbulence: Implications for bacterial degradation in oil spills

An unstable density stratification between two fluids mixes spontaneously under the effect of gravity, a phenomenon known as Rayleigh-Taylor (RT) turbulence. If the two fluids are immiscible, for example, oil and water, surface tension prevents intermixing at the molecular level. However, turbulence fragments one fluid into the other, generating an emulsion in which the typical droplet size decreases over time as a result of the competition between the rising kinetic energy and the surface energy density. Even though the first phenomenological theory describing this emulsification process was derived many years ago, it has remained elusive to experimental verification, hampering our ability to predict the fate of oil in applications such as deep-water spills. Here, we provide the first experimental and numerical verification of the immiscible RT turbulence theory, unveiling a unique turbulent state that originates at the oil-water interface due to the interaction of multiple capillary waves. We show that a single, non-dimensional, and time-independent parameter controls the range of validity of the theory. Our findings have wide-ranging implications for the understanding of the mixing of immiscible fluids. This includes in particular oil spills, where our work enables the prediction of the oil-water interface dynamics that ultimately determine the rate of oil biodegradation by marine bacteria.

In vitro investigation of the blood flow downstream of a 3D-printed aortic valve

The hemodynamics in the aorta as well as the durability of aortic valve prostheses vary greatly between different types of devices. Although placement and sizing of surgical aortic valve prostheses are excellent, the valve geometry of common devices cannot be customized to fit the patient's anatomy perfectly. Similarly, transcatheter aortic valve implantation (TAVI) devices are not customizable and may be orientated unfavorably during implantation. Imperfect fit of an aortic valve prosthesis may result in suboptimal performance and in some cases the need for additional surgery. Leveraging the advent of precision, multi-material 3D-printing, a bioinspired silicone aortic valve was developed. The manufacturing technique makes it fully customizable and significantly cheaper to develop and produce than common prostheses. In this study, we assess the hemodynamic performance of such a 3D-printed aortic valve and compare it to two TAVI devices as well as to a severely stenosed valve. We investigate the blood flow distal to the valve in an anatomically accurate, compliant aorta model via three-dimensional particle tracking velocimetry measurements. Our results demonstrate that the 3D-printed aortic valve induces flow patterns and topology compatible with the TAVI valves and showing similarity to healthy aortic blood flow. Compared to the stenosis, the 3D-printed aortic valve reduces turbulent kinetic energy levels and irreversible energy losses by over 75%, reaching values compatible with healthy subjects and conventional TAVIs. Our study substantiates that the 3D-printed heart valve displays a hemodynamic performance similar to established devices and underscores its potential for driving innovation towards patient specific valve prostheses.

An engineered Sox17 induces somatic to neural stem cell fate transitions independently from pluripotency reprogramming

Advanced strategies to interconvert cell types provide promising avenues to model cellular pathologies and to develop therapies for neurological disorders. Yet, methods to directly transdifferentiate somatic cells into multipotent induced neural stem cells (iNSCs) are slow and inefficient, and it is unclear whether cells pass through a pluripotent state with full epigenetic reset. We report iNSC reprogramming from embryonic and aged mouse fibroblasts as well as from human blood using an engineered Sox17 (eSox17FNV). eSox17FNV efficiently drives iNSC reprogramming while Sox2 or Sox17 fail. eSox17FNV acquires the capacity to bind different protein partners on regulatory DNA to scan the genome more efficiently and has a more potent transactivation domain than Sox2. Lineage tracing and time-resolved transcriptomics show that emerging iNSCs do not transit through a pluripotent state. Our work distinguishes lineage from pluripotency reprogramming with the potential to generate more authentic cell models for aging-associated neurodegenerative diseases.

Universal alignment in turbulent pair dispersion

Countless processes in nature and industry, from rain droplet nucleation to plankton interaction in the ocean, are intimately related to turbulent fluctuations of local concentrations of advected matter. These fluctuations can be described by considering the change of the separation between particle pairs, known as pair dispersion, which is believed to obey a cubic in time growth according to Richardson's theory. Our work reveals a universal, scale-invariant alignment between the relative velocity and position vectors of dispersing particles at a mean angle that we show to be a universal constant of turbulence. We connect the value of this mean angle to Richardson's traditional theory and find agreement with data from a numerical simulation and a laboratory experiment. While the Richardson's cubic regime has been observed for small initial particle separations only, the constancy of the mean angle manifests throughout the entire inertial range of turbulence. Thus, our work reveals the universal nature of turbulent pair dispersion through a geometrical paradigm whose validity goes beyond the classical theory, and provides a framework for understanding and modeling transport and mixing processes.

Global warming accelerates soil heterotrophic respiration

Carbon efflux from soils is the largest terrestrial carbon source to the atmosphere, yet it is still one of the most uncertain fluxes in the Earth's carbon budget. A dominant component of this flux is heterotrophic respiration, influenced by several environmental factors, most notably soil temperature and moisture. Here, we develop a mechanistic model from micro to global scale to explore how changes in soil water content and temperature affect soil heterotrophic respiration. Simulations, laboratory measurements, and field observations validate the new approach. Estimates from the model show that heterotrophic respiration has been increasing since the 1980s at a rate of about 2% per decade globally. Using future projections of surface temperature and soil moisture, the model predicts a global increase of about 40% in heterotrophic respiration by the end of the century under the worst-case emission scenario, where the Arctic region is expected to experience a more than two-fold increase, driven primarily by declining soil moisture rather than temperature increase.

