Recent Research

 

Fluctuations induced transition of localization of granular objects caused by degrees of crowding

**Soutaro Oda, Yoshitsugu, Kubo, Chwen-Ynaf Shew, Kenichi Yoshikawa,Physica D, 336, 39–46 (2016).**

Fluctuations are ubiquitous in both microscopic and macroscopic systems, and an investigation of confined particles under fluctuations is relevant to how living cells on the earth maintain their lives. Inspired by biological cells, we conduct the experiment through a very simple fluctuating system containing one or several large spherical granular particles and multiple smaller ones confined on a cylindrical dish under vertical vibration. We find a universal behavior that large particles preferentially locate in cavity interior due to the fact that large particles are depleted from the cavity wall by small spheres under vertical vibration in the actual experiment. This universal behavior can be understood from the standpoint of entropy.

Fig.1: Schematic representations of the experimental system with bird view in (a) and side view in (b); typical snapshots at 0 and 540 seconds (left panel) and the real-time trajectories of the large sphere (right panel) for two distinct packing fractions η = 0.1(NL = 1 and NS = 29) in (c) and 0.6(NL = 1 and NS = 229) in (d), where dL =10mm, dS =3mm and D = 60mm. The scale bar is10mm. Note that the dotted circles in the trajectory plots indicate the outermost boundary which can be reached by the center of mass of a large sphere within the cylindrical disk.

 

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Rotary motion of a micro solid particle under a stationary difference of electric potential

**Tomo Kurimura, Seori Mori, Masako Miki, and Kenichi Yoshikawa,Journal of Chemical Physics, 145, 034902 (2016).**

The periodic rotary motion of spherical sub-millimeter-sized plastic objects is generated under a direct-current electric field in an oil phase containing a small amount of anionic or cationic surfactant. Twin-rotary motion is observed between a pair of counter electrodes; i.e., two vortices are generated simultaneously, where the line between the centers of rotation lies perpendicular to the line between the tips of the electrodes. Interestingly, this twin rotational motion switches to the reverse direction when an anionic surfactant is replaced by a cationic surfactant. We discuss the mechanism of this self-rotary motion in terms of convective motion in the oil phase where nanometer-sized inverted micelles exist. The reversal of the direction of rotation between anionic and cationic surfactants is attributable to the difference in the charge sign of inverted micelles with surfactants. We show that the essential features in the experimental trends can be reproduced through a simple theoretical model, which supports the validity of the above mechanism.

FIG. 1. Self-revolution of plastic particles. (a) Initial condition at t = 0 s from when DC voltage was applied. (b) Overlap of snapshots every 0.53 s. Multiple polyethylene particles with radii of r = 50 – 175µm rotate in the oil phase with an anionic surfactant at V = 170 V. FIG. 2. (a-1, b): Angular velocity and angular acceleration depending on the angular position of the particle in the presence of an anionic surfactant (a-1), or a cationic surfactant (b). (a-2): The blue solid line is the velocity and the red dotted line is the acceleration. Videos of these experiments are shown in the Supplemental Materials.14 The radius of rotation in both the anionic and cationic surfactants depends on the initial position of a particle. Particle size: d=175 µm. Applied voltage: V =170 V and 180 V for (a) and (b), respectively.

 

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Formation of Stable Cell-Cell Contact without a Solid/Gel Scaffold:Non-invasive Manipulation by Laser under Depletion Interaction with a Polymer

**Publication of a new article by Mr. Hashimoto (MC2) as the first author in Chem. Phys. Lett., 655-656, 11-16 (2016).**

We report a novel method for constructing a stable three-dimensional cellular assembly in the absence of a solid or gel scaffold. A targeted cell was transferred to another cell, and the two were kept in contact for a few minutes by optical manipulation in an aqueous medium containing a hydrophilic polymer. Interestingly, this cell-cell adhesion was maintained even after elimination of the polymer. We discuss the mechanism of the formation of stable multi-cellular adhesion in terms of spontaneous rearrangement of the components embedded in the pair of facing membranes.

