arXiv subjects

Kenichi Yoshikawa

Publications and source records attributed to Kenichi Yoshikawa.

At least 37 records · Page 2Linked to original sources

arXiv2006

Toward the Stable Optical Trapping of a Droplet with Counter Laser Beams under Microgravity

To identify the optimum conditions for the optical trapping of a droplet under microgravity, we theoretically analyzed the efficiency of trapping with counter laser beams. We found that the distance between the two foci is an important parameter for obtaining stable trapping conditions. We also performed an optical trapping experiment with counter laser beams under microgravity. The experimental results correspond well to the theoretical prediction.

physics.optics↗

arXiv2006

Micro-Bioreactor Mimicking a Cellular Environment

We report that a cell-sized water droplet (CWD) with a diameter of several tens of microns can serve as a micro-biochemical reactor. Since the droplet inner surface is covered by a phospholipid layer, it provides an environment similar to that in living cells. The CWD is manipulated with laser tweezers and we monitor the time-development of biochemical reactions in a single CWD by fusing two droplets which contain a substrate and an enzyme, respectively. As actual examples of enzymatic reactions, we present results on the reaction of calcein with esterase and on the expression reaction of green fluorescent protein.

physics.bio-ph↗

arXiv2006

Transporting of a Cell-Sized Phospholipid Vesicle Across Water/Oil Interface

When a cell-sized water droplet, with a diameter of several tens of micro meter, is placed in oil containing phospholipids, a stable cell-sized vesicle is spontaneously formed as a water-in-oil phospholipid emulsion (W/O CE) with a phospholipid monolayer. We transferred the lipid vesicle thus formed in the oil phase to the water phase across the water/oil interface by micromanipulation, which suggests that the vesicle is transformed from a phospholipid monolayer as W/O CE into a bilayer. The lipid vesicle can then be transported back into the oil phase. This novel experimental procedure may be a useful tool for creating a model cellular system, which, together with a microreactor, is applicable as a micrometer-scale biochemical reaction field.

physics.chem-ph↗

arXiv2005

Different pathways in mechanical unfolding/folding cycle of a single semiflexible polymer

Kinetics of conformational change of a semiflexible polymer under mechanical external field were investigated with Langevin dynamics simulations. It is found that a semiflexible polymer exhibits large hysteresis in mechanical folding/unfolding cycle even with a slow operation, whereas in a flexible polymer, the hysteresis almost disappears at a sufficiently slow operation. This suggests that the essential features of the structural transition of a semiflexible polymer should be interpreted at least on a two-dimensional phase space. The appearance of such large hysteresis is discussed in relation to different pathways in the loading and unloading processes. By using a minimal two-variable model, the hysteresis loop is described in terms of different pathways on the transition between two stable states.

cond-mat.soft↗

arXiv2005

Domain Growth Kinetics in a Cell-sized Liposome

We investigated the kinetics of domain growth on liposomes consisting of a ternary mixture (unsaturated phospholipid, saturated phospholipid, and cholesterol) by temperature jump. The domain growth process was monitored by fluorescence microscopy, where the growth was mediated by the fusion of domains through the collision. It was found that an average domain size r develops with time t as r ~ t^0.15, indicating that the power is around a half of the theoretical expectation deduced from a model of Brownian motion on a 2-dimensional membrane. We discuss the mechanism of the experimental scaling behavior by considering the elasticity of the membrane.

cond-mat.soft↗

arXiv2005

Chemo-Sensitive Running Droplet

Chemical control of the spontaneous motion of a reactive oil droplet moving on a glass substrate under an aqueous phase is reported. Experimental results show that the self-motion of an oil droplet is confined on an acid-treated glass surface. The transient behavior of oil-droplet motion is also observed with a high-speed video camera. A mathematical model that incorporates the effect of the glass surface charge is built based on the experimental observation of oil-droplet motion. A numerical simulation of this mathematical model reproduced the essential features concerning confinement within a certain chemical territory of oil-droplet motion, and also its transient behavior. Our results may shed light on physical aspects of reactive spreading and a chemotaxis in living things.

nlin.AO↗

arXiv2005

Optical Levitation of a Droplet under Linear Increase of Gravitational Acceleration

Optical levitation of a liquid droplet in gas phase was investigated under timedependent change of the gravitational acceleration with specific flight pattern of an airplane. Through multiple trials under linear increase of effective gravitational acceleration, we performed the experiment of ptical trapping of a droplet from 0.3g_0 to 0.9g_0, where g_0 = 9.8 m/s^2. During such change of the effective gravitational acceleration, the trapping position on a droplet with the radius of 14 μm was found to be lowered by ca. 100 μm. The essential feature of the change of the trapping position is reproduced by a theoretical calculation under the framework of ray optics. As far as we know, the present study is the first report on optical levitation under time-dependent gravitational change.

physics.optics↗

arXiv2005

Reversible photo-switching in a cell-sized vesicle

A photosensitive amphiphilic molecule can switch the shape of an assembled vesicle as determined by microscopic observation. Photo-isomerization induces a change in membrane fluctuation behavior or a morphological transition between ellipsoid and bud shapes, depending on the asymmetrical degree of the initial shape. The mechanism of this reversible photo-switching in the vesicle morphology is interpreted in terms of a change in the effective cross-sectional area of the photosensitive molecule.

cond-mat.soft↗

arXiv2005

Self Running Droplet: Emergence of Regular Motion from Nonequilibrium Noise

Spontaneous motion of an oil droplet driven by chemical nonequilibricity is reported. It is shown that the droplet undergoes regular rhythmic motion under appropriately designed boundary conditions, whereas it exhibits random motion in an isotropic environment. This study is a novel manifestation on the direct energy transformation of chemical energy into regular spatial-motion under isothermal conditions. A simple mathematical equation including noise reproduces the essential feature of the transition from irregularity into periodic regular motion. Our results will inspire the theoretical study on the mechanism of molecular motors in living matter, working under significant influence of thermal fluctuation.