Internal Biofilm Heterogeneities Enhance Solute Mixing and Chemical Reactions in Porous Media

Bacterial biofilms can form in porous media that are of interest in industrial applications ranging from medical implants to biofilters as well as in environmental applications such as in situ groundwater remediation, where they can be critical locations for biogeochemical reactions. The presence of biofilms modifies porous media topology and hydrodynamics by clogging pores and consequently solutes transport and reactions kinetics. The interplay between highly heterogeneous flow fields found in porous media and microbial behavior, including biofilm growth, results in a spatially heterogeneous biofilm distribution in the porous media as well as internal heterogeneity across the thickness of the biofilm. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore-scale fluid flow and solute transport by considering multiple equivalent stochastically generated internal permeability fields for the biofilm. We show that the internal heterogeneous permeability mainly impacts intermediate velocities when compared with homogeneous biofilm permeability. While the equivalent internal permeability fields of the biofilm do not impact fluid-fluid mixing, they significantly control a fast reaction. For biologically driven reactions such as nutrient or contaminant uptake by the biofilm, its internal permeability field controls the efficiency of the process. This study highlights the importance of considering the internal heterogeneity of biofilms to better predict reactivity in industrial and environmental bioclogged porous systems.

TMED2 binding restricts SMO to the ER and Golgi compartments

Hedgehog (HH) signaling is important for embryonic pattering and stem cell differentiation. The G protein–coupled receptor (GPCR) Smoothened (SMO) is the key HH signal transducer modulating both transcription-dependent and transcription-independent responses. We show that SMO protects naive mouse embryonic stem cells (ESCs) from dissociation-induced cell death. We exploited this SMO dependency to perform a genetic screen in haploid ESCs where we identify the Golgi proteins TMED2 and TMED10 as factors for SMO regulation. Super-resolution microscopy shows that SMO is normally retained in the endoplasmic reticulum (ER) and Golgi compartments, and we demonstrate that TMED2 binds to SMO, preventing localization to the plasma membrane. Mutation of TMED2 allows SMO accumulation at the plasma membrane, recapitulating early events after HH stimulation. We demonstrate the physiologic relevance of this interaction in neural differentiation, where TMED2 functions to repress HH signal strength. Identification of TMED2 as a binder and upstream regulator of SMO opens the way for unraveling the events in the ER–Golgi leading to HH signaling activation.

Hedgehog signals orchestrate tissue patterning by binding the receptor Patched and restricting the signal transducer Smoothened. A genetic screen reveals Tmed2 as a new interactor of Smoothened that is required for regulating Smoothened transport from the endoplasmic reticulum and Golgi to the plasma membrane and hence modulating the strength of Hedgehog signal transduction.

Toward an accurate estimation of wall shear stress from 4D flow magnetic resonance downstream of a severe stenosis

PURPOSE

First, to investigate the agreement between velocity, velocity gradient, and Reynolds stress obtained from four-dimensional flow magnetic resonance (4D flow MRI) measurements and direct numerical simulation (DNS). Second, to propose and optimize based on DNS, 2 alternative methods for the accurate estimation of wall shear stress (WSS) when the resolution of the flow measurements is limited. Thirdly, to validate the 2 methods based on 4D flow MRI data.

METHODS

In vitro 4D MRI has been conducted in a realistic rigid stenosed aorta model under a constant flow rate of 12 L/min. A DNS of transitional stenotic flow has been performed using the same geometry and boundary conditions.

RESULTS

Time-averaged velocity and Reynolds stresses are in good agreement between in vitro 4D MRI data and DNS (errors between 2% and 8% of the reference downsampled data). WSS estimation based on the 2 proposed methods applied to MRI data provide good agreement with DNS for slice-averaged values (maximum error is less than 15% of the mean reference WSS for the first method and 25% for the second method). The performance of both models is not strongly sensitive to spatial resolution up to 1.5 mm voxel size. While the performance of model 1 deteriorates appreciably at low signal-to-noise ratios, model 2 remains robust.

CONCLUSIONS

The 2 methods for WSS magnitude give an overall better agreement than the standard approach used in the literature based on direct calculation of the velocity gradient close to the wall (relative error of 84%).

Efficient mate finding in planktonic copepods swimming in turbulence

Zooplankton live in dynamic environments where turbulence may challenge their limited swimming abilities. How this interferes with fundamental behavioral processes remains elusive. We reconstruct simultaneously the trajectories of flow tracers and calanoid copepods and we quantify their ability to find mates when ambient flow imposes physical constrains on their motion and impairs their olfactory orientation. We show that copepods achieve high encounter rates in turbulence due to the contribution of advection and vigorous swimming. Males further convert encounters within the perception radius to contacts and then to mating via directed motion toward nearby organisms within the short time frame of the encounter. Inertial effects do not result in preferential concentration, reducing the geometric collision kernel to the clearance rate, which we model accurately by superposing turbulent velocity and organism motion. This behavioral and physical coupling mechanism may account for the ability of copepods to reproduce in turbulent environments.

A Novel Estimation Approach of Pressure Gradient and Haemodynamic Stresses as Indicators of Pathological Aortic Flow Using Subvoxel Modelling

OBJECTIVE

The flow downstream from aortic stenoses is characterised by the onset of shear-induced turbulence that leads to irreversible pressure losses. These extra losses represent an increased resistance that impacts cardiac efficiency. A novel approach is suggested in this study to accurately evaluate the pressure gradient profile along the aorta centreline using modelling of haemodynamic stress at scales that are smaller than the typical resolution achieved in experiments.

METHODS

We use benchmark data obtained from direct numerical simulation (DNS) along with results from in silico and in vitro three-dimensional particle tracking velocimetry (3D-PTV) at three voxel sizes, namely 750  μm, 1 mm and 1.5 mm. A differential equation is derived for the pressure gradient, and the subvoxel-scale (SVS) stresses are closed using the Smagorinsky and a new refined model. Model constants are optimised using DNS and in silico PTV data and validated based on pulsatile in vitro 3D-PTV data and pressure catheter measurements.

RESULTS

The Smagorinsky-based model was found to be more accurate for SVS stress estimation but also more sensitive to errors especially at lower resolution, whereas the new model was found to more accurately estimate the projected pressure gradient even for larger voxel size of 1.5 mm albeit at the cost of increased sensitivity at this voxel size. A comparison with other methods in the literature shows that the new approach applied to in vitro PTV measurements estimates the irreversible pressure drop by decreasing the errors by at least 20%.

CONCLUSION

Our novel approach based on the modelling of subvoxel stress offers a validated and more accurate way to estimate pressure gradient, irreversible pressure loss and SVS stress.

