IEEE COMMUNICATIONS LETTERS, VOL. 18, NO.

11, NOVEMBER 2014

1891

Deterministic Model for Pulse Amplification in Diffusion-Based

Molecular Communication
Mehran H. Bazargani and Dogu Arifler, Member, IEEE

AbstractIn molecular communication, molecules are used to

transmit information from a nanotransmitter to a nanoreceiver. In
many molecular communication applications, the primary aim is
to send a single pulse to trigger a response at the receiver. As such,
the transmitter can emit a puff of information molecules that
will freely diffuse in a fluidic environment. In free-diffusion-based
communication, the maximum achievable pulse level rapidly decreases with increasing distance. Therefore, signal conditioning
is usually necessary for effective processing at a distant receiver.
We use Ficks diffusion equation to model pulse amplification,
which is an important stage in signal conditioning. We consider
the existence of an intermediate amplifying nanodevice that reacts
to a given particle concentration condition by emitting the same
type of particles as the transmitter. Our development differs from
an ordinary problem in partial differential equations with two
independent instantaneous point sources; here, by coupling the
activation of the amplifier to the operation of the transmitting
source, we determine the required particle allocations at these
devices for optimal signal reception.
Index TermsAmplification, diffusion equation, molecular
communication, nanonetworks.

I. I NTRODUCTION

anodevices are made up of nanoscale components and are

generally capable of performing only simple computation,
sensing, and actuation tasks. A nanonetwork is an interconnection of nanodevices that can cooperate and share information to
achieve more complex and useful tasks [1]. Nanonetworks are
expected to have a wide range of applications in biomedicine,
industry, environment, and military. Researchers foresee that
nanodevices will also interact with biological nanomachines
such as cells to form integrated nanonetworks. In particular,
healthcare applications of networks of therapeutic nanodevices
for smart drug delivery, biosensing and actuation are very
attractive [2], [3].
Interconnection of nanodevices to form a nanonetwork is
challenging since traditional silicon-based electromagnetic and
acoustic communication technologies are not feasible due to
the size, complexity, and power requirement of transceivers.
Molecular communication is one of the possible mechanisms
that have been proposed for interconnection of nanodevices and
is biocompatible [4]. In this study, we focus on nanonetworks
that employ free-diffusion-based molecular communication. In

Manuscript received June 3, 2014; accepted September 15, 2014. Date of

publication September 25, 2014; date of current version November 7, 2014.
The associate editor coordinating the review of this paper and approving it for
publication was H. Shin.
M. H. Bazargani was with the Department of Computer Engineering, Eastern
Mediterranean University, Gazimagusa, North Cyprus via Mersin 10, Turkey
(e-mail: mehran.hosseinzadeh@yahoo.com).
D. Arifler is with the Department of Computer Engineering, Eastern
Mediterranean University, Gazimagusa, North Cyprus via Mersin 10, Turkey
(e-mail: dogu.arifler@emu.edu.tr).
Digital Object Identifier 10.1109/LCOMM.2014.2360390

free diffusion, particles execute random walks due to collisions with molecules making up the fluidic medium that hosts
the nanonetwork. These erratic movements are referred to as
Brownian motion. Free diffusion results in particles moving
from regions of high concentration to regions of lower concentration and eventually having a uniform particle concentration
throughout the available space [5]. This transport mechanism
has the advantage of using only the kinetic energy possessed
by molecules without requiring input of energy from another
source. Hereafter, free diffusion will be referred to as just
diffusion.
Diffusion-based communication is the preferred means of
information transport in nanonetworks with no infrastructure.
In many applications, one is often mainly interested in sending
an alarm by transmitting a single pulse to a receiver for
triggering a response. This communication modality is said to
involve an instantaneous source [2]. As such, the transmitter
can emit a puff of particles that will freely diffuse in the
fluidic environment referred to as the molecular communication
channel. The receiver may be designed as a concentration
detector; the signal reception is successful if a prespecified
particle concentration threshold is exceeded at the receiver.
As first observed by Bossert and Wilson [6] in their systematic investigation of single-source molecular communication
systems that exist in nature, the most important shortcoming
of using freely diffusing molecules for information transport is
the limited range of communication due to the attenuation of
molecular signals with increasing distance. Hence, in order to
communicate with a destination at a long distance (100 m),
a source must release a large number of molecules, which is
generally prohibitive due to molecule production or storage
limitations, or the signal must be amplified along the way. In
order to enhance molecular signal strength, several studies have
investigated the use of multiple transmitters. Garralda et al. [7]
conjecture that coordinated activation of multiple transmitters
can improve the signal strength and hence the transmission
range. Their study, however, lacks a detailed analysis of this
conjecture. On the other hand, Meng et al. [8] investigate
multiple-inputmultiple-output techniques for lowering the error rate and improving the throughput performance of molecular communication. In their analysis, the authors assume that
the sources are capable of coordination of the transmission such
that molecular signals can be coherently summed together at the
destination, but they do not elaborate on the details of achieving such coordination. From a biological perspective, Nakano
and Shuai [9] describe the biological mechanisms involved in
propagating calcium signals from a transmitter to a receiver
over a pattern of cells which they call the repeater or relay
cells. However, the study is not general since it only considers
calcium signaling and assumes that a pattern of repeater cells
will be deployed throughout the network. In a recent study,
Ahmadzadeh et al. [10] analyze the error rate in a molecular