Hashimoto

Fig.1. Optical construction of a pyramidal assembly. The focal point of the laser is marked by the red ‘x’.

 

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Negative/positive chemotaxis of a droplet: Dynamic response to a stimulant gas

**Publication of a new article by Mr. Hiroki Sakuta (MC2) as the first author in Applied Physics Letters, 108, 203703 (2016).**

We report here the repulsive/attractive motion of an oil droplet floating on an aqueous phase caused by the application of a stimulant gas. A cm-sized droplet of oleic acid is repelled by ammonia vapor (Fig. 1). In contrast, a droplet of aniline on an aqueous phase moves toward hydrochloric acid as a stimulant (Fig. 2). The mechanisms of these characteristic behaviors of oil droplets are discussed in terms of the spatial gradient of the interfacial tension caused by the stimulant gas.

Sakuta_Fig1 Sakuta_Fig2
Fig. 1 Negative chemotactic behavior of an oleic acid droplet floating on an aqueous solution against NH3 vapor. (a) Snapshots of an oleic acid droplet moving away from ammonia vapor. (b) Spatio-temporal diagram of droplet motion, where x=0 corresponds to the center of the droplet at the initial position. Fig. 2 Positive chemotactic behavior of an aniline droplet vs. HCl vapor. Superimposed image of the aniline droplet moving toward the HCl vapor.

 

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Divalent Cation Shrinks DNA but Inhibits its Compaction with Trivalent Cation

**Publication of a new article by Miss Tongu (MC2) as the first author in Journal of Chemical Physics, 144, 205101 (2016)**

Our observation reveals the effects of divalent and trivalent cations on the higher-order structure of giant DNA (T4 DNA 166 kbp) by fluorescence microscopy. It was found that divalent cations, Mg(2+) and Ca(2+), inhibit DNA compaction induced by a trivalent cation, spermidine (SPD(3+)). On the other hand, in the absence of SPD(3+), divalent cations cause the shrinkage of DNA. As the control experiment, we have confirmed the minimum effect of monovalent cation, Na(+) on the DNA higher-order structure. We interpret the competition between 2+ and 3+ cations in terms of the change in the translational entropy of the counter ions. For the compaction with SPD(3+), we consider the increase in translational entropy due to the ion-exchange of the intrinsic monovalent cations condensing on a highly-charged polyelectrolyte, double-stranded DNA, by the 3+ cations. In contrast, the presence of 2+ cation decreases the gain of entropy contribution by the ion-exchange between monovalent and 3+ ions.

divalent_2 divalent_3

 

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Highly Concentrated Ethanol Solutions:
Good Solvents for DNA as Revealed by Single-Molecule Observation

**Publication of a new article by Mr. Oda (MC2) as the first author in ChemPhysChem, 17, 471–473 (2016)**

research_theme03We observed single DNA molecules at different ethanol concentrations by using fluorescence microscopy. Large single DNA molecules undergo reentrant conformational transitions from elongated coil into folded globule and then into elongated coil state, accompanied by the increase of the concentration of ethanol in a low-salt aqueous environment. The second transition from globule into the coil state occurs at around 70% (v/v) ethanol. From circular dichroism (CD) measurements, it is confirmed that the reentrant transition of the higher order structure proceeds together with the transitions of the secondary structure from B to C and, then, from C to A in a cooperative manner. The determined mechanism of the reentrant transition is discussed in relation to the unique characteristics of solutions with higher ethanol content, for which clathrate-like nanostructures of alcohol molecules are generated in the surrounding water.