SIGNIFICANCE

We anticipate that the approach may potentially be applied to image-based in vivo, in vitro 4D flow data or in silico data with limited spatial resolution to assess pressure loss and SVS stresses in disturbed aortic blood flow.

Mapping the local viscosity of non-Newtonian fluids flowing through disordered porous structures

Flow of non-Newtonian fluids through topologically complex structures is ubiquitous in most biological, industrial and environmental settings. The interplay between local hydrodynamics and the fluid’s constitutive law determines the distribution of flow paths. Consequently the spatial heterogeneity of the viscous resistance controls mass and solute transport from the micron to the meter scale. Examples range from oil recovery and groundwater engineering to drug delivery, filters and catalysts. Here we present a new methodology to map the spatial variation of the local viscosity of a non-Newtonian fluid flowing through a complex pore geometry. We use high resolution image velocimetry to determine local shear rates. Knowing the local shear rate in combination with a separate measurement of the fluid’s constitutive law allows to quantitatively map the local viscosity at the pore scale. Our experimental results—which closely match with three-dimensional numerical simulations—demonstrate that the exponential decay of the longitudinal velocity distributions, previously observed for Newtonian fluids, is a function of the spatial heterogeneity of the local viscosity. This work sheds light on the relationship between hydraulic properties and the viscosity at the pore scale, which is of fundamental importance for predicting transport properties, mixing, and chemical reactions in many porous systems.

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

Oct4, along with Sox2 and Klf4 (SK), can induce pluripotency but structurally similar factors like Oct6 cannot. To decode why Oct4 has this unique ability, we compare Oct4-binding, accessibility patterns and transcriptional waves with Oct6 and an Oct4 mutant defective in the dimerization with Sox2 (Oct4^defSox2). We find that initial silencing of the somatic program proceeds indistinguishably with or without Oct4. Oct6 mitigates the mesenchymal-to-epithelial transition and derails reprogramming. These effects are a consequence of differences in genome-wide binding, as the early binding profile of Oct4^defSox2 resembles Oct4, whilst Oct6 does not bind pluripotency enhancers. Nevertheless, in the Oct6-SK condition many otherwise Oct4-bound locations become accessible but chromatin opening is compromised when Oct4^defSox2 occupies these sites. We find that Sox2 predominantly facilitates chromatin opening, whilst Oct4 serves an accessory role. Formation of Oct4/Sox2 heterodimers is essential for pluripotency establishment; however, reliance on Oct4/Sox2 heterodimers declines during pluripotency maintenance.

Oct4, along with Sox2 and Klf4 can induce pluripotency, but structurally similar factors like Oct6 cannot. Here, using pluripotency competent and incompetent factors, the authors show that Sox2 plays a dominant role in facilitating chromatin opening at Oct4 bound DNA early during reprogramming to pluripotency.

Quantifying physical disintegration of faeces in sewers: Stochastic model and flow reactor experiments

We present a novel stochastic model for quantifying gross solids (GS) physical disintegration under varying turbulent flow conditions and used a unique experimental setup for model calibration and validation. The stochastic deterioration model predicts faeces size evolution over time. It conceptually entails the two main processes of solid fragmentation, namely breakage and erosion. Model parameters were calibrated on synthetic faeces and validated with real human ones. A cylindrical reactor was used, where turbulent flow was forced by an array of water jets and the physical disintegration of the faeces was monitored using a high speed camera. Image analysis of breakage experiments obtained under backlight illumination allowed determination of the evolution of the solids' size over time. The flow field in the reactor was characterised by particle image velocimetry (PIV) using tracer particles seeded into the water. We found different disintegration behaviours depending on turbulence intensity and water content of the solid. In conditions of low shear stress, dense solids hardly disintegrated. Generally, the model predictions mirrored the broad range in the solids disintegration rate imparted by the high variability in flow conditions and in solids characteristics. It is expected that, similar to our experiments, also in real sewer systems both flow conditions and solid characteristics are highly variable and the stochastic model can be tailored to capture this variability. We thus anticipate that the model can be integrated into existing sewer models predicting sewer flows and solids' movement. From these, shear stress, flow velocities and transport of individual solids can be inferred. The integration of the present solids disintegration model may provide better predictions of hot-spots for solids accumulation and blockages in sewers.

Hemodynamic Changes in the Right Ventricle Induced by Variations of Cardiac Output: A Possible Mechanism for Arrhythmia Occurrence in the Outflow Tract

The rationale of this paper is to investigate right ventricular (RV) hemodynamics in relation to changes in cardiac output, and in particular to study exercise-induced stresses at the RV outflow tract (RVOT), which is a common site of ventricular arrhythmias in the athlete’s heart. We hypothesize that the thin-walled RVOT is exposed to high wall shear stresses (WSS) during physiological states associated with high cardiac output such as exercise, and therefore, may be particularly prone to substrate formation leading to ventricular tachyarrhythmias. 3D Particle Tracking Velocimetry (3D-PTV), an optical imaging method, has been performed in a novel anatomically accurate compliant silicone right heart model derived from a high resolution MRI heart scan of a healthy male proband. RV and RVOT flow patterns at resting conditions were obtained from two healthy athletic male proband’s hearts and two patients with arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) via phase contrast magnetic resonance imaging (PC-MRI). The healthy case was used as a reference for validating the in vitro flow patterns of the silicone model, while the diseased cases were used to generalize our findings and investigate possible changes in hemodynamic stresses with RV morphological remodelling. Our results showed that both healthy and diseased geometries consistently displayed an increased WSS in the RVOT relative to the rest of the RV. We found that increases in cardiac output may lead to increases of mean kinetic energy (MKE), laminar viscous dissipation and WSS at the RVOT. Furthermore, higher peak WSS magnitudes were found for the diseased cases. The identified high WSS regions may correlate with the common site of RVOT ventricular tachycardia in athletes and patients with ARVC/D. Our results imply that exercise, as well as anatomical and functional remodeling might alter RV wall shear stress both in magnitude and spatial distribution, leading to increased hemodynamic stresses in the RVOT.