1089-7798 2014 IEEE. Personal use is permitted, but republication/redistribution requires IEEE permission.
See http://www.ieee.org/publications_standards/publications/rights/index.html for more information.

1892

IEEE COMMUNICATIONS LETTERS, VOL. 18, NO. 11, NOVEMBER 2014

dilute. With these assumptions, diffusion of particles in an

isotropic fluidic medium is described in mathematical terms by
Ficks diffusion equation [5]:
c(x, t)
= D2 c(x, t),
t

Fig. 1. An example nanonetwork deployment with a transmitter, an amplifier,

and a receiver. The amplifier deployed in region B senses nearby information
particles released by the transmitter and is triggered when a given concentration
condition is satisfied.

communication system that transmits a stream of bits encoded

by on-off keying when a relay is used between a source and a
destination nanodevice. Yet, the detection thresholds required at
the nodes must be determined numerically for different values
chosen as bit intervals.
In this work, we consider the existence of an intermediate
amplifying nanodevice for enhancing molecular signals. The
amplifier reacts to a given particle concentration condition
by emitting the same type of particles as the transmitter. We
propose a general deterministic model that may be used for
predicting the tradeoffs involved in amplifier deployment and
operation with a fixed molecule budget for communication. In
particular, we provide an analysis on optimal activation time as
a function of spatial placement of amplifiers. We assume that
the transmitter is a nanodevice that can generally be located
at the boundary of the medium and can easily be activated
by an external stimulus. On the other hand, the amplifier
is usually a simple, limited-capability, special-purpose entity
(possibly of low mobility) that is injected or released into
the fluidic medium to help the transmitter relay information
to a destination which may be embedded further inside the
medium. Fig. 1 depicts an example nanonetwork deployment
with a transmitter, an amplifier, and a receiver. We consider
scenarios in which signals are generated in a time scale much
larger than that of their fadeout times;1 this implies that we can
assume there is no interference from successive pulses to affect
the operation of the amplifier. The primary contribution of the
presented work is coupling the operation of sources of particles
in the diffusion equation so as to determine the required particle
allocations for achieving the maximum concentration level at
the destination for robust detection and effective processing;
this differs significantly from ordinary diffusion models with
particle sources acting independently.
II. M ODEL
In modeling diffusion, we make the usual assumption that
particles diffuse freely in the environment forever without being
absorbed by the medium or by the nanodevices. Also, we suppose that information-carrying particles move independently
of each other and do not interact; this holds provided that
the suspension of information-carrying particles is sufficiently
1 For instance, in nanomedical applications, simple alarm signals generated
by instantaneous sources fade out in a few seconds [2].

(1)

where c(x, t) is the concentration of particles at a position

x Rd , d {1, 2, 3} at time t > 0, D is the diffusion co
efficient, and 2 = di=1 2 /x2i is the Laplacian operator.
When sources s(x, t) are present, we have the inhomogeneous
diffusion equation:
c(x, t)
= D2 c(x, t) + s(x, t).
t

(2)

