217 research outputs found
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
A Path Intergal Approach to Current
Discontinuous initial wave functions or wave functions with discontintuous
derivative and with bounded support arise in a natural way in various
situations in physics, in particular in measurement theory. The propagation of
such initial wave functions is not well described by the Schr\"odinger current
which vanishes on the boundary of the support of the wave function. This
propagation gives rise to a uni-directional current at the boundary of the
support. We use path integrals to define current and uni-directional current
and give a direct derivation of the expression for current from the path
integral formulation for both diffusion and quantum mechanics. Furthermore, we
give an explicit asymptotic expression for the short time propagation of
initial wave function with compact support for both the cases of discontinuous
derivative and discontinuous wave function. We show that in the former case the
probability propagated across the boundary of the support in time is
and the initial uni-directional current is . This recovers the Zeno effect for continuous detection of a particle
in a given domain. For the latter case the probability propagated across the
boundary of the support in time is and the
initial uni-directional current is . This is an anti-Zeno
effect. However, the probability propagated across a point located at a finite
distance from the boundary of the support is . This gives a decay
law.Comment: 17 pages, Late
Robust synchronization of a class of coupled delayed networks with multiple stochastic disturbances: The continuous-time case
In this paper, the robust synchronization problem is investigated for a new class of continuous-time complex networks that involve parameter uncertainties, time-varying delays, constant and delayed couplings, as well as multiple stochastic
disturbances. The norm-bounded uncertainties exist in all the network parameters after decoupling, and the stochastic disturbances are assumed to be Brownian motions that act on the constant coupling term, the delayed coupling term as well as the overall network dynamics. Such multiple stochastic disturbances could reflect more realistic dynamical behaviors of the coupled complex network presented within a noisy environment. By using a combination of the Lyapunov functional method, the robust analysis tool, the stochastic analysis techniques and the properties of Kronecker product, we derive several delay-dependent sufficient conditions that ensure the coupled complex network to be globally robustly synchronized in the mean square for all admissible parameter uncertainties. The criteria obtained in this paper are in the form of linear matrix inequalities (LMIs) whose solution can be easily calculated by using the standard numerical software. The main results are shown to be general enough to cover many existing ones reported in the literature. Simulation examples are presented to demonstrate the feasibility and applicability of the proposed results
Measurement as Absorption of Feynman Trajectories: Collapse of the Wave Function Can be Avoided
We define a measuring device (detector) of the coordinate of quantum particle
as an absorbing wall that cuts off the particle's wave function. The wave
function in the presence of such detector vanishes on the detector. The trace
the absorbed particles leave on the detector is identifies as the absorption
current density on the detector. This density is calculated from the solution
of Schr\"odinger's equation with a reflecting boundary at the detector. This
current density is not the usual Schr\"odinger current density. We define the
probability distribution of the time of arrival to a detector in terms of the
absorption current density. We define coordinate measurement by an absorbing
wall in terms of 4 postulates. We postulate, among others, that a quantum
particle has a trajectory. In the resulting theory the quantum mechanical
collapse of the wave function is replaced with the usual collapse of the
probability distribution after observation. Two examples are presented, that of
the slit experiment and the slit experiment with absorbing boundaries to
measure time of arrival. A calculation is given of the two dimensional
probability density function of a free particle from the measurement of the
absorption current on two planes.Comment: 20 pages, latex, no figure
Ions in Fluctuating Channels: Transistors Alive
Ion channels are proteins with a hole down the middle embedded in cell
membranes. Membranes form insulating structures and the channels through them
allow and control the movement of charged particles, spherical ions, mostly
Na+, K+, Ca++, and Cl-. Membranes contain hundreds or thousands of types of
channels, fluctuating between open conducting, and closed insulating states.
