The effect of groyne field on trapping macroplastic. Preliminary results from laboratory experiments

Macroplastic, a precursor of microplastic pollution, has become a new scope of research interest. However, the physical processes of macroplastic transport and deposition in rivers are poorly understood, which makes the decisions of where to locate macroplastic trapping infrastructure difficult. In this research, we conducted a series of experiments in a laboratory channel, exploring the impact of groynes and flexible artificial vegetation on the floating macroplastic litter. The goal was to investigate the litter paths with different obstruction arrangements, which was done by implementing a particle tracking technique on video recordings from each experimental run. We found that increasing discharge correlated with the number of plastic litter floating into the recirculation zone within the groyne fields, especially if the upstream groyne had an extended length. This produced a strong mixing interface between the main flow and the groyne field, while a vegetation patch added in the same groyne field changed the paths of plastic litter by deflecting the flow. We noticed that during a moderate discharge rate, the litter pieces flowing into the groyne field with the vegetation circulated there for the longest period, and some of them got entangled between floating stems when discharge was at its lowest. This phenomenon points to the conclusion that low flow velocity paired with the presence of vegetation can be a primer for plastic deposition and consequently, its degradation. The insights from the experiment allowed us to recommend a place downstream of an extended groyne as the desirable (efficient) area for installing a plastic trapping infrastructure or conducting plastic cleaning actions.

A counter-swirl design concept for dry powder inhalers

A swirling airflow is incorporated in several dry powder inhalers (DPIs) for effective powder de-agglomeration. This commonly requires the use of a flow-straightening grid in the DPI to reduce drug deposition loss caused by large lateral spreading of the emerging aerosol. Here, we propose a novel grid-free DPI design concept that improves the aerosol flow characteristics and reduces the aforementioned drug loss. The basis of this design is the implementation of a secondary airflow that swirls in the opposite direction (counter-swirl) to that of a primary swirling airflow. In-vitro deposition, computational fluid dynamics simulations and particle image velocimetry measurements are used to evaluate the counter-swirl DPI aerosol performance and flow characteristics. In comparison with a baseline-DPI that has only a primary swirling airflow, the counter-swirl DPI has 20% less deposition of the emitted drug dose in the induction port and pre-separator of a next generation impactor (NGI). This occurs as a result of the lower flow-swirl generated from the counter-swirl DPI which eliminates the axial reverse flow outside of the mouthpiece and substantially reduces lateral spreading in the exiting aerosol. Modifications to the counter-swirl DPI design were made to prevent drug loss from the secondary airflow tangential inlets, which involved the addition of wall perforations in the tangential inlets and the separation of the primary and secondary swirling airflows by an annular channel. These modified DPI devices were successful in that aspect but had higher flow-swirl than that in the counter-swirl DPI and thus had higher drug mass retained in the device and deposited in the induction port and pre-separator of the NGI. The fine particle fraction in the aerosols generated from all the counter-swirl-based DPIs and the baseline-DPI are found to be statistically similar to each other.

Rotational and translational drags of a Janus particle close to a wall and a lipid membrane

HYPOTHESIS

Measuring rotational and translational Brownian motion of single spherical particles reveals dissipations due to the interaction between the particle and the environment.

EXPERIMENTS

In this article, we show experiments where the in-plane translational and the two rotational drag coefficients of a single spherical Brownian particle can be measured. These particle drags are functions of the particle size and of the particle-wall distance, and of the viscous dissipations at play. We measure drag coefficients for Janus particles close to a solid wall and close to a lipid bilayer membrane.

FINDINGS

For a particle close to a wall, we show that according to hydrodynamic models, particle-wall distance and particle size can be determined. For a particle partially wrapped by lipid membranes, in absence of strong binding interactions, translational and rotational drags are significantly larger than the ones of non-wrapped particles. Beside the effect of the membrane viscosity, we show that dissipations in the deformed membrane cap region strongly contribute to the drag coefficients.

4D Flow Patterns and Relative Pressure Distribution in a Left Ventricle Model by Shake-the-Box and Proper Orthogonal Decomposition Analysis

PURPOSE

Intraventricular blood flow dynamics are associated with cardiac function. Accurate, noninvasive, and easy assessments of hemodynamic quantities (such as velocity, vortex, and pressure) could be an important addition to the clinical diagnosis and treatment of heart diseases. However, the complex time-varying flow brings many challenges to the existing noninvasive image-based hemodynamic assessments. The development of reliable techniques and analysis tools is essential for the application of hemodynamic biomarkers in clinical practice.

METHODS

In this study, a time-resolved particle tracking method, Shake-the-Box, was applied to reconstruct the flow in a realistic left ventricle (LV) silicone model with biological valves. Based on the obtained velocity, 4D pressure field was calculated using a Poisson equation-based pressure solver. Furthermore, flow analysis by proper orthogonal decomposition (POD) of the 4D velocity field has been performed.

RESULTS

As a result of the Shake-the-Box algorithm, we have extracted: (i) particle positions, (ii) particle tracks, and finally, (iii) 4D velocity fields. From the latter, the temporal evolution of the 3D pressure field during the full cardiac cycle was obtained. The obtained maximal pressure difference extracted along the base-to-apex was about 2.7 mmHg, which is in good agreement with those reported in vivo. The POD analysis results showed a clear picture of different scale of vortices in the pulsatile LV flow, together with their time-varying information and corresponding kinetic energy content. To reconstruct 95% of the kinetic energy of the LV flow, only the first six POD modes would be required, leading to significant data reduction.

CONCLUSIONS

This work demonstrated Shake-the-Box is a promising technique to accurately reconstruct the left ventricle flow field in vitro. The good spatial and temporal resolutions of the velocity measurements enabled a 4D reconstruction of the pressure field in the left ventricle. The application of POD analysis showed its potential in reducing the complexity of the high-resolution left ventricle flow measurements. For future work, image analysis, multi-modality flow assessments, and the development of new flow-derived biomarkers can benefit from fast and data-reducing POD analysis.

Estimation of the Deformation Gradient Tensor by Particle Tracking Near a Free Boundary with Quantified Error

Background

Obtaining accurate displacement measurements for large material deformation and/or rotation presents a distinct challenge to digital image correlation (DIC) due to cumulative and decorrelation errors, particularly near material boundaries.

Objective

We aim to accurately measure the deformation gradient tensor near boundary discontinuities in situations of large deformation and large deformation gradients.

Methods

To achieve this goal, the locations of randomly distributed particles are tracked using an open-source particle-tracking software, Trackpy. A least-squares estimate of the deformation gradient tensor field uses nearest-neighbor material vectors and a first-order Finite Difference (FD) approximation, circumventing common errors in other methods. The error caused by FD approximation and that incurred by measurement are derived and tested with exhaustive numerical simulations. Furthermore, a uniaxial tensile test and mode-I fracture experiment are conducted with particle-embedded hydrogels to validate the method.

Results

Numerical results corroborate a theoretical expression of measurement error. They show that the FD error increases while the measurement error decreases for a growing estimating radius. Moreover, measurement error is linearly correlated to displacement noise. A benchmark uniaxial tensile test validates the accuracy of the proposed estimator, and the near-crack-tip measurements in a tensile fracture experiment demonstrate the estimator's capabilities near a free surface, when a material undergoes large deformation and rotation. The results of the displacement and strain data are benchmarked against kinematic data obtained using an open-source DIC software, Ncorr. Computation time for both methods is compared.

Conclusions

A deformation gradient tensor estimator is developed based on a particle tracking technique and a least squares routine. Theoretical error bounds on the estimator are verified by numerical simulations, and the method's capability is confirmed by physical experiments in evaluating large deformation and rotation near a free boundary. The proposed estimator is expected to open a door towards future material tests and experimental mechanics studies, especially in large deformation and large rotation scenarios.

