Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes.

Functionalizing nucleic acids using DNA polymerases is essential in biophysical and biotechnology applications. This study focuses on understanding how DNA polymerases recognize and incorporate nucleotides with diverse chemical modifications, aiming to develop advanced nucleotide probes. We present the crystal structures of ternary complexes of Thermus aquaticus DNA polymerase (KlenTaq) with C5-heterocycle-modified environment-sensitive 2'-deoxyuridine-5'-triphosphate (dUTP) probes.

Particle-wall alignment interaction and active Brownian diffusion through narrow channels.

We numerically examine the impacts of particle-wall alignment interactions on active species diffusion through a structureless narrow two-dimensional channel. We consider particle-wall interaction to depend on the self-propulsion velocity direction whereby some specific particle's alignments with respect to the boundary walls are stabilized more. Further, the alignment interaction is meaningful as long as particles are close to the confining boundaries.

Ratcheting by Stochastic Resetting With Fat-Tailed Time Distributions.

We investigated both numerically and analytically the drift of a Brownian particle in a ratchet potential under stochastic resetting with fat-tailed distributions. As a study case we chose a Pareto time distribution with tail index β. We observed that for rectification occurs even if for the mean resetting time is infinite.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Chloride Transport across Liposomes and Cells by Nontoxic 3-(1-1,2,3-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-(1-1,2,3-triazol-1-yl)benzamides as transmembrane anion carriers, nontoxic to cells.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

Hydrodynamic interaction of trapped active Janus particles in two dimensions.

The dynamics of a pair of identical artificial microswimmers bound inside two harmonic traps, in a thin sheared fluid film, is numerically investigated. In a two-dimensional Oseen approximation, the hydrodynamic pair coupling is long-ranged and proportional to the particle radius to film thickness ratio. On increasing such ratio above a certain threshold, a transition occurs between a free regime, where each swimmer orbits in its own trap with random phase, and a strong synchronization regime, where the two swimmers strongly repel each other to an average distance larger than both the trap distance and their free orbit diameter.

Two-dimensional dynamics of a trapped active Brownian particle in a shear flow.

We model the two-dimensional dynamics of a pointlike artificial microswimmer diffusing in a harmonic trap subject to the shear flow of a highly viscous medium. The particle is driven simultaneously by the linear restoring force of the trap, the drag force exerted by the flow, and the torque due to the shear gradient. For a Couette flow, elliptical orbits in the noiseless regime, and the correlation functions between the particle's displacements parallel and orthogonal to the flow are computed analytically.