Channels control an enormous range of biological function by opening and
closing in response to specific stimuli using mechanisms that are not yet
understood in physical language. Open channels conduct current of charged
particles following laws of Brownian movement of charged spheres rather like
the laws of electrodiffusion of quasi-particles in semiconductors. Open
channels select between similar ions using a combination of electrostatic and
'crowded charge' (Lennard-Jones) forces. The specific location of atoms and the
exact atomic structure of the channel protein seems much less important than
certain properties of the structure, namely the volume accessible to ions and
the effective density of fixed and polarization charge. There is no sign of
other chemical effects like delocalization of electron orbitals between ions
and the channel protein. Channels play a role in biology as important as
transistors in computers, and they use rather similar physics to perform part
of that role. Understanding their fluctuations awaits physical insight into the
source of the variance and mathematical analysis of the coupling of the
fluctuations to the other components and forces of the system.Comment: Revised version of earlier submission, as invited, refereed, and
published by journa
Distributed state estimation in sensor networks with randomly occurring nonlinearities subject to time delays
This is the post-print version of the Article. The official published version can be accessed from the links below - Copyright @ 2012 ACM.This article is concerned with a new distributed state estimation problem for a class of dynamical systems in sensor networks. The target plant is described by a set of differential equations disturbed by a Brownian motion and randomly occurring nonlinearities (RONs) subject to time delays. The RONs are investigated here to reflect network-induced randomly occurring regulation of the delayed states on the current ones. Through available measurement output transmitted from the sensors, a distributed state estimator is designed to estimate the states of the target system, where each sensor can communicate with the neighboring sensors according to the given topology by means of a directed graph. The state estimation is carried out in a distributed way and is therefore applicable to online application. By resorting to the Lyapunov functional combined with stochastic analysis techniques, several delay-dependent criteria are established that not only ensure the estimation error to be globally asymptotically stable in the mean square, but also guarantee the existence of the desired estimator gains that can then be explicitly expressed when certain matrix inequalities are solved. A numerical example is given to verify the designed distributed state estimators.This work was supported in part by the National Natural Science Foundation of China under Grants 61028008, 60804028 and 61174136, the Qing Lan Project of Jiangsu Province of China, the Project sponsored by SRF for ROCS of SEM of China, the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the Royal Society of the UK,
and the Alexander von Humboldt Foundation of Germany
Temporal dynamics of tunneling. Hydrodynamic approach
We use the hydrodynamic representation of the Gross -Pitaevskii/Nonlinear
Schroedinger equation in order to analyze the dynamics of macroscopic tunneling
process. We observe a tendency to a wave breaking and shock formation during
the early stages of the tunneling process. A blip in the density distribution
appears in the outskirts of the barrier and under proper conditions it may
transform into a bright soliton. Our approach, based on the theory of shock
formation in solutions of Burgers equation, allows us to find the parameters of
the ejected blip (or soliton if formed) including the velocity of its
propagation. The blip in the density is formed regardless of the value and sign
of the nonlinearity parameter. However a soliton may be formed only if this
parameter is negative (attraction) and large enough. A criterion is proposed.
An ejection of a soliton is also observed numerically. We demonstrate,
theoretically and numerically, controlled formation of soliton through
tunneling. The mass of the ejected soliton is controlled by the initial state.Comment: 11 pages, 6 figures, expanded and more detailed verions of the
previous submissio
Non-Markovian dynamics of clusters during nucleation
Most theories of homogeneous nucleation are based on a Fokker-Planck-like
description of the behavior of the mass of clusters. Here we will show that
these approaches are incomplete for a large class of nucleating systems, as
they assume the effective dynamics of the clusters to be Markovian, i.e.,
memoryless. We characterize these non-Markovian dynamics and show how this
influences the dynamics of clusters during nucleation. Our results are
validated by simulations of a three-dimensional Ising model with locally
conserved magnetization.Comment: 4 pages, 4 figure
Realistic boundary conditions for stochastic simulations of reaction-diffusion processes
Many cellular and subcellular biological processes can be described in terms
of diffusing and chemically reacting species (e.g. enzymes). Such
reaction-diffusion processes can be mathematically modelled using either
deterministic partial-differential equations or stochastic simulation
algorithms. The latter provide a more detailed and precise picture, and several
stochastic simulation algorithms have been proposed in recent years. Such
models typically give the same description of the reaction-diffusion processes
far from the boundary of the simulated domain, but the behaviour close to a
reactive boundary (e.g. a membrane with receptors) is unfortunately
model-dependent. In this paper, we study four different approaches to
stochastic modelling of reaction-diffusion problems and show the correct choice
of the boundary condition for each model. The reactive boundary is treated as
partially reflective, which means that some molecules hitting the boundary are
adsorbed (e.g. bound to the receptor) and some molecules are reflected. The
probability that the molecule is adsorbed rather than reflected depends on the
reactivity of the boundary (e.g. on the rate constant of the adsorbing chemical
reaction and on the number of available receptors), and on the stochastic model
used. This dependence is derived for each model.Comment: 24 pages, submitted to Physical Biolog
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