Biomedical subjects

Jun Ohkubo

Publications and source records attributed to Jun Ohkubo.

4 recordsLinked to original sources

PubMed2005

Preferential urn model and nongrowing complex networks.

A preferential urn model, which is based on the concept "the rich get richer," is proposed. From a relationship between a nongrowing model for complex networks and the preferential urn model in regard to degree distributions, it is revealed that a fitness parameter in the nongrowing model is interpreted as an inverse local temperature in the preferential urn model. Furthermore, it is clarified that the preferential urn model with randomness generates a fat-tailed occupation distribution; the concept of the local temperature enables us to understand the fat-tailed occupation distribution intuitively. Since the preferential urn model is a simple stochastic model, it can be applied to research on not only the nongrowing complex networks, but also many other fields such as econophysics and social sciences.

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PubMed2005

Statistical-mechanical iterative algorithms on complex networks.

The Ising models have been applied for various problems on information sciences, social sciences, and so on. In many cases, solving these problems corresponds to minimizing the Bethe free energy. To minimize the Bethe free energy, a statistical-mechanical iterative algorithm is often used. We study the statistical-mechanical iterative algorithm on complex networks. To investigate effects of heterogeneous structures on the iterative algorithm, we introduce an iterative algorithm based on information of heterogeneity of complex networks, in which higher-degree nodes are likely to be updated more frequently than lower-degree ones. Numerical experiments clarified that the usage of the information of heterogeneity affects the algorithm in Barabási and Albert networks, but does not influence that in Erdös and Rényi networks. It is revealed that information of the whole system propagates rapidly through such high-degree nodes in the case of Barabási-Albert's scale-free networks.

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PubMed2005

Generation of complex bipartite graphs by using a preferential rewiring process.

It is important in computer science, sociology, and so on to investigate complex bipartite graphs from a viewpoint of statistical physics. We propose a model to generate complex bipartite graphs without growing; the bipartite graphs are assumed to have two sets of the fixed numbers of nodes and a fixed number of edges between nodes belonging to different sets of nodes. In this model, essential ingredients are a preferential rewiring process and a fitness distribution function. By using the preferential rewiring process, we confirm that a bipartite graph reaches a stationary state after a sufficiently long time has passed. We find that the obtained bipartite graph has a scale-free-like property when a suitable fitness distribution is used. It turns out that a condensation of edges takes place in the cases of certain fitness distributions.

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PubMed2004

Molecular alignment in a liquid induced by a nonresonant laser field: Molecular dynamics simulation.

We carried out molecular dynamics (MD) simulations for a dilute aqueous solution of pyrimidine in order to investigate the mechanisms of field-induced molecular alignment in a liquid phase. An anisotopically polarizable molecule can be aligned in a liquid phase by the interaction with a nonresonant intense laser field. We derived the effective forces induced by a nonresonant field on the basis of the concept of the average of the total potential over one optical cycle. The results of MD simulations show that a pyrimidine molecule is aligned in an aqueous solution by a linearly polarized field of light intensity I approximately 10(13) W/cm2 and wavelength lambda = 800 nm. The temporal behavior of field-induced alignment is adequately reproduced by the solution of the Fokker-Planck equation for a model system in which environmental fluctuations are represented by Gaussian white noise. From this analysis, we have revealed that the time required for alignment in a liquid phase is in the order of the reciprocals of rotational diffusion coefficients of a solute molecule. The degree of alignment is determined by the anisotropy of the polarizability of a molecule, light intensity, and temperature. We also discuss differences between the mechanisms of optical alignment in a gas phase and a liquid phase.

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