Tracking the pumice rafts from the Fukutoku-Okanoba submarine volcano with Satellites and a Lagrangian Particles trajectory model

On August 13th, 2021, the Fukutoku-Okanoba, a submarine volcano in the Northwest Pacific Ocean, erupted. Satellites detected various pumice rafts that had drifted westward to reach southern Japan over two months. To cope with the potential danger from pumice rafts, predicting their trajectories is crucial. Using a Lagrangian particle tracking model, the trajectories of the rafts were investigated. The model results showed strong sensitivity to the windage coefficient of pumice rafts, which is uncertain and could cause significant errors. An optimal windage coefficient was estimated by comparing the model results with satellite images using a skill score based on the distance between simulated particles and the nearest observed rafts divided by the travel distance of the particles. The optimal windage coefficients ranged between 2 and 3 % and produced pathways comparable to the observations from satellites. The simulation results showed that the pumice rafts moved from Fukutoku-Okanoba toward the Ryukyu Islands for approximately two months prior to being pushed by the north-easterly wind toward Taiwan against the Kuroshio. The methods presented here may become a valuable tool in managing coastal hazards due to diverse marine debris.

Combined use of UAV-SfM surveys, soil particle tracking with RFID tags and a sediment connectivity index to study plot-scale sediment transport

To explore the processes of soil erosion at the plot scale, Digital surface model of Differences (DoD) maps (Unmanned Aerial Vehicle - Structure from Motion (UAV-SfM) method) and data from Radio Frequency Identification (RFID) tags were analysed. The comparison of differences in accuracy of UAV-SfM and 3D terrestrial laser scanner (TLS) measurements, and the integration of the UAV-SfM method and soil particle tracing with RFID tag locations were conducted to assess sediment transport in a plot in Fukushima prefecture, Japan. The Universal Soil Loss Equation (USLE) plot was installed and kept with no vegetation and no cultivation. Water and sediment discharges were measured at the outlet of the plot, and the topographic index of runoff and sediment connectivity (IC) -focused on surface roughness- was also estimated. Based on field surveys, four periods were defined. Locations of RFID tags were firstly determined by using orthoimages derived from the UAV-SfM method and then compared with those locations measured with a laser total station. The mean and standard deviation of difference amounts of UAV-SfM were of 1 and 3.3 mm, respectively. On average, the RFID tags were located with an accuracy of 3.1 cm (RMSE). Although data of tags tracing showed short transport distances with rill erosion, the results of the UAV-SfM surveys showed an increase of sediment connectivity (SC) over the study period that may explain the largest sediment discharge, especially of fine soil particles. The concurrence of higher values of SC as well as the development of new and longer rills demonstrated the important activity of net soil loss in our study site. The combination of distinct methods and techniques, all providing accurate measurements, shed light on the sediment transport process at short distances, which affects the net water and sediment discharge at larger scales.

Particle-tracking-based strategy for the optimization of agitation conditions in a suspension culture of human induced pluripotent stem cells in a shaking vessel

Suspension cultures are widely used for cell expansion in regenerative medicine and production. Shaking culture is one of the useful suspension culture methods that ensures gentle agitation. There are other shaking methods, including orbital shaking, reciprocating, and rocking; however, optimizing the shaking conditions for each method to meet cell culture requirements is time-consuming. In this study, we used a particle-tracking-based strategy for optimizing the agitation conditions. When the average accelerations of aggregates were calculated, high acceleration occurred periodically, and acceleration of the aggregates in orbital shaking was stable. Furthermore, the number of dead cells correlated with the average time of acceleration. We observed that cell growth was ideally maintained by factors such as optimal acceleration, aggregate formation, and cell death. These results indicate that the image-based analyses of aggregates help optimize the agitation conditions for the shaking suspension culture of induced pluripotent stem cells (iPSCs).

Out-of-field measurements and simulations of a proton pencil beam in a wide range of dose rates using a Timepix3 detector: Dose rate, flux and LET

Stray radiation produced by ultra-high dose-rates (UHDR) proton pencil beams is characterized using ASIC-chip semiconductor pixel detectors. A proton pencil beam with an energy of 220 MeV was utilized to deliver dose rates (DR) ranging from conventional radiotherapy DRs up to 270 Gy/s. A MiniPIX Timepix3 detector equipped with a silicon sensor and integrated readout electronics was used. The chip-sensor assembly and chipboard on water-equivalent backing were detached and immersed in the water-phantom. The deposited energy, particle flux, DR, and the linear energy transfer (LET(Si)) spectra were measured in the silicon sensor at different positions both laterally, at different depths, and behind the Bragg peak. At low-intensity beams, the detector is operated in the event-by-event data-driven mode for high-resolution spectral tracking of individual particles. This technique provides precise energy loss response and LET(Si) spectra with radiation field composition resolving power. At higher beam intensities a rescaling of LET(Si) can be performed as the distribution of the LET(Si) spectra exhibits the same characteristics regardless of the delivered DR. The integrated deposited energy and the absorbed dose can be thus measured in a wide range. A linear response of measured absorbed dose was obtained by gradually increasing the delivered DR to reach UHDR beams. Particle tracking of scattered radiation in data-driven mode could be performed at DRs up to 0.27 Gy/s. In integrated mode, the saturation limits were not reached at the measured out-of-field locations up to the delivered DR of over 270 Gy/s. A good agreement was found between measured and simulated absorbed doses.

Is safe distance enough to prevent COVID-19? Dispersion and tracking of aerosols in various artificial ventilation conditions using OpenFOAM

The current COVID-19 pandemic has underlined the importance of learning more about aerosols and particles that migrate through the airways when a person sneezes, coughs and speaks. The coronavirus transmission is influenced by particle movement, which contributes to the emergence of regulations on social distance, use of masks and face shield, crowded assemblies, and daily social activity in domestic, public, and corporate areas. Understanding the transmission of aerosols under different micro-environmental conditions, closed, or ventilated, has become extremely important to regulate safe social distances. The present work attempts to simulate the airborne transmission of coronavirus-laden particles under different respiratory-related activities, i.e., coughing and speaking, using CFD modelling through OpenFOAM v8. The dispersion coupled with the Discrete Phase Method (DPM) has been simulated to develop a better understanding of virus carrier particles transmission processes and their path trailing under different ventilation scenarios. The preliminary results of this study with respect to flow fields were in close agreement with published literature, which was then extended under varied ventilation scenarios and respiratory-related activities. The study observed that improper wearing of mask leads to escape of SARS-CoV-2 containminated aerosols having a smaller aerodynamic diameter from the gap between face mask and face, infecting different surfaces in the vicinity. It was also observed that aerosol propagation infecting the area through coughing is a faster phenomenon compared to the propagation of coronavirus-laden particles during speaking. The study's findings will help decision-makers formulate common but differentiated guidelines for safe distancing under different micro-environmental conditions.

Dispersal and transport of microplastic particles under different flow conditions in riverine ecosystem

Microplastic (MP) pollution is a global issue owing to its potential threats to ecosystems and human health. MP pollution in river ecosystems is widely investigated, but the transport process under different hydrological conditions remain unclear. In this study, an approach of particle tracking in conjunction with hydrodynamic modeling was developed to investigate the dispersal and transport processes of microplastic particles in riverine ecosystem. The concentration and dispersal pattern of polyamide (PA), polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyethylene terephthalate (PET) particles under base flow and flood events with recurrence intervals of 10-year, 20-year and 50-year were identified. Results indicated that rainfall intensity had a significant impact on the microplastic transport in rivers. Higher suspension concentration and lower sedimented concentration were observed in high flow periods, and the sedimented concentration showed a slow increasing trend in the flood recession stage. High water velocity facilitated the microplastic particles to be migrated for a longer distance, and high water flow was conducive to transport more microplastics from source points. Besides, microplastic particles with high density had worse mobility in water and more prone to deposition. PET were likely to be transported for a relatively shorter distance, while PP had higher mobility and took less time to reach the same simulation point. This study put forward an effective approach to understand the transport of MPs in the river. The results obtained are useful to identify pollution hotspots and track pollution paths.

