Biomedical subjects

Isamu Kusaka

Publications and source records attributed to Isamu Kusaka.

6 recordsLinked to original sources

PubMed2006

Direct calculation of solid-vapor coexistence points by thermodynamic integration: application to single component and binary systems.

We present a new thermodynamic integration method that directly connects the vapor and solid phases by a reversible path. The thermodynamic integration in the isothermal-isobaric ensemble yields the Gibbs free energy difference between the two phases, from which the sublimation temperature can be easily calculated. The method extends to the binary mixture without any modification to the integration path simply by employing the isothermal-isobaric semigrand ensemble. The thermodynamic integration, in this case, yields the chemical potential difference between the solid and vapor phases for one of the components, from which the binary sublimation temperature can be calculated. The coexistence temperatures predicted by our method agree well with those in the literature for single component and binary Lennard-Jones systems.

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PubMed2006

Statistical mechanics of nucleation: incorporating translational and rotational free energy into thermodynamics of a microdroplet.

Motivated by the original Lothe-Pound prescription, we derive a formula for the replacement partition function that is suitable for vapor to liquid phase nucleation in terms of the classical phase integral. The resulting expression was evaluated for truncated and shifted Lennard-Jones fluids by means of computer simulation. The corresponding Lothe-Pound correction factor, which is to multiply the classical expression for the nucleation rate, decreases significantly with increasing temperature and decreasing cluster size, and is in the range of 10(9)-10(13) for the temperatures and the cluster sizes we studied. This is somewhat smaller than the original estimate of 10(17) by Lothe and Pound.

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PubMed2006

Evaluation of the translational free energy in a melting temperature calculation by simulation.

We present two methods suitable for controlling the translational degrees of freedom of a system when evaluating directly the free energy difference between the liquid and the solid phases by thermodynamic integration along a reversible path connecting these two phases. Such a constraint is crucial for an accurate prediction of the melting point by means of simulation. In one of the methods, the free energy difference was calculated by fixing one of the particles of the system at the center of the simulation box. In the second method, the free energy difference was calculated by constraining the center of mass of the system to a small region taken around the center of the simulation box. The correction to the free energy difference due to each constraint must be evaluated by a direct simulation. Both methods give consistent results when applied to a truncated and shifted Lennard-Jones system with cutoff radius of 2.5sigma. However, the fixed particle constraint method is found to be more efficient computationally.

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PubMed2005

Direct calculation of solid-liquid coexistence points of a binary mixture by thermodynamic integration.

We present a new thermodynamic integration method that directly connects the liquid and the solid phases of a binary mixture by a reversible path. The states along the path are simulated in the isothermal-isobaric semigrand canonical ensemble, in which temperature, pressure, the total number of particles, and the fugacity fractions of the components are held fixed. The thermodynamic integration yields the chemical-potential difference between the two phases for one of the components and this information is then used to locate the solid-liquid coexistence points. The melting temperatures predicted by our method agree well with those predicted by the Gibbs-Duhem integration for a truncated and shifted Lennard-Jones system with a cutoff radius of 2.5sigma.

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PubMed2005

Distinct functional units of the Golgi complex in Drosophila cells.

A striking variety of glycosylation occur in the Golgi complex in a protein-specific manner, but how this diversity and specificity are achieved remains unclear. Here we show that stacked fragments (units) of the Golgi complex dispersed in Drosophila imaginal disk cells are functionally diverse. The UDP-sugar transporter FRINGE-CONNECTION (FRC) is localized to a subset of the Golgi units distinct from those harboring SULFATELESS (SFL), which modifies glucosaminoglycans (GAGs), and from those harboring the protease RHOMBOID (RHO), which processes the glycoprotein SPITZ (SPI). Whereas the glycosylation and function of NOTCH are affected in imaginal disks of frc mutants, those of SPI and of GAG core proteins are not, even though FRC transports a broad range of glycosylation substrates, suggesting that Golgi units containing FRC and those containing SFL or RHO are functionally separable. Distinct Golgi units containing FRC and RHO in embryos could also be separated biochemically by immunoisolation techniques. We also show that Tn-antigen glycan is localized only in a subset of the Golgi units distributed basally in a polarized cell. We propose that the different localizations among distinct Golgi units of molecules involved in glycosylation underlie the diversity of glycan modification.

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PubMed2004

Bubble nucleation in micellar solution: a density functional study.

We explore the free energetics of bubble nucleation in the micellar solution subjected to a negative pressure using a density functional model of a non-ionic surfactant solution. In this two-component model, the solvent is represented by a single hard-core sphere and the surfactant is represented by two tangent hard-core spheres connected by a rigid bond. The attractive interactions between the particles are modeled by the simple 1/R(6) form. Under all conditions of pressure and interparticle interactions we studied, the free energy barrier of bubble nucleation is found to be lower in the binary surfactant solution than that in a pure solvent and to continue to decrease as the mole fraction of the surfactant in the solution increases. We analyze the free energy surface of the model system under the conditions where both the critical bubble nucleus and the stable micelle exist in equilibrium with the same metastable solution. Our study shows that at moderately low pressures, bubbles can nucleate from the stable micelle and that the resulting free energy barrier of bubble nucleation is expected to be lower than that in the absence of this mechanism. However, as the spinodal is approached at lower pressures, the mechanism of micelle-assisted bubble nucleation becomes less effective. The liquid-liquid miscibility of the model system correlates well with the mechanism of bubble nucleation from the stable micelle.

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