Driven transport of active particles through arrays of symmetric obstacles.

We numerically examine the driven transport of an overdamped self-propelled particle through a two-dimensional array of circular obstacles. A detailed analysis of transport quantifiers (mobility and diffusivity) has been performed for two types of channels, channel I and channel II, that respectively correspond to the parallel and diagonal drives with respect to the array axis. Our simulation results show that the signatures of pinning actions and depinning processes in the array of obstacles are manifested through excess diffusion peaks or sudden drops in diffusivity, and abrupt jumps in mobility with varying amplitude of the drive. The underlying depinning mechanisms and the associated threshold driving strength largely depend on the persistent length of self-propulsion. For low driving strength, both diffusivity and mobility are noticeably suppressed by the array of obstacles, irrespective of the self-propulsion parameters and direction of the drive. When self-propulsion length is larger than a channel compartment size, transport quantifiers are insensitive to the rotational relaxation time. Transport with diagonal drives features self-propulsion-dependent negative differential mobility. The amplitude of the negative differential mobility of an active particle is much larger than that of a passive one. The present analysis aims at understanding the driven transport of active species like, bacteria, virus, Janus particle etc. in porous medium.

Association Between a State-Level Fat Tax and Fast Food Purchases.

Importance: India faces an increasing obesity problem, including in the Indian state of Kerala in which the fat tax was implemented but was nullified 11 months later. A fat tax, defined as a tax on unhealthy foods, may be associated with changes in food purchases and outcomes for multiple diet-related diseases. Objective: To investigate the association between the state-level fat tax and fast food purchases in Kerala, India. Design, Setting, and Participants: This cohort study analyzed a large-scale credit and debit card transaction data set and aggregated this sample at the account-year-month level of fast food purchases in Kerala state and 9 major cities in other Indian states (Ahmedabad, Bangalore, Bhubaneswar, Chennai, Delhi, Gurgaon, Kolkata, Mumbai, and Surat). Purchase records were obtained for January 1, 2016, to December 31, 2017. The association between the fat tax and fast food purchases was examined using the difference-in-differences method. This analysis was initiated on December 1, 2022. Exposures: The exposure was the fat tax. Kerala was the exposed group, and 9 major Indian cities were the control group. Main Outcomes and Measures: The main outcome was the fast food purchase ratio, defined as the proportion of fast food purchases of the total food purchases. Changes in the fast food purchase ratio were estimated in Kerala across the sample period and then compared with 9 major cities. Results: The sample for analysis included 238 015 credit and debit card accounts, of which 36.7% were in Kerala and 63.3% were in 9 major cities. The cardholders included 191 603 males (80.5%) with a mean (SD) age of 36.6 (12.8) years. During the fat tax implementation (August 2016-June 2017), Kerala's fast food purchase ratio decreased by 3.9 percentage points (ß [SE], -0.039 [0.002]; 95% CI, -0.042 to -0.036), compared with 9 major cities. After the fat tax was nullified, the fast food purchase ratio reduced by 5.6 percentage points (γ [SE], -0.056 [0.002]; 95% CI, -0.059 to -0.052) compared with 9 major cities and using the pretax period as the benchmark. Conclusions and Relevance: Results of this cohort study suggest that the Kerala fat tax was associated with fewer fast food purchases. Food tax policies need to have an elaborate design, and related issues, such as social inequality, nutritional deficiency, and political concerns, need to be evaluated in future studies.

Autonomous ratcheting by stochastic resetting.

We propose a generalization of the stochastic resetting mechanism for a Brownian particle diffusing in a one-dimensional periodic potential: randomly in time, the particle gets reset at the bottom of the potential well it was in. Numerical simulations show that in mirror asymmetric potentials, stochastic resetting rectifies the particle's dynamics, with a maximum drift speed for an optimal average resetting time. Accordingly, an unbiased Brownian tracer diffusing on an asymmetric substrate can rectify its motion by adopting an adaptive stop-and-go strategy. Our proposed ratchet mechanism can model the directed autonomous motion of molecular motors and micro-organisms.

A multiplicative structural nested mean model for zero-inflated outcomes.

