Phase separation organizes the site of autophagosome formation.

Many biomolecules undergo liquid-liquid phase separation to form liquid-like condensates that mediate diverse cellular functions. Autophagy is able to degrade such condensates using autophagosomes-double-membrane structures that are synthesized de novo at the pre-autophagosomal structure (PAS) in yeast. Whereas Atg proteins that associate with the PAS have been characterized, the physicochemical and functional properties of the PAS remain unclear owing to its small size and fragility.

Optimality conditions for cell-fate heterogeneity that maximize the effects of growth factors in PC12 cells.

Recently, the heterogeneity that arises from stochastic fate decisions has been reported for several types of cancer-derived cell lines and several types of clonal cells grown under constant environmental conditions. However, the relation between this stochasticity and the responsiveness to extracellular stimuli remains largely unknown. Here we focused on the fate decisions of the PC12 cell line, which was derived from rat pheochromocytoma, and is a model system to study differentiation into sympathetic neurons.

A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM.

Background: After IR stress, DNA double-strand breaks (DSBs) occur and repair proteins (RPs) bind to them, generating DSB-RP complexes (DSBCs), which results in repaired DSBs (RDSBs). In recent experimental studies, it is suggested that the ATM proteins detect these DNA lesions depending on the autophosphorylation of ATM which exists as a dimer before phosphorylation. Interestingly, the ATM proteins can work as a sensor for a small number of DSBs (approximately 18 DSBs in a cell after exposure to IR).

The Fokker-Planck approach for the cooperative molecular motor model with finite number of motors.

We provide the methodology for the analysis of the cooperative molecular motor model with finite number of motors, which are linearly and rigidly coupled, based on the Fokker-Planck approach. The probability density functions for the position of motors are solved numerically from the stationary Fokker-Planck equations. By using these probability density functions, we provide the analytical expressions, such as the velocity, the rate of the ATP consumption, the energetic efficiency, and the dissipation energy rates.

The enhancement of the energetic efficiency by the cooperation of low-efficient flashing ratchets.

The energetic efficiency of the classical flashing ratchet model is much lower (around 1%) than the experimental results (around 50%). Jülicher and Prost have provided a prototype of the cooperative ratchet model [Jülicher, F., Prost, J.