Biofilms in 3D porous media: Delineating the influence of the pore network geometry, flow and mass transfer on biofilm development

This study investigates the functional correspondence between porescale hydrodynamics, mass transfer, pore structure and biofilm morphology during progressive biofilm colonization of a porous medium. Hydrodynamics and the structure of both the porous medium and the biofilm are experimentally measured with 3D particle tracking velocimetry and micro X-ray Computed Tomography, respectively. The analysis focuses on data obtained in a clean porous medium after 36 h of biofilm growth. Registration of the particle tracking and X-ray data sets allows to delineate the interplay between porous medium geometry, hydrodynamic and mass transfer processes on the morphology of the developing biofilm. A local analysis revealed wide distributions of wall shear stresses and concentration boundary layer thicknesses. The spatial distribution of the biofilm patches uncovered that the wall shear stresses controlled the biofilm development. Neither external nor internal mass transfer limitations were noticeable in the considered system, consistent with the excess supply of nutrient and electron acceptors. The wall shear stress remained constant in the vicinity of the biofilm but increased substantially elsewhere.

Pore-Scale Hydrodynamics in a Progressively Bioclogged Three-Dimensional Porous Medium: 3-D Particle Tracking Experiments and Stochastic Transport Modeling

Biofilms are ubiquitous bacterial communities that grow in various porous media including soils, trickling, and sand filters. In these environments, they play a central role in services ranging from degradation of pollutants to water purification. Biofilms dynamically change the pore structure of the medium through selective clogging of pores, a process known as bioclogging. This affects how solutes are transported and spread through the porous matrix, but the temporal changes to transport behavior during bioclogging are not well understood. To address this uncertainty, we experimentally study the hydrodynamic changes of a transparent 3-D porous medium as it experiences progressive bioclogging. Statistical analyses of the system's hydrodynamics at four time points of bioclogging (0, 24, 36, and 48 h in the exponential growth phase) reveal exponential increases in both average and variance of the flow velocity, as well as its correlation length. Measurements for spreading, as mean-squared displacements, are found to be non-Fickian and more intensely superdiffusive with progressive bioclogging, indicating the formation of preferential flow pathways and stagnation zones. A gamma distribution describes well the Lagrangian velocity distributions and provides parameters that quantify changes to the flow, which evolves from a parallel pore arrangement under unclogged conditions, toward a more serial arrangement with increasing clogging. Exponentially evolving hydrodynamic metrics agree with an exponential bacterial growth phase and are used to parameterize a correlated continuous time random walk model with a stochastic velocity relaxation. The model accurately reproduces transport observations and can be used to resolve transport behavior at intermediate time points within the exponential growth phase considered.

Zooplankton can actively adjust their motility to turbulent flow

Calanoid copepods are among the most abundant metazoans in the ocean and constitute a vital trophic link within marine food webs. They possess relatively narrow swimming capabilities, yet are capable of significant self-locomotion under strong hydrodynamic conditions. Here we provide evidence for an active adaptation that allows these small organisms to adjust their motility in response to background flow. We track simultaneously and in three dimensions the motion of flow tracers and planktonic copepods swimming freely at several intensities of quasi-homogeneous, isotropic turbulence. We show that copepods synchronize the frequency of their relocation jumps with the frequency of small-scale turbulence by performing frequent relocation jumps of low amplitude that seem unrelated to localized hydrodynamic signals. We develop a model of plankton motion in turbulence that shows excellent quantitative agreement with our measurements when turbulence is significant. We find that, compared with passive tracers, active motion enhances the diffusion of organisms at low turbulence intensity whereas it dampens diffusion at higher turbulence levels. The existence of frequent jumps in a motion that is otherwise dominated by turbulent transport allows for the possibility of active locomotion and hence to transition from being passively advected to being capable of controlling diffusion. This behavioral response provides zooplankton with the capability to retain the benefits of self-locomotion despite turbulence advection and may help these organisms to actively control their distribution in dynamic environments. Our study reveals an active adaptation that carries strong fitness advantages and provides a realistic model of plankton motion in turbulence.

Clogging of an Alpine streambed by silt-sized particles - Insights from laboratory and field experiments

Clogging of streambeds by suspended particles (SP) can cause environmental problems, as it can negatively influence, e.g., habitats for macrozoobenthos, fish reproduction and groundwater recharge. This especially applies in the case of silt-sized SP. Until now, most research has dealt with coarse SP and was carried out in laboratory systems. The aims of this study are to examine (1) whether physical clogging by silt-sized SP exhibits the same dynamics and patterns as by sand-sized SP, and (2) the comparability of results between laboratory and field experiments. We carried out vertical column experiments with sand-sized bed material and silt-sized SP, which are rich in mica minerals. In laboratory experiments, we investigated the degree of clogging quantified by the reduction of porosity and hydraulic conductivity and the maximum clogging depth as a function of size and shape of bed material, size of SP, pore water flow velocity, and concentration of calcium cations. The SP were collected from an Alpine sedimentation basin, where our field experiments were carried out. To investigate the clogging process in the field, we buried columns filled with sand-sized quartz in the stream bed. We found that the maximal bed-to-grain ratio where clogging still occurs is larger for silt-sized SP than for sand-sized SP. The observed clogging depths and the reduction of flow rate through the column from our laboratory experiments were comparable to those from the field. However, our field results showed that the extent of clogging strongly depends on the naturally-occurring hydrological dynamics. The field location was characterized by a more polydisperse suspension, a strongly fluctuating water regime, and high SP concentrations at times, leading to more heterogeneous and more pronounced clogging when compared to laboratory results.

Investigation of Atrial Vortices Using a Novel Right Heart Model and Possible Implications for Atrial Thrombus Formation

The main aim of this paper is to characterize vortical flow structures in the healthy human right atrium, their impact on wall shear stresses and possible implications for atrial thrombus formation. 3D Particle Tracking Velocimetry is applied to a novel anatomically accurate compliant silicone right heart model to study the phase averaged and fluctuating flow velocity within the right atrium, inferior vena cava and superior vena cava under physiological conditions. We identify the development of two vortex rings in the bulk of the right atrium during the atrial filling phase leading to a rinsing effect at the atrial wall which break down during ventricular filling. We show that the vortex ring formation affects the hemodynamics of the atrial flow by a strong correlation (ρ = 0.7) between the vortical structures and local wall shear stresses. Low wall shear stress regions are associated with absence of the coherent vortical structures which might be potential risk regions for atrial thrombus formation. We discuss possible implications for atrial thrombus formation in different regions of the right atrium.