Zero-inflated nonnegative outcomes are common in many applications. In this work, motivated by freemium mobile game data, we propose a class of multiplicative structural nested mean models for zero-inflated nonnegative outcomes which flexibly describes the joint effect of a sequence of treatments in the presence of time-varying confounders. The proposed estimator solves a doubly robust estimating equation, where the nuisance functions, namely the propensity score and conditional outcome means given confounders, are estimated parametrically or nonparametrically. To improve the accuracy, we leverage the characteristic of zero-inflated outcomes by estimating the conditional means in two parts, that is, separately modelling the probability of having positive outcomes given confounders, and the mean outcome conditional on its being positive and given the confounders. We show that the proposed estimator is consistent and asymptotically normal as either the sample size or the follow-up time goes to infinity. Moreover, the typical sandwich formula can be used to estimate the variance of treatment effect estimators consistently, without accounting for the variation due to estimating nuisance functions. Simulation studies and an application to a freemium mobile game dataset are presented to demonstrate the empirical performance of the proposed method and support our theoretical findings.

Narrow Pore Crossing of Active Particles under Stochastic Resetting.

We propose a two-dimensional model of biochemical activation process, whereby self-propelling particles of finite correlation times are injected at the center of a circular cavity with constant rate equal to the inverse of their lifetime; activation is triggered when one such particle hits a receptor on the cavity boundary, modeled as a narrow pore. We numerically investigated this process by computing the particle mean-first exit times through the cavity pore as a function of the correlation and injection time constants. Due to the breach of the circular symmetry associated with the positioning of the receptor, the exit times may depend on the orientation of the self-propelling velocity at injection. Stochastic resetting appears to favor activation for large particle correlation times, where most of the underlying diffusion process occurs at the cavity boundary.

Binary Mixtures in Linear Convection Arrays.

We numerically investigated the dynamics of a mixture of finite-size active and passive disks in a linear array of two-dimensional convection rolls. The interplay of advection and steric interactions produces a number of interesting effects, like the stirring of a passive colloidal fluid by a small fraction of slow active particles, or the separation of the mixture active and passive colloidal fractions by increasing the motility of the active one, which eventually clusters in stagnation areas along the array walls. These mechanisms are quantitatively characterized by studying the dependence of the diffusion constants of the active and passive particles on the parameters of the active mixture fraction.

Directed Autonomous Motion and Chiral Separation of Self-Propelled Janus Particles in Convection Roll Arrays.

Self-propelled Janus particles exhibit autonomous motion thanks to engines of their own. However, due to the randomly changing direction of such motion they are of little use for emerging nanotechnological and biomedical applications. Here, we numerically show that the motion of chiral active Janus particles can be directed, subjecting them to a linear array of convection rolls. The rectification power of self-propulsion motion here can be made to be more than 60%, which is much larger than earlier reports. We show that rectification of a chiral Janus particle's motion leads to conspicuous segregation of dextrogyre and levogyre active particles from a racemic binary mixture. Further, we demonstrate how efficiently the rectification effect can be exploited to separate dextrogyre and levogyre particles when their intrinsic torques are distributed with Gaussian statistics.

Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases.

DNA polymerases can process a wide variety of structurally diverse nucleotide substrates, but the molecular basis by which the analogs are processed is not completely understood. Here, we demonstrate the utility of environment-sensitive heterocycle-modified fluorescent nucleotide substrates in probing the incorporation mechanism of DNA polymerases in real time and at the atomic level. The nucleotide analogs containing a selenophene, benzofuran, or benzothiophene moiety at the C5 position of 2'-deoxyuridine are incorporated into oligonucleotides (ONs) with varying efficiency, which depends on the size of the heterocycle modification and the DNA polymerase sequence family used. KlenTaq (A family DNA polymerase) is sensitive to the size of the modification as it incorporates only one heterobicycle-modified nucleotide into the growing polymer, whereas it efficiently incorporates the selenophene-modified nucleotide analog at multiple positions. Notably, in the single nucleotide incorporation assay, irrespective of the heterocycle size, it exclusively adds a single nucleotide at the 3'-end of a primer, which enabled devising a simple two-step site-specific ON labeling technique. KOD and Vent(exo-) DNA polymerases, belonging to the B family, tolerate all the three modified nucleotides and produce ONs with multiple labels. Importantly, the benzofuran-modified nucleotide (BFdUTP) serves as an excellent reporter by providing real-time fluorescence readouts to monitor enzyme activity and estimate the binding events in the catalytic cycle. Further, a direct comparison of the incorporation profiles, fluorescence data, and crystal structure of a ternary complex of KlenTaq DNA polymerase with BFdUTP poised for catalysis provides a detailed understanding of the mechanism of incorporation of heterocycle-modified nucleotides.

