# Yukitaka IshimotoSaga University · Faculty of Sciences & Engineering

Yukitaka Ishimoto

PhD

## About

72

Publications

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299

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Introduction

Yukitaka Ishimoto has just moved to Faculty of Science and Engineering, Saga Univ. from Dept. of Mechanical Engineering, Akita Prefectural Univ. Yukitaka does research in Applied Mathematics, Mathematical Physics, Fluid Science, Bioinformatics, Biophysics, and Bioengineering by using mathematical/physical/biological/engineering techniques. One of the lab's current projects is 'Tissue mechanics by bubbly vertex dynamics model and other means'.

Additional affiliations

Education

October 1999 - March 2004

## Publications

Publications (72)

In south India, there are traditional patterns of line-drawings encircling
dots, called ``Kolam'', among which one-line drawings or the ``infinite Kolam''
provide very interesting questions in mathematics. For example, we address the
following simple question: how many patterns of infinite Kolam can we draw for
a given grid pattern of dots? The sim...

In order to describe two-dimensionally packed cells in epithelial tissues
both mathematically and physically, there have been developed several sorts of
geometrical models, such as the vertex model, the finite element model, the
cell-centered model, the cellular Potts model. So far, in any case, pressures
have not neatly been dealt with and curvatu...

Plant zygote cells exhibit tip growth, producing a hemisphere-like tip. To understand how this hemisphere-like tip shape is formed, we revisited a viscoelastic-plastic deformation model that enabled us to simultaneously evaluate the shape, stress, and strain of Arabidopsis ( Arabidopsis thaliana ) zygote cells undergoing tip growth. Altering the sp...

Comprehensive analysis of cellular dynamics during the process of morphogenesis is fundamental to understanding the principles of animal development. Despite recent advancements in light microscopy, how successive cell shape changes lead to complex three-dimensional tissue morphogenesis is still largely unresolved. Using in vivo live imaging of Dro...

In medical and biological research, measurements of cellular dynamics have been paid much attention in recent years. Among such quantifications, particle tracking velocimetry (PTV) of cells is one of the major tools to elucidate the dynamics. For this purpose, it is critical to establish precise detection of individual cell positions at different t...

In most plants, the zygote divides asymmetrically to define the body axis. In Arabidopsis thaliana, the zygote undergoes polar elongation maintaining a transverse band of cortical microtubules (MTs), and divides asymmetrically forming another MT band, preprophase band (PPB). How the MT band is maintained at the actively growing cell tip and whether...

The dynamics of microtubule-mediated protrusions, termed Interplanar Amida Network (IPAN) in Drosophila pupal wing, involve cell shape changes. The molecular mechanisms underlying these processes are yet to be fully understood. This study delineates the stages of cell shape alterations during the disassembly of microtubule protrusions and underscor...

Lodging of cereal crops significantly reduces grain yield and quality, making lodging resistance a prime target for breeding programs. However, lodging resistance among different rice (Oryza sativa L.) cultivars in the field remains largely unknown, as is the relationship between the major properties of culms such as their morphological and mechani...

Polarization of the zygote defines the body axis during plant development. In Arabidopsis (Arabidopsis thaliana), the zygote becomes polarized and elongates in the longitudinal direction, ultimately forming the apical-basal axis of the mature plant. Despite its importance, the mechanism for this elongation remains poorly understood. Based on live-c...

Plant roots have three-dimensional branching structure to mechanically support the above-ground portion of the plant. In addition, it is probable that each root forms an optimal morphology for the environment in which it is placed. If we can identify and analyse this three-dimensional morphology and physical properties such as rigidity and stress p...

The mechanisms of chromosome condensation and decondensation processes plays a key role in regulating transcriptions and gene expressions, but it is not sufficiently understood, especially in human cells. So far, three types of chromosome models have been proposed and widely known, while recent experiments have shown that there is polymer-melt-like...

Many biological systems including humans are made up of various cells. In addition, cells of a specific type gather together to form tissues, and organs are organized as an aggregate of multiple tissues. One of the tissues constituting organs is epithelial tissue. Epithelial tissue is composed of epithelial cells, and almost all the surfaces inside...