Microparticle Brownian motion near an air-water interface governed by direction-dependent boundary conditions

HYPOTHESIS

Although the dynamics of colloids in the vicinity of a solid interface has been widely characterized in the past, experimental studies of Brownian diffusion close to an air-water interface are rare and limited to particle-interface gap distances larger than the particle size. At the still unexplored lower distances, the dynamics is expected to be extremely sensitive to boundary conditions at the air-water interface. There, ad hoc experiments would provide a quantitative validation of predictions.

EXPERIMENTS

Using a specially designed dual wave interferometric setup, the 3D dynamics of 9 μm diameter particles at a few hundreds of nanometers from an air-water interface is here measured in thermal equilibrium.

FINDINGS

Intriguingly, while the measured dynamics parallel to the interface approaches expected predictions for slip boundary conditions, the Brownian motion normal to the interface is very close to the predictions for no-slip boundary conditions. These puzzling results are rationalized considering current models of incompressible interfacial flow and deepened developing an ad hoc model which considers the contribution of tiny concentrations of surface active particles at the interface. We argue that such condition governs the particle dynamics in a large spectrum of systems ranging from biofilm formation to flotation process.

Small Volume Microrheology to Evaluate Viscoelastic Properties of Nucleic Acid-Based Supra-Assemblies

Particle tracking (PT) microrheology is a passive microrheological approach that characterizes material properties of soft matter. Multicomponent materials with the ability to create extensive crosslinking, such as supra-assemblies, may exhibit a complex interplay of viscous and elastic properties with a substantial contribution of liquid phase still diffusing through the system. Microrheology analyzes the motion of microscopic beads immersed in a sample, making it possible to evaluate the rheological properties of biological supra-assemblies. This method requires only a small volume of the sample and a relatively simple, inexpensive experimental setup. The objective of this chapter is to describe the experimental procedures for the observation of particle motion, calibration of an optical setup for particle tracking, preparation of imaging chambers, and the use of image analysis software for particle tracking in viscoelastic nucleic acid-based supra-assemblies.

Simulating degradation of organic compounds accounting for the growth of microorganisms (Monod kinetics) in a fully Lagrangian framework

Biologically mediated degradation of organic compounds in porous media is a complex mathematical problem, described by a non-linear differential equation. The organic compound gets in contact with the biomass, and an enzyme-catalysed reaction takes place. The net result is that part of the parent compound degrades into some daughter product, while some of the organic carbon is used for microbial growth. The rate of biomass growth in the presence of a limiting nutrient supply is usually modelled with the experimentally derived Monod equation, i.e., it is proportional to the actual existing biomass multiplied by a factor that is non-linear in terms of available organic matter. This non-linearity in the degradation equation implies a strong difficulty in directly implementing a numerical solution within a fully Lagrangian framework, and thus, numerical solutions have traditionally been sought in either an Eulerian, or else an Eulerian-Lagrangian framework. Here we pursue a fully Lagrangian solution to the problem. First, the Monod empirical equation is formulated as the outcome of a two-step reaction; while the approach is less general than other derivations existing in the literature based on a full understanding of the thermodynamics of the process, it allows two things: 1) providing some physical meaning to the actual parameters in the Monod equation, and more interestingly, 2) formulating a methodology for the solution of the degradation equation incorporating Monod kinetics by means of a particle tracking formulation. For the latter purpose, both reactants and biomass are represented by particles, and their location at any given time is represented by a kernel that accounts for the uncertainty in the actual physical location. By solving the reaction equation in a kernel framework, we can reproduce the Monod kinetics and, as a particular result in the case no biomass growth is allowed, the Michaelis-Menten kinetics. The methodology proposed is then successfully applied to reproduce two studies of microbially induced degradation of organic compounds in porous media, first, the observed kinetics of Pseudomonas putida F1 in batch reactors while growing on benzene, toluene and phenol, and second, the column study of carbon tetrachloride biodegradation by the denitrifying bacterium Pseudomonas Stutzeri KC.

A numerical framework for modeling fate and transport of microplastics in inland and coastal waters

Proliferation of microplastics in rivers, lakes, estuaries, coastal waters and oceans is a major global challenge and threat to the environment, livelihoods and human health. Reliable predictive tools can play an essential role in developing an improved understanding of microplastics behaviour, exposure and risk in water bodies, and facilitate identification of sources and accumulation hot spots, thereby enabling informed decision-making for targeted prevention and clean-up activities. This study presents a new numerical framework (CaMPSim-3D) for predicting microplastics fate and transport in different aquatic settings, which consists of a Lagrangian, three-dimensional (3D) particle-tracking model (PTM) coupled with an Eulerian-based hydrodynamic modeling system (TELEMAC). The 3D PTM has several innovative features that enable accurate simulation and efficient coupling with TELEMAC, which utilizes an unstructured computational mesh. The PTM is capable of considering spatio-temporally varying diffusivity, and uses an innovative algorithm to locate particles within the Eulerian mesh. Model accuracy associated with different advection schemes was verified by comparing numerical predictions to known analytical solutions for several test cases. The implications of choosing different advection schemes for modeling microplastics transport was then investigated by applying the PTM to simulate particle transport in the lower Saint John River Estuary in eastern Canada. The sensitivity of the PTM predictions to the advection scheme was investigated using six numerical schemes with different levels of complexity. Predicted particle distributions and residence times based on the fourth-order Runge-Kutta (RK4) scheme differed significantly (residence times by up to 100 %) from those computed using the traditional first-order (Euler) method. The Third Order Total Variation Diminishing (TVD3) Runge-Kutta method was found to be optimal, providing the closest results to RK4 with approximately 27 % lower computational cost.

Assessing a model of Pacific Northwest harmful algal bloom transport as a decision-support tool

In the Pacific Northwest, blooms of the diatom Pseudo-nitzschia (PN) sometimes produce domoic acid, a neurotoxin that causes amnesic shellfish poisoning, leading to a Harmful Algal Bloom (HAB) event. The Pacific Northwest (PNW) HAB Bulletin project, a partnership between academic, government, and tribal stakeholders, uses a combination of beach and offshore monitoring data and ocean forecast modeling to better understand the formation, evolution, and transport of HABs in this region. This project produces periodic Bulletins to inform local stakeholders of current and forecasted conditions. The goal of this study was to help improve how the forecast model is used in the Bulletin's preparation through a retrospective particle-tracking experiment. Using past observations of beach PN cell counts, events were identified that likely originated in the Juan de Fuca eddy, a known PN hotspot, and then particle tracks were used in the model to simulate these events. A variety of "beaching definitions" were tested, based on both water depth and distance offshore, to define when a particle in the model was close enough to the coast that it was likely to correspond to cells appearing in the intertidal zone and in shellfish diets, as well as a variety of observed PN cell thresholds to determine what cell count should be used to describe an event that would warrant further action. The skill of these criteria was assessed by determining the fraction of true positives, true negatives, false positives, and false negatives within the model in comparison with observations, as well as a variety of derived model performance metrics. This analysis suggested that for our stakeholders' purposes, the most useful beaching definition is the 30 m isobath and the most useful PN cell threshold for coincident field-based sample PN density estimates is 10,000 PN cells/L. Lastly, the performance of a medium-resolution (1.5 km horizontal resolution) version of the model was compared with that of a high-resolution (0.5 km horizontal resolution) version, the latter currently used in forecasting for the PNW HAB Bulletin project. This analysis includes a direct comparison of the two model resolutions for one overlapping year (2017). These results suggested that a narrower, more realistic beaching definition is most useful in a high-resolution model, while a wider beaching definition is more appropriate in a lower resolution model like the medium-resolution version used in this analysis. Overall, this analysis demonstrated the importance of incorporating stakeholder needs into the statistical approach in order to generate the most effective decision-support information from oceanographic modeling.