Short-term exposure to gold nanoparticle suspension impairs swimming behavior in a widespread calanoid copepod

Calanoid copepods play an important role in the functioning of marine and brackish ecosystems. Information is scarce on the behavioral toxicity of engineered nanoparticles to these abundant planktonic organisms. We assessed the effects of short-term exposure to nonfunctionalized gold nanoparticles on the swimming behavior of the widespread estuarine copepod Eurytemora affinis. By means of three-dimensional particle tracking velocimetry, we reconstructed the trajectories of males, ovigerous and non-ovigerous females. We quantified changes in their swimming activity and in the kinematics and geometrical properties of their motion, three important descriptors of the motility patterns of zooplankters. In females, exposure to gold nanoparticles in suspension (11.4 μg L^-1) for 30 min caused depressed activity and lower velocity and acceleration, whereas the same exposure caused minimal effects in males. This response differs clearly from the hyperactive behavior that is commonly observed in zooplankters exposed to pollutants, and from the generally lower sensitivity of female copepods to toxicants. Accumulation of gold nanoparticles on the external appendages was not observed, precluding mechanical effects. Only very few nanoparticles appeared sporadically in the inner part of the gut in some samples, either as aggregates or as isolated nanoparticles, which does not suggest systemic toxicity resulting from pronounced ingestion. Hence, the precise mechanisms underlying the behavioral toxicity observed here remain to be elucidated. These results demonstrate that gold nanoparticles can induce marked behavioral alterations at very low concentration and short exposure duration. They illustrate the applicability of swimming behavior as a suitable and sensitive endpoint for investigating the toxicity of nanomaterials present in estuarine and marine environments. Changes in swimming behavior may impair the ability of planktonic copepods to interact with their environment and with other organisms, with possible impacts on population dynamics and community structure.

Biofilm imaging in porous media by laboratory X-Ray tomography: Combining a non-destructive contrast agent with propagation-based phase-contrast imaging tools

X-ray tomography is a powerful tool giving access to the morphology of biofilms, in 3D porous media, at the mesoscale. Due to the high water content of biofilms, the attenuation coefficient of biofilms and water are very close, hindering the distinction between biofilms and water without the use of contrast agents. Until now, the use of contrast agents such as barium sulfate, silver-coated micro-particles or 1-chloronaphtalene added to the liquid phase allowed imaging the biofilm 3D morphology. However, these contrast agents are not passive and potentially interact with the biofilm when injected into the sample. Here, we use a natural inorganic compound, namely iron sulfate, as a contrast agent progressively bounded in dilute or colloidal form into the EPS matrix during biofilm growth. By combining a very long source-to-detector distance on a X-ray laboratory source with a Lorentzian filter implemented prior to tomographic reconstruction, we substantially increase the contrast between the biofilm and the surrounding liquid, which allows revealing the 3D biofilm morphology. A comparison of this new method with the method proposed by Davit et al (Davit et al., 2011), which uses barium sulfate as a contrast agent to mark the liquid phase was performed. Quantitative evaluations between the methods revealed substantial differences for the volumetric fractions obtained from both methods. Namely, contrast agent—biofilm interactions (e.g. biofilm detachment) occurring during barium sulfate injection caused a reduction of the biofilm volumetric fraction of more than 50% and displacement of biofilm patches elsewhere in the column. Two key advantages of the newly proposed method are that passive addition of iron sulfate maintains the integrity of the biofilm prior to imaging, and that the biofilm itself is marked by the contrast agent, rather than the liquid phase as in other available methods. The iron sulfate method presented can be applied to understand biofilm development and bioclogging mechanisms in porous materials and the obtained biofilm morphology could be an ideal basis for 3D numerical calculations of hydrodynamic conditions to investigate biofilm-flow coupling.

Shear-scaling-based approach for irreversible energy loss estimation in stenotic aortic flow - An in vitro study

Today, the functional and risk assessment of stenosed arteries is mostly based on ultrasound Doppler blood flow velocity measurements or catheter pressure measurements, which rely on several assumptions. Alternatively, blood velocity including turbulent kinetic energy (TKE) may be measured using MRI. The aim of the present study is to validate a TKE-based approach that relies on the fact that turbulence production is dominated by the flow's shear to determine the total irreversible energy loss from MRI scans. Three-dimensional particle tracking velocimetry (3D-PTV) and phase-contrast magnetic resonance imaging (PC-MRI) simulations were performed in an anatomically accurate, compliant, silicon aortic phantom. We found that measuring only the laminar viscous losses does not reflect the true losses of stenotic flows since the contribution of the turbulent losses to the total loss become more dominant for more severe stenosis types (for example, the laminar loss is 0.0094±0.0015W and the turbulent loss is 0.0361±0.0015W for the Re_max=13,800 case, where Re_max is the Reynolds number based on the velocity in the vena-contracta). We show that the commonly used simplified and modified Bernoulli's approaches overestimate the total loss, while the new TKE-based method proposed here, referred to as "shear scaling" approach, results in a good agreement between 3D-PTV and simulated PC-MRI (mean error is around 10%). In addition, we validated the shear scaling approach on a geometry with post-stenotic dilatation using numerical data by Casas et al. (2016). The shear scaling-based method may hence be an interesting alternative for irreversible energy loss estimation to replace traditional approaches for clinical use. We expect that our results will evoke further research, in particular patient studies for clinical implementation of the new method.

