Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable model

Active loop extrusion-the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes-is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the equilibrium ensemble. This framework allows us to arrive at the closed-form analytical expression for the mean-squared distance between pairs of genomic loci, which is valid beyond the one-loop approximation in diagrammatic representation. In addition, we analyze the loop-induced deviation of chain conformations from the Gaussian statistics by calculating kurtosis of probability density of the pairwise separation vector. The presented results suggest the possible ways of estimating the characteristics of the loop extrusion process based on the experimental data on the scale-dependent statistics of intra-chromosomal pair-wise distances.

Crumpled polymer with loops recapitulates key features of chromosome organization

Chromosomes are exceedingly long topologically-constrained polymers compacted in a cell nucleus. We recently suggested that chromosomes are organized into loops by an active process of loop extrusion. Yet loops remain elusive to direct observations in living cells; detection and characterization of myriads of such loops is a major challenge. The lack of a tractable physical model of a polymer folded into loops limits our ability to interpret experimental data and detect loops. Here, we introduce a new physical model - a polymer folded into a sequence of loops, and solve it analytically. Our model and a simple geometrical argument show how loops affect statistics of contacts in a polymer across different scales, explaining universally observed shapes of the contact probability. Moreover, we reveal that folding into loops reduces the density of topological entanglements, a novel phenomenon we refer as "the dilution of entanglements". Supported by simulations this finding suggests that up to ~ 1 - 2Mb chromosomes with loops are not topologically constrained, yet become crumpled at larger scales. Our theoretical framework allows inference of loop characteristics, draws a new picture of chromosome organization, and shows how folding into loops affects topological properties of crumpled polymers.

Universal performance bounds of restart

As has long been known to computer scientists, the performance of probabilistic algorithms characterized by relatively large runtime fluctuations can be improved by applying a restart, i.e., episodic interruption of a randomized computational procedure followed by initialization of its new statistically independent realization. A similar effect of restart-induced process acceleration could potentially be possible in the context of enzymatic reactions, where dissociation of the enzyme-substrate intermediate corresponds to restarting the catalytic step of the reaction. To date, a significant number of analytical results have been obtained in physics and computer science regarding the effect of restart on the completion time statistics in various model problems, however, the fundamental limits of restart efficiency remain unknown. Here we derive a range of universal statistical inequalities that offer constraints on the effect that restart could impose on the completion time of a generic stochastic process. The corresponding bounds are expressed via simple statistical metrics of the original process such as harmonic mean h, median value m, and mode M, and, thus, are remarkably practical. We test our analytical predictions with multiple numerical examples, discuss implications arising from them and important avenues of future work.

Second-harmonic generation as a minimal model of turbulence

When two resonantly interacting modes are in contact with a thermostat, their statistics is exactly Gaussian and the modes are statistically independent despite strong interaction. Considering a noise-driven system, we show that when one mode is pumped and another dissipates, the statistics of such cascades is never close to Gaussian, no matter what is the relation between interaction and noise. One finds substantial phase correlation in the limit of strong interaction or weak noise. Surprisingly, the mutual information between modes increases and entropy decreases when interaction strength decreases. We use the model to elucidate the fundamental problem of far-from equilibrium physics: where the information, or entropy deficit, is encoded, and how singular measures form. For an instability-driven system, such as laser, even a small added noise leads to large fluctuations of the relative phase near the stability threshold, while far from the equilibrium the conversion into the second harmonic is weakly affected by noise.

Conformational statistics of non-equilibrium polymer loops in Rouse model with active loop extrusion

Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper, we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is characterized statistically by the mean gyration radius and the pairwise contact probabilities. It turns out that a single dimensionless parameter, which is given by the ratio of the loop relaxation time over the time elapsed since the start of extrusion, controls the crossover between near-equilibrium and highly non-equilibrium asymptotics in the statistics of the extruded loop, regardless of the specific time dependence of the extrusion velocity. In addition, we show that two-sided and one-sided loop extruding motors produce the loops with almost identical properties. Our predictions are based on two rigorous semi-analytical methods accompanied by asymptotic analysis of slow and fast extrusion limits.

Active motion of passive asymmetric dumbbells in a non-equilibrium bath

Persistent motion of passive asymmetric bodies in non-equilibrium media has been experimentally observed in a variety of settings. However, fundamental constraints on the efficiency of such motion are not fully explored. Understanding such limits, and ways to circumvent them, is important for efficient utilization of energy stored in agitated surroundings for purposes of taxis and transport. Here, we examine such issues in the context of erratic movements of a passive asymmetric dumbbell driven by non-equilibrium noise. For uncorrelated (white) noise, we find a (non-Boltzmann) joint probability distribution for the velocity and orientation, which indicates that the dumbbell preferentially moves along its symmetry axis. The dumbbell thus behaves as an Ornstein-Uhlenbeck walker, a prototype of active matter. Exploring the efficiency of this active motion, we show that in the over-damped limit, the persistence length l of the dumbbell is bound from above by half its mean size, while the propulsion speed v_∥ is proportional to its inverse size. The persistence length can be increased by exploiting inertial effects beyond the over-damped regime, but this improvement always comes at the price of smaller propulsion speeds. This limitation is explained by noting that the diffusivity of a dumbbell, related to the product v_∥l, is always less than that of its components, thus severely constraining the usefulness of passive dumbbells as active particles.