Applying finite-time lyapunov exponent to study the tidal dispersion on oil spill trajectory in Burrard Inlet

This study used a combination of Finite-Time Lyapunov Exponent (FTLE) values, residual currents, and tidal excursion lengths to systematically investigate the effects of tidal dispersion on oil spill trajectories in Burrard Inlet, BC, Canada, which is a tidally dominated estuary. The FTLE analysis results showed that tidal type and tidal phase significantly influenced the FTLE fields because the flow structure and the location of saddle points varied as a function of the tidal type and tidal phase. Some transport barriers formed in the Inner Harbour, which blocked the water exchange between the western and eastern parts of the inlet. Moreover, tidal mixing in the wider regions of Burrard Inlet (i.e., the western Outer Harbour) was relatively weak than in the narrower areas (i.e., First Narrows and Second Narrows). The observations from the FTLE analysis agreed well with the residual currents and tidal excursion results. The drifter trajectories were consistent with the Lagrangian coherent structure lines extracted from the FTLE analysis. To verify the tidal dispersion impact on an oil spill trajectory in the inlet, the FTLE fields were compared with a real oil spill that occurred in Burrard Inlet in 2015 (the M/V Marathassa oil spill). The FTLE fields reasonably explained the spilled oil's trajectories from the real event. In addition, a set of stochastic oil spill models were run in this study and found that the FTLE analysis was a reliable tool for oil spill tracking. Overall, the FTLE method would be a valuable addition to practical oil spill response planning.

Arsenic contamination at the Bagnoli Bay seabed (South Italy) via particle tracking numerical modeling: Pollution patterns from stationary climatic forcings

Almost 140 years of industrial exploitation have severely degraded the environment of Bagnoli Coroglio (BC), the westernmost neighborhood of the city of Naples (Italy). In this peculiar area, however, geogenic processes overlap with the impact of human activities, making it difficult to distinguish between anthropogenic and geogenic pollution sources. This is particularly true for Arsenic, the concentration of which in the marine sediments largely exceeds the tolerable level for human health and the background value for local pyroclastics. After several studies have used traditional tools based on multivariate statistics, this article attempts at tackling the problem via numerical modeling, which provides a deeper insight into the physics that governs the pollution process. Therefore, we use a particle tracking model to assess whether arsenic levels in the seabed can be affected by the influx of thermal water from an artificial channel outfalling at the westernmost part of the coast The climatic forcings that drive the marine circulation are simplified to basic "scenarios", in which wind and waves are stationary in strength and direction. Since the simulation time is much less than the contamination timescale, the comparison between numerical results and measurements is essentially qualitative and concerns the shape of contamination contours. It was found the primary forcing that enables seabed pollution is the tidal circulation, which, moreover, acts continuously in time. Quantitative arguments based on regression analysis suggest the discharge of thermal water explains almost a quarter of the observed pollution, which is consistent with previous research based on multivariate statistics.

Organotypic whole hemisphere brain slice models to study the effects of donor age and oxygen-glucose-deprivation on the extracellular properties of cortical and striatal tissue

BACKGROUND

The brain extracellular environment is involved in many critical processes associated with neurodevelopment, neural function, and repair following injury. Organization of the extracellular matrix and properties of the extracellular space vary throughout development and across different brain regions, motivating the need for platforms that provide access to multiple brain regions at different stages of development. We demonstrate the utility of organotypic whole hemisphere brain slices as a platform to probe regional and developmental changes in the brain extracellular environment. We also leverage whole hemisphere brain slices to characterize the impact of cerebral ischemia on different regions of brain tissue.

RESULTS

Whole hemisphere brain slices taken from postnatal (P) day 10 and P17 rats retained viable, metabolically active cells through 14 days in vitro (DIV). Oxygen-glucose-deprivation (OGD), used to model a cerebral ischemic event in vivo, resulted in reduced slice metabolic activity and elevated cell death, regardless of slice age. Slices from P10 and P17 brains showed an oligodendrocyte and microglia-driven proliferative response after OGD exposure, higher than the proliferative response seen in DIV-matched normal control slices. Multiple particle tracking in oxygen-glucose-deprived brain slices revealed that oxygen-glucose-deprivation impacts the extracellular environment of brain tissue differently depending on brain age and brain region. In most instances, the extracellular space was most difficult to navigate immediately following insult, then gradually provided less hindrance to extracellular nanoparticle diffusion as time progressed. However, changes in diffusion were not universal across all brain regions and ages.

CONCLUSIONS

We demonstrate whole hemisphere brain slices from P10 and P17 rats can be cultured up to two weeks in vitro. These brain slices provide a viable platform for studying both normal physiological processes and injury associated mechanisms with control over brain age and region. Ex vivo OGD impacted cortical and striatal brain tissue differently, aligning with preexisting data generated in in vivo models. These data motivate the need to account for both brain region and age when investigating mechanisms of injury and designing potential therapies for cerebral ischemia.

How does Three Gorges Dam regulate heavy metal footprints in the largest freshwater lake of China

Herein, a two-dimensional (2-D) vertically-averaged hydrodynamic model was applied to study the heavy metal particle footprints pre- and post-Three Gorges Dam (TGD) in Poyang Lake. Two defined indexes-Reserve Impact Index (σ_RII) and Species Impact Index (η_SII) were applied to assess the potential impact of the copper footprint on nature reserves and sensitive species quantitatively. The results demonstrated that the movement speed, distribution, and trajectory of copper particle footprints differed enormously pre- and post-TGD. By contrast, the post-TGD footprints were more complex because of the dam-induced variations in hydrology and meteorology. TGD had both pros and cons for the copper footprint on the reserves based on the results of σ_RII. It had changed the way for the transport of heavy metals and altered the patterns of exposure risk in the reserves. Sustainable management of Poyang Lake could be achieved by optimizing daily monitoring works. The η_SII for Finless Porpoises do not differ significantly between scenarios, but the η_SII for Siberian White Cranes increased by 0.92 and 0.83 for the two periods pre- and post-TGD, respectively. Heavy metals in food sources and the excreta of Siberian White Cranes could be of great concern in future studies. This study provides a theoretical basis for the in-depth study of the TGD-induced impact on Poyang Lake and provides a reference for the long-term treatment of Poyang Lake and the protection of key species.

Roughness induced rotational slowdown near the colloidal glass transition

HYPOTHESIS

In concentrated suspensions, the dynamics of colloids are strongly influenced by the shape and topographical surface characteristics of the particles. As the particles get into close proximity, surface roughness alters the translational and rotational Brownian motions in different ways. Eventually, the rotations will get frustrated due to geometric hindrance from interacting asperities.

EXPERIMENTS

We use model raspberry-like colloids to study the effect of roughness on the translational and rotational dynamics. Using Confocal Scanning Laser Microscopy and particle tracking, we simultaneously resolve the two types of Brownian motion and obtain the corresponding Mean Squared Displacements for varying concentrations up to the maximum packing fraction.

FINDINGS

Roughness not only lowers the concentration of the translational colloidal glass transition, but also generates a broad concentration range in which the rotational Brownian motion changes signature from high-amplitude diffusive to low-amplitude rattling. This hitherto not reported second glass transition for rough spherical colloids emerges when the particle intersurface distance becomes comparable to the roughness length scale. Our work provides a unifying understanding of the surface characteristics' effect on the rotational dynamics during glass formation and provides a microscopic foundation for many roughness-related macroscale phenomena in nature and technology.

