In this article we present a comprehensive study of the totally asymmetric simple exclusion process with pausing particles (pTASEP), a model initially introduced to describe RNAP dynamics during transcription. We extend previous mean-field approaches and demonstrate that the pTASEP is equivalent to the exclusion process with dynamical defects (ddTASEP), thus broadening the scope of our investigation to a larger class of problems related to transcription and translation. We extend the mean-field theory to the open boundary case, revealing the system's phase diagram and critical values of entry and exit rates. However, we identify a significant discrepancy between theory and simulations in a region of the parameter space, indicating severe finite-size effects. To address this, we develop a single-cluster approximation that captures the relationship between current and lattice size, providing a more accurate representation of the system's dynamics. Finally, we extend our approach to open boundary conditions, demonstrating its applicability in different scenarios. Our findings underscore the importance of considering finite-size effects, often overlooked in the literature, when modelling biological processes such as transcription and translation.

The emergence of surprising collective behaviors in systems driven out of equilibrium by local energy injection at the particle level remains a central theme in the study of active matter. Recently, chaotic flows reminiscent of turbulence have garnered significant attention due to their appearance in diverse biological and physical active matter systems. In this talk, I will demonstrate how even the simplest model of active particles — self-propelled point particles — can exhibit mesoscale flows, characterized by streams and vortices, when very persistent active forces compete with crowding at high densities.In the second part, I will introduce a minimal model of non-reciprocal interactions inspired by human crowds, which generates collective flows strikingly similar to those of the self-propelled particles. Interestingly, as the system approaches the equilibrium limit by reducing non-reciprocity, it undergoes an absorbing phase transition characterized by an infinite number of absorbing states and critical exponents consistent with the conserved directed percolation universality class.

We address the question of how viscosity impacts the growth of gravitation waves, such as those on the ocean, when they are driven by wind. There is so far no general rigorous theory for this energy transfer. We extend Miles' approach [J. W. Miles, “On the generation of surface waves by shear flows,” J. Fluid Mech. 3, 185–204 (1957)], using the same logarithmic wind profile, to incorporate bulk viscosity and derive modified growth rates. Exploiting the fact that water waves fall into the “weak viscosity” regime, we produce analytical expressions for the growth rate, which we solve using the numerical method proposed by Beji and Nadaoka [“Solution of Rayleigh's instability equation for arbitrary wind profiles,” J. Fluid Mech. 500, 65–73 (2004)]. Our results confirm that corrections to the growth rates are significant for wavelengths below a meter, and for weak to modest wind strengths. We show that all wave growth is suppressed, due to viscous effects, below a critical wind strength. We also show that the wave age corresponding to a developed sea is reduced by viscosity. We quantitatively characterize the zones, in terms of wind strength and wavelength, for which the wave growth is suppressed by viscosity.

We study two models of overdamped self-propelled disks in two dimensions, with and without aligning interactions. Both models support active mesoscale flows, leading to chaotic advection and transport over large length scales in their homogeneous dense fluid states, away from dynamical arrest. They form streams and vortices reminiscent of multiscale flow patterns in turbulence. We show that the characteristics of these flows do not depend on the specific details of the active fluids, and result from the competition between crowding effects and persistent propulsions. This observation suggests that dense active suspensions of self-propelled particles present a type of “active turbulence” distinct from collective flows reported in other types of active systems. Published by the American Physical Society 2024