Tagged Particle Research Articles

Confined fluid dynamics in a viscoelastic, amorphous, and microporous medium: Study of a kerogen by molecular simulations and the generalized Langevin equation.

We combine the use of molecular dynamics simulations and the generalized Langevin equation to study the diffusion of a fluid adsorbed within kerogen, the main organic phase of shales. As a class of microporous and amorphous materials that can exhibit significant adsorption-induced swelling, the dynamics of the kerogen's microstructure is expected to play an important role in the confined fluid dynamics. This role is investigated by conducting all-atom simulations with or without solid dynamics. Whenever the dynamics coupling between the fluid and solid is accounted for, we show that the fluid dynamics displays some qualitative differences compared to bulk fluids, which can be modulated by the amount of adsorbed fluid owing to adsorption-induced swelling. We highlight that working with the memory kernel, the central time correlation function of the generalized Langevin equation, allows the fingerprint of the dynamics of the solid to appear on that of the fluid. Interestingly, we observe that the memory kernels of fluid diffusion in kerogen qualitatively behave as those of tagged particles in supercooled liquids. We emphasize the importance of reproducing the velocity-force correlation function to validate the memory kernel numerically obtained as confinement enhances the numerical instabilities. This route is interesting as it opens the way for modeling the impact of fluid concentration on the diffusion coefficient in such ultra-confining cases.

Tagged particle behavior in a harmonic chain of direction-reversing active Brownian particles

Abstract We study the tagged particle dynamics in a harmonic chain of direction-reversing active Brownian particles, with the spring constant k, rotation diffusion coefficient D R , and directional reversal rate γ. We exactly compute the tagged particle position variance for quenched and annealed initial orientations of the particles. For well-separated time-scales, k − 1 , D R − 1 and γ −1, the strength of the spring constant k relative to D R and γ gives rise to different coupling limits, and for each coupling limit there are short, intermediate, and long-time regimes. In the thermodynamic limit, we show that, to the leading order, the tagged particle variance exhibits an algebraic growth t ν , where the value of the exponent ν depends on the specific regime. For a quenched initial orientation, the exponent ν crosses over from 3 to 1 / 2 , via intermediate values 5 / 2 or 1, depending on the specific coupling limits. However, for the annealed initial orientation, ν crosses over from 2 to 1 / 2 via an intermediate value 3 / 2 or 1 for the strong coupling limit and the weak coupling limit, respectively. An additional time-scale t N = N 2 / k emerges for a system with a finite number of oscillators N. We show that the behavior of the tagged particle variance across tN can be expressed in terms of a crossover scaling function, which we find exactly. Moreover, we study the velocity autocorrelation. Finally, we characterize the stationary state behavior of the separation between two consecutive particles by calculating the corresponding spatio-temporal correlation function.

Vanishing self-diffusivity in Ginibre interacting Brownian motions in two dimensions

AbstractWe prove that the tagged particles of infinitely many Brownian particles in $$ {\mathbb {R}} ^2$$ R 2 interacting via a logarithmic (two-dimensional Coulomb) potential with inverse temperature $$ \beta = 2 $$ β = 2 are sub-diffusive. The associated unlabeled diffusion is reversible with respect to the Ginibre random point field, and the dynamics are thus referred to as the Ginibre interacting Brownian motion. If the interacting Brownian particles have interaction potential $$ \Psi $$ Ψ of Ruelle class and the total system starts in a translation invariant equilibrium state, then the tagged particles are always diffusive if the dimension $$ d$$ d of the space $$ {\mathbb {R}}^{d} $$ R d is greater than or equal to two. That is, the tagged particles are always non-degenerate under diffusive scaling. Our result is, therefore, contrary to known results. The Ginibre random point field has various levels of geometric rigidity. Our results reveal that the geometric property of infinite particle systems affects the dynamical property of the associated stochastic dynamics.

