2,587 research outputs found
Algorithm for Mesoscopic Advection-Diffusion
In this paper, an algorithm is presented to calculate the transition rates
between adjacent mesoscopic subvolumes in the presence of flow and diffusion.
These rates can be integrated in stochastic simulations of reaction-diffusion
systems that follow a mesoscopic approach, i.e., that partition the environment
into homogeneous subvolumes and apply the spatial stochastic simulation
algorithm (spatial SSA). The rates are derived by integrating Fick's second law
over a single subvolume in one dimension (1D), and are also shown to apply in
three dimensions (3D). The proposed algorithm corrects the derived rates to
ensure that they are physically meaningful and it is implemented in the AcCoRD
simulator (Actor-based Communication via Reaction-Diffusion). Simulations using
the proposed method are compared with a naive mesoscopic approach, microscopic
simulations that track every molecule, and analytical results that are exact in
1D and an approximation in 3D. By choosing subvolumes that are sufficiently
small, such that the Peclet number associated with a subvolume is sufficiently
less than 2, the accuracy of the proposed method is comparable with the
microscopic method, thus enabling the simulation of
advection-reaction-diffusion systems with the spatial SSA.Comment: 12 pages, 9 figures. Submitted to IEEE Transactions on NanoBioscienc
A Novel A Priori Simulation Algorithm for Absorbing Receivers in Diffusion-Based Molecular Communication Systems
A novel a priori Monte Carlo (APMC) algorithm is proposed to accurately
simulate the molecules absorbed at spherical receiver(s) with low computational
complexity in diffusion-based molecular communication (MC) systems. It is
demonstrated that the APMC algorithm achieves high simulation efficiency since
by using this algorithm, the fraction of molecules absorbed for a relatively
large time step length precisely matches the analytical result. Therefore, the
APMC algorithm overcomes the shortcoming of the existing refined Monte Carlo
(RMC) algorithm which enables accurate simulation for a relatively small time
step length only. Moreover, for the RMC algorithm, an expression is proposed to
quickly predict the simulation accuracy as a function of the time step length
and system parameters, which facilitates the choice of simulation time step for
a given system. Furthermore, a rejection threshold is proposed for both the RMC
and APMC algorithms to significantly save computational complexity while
causing an extremely small loss in accuracy.Comment: 11 pages, 14 figures, submitted to IEEE Transactions on
NanoBioscience. arXiv admin note: text overlap with arXiv:1803.0463
Improving Receiver Performance of Diffusive Molecular Communication with Enzymes
This paper studies the mitigation of intersymbol interference in a diffusive
molecular communication system using enzymes that freely diffuse in the
propagation environment. The enzymes form reaction intermediates with
information molecules and then degrade them so that they cannot interfere with
future transmissions. A lower bound expression on the expected number of
molecules measured at the receiver is derived. A simple binary receiver
detection scheme is proposed where the number of observed molecules is sampled
at the time when the maximum number of molecules is expected. Insight is also
provided into the selection of an appropriate bit interval. The expected bit
error probability is derived as a function of the current and all previously
transmitted bits. Simulation results show the accuracy of the bit error
probability expression and the improvement in communication performance by
having active enzymes present.Comment: 13 pages, 8 figures, 1 table. To appear in IEEE Transactions on
Nanobioscience (submitted January 22, 2013; minor revision October 16, 2013;
accepted December 4, 2013
Using Dimensional Analysis to Assess Scalability and Accuracy in Molecular Communication
In this paper, we apply dimensional analysis to study a diffusive molecular
communication system that uses diffusing enzymes in the propagation environment
to mitigate intersymbol interference. The enzymes bind to information molecules
and then degrade them so that they cannot interfere with the detection of
future transmissions at the receiver. We determine when it is accurate to
assume that the concentration of information molecules throughout the receiver
is constant and equal to that expected at the center of the receiver. We show
that a lower bound on the expected number of molecules observed at the receiver
can be arbitrarily scaled over the environmental parameters, and generalize how
the accuracy of the lower bound is qualitatively impacted by those parameters.Comment: 6 pages, 2 figures, will be presented at the 3rd IEEE International
Workshop on Molecular and Nanoscale Communications (MoNaCom 2013) in
Budapest, Hungar
Optimal Receiver Design for Diffusive Molecular Communication With Flow and Additive Noise
In this paper, we perform receiver design for a diffusive molecular
