Inertia and activity: spiral transitions in semi-flexible, self-avoiding polymers.

We consider a two-dimensional, tangentially active, semi-flexible, self-avoiding polymer to find a dynamical re-entrant transition between motile open chains and spinning achiral spirals with increasing activity. Utilizing probability distributions of the turning number, we ascertain the comparative stability of the spiral structure and present a detailed phase diagram within the activity inertia plane. The onset of spiral formation at low activity levels is governed by a torque balance and is independent of inertia.

Anomalous dynamics of a passive droplet in active turbulence.

Motion of a passive deformable object in an active environment serves as a representative of both in-vivo systems such as intracellular particle motion in Acanthamoeba castellanii, or in-vitro systems such as suspension of beads inside dense swarms of Escherichia coli. Theoretical modeling of such systems is challenging due to the requirement of well resolved hydrodynamics which can explore the spatiotemporal correlations around the suspended passive object in the active fluid. We address this critical lack of understanding using coupled hydrodynamic equations for nematic liquid crystals with finite active stress to model the active bath, and a suspended nematic droplet with zero activity.

Homopolymer and heteropolymer translocation through patterned pores under fluctuating forces.

We investigate the translocation of a semiflexible polymer through extended patterned pores using Langevin dynamics simulations, specifically focusing on the influence of a time-dependent driving force. Our findings reveal that, akin to its flexible counterpart, a rigid chain-like molecule translocates faster when subjected to an oscillating force than a constant force of equivalent average magnitude. The enhanced translocation is strongly correlated with the stiffness of the polymer and the stickiness of the pores.

Emergence of slip-ideal-slip behavior in tip-links serve as force filters of sound in hearing.

Tip-links in the inner ear convey force from sound and trigger mechanotransduction. Here, we present evidence that tip-links (collectively as heterotetrameric complexes of cadherins) function as force filters during mechanotransduction. Our force-clamp experiments reveal that the tip-link complexes show slip-ideal-slip bond dynamics.

Gain reversal in the translocation dynamics of a semiflexible polymer through a flickering pore.

We study the driven translocation of a semiflexible polymer through an attractive extended pore with a periodically oscillating width. Similar to its flexible counterpart, a stiff polymer translocates through an oscillating pore more quickly than a static pore whose width is equal to the oscillating pore's mean width. This efficiency quantified as a gain in the translocation time, highlights a considerable dependence of the translocation dynamics on the stiffness of the polymer and the attractive nature of the pore.

Stochastic resonance in a model of a periodically driven DNA: Multiple transitions, scaling, and sequence dependence.

We numerically study stochastic resonance in the unzipping of a model double-stranded DNA by a periodic force. We observe multiple peaks in stochastic resonance in the output signal as the driving force frequency is varied for different force amplitudes, temperature, chain length, and chain heterogeneity. Multiple peaks point to the existence of multiple stable and metastable states, which correspond to dynamical states of partially zipped and unzipped conformations and transitions between them.

Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions.

We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible polymer through an extended channel as control, we first show that the asymmetric shape of the channel gives rise to non-monotonic features in the total translocation time as a function of the apex angle of the channel. The waiting time distributions of individual monomer beads inside the channel show unique features strongly dependent on the driving force and the surface interactions.

Effectiveness of Arsenicum album 30C in Prevention of COVID-19 in Individuals Residing in Containment Zones of Delhi-A Prospective, Community-based, Parallel Cohort Study.

Objective: This work was undertaken to evaluate the protective effect of 30C against COVID-19.

Design: The work was designed as a prospective parallel cluster cohort study.

Intervention: Participants were enrolled in a homeopathy intervention (HI) cohort (who received ) or in a non-intervention (NI) cohort (who received no systematic intervention) from COVID-19 containment areas of Delhi.

Deconstructing the role of myosin contractility in force fluctuations within focal adhesions.

Force fluctuations exhibited in focal adhesions that connect a cell to its extracellular environment point to the complex role of the underlying machinery that controls cell migration. To elucidate the explicit role of myosin motors in the temporal traction force oscillations, we vary the contractility of these motors in a dynamical model based on the molecular clutch hypothesis. As the contractility is lowered, effected both by changing the motor velocity and the rate of attachment/detachment, we show analytically in an experimentally relevant parameter space, that the system goes from decaying oscillations to stable limit cycle oscillations through a supercritical Hopf bifurcation.

A semiflexible polymer in a gliding assay: reentrant transition, role of turnover and activity.

We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a capture radius, and extend along the filament in a directed fashion before detaching. Both the extension and detachment rates are load-dependent and generate an active drive on the filament.

Morphological and dynamical properties of semiflexible filaments driven by molecular motors.

We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load experienced. Attached motor proteins move along the filament to one of its ends with a velocity that varies nonlinearly with the motor protein extension. The resultant force on the filament drives it out of equilibrium.

Force-activated catalytic pathway accelerates bacterial adhesion against flow.

Mechanical cues often influence the factors affecting the transition states of catalytic reactions and alter the activation pathway. However, tracking the real-time dynamics of such activation pathways is limited. Using single-molecule trapping of reaction intermediates, we developed a method that enabled us to perform one reaction at one site and simultaneously study the real-time dynamics of the catalytic pathway.

