(1) Tomohiro Yanao, Sosuke Sano and *Kenichi Yoshikawa, Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity, AIMS Biophysics 2(4), 666–694 (2015).

Abstract: Wrapping, crossover, and braiding of DNA are the motifs of fundamental interest in genome packaging, gene regulation, and enzyme recognition. This study explores elastic mechanisms for the selection of chirality in wrapping, crossover, and braiding of DNA based on a coarse-grained model. The DNA model consists of two elastic chains that mutually intertwine in a right-handed manner forming a double-stranded helix with the distinction between major and minor grooves. Although individual potential energy functions of the DNA model have no asymmetry in terms of left and right twist, the model as a whole exhibits an asymmetric propensity to writhe in the left direction upon bending due to the right-handed helical geometry. Monte Carlo simulations of this model suggest that DNA has a propensity to prefer left-handed wrapping around a spherical core particle and also around a uniform rod due to the asymmetric elastic coupling between bending and writhing. This result indicates an elastic origin of the uniform left-handed wrapping of DNA in nucleosomes and also has implications on the wrapping of double-stranded DNA around rod-like molecules. Monte Carlo simulations of the DNA model also suggest that two juxtaposed DNA molecules can braid each other spontaneously under moderate attractive interactions with the preference for left-handed braiding due to the asymmetric coupling between bending and writhing. This result suggests the importance of asymmetric elasticity in the selection of chirality in braiding of a pair of DNA molecules.

Masanobu Tanaka, Marcel Hörning, Hiroyuki Kitahata and *Kenichi Yoshikawa, Elimination of a spiral wave pinned at an obstacle by a train of plane waves: Effect of diffusion between obstacles and surrounding media, Chaos 25, 103127 (2015).

Abstract: In excitable media such as cardiac tissue and Belousov-Zhabotinsky reaction medium, spiral waves tend to anchor (pin) to local heterogeneities. In general, such pinned waves are difficult to eliminate and may progress to spatio-temporal chaos. Heterogeneities can be classified as either the absence or presence of diffusive interaction with the surrounding medium. In this study, we investigated the difference in the unpinning of spiral waves from obstacles with and without diffusive interaction, and found a profound difference. The pacing period required for unpinning at fixed obstacle size is larger in case of diffusive obstacles. Further, we deduced a generic theoretical framework that can predict the minimal unpinning period. Our results explain the difference in pacing periods between for the obstacles with and without diffusive interaction, and the difference is interpreted in terms of the local decrease of spiral wave velocity close to the obstacle boundary caused in the case of diffusive interaction.

Yue Ma, Naoki Ogawa, Yuko Yoshikawa, Toshiaki Mori, Tadayuki Imanaka, Yoshiaki Watanabe and *Kenichi Yoshikawa, Protective Effect of Ascorbic Acid against Double-strand Breaks in Giant DNA: Marked Differences among the Damage Induced by Photo-irradiation, Gamma-rays and Ultrasound, Chemical Physics Letters 638, 205-209 (2015).

Abstract: The protective effect of ascorbic acid against double-strand breaks in DNA was evaluated by single-molecule observation of giant DNA (T4 DNA; 166 kbp) through fluorescence microscopy. Samples were exposed to three different forms of radiation: visible light, -ray and ultrasound. With regard to irradiation with visible light, 1 mM AA reduced the damage down to ca. 30%. Same concentration of AA decreased the damage done by -ray to ca. 70%. However, AA had almost no protective effect against the damage causedby ultrasound. This significant difference is discussed in relation to the physico-chemical mechanism of double-strand breaks depending on the radiation source.

Yong-jun Chen, Kosuke Suzuki and *Kenichi Yoshikawa, Self-organized Target and Spiral Patterns through the “Coffee Ring” Effect, Journal of Chemical Physics 143, 084702 (2015).

Abstract: We studied the precipitation pattern of fullerene C60 nanocrystals generated through the evaporation of a confined liquid bridge. In contrast to the usual “coffee ring” pattern, both target and spiral patterns were observed. The characteristics of the pattern critically depended on the concentration of the solution, the temperature, and the level of vacuum. In addition, the morphology of the microscopic precipitates varied greatly as a function of these experimental parameters. This pattern formation can be interpreted as a two-step rhythmic nucleation/precipitation of fullerene crystals during receding motion of the contact line. Symmetric motion of the contact line produces a target pattern, and the propagation of distortion of the liquid interface caused by a disturbance generates a spiral pattern.

Naoki Umezawa, Yuhei Horai, Yuki Imamura, Makoto Kawakubo, Mariko Nakahira, Nobuki Kato, Akira Muramatsu, Yuko Yoshikawa, *Kenichi Yoshikawa and Tsunehiko Higuchi, Structurally Diverse Polyamines: Solid-Phase Synthesis and Interaction with DNA, ChemBioChem 16, 1811-1819 (2015).

Abstract: A versatile solid-phase approach based on peptide chemistry was used to construct four classes of structurally diverse polyamines with modified backbones: linear, partially constrained, branched, and cyclic. Their effects on DNA duplex stability and structure were examined. The polyamines showed distinct activities, thus highlighting the importance of polyamine backbone structure. Interestingly, the rank order of polyamine ability for DNA compaction was different to that for their effects on circular dichroism and melting temperature, thus indicating that these polyamines have distinct effects on secondary and higher-order structures of DNA.