Small-scale entrainment in inclined gravity currents

We investigate the effect of buoyancy on the small-scale aspects of turbulent entrainment by performing direct numerical simulation of a gravity current and a wall jet. In both flows, we detect the turbulent/nonturbulent interface separating turbulent from irrotational ambient flow regions using a range of enstrophy iso-levels spanning many orders of magnitude. Conform to expectation, the relative enstrophy isosurface velocity v n in the viscous superlayer scales with the Kolmogorov velocity for both flow cases. We connect the integral entrainment coefficient E to the small-scale entrainment and observe excellent agreement between the two estimates throughout the viscous superlayer. The contribution of baroclinic torque to v n is negligible, and we show that the primary reason for reduced entrainment in the gravity current as compared to the wall-jet are 1) the reduction of v n relative to the integral velocity scale u T ; and 2) the reduction in the surface area of the isosurfaces.

Solvable continuous-time random walk model of the motion of tracer particles through porous media

We consider the continuous-time random walk (CTRW) model of tracer motion in porous medium flows based on the experimentally determined distributions of pore velocity and pore size reported by Holzner et al. [M. Holzner et al., Phys. Rev. E 92, 013015 (2015)PLEEE81539-375510.1103/PhysRevE.92.013015]. The particle's passing through one channel is modeled as one step of the walk. The step (channel) length is random and the walker's velocity at consecutive steps of the walk is conserved with finite probability, mimicking that at the turning point there could be no abrupt change of velocity. We provide the Laplace transform of the characteristic function of the walker's position and reductions for different cases of independence of the CTRW's step duration τ, length l, and velocity v. We solve our model with independent l and v. The model incorporates different forms of the tail of the probability density of small velocities that vary with the model parameter α. Depending on that parameter, all types of anomalous diffusion can hold, from super- to subdiffusion. In a finite interval of α, ballistic behavior with logarithmic corrections holds, which was observed in a previously introduced CTRW model with independent l and τ. Universality of tracer diffusion in the porous medium is considered.

Clustering of particles in turbulence due to phoresis

We demonstrate that diffusiophoretic, thermophoretic, and chemotactic phenomena in turbulence lead to clustering of particles on multifractal sets that can be described using one single framework, valid when the particle size is much smaller than the smallest length scale of turbulence l_{0}. To quantify the clustering, we derive positive pair correlations and fractal dimensions that hold for scales smaller than l_{0}. For scales larger than l_{0} the pair-correlation function is predicted to show a stretched exponential decay towards 1. In the case of inhomogeneous turbulence we find that the fractal dimension depends on the direction of inhomogeneity. By performing experiments with particles in a turbulent gravity current we demonstrate clustering induced by salinity gradients in conformity to the theory. The particle size in the experiment is comparable to l_{0}, outside the strict validity region of the theory, suggesting that the theoretical predictions transfer to this practically relevant regime. This clustering mechanism may provide the key to the understanding of a multitude of processes such as formation of marine snow in the ocean and population dynamics of chemotactic bacteria.

Turbulence triggers vigorous swimming but hinders motion strategy in planktonic copepods

Calanoid copepods represent a major component of the plankton community. These small animals reside in constantly flowing environments. Given the fundamental role of behaviour in their ecology, it is especially relevant to know how copepods perform in turbulent flows. By means of three-dimensional particle tracking velocimetry, we reconstructed the trajectories of hundreds of adult Eurytemora affinis swimming freely under realistic intensities of homogeneous turbulence. We demonstrate that swimming contributes substantially to the dynamics of copepods even when turbulence is significant. We show that the contribution of behaviour to the overall dynamics gradually reduces with turbulence intensity but regains significance at moderate intensity, allowing copepods to maintain a certain velocity relative to the flow. These results suggest that E. affinis has evolved an adaptive behavioural mechanism to retain swimming efficiency in turbulent flows. They suggest the ability of some copepods to respond to the hydrodynamic features of the surrounding flow. Such ability may improve survival and mating performance in complex and dynamic environments. However, moderate levels of turbulence cancelled gender-specific differences in the degree of space occupation and innate movement strategies. Our results suggest that the broadly accepted mate-searching strategies based on trajectory complexity and movement patterns are inefficient in energetic environments.

Breakup of Finite-Size Colloidal Aggregates in Turbulent Flow Investigated by Three-Dimensional (3D) Particle Tracking Velocimetry

Aggregates grown in mild shear flow are released, one at a time, into homogeneous isotropic turbulence, where their motion and intermittent breakup is recorded by three-dimensional particle tracking velocimetry (3D-PTV). The aggregates have an open structure with a fractal dimension of ∼2.2, and their size is 1.4 ± 0.4 mm, which is large, compared to the Kolmogorov length scale (η = 0.15 mm). 3D-PTV of flow tracers allows for the simultaneous measurement of aggregate trajectories and the full velocity gradient tensor along their pathlines, which enables us to access the Lagrangian stress history of individual breakup events. From this data, we found no consistent pattern that relates breakup to the local flow properties at the point of breakup. Also, the correlation between the aggregate size and both shear stress and normal stress at the location of breakage is found to be weaker, when compared with the correlation between size and drag stress. The analysis suggests that the aggregates are mostly broken due to the accumulation of the drag stress over a time lag on the order of the Kolmogorov time scale. This finding is explained by the fact that the aggregates are large, which gives their motion inertia and increases the time for stress propagation inside the aggregate. Furthermore, it is found that the scaling of the largest fragment and the accumulated stress at breakup follows an earlier established power law, i.e., dfrag ∼ σ(-0.6) obtained from laminar nozzle experiments. This indicates that, despite the large size and the different type of hydrodynamic stress, the microscopic mechanism causing breakup is consistent over a wide range of aggregate size and stress magnitude.