Sequencing of semiflexible polymers of varying bending rigidity using patterned pores.

We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and depends strongly on the interplay of polymer stiffness and pore-polymer interactions. For heterogeneous polymers with periodically varying stiffness along their lengths, we find that variation of the block size of the sequences and the orientation results in large variations in the translocation time distributions.

Effect of catch bonding on transport of cellular cargo by dynein motors.

Recent experiments have demonstrated that dynein motors exhibit catch bonding behavior, in which the unbinding rate of a single dynein decreases with increasing force, for a certain range of force. Motivated by these experiments, we study the effect of catch bonding on unidirectional transport properties of cellular cargo carried by multiple dynein motors. We introduce a threshold force bond deformation (TFBD) model, consistent with the experiments, wherein catch bonding sets in beyond a critical applied load force.

Forced desorption of semiflexible polymers, adsorbed and driven by molecular motors.

We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the filament. The stochastic binding-unbinding of the motor proteins and their ability to move along the polymer generate active forces. As the pulling force reaches a threshold value, the polymer eventually desorbs from the substrate.

Translocation through environments with time dependent mobility.

We consider single particle and polymer translocation where the frictional properties experienced from the environment are changing in time. This work is motivated by the interesting frequency responsive behaviour observed when a polymer is passing through a pore with an oscillating width. In order to explain this better we construct general diffusive and non-diffusive frequency response of the gain in translocation time for a single particle in changing environments and look at some specific variations.

Modified fluctuation-dissipation and Einstein relation at nonequilibrium steady states.

Starting from the pioneering work of Agarwal [G. S. Agarwal, Zeitschrift für Physik 252, 25 (1972)], we present a unified derivation of a number of modified fluctuation-dissipation relations (MFDR) that relate response to small perturbations around nonequilibrium steady states to steady-state correlations.

Active polymer translocation through flickering pores.

Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to significantly more efficient translocation as compared to a static channel that has a width equal to the mean width of the oscillating pore. The gain in translocation exhibits a strong dependence on the stickiness of the pore, which could allow the polymer translocation process to be highly selective.

Spatiotemporal regulation of chemical reactions by active cytoskeletal remodeling.

Efficient and reproducible construction of signaling and sorting complexes, both on the surface and within the living cell, is contingent on local regulation of biochemical reactions by the cellular milieu. We propose that in many cases this spatiotemporal regulation can be mediated by interaction with components of the dynamic cytoskeleton. We show how the interplay between active contractility and remodeling of the cytoskeleton can result in transient focusing of passive molecules to form clusters, leading to a dramatic increase in the reaction efficiency and output levels.

The effect of interactions on the cellular uptake of nanoparticles.

We present a simple two-state model to understand the size-dependent endocytosis of nanoparticles. Using this model, we elucidate the relevant energy terms required to understand the size-dependent uptake mechanism and verify it by correctly predicting the behavior at large and small particle sizes. In the absence of interactions between the nanoparticles, we observe an asymmetric distribution of sizes with maximum uptake at intermediate sizes and a minimum size cut-off below which there can be no endocytosis.

Driving particle current through narrow channels using a classical pump.

We study a symmetric exclusion process in which the hopping rates at two chosen adjacent sites vary periodically in time and have a relative phase difference. This mimics a colloidal suspension subjected to external time-dependent modulation of the local chemical potential. The two special sites act as a classical pump by generating an oscillatory current with a nonzero dc value whose direction depends on the applied phase difference.

Fluctuations at a constrained liquid-solid interface.

We study the interface between a solid trapped within a bath of liquid by a suitably shaped nonuniform external potential. Such a potential may be constructed using lasers, external electric or magnetic fields, or a surface template. We study a two-dimensional case where a thin strip of solid, created in this way, is surrounded on either side by a bath of liquid with which it can easily exchange particles.

Stress relaxation in a perfect nanocrystal by coherent ejection of lattice layers.

We show that a small crystal trapped within a potential well and in contact with its own fluid responds to large compressive stresses by a novel mechanism--the transfer of complete lattice layers across the solid-fluid interface. Further, when the solid is impacted by a momentum impulse set up in the fluid, a coherently ejected lattice layer carries away a definite quantity of energy and momentum, resulting in a sharp peak in the calculated phonon absorption spectrum. Apart from its relevance to studies of stability and failure of small sized solids, such coherent nanospallation may be used to make atomic wires or monolayer films.

Growing smooth interfaces with inhomogeneous moving external fields: dynamical transitions, devil's staircases, and self-assembled ripples.

We study the steady state structure and dynamics of an interface in a pure Ising system on a square lattice placed in an inhomogeneous external field with a profile designed to stabilize a flat interface and translated with velocity v(e). For small v(e), the interface is stuck to the profile, is macroscopically smooth, and is rippled with a periodicity in general incommensurate with the lattice parameter. For arbitrary orientations of the profile, the local slope of the interface locks in to one of infinitely many rational values (devil's staircase) which most closely approximates the profile.