arXiv subjects

Yuki Norizoe

Publications and source records attributed to Yuki Norizoe.

9 recordsLinked to original sources

arXiv2024

Phase separation in soft repulsive polymer mixtures: foundation and implication for chromatin organization

Given the wide range of length scales, the analysis of polymer systems often requires coarse-graining, for which various levels of description may be possible depending on the phenomenon under consideration. Here, we provide a super-coarse grained description, where polymers are represented as a succession of mesosopic soft beads which are allowed to overlap with others. We then investigate the phase separation behaviors in a mixture of such homopolymers based on mean-field theory, and discuss universal aspects of the miscibility phase diagram in comparison with the numerical simulation. We also discuss an extension of our analysis to mixtures involving random copolymers, which might be interesting in the context of chromatin organization in a cell nucleus.

cond-mat.soft↗

arXiv2021

Molecular-shape- and size-independent power-law dependence of percolation thresholds on radius of gyration in ideal molecular systems

Three-dimensional single-component ideal gas systems composed of model homogeneous rigid molecules in various molecular shapes and sizes are simulated by a molecular Monte Carlo simulation technique. We reveal that percolation thresholds of such single-component systems result in, when the molecular volume is fixed, power-law decreasing functions of the radius of gyration (gyradius) of the molecules. The systems with the same parameter set of the molecular volume and radius of gyration, but in different molecular shapes, show the identical value of the percolation threshold. Moreover, we also reveal that a dimensionless scale-free parameter, which is the ratio between the radius of gyration and real cube root of the molecular volume, uniquely determines the percolation threshold.

cond-mat.soft↗

arXiv2019

Conducting transition analysis of thin films composed of long flexible macromolecules: Percolation study

Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting transition and critical phenomena upon both thermal movement, i.e. spontaneous mobility, and extra-molecular topological constraints of the molecules. Systems containing topological constraints and/or composed of immobile particles, e.g. lattice models and chemical gelation, were studied in conventional works on percolation. Coordinates of the randomly distributed particles in the conventional lattice models are limited to discrete lattice points. Moreover, each particle is spatially fixed at the distributed position, which results in a temporally unchanged network structure. Although each polymer in the chemical gels can spontaneously move in the continuous space, the network structure is fixed when cross-linking reaction ends. By contrast to these conventional systems, all the molecules in the present system freely move and spontaneously diffuse in the continuous space. The network structure of the present molecules continues changing dynamically. The percolation and critical phenomena of such dynamic network structures are examined here. We reveal that these phenomena also occur in the present system, and that both the universality class and percolation threshold are independent from the extra-molecular topological constraints.

cond-mat.soft↗

arXiv2018

Thermodynamic stability of multicomponent ideal gas

We present an example counter to the widely-accepted concept on equilibrium states that "Any thermodynamic equilibrium state of two component systems is determined by specifying 4 thermodynamic variables that include at least 1 extensive variable." which is equivalent to Gibbs' phase rule. We demonstrate this fact by thought experiments on an A/B binary mixture where temperature, pressure and chemical potential of the A-species are chosen as the 3 intensive variables while the number of B-molecules is chosen as the 1 extensive variable. Our findings also apply to $M (>2)$-component systems.

cond-mat.soft↗

arXiv2014

Two-dimensional percolation phenomena of single-component linear homopolymer brushes

Percolation phenomena of homopolymer brushes on a planar substrate are simulated using the molecular Monte Carlo method in 3 dimensions. The grafted polymers are isolated from each other at extremely low grafting density, whereas a continuous polymer layer covers the whole substrate when the density rises to extremely high values. This indicates that percolation clusters of the grafted polymers, bridging both the edges of the substrate, appear at an intermediate density. We construct phase diagrams of this percolation phenomenon. Critical phenomena at the transition are also studied.

cond-mat.soft↗

arXiv2011

Particle Monte Carlo simulation of string-like colloidal assembly in 2 dimensions

