Particle Tracking Experiments Research Articles

Role of Japan Sea Throughflow in the spatial variability of the long-term sea surface temperature trend

AbstractThe Japan Sea shows a much stronger warming of long-term sea surface temperature (SST) than surrounding oceans. The warming trend possesses a meridionally alternating zonal band pattern, with weak trends along the paths of the Japan Sea Throughflow and strong trends in the remaining interior region. Using idealized models of the Japan Sea Throughflow and atmospheric heating, this study examines the process behind the formation of such spatial patterns in the SST trend. We find that zonal band structures form in a flat rectangular coastline model, and heat budget analysis shows that horizontal heat transport, due to throughflow, reduces the warming effect created by the surface heat flux. A weak SST trend appears around the jet, while a strong SST trend appears elsewhere. Bathymetric effects are also examined using a model with realistic coastline settings. The location of the western boundary current stabilizes, and the coastal branch begins to disconnect from the Japanese coastline toward the north, allowing a more stable SST warming region to form in the southern interior region. Lagrangian particle tracking experiments confirm that a weak (strong) SST trend corresponds to a short (long) residence time, and eddies in the Japan Sea prolong the residence time in interior regions. The model results suggest that the accumulation time of surface heating is essential to the spatial distribution of the long-term SST warming trend.

Transport and retention of sinking microplastics in a well-mixed estuary

Estuaries have been shown to be potential hotspots of microplastic accumulation, but the hydrodynamic conditions and particle properties that control this process need further investigation. We have designed a series of numerical particle-tracking experiments to examine the sensitivity of retention in estuaries to particle size, particle density and varying tides and freshwater flow. At the end of the simulation, over 90 % of sinking particles are retained in the estuary, and the retention rate is further increased by high river runoff. In contrast, increased river discharge increases the number of marginally-buoyant (i.e. density close to estuarine water) particles that escape the estuary. Larger particle size tends to limit the downstream transport of sinking particles but can facilitate the transport of marginally-buoyant particles. Tidal asymmetry, vertical turbulent mixing and the vertical structure of the subtidal circulation are proposed as the underlying mechanisms controlling the fate of particles.

An open-source, high-resolution, automated fluorescence microscope

Fluorescence microscopy is a fundamental tool in the life sciences, but the availability of sophisticated equipment required to yield high-quality, quantitative data is a major bottleneck in data production in many laboratories worldwide. This problem has long been recognized and the abundancy of low-cost electronics and the simplification of fabrication through 3D-printing have led to the emergence of open-source scientific hardware as a research field. Cost effective fluorescence microscopes can be assembled from cheaply mass-produced components, but lag behind commercial solutions in image quality. On the other hand, blueprints of sophisticated microscopes such as light-sheet or super-resolution systems, custom-assembled from high quality parts, are available, but require a high level of expertise from the user. Here, we combine the UC2 microscopy toolbox with high-quality components and integrated electronics and software to assemble an automated high-resolution fluorescence microscope. Using this microscope, we demonstrate high resolution fluorescence imaging for fixed and live samples. When operated inside an incubator, long-term live-cell imaging over several days was possible. Our microscope reaches single molecule sensitivity, and we performed single particle tracking and SMLM super-resolution microscopy experiments in cells. Our setup costs a fraction of its commercially available counterparts but still provides a maximum of capabilities and image quality. We thus provide a proof of concept that high quality scientific data can be generated by lay users with a low-budget system and open-source software. Our system can be used for routine imaging in laboratories that do not have the means to acquire commercial systems and through its affordability can serve as teaching material to students.

An open-source, high-resolution, automated fluorescence microscope.

