267 research outputs found
Discreteness-Induced Slow Relaxation in Reversible Catalytic Reaction Networks
Slowing down of the relaxation of the fluctuations around equilibrium is
investigated both by stochastic simulations and by analysis of Master equation
of reversible reaction networks consisting of resources and the corresponding
products that work as catalysts. As the number of molecules is decreased,
the relaxation time to equilibrium is prolonged due to the deficiency of
catalysts, as demonstrated by the amplification compared to that by the
continuum limit. This amplification ratio of the relaxation time is represented
by a scaling function as , and it becomes prominent as
becomes less than a critical value , where is the inverse
temperature and is the energy gap between a product and a resource
Counter Chemotactic Flow in Quasi-One-Dimensional Path
Quasi-one-dimensional bidirectional particle flow including the effect of
chemotaxis is investigated through a modification of the
John-Schadschneider-Chowdhury-Nishinari model. Specifically, we permit multiple
lanes to be shared by both directionally traveling particles. The relation
between particle density and flux is studied for several evaporation rates of
pheromone, and the following results are obtained: i) in the
low-particle-density range, the flux is enlarged by pheromone if the pheromone
evaporation rate is sufficiently low, ii) in the high particle-density range,
the flux is largest at a reasonably high evaporation rate and, iii) if the
evaporation rate is at the level intermediate between the above two cases, the
flux is kept small in the entire range of particle densities. The mechanism of
these behaviors is investigated by observing the spatial-temporal evolution of
particles and the average cluster size in the system.Comment: 4 pages, 9 figure
Discreteness-induced Transition in Catalytic Reaction Networks
Drastic change in dynamics and statistics in a chemical reaction system,
induced by smallness in the molecule number, is reported. Through stochastic
simulations for random catalytic reaction networks, transition to a novel state
is observed with the decrease in the total molecule number N, characterized by:
i) large fluctuations in chemical concentrations as a result of intermittent
switching over several states with extinction of some molecule species and ii)
strong deviation of time averaged distribution of chemical concentrations from
that expected in the continuum limit, i.e., . The origin of
transition is explained by the deficiency of molecule leading to termination of
some reactions. The critical number of molecules for the transition is obtained
as a function of the number of molecules species M and that of reaction paths
K, while total reaction rates, scaled properly, are shown to follow a universal
form as a function of NK/M
Segregation and Phase Inversion in a Simple Granular System
The segregation and the phase inversion are investigated through a simple
granular system which consists of only two inelastic hard spheres in a square
box with an energy source. With the variation of the coefficient of
restitution, the mass ratio between two spheres or the box size, we show that
two types of segregated states and crossover between them are realized in such
a small simple system.Comment: 7 pages, 3 figure
Size Segregation and Convection of Granular Mixtures Almost Completely Packed in the Rotating Thin Box
Size segregation of granular mixtures which are almost completely packed in a
rotating drum is discussed with an effective simulation and a brief analysis.
Instead of a 3D drum, we simulate 2D rotating thin box which is almost
completely packed with granular mixtures. The phase inversion of radially
segregated pattern which was found in a 3D experiment are qualitatively
reproduced with this simulation, and a brief analysis is followed. Moreover in
our simulation, a global convection appears after radial segregation pattern is
formed, and this convection induces axially segregated pattern.Comment: 9 pages, 5 figures, PACS number(s): 45.70.-n, 45.70.M
Liquid-Solid Phase Transition of the System with Two particles in a Rectangular Box
We study the statistical properties of two hard spheres in a two dimensional
rectangular box. In this system, the relation like Van der Waals equation loop
is obtained between the width of the box and the pressure working on side
walls. The auto-correlation function of each particle's position is calculated
numerically. By this calculation near the critical width, the time at which the
correlation become zero gets longer according to the increase of the height of
the box. Moreover, fast and slow relaxation processes like and
relaxations observed in supper cooled liquid are observed when the height of
the box is sufficiently large. These relaxation processes are discussed with
the probability distribution of relative position of two particles.Comment: 6 figure
Influences of Excluded Volume of Molecules on Signaling Processes on Biomembrane
We investigate the influences of the excluded volume of molecules on
biochemical reaction processes on 2-dimensional surfaces using a model of
signal transduction processes on biomembranes. We perform simulations of the
2-dimensional cell-based model, which describes the reactions and diffusion of
the receptors, signaling proteins, target proteins, and crowders on the cell
membrane. The signaling proteins are activated by receptors, and these
activated signaling proteins activate target proteins that bind autonomously
from the cytoplasm to the membrane, and unbind from the membrane if activated.
If the target proteins bind frequently, the volume fraction of molecules on the
membrane becomes so large that the excluded volume of the molecules for the
reaction and diffusion dynamics cannot be negligible. We find that such
excluded volume effects of the molecules induce non-trivial variations of the
signal flow, defined as the activation frequency of target proteins, as
follows. With an increase in the binding rate of target proteins, the signal
flow varies by i) monotonically increasing; ii) increasing then decreasing in a
bell-shaped curve; or iii) increasing, decreasing, then increasing in an
S-shaped curve. We further demonstrate that the excluded volume of molecules
influences the hierarchical molecular distributions throughout the reaction
processes. In particular, when the system exhibits a large signal flow, the
signaling proteins tend to surround the receptors to form receptor-signaling
protein clusters, and the target proteins tend to become distributed around
such clusters. To explain these phenomena, we analyze the stochastic model of
the local motions of molecules around the receptor.Comment: 31 pages, 10 figure
Required Levels of Catalysis for Emergence of Autocatalytic Sets in Models of Chemical Reaction Systems
The formation of a self-sustaining autocatalytic chemical network is a necessary but not sufficient condition for the origin of life. The question of whether such a network could form âby chanceâ within a sufficiently complex suite of molecules and reactions is one that we have investigated for a simple chemical reaction model based on polymer ligation and cleavage. In this paper, we extend this work in several further directions. In particular, we investigate in more detail the levels of catalysis required for a self-sustaining autocatalytic network to form. We study the size of chemical networks within which we might expect to find such an autocatalytic subset, and we extend the theoretical and computational analyses to models in which catalysis requires template matching
Understanding and simulating the material behavior during multi-particle irradiations
A number of studies have suggested that the irradiation behavior and damage processes occurring during sequential and simultaneous particle irradiations can significantly differ. Currently, there is no definite answer as to why and when such differences are seen. Additionally, the conventional multi-particle irradiation facilities cannot correctly reproduce the complex irradiation scenarios experienced in a number of environments like space and nuclear reactors. Therefore, a better understanding of multi-particle irradiation problems and possible alternatives are needed. This study shows ionization induced thermal spike and defect recovery during sequential and simultaneous ion irradiation of amorphous silica. The simultaneous irradiation scenario is shown to be equivalent to multiple small sequential irradiation scenarios containing latent damage formation and recovery mechanisms. The results highlight the absence of any new damage mechanism and time-space correlation between various damage events during simultaneous irradiation of amorphous silica. This offers a new and convenient way to simulate and understand complex multi-particle irradiation problems
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