Pair dispersion in dilute suspension of active swimmers

Ensembles of biological and artificial microswimmers produce long-range velocity fields with strong nonequilibrium fluctuations, which result in a dramatic increase in diffusivity of embedded particles (tracers). While such enhanced diffusivity may point to enhanced mixing of the fluid, a rigorous quantification of the mixing efficiency requires analysis of pair dispersion of tracers, rather than simple one-particle diffusivity. Here, we calculate analytically the scale-dependent coefficient of relative diffusivity of passive tracers embedded in a dilute suspension of run-and-tumble microswimmers. Although each tracer is subject to strong fluctuations resulting in large absolute diffusivity, the small-scale relative dispersion is suppressed due to the correlations in fluid velocity which are relevant when the inter-tracer separation is below the persistence length of the swimmer's motion. Our results suggest that the reorientation of swimming direction plays an important role in biological mixing and should be accounted in the design of potential active matter devices capable of effective fluid mixing at microscale.

Inelastic collapse and near-wall localization of randomly accelerated particles

Inelastic collapse of stochastic trajectories of a randomly accelerated particle moving in half-space z>0 has been discovered by McKean [J. Math. Kyoto Univ. 2, 227 (1963)] and then independently rediscovered by Cornell et al. [Phys. Rev. Lett. 81, 1142 (1998)PRLTAO0031-900710.1103/PhysRevLett.81.1142]. The essence of this phenomenon is that the particle arrives at the wall at z=0 with zero velocity after an infinite number of inelastic collisions if the restitution coefficient β of particle velocity is smaller than the critical value β_{c}=exp(-π/sqrt[3]). We demonstrate that inelastic collapse takes place also in a wide class of models with spatially inhomogeneous random forcing and, what is more, that the critical value β_{c} is universal. That class includes an important case of inertial particles in wall-bounded random flows. To establish how inelastic collapse influences the particle distribution, we derive the exact equilibrium probability density function ρ(z,v) for the particle position and velocity. The equilibrium distribution exists only at β<β_{c} and indicates that inelastic collapse does not necessarily imply near-wall localization.

Synchronization dynamics in diverse ensemble of noisy phase oscillators with asynchronous phase updates

Decentralized control of autonomous phase oscillators integrated into networked systems is of great interest for many technological applications, from clock synchronization in sensor nets to coordinated motion in swarm robotics. In the simplest distributed synchronization scheme, each oscillator updates its phase from time to time to a new value equal to the average of its present phase and the phases of its neighbors. Here we describe the resulting synchronization dynamics within a mean-field model where the update actions of different oscillators are completely asynchronous. In particular, it is shown how the steady-state level of synchrony depends on noise intensity and frequency diversity for any given rate of updates. The central part of the analysis is devoted to the case when the correction rate positively correlates with the degree of macroscopic coherence. We demonstrate that depending on relation between correction rate and phase coherence the oscillators may exhibit both continuous and discontinuous transition from incoherence to synchrony upon the change of interaction constant. To illustrate our analytical results, numerical simulations have been performed for a large population of phase oscillators with the proposed type of coupling.

Localization-delocalization transitions in turbophoresis of inertial particles

Small aerosols drift down a temperature or turbulence gradient since faster particles fly longer distances before equilibration. That fundamental phenomenon, called thermophoresis or turbophoresis, is widely encountered in nature and used in industry. It is universally believed that particles moving down the kinetic energy gradient must concentrate in minima (say, on walls in turbulence). Here, we show that this is incorrect: escaping minima is possible for inertial particles whose time of equilibration is longer than the time to reach the minimum. "The best way out is always through": particles escape by flying through minima or reflecting from walls. We solve the problem analytically and find the phase transition as a sign change of the mean velocity. That means separation: light particles concentrate in a minimum while heavy particles spread away from it (gravity can reverse the effect). That discovery changes our understanding of that fundamental phenomenon and may find numerous applications.

Adjustable subwavelength localization in a hybrid plasmonic waveguide

The hybrid plasmonic waveguide consists of a high-permittivity dielectric nanofiber embedded in a low-permittivity dielectric near a metal surface. This architecture is considered as one of the most perspective candidates for long-range subwavelength guiding. We present qualitative analysis and numerical results which reveal advantages of the special waveguide design when dielectric constant of the cylinder is greater than the absolute value of the dielectric constant of the metal. In this case the arbitrary subwavelength mode size can be achieved by controlling the gap width. Our qualitative analysis is based on consideration of sandwich-like conductor-gap-dielectric system. The numerical solution is obtained by expansion of the hybrid plasmonic mode over single cylinder modes and the surface plasmon-polariton modes of the metal screen and matching the boundary conditions.

Magnetic resonance imaging in children receiving quinolones: no evidence of quinolone-induced arthropathy. A multicenter survey

Twenty-nine children with cystic fibrosis (CF) were investigated for quinolone-induced arthropathy. Magnetic resonance imaging (MRI) was performed in 14/14 children treated with ofloxacin or ciprofloxacin and in 10/15 of those never treated with quinolones. The frequency of pathologic MRI findings, concerning cartilage thickness, careful analysis of the cartilage structure, presence of edema, cartilage-bone borderline and the presence of fluid in joints did not show any difference between both groups. Thus the presence of quinolone-induced arthrotoxicity cannot be confirmed in this study.