Fluorescence microscopy is a fundamental tool in the life sciences, but the availability of sophisticated equipment required to yield high-quality, quantitative data is a major bottleneck in data production in many laboratories worldwide. This problem has long been recognized and the abundancy of low-cost electronics and the simplification of fabrication through 3D-printing have led to the emergence of open-source scientific hardware as a research field. Cost effective fluorescence microscopes can be assembled from cheaply mass-produced components, but lag behind commercial solutions in image quality. On the other hand, blueprints of sophisticated microscopes such as light-sheet or super-resolution systems, custom-assembled from high quality parts, are available, but require a high level of expertise from the user. Here, we combine the UC2 microscopy toolbox with high-quality components and integrated electronics and software to assemble an automated high-resolution fluorescence microscope. Using this microscope, we demonstrate high resolution fluorescence imaging for fixed and live samples. When operated inside an incubator, long-term live-cell imaging over several days was possible. Our microscope reaches single molecule sensitivity, and we performed single particle tracking and SMLM super-resolution microscopy experiments in cells. Our setup costs a fraction of its commercially available counterparts but still provides a maximum of capabilities and image quality. We thus provide a proof of concept that high quality scientific data can be generated by lay users with a low-budget system and open-source software. Our system can be used for routine imaging in laboratories that do not have the means to acquire commercial systems and through its affordability can serve as teaching material to students.

Deep Learning-Assisted Automated Multidimensional Single Particle Tracking in Living Cells.

The translational and rotational dynamics of anisotropic optical nanoprobes revealed in single particle tracking (SPT) experiments offer molecular-level information about cellular activities. Here, we report an automated high-speed multidimensional SPT system integrated with a deep learning algorithm for tracking the 3D orientation of anisotropic gold nanoparticle probes in living cells with high localization precision (<10 nm) and temporal resolution (0.9 ms), overcoming the limitations of rotational tracking under low signal-to-noise ratio (S/N) conditions. This method can resolve the azimuth (0°-360°) and polar angles (0°-90°) with errors of less than 2° on the experimental and simulated data under S/N of ∼4. Even when the S/N approaches the limit of 1, this method still maintains better robustness and noise resistance than the conventional pattern matching methods. The usefulness of this multidimensional SPT system has been demonstrated with a study of the motions of cargos transported along the microtubules within living cells.

Altered Weddell Sea warm- and dense-water pathways in response to 21st-century climate change

Abstract. The transport of water masses with ocean circulation is a key component of the global climate system. In this context, the Filchner Trough in the southern Weddell Sea is critical, as it is a hotspot for the cross-shelf-break exchange of Dense Shelf Water and Warm Deep Water. We present results from Lagrangian particle tracking experiments in a global-ocean–sea-ice model (FESOM-1.4) which includes ice-shelf cavities and has eddy-permitting resolution on the southern Weddell Sea continental shelf. With backward and forward experiments, we assess changes between a present-day and a future (SSP5-8.5) time slice in the origin of waters reaching the Filchner Ice Shelf front and the fate of waters leaving it. We show that particles reaching the ice-shelf front from the open ocean originate from 173 % greater depths by 2100 (median; 776 m as compared to 284 m for the present day), while waters leaving the cavity towards the open ocean end up at 35 % shallower depths (550 m as compared to 850 m for the present day). Pathways of water leaving the continental shelf increasingly occur in the upper ocean, while the on-shelf flow of waters that might reach the ice-shelf cavity, i.e., at deeper layers, becomes more important by 2100. Simultaneously, median transit times between the Filchner Ice Shelf front and the continental shelf break decrease (increase) by 6 (9.5) months in the backward (forward) experiments. In conclusion, our study demonstrates the sensitivity of regional circulation patterns in the southern Weddell Sea to ongoing climate change, with direct implications for ice-shelf basal melt rates and local ecosystems.

Advanced System-on-Chip Field-Programmable-Gate-Array-Powered Data Acquisition System for Pixel Detectors.

Particle detector systems require data acquisition systems (DAQs) as their back-end. This paper presents a new edge-computing DAQ that is capable of handling multiple pixel detectors simultaneously and was designed for particle-tracking experiments. The system was designed for the ROC4SENS readout chip, but its control logic can be adapted for other pixel detectors. The DAQ was based on a system-on-chip FPGA (SoC FPGA), which includes an embedded microprocessor running a fully functional Linux system. An application using a client-server architecture was developed to facilitate remote control and data visualization. The comprehensive DAQ is very compact, thus reducing the typical hardware load in particle tracking experiments, especially during the obligatory characterization of particle telescopes.