Hisako Takigawa-Imamura, Ritsuko Morita, Takafumi Iwaki, Takashi Tsuji and *Kenichi Yoshikawa, Tooth germ invagination from cell–cell interaction: Working hypothesis on mechanical instability, Journal of Theoretical Biology 382, 284 (2015).

Abstract: In the early stage of tooth germ development, the bud of the dental epithelium is invaginated by the underlying mesenchyme, resulting in the formation of a cap-like folded shape. This bud-to-cap transition plays a critical role in determining the steric design of the tooth. The epithelial- mesenchymal interaction within a tooth germ is essential for mediating the bud-to-cap transition. Here, we present a theoretical model to describe the autonomous process of the morphological transition, in which we introduce mechanical interactions among cells. Based on our observations, we assumed that peripheral cells of the dental epithelium bound tightly to each other to form an elastic sheet, and mesenchymal cells that covered the tooth germ would restrict its growth. By considering the time-dependent growth of cells, we were able to numerically show that the epithelium within the tooth germ buckled spontaneously, which is reminiscent of the cap-stage form. The difference in growth rates between the peripheral and interior parts of the dental epithelium, together with the steric size of the tooth germ, were determining factors for the number of invaginations. Our theoretical results provide a new hypothesis to explain the histological features of the tooth germ.

Daigo Yamamoto, Tsuyoshi Takada, Masashi Tachibana, Yuta Iijima, Akihisa Shioi and Kenichi Yoshikawa, Micromotors working in water through artificial aerobic metabolism, Nanoscale 7, 13186–13190 (2015).

Abstract: Most catalytic micro/nanomotors that have been developed so far use hydrogen peroxide as fuel, while some use hydrazine. These fuels are difficult to apply because they can cause skin irritation, and often form and store disruptive bubbles. In this paper, we demonstrate a novel catalytic Pt micromotor that does not produce bubbles, and is driven by the oxidation of stable, non-toxic primary alcohols and aldehydes with dissolved oxygen. This use of organic oxidation mirrors living systems, and lends this new motor essentially the same characteristics, including decreased motility in low oxygen environments and the direct isothermal conversion of chemical energy into mechanical energy. Interestingly, the motility direction is reversed by replacing the reducing fuels with hydrogen peroxide. Therefore, these micromotors not only provide a novel system in nanotechnology, but also help in further revealing the underlining mechanisms of motility of living organisms.

Masa Tsuchiya, Alessandro Giuliani, Midori Hashimoto, Jekaterina Erenpreisa and Kenichi Yoshikawa, Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer
Cell Line, PLOS ONE 10(6), e0128565 (2015).

Abstract: Emergent properties of SOC through a mean field approach are revealed: i) SOC, as a form of genomic phase transition, consolidates distinct critical states of expression, ii) Coupling of coherent stochastic oscillations between critical states on different time-scales gives rise to SOC, and iii) Specific gene clusters (barcode genes) ranging in size from kbp to Mbp reveal similar SOC to genome-wide mRNA expression and ON-OFF synchronization to critical states. This suggests that the cooperative gene regulation of topological genome sub-units is mediated by the coherent phase transitions of megadomain-scaled conformations between compact and swollen chromatin states. In summary, our study provides not only a systemic method to demonstrate SOC in whole-genome expression, but also introduces novel, physically grounded concepts for a breakthrough in the study of biological regulation.

Yong-jun Chen, Shun N. Watanabe and *Kenichi Yoshikawa, Roughening Dynamics of Radial Imbibition in a Porous Medium, Journal of Physical Chemistry C 199(22), 12508–12513 (2015).

Abstract: We report radial imbibition of water in a porous medium in a Hele−Shaw cell, including forced imbibition and spontaneous imbibition. Washburn’s law is confirmed in our experiment. Radial imbibition follows scaling dynamics. For forced radial imbibition, anomalous roughening dynamics is found when the front invades the porous medium, and the roughening dynamics depend on the flow rate of the injected fluid. The growth exponents increase linearly with an increase in the flow rate while the roughness exponents decrease with an increase in the flow rate. For spontaneous imbibition, we found a growth exponent (β = 0.6) that was independent of the pressure applied at the liquid inlet, and the roughness exponent decreased with an increase in pressure. Thus, it has become evident that the roughening dynamics of radial imbibition is markedly different from one-dimensional imbibition with a planar interface window.

Kingo Takiguchi, Makiko Egishi, Yohko Tanaka-Takiguchi, Masahito Hayashi and Kenichi Yoshikawa, Specific Transformation of Assembly with Actin Filaments and Molecular Motors in a Cell-Sized Self-Emerged Liposome, Origins of Life and Evolution of Biospheres 44(4), 325-329 (2015).

Abstract: Eukaryotes, by the same combination of cytoskeleton and molecular motor, for example actin filament and myosin, can generate a variety of movements. For this diversity, the organization of biological machineries caused by the confinement and/or crowding effects of internal living cells, may play very important roles.