Lipid nanocapsules for behavioural testing in aquatic toxicology: Time-response of Eurytemora affinis to environmental concentrations of PAHs and PCB

The increasing interest for behavioural investigations in aquatic toxicology has heightened the need for developing tools that allow realistic exposure conditions and provide robust quantitative data. Calanoid copepods dominate the zooplankton community in marine and brackish environments. These small organisms have emerged as attractive models because of the sensitivity of their behaviour to important environmental parameters and the significance of self-induced motion in their ecology. Estuarine copepods are particularly relevant in this context because of their incessant exposure to high levels of pollution. We used lipid nanocapsules to deliver sub-lethal concentrations of PAHs (pyrene, phenanthrene and fluoranthene) and PCB 153 into the digestive track of males and females Eurytemora affinis. This novel approach enabled us to achieve both contact and trophic exposure without using phytoplankton, and to expose copepods to small hydrophobic molecules without using organic solvent. We reconstructed the motion of many copepods swimming simultaneously by means of three-dimensional particle tracking velocimetry. We quantified the combined effects of contact and trophic toxicity by comparing the kinematic and diffusive properties of their motion immediately and after 3h and 24h of exposure. Despite the lack of toxicity of their excipients, both empty and loaded capsules increased swimming activity and velocity immediately after exposure. Laser microscopy imaging shows adhesion of nanocapsules on the exoskeleton of the animals, suggesting contact toxicity. The behavioural response resembles an escape reaction allowing copepods to escape stressful conditions. The contact toxicity of empty capsules and pollutants appeared to be additive and nanocapsules loaded with PCB caused the greatest effects. We observed a progressive accumulation of capsules in the digestive track of the animals after 3h and 24h of exposure, which suggests an increasing contribution of systemic toxicity. Nanocapsules filled with PAHs caused a smaller response compared to empty capsules, which we attribute to the narcotic properties of these toxicants. The sharp decrease in velocity after 24h of exposure to capsules loaded with PCB suggests physiological incapacitation following systemic toxicity. Clear differences are visible between genders in their response to empty and loaded capsules, for all exposure durations. Females appear to be less sensitive than males, suggesting different tolerance to stress conditions. Our results confirm the feasibility of using lipid nanocapsules to identify pollutant-induced behavioural alteration in the plankton. They also add new insights into the contact and systemic toxicity of common pollutants. We expect that our results will assist and evoke further research to develop suitable nanocarrier systems for behavioural testing.

Characterization of intermittency in zooplankton behaviour in turbulence

We consider Lagrangian velocity differences of zooplankters swimming in still water and in turbulence. Using cumulants, we quantify the intermittency properties of their motion recorded using three-dimensional particle tracking velocimetry. Copepods swimming in still water display an intermittent behaviour characterized by a high probability of small velocity increments, and by stretched exponential tails. Low values arise from their steady cruising behaviour while heavy tails result from frequent relocation jumps. In turbulence, we show that at short time scales, the intermittency signature of active copepods clearly differs from that of the underlying flow, and reflects the frequent relocation jumps displayed by these small animals. Despite these differences, we show that copepods swimming in still and turbulent flow belong to the same intermittency class that can be modelled by a log-stable model with non-analytical cumulant generating function. Intermittency in swimming behaviour and relocation jumps may enable copepods to display oriented, collective motion under strong hydrodynamic conditions and thus, may contribute to the formation of zooplankton patches in energetic environments.

On the accuracy of viscous and turbulent loss quantification in stenotic aortic flow using phase-contrast MRI

PURPOSE

To investigate the limits of phase contrast MRI (PC-MRI)-based measurements of viscous losses and turbulent kinetic energy (TKE) pertaining to spatial resolution, signal-to-noise ratio (SNR), and non-Gaussian intravoxel velocity distributions.

THEORY AND METHODS

High-resolution particle tracking velocimetry data obtained in a realistic aortic phantom with stenotic flow were used to simulate PC-MRI measurements at different resolutions and noise levels. Laminar viscous losses were computed using the spatial gradients of the mean velocity vector field, and TKE levels were derived based on the intravoxel phase dispersion of flow-sensitized PC-MRI measurements.

RESULTS

Increasing the voxel size from 0.625 to 2.5 mm resulted in an underestimation of viscous losses of up to 83%, whereas total TKE values showed errors of <15% and reduced sensitivity to voxel size. Relative errors in viscous loss quantification were found to be less dependent on noise levels when compared with TKE values. In general, a SNR of 20-30 is required for both methods.

CONCLUSION

At spatial resolutions feasible in clinical three-dimensional PC-MRI measurements, viscous losses of stenotic flows are significantly underestimated, whereas TKE shows smaller errors and reduced sensitivity to spatial resolution. Magn Reson Med 76:191-196, 2016. © 2015 Wiley Periodicals, Inc.

Intermittent Lagrangian velocities and accelerations in three-dimensional porous medium flow

Intermittency of Lagrangian velocity and acceleration is a key to understanding transport in complex systems ranging from fluid turbulence to flow in porous media. High-resolution optical particle tracking in a three-dimensional (3D) porous medium provides detailed 3D information on Lagrangian velocities and accelerations. We find sharp transitions close to pore throats, and low flow variability in the pore bodies, which gives rise to stretched exponential Lagrangian velocity and acceleration distributions characterized by a sharp peak at low velocity, superlinear evolution of particle dispersion, and double-peak behavior in the propagators. The velocity distribution is quantified in terms of pore geometry and flow connectivity, which forms the basis for a continuous-time random-walk model that sheds light on the observed Lagrangian flow and transport behaviors.

Experimental characterization of breakage rate of colloidal aggregates in axisymmetric extensional flow

Aggregates prepared under fully destabilized conditions by the action of Brownian motion were exposed to an extensional flow generated at the entrance of a sudden contraction. Two noninvasive techniques were used to monitor their breakup process [i.e. light scattering and three-dimensional (3D) particle tracking velocimetry (3D-PTV)]. While the first one can be used to measure the size and the morphology of formed fragments after the breakage event, the latter is capable of resolving trajectories of individual aggregates up to the breakage point as well as the trajectories of formed fragments. Furthermore, measured velocity gradients were used to determine the local hydrodynamic conditions at the breakage point. All this information was combined to experimentally determine for the first time the breakage rate of individual aggregates, given in the form of a size reduction rate K(R), as a function of the applied strain rate, as well as the properties of the formed fragments (i.e., the number of formed fragments and the size ratio between the largest fragment and the original aggregate). It was found that K(R) scales with the applied strain rate according to a power law with the slope being dependent on the initial fractal dimension only, while the obtained data indicates a linear dependency of K(R) with the initial aggregate size. Furthermore, the probability distribution function (PDF) of the number of formed fragments and the PDF of the size ratio between the largest fragment and the original aggregate indicate that breakage will result with high probability (75%) in the formation of two to three fragments with a rather asymmetric ratio of sizes of about 0.8. The obtained results are well in agreement with the results from the numerical simulations published in the literature.