Significance
Tissue morphogenesis is a dynamic process often accompanied by cell patterning and differentiation. Although how conserved growth factor signaling affects cell and tissue shapes has been actively studied, much less is known about how signaling and dynamic morphogenesis are mutually coordinated. Our study shows that BMP signaling and 3D...

For isolated single cells on a substrate, the intracellular stiffness, which is often measured as the Young's modulus, E, by atomic force microscopy (AFM), depends on the substrate rigidity. However, little is known about how the E of cells is influenced by the surrounding cells in a cell population system in which cells physically and tightly cont...

At the level of organ formation, tissue morphogenesis drives developmental processes in animals, often involving the rearrangement of two-dimensional (2D) structures into more complex three-dimensional (3D) tissues. These processes can be directed by growth factor signaling pathways. However, little is known about how such morphological changes aff...

The wings in different insect species are morphologically distinct with regards to their size, outer contour (margin) shape, venation, and pigmentation. The basis of the diversity of wing margin shapes remains unknown, despite the fact that gene networks governing the Drosophila wing development have been well characterised. Among the different typ...

This paper describes microstreaming flows generated by oscillating interface of magnetic fluid adsorbed on a circular cylindrical permanent magnet in alternating magnetic field. The interface of magnetic fluid adsorbed on the NdFeB magnet responds to the external alternating magnetic flied as harmonic oscillation. The directions of alternating magn...

The morphologies of ectodermal organs are shaped by appropriate combinations of several deformation modes, such as invagination and anisotropic tissue elongation. However, how multicellular dynamics are coordinated during deformation processes remains to be elucidated. Here, we developed a four-dimensional (4D) analysis system for tracking cell mov...

Deformation analysis of developing tooth epithelium (related to Fig 2).
(A) The trajectories of epithelial cells over 5 hours are shown on fluorescent images (upper panel) and wire frames (lower panel) at each time point of the long-term live imaging. The scale bars represent 100 ?m. (B) The raw data for the epithelial tissue deformation analysis....

The epithelial tissue elongation direction is subject to spatial restriction by the surrounding mesenchyme.
(A) Histological analysis of the E14.5 molar tooth germ. The yellow dashed line indicates the border between the tooth germ mesenchyme and the oral mesenchyme. The scale bars represent 100 ?m. E, epithelium; M, mesenchyme; DF, dental follicle...

Ex vivo live imaging of a developing tooth germ.
Time-lapse imaging of a developing tooth germ derived from a transgenic mouse embryo co-expressing Fucci-G0/G1 probe and H2BEGFP. The tooth germ was cultured for 5 days ex vivo, and the images were taken at 30-min intervals. The lingual side is on the left. Also see Fig 1E.
(MP4)

Time-lapse recording of epithelial shape changes following treatment with dispase.
Time-lapse recording of epithelial shape changes when an E14.5 tooth germ was treated with dispase. The lingual side is on the left. Also see S5 Fig.
(MP4)

The quantitative kinetic analysis of tooth morphogenesis (related to Fig 2).
(A) Photographs showing the cutting surface region (z < 30 ?m, upper panels) and the deeper region (z > 30 ?m, lower panels) in ex vivo cultured tooth germ. The white arrowheads indicate mitotic cells. (B) The relative numbers of cell divisions per tissue volume in the sur...

Ex vivo time-lapse tooth germ imaging system.
The molar tooth germ was reconstructed three-dimensionally from frontal sections of the tooth germ derived from a transgenic mouse embryo co-expressing Fucci-G0/G1 probe and H2BEGFP. The molar tooth germs were cut into 250?300 ?m-thick frontal slices and then cultured on a glass-bottomed dish for ex viv...

