Nen Saito

A method based on multicanonical Monte Carlo is applied to the calculation of large deviations in the largest eigenvalue of random matrices. The method is successfully tested with the Gaussian orthogonal ensemble, sparse random matrices, and matrices whose components are subject to uniform density. Specifically, the probability that all eigenvalues of a matrix are negative is estimated in these cases down to the values of ∼10(-200), a region where simple random sampling is ineffective. The metho

Shape measurements are crucial for evolutionary and developmental biology; however, they present difficulties in the objective and automatic quantification of arbitrary shapes. Conventional approaches are based on anatomically prominent landmarks, which require manual annotations by experts. Here, we develop a machine-learning approach by presenting morphological regulated variational AutoEncoder (Morpho-VAE), an image-based deep learning framework, to conduct landmark-free shape analysis. The p

Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in molecule number have attracted much attention. Here, a method based on a Markov process with a tridiagonal transition matrix is applied to the analysis of this transition in reaction dynamics. The transition to bistability due to the small-number effect and the mean switching time between the bistable states are analytically calculated in agreement with numerical simulations. In addition, a novel transition

Macropinocytosis refers to the non-specific uptake of extracellular fluid, which plays ubiquitous roles in cell growth, immune surveillance, and virus entry. Despite its widespread occurrence, it remains unclear how its initial cup-shaped plasma membrane extensions form without any external solid support, as opposed to the process of particle uptake during phagocytosis. Here, by developing a computational framework that describes the coupling between the bistable reaction-diffusion processes of

Phenotypic fluctuations and plasticity can generally affect the course of evolution, a process known as the Baldwin effect. Several studies have recast this effect and claimed that phenotypic plasticity accelerates evolutionary rate (the Baldwin expediting effect); however, the validity of this claim is still controversial. In this study, we investigate the evolutionary population dynamics of a quantitative genetic model under a multipeaked fitness landscape, in order to evaluate the validity of

Protein motors, such as kinesins and dyneins, bind to a microtubule and travel along it in a specific direction. Previously, it was thought that the directionality for a given motor was constant in the absence of an external force. However, the directionality of the kinesin-5 Cin8 was recently found to change as the number of motors that bind to the same microtubule is increased. Here, we introduce a simple mechanical model of a microtubule-sliding assay in which multiple motors interact with th

The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen and been maintained during evolution, it may have been preserved under selection pressure. Theoretical studies comparing the SGC and numerically created hypothetical random genetic codes have suggested that the SGC has been subject to strong selection pressure f

Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for tissue homeostasis and stable developmental processes. However, large-scale simulations of deformable cells have been restricted to those of polygonal-shaped cells, limiting our understanding of populations of arbitrarily deformable cells, such as mesenchymal, amoeboid cells, and nonconfluent epithelial cells. Here, we present an efficient approach for simulat

• Abstract Macropinocytosis is non-specific uptake of the extracellular fluid playing ubiquitous roles in cell growth, immune-surveillance as well as virus entry. Despite its widespread occurrence, it remains unclear how its initial cup-shaped plasma membrane extensions forms without external physical support as in phagocytosis or curvature inducing proteins as in clathrin-mediated endocytosis. Here, by developing a novel computational framework that describes the coupling between bistable react

Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations for the collective dynamics of cells with arbitral cell deformations akin to mesenchymal, ameboid, and epithelial cells in a non-confluent situation need high computational costs and are still challenging. Here we propose a new method that allows us to study sig

Studies on the effects of nonmagnetic (SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ) intermediate layers of various thicknesses in amorphous Co-Zr-Nb films are described. Both SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and amorphous Co-Zr-Nb layers were formed by ion beam sputtering, and samples were annealed in rotating and dc magnetic fields to induce a uniaxial anisot

A 62-year-old man with Wegener's granulomatosis developed sclerocorneal ulcer. The general condition of the patient became well with steroid and presented cyclophosphamide therapy, he developed sclerocorneal ulcer. The sclerocorneal ulcer was present at the nasal limbus of the right eye. The ulcer was marked and presented descemetocele. Although lamellar keratoplasty was performed, the scleral ulcer recurred after two weeks. Excision of the affected sclera and autoscleroplasty was performed. The

Dynamics in biological networks are in general robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems which are robust against phenotypic perturbations (perturbations in dynamics), as well as systems which are robust against mutation (perturbations in network structure). To achieve such a design, we apply a multicanonical Monte Carlo method. Analysis based on the maximum Lyapunov exponent and parameter sensit