Measurement of the amplitude and phase of the electrophoretic and electroosmotic mobility based on fast single-particle tracking

The electrophoretic mobility of micron-scale particles is of crucial importance in applications related to pharmacy, electronic ink displays, printing, and food technology as well as in fundamental studies in these fields. Particle mobility measurements are often limited in accuracy because they are based on ensemble averages and because a correction for electroosmosis needs to be made based on a model. Single-particle approaches are better suited for examining polydisperse samples, but existing implementations either require multiple measurements to take the effect of electroosmosis into account or are limited in accuracy by short measurement times. In this work, accurate characterization of monodisperse and polydisperse samples is achieved by measuring the electrophoretic mobility on a particle-to-particle basis while suppressing electroosmosis. Electroosmosis can be suppressed by measuring in the middle of a microchannel while applying an AC voltage with a sufficiently high frequency. An accurate measurement of the electrophoretic mobility is obtained by analyzing the oscillating particle motion for 1.5 s per particle with a high-speed camera measuring at 850 Hz , synchronized to the applied electric field. Attention is paid to take into account the effect of the rolling shutter and the non-uniform sampling in order to obtain the accurate amplitude and phase of the electrophoretic mobility. The accuracy of method is experimentally verified and compared with a commercial apparatus for polystyrene microspheres in water. The method is further demonstrated on a range of particle materials and particle sizes and for a mixture of positively and negatively charged particles.

Pathways of floating marine debris in Jakarta Bay, Indonesia

Jakarta is the capital of Indonesia with a high population density, which affects the amount of waste generated. The waste that ends up in Jakarta Bay has become an environmental problem. Understanding the pathway of marine debris in the ocean is important to identify the mitigation strategies. Before this study, the pathways and sources of marine debris in Jakarta Bay were unknown. By using virtual floating marine debris particles in a high-resolution ocean model, the fate of marine debris based on the pathways of particles released in Jakarta Bay in both forward and backward tracking experiments was analyzed. It was found that most of the particles from Jakarta Bay flow toward the Indian Ocean in all seasons. They flow off through the Sunda Strait and reach the open Indian Ocean after a few weeks. With regard to the source location, most particles that end up in Jakarta Bay come from the north of Java Island locally and from the Gulf of Thailand, Sumatra, and Kalimantan coasts. The particles do not appear to vary significantly across all seasons and identifying the pathway of marine debris might be useful in pollution reduction.

Data fusion and smoothing for probabilistic tracking of viral structures in fluorescence microscopy images

Automatic tracking of viral structures displayed as small spots in fluorescence microscopy images is an important task to determine quantitative information about cellular processes. We introduce a novel probabilistic approach for tracking multiple particles based on multi-sensor data fusion and Bayesian smoothing methods. The approach exploits multiple measurements as in a particle filter, both detection-based measurements and prediction-based measurements from a Kalman filter using probabilistic data association with elliptical sampling. Compared to previous probabilistic tracking methods, our approach exploits separate uncertainties for the detection-based and prediction-based measurements, and integrates them by a sequential multi-sensor data fusion method. In addition, information from both past and future time points is taken into account by a Bayesian smoothing method in conjunction with the covariance intersection algorithm for data fusion. Also, motion information based on displacements is used to improve correspondence finding. Our approach has been evaluated on data of the Particle Tracking Challenge and yielded state-of-the-art results or outperformed previous approaches. We also applied our approach to challenging time-lapse fluorescence microscopy data of human immunodeficiency virus type 1 and hepatitis C virus proteins acquired with different types of microscopes and spatial-temporal resolutions. It turned out, that our approach outperforms existing methods.

Modelling the distribution of microplastics released by wastewater treatment plants in Ria de Vigo (NW Iberian Peninsula)

The accumulation of plastic waste in estuaries is growing due to the increase in their use in daily life and their inadequate treatment on wastewater plants (WWTPs). Hydrodynamic and particle-tracking models were validated and used to improve the knowledge about the distribution and concentration of microplastics released by WWTPs in the Ria de Vigo. Results showed that the Vigo WWTP is the main driver of microplastics to the Ria de Vigo. Besides, 21% of the released microplastics reach the adjacent ocean, 24% remain anchored around the Cies Islands, and a negligible percentage reaches the upper estuary when the emission occurs under ebb on spring tide conditions. A negligible number of released microplastics is exported to the nearby ocean when the emission occurs under neap tide conditions. This research can provide a useful tool to support the identification of monitoring processes and debris removal.

Pollutant transport and residence time of a shallow and narrow coastal lagoon estimated using a numerical model

Setiu Wetland is rapidly developing into an aquaculture and agriculture hub, causing concern about its water quality condition. To address this issue, it is imperative to acquire knowledge of the spatial and temporal distributions of pollutants. Consequently, this study applied combinations of hydrodynamic and particle tracking models to identify the transport behaviour of pollutants and calculate the residence time in Setiu Lagoon. The particle tracking results indicated that the residence time in Setiu Lagoon was highly influenced by the release location, where particles released closer to the river mouth exhibited shorter residence times than those released further upstream. Despite this fact, the pulse of river discharges successfully reduced the residence time in the order of two to twelve times shorter. Under different tidal phases, the residence time during the neap tide was longer regardless of heavy rainfalls, implying the domination of tidal flow in the water renewal within the lagoon.

Cauliflower mosaic virus P6 inclusion body formation: A dynamic and intricate process

During an infection, Cauliflower mosaic virus (CaMV) forms inclusion bodies (IBs) mainly composed of viral protein P6, where viral activities occur. Because viral processes occur in IBs, understanding the mechanisms by which they are formed is crucial. FL-P6 expressed in N. benthamiana leaves formed IBs of a variety of shapes and sizes. Small IBs were dynamic, undergoing fusion/dissociation events. Co-expression of actin-binding polypeptides with FL-P6 altered IB size distribution and inhibited movement. This suggests that IB movement is required for fusion and growth. A P6 deletion mutant was discovered that formed a single large IB per cell, which suggests it exhibited altered fusion/dissociation dynamics. Myosin-inhibiting drugs did not affect small IB movement, while those inhibiting actin polymerization did. Large IBs colocalized with components of the aggresome pathway, while small ones generally did not. This suggests a possible involvement of the aggresome pathway in large IB formation.

How litter moves along a macro tidal mid-latitude coast exposed to a coastal current

A simplified particle-tracking model with an idealised coastline was used to investigate how the interaction between variable winds and water level (VaWWL) operates spatially along a coast. The model included a constant along-coast current, horizontal diffusion, onshore/offshore wind drift, beach/cliff combinations and point/distributed litter sources. The default model reproduced basic properties of observed beach litter loadings (zero net accumulation, negatively skewed loading distributions) and the observed spatial pattern along the Scottish east coast, with average loadings increasing in the coastal current direction. The VaWWL effect moved the along-coast flux of floating litter offshore as debeaching events occur during offshore winds. Varying diffusion, coastal current speed, windage, beach/cliff combinations and different foreshore boundary conditions were investigated. Reconciling model predictions with previous estimates of plastic inflow suggested sinking rates of up to 90% soon after first entry into the sea. The VaWWL effect offers a realistic boundary condition for particle-tracking models.

