Dynamical pattern formations in two dimensional fluid and Landau pole bifurcation

A phenomenological theory is proposed to analyze the asymptotic dynamics of perturbed inviscid Kolmogorov shear flows in two dimensions. The phase diagram provided by the theory is in qualitative agreement with numerical observations, which include three phases depending on the aspect ratio of the domain and the size of the perturbation: a steady shear flow, a stationary dipole, and four traveling vortices. The theory is based on a precise study of the inviscid damping of the linearized equation and on an analysis of nonlinear effects. In particular, we show that the dominant Landau pole controlling the inviscid damping undergoes a bifurcation, which has important consequences on the asymptotic fate of the perturbation.Comment: 9 pages, 7 figure

Residue network in protein native structure belongs to the universality class of three dimensional critical percolation cluster

A single protein molecule is regarded as a contact network of amino-acid residues. Some studies have indicated that this network is a small world network (SWN), while other results have implied that this is a fractal network (FN). However, SWN and FN are essentially different in the dependence of the shortest path length on the number of nodes. In this paper, we investigate this dependence in the residue contact networks of proteins in native structures, and show that the networks are not SWN but FN. FN is generally characterized by several dimensions. Among them, we focus on three dimensions; the network topological dimension $D_c$, the fractal dimension $D_f$, and the spectral dimension $D_s$. We find that proteins universally yield $D_c \approx 1.9$, $D_f \approx 2.5$ and $Ds \approx 1.3$. These values are in surprisingly good coincidence with those in three dimensional critical percolation cluster. Hence the residue contact networks in the protein native structures belong to the universality class of three dimensional percolation cluster. The criticality is relevant to the ambivalent nature of the protein native structures, i.e., the coexistence of stability and instability, both of which are necessary for a protein to function as a molecular machine or an allosteric enzyme.Comment: 4 pages, 3 figure

Alzheimer’s disease : Relationship between the Alzheimer’s disease and human microbiome

Alzheimer’s disease (AD) is a progressive, neurodegenerative disease characterized by memory and language disorder. The accumulation of senile plaques called β-amyloid and neurofibrillary tangles involving protein tau in the brains of AD patients have been considered as two hallmarks of AD. In AD, it is reported that accumulation of β-amyloid may be observed 25 years before onset, supporting early diagnosis and treatment by brain image analysis, because several techniques have recently been developed to detect β-amyloid and tau protein in brains of persons diagnosed with AD. AD patients are usually suffering from other diseases such as diabetes or periodontal disease, and there is accumulating data to show that these diseases associate with the human microbiome, such as gut and oral microbiota. In this report, the relation ship between AD and the human microbiome is reviewed

Comparative Genomic Analysis of Lactococcus garvieae Strains Isolated from Different Sources Reveals Candidate Virulence Genes

Lactococcus garvieae is a major pathogen for fish. Two complete (ATCC 49156 and Lg2) and three draft (UNIUD074, 8831, and 21881) genome sequences of L. garvieae have recently been released. We here present the results of a comparative genomic analysis of these fish and human isolates of L. garvieae. The pangenome comprised 1,542 core and 1,378 dispensable genes. The sequenced L. garvieae strains shared most of the possible virulence genes, but the capsule gene cluster was found only in fish-pathogenic strain Lg2. The absence of the capsule gene cluster in other nonpathogenic strains isolated from mastitis and vegetable was also confirmed by PCR. The fish and human isolates of L. garvieae contained the specific two and four adhesin genes, respectively, indicating that these adhesion proteins may be involved in the host specificity differences of L. garvieae. The discoveries revealed by the pangenomic analysis may provide significant insights into the biology of L. garvieae

Roundabout relaxation: collective excitation requires a detour to equilibrium

Relaxation to equilibrium after strong and collective excitation is studied, by using a Hamiltonian dynamical system of one dimensional XY model. After an excitation of a domain of $K$ elements, the excitation is concentrated to fewer elements, which are made farther away from equilibrium, and the excitation intensity increases logarithmically with $K$. Equilibrium is reached only after taking this ``roundabout'' route, with the time for relaxation diverging asymptotically as $K^\gamma$ with $\gamma \approx 4.2$.Comment: 4 pages, 5 figure

Surface terms on the Nishimori line of the Gaussian Edwards-Anderson model

For the Edwards-Anderson model we find an integral representation for some surface terms on the Nishimori line. Among the results are expressions for the surface pressure for free and periodic boundary conditions and the adjacency pressure, i.e., the difference between the pressure of a box and the sum of the pressures of adjacent sub-boxes in which the box can been decomposed. We show that all those terms indeed behave proportionally to the surface size and prove the existence in the thermodynamic limit of the adjacency pressure.Comment: Final version with minor corrections. To appear in Journal of Statistical Physic