We simulate structural phase behavior of polymer-grafted colloidal particles by molecular Monte Carlo technique. Interparticle potential, which has a finite repulsive square-step outside a rigid core of the colloid, was previously confirmed via numerical self-consistent field calculation. This model potential is purely repulsive. We simulate these model colloids in the canonical ensemble in 2 dimensions and find that these particles containing no interparticle attraction self-assemble and align in a string-like assembly, at low temperature and high density. This string-like colloidal assembly is related to percolation phenomena. Analyzing the cluster size distribution and the average string length, we build phase diagrams and discover that the average string length diverges around the region where the melting transition line and the percolation transition line cross. This result is similar to Ising spin systems, in which the percolation transition line and the order-disorder line meet at a critical point.

cond-mat.soft↗

arXiv2011

Molecular Monte Carlo simulation method of systems connected to three reservoirs

In conventional molecular simulation, metastable structures often survive over considerable computational time, resulting in difficulties in simulating equilibrium states. In order to overcome this difficulty, here we propose a newly devised method, molecular Monte Carlo simulation of systems connected to three reservoirs: chemical potential, pressure, and temperature. Gibbs-Duhem equation thermodynamically limits the number of reservoirs to 2 for single component systems. However, in conventional simulations utilizing 2 or fewer reservoirs, the system tends to be trapped in metastable states. Even if the system is allowed to escape from such metastable states in conventional simulations, the fixed system size and/or the fixed number of particles result in creation of defects in ordered structures. This situation breaks global anisotropy of ordered structures and forces the periodicity of the structure to be commensurate to the system size. Here we connect the such three reservoirs to overcome these difficulties. A method of adjusting the three reservoirs and obtaining thermodynamically stable states is also designed, based on Gibbs-Duhem equation. Unlike the other conventional simulation techniques utilizing no more than 2 reservoirs, our method allows the system itself to simultaneously tune the system size and the number of particles to periodicity and anisotropy of ordered structures. Our method requires fewer efforts for preliminary simulations prior to production runs, compared with the other advanced simulation techniques such as multicanonical method. A free energy measurement method, suitable for the system with the three reservoirs, is also discussed, based on Euler equation of thermodynamics. This measurement method needs fewer computational efforts than other free energy measurement methods do.

physics.comp-ph↗

arXiv2011

Simulation of Equilibrated States via Molecular Monte Carlo Method of Systems Connected to 3 Reservoirs

Metastable structures in macromolecular and colloidal systems are non-equilibrium states that often have long lifetimes and cause difficulties in simulating equilibrium. In order to escape from the long-lived metastable states, we propose a newly devised method, molecular Monte-Carlo simulation of systems connected to 3 reservoirs: chemical potential $μ$, pressure $P$, and temperature $T$. One of these reservoirs is adjusted for the thermodynamic equilibrium condition according to Gibbs-Duhem equation, so that this adjusted 3rd reservoir does not thermodynamically affect phases and states. Additional degrees of freedom, i.e. system volume $V$ and the number of particles $N$, reduce kinetic barriers of non-equilibrium states and facilitate quick equilibration. We show globally-anisotropic defect-free ordered structures, e.g. string-like colloidal assembly, are obtained via our method.

cond-mat.soft↗

arXiv2005

Monte-Carlo simulation of string-like colloidal assembly

We study structural phase transition of polymer-grafted colloidal particles by Monte Carlo simulations on hard spherical particles. The interaction potential, which has a weak repulsive step outside the hard core, was validated with use of the self-consistent field calculations. With this potential, canonical Monte Carlo simulations have been carried out in two and three dimensions using the Metropolis algorithm. At low temperature and high density, we find that the particles start to self-assemble and finally align in strings. By analyzing the cluster size distribution and string length distribution, we construct a phase diagram and find that this string-like assembly is related to the percolation phenomena. The average string length diverges in the region where the melting transition line and the percolation transition line cross, which is similar to Ising spin systems where the percolation transition line and the order-disorder line meet on the critical point.

cond-mat.soft↗