Understanding the effect of effective metal surface area of flow diverter stent's on the patient-specific intracranial aneurysm numerical model using Lagrangian coherent structures

The effective metal surface area (EMSA) of flow diversions plays an essential role in the occlusion mechanism inside the aneurysm since the value of EMSA determines the amount of blood flow into the aneurysm sac. In the present study, three different models of a flow diverter stent, namely FRED 4017, FRED 4038, and FRED 4539, were virtually placed at the aneurysm neck of a 52-years-old female patient to identify the effect of EMSA on stagnation region formation inside the aneurysm sac. Lagrangian coherent structures (LCSs), hyperbolic time, and particle tracking analysis were employed to the velocity vectors obtained from computational fluid dynamics (CFD). It is noticed that use of FRED 4017 stent with 0.42 EMSA value caused nearly 40% of the weightless blood flow particles (more than FRED 4038 and FRED 4539) to stay inside the aneurysm while only 0.35% of the blood flow was remaining inside the aneurysm sac when no stent was placed into the aneurysm site. Furthermore, hyperbolic time computations illustrated the formation of stagnation fluid flow zones that can be associated with the residence time of the blood flow particles. Lastly, the results of hyperbolic time analysis are in good agreement with digital subtraction angiography (DSA) images taken in the clinic a few minutes after a FRED 4017 implantation.

Methods for characterizing the material properties of biomolecular condensates

Biomolecular condensates are membrane-less sub-cellular compartments that perform a plethora of important functions in signaling and storage. The material properties of biomolecular condensates such as viscosity, surface tension, viscoelasticity, and macromolecular diffusion play important roles in regulating their biological functions. Aberrations in these properties have been implicated in various neurodegenerative disorders and certain types of cancer. Unraveling the molecular driving forces that control the fluid structure and dynamics of biomolecular condensates across different length- and time-scales necessitates the application of innovative biophysical methodologies. In this chapter, we discuss major experimental techniques that are widely used to study the material states and dynamics of biomolecular condensates as well as their practical and conceptual limitations. We end this chapter with a discussion on more advanced tools that are currently emerging to address the complex fluid dynamics of these condensates.

Live-Cell Imaging and Analysis of Nuclear Body Mobility

The cell nucleus contains different domains and nuclear bodies, whose position relative to each other inside the nucleus can vary depending on the physiological state of the cell. Changes in the three-dimensional organization are associated with the mobility of individual components of the nucleus. In this chapter, we present a protocol for live-cell imaging and analysis of nuclear body mobility. Unlike other similar protocols, our image analysis pipeline includes non-rigid compensation for global motion of the nucleus before particle tracking and trajectory analysis, leading to precise detection of intranuclear movements. The protocol described can be easily adapted to work with most cell lines and nuclear bodies.

Imaging the delivery and behavior of cellulose synthases in Arabidopsis thaliana using confocal microscopy

Confocal microscopy has been a key tool for characterizing the behavior of cellulose synthase (CESA) proteins as they extrude cellulose into the apoplast to help construct plant cell walls. While other microscopy techniques like electron microscopy can achieve higher resolution images of CESAs, confocal microscopy is still the most accessible way to image these proteins in living plants as they are trafficked to and from the cell surface and move through the plasma membrane. Here, we describe a method for imaging fluorescently tagged CESA proteins in seedlings of Arabidopsis thaliana using spinning disk confocal microscopy, with a focus on quantifying the speed, density, and delivery rate of CESA particles. Many of these techniques can be adapted and applied to imaging other membrane-localized proteins and other plant species. In addition to imaging techniques, we describe several options for image analysis that can be optimized for different datasets.

Tracking organelle movements in plant cells

Cytoplasmic streaming is characterized by the rapid movement of organelles and other cellular components throughout the cell. In plants, the process depends on actin filaments and myosin motor proteins and plays an important role in cell growth. Detailed quantification of organelle movements can yield important insights into the dynamics of intracellular organization and its functional aspects. This quantification is hindered by a lack of knowledge of the different types of movements and generic tracking algorithms that yield erroneous output. This protocol provides a step-by-step guide to the detection and measurement of organelle motility as well as a description of additional analysis steps distinguishing undirected, diffusion-like movements from directional movements along the actin cytoskeleton.

Massive pollutants released to Galveston Bay during Hurricane Harvey: Understanding their retention and pathway using Lagrangian numerical simulations

Increasing frequency of extreme precipitation events under the future warming climate makes the storm-related pollutant release more and more threatening to coastal ecosystems. Hurricane Harvey, a 1000-year extreme precipitation event, caused massive pollutant release from the Houston metropolitan area to the adjacent Galveston Bay. 0.57 × 10⁶ tons of raw sewage and 22,000 barrels of oil, refined fuels and chemicals were reportly released during Harvey, which would likely deteriorate the water quality and damage the coastal ecosystem. Using a Lagrangian particle-tracking method coupled with a validated 3D hydrodynamic model, we examined the retention, pathway, and fate of the released pollutants. A new timescale, local exposure time (LET), is introduced to quantitatively evaluate the spatially varying susceptibility inside the bay and over the shelf, with a larger LET indicating the region is more susceptible to the released pollutants. We found LET inside the bay is at least one order of magnitude larger for post-storm release than storm release due to a quick recovery in the system's flushing. More than 90% of pollutants released during the storm exited the bay within two days, while those released after the storm could stay inside the bay for up to three months. This implies that post-storm release is potentially more damaging to water quality and ecosystem health. Our results suggest that not only the amount of total pollutant load but also the release timing should be considered when assessing a storm's environmental and ecological influence, because there could be large amounts of pollutants steadily and slowly discharged after storm through groundwater, sewage systems, and reservoirs.

FM-Track: A fiducial marker tracking software for studying cell mechanics in a three-dimensional environment

Tracking the deformation of fiducial markers in the vicinity of living cells embedded in compliant synthetic or biological gels is a powerful means to study cell mechanics and mechanobiology in three-dimensional environments. However, current approaches to track and quantify three-dimensional (3D) fiducial marker displacements remain ad-hoc, can be difficult to implement, and may not produce reliable results. Herein, we present a compact software package entitled "FM-Track," written in the popular Python language, to facilitate feature-based particle tracking tailored for 3D cell micromechanical environment studies. FM-Track contains functions for pre-processing images, running fiducial marker tracking, and post-processing and visualization. FM-Track can thus aid the study of cellular mechanics and mechanobiology by providing an extensible software platform to more reliably extract complex local 3D cell contractile information in transparent compliant gel systems.

Shape anisotropic colloidal particle fabrication using 2-photon polymerization

HYPOTHESIS

Our ability to dictate the colloid geometry is intimately related to self-assembly. The synthesis of anisotropic colloidal particles is currently dominated by wet chemistry and lithographic techniques. The wet chemical synthesis offers limited particle geometries at bulk quantities. Lithographic techniques, on the other hand, provide precise control over the particle shape, although at lower yields. In this respect, two-photon polymerization (2PP)¹ has attracted growing attention due to its ability to automatically fabricate complex micro/nano structures with high resolution.

EXPERIMENTS

We manufacture precisely designed colloids with sizes ranging from 1 µm to 10 µm with 2PP and optimize the process parameters for each dimension. Moreover, we study the shape dependent Brownian motion of these particles with video microscopy and estimate their diffusion coefficients.

FINDINGS

We observe that increasing the geometrical anisotropy leads to a pronounced deviation from the analytically predicted diffusion coefficient for disks with a given aspect ratio. The deviation is attributed to stronger hydrodynamic coupling with increasing anisotropy. We demonstrate, for the first time, 2PP manufacturing of colloids with tailored geometry. This study opens synthesis of colloidal building blocks to a broader audience with limited access to cleanrooms or wet-chemistry know-how.

