Controlling topological defects and contractile flow in confined nematic cell population

Topological defects in an orientation field play a vital role for controlling the collective motion of nematic cell populations within epithelia and tissue. In this study, we study the geometric control of the collective motion in a nematic cell population to further explore the interplay between topology and dynamics in active nematics. By applying spatial constraints consisting of two or three overlapping circle boundaries, we demonstrate an ordered pairing of half-integer topological defects in a confined cell population. The defects facing each other can induce a contractile cellular flow at broad geometric conditions. This robust contractile flow contributes to mechanical stimulation while altering the cell nucleus, which may be relevant to geometry-dependent morphogenesis.Comment: 8 pages, 5 figure

Geometry-Induced Dynamics of Confined Chiral Active Matter

Controlling the motion of active matter is a central issue that has recently garnered significant attention in fields ranging from non-equilibrium physics to chemical engineering and biology. Distinct methods for controlling active matter have been developed, and physical confinement to limited space and active matter with broken rotational symmetry (chirality) are two prominent mechanisms. However, the interplay between pattern formation due to physical constraints and the ordering by chiral motion needs to be better understood. In this study, we conduct numerical simulations of chiral self-propelled particles under circular boundary confinement. The collective motion of confined self-propelled particles can take drastically different forms depending on their chirality. The balance of orientation changes between particle interaction and the boundary wall is essential for generating ordered collective motion. Our results clarify the role of the steric boundary effect in controlling chiral active matter.Comment: 13 pages, 8 figures. Updated the list of reference

Geometric Effect for Biological Reactors and Biological Fluids

As expressed “God made the bulk; the surface was invented by the devil„ by W. Pauli, the surface has remarkable properties because broken symmetry in surface alters the material properties. In biological systems, the smallest functional and structural unit, which has a functional bulk space enclosed by a thin interface, is a cell. Cells contain inner cytosolic soup in which genetic information stored in DNA can be expressed through transcription (TX) and translation (TL). The exploration of cell-sized confinement has been recently investigated by using micron-scale droplets and microfluidic devices. In the first part of this review article, we describe recent developments of cell-free bioreactors where bacterial TX-TL machinery and DNA are encapsulated in these cell-sized compartments. Since synthetic biology and microfluidics meet toward the bottom-up assembly of cell-free bioreactors, the interplay between cellular geometry and TX-TL advances better control of biological structure and dynamics in vitro system. Furthermore, biological systems that show self-organization in confined space are not limited to a single cell, but are also involved in the collective behavior of motile cells, named active matter. In the second part, we describe recent studies where collectively ordered patterns of active matter, from bacterial suspensions to active cytoskeleton, are self-organized. Since geometry and topology are vital concepts to understand the ordered phase of active matter, a microfluidic device with designed compartments allows one to explore geometric principles behind self-organization across the molecular scale to cellular scale. Finally, we discuss the future perspectives of a microfluidic approach to explore the further understanding of biological systems from geometric and topological aspects