Flowpattern in hydrocyclones, numerical simulations with experimental verification

This paper reports a detailed study of the flow in cyclone separators, with the use of most up to date computational fluid dynamics simulations, which are validated with positron emission particle tracking (PEPT) experiments tracing the movement of particles through the cyclone. The parameters varied were the viscosity of the carrier liquid, the flowrate and, in the numerical simulations, the inlet configurations of the cyclone, namely one and two inlets and, with the two inlets, a) both at right angles to the cyclone axis and b) angled downwards. The study reveals features of the flow, which have not been seen till now, but are necessary for the understanding and modelling of the separation and purification efficiency of cyclones. The results of the simulations and the close agreement with experiment are a testament to the reliability and accuracy of large eddy simulation (LES), even for flow features as difficult to simulate as the confined strongly swirling flows in cyclone separators. The results show that a contiguous, smooth surface of zero axial velocity does exist and has approximately the shape that has been assumed by modellers. The significant effects of fluid viscosity, underflow and modifications to the inlet are also shown.

New diagnostic sea surface current fields to trace floating algae in the Yellow Sea

The new velocity fields based on the Generalized Ekman (GE) theory to trace floating algae were derived and verified by drifter observations and compared to reanalysis datasets in the Yellow Sea (YS). Two velocity fields using diagnostic approaches and two velocity fields from reanalysis datasets were examined. The results revealed that the diagnostic velocity fields had comparable accuracy to the reanalysis datasets, even locally better. Then, we applied each velocity field to trace green algae, Ulva prolifera, in July 2011 and brown algae, Sargassum horneri, in May 2017 using particle tracking experiments. In addition, drifter trajectories were simulated, and error accumulation speed was estimated for each velocity field. Simulation results using the diagnostic velocity fields consistently showed better agreement with satellite images and in situ observations than those using reanalysis datasets, demonstrating that the diagnostic velocity could be a superior tool for simulating surface-floating substances and organisms. The approach to derive diagnostic velocity fields can be easily applied instead of relying on heavy computing numerical models.

Asymmetric Drifter Trajectories in an Anticyclonic Mesoscale Eddy

The influences of sea surface wind on the oceanic mesoscale eddy are complex. By integrating our self-developed surface drifters with satellite observations, we examined the influence of sea surface wind on the distribution of water masses and biomass within the interior of an anticyclonic eddy. Ten drifters were deployed in the northern South China Sea in the spring of 2021. Eventually, six were trapped in an anticyclonic mesoscale eddy for an extended period. Interestingly, the drifters’ trajectories were not symmetric around the eddy center, displaying a significant offset of the distance from the wind turns to the southerly wind. Particle tracking experiments demonstrated that this departure could mainly be attributed to wind-driven ageostrophic currents. This is due to the strength of wind-driven ageostrophic currents being more comparable to geostrophic currents when accompanied by a deflection between the directions of the wind-driven current and the eddy’s translation. The drifters’ derived data indicated that sub-mesoscale ageostrophic currents within the eddy contributed to this asymmetric trajectory, with Ekman and non-Ekman components playing a role. Furthermore, the evolution of ocean color data provided corroborating evidence of these dynamic processes, highlighting the importance of ageostrophic processes within mesoscale eddies.