Time-lapse recording of the DL, EK and GAE regions.
Time-lapse recording of the DL, EK and GAE regions showing cell motility. Also see Fig 3A.
(MP4)

Tooth morphogenesis and spatial-temporal cell proliferation (related to Fig 1).
Frontal sections of the mandibular molar tooth germ derived from Fucci transgenic mice at E13.5?18.5. Hoechst (upper), Fucci fluorescence (middle), and merged (lower) images are shown. The lingual side is on the left in all panels. The scale bars represent 100 ?m.
(TIF)

Deformation analysis of the epithelial tissue over 25?30 hours (A) and 30?35 hours (B) at different z positions.
The upper and lower panels illustrate the spatial patterns of the volume growth rate and anisotropic tissue stretching, respectively. In the lower panels, the colors indicate the degree of anisotropy, and the arrows indicate the major ax...

Cofilin activity is regulated spatiotemporally during tooth development (related to Fig 4).
(A) The localizations of p-cofilin, cofilin and F-actin in the tooth germ were detected by immunohistochemistry at E13.5?16.5. G0/G1 phase cells (red, center) are visualized with the Fucci probe. The lingual side is on the left in all panels. The scale bars...

Quantitative kinetic analysis of epithelial morphogenesis.
The trajectories of epithelial cells over 20 hours acquired from quantitative kinetic analysis are illustrated with raw live imaging data (left) and a wire frame (right). The lingual side is on the left. Also see Fig 2A.
(MP4)

This paper describes the characteristics of water flow induced by the bridge oscillation of magnetic fluid between two permanent magnets subject to external alternating magnetic field. The magnetic fluid bridge is formed in the space between a pair of identical coaxial cylindrical permanent magnets submerged in water. The directions of alternating...

In the olfactory epithelium (OE), olfactory cells (OCs) and supporting cells (SCs), which express different cadherins, are arranged in a characteristic mosaic pattern in which OCs are enclosed by SCs. However, the mechanism underlying this cellular patterning is unclear. Here, we show that the cellular pattern of the OE is established by cellular r...

A family of models of liquid on a two-dimensional lattice (2D lattice liquid models) have been proposed as primitive models of soft-material membrane. As a first step, we have formulated them as single-component, single-layered, classical particle systems on a two-dimensional surface with no explicit viscosity. Among the family of the models, we ha...

We investigate how different microscopic interactions between semiflexible chain segments can qualitatively alter the physical properties of the condensed toroid. We propose a general form of the Hamiltonian of the toroid and discuss its analytic properties. For different interactions, the theory predicts different scaling behaviors of the mean tor...

It now becomes apparent that condensed DNA toroid which emerges in a poor solvent condition can be realised in the framework of the non-linear sigma model on a line segment. In fact, the classical solutions of the model, i.e., of the bending potential exhibit toroidal forms, and fit well with the delta-function term of the attractive interaction. T...

We investigate how different microscopic interactions between semiflexible
chain segments can qualitatively alter the physical properties of the condensed
toroid. We propose a general form of the Hamiltonian of the toroid and discuss
its analytic properties. For different interactions, the theory predicts
different scaling behaviours of the mean to...

We consider moduli integrals appearing in four-point correlation functions of the (p, q) minimal models coupled to Liouville gravity on a sphere, which is sometimes called 2D minimal gravity or minimal string
theory on a sphere. Liouville gravity on a sphere is the quantized metric of the spherical topology in the conformal gauge.
Reviewing the pre...

We establish a general model for the whip-toroid transitions of a semiflexible homopolymer chain using the path integral method and the O3 nonlinear sigma model on a line segment with the local inextensibility constraint. We exactly solve the energy levels of classical solutions and show that some of its classical configurations exhibit toroidal fo...

We consider the partition function of the two-dimensional free massive Majorana fermion coupled to the quantized metric of
the spherical topology. By adding an arbitrary conformal “spectator” matter, we gain control over the total matter central
charge. This provides an interesting continuously parameterized family of critical points and also allow...

We consider four-point functions of the (p,q) minimal models coupled to the quantised metric of the spherical topology, which is called 2D minimal gravity or minimal string theory on a sphere. Reviewing the previous results on such four-point functions, we show logarithmic correlation functions of ‘tachyons’ in the Liouville sector, and its moduli...

