Accelerated preprocessing of large numbers of brain images by parallel computing on supercomputers.

"Preprocessing" is the first step required in brain image analysis that improves the overall quality and reliability of the results. However, it is computationally demanding and time-consuming, particularly to handle and parcellate complicatedly folded cortical ribbons of the human brain. In this study, we aimed to shorten the analysis time for data preprocessing of 1410 brain images simultaneously on one of the world's highest-performing supercomputers, "Fugaku." The FreeSurfer was used as a benchmark preprocessing software for cortical surface reconstruction. All the brain images were processed simultaneously and successfully analyzed in a calculation time of 17.33 h. This result indicates that using a supercomputer for brain image preprocessing allows big data analysis to be completed shortly and flexibly, thus suggesting the possibility of supercomputers being used for expanding large data analysis and parameter optimization of preprocessing in the future.

DNA Length-dependent Division of a Giant Vesicle-based Model Protocell.

DNA is an essential carrier of sequence-based genetic information for all life today. However, the chemical and physical properties of DNA may also affect the structure and dynamics of a vesicle-based model protocell in which it is encapsulated. To test these effects, we constructed a polyethylene glycol-grafted giant vesicle system capable of undergoing growth and division. The system incorporates a specific interaction between DNA and lipophilic catalysts as well as components of PCR. We found that vesicle division depends on the length of the encapsulated DNA, and the self-assembly of an internal supramolecular catalyst possibly leads to the direct causal relationship between DNA length and the capacity of the vesicle to self-reproduce. These results may help elucidate how nucleic acids could have functioned in the division of prebiotic protocells.

Migration of Deformable Vesicles Induced by Ionic Stimuli.

We have investigated the dynamics of phospholipid vesicles composed of 1,2-dioleoyl- sn-glycero-3-phosphocholine triggered by ionic stimuli using electrolytes such as CaCl2, NaCl, and NaOH. The ionic stimuli induce two characteristic vesicle dynamics, deformation due to the ion binding to the lipids in the outer leaflet of the vesicle and migration due to the concentration gradient of ions, that is, diffusiophoresis or the interfacial energy gradient mechanism. We examined the deformation pathway for each electrolyte as a function of time and analyzed it based on the surface dissociation model and the area difference elasticity model, which reveals the change of the cross-sectional area of the phospholipid by the ion binding. The metal ions such as Ca2+ and Na+ encourage inward budding deformation by decreasing the cross-sectional area of a lipid, whereas the hydroxide ion (OH-) encourages outward budding deformation by increasing the cross-sectional area of a lipid. When we microinjected these electrolytes toward the vesicles, a strong coupling between the deformation and the migration of the vesicle was observed for CaCl2 and NaOH, whereas for NaCl, the coupling was very weak. This difference probably originates from the binding constants of the ions.

Molecular mechanism of vesicle division induced by coupling between lipid geometry and membrane curvatures.

We investigated the effects of lipid geometry on vesicle division using coarse grained molecular dynamics simulations. When the vesicle is composed of zero and negative spontaneous curvature lipids (ZSLs and NSLs), the difference in their molecular spontaneous curvatures destabilizes the neck of the limiting shape vesicle. In the vesicle division pathway, the neck developed into the stalk intermediates. The stalk was broken when the NSLs were expelled from the stalk. Free energy analysis shows that the coupling between the lipid geometry and the Gaussian rigidity is responsible for the observed vesicle division.

Role of Inverse-Cone-Shape Lipids in Temperature-Controlled Self-Reproduction of Binary Vesicles.

We investigate a temperature-driven recursive division of binary giant unilamellar vesicles (GUVs). During the heating step of the heating-cooling cycle, the spherical mother vesicle deforms to a budded limiting shape using up the excess area produced by the chain melting of the lipids and then splits off into two daughter vesicles. Upon cooling, the daughter vesicle opens a pore and recovers the spherical shape of the mother vesicle. Our GUVs are composed of DLPE (1,2-dilauroyl-sn-glycero-3-phosphoethanolamine) and DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine). During each cycle, vesicle deformation is monitored by a fast confocal microscope and the images are analyzed to obtain the time evolution of reduced volume and reduced monolayer area difference as the key geometric parameters that quantify vesicle shape. By interpreting the deformation pathway using the area-difference elasticity theory, we conclude that vesicle division relies on (1) a tiny asymmetric distribution of DLPE within the bilayer, which controls the observed deformation from the sphere to the budded shape; and (2) redistribution of DLPE during the deformation-division stage, which ensures that the process is recursive. The spontaneous coupling between membrane curvature and PE lipid distribution is responsible for the observed recursive division of GUVs. These results shed light on the mechanisms of vesicle self-reproduction.

Dynamics of fatty acid vesicles in response to pH stimuli.

We investigate the dynamics of decanoic acid/decanoate (DA) vesicles in response to pH stimuli. Two types of dynamic processes induced by the micro-injection of NaOH solutions are sequentially observed: deformations and topological transitions. In the deformation stage, DA vesicles show a series of shape deformations, i.e., prolate-oblate-stomatocyte-sphere. In the topological transition stage, spherical DA vesicles follow either of the two pathways, pore formation and vesicle fusion. The pH stimuli modify a critical aggregation concentration of DA molecules, which causes the solubilization of DA molecules in the outer leaflet of the vesicle bilayers. This solubilization decreases the outer surface area of the vesicle, thereby increasing surface tension. A kinetic model based on area difference elasticity theory can accurately describe the dynamics of DA vesicles triggered by pH stimuli.