Tracer dynamics in the active random average process

We investigate the dynamics of tracer particles in the random average process (RAP), a single-file system in one dimension. In addition to the position, every particle possesses an internal spin variable σ(t) that can alternate between two values, ±1, at a constant rate γ. Physically, the value of σ(t) dictates the direction of motion of the corresponding particle and, for finite γ, every particle performs non-Markovian active dynamics. Herein, we study the effect of this non-Markovian behavior in the fluctuations and correlations of the positions of tracer particles. We analytically show that the variance of the position of a tagged particle grows sub-diffusively as ∼ζqt at large times for the quenched uniform initial conditions. While this sub-diffusive growth is identical to that of the Markovian/non-persistent RAP, the coefficient ζq is rather different and bears the signature of the persistent motion of active particles through higher-point correlations (unlike in the Markovian case). Similarly, for the annealed (steady-state) initial conditions, we find that the variance scales as ∼ζat at large times, with the coefficient ζa once again different from the non-persistent case. Although both ζ q and ζa individually depart from their Markovian counterparts, their ratio ζa/ζq is still equal to 2 , a condition observed for other diffusive single-file systems. This condition turns out to be true even in the strongly active regimes, as corroborated by extensive simulations and calculations. Finally, we study the correlation between the positions of two tagged particles in both quenched uniform and annealed initial conditions. We verify all our analytical results using extensive numerical simulations.

Kinetic Theory of Motility Induced Phase Separation for Active Brownian Particles.

When two active Brownian particles collide, they slide along each other until they can continue their free motion. For persistence lengths much larger than the particle diameter, the directors do not change, but the collision can be modeled as producing a net displacement on the particles compared to their free motion in the absence of the encounter. With these elements, a Boltzmann-Enskog-like kinetic theory is built. A linear stability analysis of the homogeneous state predicts a density instability resulting from the effective velocity reduction of tagged particles predicted by the theory.

Tracking coarse sediment in an Alpine subglacial channel using radio-tagged particles

Abstract We present a method for tracking radio-tagged pebbles and cobbles through subglacial meltwater channels under shallow temperate glaciers. Natural particles tagged with active radio transmitters were injected directly into a large subglacial channel 300 m up-glacier from the terminus of the Glacier d'Otemma, Switzerland. A roving antenna was developed to localise tagged particles planimetrically in subglacial and proglacial channel reaches (350 and 150 m long, respectively) using a probabilistic technique, delivering records of the change in particle location and transport distance over time with uncertainty. The roving antenna had a ±5−15 m planimetric precision, a 75% particle localisation rate and operated at a maximum ice depth of 47 m. Additionally, stationary supraglacial and proglacial antennas continuously monitored the passage of tagged particles through consecutive reaches of the channel, constraining the timing of particle transport events. The proglacial antenna system had a 98.1% detection rate and was operational to 0.89 m water depth during testing. Roving and stationary antenna records were combined to create a transport distance model for each particle, which may be used in conjunction with hydraulic data to investigate the kinematics of particle motion. When applied at scale in future studies, this method may be used to reveal the mechanisms and timescales of coarse sediment export from Alpine glaciers.

Moderate deviations for the current and tagged particle in symmetric simple exclusion processes

We prove moderate deviation principles for the tagged particle position and current in one dimensional symmetric simple exclusion processes. There is at most one particle per site. A particle jumps to one of its two neighbors at rate 1/2, and the jump is suppressed if there is already one at the target site. We distinguish one particular particle which is called the tagged particle. We first establish a variational formula for the moderate deviation rate functions of the tagged particle positions based on moderate deviation principles from hydrodynamic limits proved by Gao and Quastel (2003). Then we construct a minimizer of the variational formula and obtain explicit expressions for the moderate deviation rate functions.

Assessing solid particle mixing using X-ray radiographic particle tracking

Mixture homogeneity values are obtained from a binary mixture in a vertically bladed mixer utilizing data extracted from a single tagged particle. X-ray radiography was performed to image the mixer vessel during the mixing process, and the location of the tagged particle was tracked throughout. Mixture homogeneity is quantified using a standard deviation-based Location Distribution Mixing Index (LDMI), the Modified Generalized Mixing Mean Mixing Index (MGMMI), and the Gini Index, all adapted to single-particle data. Mixture homogeneity values obtained using these indices were compared to data extracted using X-ray Computed Tomography (CT), which was quantified using a particle scale mixing index. It was observed that the LDMI was superior in determining the magnitude of mixing, whereas the Gini index was more suited to predicting mixing endpoints. Methods presented in this study pave the way for new process analytical technologies that extract in-line mixture homogeneity values using velocimetric methods while removing the necessity of uniquely identifying and discriminating between tagged particles.

Scaling laws for single-file diffusion of adhesive particles.

