Hiroki Miyazako

Turing instability in reaction-diffusion systems with a single diffuser: Characterization based on root locus

Cooperative behaviors arising from bacterial cell-to-cell communication can be modeled by reaction-diffusion equations having only a single diffusible component. This paper presents the following three contributions for the systematic analysis of Turing instability in such reaction-diffusion systems. (i) We first introduce a unified framework to formulate the reaction-diffusion system as an interconnected multi-agent dynamical system. (ii) Then, we mathematically classify biologically plausible and implausible Turing instabilities and characterize them by the root locus of each agents dynamics, or the local reaction dynamics. (iii) Using this characterization, we derive analytic conditions for biologically plausible Turing instability, which provide useful guidance for the design and the analysis of biological networks. These results are demonstrated on an extended Gray-Scott model with a single diffuser.

Spatiotemporal Control of Electrokinetic Transport in Nanofluidics Using an Inverted Electron-Beam Lithography System

Manipulation techniques of biomolecules have been proposed for biochemical analysis which combine electrokinetic dynamics, such as electrophoresis or electroosmotic flow, with optical manipulation to provide high throughput and high spatial degrees of freedom. However, there are still challenging problems in nanoscale manipulation due to the diffraction limit of optics. We propose here a new manipulation technique for spatiotemporal control of chemical transport in nanofluids using an inverted electron-beam (EB) lithography system for liquid samples. By irradiating a 2.5 keV EB to a liquid sample through a 100-nm-thick SiN membrane, negative charges can be generated within the SiN membrane, and these negative charges can induce a highly focused electric field in the liquid sample. We showed that the EB-induced negative charges could induce fluid flow, which was strong enough to manipulate 240 nm nanoparticles in water, and we verified that the main dynamics of this EB-induced fluid flow was electroosmosis caused by changing the zeta potential of the SiN membrane surface. Moreover, we demonstrated manipulation of a single nanoparticle and concentration patterning of nanoparticles by scanning EB. Considering the shortness of the EB wavelength and Debye length in buffer solutions, we expect that our manipulation technique will be applied to nanomanipulation of biomolecules in biochemical analysis and control.

In situ patterning of organic molecules in aqueous solutions using an inverted electron-beam lithography system

A method for in situ controlling the detachment and deposition of organic molecules such as sugars and biocompatible polymers in aqueous solutions by electron-beam (EB) scan is proposed and evaluated. It was demonstrated that EB irradiation could detach 2-methacryloyloxyethyl phosphorylcholine (MPC) polymers from a silicon nitride membrane. Moreover, organic molecules such as cationic polymers and sugars could be deposited on the membrane by EB irradiation. Spatial distributions of scattered electrons were numerically simulated, and acceleration voltage dependences of the detachment and deposition phenomena were experimentally measured. The simulations and experimental results suggest that the detachment of MPC polymers is mainly due to electrical effects of primary electrons, and that the deposition of organic molecules is mainly due to chemical reactions induced by primary electrons. In view of these findings, the proposed method can be applied to in situ and nanoscale patterning such as the fabrication of cell scaffolds.

Coordinated Spatial Pattern Formation in Biomolecular Communication Networks

This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular communication networks, bionanomachines, or biological cells, communicate with each other using a cell-to-cell communication mechanism mediated by a diffusible signaling molecule, thereby the dynamics of molecular concentrations are approximately modeled as a reaction-diffusion system with a single diffuser. We first introduce a feedback model representation of the reaction- diffusion system and provide a systematic local stability/instability analysis tool using the root locus of the feedback system. The instability analysis then allows us to analytically derive the conditions for the self-organized spatial pattern formation, or Turing pattern formation, of the bionanomachines. We propose a novel synthetic biocircuit motif called activator-repressor-diffuser system and show that it is one of the minimum biomolecular circuits that admit self-organized patterns over cell population.

Single-cell membrane surgery by virtual electrodes using an inverted electron beam lithography system

Single cell manipulation had been applied to various analyses of cell functions, however, the nanometer size surgery tools for the single cell analysis was limited the resolution and rapidly. We proposed here a single cell manipulation using a fine focused electron beam. Since the electron beam could provide virtual electrodes which promoted electric influences and they were focused in sub-micrometers, the fine manipulation could performed subcellular surgery of the single living cell. By using our method with an inverted electron beam lithography system, we reported here the electrokinetic induced poration of localized single cells and subcellular detachment. Observing this poration, the electron beam irradiation induced PI dye inflow into the single living cells and their fluorescence were confirmed. Although the viability of the treated cells was still unclear, the poration probability by our method was demonstrated.