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Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active perturbation affects fluctuating dynamics of an inclusion in the chromatic medium. Using numerical simulations and a versatile effective model, we categorize inclusion dynamics into three distinct modes. The transient-link-and-pass activity speeds up inclusion dynamics by affecting a slow mode related to chromatin remodeling, viz., size and shape of the chromatin meshes.

Spatial organization of chromatin plays a critical role in genome regulation. Various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at the mechanistic level, enzymes act in their unique ways. Here, we construct a polymer physics model following the mechanistic scheme of Topoisomerase-II, an enzyme resolving topological constraints of chromatin, and investigate its role on interphase chromatin organization. Our computer simulations demonstrate Topoisomerase-II's ability to phase separate chromatin into eu- and heterochromatic regions with a characteristic wall-like organization of the euchromatic regions. Exploiting a mean-field framework, we argue that the ability of the euchromatic regions crossing each other due to enzymatic activity of Topoisomerase-II induces this phase separation. Motivated from a recent experimental observation on different structural states of the eu- and the heterochromatic units, we further extend our model to a bidisperse setting and show that the characteristic features of the enzymatic activity driven phase separation survives there. The existence of these characteristic features, even under the non-localized action of the enzyme, highlights the critical role of enzymatic activity in chromatin organization, and points out the importance of further experiments along this line., Comment: 4 figures, 3 supplementary figures

Tissues are characterized by layers of functional units such as cells and extracellular matrix (ECM). Nevertheless, how dynamics at interlayer interfaces help transmit cellular forces in tissues remains overlooked. Here, we investigate a multi-layer system where a layer of epithelial cells is seeded upon an elastic substrate in contact with a hard surface. Our experiments show that, upon a cell extrusion event in the cellular layer, long-range wave propagation emerges in the substrate only when the two substrate layers were weakly attached to each other. We then derive a theoretical model which quantitatively reproduces the wave dynamics and explains how frictional sliding between substrate layers helps propagate cellular forces at a variety of scales, depending on the stiffness, thickness, and slipperiness of the substrate. These results highlight the importance of interfacial friction between layers in transmitting mechanical cues in tissues in vivo., Comment: Main texts: 22 pages, 5 figures, 1 table. Supplementary Information: 21 pages including 5 figures. Movies are not available here

It is still challenging to control dynamic self-organization patterns of self-propelled particles. Although varieties of patterns associated with chirality have been observed, essential control factors determining patterns remain unclear. Here, we explore numerically how torque upon particle collision affects dynamic self-organization. Based on the particle-based model with both collision-induced torque and torque in self-propulsion, we find that introducing collision-induced torque turns homogeneous bi-polar orientation templated by bi-directional alignment into rotating mono-polar flocks., Comment: 24 pages, 7 figures

Various multicellular tissues show chiral morphology. Experimental studies have shown this can originate from cell chirality. However, no theory has been proposed to connect the cellular chiral torque and multicellular chiral morphogenesis. We propose a model of confluent tissue dynamics with cellular chiral torque. We found that cells migrate unidirectionally under a gradient of cellular chiral torque. While the migration speed varies depending on the tissue's mechanical parameters, it is scaled solely by a structural order parameter for liquid-to-solid transition in confluent tissues., Comment: 9 pages, 9 figures

Active matter consists of self-propelled elements exhibits fascinating collective motions ranging from biological to artificial systems. Among wide varieties of active matter systems, reconstituted bio-filaments moving on molecular motor turf interacting purely by physical interactions provides the fundamental test ground for understanding biological motility. However, until now, multi-filament collisions,depletion agents or binding molecules has been required for the emergence of ordered patterns in motility assay. Thus, whether simple physical interactions during collisions such as steric effect without depletion nor binding agents are sufficient or not for producing ordered patterns in motility assays remains still elusive. In this article, we constructed a motility assay purely consists of kinesin motor and microtubule in which the frequency of binary collision can be controlled without using depletion nor binding agents. By controlling strength of steric interaction and density of microtubules, we found different states; disordered state, long-range orientationally ordered state, liquid-gas-like phase separated state, and transitions between them. We found that a balance between cross over and aligning events in collisions controls transition from disorder to global ordered state, while excessively strong steric effect leads to the phase separated clusters. Furthermore, macroscopic chiral symmetry breaking observed as a global rotation of nematic order observed in this experiment could be attributed to the chirality at molecular level. Numerical simulations in which we change strength of volume exclusion reproduce these experimental results. Moreover, it reveals the transition from long-range alignment to nematic bands then to aggregations. This study may provide new insights into dynamic ordering by self-propelled elements through a purely physical interaction., Comment: 18 pages, 11 figures

We study the effect of turnover of cross linkers, motors and filaments on the generation of a contractile stress in a network of filaments connected by passive crosslinkers and subjected to the forces exerted by molecular motors. We perform numerical simulations where filaments are treated as rigid rods and molecular motors move fast compared to the timescale of exchange of crosslinkers. We show that molecular motors create a contractile stress above a critical number of crosslinkers. When passive crosslinkers are allowed to turn over, the stress exerted by the network vanishes, due to the formation of clusters. When both filaments and passive crosslinkers turn over, clustering is prevented and the network reaches a dynamic contractile steady-state. A maximum stress is reached for an optimum ratio of the filament and crosslinker turnover rates., Comment: 17 pages, 8 figures, 5 supplementary movies (included in the source) In the latest version, appendices D and E have been added, text has been updated, Figure 2 has been corrected, and Figure 4 has been replaced by simulation results with higher precision

Chemotactic cells establish cell polarity in the absence of external guidance cues. Such self-organized polarity is induced by spontaneous symmetry breaking in the intracellular activities, which produces an emergent memory effect associated with slow-changing mode. Therefore, spontaneously established polarity should play a pivotal role in efficient chemotaxis. In this study, we develop a model of chemotactic cell migration that demonstrates the connection between intracellular polarity and chemotactic accuracy. Spontaneous polarity formation and gradient sensing are described by a stochastic differential equation. We demonstrate that the direction of polarity persists over a characteristic time that is predicted to depend on the chemoattractant concentration. Next, we theoretically derive the chemotactic accuracy as a function of both the gradient sensing ability and the characteristic time of polarity direction. The results indicate that the accuracy can be improved by the polarity. Furthermore, the analysis of chemotactic accuracy suggests that accuracy is maximized at some optimal responsiveness to extracellular perturbations. To obtain the model parameters, we studied the correlation time of random cell migration in cell tracking analysis of Dictyostelium cells. As predicted, the persistence time depended on the chemoattractant concentration. From the fitted parameters, we inferred that polarized Dictyosteium cells can respond optimally to a chemical gradient. Chemotactic accuracy was almost 10 times larger than can be achieved by non-polarized gradient sensing. Using the obtained parameter values, we show that polarity also improves the dynamic range of chemotaxis., Comment: In page 3, typo has been corrected