Single-file diffusion refers to the Brownian motion in narrow channels where particles cannot pass each other. In such processes, the diffusion of a tagged particle is typically normal at short times and becomes subdiffusive at long times. For hard-sphere interparticle interaction, the time-dependent mean squared displacement of a tracer is well understood. Here we develop a scaling theory for adhesive particles. It provides a full description of the time-dependent diffusive behavior with a scaling function that depends on an effective strength of adhesive interaction. Particle clustering induced by the adhesive interaction slows down the diffusion at short times, while it enhances subdiffusion at long times. The enhancement effect can be quantified in measurements irrespective of how tagged particles are injected into the system. Combined effects of pore structure and particle adhesiveness should speed up translocation of molecules through narrow pores.

Uptake and Effects of Nanoplastics on the Dinoflagellate Gymnodinium corollarium.

Plastic nanoparticles (NPs) are the final state of plastic degradation in the environment before they disintegrate into low-molecular-weight organic compounds. Unicellular organisms are highly sensitive to the toxic effects of nanoplastics, because they are often capable of phagotrophy but are unable to consume a foreign material such as synthetic plastic. We studied the effect of polystyrene, poly(vinyl chloride), poly(methyl acrylate), and poly(methyl methacrylate) NPs on the photosynthetic dinoflagellate Gymnodinium corollarium Sundström, Kremp et Daugbjerg. Fluorescent tagged particles were used to visualize plastic capture by dinoflagellate cells. We found that these dinoflagellates are capable of phagotrophic nutrition and thus should be regarded as mixotrophic species. This causes their susceptibility to the toxic effects of plastic NPs. Living cells ingest plastic NPs and accumulate in the cytoplasm as micrometer-level aggregates, probably in food vacuoles. The action of nanoplastics leads to a dose-dependent increase in the level of reactive oxygen species in dinoflagellate cells, indicating plastic degradation in the cells. The introduction of a methyl group into the main chain in the α-position in the case of poly(methyl methacrylate) causes a drastic reduction in toxicity. We expect that such NPs can be a tool for testing unicellular organisms in terms of heterotrophic feeding ability. We suggest a dual role of dinoflagellates in the ecological fate of plastic waste: the involvement of nanoplastics in the food chain and its biochemical destruction. Environ Toxicol Chem 2023;42:1124-1133. © 2023 SETAC.

Simple and efficient algorithms based on Volterra equations to compute memory kernels and projected cross-correlation functions from molecular dynamics.

Starting from the orthogonal dynamics of any given set of variables with respect to the projection variable used to derive the Mori-Zwanzig equation, a set of coupled Volterra equations is obtained that relate the projected time correlation functions between all the variables of interest. This set of equations can be solved using standard numerical inversion methods for Volterra equations, leading to a very convenient yet efficient strategy to obtain any projected time correlation function or contribution to the memory kernel entering a generalized Langevin equation. Using this strategy, the memory kernel related to the diffusion of tagged particles in a bulk Lennard-Jones fluid is investigated up to the long-term regime to show that the repulsive-attractive cross-contribution to memory effects represents a small but non-zero contribution to the self-diffusion coefficient.

Dual-Affinity Graphene Sheets for High-Resolution Cryo-Electron Microscopy.

With the development of cryo-electron microscopy (cryo-EM), high-resolution structures of macromolecules can be reconstructed by the single particle method efficiently. However, challenges may still persist during the specimen preparation stage. Specifically, proteins tend to adsorb at the air-water interface and exhibit a preferred orientation in vitreous ice. To overcome these challenges, we have explored dual-affinity graphene (DAG) modified with two different affinity ligands as a supporting material for cryo-EM sample preparation. The ligands can bind to distinct sites on the corresponding tagged particles, which in turn generates various orientation distributions of particles and prevents the adsorption of protein particles onto the air-water interface. As expected, the DAG exhibited high binding specificity and affinity to target macromolecules, resulting in more balanced particle Euler angular distributions compared to single functionalized graphene on two different protein cases, including the SARS -CoV-2 spike glycoprotein. We anticipate that the DAG grids will enable facile and efficient three-dimensional (3D) reconstruction for cryo-EM structural determination, providing a robust and general technique for future studies.