An improved position reconstruction method for radioactive particle tracking

This work introduces a novel reconstruction method exploiting the inverse of Finite Element Method (FEM) to reconstruct positions from ray tracing experimental measurement such as those obtained by radioactive particle tracking. FEM based Position Reconstruction (FEM-PR) relies on shape function evaluation within simplex elements (i.a tetrahedron) for position reconstruction using a mean-square problem, which has proven to be robust, accurate, and fast. Tracer positions are reconstructed under the condition that least-squares compatibility is maintained between experimental counts and interpolated values within inverse elements. This approach is implemented in a module within the open-source software, Lethe-RPT, enabling user to carry out radioactive particle tracking (RPT) experiments from calibration to tracer position reconstruction. The test benchmark and experimental setup are described. For the same test cases, the reconstruction error is investigated using an increasing number of inverse elements and Monte Carlo (MC) iterations. The accuracy and robustness of FEM-PR concerning the inevitable measurement errors due to calibration, measurement systems, and the quantized nature of γ-rays is demonstrated. This approach provides a new view for immediate and precise position reconstruction. FEM-PR reconstructs the tracer position with an accuracy of 0.08mm. Approximately 3.37ms is required to reconstruct one position on a desktop computer, which is less than the sampling time for experimental data collection.

Effects of High‐Frequency Flow Variability on the Pathways of the Indonesian Throughflow

AbstractPrevious studies have shown the presence of strong mesoscale eddy activities in the Indonesian Seas and their influence on the transport and water mass properties of the Indonesian Throughflow (ITF), a mean flow from the Pacific Ocean to the Indian Ocean through the Indonesian Archipelago. This study explores the effects of these eddy activities, or high‐frequency flow variability (HFFV), on residence time and pathway of the ITF by conducting Lagrangian particle tracking experiments using a velocity field from an eddy‐resolving ocean general circulation model. Particles are released at key locations in the western and eastern routes of the ITF and tracked both backward and forward in time. To assess the effects of flow variability that has a time scale longer than a day but shorter than a month, the definition of HFFV in this study, we conduct parallel experiments using daily and monthly averaged velocity fields. Particle trajectories reveal the contrasting circulation characteristics of the Sulawesi and Banda Seas. HFFV in the Sulawesi Sea (in the western route) is high, causing water to circulate longer over a broader area. The longer residence time in the Sulawesi Sea helps the upwelling of the inflowing Pacific waters, especially the intermediate water masses, to rise above 300 m at the Makassar Strait, and also has the potential to allow mixing processes to modify the water mass properties of the ITF. In contrast, HFFV is much lower in the Banda Sea and has minimal effects on the ITF.

Large-scale particle shadow tracking and orientation measurement with collimated light

Lagrangian particle tracking experiments are a key tool to understanding particle transport in fluid flows. However, tracking particles over long distances is expensive and limited by both the intensity of light and number of cameras. In order to increase the length of measured particle trajectories in a large fluid volume with minimal cost, we developed a large-scale particle-shadow-tracking method. This technique is able to accurately track millimeter-scale particles and their orientations in meter-scale laboratory fluid flows. By tracking the particles’ shadows cast by a wide beam of collimated light from a high-power LED, 2D particle position and velocity can be obtained, as well as their 3D orientation. Compared with traditional volumetric particle tracking techniques, this method is able to measure particle kinematics over a larger area using much simpler imaging and tracking techniques. We demonstrate the method on sphere, disk, and rod particles in a wavy wind-driven flow, where we successfully track particles and reconstruct their orientations.

How do topography and thermal front influence the water transport from the northern Laotieshan Channel to the Bohai Sea interior in summer?