Pixel by pixel: real-time observation and quantification of passive flotation speeds of three common equine endoparasite egg types

The efficacy of anthelmintic treatments against populations of endoparasites infecting livestock throughout the world is decreasing. To mitigate this, the use of fecal egg counts is recommended to determine both the necessity, and to ensure the appropriate choice, of anthelmintic treatment. Traditionally, and in order to facilitate easier identification and/or enumeration, samples are analysed after separating eggs from other fecal particulates by exposing them to a solution with a density higher than that of the eggs, but lower than the remaining fecal contents. While many parasite egg flotation protocols exist, little is known about the characteristics of these eggs with respect to their movement through a flotation solution. In this study, we have demonstrated a novel method for the observation and quantification of microscopic (65-100 µm) objects as they experience unassisted flotation. This also represents, to our knowledge for the first time, that the flotation of parasite eggs has been observed and their movement characteristics quantified as they float through solution. Particle tracking and video analysis software were utilised to automatically detect and track the movement of individual eggs as they floated. Three 30 s videos and one 2 min video of each egg type were analysed. If the first 30 s of video were discounted, the differences in mean flotation speed among all videos was statistically significant between egg types (P = 0.0004). Strongyle type eggs (n = 201) moved the fastest with a mean 51.08 µm/s (95% confidence interval: 47.54-54.62). This was followed by Parascaris spp. (n = 131) and Anoplocephala perfoliata eggs (n = 322), with mean speeds of 44.43 µm/s (95% confidence interval: 39.47-49.4) and 31.11 µm/s (95% confidence interval: 29.6-32.61), respectively. This method for evaluating the mean speed of passive flotation may represent a first step towards further optimizing fecal egg flotation and be of interest to parasitologists and veterinary practitioners.

Mixed impact of torsion on LV hemodynamics: A CFD study based on the Chimera technique

Image-based patient-specific Computational Fluid Dynamics (CFD) models of the Left Ventricle (LV) can be used to quantify hemodynamics-based biomarkers that can support the clinicians in the early diagnosis, follow-up and treatment planning of patients, beyond the capabilities of the current imaging modalities. We propose a workflow to build patient-specific CFD models of the LV with moving boundaries based on the Chimera technique to overcome the convergence issues previously encountered by means of the Arbitrarian Lagrangian Eulerian approach. The workflow was tested while investigating whether the torsional motion has an impact on LV fluid dynamics. Starting from 3D cine MRI scans of a healthy volunteer, six cardiac cycles were simulated in three CFD LV models: with no, physiological, and exaggerated torsion. The Chimera technique was robust in handling the impulsive motion of the LV endocardium, allowing to notice cycle-to-cycle variations in every simulated case. Torsion affected slightly velocity, vorticity, WSS. It did not affect energy loss and induced a double-sided effect in terms of residence time: the particles ejected in one beat decreased, whereas the motility of the particles remaining in the LV was affected only in the exaggerated torsion case, indicating that implementation of torsion can be discarded in case of physiological levels. Nonetheless, caution is warranted when interpreting these results given the absence of the mitral valve, the papillary muscles, and the trabeculae. The effects of the mitral valve will be evaluated within an Fluid Structure Interaction simulation framework as further development of the current model.

Antibody-Mediated Immobilization of Virions in Mucus

Antibodies have been shown to hinder the movement of herpes simplex virus virions in cervicovaginal mucus, as well as other viruses in other mucus secretions. However, it has not been possible to directly observe the mechanisms underlying this phenomenon, so the nature of virion-antibody-mucin interactions remain poorly understood. In this work, we analyzed thousands of virion traces from single particle tracking experiments to explicate how antibodies must cooperate to immobilize virions for relatively long time periods. First, using a clustering analysis, we observed a clear separation between two classes of virion behavior: freely diffusing and immobilized. While the proportion of freely diffusing virions decreased with antibody concentration, the magnitude of their diffusivity did not, implying an all-or-nothing dichotomy in the pathwise effect of the antibodies. Proceeding under the assumption that all binding events are reversible, we used a novel switch-point detection method to conclude that there are very few, if any, state switches on the experimental timescale of 20 s. To understand this slow state switching, we analyzed a recently proposed continuous-time Markov chain model for binding kinetics and virion movement. Model analysis implied that virion immobilization requires cooperation by multiple antibodies that are simultaneously bound to the virion and mucin matrix and that there is an entanglement phenomenon that accelerates antibody-mucin binding when a virion is immobilized. In addition to developing a widely applicable framework for analyzing multistate particle behavior, this work substantially enhances our mechanistic understanding of how antibodies can reinforce a mucus barrier against passive invasive species.

Identification of groundwater pollution sources in a landfill site using artificial sweeteners, multivariate analysis and transport modeling

In this study, sources of groundwater pollution in a landfill site were identified, using artificial sweeteners as chemical tracers, multivariate statistical analysis and a quantitative analysis of the groundwater flow system through particle tracking and transport modeling. The study area, located in northern Italy, hosts an older unlined landfill and a newer lined municipal solid waste landfill placed downstream of the former. Groundwater, surface water, treated wastewater, and leachate samples were collected in March 2017 for analysis of the artificial sweeteners saccharin, cyclamate, acesulfame and sucralose together with major cations and anions, inorganic nitrogen compounds, total phosphorus, COD and some further parameters. The interpretation of the results suggests that two main leachate leaks/spills are affecting the study area. The first one concerns leachate probably spilling out of the leachate collection system serving the younger lined landfill, the other one involves leachate from the older unlined landfill that also seems to affect an area downstream of the lined landfill. Direct leachate leaks from the lined landfill seem unlikely, although they cannot be definitively excluded. This work underlines the importance of a multi-methods approach, which integrates here chemical tracers, multivariate analysis and transport modeling, for assessing groundwater pollution sources generated from complex landfill sites, where multiple and different sources may exist. In particular, this work highlights how artificial sweeteners can be used for tracing leachate plumes from landfills. The methodology applied in this study can have a broad applicability also in other polluted landfill sites worldwide.

Hydrodynamic Modeling Coupled with Long-term Field Data Provide Evidence for Suppression of Phytoplankton by Invasive Clams and Freshwater Exports in the San Francisco Estuary

The San Francisco Estuary (California, USA) had abundant pelagic fish in the late 1960s, but has few pelagic fish today. A primary cause for this decline in fish is thought to be a trophic cascade, triggered by declining phytoplankton. Here, we describe the changes in pelagic community structure of the San Francisco Estuary. Then, we examine whether changes in hydrodynamics due to freshwater exports, which increased exponentially beginning in 1967, in addition to the 1986 invasion by the clam Potamocorbula amurensis, explain the phytoplankton loss. Hydrodynamic variables were reconstructed back to 1956 using statistical models fit to, and cross-validated against, output from a hydrodynamic model. Then, we regressed mean summer/fall chlorophyll a-the season with the largest phytoplankton decline-against the reconstructed hydrodynamic variables and the presence/absence of P. amurensis for 1969-2014. The regression model, which explained 78% of the interannual variation in chlorophyll a, was then used to quantify the influence of P. amurensis and exports on chlorophyll a. Based on monitoring data, chlorophyll a declined 22-fold from 1969-2014, zooplankton declined 32-fold from 1972-2014, and pelagic fish declined 92-fold from 1968-2014. Averaged over 1990-2014, the chlorophyll a model ascribed an 88% decline in chlorophyll a to P. amurensis, a 74% decline to exports (at minimum), and a 97% decline to the combined influence of P. amurensis and exports (at minimum). Thus, the decline in pelagic productivity in the San Francisco Estuary has occurred largely due to the combined impacts of the P. amurensis invasion and increased freshwater exports.

