37,569 research outputs found
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
Noise-Induced Spatial Pattern Formation in Stochastic Reaction-Diffusion Systems
This paper is concerned with stochastic reaction-diffusion kinetics governed
by the reaction-diffusion master equation. Specifically, the primary goal of
this paper is to provide a mechanistic basis of Turing pattern formation that
is induced by intrinsic noise. To this end, we first derive an approximate
reaction-diffusion system by using linear noise approximation. We show that the
approximated system has a certain structure that is associated with a coupled
dynamic multi-agent system. This observation then helps us derive an efficient
computation tool to examine the spatial power spectrum of the intrinsic noise.
We numerically demonstrate that the result is quite effective to analyze
noise-induced Turing pattern. Finally, we illustrate the theoretical mechanism
behind the noise-induced pattern formation with a H2 norm interpretation of the
multi-agent system
Transitions Induced by the Discreteness of Molecules in a Small Autocatalytic System
Autocatalytic reaction system with a small number of molecules is studied
numerically by stochastic particle simulations. A novel state due to
fluctuation and discreteness in molecular numbers is found, characterized as
extinction of molecule species alternately in the autocatalytic reaction loop.
Phase transition to this state with the change of the system size and flow is
studied, while a single-molecule switch of the molecule distributions is
reported. Relevance of the results to intracellular processes are briefly
discussed.Comment: 5 pages, 4 figure
Stochastic Approach to Enantiomeric Excess Amplification and Chiral Symmetry Breaking
Stochastic aspects of chemical reaction models related to the Soai reactions
as well as to the homochirality in life are studied analytically and
numerically by the use of the master equation and random walk model. For
systems with a recycling process, a unique final probability distribution is
obtained by means of detailed balance conditions. With a nonlinear
autocatalysis the distribution has a double-peak structure, indicating the
chiral symmetry breaking. This problem is further analyzed by examining
eigenvalues and eigenfunctions of the master equation. In the case without
recycling process, final probability distributions depend on the initial
conditions. In the nonlinear autocatalytic case, time-evolution starting from a
complete achiral state leads to a final distribution which differs from that
deduced from the nonzero recycling result. This is due to the absence of the
detailed balance, and a directed random walk model is shown to give the correct
final profile. When the nonlinear autocatalysis is sufficiently strong and the
initial state is achiral, the final probability distribution has a double-peak
structure, related to the enantiomeric excess amplification. It is argued that
with autocatalyses and a very small but nonzero spontaneous production, a
single mother scenario could be a main mechanism to produce the homochirality.Comment: 25 pages, 6 figure
Stochastic Chemical Reactions in Micro-domains
Traditional chemical kinetics may be inappropriate to describe chemical
reactions in micro-domains involving only a small number of substrate and
reactant molecules. Starting with the stochastic dynamics of the molecules, we
derive a master-diffusion equation for the joint probability density of a
mobile reactant and the number of bound substrate in a confined domain. We use
the equation to calculate the fluctuations in the number of bound substrate
molecules as a function of initial reactant distribution. A second model is
presented based on a Markov description of the binding and unbinding and on the
mean first passage time of a molecule to a small portion of the boundary. These
models can be used for the description of noise due to gating of ionic channels
by random binding and unbinding of ligands in biological sensor cells, such as
olfactory cilia, photo-receptors, hair cells in the cochlea.Comment: 33 pages, Journal Chemical Physic
Single-molecule experiments in biological physics: methods and applications
I review single-molecule experiments (SME) in biological physics. Recent
technological developments have provided the tools to design and build
scientific instruments of high enough sensitivity and precision to manipulate
and visualize individual molecules and measure microscopic forces. Using SME it
is possible to: manipulate molecules one at a time and measure distributions
describing molecular properties; characterize the kinetics of biomolecular
reactions and; detect molecular intermediates. SME provide the additional
information about thermodynamics and kinetics of biomolecular processes. This
complements information obtained in traditional bulk assays. In SME it is also
possible to measure small energies and detect large Brownian deviations in
biomolecular reactions, thereby offering new methods and systems to scrutinize
the basic foundations of statistical mechanics. This review is written at a
very introductory level emphasizing the importance of SME to scientists
interested in knowing the common playground of ideas and the interdisciplinary
topics accessible by these techniques. The review discusses SME from an
experimental perspective, first exposing the most common experimental
methodologies and later presenting various molecular systems where such
techniques have been applied. I briefly discuss experimental techniques such as
atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers
(MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I
then present several applications of SME to the study of nucleic acids (DNA,
RNA and DNA condensation), proteins (protein-protein interactions, protein
folding and molecular motors). Finally, I discuss applications of SME to the
study of the nonequilibrium thermodynamics of small systems and the
experimental verification of fluctuation theorems. I conclude with a discussion
of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond.
Matt
Switching Dynamics in Reaction Networks Induced by Molecular Discreteness
To study the fluctuations and dynamics in chemical reaction processes,
stochastic differential equations based on the rate equation involving chemical
concentrations are often adopted. When the number of molecules is very small,
however, the discreteness in the number of molecules cannot be neglected since
the number of molecules must be an integer. This discreteness can be important
in biochemical reactions, where the total number of molecules is not
significantly larger than the number of chemical species. To elucidate the
effects of such discreteness, we study autocatalytic reaction systems
comprising several chemical species through stochastic particle simulations.
The generation of novel states is observed; it is caused by the extinction of
some molecular species due to the discreteness in their number. We demonstrate
that the reaction dynamics are switched by a single molecule, which leads to
the reconstruction of the acting network structure. We also show the strong
dependence of the chemical concentrations on the system size, which is caused
by transitions to discreteness-induced novel states.Comment: 11 pages, 5 figure
- …