nlin.AO↗

arXiv2005

Smooth/rough layering in liquid-crystalline/gel state of dry phospholipid film, in relation to its ability to generate giant vesicles

Morphological changes in a dry phospholipid film on a solid substrate were studied below and above the main transition temperature, between the gel and liquid-crystalline phases by phase-contrast microscopy and AFM. A Phospholipid film in the liquid-crystalline phase exhibits flat, smooth layering, whereas that in the gel phase shows rough, random layering. These film morphologies are discussed in relation to the ability to form giant vesicles through the natural swelling method.

physics.chem-ph↗

arXiv2005

Mode Selection in the Spontaneous Motion of an Alcohol Droplet

An alcohol (pentanol) droplet exhibits spontaneous agitation on an aqueous solution, driven by a solutal Marangoni effect. We found that the droplet's mode of motion is controlled by its volume. A droplet with a volume of less than $0.1 μ\rm{l}$ shows irregular translational motion, whereas intermediate-sized droplets of $0.1-200 μ\rm{l}$ show vectorial motion. When the volume is above $300 μ\rm{l}$, the droplet splits into smaller drops. These experimental results regarding mode selection are interpreted in terms of the wave number selection depending on the droplet volume.

nlin.AO↗

arXiv2005

Dynamics of micrometer-scale phase separation in a polymer mixture upon laser irradiation

Ten $μ$m -sized droplets in an aqueous-two-phase system (water/ polyethylene-glycol (PEG)/ dextran) dissapear upon irradiation with a focused YAG laser. The interface of the dextran-rich droplet broadens, indicating smoothing of the concentration profile, whereas, the PEG-rich droplet shrinks and disappears. These phenomena can be described in terms of the Ginzburg-Landau free energy, by considering the laser-induced dielectric potential.

cond-mat.other↗

arXiv2005

Slowing and stopping of chemical waves in a narrowing canal

The propagation of a chemical wave in a narrow, cone-shaped glass capillary was investigated. When a chemical wave propagates from the wider end to the narrower end, it slows, stops, and then disappears. A phenomenological model that considers the surface effect of the glass is proposed, and this model reproduces the experimental trends.

nlin.PS↗

arXiv2004

Why is the condensed phase of DNA preferred at higher temperature? DNA compaction in the presence of a multivalent cation

Upon the addition of multivalent cations, a giant DNA chain exhibits a large discrete transition from an elongated coil into a folded compact state. We performed single-chain observation of long DNAs in the presence of a tetravalent cation (spermine), at various temperatures and monovalent salt concentrations. We confirmed that the compact state is preferred at higher temperatures and at lower monovalent salt concentrations. This result is interpreted in terms of an increase in the net translational entropy of small ions due to ionic exchange between higher and lower valence ions.

cond-mat.soft↗

arXiv2004

Phase Transition in Reconstituted Chromatin

By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed states in reconstituted chromatin. Based on an analysis of the spatial distribution of nucleosome cores, we deduced an effective thermodynamic potential as a function of the nucleosome-nucleosome distance. This enabled us to interpret the folding transition of chromatin in terms of a first-order phase transition. This mechanism for the condensation of chromatin is discussed in terms of its biological significance.

q-bio.SC↗

arXiv2004

Entrapping a polymer chain in a light well under a good solvent condition

During the last decade, the laser trapping technique has been actively applied to elucidate the property of macromolecules, DNA, RNA, cytoskeleton fibres, etc. Due to the inherent difficulty in the direct trapping of single molecules at approximately 300 K, most of the current studies on laser trapping utilize the experimental technique to grasp microbeads that are attached to a single macromolecule, instead of using direct trapping. A few studies have demonstrated the applicability of laser trapping for highly packed compact DNA under a `poor' solvent condition without any beads. The present study achieves laser trapping on a single DNA molecule under a `good' solvent condition without any microbeads. The time-dependent change of the conformation accompanied by ON/OFF laser irradiation was measured and analysed in terms of the entrapment and release of a coiled polymer around a micrometer-sized potential.

cond-mat.soft↗

arXiv2004

All-or-none switching of transcriptional activity on single DNA molecules caused by a discrete conformational transition

Recently, it has been confirmed that long duplex DNA molecules with sizes larger than several tens of kilo-base pairs (kbp), exhibit a discrete conformational transition from an elongated coil state to a compact globule state upon the addition of various kinds of chemical species that usually induce DNA condensation. In this study, we performed a single-molecule observation on a large DNA, Lambda ZAP II DNA (ca. 41 kbp), in a solution containing RNA polymerase and substrates along with spermine, a tetravalent cation, at different concentrations, by use of fluorescence staining of both DNA and RNA. We found that transcription, or RNA production, is completely inhibited in the compact state, but is actively performed in the unfolded coil state. Such an all-or-none effect on transcriptional activity induced by the discrete conformational transition of single DNA molecules is discussed in relation to the mechanism of the regulation of large-scale genetic activity.

q-bio.BM↗

arXiv2004

Direction Detector on an Excitable Field: Field Computation with Coincidence Detection

Living organisms process information without any central control unit and without any ruling clock. We have been studying a novel computational strategy that uses a geometrically arranged excitable field, i.e., "field computation." As an extension of this research, in the present article we report the construction of a "direction detector" on an excitable field. Using a numerical simulation, we show that the direction of a input source signal can be detected by applying the characteristic as a "coincidence detector" embedded on an excitable field. In addition, we show that this direction detection actually works in an experiment using an excitable chemical system. These results are discussed in relation to the future development of "field computation."

nlin.PS↗