Effect of blade configuration on the mixing process of particles in an intensive mixer

DEM simulations of particle mixing process in the intensive mixer were conducted to study the influence of blade configuration and impeller speed on the particle dynamics and mixing performance. Two tagged particles at different locations were used to discuss the influence of blade configuration on the particle trajectory and residence time in the intensive mixing region. The average magnitude velocity in the intensive mixing region, time-averaged velocity fluctuation, coordination number, impeller torque and relative standard deviation (RSD) were adopted to quantify the mixing performance during the mixing process. It was found that the blade configuration plays a vital role in the mixing process as it affects the residence time, particle velocity and mixing performance. The magnitude velocity of particles agitated by the thread blades is lower than that agitated by the arc and straight blades. The residence time for the thread blade mixer is longer than that for the arc and straight blade mixers. The mixing performance of particles in the thread blade mixer is better than that in the arc and straight blade mixers. Results obtained show that a proper impeller speed is very important for the mixing of particles, and the optimal impeller speed for granular mixing in the intensive mixer is 150 rpm.

Distinction between transport and Rényi entropy growth in kinetically constrained models

Conservation laws and the associated hydrodynamic modes have important consequences on the growth of higher R\'enyi entropies in isolated quantum systems. It has been shown in various random unitary circuits and Hamiltonian systems that the dynamics of the R\'enyi entropies in the presence of a U(1) symmetry obey ${S}^{(n\ensuremath{\ge}2)}(t)\ensuremath{\propto}{t}^{1/z}$, where $z$ is identified as the dynamical exponent characterizing transport of the conserved charges. Here, however, we demonstrate that this simple identification may not hold in certain quantum systems with kinetic constraints. In particular, we study two types of U(1)-symmetric quantum automaton circuits with XNOR (exclusive NOR) and Fredkin constraints, respectively. We find numerically that while spin transport in both models is subdiffusive, the second R\'enyi entropy grows diffusively in the XNOR model, and superdiffusively in the Fredkin model. For systems with the XNOR constraint, this distinction arises since the spin correlation function can be attributed to an emergent tracer dynamics of tagged particles, whereas the R\'enyi entropies are constrained by collective transport of the particles. Our results suggest that care must be taken when relating transport and entanglement entropy dynamics in generic quantum systems with conservation laws.

Dynamics of an inelastic tagged particle under strong confinement

The dynamics of a tagged particle immersed in a fluid of particles of the same size but different mass is studied when the system is confined between two hard parallel plates separated by a distance smaller than twice the diameter of the particles. The collisions between particles are inelastic while the collisions of the particles with the hard walls inject energy in the direction perpendicular to the wall, so that stationary states can be reached in the long-time limit. The velocity distribution of the tagged particle verifies a Boltzmann–Lorentz-like equation that is solved assuming that it is a spatially homogeneous Gaussian distribution with two different temperatures (one associated with the motion parallel to the wall and another associated with the perpendicular direction). It is found that the temperature perpendicular to the wall diverges when the tagged particle mass approaches a critical mass from below, while the parallel temperature remains finite. Molecular dynamics simulation results agree very well with the theoretical predictions for tagged particle masses below the critical mass. The measurements of the velocity distribution function of the tagged particle confirm that it is Gaussian if the mass is not close to the critical mass, while it deviates from Gaussianity when approaching the critical mass. Above the critical mass, the velocity distribution function is very far from a Gaussian, being the marginal distribution in the perpendicular direction bimodal and with a much larger variance than the one in the parallel direction.

Interacting particle systems with long-range interactions: Approximation by tagged particles in random fields

In this paper, we continue the study of the derivation of different types of kinetic equations which arise from scaling limits of interacting particle systems. We began this study in [Atti Accad. Naz. Lincei Rend. Lincei Mat. Appl. 32 (2021), 335–377]. More precisely, we consider the derivation of the kinetic equations for systems with long-range interaction. Particular emphasis is put on the fact that all the kinetic regimes can be obtained approximating the dynamics of interacting particle systems, as well as the dynamics of Rayleigh gases, by a stochastic Langevin-type dynamics for a single particle. We will present this approximation in detail and we will obtain precise formulas for the diffusion and friction coefficients appearing in the limit Fokker–Planck equation for the probability density of the tagged particle f(x,v,t) , for three different classes of potentials. The case of interaction potentials behaving as Coulombian potentials at large distances will be considered in detail. In particular, we will discuss the onset of the the so-called Coulombian logarithm.