communication environment. Our model includes flow in any direction, sources of
information molecules in addition to the transmitter, and enzymes in the
propagation environment to mitigate intersymbol interference. We characterize
the mutual information between receiver observations to show how often
independent observations can be made. We derive the maximum likelihood sequence
detector to provide a lower bound on the bit error probability. We propose the
family of weighted sum detectors for more practical implementation and derive
their expected bit error probability. Under certain conditions, the performance
of the optimal weighted sum detector is shown to be equivalent to a matched
filter. Receiver simulation results show the tradeoff in detector complexity
versus achievable bit error probability, and that a slow flow in any direction
can improve the performance of a weighted sum detector.Comment: 14 pages, 7 figures, 1 appendix. To appear in IEEE Transactions on
NanoBioscience (submitted July 31, 2013, revised June 18, 2014, accepted July
7, 2014
Root Mean Square Error of Neural Spike Train Sequence Matching with Optogenetics
Optogenetics is an emerging field of neuroscience where neurons are
genetically modified to express light-sensitive receptors that enable external
control over when the neurons fire. Given the prominence of neuronal signaling
within the brain and throughout the body, optogenetics has significant
potential to improve the understanding of the nervous system and to develop
treatments for neurological diseases. This paper uses a simple optogenetic
model to compare the timing distortion between a randomly-generated target
spike sequence and an externally-stimulated neuron spike sequence. The
distortion is measured by filtering each sequence and finding the root mean
square error between the two filter outputs. The expected distortion is derived
in closed form when the target sequence generation rate is sufficiently low.
Derivations are verified via simulations.Comment: 6 pages, 5 figures. Will be presented at IEEE Global Communications
Conference (IEEE GLOBECOM 2017) in December 201
Diffusive Molecular Communication with Disruptive Flows
In this paper, we study the performance of detectors in a diffusive molecular
communication environment where steady uniform flow is present. We derive the
expected number of information molecules to be observed in a passive spherical
receiver, and determine the impact of flow on the assumption that the
concentration of molecules throughout the receiver is uniform. Simulation
results show the impact of advection on detector performance as a function of
the flow's magnitude and direction. We highlight that there are disruptive
flows, i.e., flows that are not in the direction of information transmission,
that lead to an improvement in detector performance as long as the disruptive
flow does not dominate diffusion and sufficient samples are taken.Comment: 7 pages, 1 table, 5 figures. Will be presented at the 2014 IEEE
International Conference on Communications (ICC) in Sydney, Australia, on
September 12, 201
Bounds on Distance Estimation via Diffusive Molecular Communication
This paper studies distance estimation for diffusive molecular communication.
The Cramer-Rao lower bound on the variance of the distance estimation error is
derived. The lower bound is derived for a physically unbounded environment with
molecule degradation and steady uniform flow. The maximum likelihood distance
estimator is derived and its accuracy is shown via simulation to perform very
close to the Cramer-Rao lower bound. An existing protocol is shown to be
equivalent to the maximum likelihood distance estimator if only one observation
is made. Simulation results also show the accuracy of existing protocols with
respect to the Cramer-Rao lower bound.Comment: 7 pages, 5 figures, 1 table. Will be presented at the 2014 IEEE
Global Communications Conference (GLOBECOM) in Austin, TX, USA, on December
9, 201
On the Statistics of Reaction-Diffusion Simulations for Molecular Communication
A molecule traveling in a realistic propagation environment can experience
stochastic interactions with other molecules and the environment boundary. The
statistical behavior of some isolated phenomena, such as dilute unbounded
molecular diffusion, are well understood. However, the coupling of multiple
interactions can impede closed-form analysis, such that simulations are
required to determine the statistics. This paper compares the statistics of
molecular reaction-diffusion simulation models from the perspective of
molecular communication systems. Microscopic methods track the location and
state of every molecule, whereas mesoscopic methods partition the environment
into virtual containers that hold molecules. The properties of each model are
described and compared with a hybrid of both models. Simulation results also
assess the accuracy of Poisson and Gaussian approximations of the underlying
Binomial statistics.Comment: 6 pages, 1 table, 10 figures. Submitted to the 2nd ACM International
Conference on Nanoscale Computing and Communication (ACM NANOCOM 2015) on May
16, 201
- …