Effective nonlocal kernels on Reaction-diffusion networks

A new method to derive an essential integral kernel from any given reaction-diffusion network is proposed. Any network describing metabolites or signals with arbitrary many factors can be reduced to a single or a simpler system of integro-differential equations called "effective equation" including the reduced integral kernel (called "effective kernel" ) in the convolution type. As one typical example, the Mexican hat shaped kernel is theoretically derived from two component activator-inhibitor systems. It is also shown that a three component system with quite different appearance from activator-inhibitor systems is reduced to an effective equation with the Mexican hat shaped kernel. It means that the two different systems have essentially the same effective equations and that they exhibit essentially the same spatial and temporal patterns. Thus, we can identify two different systems with the understanding in unified concept through the reduced effective kernels. Other two applications of this method are also given: Applications to pigment patterns on skins (two factors network with long range interaction) and waves of differentiation (called proneural waves) in visual systems on brains (four factors network with long range interaction). In the applications, we observe the reproduction of the same spatial and temporal patterns as those appearing in pre-existing models through the numerical simulations of the effective equations

Renormalization-group Method for Reduction of Evolution Equations; invariant manifolds and envelopes

The renormalization group (RG) method as a powerful tool for reduction of evolution equations is formulated in terms of the notion of invariant manifolds. We start with derivation of an exact RG equation which is analogous to the Wilsonian RG equations in statistical physics and quantum field theory. It is clarified that the perturbative RG method constructs invariant manifolds successively as the initial value of evolution equations, thereby the meaning to set $t_0=t$ is naturally understood where $t_0$ is the arbitrary initial time. We show that the integral constants in the unperturbative solution constitutes natural coordinates of the invariant manifold when the linear operator $A$ in the evolution equation has no Jordan cell; when $A$ has a Jordan cell, a slight modification is necessary because the dimension of the invariant manifold is increased by the perturbation. The RG equation determines the slow motion of the would-be integral constants in the unperturbative solution on the invariant manifold. We present the mechanical procedure to construct the perturbative solutions hence the initial values with which the RG equation gives meaningful results. The underlying structure of the reduction by the RG method as formulated in the present work turns out to completely fit to the universal one elucidated by Kuramoto some years ago. We indicate that the reduction procedure of evolution equations has a good correspondence with the renormalization procedure in quantum field theory; the counter part of the universal structure of reduction elucidated by Kuramoto may be the Polchinski's theorem for renormalizable field theories. We apply the method to interface dynamics such as kink-anti-kink and soliton-soliton interactions in the latter of which a linear operator having a Jordan-cell structure appears.Comment: 67 pages. No figures. v2: Additional discussions on the unstable motion in the the double-well potential are given in the text and the appendix added. Some references are also added. Introduction is somewhat reshape

Improvement in organophosphorus hydrolase activity of cell surface-engineered yeast strain using Flo1p anchor system

Organophosphorus hydrolase (OPH) hydrolyzes organophosphorus esters. We constructed the yeast-displayed OPH using Flo1p anchor system. In this system, the N-terminal region of the protein was fused to Flo1p and the fusion protein was displayed on the cell surface. Hydrolytic reactions with paraoxon were carried out during 24 h of incubation of OPH-displaying cells at 30°C. p-Nitrophenol produced in the reaction mixture was detected by HPLC. The strain with highest activity showed 8-fold greater OPH activity compared with cells engineered using glycosylphosphatidylinositol anchor system, and showed 20-fold greater activity than Escherichia coli using the ice nucleation protein anchor system. These results indicate that Flo1p anchor system is suitable for display of OPH in the cell surface-expression systems