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Ito, Nobuyasu (24)

Watanabe, Hiroshi (8)Shimada, Takashi (7)Yukawa, Satoshi (4)Inaoka, Hajime (3)View MoreJournalPhysical Review E (10)Physica A: Statistical Mechanics and its Applications (3)Computer Physics Communications (2)Progress of Theoretical Physics Supplement (2)International Journal of Modern Physics C (1)View MoreKAUST Grant NumberKUK-I1-005-04 (22)KUK-I1-00504 (1)KUKI1-005-04 (1)PublisherAmerican Physical Society (APS) (11)Elsevier BV (7)Oxford University Press (OUP) (2)AIP Publishing (1)IOP Publishing (1)View MoreSubjectMolecular dynamics simulation (4)Lennard-Jones particle system (3)Community assembly (1)Coordinated stasis (1)Current distribution (1)View MoreTypeArticle (23)Conference Paper (1)Year (Issue Date)2014 (1)2013 (2)2012 (3)2011 (3)2010 (10)View MoreItem AvailabilityMetadata Only (22)Open Access (2)

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Dynamical study of a polydisperse hard-sphere system

Nogawa, Tomoaki; Ito, Nobuyasu; Watanabe, Hiroshi (Physical Review E, American Physical Society (APS), 2010-08-10) [Article]

We study the interplay between the fluid-crystal transition and the glass transition of elastic sphere system with polydispersity using nonequilibrium molecular dynamics simulations. It is found that the end point of the crystal-fluid transition line, which corresponds to the critical polydispersity above which the crystal state is unstable, is on the glass transition line. This means that crystal and fluid states at the melting point becomes less distinguishable as polydispersity increases and finally they become identical state, i.e., marginal glass state, at critical polydispersity. © 2010 The American Physical Society.

Distribution in flowing reaction-diffusion systems

Kamimura, Atsushi; Herrmann, Hans J.; Ito, Nobuyasu (Physical Review E, American Physical Society (APS), 2009-12-28) [Article]

A power-law distribution is found in the density profile of reacting systems A+B→C+D and 2A→2C under a flow in two and three dimensions. Different densities of reactants A and B are fixed at both ends. For the reaction A+B, the concentration of reactants asymptotically decay in space as x-1/2 and x-3/4 in two dimensions and three dimensions, respectively. For 2A, it decays as log (x) /x in two dimensions. The decay of A+B is explained considering the effect of segregation of reactants in the isotropic case. The decay for 2A is explained by the marginal behavior of two-dimensional diffusion. A logarithmic divergence of the diffusion constant with system size is found in two dimensions. © 2009 The American Physical Society.

Effects of demographic stochasticity on biological community assembly on evolutionary time scales

Murase, Yohsuke; Shimada, Takashi; Ito, Nobuyasu; Rikvold, Per Arne (Physical Review E, American Physical Society (APS), 2010-04-13) [Article]

We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the noise consist of species strongly coupled with each other and have stronger linear stability around the fixed-point populations than the corresponding noiseless model. The dynamics on evolutionary time scales for the predator-prey model are also altered by the noise. Approximate 1/f fluctuations are observed with noise, while 1/ f2 fluctuations are found for the model without demographic noise. © 2010 The American Physical Society.

Cluster-cluster aggregation of Ising dipolar particles under thermal noise

Suzuki, Masaru; Kun, Ferenc; Ito, Nobuyasu (Physical Review E, American Physical Society (APS), 2009-08-14) [Article]

The cluster-cluster aggregation processes of Ising dipolar particles under thermal noise are investigated in the dilute condition. As the temperature increases, changes in the typical structures of clusters are observed from chainlike (D1) to crystalline (D2) through fractal structures (D1.45), where D is the fractal dimension. By calculating the bending energy of the chainlike structure, it is found that the transition temperature is associated with the energy gap between the chainlike and crystalline configurations. The aggregation dynamics changes from being dominated by attraction to diffusion involving changes in the dynamic exponent z=0.2 to 0.5. In the region of temperature where the fractal clusters grow, different growth rates are observed between charged and neutral clusters. Using the Smoluchowski equation with a twofold kernel, this hetero-aggregation process is found to result from two types of dynamics: the diffusive motion of neutral clusters and the weak attractive motion between charged clusters. The fact that changes in structures and dynamics take place at the same time suggests that transitions in the structure of clusters involve marked changes in the dynamics of the aggregation processes. © 2009 The American Physical Society.