Behavioral responses of the estuarine calanoid copepod Eurytemora affinis to sub-lethal concentrations of waterborne pollutants

Estuarine waters contain a variety of chemicals which affect to various extents the behavior of aquatic organisms. Little is known, however, on the behavioral response of copepods. The present study shows the results of laboratory experiments investigating the immediate effects of sub-lethal concentrations of three commonly found contaminants on the three-dimensional swimming behavior of the estuarine calanoid copepod Eurytemora affinis. Nonylphenol at 2 μg L⁻¹, cadmium at 45 n gL⁻¹ and a mixture of low to medium molecular weight polycyclic aromatic hydrocarbons at 40 ng L⁻¹ all affected the swimming behavior of E. affinis adults, increasing both swimming speed and activity. In most cases, effects were observable within 30 min of exposure and persisted or faded during a period of depuration in uncontaminated water of similar duration. In ovigerous females exposed to Cd and PAHs, effects appeared to be more pronounced during the depuration period, suggesting that carrying ovisacs may impair recovery. We quantified differences in the distribution of swimming speed values by considering the relative frequencies of periods of break, slow and fast swimming and we observed a trend toward faster movements in the presence of pollutants. The degree of trajectory complexity, estimated through their fractal dimension, was unaffected by pollutants. Since both narcotic and non-narcotic pollutants induced hyperactivity, our results suggest that changes in behavior after a short-term exposure may be independent of the general mode of action of the chemicals. The increase in speed and activity resembles an escape reaction permitting copepods to evade stressful conditions. Overall, these results indicate that environment-relevant concentrations of pollutants can induce rapid changes in copepod behavior. Since behavioral processes represent a fundamental element in the ecology of copepods, our results raise concern about the effects of background levels of pollution on a major component of the plankton community. The long-term response of copepods to waterborne pollutants, their synergistic effects and their interactions with other environmental factors need further investigation.

Mapping mean and fluctuating velocities by Bayesian multipoint MR velocity encoding-validation against 3D particle tracking velocimetry

PURPOSE

To validate Bayesian multipoint MR velocity encoding against particle tracking velocimetry for measuring velocity vector fields and fluctuating velocities in a realistic aortic model.

METHODS

An elastic cast of a human aortic arch equipped with an 80 or 64% stenotic section was driven by a pulsatile pump. Peak velocities and peak turbulent kinetic energies of more than 3 m/s and 1000 J/m(3) could be generated. Velocity vector fields and fluctuating velocities were assessed using Bayesian multipoint MR velocity encoding with varying numbers of velocity encoding points and particle tracking velocimetry in the ascending aorta.

RESULTS

Velocities and turbulent kinetic energies measured with 5-fold k-t undersampled 10-point MR velocity encoding and particle tracking velocimetry were found to reveal good correlation with mean differences of -4.8 ± 13.3 cm/s and r(2) = 0.98 for velocities and -21.8 ± 53.9 J/m(3) and r(2) = 0.98 for turbulent kinetic energies, respectively. Three-dimensional velocity patterns of fast flow downstream of the stenoses and regions of elevated velocity fluctuations were found to agree well.

CONCLUSION

Accelerated Bayesian multipoint MR velocity encoding has been demonstrated to be accurate for assessing mean and fluctuating velocities against the reference standard particle tracking velocimetry. The MR method holds considerable potential to map velocity vector fields and turbulent kinetic energies in clinically feasible exam times of <15 min.

Laminar superlayer at the turbulence boundary

In this Letter we present results from particle tracking velocimetry and direct numerical simulation that are congruent with the existence of a laminar superlayer, as proposed in the pioneering work of Corrsin and Kistler (NACA, Technical Report No. 1244, 1955). We find that the local superlayer velocity is dominated by a viscous component and its magnitude is comparable to the characteristic velocity of the smallest scales of motion. This slow viscous process involves a large surface area so that the global rate of turbulence spreading is set by the largest scales of motion. These findings are important for a better understanding of mixing of mass and momentum in a variety of flows where thin layers of shear exist. Examples are boundary layers, clouds, planetary atmospheres, and oceans.

p16INK4A sensitizes human leukemia cells to FAS- and glucocorticoid-induced apoptosis via induction of BBC3/Puma and repression of MCL1 and BCL2

Loss of CDKN2A/p16(INK4A) in hematopoietic stem cells is associated with enhanced self-renewal capacity and might facilitate progression of damaged stem cells into pre-cancerous cells that give rise to leukemia. This is also reflected by the frequent loss of the INK4A locus in acute lymphoblastic T-cell leukemia. T-cell acute lymphoblastic leukemia cells designed to conditionally express p16(INK4A) arrest in the G(0)/G(1) phase of the cell cycle and show increased sensitivity to glucocorticoid- and tumor necrosis factor receptor superfamily 6-induced apoptosis. To investigate the underlying molecular mechanism for increased death sensitivity, we interfered with specific steps of apoptosis signaling by expression of anti-apoptotic proteins. We found that alterations in cell death susceptibility resulted from changes in the composition of pro- and anti-apoptotic BCL2 proteins, i.e. repression of MCL1, BCL2, and PMAIP1/Noxa and the induction of pro-apoptotic BBC3/Puma. Interference with Puma induction by short hairpin RNA technology or retroviral expression of MCL1 or BCL2 significantly reduced both glucocorticoid- and FAS-induced cell death in p16(INK4A)-reconstituted leukemia cells. These results suggest that Puma, in concert with MCL1 and BCL2 repression, critically mediates p16(INK4A)-induced death sensitization and that in human T-cell leukemia the deletion of p16(INK4A) confers apoptosis resistance by shifting the balance of pro- and anti-apoptotic BCL2 proteins toward apoptosis protection.