Effect of low-cost recirculating portable air filtration on aerosol particle deposition and concentration in a conference room: Experiment, theory, and simulation comparison

Respiratory particles exhaled when an individual speaks and breathes can facilitate respiratory virus transmission. Portable air purification units can potentially reduce transmission risk by decreasing the overall infectious particle concentration in a room. This is particularly important for rooms with an inability to be ventilated with adequate amounts of filtered or outdoor air. While the efficacy of portable air filtration units on particle concentrations has been well-studied, the impact of portable air purification units on particle deposition and, hence, indirect aerosol transmission, has received lesser study but may be important for smaller spaces with greater surface area-to-volume ratios. We conducted a series of experiments in a simulated, small conference room (34.4 m3, mimicking a common office meeting room) assessing (1) particle removal rates and (2) changes in deposition rate owing to the presence of a low-cost box fan air purifier (BFAP). To mimic an infectious aerosol source, a breathing simulator manikin was utilized in these experiments, which ejected fluorescein tagged particles in the 1–3 μm size range throughout each experimental condition, with a prescribed, periodic, breathing waveform mimicking human exhalation. We measured deposition flux on upward- and downward-facing horizontal surfaces throughout the room and determined aerosol mass concentrations using impingers; combined, these data enabled estimates of surface-specific deposition velocities. Aerosol size distributions within the room were also quantified using an optical particle spectrometer. CFD simulations and theoretical calculations were simultaneously conducted for comparison to the experimental data. Results suggested the BFAP unit, which had an effective clean air delivery rate of 540 m3 h−1, increased the effective air exchange rate by 4.4x over baseline (20.1 vs. 4.5 h−1). Notably, BFAP unit operation introduced greater deposition to surfaces near the breathing simulator manikin vs. baseline, with deposition velocities within 2 m of the breathing simulator being 100 cm s−1 during BFAP operation, compared to 10−2 cm s−1 during baseline. Deposition velocities and air exchange rates generated from the CFD and theoretical calculations largely agreed with those derived from experiments. Taken together, data suggest that in smaller rooms, such as conference rooms, deposition is not negligible as a mechanism of aerosol clearance, even for particles near 1–3 μm in diameter.

Detecting Intact Virus Using Exogenous Oligonucleotide Labels.

The COVID-19 pandemic has revealed how an emerging pathogen can cause a sudden and dramatic increase in demand for viral testing. Testing pooled samples could meet this demand; however, the sensitivity of reverse transcription quantitative polymerase chain reaction (RT-qPCR), the gold standard, significantly decreases with an increasing number of samples pooled. Here, we introduce detection of intact virus by exogenous-nucleotide reaction (DIVER), a method that quantifies intact virus and is robust to sample dilution. As demonstrated using two models of severe acute respiratory syndrome coronavirus 2, DIVER first tags membraned particles with exogenous oligonucleotides, then captures the tagged particles on beads functionalized with a virus-specific capture agent (in this instance, angiotensin-converting enzyme 2), and finally quantifies the oligonucleotide tags using qPCR. Using spike-presenting liposomes and spike-pseudotyped lentivirus, we show that DIVER can detect 1 × 105 liposomes and 100 plaque-forming units of lentivirus and can successfully identify positive samples in pooling experiments. Overall, DIVER is well positioned for efficient sample pooling and clinical validation.

A driven tagged particle in asymmetric exclusion processes

We consider the asymmetric exclusion process with a driven tagged particle on Z which has different jump rates from other particles. When the non-tagged particles have non-nearest-neighbor jump rates , we show that the tagged particle can have a speed which has a different sign from the mean derived from its jump rates. We also show the existence of some non-trivial invariant measures for the environment process viewed from the tagged particle. Our arguments are based on coupling, martingale methods, and analyzing currents through fixed bonds.

Swarming Bottom Feeders: Flocking at Solid-Liquid Interfaces.

We present the hydrodynamic theory of coherent collective motion ("flocking") at a solid-liquid interface, and many of its predictions for experiment. We find that such systems are stable, and have long-range orientational order, over a wide range of parameters. When stable, these systems exhibit "giant number fluctuations," which grow as the 3/4th power of the mean number. Stable systems also exhibit anomalous rapid diffusion of tagged particles suspended in the passive fluid along any directions in a plane parallel to the solid-liquid interface, whereas the diffusivity along the direction perpendicular to the plane is not anomalous. In the remaining parameter space, the system becomes unstable.