Water renewal through the Bohai Strait largely dominates the water quality of the semi-enclosed Bohai Sea (BS), which connects only to the northern Yellow Sea (NYS) through the strait. Although the peak water transport through the Bohai Strait occurs in summer, the spatially averaged water residence time of the BS shows no significant decrease compared to other periods. A three-dimensional model is applied to unravel the detailed structure and dynamic processes of the summertime NYS water transport from the northern Laotieshan Channel to the BS interior. Model results from both climatological and hindcasting cases show that despite a large amount of the NYS water enters the strait, they are confined to the Laotieshan Channel between the Central Bank and Dalian surrounded by a strong Ω-shaped tidal front and could not move further north into the Liaodong Bay. The strong along-front flow steered by the topography forms a counter-clockwise circulation pattern in the strait zone, resulting in most of water southward movement east of the Central Bank, then join the outflow south of the strait and leave for the NYS. The Central Bank and the topographic sill north of the Laotieshan Channel act as a barrier that significantly reduces the water exchange between the strait zone and the BS interior, in particular the Liaodong Bay. Particle-tracking experiments suggest that less than 10% of particles released in the NYS could finally reach the BS interior, and among of them only a small portion of them could move further north into the Liaodong Bay. Momentum diagnostics suggest that the water transport northwest of the strait is dominated by geostrophic balance in the Ω-shaped frontal region. Sensitivity experiments indicate that tides promote the surface water transport from the NYS to the BS interior. The realistic wind forcing including synoptic events may facilitate the water transport from the strait to the BS interior by modulating the barotropic and baroclinic pressure gradient than that with the climatological wind case.

Does Supramolecular Gelation Require an External Trigger?

The supramolecular gelation of small molecules is typically preceded by an external stimulus to trigger the self-assembly. The need for this trigger stems from the metastable nature of most supramolecular gels and can limit their applicability. Herein, we present a small urea-based molecule that spontaneously forms a stable hydrogel by simple mixing without the addition of an external trigger. Single particle tracking experiments and observations made from scanning electron microscopy indicated that triggerless gelation occurred in a similar fashion as the archetypical heat-triggered gelation. These results could stimulate the search for other supramolecular hydrogels that can be obtained by simple mixing. Furthermore, the mechanism of the heat-triggered supramolecular gelation was elucidated by a combination of molecular dynamics simulations and quantitative NMR experiments. Surprisingly, hydrogelation seemingly occurs via a stepwise self-assembly in which spherical nanoparticles mature into an entangled fibrillary network.

Particle-tracking experiments of coastal-origin sea ice that could induce high biological productivity in the Sea of Okhotsk

Particle-tracking experiments of coastal-origin sea ice that could induce high biological productivity in the Sea of Okhotsk

Hopping Behavior Mediates the Anomalous Confined Diffusion of Nanoparticles in Porous Hydrogels.

Diffusion is an essential means of mass transport in porous materials such as hydrogels, which are appealing in various biomedical applications. Herein, we investigate the diffusive motion of nanoparticles (NPs) in porous hydrogels to provide a microscopic view of confined diffusion. Based on the mean square displacement from particle tracking experiments, we elucidate the anomalous diffusion dynamics of the embedded NPs and reveal the heterogeneous pore structures in hydrogels. The results demonstrate that diffusive NPs can intermittently escape from single pores through void connective pathways and exhibit non-Gaussian displacement probability distribution. We simulate this scenario using the Monte Carlo method and clarify the existence of hopping events in porous diffusion. The resultant anomalous diffusion can be fully depicted by combining the hopping mechanism and the hydrodynamic effect. Our results highlight the hopping behavior through the connective pathways and establish a hybrid model to predict NP transport in porous environments.

Combined biophysical and genetic modelling approaches reveal new insights into population connectivity of New Zealand green-lipped mussels

Understanding how ocean currents affect larval transport is crucial for understanding population connectivity in sessile marine invertebrates whose primary dispersal opportunity occurs during the pelagic larval stage. This study used Lagrangian particle tracking experiments to examine population connectivity in New Zealand green-lipped mussels (Perna canaliculus) at the national scale. Predicted patterns of larval dispersal were compared to published multi-locus microsatellite data of observed population genetic structure. Estimates of oceanographic circulation correlated significantly with FST, and we conclude that hydrodynamic processes are important in driving genetic connectivity. However, no evidence was found for an oceanographic barrier to gene flow south of Cook Strait, an important feature of genetic structure observed across several marine invertebrate species. Discrepancies between genetic and biophysical data may be explained by several factors including the different timescales of connectivity described by the two methods and the impact of localised ecological conditions and corresponding adaptations in genetic structure not captured by the bipohysical model. Population genetic analyses provide empirical data on realised connectivity and Lagrangian particle tracking experiments reveal information about directionality and asymmetry of connections that often cannot be determined by molecular analyses alone, thus a multidisciplinary approach is recommended.

