No abstract

Cells communicate with each other to coordinate their gene activities at the population level through signaling pathways. It has been shown that many gene activities are oscillatory and that the frequency and phase of oscillatory gene expression encode various types of information. However, whether or how such oscillatory information is transmitted from cell to cell remains unknown. Here, we developed an integrated approach that combines optogenetic perturbations and single-cell bioluminescence imaging to visualize and reconstitute synchronized oscillatory gene expression in signal-sending and signal-receiving processes. We found that intracellular and intercellular periodic inputs of Notch signaling entrain intrinsic oscillations by frequency tuning and phase shifting at the singlecell level. In this way, the oscillation dynamics are transmitted through Notch signaling, thereby synchronizing the population of oscillators. Thus, this approach enabled us to control and monitor dynamic cell-to-cell transfer of oscillatory information to coordinate gene expression patterns at the population level.

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.

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We study slip-avalanches in two-dimensional soft athermal disks by quasi-static simulations of simple shear deformations. Sharp drops in shear stress, or slip-avalanches, are observed intermittently during steady state. Such the stress drop is caused by restructuring of the contact networks, accompanied by drastic changes of the interaction forces, ∆ f . The changes of the forces happen heterogeneously in space, indicating that collective non-affine motions of the disks are most pronounced when slip-avalanches occur. We analyze and predict statistics for the force changes, ∆ f , by transition rates of the force and contact angle, where slip-avalanches are characterized by their wide power-law tails. We find that the transition rates are described as a q-Gaussian distribution regardless of the area fraction of the disks. Because the transition rates quantify structural changes of the force-chains, our findings are an important step towards a microscopic theory of slip-avalanches in the experimentally accessible quasi-static regime.The mechanics of amorphous solids, e.g. glasses, ceramics, colloidal suspensions, and granular materials, is of crucial importance in engineering science 1 . Continuously shearing amorphous solids, one observes plastic deformations after a yielding point, where stress exhibits intermittent fluctuations around a mean In this Communication, we investigate microscopic structural changes of force-chain networks by QS simulations. As a model of amorphous solids, we simulate disordered soft athermal disks in two dimensions. In our system, slip-avalanches are caused by restructuring of the force-chain networks (accompanied by drastic changes of the forces between the disks) under shear. These structural changes of force-chains are analyzed by introducing transition rates as previously studied for isotropic deformations 31 . The transition rates describe the development of force distributions through a master equation. We find that (i) despite J o u r n a l N a me , [ y e a r ] , [ v o l . ] , 1-5 | 1 arXiv:1809.10487v1 [cond-mat.soft]