Robust antigen-specific tuning of the nanoscale barrier properties of biogels using matrix-associating IgG and IgM antibodies

Biological hydrogels (biogels) are selective barriers that restrict passage of harmful substances yet allow the rapid movement of nutrients and select cells. Current methods to modulate the barrier properties of biogels typically involve bulk changes in order to restrict diffusion by either steric hindrance or direct high-affinity interactions with microstructural constituents. Here, we introduce a third mechanism, based on antibody-based third party anchors that bind specific foreign species but form only weak and transient bonds with biogel constituents. The weak affinity to biogel constituents allows antibody anchors to quickly accumulate on the surface of specific foreign species and facilitates immobilization via multiple crosslinks with the biogel matrix. Using the basement membrane Matrigel® and a mixture of laminin/entactin, we demonstrate that antigen-specific, but not control, IgG and IgM efficiently immobilize a variety of individual nanoparticles. The addition of Salmonella typhimurium-binding IgG to biogel markedly reduced the invasion of these highly motile bacteria. These results underscore a generalized strategy through which the barrier properties of biogels can be readily tuned with molecular specificity against a diverse array of particulates. STATEMENT OF SIGNIFICANCE: Biological hydrogels (biogels) are essential in living systems to control the movement of cells and unwanted substances. However, current methods to control transport within biogels rely on altering the microstructure of the biogel matrix at a gross level, either by reducing the pore size to restrict passage through steric hindrance or by chemically modifying the matrix itself. Both methods are either nonspecific or not scalable. Here, we offer a new approach, based on weakly adhesive third-party molecular anchors, that allow for a variety of foreign entities to be trapped within a biogel simultaneously with exceptional potency and molecular specificity, without perturbing the bulk properties of the biogel. This strategy greatly increases our ability to control the properties of biogels at the nanoscale, including those used for wound healing or tissue engineering applications.

Assessment of vulnerability and control measures to protect the Salbarua ecosystem from hypothetical spill sites

Population pressure, urbanization, and industrial developments, among other factors, have resulted in severe degradation of environmental resources such as wetlands. Thus, a groundwater model (MODFLOW) was integrated with a particle tracking MODPATH model to simulate the hydrodynamic flow head field and to analyze the vulnerability of the Salburua ecosystem and propose control measures to protect the riparian area. The simulations show that pathways of particle tracking originating at potential contaminant sources will tend to migrate downwards towards the sensitive ecosystem, which suggests that the quality of the hydrological ecosystem is likely to deteriorate in the future. Variation in exit points of particles indicates that the time-related capture areas are affected by changes of the hydraulic gradients. Two control measures of potential sources of pollutants in the vicinity of the Salbarua ecosystem were analyzed. The study results suggest that the travel time-related capture zone with a funnel-and-gate system is much smaller than without the control alternative, which indicates that the gate configuration has an effect on capture zone size and shape and on the residence time with a better attenuation performance. It is also shown that a leakage-proof barrier is less effective for point-source containment, assuming that hydraulic control performance and cost-efficiency are the criteria for pollution control effectiveness. Instead, a program of monitoring wells would effectively characterize water quality in the aquifer and provide a decision support system. This approach may be used in helping water managers to develop more physically based and quantitative protection strategies.

Microrheology, advances in methods and insights

Microrheology is an emerging technique that probes mechanical response of soft material at micro-scale. Generally, microrheology technique can be divided into active and passive versions. During last two decades, extensive efforts have been paid to improve both the experiment techniques and data analysis methods, especially about how to link consequential particle positions into trajectories. We review the recent advances in microrheology, including improvements in labeling, imaging, data acquiring, data processing and data interpretation. Some of the recent insights in soft matter and living systems gained by using this technique are given. Before these, we also give a very brief description of the basic principles of both active and passive microrheology techniques, and some details about optical particle tracking and DWS.

Massively parallel approximate Bayesian computation for estimating nanoparticle diffusion coefficients, sizes and concentrations using confocal laser scanning microscopy

We implement a massively parallel population Monte Carlo approximate Bayesian computation (PMC-ABC) method for estimating diffusion coefficients, sizes and concentrations of diffusing nanoparticles in liquid suspension using confocal laser scanning microscopy and particle tracking. The method is based on the joint probability distribution of diffusion coefficients and the time spent by a particle inside a detection region where particles are tracked. We present freely available central processing unit (CPU) and graphics processing unit (GPU) versions of the analysis software, and we apply the method to characterize mono- and bidisperse samples of fluorescent polystyrene beads.

Automated Analysis of Intracellular Dynamic Processes

The study of intracellular dynamic processes is of fundamental importance for understanding a wide variety of diseases and developing effective drugs and therapies. Advanced fluorescence microscopy imaging systems nowadays allow the recording of virtually any type of process in space and time with super-resolved detail and with high sensitivity and specificity. The large volume and high information content of the resulting image data, and the desire to obtain objective, quantitative descriptions and biophysical models of the processes of interest, require a high level of automation in data analysis. Two key tasks in extracting biologically meaningful information about intracellular dynamics from image data are particle tracking and particle trajectory analysis. Here we present state-of-the-art software tools for these tasks and describe how to use them.

Live Imaging of Influenza Viral Ribonucleoproteins Using Light-Sheet Microscopy

Influenza viruses exhibit a complex life cycle that is still poorly understood. It involves independent replication of each of the eight segments that make up its genome and subsequent coordinated assembly as they egress from the host cell. Fast, time-resolved volumetric live cell imaging offers a powerful tool for understanding the various host mechanisms hijacked by the virus. Here, we describe the methods necessary for generating influenza viruses that carry a fluorescently tagged polymerase complex, infection of biologically relevant cells with these viruses, and finally protocols for live cell imaging and analysis.

Development of groundwater vulnerability zones in a data-scarce eogenetic karst area using Head-Guided Zonation and particle-tracking simulation methods

Delineation of groundwater vulnerability zones based on a valid groundwater model is crucial towards an accurate design of management strategies. However, limited data often restrain the development of a robust groundwater model. This study presents a methodology to develop groundwater vulnerability zones in a data-scarce area. The Head-Guided Zonation (HGZ) method was applied on the recharge area of Oemau Spring in Rote Island, Indonesia, which is under potential risk of contamination from rapid land use changes. In this method the model domain is divided into zones of piecewise constant into which the values of subsurface properties are assigned in the parameterisation step. Using reverse particle-tracking simulation on the calibrated and validated groundwater model, the simulation results (travel time and pathline trajectory) were combined with the potential groundwater contamination risk from human activities (land use type and current practice) to develop three vulnerability zones. The corresponding preventive management strategies were proposed to protect the spring from contamination and to ensure provision of safe and good quality water from the spring.

Wavelet-based tracking of bacteria in unreconstructed off-axis holograms

We propose an automated wavelet-based method of tracking particles in unreconstructed off-axis holograms to provide rough estimates of the presence of motion and particle trajectories in digital holographic microscopy (DHM) time series. The wavelet transform modulus maxima segmentation method is adapted and tailored to extract Airy-like diffraction disks, which represent bacteria, from DHM time series. In this exploratory analysis, the method shows potential for estimating bacterial tracks in low-particle-density time series, based on a preliminary analysis of both living and dead Serratia marcescens, and for rapidly providing a single-bit answer to whether a sample chamber contains living or dead microbes or is empty.

Particle sizing of pharmaceutical aerosols via direct imaging of particle settling velocities

We present a novel method for characterizing in near real-time the aerodynamic particle size distributions from pharmaceutical inhalers. The proposed method is based on direct imaging of airborne particles followed by a particle-by-particle measurement of settling velocities using image analysis and particle tracking algorithms. Due to the simplicity of the principle of operation, this method has the potential of circumventing potential biases of current real-time particle analyzers (e.g. Time of Flight analysis), while offering a cost effective solution. The simple device can also be constructed in laboratory settings from off-the-shelf materials for research purposes. To demonstrate the feasibility and robustness of the measurement technique, we have conducted benchmark experiments whereby aerodynamic particle size distributions are obtained from several commercially-available dry powder inhalers (DPIs). Our measurements yield size distributions (i.e. MMAD and GSD) that are closely in line with those obtained from Time of Flight analysis and cascade impactors suggesting that our imaging-based method may embody an attractive methodology for rapid inhaler testing and characterization. In a final step, we discuss some of the ongoing limitations of the current prototype and conceivable routes for improving the technique.