この論文は国立情報学研究所の電子図書館事業により電子化されました。 研究会報告 完全屈曲性を持つ高分子ガウス鎖の連続理論は、場の理論による相転移の記述等よく知られている。一方、DNA等のより一般の半屈曲性高分子鎖については、数値計算で一定の理解は得られたが、予言性を持つ解析理論に至っていなかった。我々はこのモデルを経路積分において引力項付きで定式化し、DNA凝縮に特徴的なトロイド状態を解析的に導き出した[1]。更に実験との一致を見、ウィップートロイド相転移を発見した。これを発展させ、異なる引力相互作用によるトロイド半径のスケーリング則、例えばクーロンカの場合トロイド半径r_cが全長Lに対してr_c～L^<-1/3>となることを示す[2]。

An International Workshop dedicated to the anniversary of the Polyakov's String (of course today there is no need to remind the meaning and the role of this theory) was held in Chernogolovka in June 2005. Apart from the 25-th anniversary of the first appearance of the Polyakov's String theory, this conference, to our mind, might be also thought of...

We introduce a novel model for DNA condensation (whip-toroid transition) using the path integral method in the framework of the non-linear sigma model on a line segment. We show that some of its classical configurations exhibit toroidal forms, and the system has phase transitions from a whip to toroidal phases with a parameter $c=W/(2l) (L/(2\pi))^...

この論文は国立情報学研究所の電子図書館事業により電子化されました。 完全屈曲性高分子鎖の連続理論は、場の理論による相転移の記述等よく知られている。一方、より一般の半屈曲性高分子鎖については、MD法やモンテカルロ計算で一定の理解は得られたが、予言性を持つ解析理論に至っていない。我々はこのモデルを経路積分において引力項付きで定式化し、DNA凝縮に特徴的なトロイド状態を導出した。更にウィップ-トロイド相転移等を議論する。

We study the simplest examples of minimal string theory whose worldsheet description is the unitary (p,q) minimal model coupled to two-dimensional gravity ( Liouville field theory). In the Liouville sector, we show that four-point correlation functions of ‘tachyons’ exhibit logarithmic singularities, and that the theory turns out to be logarithmic....

Amongst conformal field theories, there exist logarithmic conformal field theories such as $c_{p,1}$ models. We have investigated $c_{p,q}$ models with a boundary in search of logarithmic theories and have found logarithmic solutions of two-point functions in the context of the Coulomb gas picture. We have also found the relations between coefficie...

It is well known that LCFT generally contains Jordan cell structure and, in our previous paper, we have proposed a conjecture that one and only one boundary sate is allowed in the rank-2 cell. With these states in c=-2 rational LCFT, we can express boundary states in the closed string picture, in regard to corresponding boundary conditions in the o...

There exist logarithmic CFTs (LCFTs) such as the c(p,1) models. It is also well known that it generally contains Jordan cell structure. In this paper, we obtain the boundary Ishibashi state for a rank-2 Jordan cell structure and, with these states in c = -2 rational LCFT, we derive boundary states in the closed string picture, which correspond to b...

3d Chern–Simons gauge theory has a strong connection with 2d CFT and link invariants in knot theory. We impose some constraints on the D(2|1;α) CS theory in the similar context of the hamiltonian reduction of 2d superconformal algebras. There Hilbert states in D(2|1;α) CS theory are partly identified with characters of the large N=4 SCFT by their t...

We study a Wess-Zumino-Witten model with target space
AdS3× (S3× S3× S1)/2. This allows us to
construct space-time = 3 superconformal theories. By
combining left-, and right-moving parts through a GSO and a 2
projections, a new asymmetric (,bar−) = (3,1)
model is obtained. It has an extra gauge (affine) SU(2) symmetry in
the target space of the typ...

The $N=4$ SU(2)$_k$ superconformal algebra has the global automorphism of
SO(4) $\approx$ SU(2)$\times$SU(2) with the {\it left} factor as the Kac-Moody
gauge symmetry. As a consequence, an infinite set of independent algebras
labeled by $\rho$ corresponding to the conjugate classes of the {\it outer}
automorphism group SO(4)/SU(2)=SU(2) are obtain...