The Natal Bight Coastal Counter-Current: A modeling study

Output from a high-resolution ocean model, a wind reanalysis and a particle tracking tool are used to improve our understanding of the shelf circulation in an embayment off South Africa's east coast, known as the KwaZulu-Natal Bight. This region spans across roughly 140 km of coastline and is located between 29°S and 30°S. It is influenced by the strong, south-westward flowing Agulhas Current on its offshore edge, while its shelf is dominated by weak and variable currents. On the KwaZulu-Natal Bight's shelf, realistic high-resolution model simulations indicate the presence of a mean north-eastward flow: the Natal Bight Coastal Counter-Current. The mean surface circulation depicts a Natal Bight Coastal Counter Current stretching along the 50 m isobath from the southern to the northern section of the KwaZulu-Natal Bight while progressively becoming narrower and weaker northwards. The mean vertical structure of this counter current extends throughout the water column and at its origin, it almost connects with the Agulhas Undercurrent. In this region, the Natal Bight Coastal Counter-Current is about 20 km wide and has an average speed of 20 cm/s at its core, which may exceed 100 cm/s during individual events. The passage of southward propagating anticyclonic eddies offshore of the Agulhas Current are associated with a southward flow along the southern KwaZulu-Natal Bight region and the interruption of the otherwise north-eastward shelf currents. While the circulation in the KwaZulu-Natal Bight is primarily driven by perturbations at the Agulhas Current front, there is also some indication of a direct wind-driven influence in coastal waters, inshore of the 50 m isobath and north of 29.5°S. Virtual particle tracking experiments show that the Natal Bight Coastal Counter Current may increase connectivity between Marine Protected Areas within the KwaZulu-Natal Bight, where the current greatly increases the water retention. This may trap nutrients from coastal origins on the shelf, together with any suspended particles such as larvae. Therefore, the Natal Bight Coastal Counter-Current has the potential to increase the suitability of this habitat for larval settlement.

Fate of river-derived microplastics from the South China Sea: Sources to surrounding seas, shores, and abysses

Microplastics (MPs) in the ocean have been widely recognized as causing global marine environmental problems. To gain a quantitative and comprehensive understanding of oceanic MP contamination, detailed numerical Lagrangian particle tracking experiments were conducted to evaluate the regional oceanic transport and dispersal of MPs in the South China Sea (SCS) derived from three major rivers, Pearl (China), Mekong (Vietnam), and Pasig (the Philippines), which are known to discharge large amounts of plastic waste into the SCS. As previous field surveys have suggested, MP contamination spreads from the surface to the deeper ocean in the water column, we thus considered three types of MPs: (1) positively buoyant (light) MPs, (2) positively buoyant (light) MPs with random walk diffusion, and (3) full 3-D tracking of non-buoyant MPs that are passively transported by ambient currents. Transport patterns of these MPs from the three rivers clearly showed the intra-annual variability associated with seasonally varying circulations driven by the Asian monsoons in the SCS. Many MPs floating during the prevailing southwest monsoon are transported to the northwest Pacific Ocean and the East China Sea through the Luzon Strait and the Taiwan Strait to form MP hotspots. Non-buoyant MPs are broadly transported from the surface layer to depths of approximately 100 m or deeper, where in situ observations are rare. In addition, the buoyant MPs drifting on the continental shelf originating from southern China tend to be pushed toward the shore and beached by northward wind-induced currents more pronouncedly than the non-buoyant MPs. Therefore, the river-derived MPs to the SCS were found to serve as sources to adjacent basins and oceans, to be distributed not only in the upper layer but also in the abyssal ocean (non-buoyant MPs), and to be transported to the shores (buoyant MPs).