Chloride Transport across Liposomes and Cells by Nontoxic 3-(1H-1,2,3-Triazol-1-yl)benzamides.

Synthetic anion transmembrane transporters are adding new aspirations for treating channelopathies by replacing defective ion channels. The availability of such suitable candidates is still infrequent due to the associated toxicity. Here, we report 3-(1H-1,2,3-triazol-1-yl)benzamides as transmembrane anion carriers, nontoxic to cells. The selective and electrogenic chloride transport activity was established by fluorescence and ion selective electrode-based assays. MQAE assay confirmed the chloride uptake into the cells by the nontoxic compounds.

Colloidal clustering and diffusion in a convection cell array.

We numerically investigated the clustering of a uniform suspension of finite-size disks in a linear array of two-dimensional convection cells. We observed that, due to steric interactions, the disks tend to form coherently rotating spatial structures at the center of each cell, as a combined effect of advection and pair collisions. Micellar, ring-like and hexatic patterns emerge in the deterministic regime, depending on the suspension density, but dissolve in the presence of thermal fluctuations. Moreover, pair collisions suffice to activate cell crossings even by noiseless disks and, therefore, cause athermal diffusion. The robustness of such collision induced effects is studied against the opposing action of thermal noise, transverse biases, and particle self-propulsion.

Measuring vaccine effectiveness from limited public health datasets: Framework and estimates from India's second COVID wave.

Despite an urgent need, authorities in many countries are struggling to track COVID vaccine effectiveness (VE) because standard VE measures cannot be calculated from their public health data. Here, we use regression discontinuity design (RDD) to estimate VE, motivated by such limitations in public health records from West Bengal, India. These data cover 8,755,414 COVID vaccinations (90% ChAdOx1 NCov-19, almost all first doses, until May 2021), 8,179,635 tests, and 141,800 hospitalizations. The standard RDD exploits age-based vaccine eligibility; we also introduce a new RDD-based VE measure that improves on the standard one when better data are available. Applying these measures, we find a VE of 55.2% (95% confidence interval: 44.5 to 65.0%) against symptomatic disease, 80.1% (63.3 to 88.8%) against hospitalizations, and 85.5% (24.8 to 99.2%) against intensive care/critical care/high dependency admissions or deaths. Other data-deficient countries with age-based eligibility for any vaccine-and not just COVID vaccines-can also use these easy-to-implement measures to inform their own immunization policies.

Escape kinetics of self-propelled particles from a circular cavity.

We numerically investigate the mean exit time of an inertial active Brownian particle from a circular cavity with single or multiple exit windows. Our simulation results witness distinct escape mechanisms depending on the relative amplitudes of the thermal length and self-propulsion length compared to the cavity and pore sizes. For exceedingly large self-propulsion lengths, overdamped active particles diffuse on the cavity surface, and rotational dynamics solely governs the exit process. On the other hand, the escape kinetics of a very weakly damped active particle is largely dictated by bouncing effects on the cavity walls irrespective of the amplitude of self-propulsion persistence lengths. We show that the exit rate can be maximized for an optimal self-propulsion persistence length, which depends on the damping strength, self-propulsion velocity, and cavity size. However, the optimal persistence length is insensitive to the opening windows' size, number, and arrangement. Numerical results have been interpreted analytically based on qualitative arguments. The present analysis aims at understanding the transport controlling mechanism of active matter in confined structures.

Active particle diffusion in convection roll arrays.

Undesired advection effects are unavoidable in most nano-technological applications involving active matter. However, it is conceivable to govern the transport of active particles at the small scales by suitably tuning the relevant advection and self-propulsion parameters. To this purpose, we numerically investigated the Brownian motion of active Janus particles in a linear array of planar counter-rotating convection rolls at high Péclet numbers. Similarly to passive particles, active microswimmers exhibit advection enhanced diffusion, but only for self-propulsion speeds up to a critical value. The diffusion of faster Janus particles is governed by advection along the array's edges, whereby distinct diffusion regimes are observed and characterized. Contrary to passive particles, the relevant spatial distributions of active Janus particles are inhomogeneous. These peculiar properties of active matter are related to the combined action of noise and self-propulsion in a confined geometry and hold regardless of the actual flow boundary conditions.