 

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Protection against double-strand breaks of DNA by ascorbic acid: Comparison among visible light, γ-ray and ultrasound

**Publication of a new article by Mr. Ma (PhD student) as the first author in Chem. Phys. Lett., 638, 205–209 (2015).**

research_theme02The protective effect of ascorbic acid (AA) against double-strand breaks (DSBs) in DNA caused by various sources of radiation was evaluated by single-molecule observation of giant DNA. The following conclusions were obtained: 1) The significant protective effect of AA against photo-induced damage may reflect the effective diminish of reactive oxygen species (ROS) by AA. 2) As for γ-ray, there exist the protective effect by AA but a little bit weaker than the case of photo irradiation. This may be due to the generation of plural number of ROS by single photon of γ-ray. Surviving ROS against the diminishment effect by AA may cause DSBs. 3) As for the DSBs by ultrasound, physical damage caused by the shockwave through the generation of cavitation dominates. Thus, the chemical effect of AA is considered to be negligible small for the protection of DSBs.

 

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Structurally Diverse Polyamines: Solid-Phase Synthesis and Interaction with DNA

**A new research article by Mr. A. Muramatsu (MC2) as the collaboration with Nagoya City Univ. has been published in Journal of Chemical Physics, 145, 235103 (2016)**

research_theme01

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.


 

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Lamellar/Disorder Phase Transition in a Mixture of Water/2,6-Dimethylpyridine/Antagonistic Salty

The effects of adding an antagonistic salt, sodium tetraphenylborate (NaBPh4), to a binary mixture of deuterated water and 2,6-dimethylpyridine were investigated by visual inspection, optical microscopy, and small-angle neutron scattering. With increasing salt concentration, the two-phase region shrinks. When the concentration of NaBPh4 is 85 mmol·L-1, a temperature-induced lamellar/disorder phase transition is observed at 338 K. These trends are similar to those observed for a mixture of water/3-methylpyridine/ NaBPh4 (Sadakane et al., Phys. Rev. Lett. 103, 167803 (2009)).

 

[1] K. Sadakane, H. Endo, K. Nishida, H. Seto, “Lamellar/Disorder Phase Transition in a Mixture of Water/2,6-Dimethylpyridine/Antagonistic Salty”, Journal of Solution Chemistry, 43, 1722-1731 (2014).

[2] K. Sadakane, M. Nagao, H. Endo, H. Seto, “Membrane formation by preferential solvation of ions in mixture of water, 3-methylpyridine, and sodium tetraphenylborate”, The Journal of Chemical Physics, 139, 234905 (2013).

[3] K. Sadakane, A. Onuki, K. Nishida, S. Koizumi and H. Seto, “Multilamellar Structures Induced by Hydrophilic and Hydrophobic Ions Added to a Binary Mixture of D2O and 3-Methylpyridine”, Phys. Rev.Lett., 103, pp. 167803(1)-(4) (2009).

Fig1

 

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Marked difference in conformational fluctuation between giant DNA molecules in circular and linear forms

We performed monomolecular observations on linear and circular giant DNAs (208 kbp) in anaqueous solution by the use of fluorescence microscopy. The results showed that the degree of conformational fluctuation in circular DNA was ca. 40% less than that in linear DNA, although the long-axis length of circular DNA was only 10% smaller than that of linear DNA. Additionally, the relaxation time of a circular chain was shorter than that of a linear chain by at least one order of magnitude. The essential features of this marked difference between linear and circular DNAs were reproduced by numerical simulations on a ribbon-like macromolecule as a coarse-grained model of a long semi flexible, double-helical DNA molecule. In addition, we calculated the radius of gyration of an interacting chain in a circular form on the basis of the mean field model, which provides a better understanding of the present experimental trend than a traditional theoretical equation.

  1. Iwaki, T. Ishido, L\K. Hirano, A. A. Lazutin, V. V. Vashievskaya, T. Kenmotsu, K. Yoshikawa, “Marked difference in conformational fluctuation between giant DNA molecules in circular and linear forms”, J. Chem. Phys. Vol. 142, Issue 14, 145101, 2015

Fig2

 

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*b>b.