Evaporation-condensation transition of the two-dimensional Potts model in the microcanonical ensemble

Nogawa, Tomoaki; Ito, Nobuyasu; Watanabe, Hiroshi (Physical Review E, American Physical Society (APS), 2011-12-05) [Article]

The evaporation-condensation transition of the Potts model on a square lattice is numerically investigated by the Wang-Landau sampling method. An intrinsically system-size-dependent discrete transition between supersaturation state and phase-separation state is observed in the microcanonical ensemble by changing constrained internal energy. We calculate the microcanonical temperature, as a derivative of microcanonical entropy, and condensation ratio, and perform a finite-size scaling of them to indicate the clear tendency of numerical data to converge to the infinite-size limit predicted by phenomenological theory for the isotherm lattice gas model. © 2011 American Physical Society.

Efficiency of rejection-free methods for dynamic Monte Carlo studies of off-lattice interacting particles

Guerra, Marta L.; Novotny, M. A.; Watanabe, Hiroshi; Ito, Nobuyasu (Physical Review E, American Physical Society (APS), 2009-02-23) [Article]

We calculate the efficiency of a rejection-free dynamic Monte Carlo method for d -dimensional off-lattice homogeneous particles interacting through a repulsive power-law potential r-p. Theoretically we find the algorithmic efficiency in the limit of low temperatures and/or high densities is asymptotically proportional to ρ (p+2) /2 T-d/2 with the particle density ρ and the temperature T. Dynamic Monte Carlo simulations are performed in one-, two-, and three-dimensional systems with different powers p, and the results agree with the theoretical predictions. © 2009 The American Physical Society.

Huge-scale molecular dynamics simulation of multibubble nuclei

Watanabe, Hiroshi; Suzuki, Masaru; Ito, Nobuyasu (Computer Physics Communications, Elsevier BV, 2013-12) [Article]

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.

Random walk in genome space: A key ingredient of intermittent dynamics of community assembly on evolutionary time scales

Murase, Yohsuke; Shimada, Takashi; Ito, Nobuyasu; Rikvold, Per Arne (Journal of Theoretical Biology, Elsevier BV, 2010-06) [Article]

Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species, while migrants have no correlation with the resident species. It is found that the dynamics of community assembly with mutations are quite different from the case with migrations. In contrast to mutation models, which show intermittent dynamics of quasi-steady states interrupted by sudden reorganizations of the community, migration models show smooth and gradual renewal of the community. As a consequence, instead of the 1/f diversity fluctuations found for the mutation models, 1/f2, random-walk like fluctuations are observed for the migration models. In addition, a characteristic species-lifetime distribution is found: a power law that is cut off by a "skewed" distribution in the long-lifetime regime. The latter has a longer tail than a simple exponential function, which indicates an age-dependent species-mortality function. Since this characteristic profile has been observed, both in fossil data and in several other mathematical models, we conclude that it is a universal feature of macroevolution. © 2010 Elsevier Ltd.

Kertész line of thermally activated breakdown phenomena

Yoshioka, Naoki; Kun, Ferenc; Ito, Nobuyasu (Physical Review E, American Physical Society (APS), 2010-11-12) [Article]

Based on a fiber bundle model we substantially extend the phase-transition analogy of thermally activated breakdown of homogeneous materials. We show that the competition of breaking due to stress enhancement and due to thermal fluctuations leads to an astonishing complexity of the phase space of the system: varying the load and the temperature a phase boundary emerges, separating a Griffith-type regime of abrupt failure analogous to first-order phase transitions from disorder dominated fracture where a spanning cluster of cracks emerges. We demonstrate that the phase boundary is the Kertész line of the system along which thermally activated fracture appears as a continuous phase transition analogous to percolation. The Kertész line has technological relevance setting the boundary of safe operation for construction components under high thermal loads. © 2010 The American Physical Society.

Efficiencies of dynamic Monte Carlo algorithms for off-lattice particle systems with a single impurity

Novotny, M.A.; Watanabe, Hiroshi; Ito, Nobuyasu (Physics Procedia, Elsevier BV, 2010-02) [Conference Paper]

The efficiency of dynamic Monte Carlo algorithms for off-lattice systems composed of particles is studied for the case of a single impurity particle. The theoretical efficiencies of the rejection-free method and of the Monte Carlo with Absorbing Markov Chains method are given. Simulation results are presented to confirm the theoretical efficiencies. © 2010.

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