Anisotropic Diffusion in Driven Convection Arrays.

We numerically investigate the transport of a Brownian colloidal particle in a square array of planar counter-rotating convection rolls at high Péclet numbers. We show that an external force produces huge excess peaks of the particle's diffusion constant with a height that depends on the force orientation and intensity. In sharp contrast, the particle's mobility is isotropic and force independent. We relate such a nonlinear response of the system to the advection properties of the laminar flow in the suspension fluid.

Advection-enhanced diffusion in biased convection arrays.

We numerically investigated the transport of a passive colloidal particle in a one-dimensional periodic array of planar counter-rotating convection rolls at high Péclet numbers. We show that advection-enhanced diffusion is drastically suppressed by an external transverse bias but strongly reinforced by a longitudinal drive of appropriate intensity. Both effects are magnified by imposing free-slip flows at the array's edges. The dependence of the diffusion constant on an external forcing is interpreted as a measure of the fluid-mechanical robustness of the flow boundary layer mechanism governing diffusion in convection rolls.

Diffusion of active particles in convective flows.

We numerically investigated the diffusion of an active Janus particle in periodic arrays of planar counter-rotating convection rolls at high Péclet numbers. We considered convection patterns with distinct longitudinal and transverse advection properties and characterized the dependence of the relevant diffusion constants on the particle's dynamical parameters, namely, self-propulsion speed, correlation time and chirality. Numerical results are interpreted analytically based on qualitative arguments of classical transport theory. The purpose of the present analysis is controlling active matter transport in microfluidic devices.

Enhanced motility in a binary mixture of active nano/microswimmers.

It is often desirable to enhance the motility of active nano- or microscale swimmers such as, e.g., self-propelled Janus particles as agents of chemical reactions or weak sperm cells for better chances of successful fertilization. Here we tackle this problem based on the idea that motility can be transferred from a more active guest species to a less active host species. We performed numerical simulations of motility transfer in two typical cases, namely for interacting particles with a weak inertia effect, by analyzing their velocity distributions, and for interacting overdamped particles, by studying their effusion rate. In both cases, we detected motility transfer with a motility enhancement of the host species of up to a factor of four. This technique of motility enhancement can find applications in chemistry, biology and medicine.

Active diffusion limited reactions.

We investigate the one- and two-dimensional diffusion limited reactions A + A → 0 and A + B → 0 with A active Janus particles and B passive particles in thermal equilibrium. We show that by increasing the self-propulsion time of the A particles, the reactant densities decay faster, at least for time transients of potential interest for chemical applications, e.g., to develop smart drug delivery protocols. Asymptotic and transient density decays obey power laws with exponents that depend on the actual annihilation reaction and its dimensionality.

Active microswimmers in a finite two dimensional trap: The role of hydrodynamic interaction.

We investigate the dynamics of two identical artificial active particles suspended in a free-standing fluid film with a trap of finite radius in an acoustic tweezer. In the two dimensional Oseen approximation, their hydrodynamic coupling is long ranged, which naturally raises the question as under what conditions they can simultaneously reside in the trap. We determine a critical value of the hydrodynamic coupling below which that happens and study the ensuing active pair dynamics inside the trap. For larger couplings, only one particle sits in the trap, while the other diffuses freely until it eventually replaces the particle in the trap. Such a mechanism repeats itself with a characteristic noise-dependent mean residence-retrapping time.

Activated barrier crossing dynamics of a Janus particle carrying cargo.

We numerically study the escape kinetics of a self-propelled Janus particle, carrying a cargo, from a meta-stable state. We assume that the cargo is attached to the Janus particle by a flexible harmonic spring. We take into account the effect of the velocity field created in the fluid due to movements of the dimer's components, by considering a space-dependent diffusion tensor (Oseen tensor). Our simulation results show that the synchronization between barrier crossing events and the rotational relaxation process can enhance the escape rate to a large extent. Also, the load carrying capability of a Janus particle is largely controlled by its rotational dynamics and self-propulsion velocity. Moreover, the hydrodynamic interaction, conspicuously, enhances the escape rate of the Janus-cargo dimer. The most important features in escape kinetics have been justified based on analytic arguments.