| 09/2023 Escaping kinetic traps using non-reciprocal interactions Saeed Osat et al. Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system to low energy configurations. Using multifarious self-assembly as a model system, we introduce a mechanism to escape kinetic traps by utilizing non-reciprocal interactions between components. Introducing non-equilibrium effects offered by broken action-reaction … |
| 08/2023 The motility-matrix production switch in Bacillus subtilis — a modeling perspective Simon Dannenberg et al. Phenotype switching can be triggered by external stimuli and by intrinsic stochasticity. Here, we focus on the motility-matrix production switch in Bacillus subtilis. We use modeling to describe the SinR-SlrR bistable switch its regulation by SinI, and to distinguish different sources of stochasticity. Our simulations indicate that intrinsic fluctuations in the synthesis of SinI are insufficient t … |
| 08/2023 Motility induced phase separation of deformable cells Austin Hopkins et al. Using a multi-phase field model, we examine how particle deformability, which is a proxy for cell stiffness, affects motility induced phase separation (MIPS). We show that purely repulsive deformable, i.e., squishy, cells phase separate more effectively than their rigid counterparts. This can be understood as due to the fact that deformability increases the effective duration of collisions. In add … |
| 08/2023 A unified-field theory of genome organization and gene regulation Giuseppe Negro Massimiliano Semeraro Perter R Cook Davide Marenduzzo et al. Our aim is to predict how often genic and non-genic promoters fire within a cell. We first review a parsimonious pan-genomic model for genome organization and gene regulation, where transcription rate is determined by proximity in 3D space of promoters to clusters containing appropriate factors and RNA polymerases — structures variously called transcription factories, hubs, and condensates. This … |
| 07/2023 Scaling transition of active turbulence from two to three dimensions Da Wei et al. Turbulent flows are observed in low-Reynolds active fluids. They are intrinsically different from the classical inertial turbulence and behave distinctively in two- and three-dimensions. Understanding the behaviors of this new type of turbulence and their dependence on the system dimensionality is a fundamental challenge in non-equilibrium physics. We experimentally measure flow structures and ene … |
| 07/2023 Thawed Matrix method for computing Local Mechanical Properties of Amorphous Solids Jörg Rottler et al. We present a method for computing locally varying nonlinear mechanical properties in particle simulations of amorphous solids. Plastic rearrangements outside a probed region are suppressed by introducing an external field that directly penalizes large nonaffine displacements. With increasing strength of the field, plastic deformation can be localized. We characterize the distribution of local plas … |
| 07/2023 Available observation time regulates optimal balance between sensitivity and confidence Sahel Azizpour et al. Tasks that require information about the world imply a trade-off between the time spent on observation and the variance of the response. In particular, fast decisions need to rely on uncertain information. However, standard estimates of information processing capabilities, such as the dynamic range, are defined based on mean values that assume infinite observation times. Here, we show that limitin … |
| 07/2023 Energetic cost of microswimmer navigation: the role of body shape Lorenzo Piro et al. We study the energetic efficiency of navigating microswimmers by explicitly taking into account the geometry of their body. We show that, as their shape transitions from prolate to oblate, non-steering microswimmers rotated by flow gradients naturally follow increasingly time-optimal trajectories. At the same time, they also require larger dissipation to swim. The coupling between body geometry an … |
| 07/2023 Theory of Elastic Microphase Separation Yicheng Qiang et al. Elastic microphase separation refers to equilibrium patterns that form by phase separation in elastic gels. Recent experiments revealed a continuous phase transition from the homogeneous phase to a regularly patterned phase, whose period decreased for stiffer systems. We here propose a model that captures these observations. The model combines a continuous field of the elastic component to describ … |
| 07/2023 Enhanced diffusion of tracer particles in non-reciprocal mixtures Anthony Benois et al. We study the diffusivity of a tagged particle in a binary mixture of Brownian particles with non-reciprocal interactions. Numerical simulations reveal that, for a broad class of interaction potentials, non-reciprocity can significantly increase the effective diffusion coefficient of tracer particles, and that this diffusion enhancement is associated with a breakdown of the Einstein relation. These … |