In this study, we consider point-like sources that instantaneously emit particles. For example, if a transmitting source at
the origin emits m1 particles at time 0, i.e., s(x, t) = m1 (x, t)
where () is the unit-impulse function, the spatio-temporal
concentration of molecules is given by


x2
m1
c(x, t) =
exp
.
(3)
4Dt
(4Dt)d/2
If, in addition, an amplifying device at location r Rd instantaneously emits m2 particles at time > 0, i.e., s(x, t) =
m1 (x, t) + m2 (x r, t ), due to the linearity of (2),


x2
m1
c(x, t) =
exp
4Dt
(4Dt)d/2


x r2
m2
+
exp
u(t ),
4D(t )
(4D(t ))d/2
(4)
where u() is the unit-step function. The concentration given
in (4) can be considered as the time-dependent signal strength
at that point. We also note that in general m2  m1 since an
amplifier is usually a device of much lower capability compared
to the transmitter.
We will now fix x and consider a target receiver device
located at that position. Since the system described by (2) is
linear, the principle of superposition dictates that the maximum
concentration at the receiver due to the transmitting source
and the amplifier together is obtained by adding their respective maximum concentrations. By equating the time derivative
of the function in (3) to zero, we find that the maximum
concentration due to the source is achieved at time tS =
x2 /(2dD) and that due to the amplifier is achieved at time
tA = p2 /(2dD) + , where p = x r. The maximum due
to both is then obtained when the times for peak concentrations coincide: t = tS = tA . Therefore, the concentration at
the receiver located at x is maximized if the time of activation
of an amplifier located at r is
=

x2 p2
.
2dD

(5)

Throughout, we will require that x p since > 0.

Note that is independent of particle allocations m1 and m2 .

BAZARGANI AND ARIFLER: PULSE AMPLIFICATION IN DIFFUSION-BASED MOLECULAR COMMUNICATION

Substitution of the maximizer t into (4) yields the maximum

concentration achieved at the receiver:
c(x, t ) =

d
2e

d/2 

m1
m2
+
d
x
pd

released by the source must satisfy


m1

(6)

1893


2 
x2 p2
d

d/2
exp

dr2
2 (x2 p2 )


.
(9)

The quantity in (6) represents the achievable signal strength and

is independent of D. Now, consider an overall particle budget
M = m1 + m2 available for communication. Alternatively, let
= m2 /M be the fraction of particle budget that can be
generated by the amplifier. We can define the gain G due to
using an amplifier as the ratio of the maximum concentration
achieved at the receiver with the aid of the amplifier ((6))
to the maximum concentration achieved without the amplifier
(with all M particles released by the transmitting source, i.e.
m1 = M and m2 = 0):


d
x
G=1+
1 .
(7)
p

Hence, the lower bound on m1 gives the number of particles

that must be allocated at the source. The rest m2 = M m1 of
the particles must be allocated at the amplifier for the highest
signal strength at the target. We also let = ad bd denote the
minimum number of particles that must be in the vicinity of the
amplifier for its activation.
The optimal activation time can be translated into a concentration condition necessary for activating the amplifier. Note
that for r B, the concentration at the amplifier reaches its
peak before . Hence, corresponds to an instant at which
c(r, t) is decreasing with respect to time. For optimal operation,
the amplifier thus needs to be activated when this decreasing
concentration first falls below c(r, ).

The gain is larger than or equal to 1 since x p as

argued before. Also, the gain is large if the amplifier is closer
to the destination or if the fraction of particles released by
the amplifier is large. However, the following facts make amplifier placement and particle allocation non-trivial: i) Since
amplifiers are envisioned as very primitive devices injected into
the medium and having limited particle generation capability,
one usually expects  1, and ii) deploying the amplifier
too close to the receiver will make its reachability and hence
activation by the actual transmitting source difficult due to
attenuation. Accordingly, the deployment and activation time
of the amplifier must be carefully engineered.
In this study, we assume ideal point-like nanodevices that
perform signal detection by continuously sampling the number
of particles in their immediate vicinity. As in [11], the ideality
assumption makes the results of the analysis independent of
the reception process. In particular, we consider an amplifier
that is located in a region defined by B = {r Rd : r2
x2 p2 }. This region corresponds to a line segment between the origin and x in a one-dimensional space, or a
circle or a sphere with a radius x/2 and centered at x/2
in a two- or three-dimensional space. We can assume that
the vicinity of the amplifier is ball-shaped and is defined by
V = {w Rd : w r b}, where the radius of the ball is
denoted by b  x. Once the number of particles in the
ball is obtained, the concentration in units of particles per unit
volume at the position of the detecting device is estimated as
/(ad bd ) where a1 = 2, a2 = , and a3 = 4/3 are the volumes of d-dimensional unit balls. The amplifier can react and
emit its particles only if the detected concentration exceeds a
threshold .
Just before its activation at time , the concentration at the
amplifier that is positioned at r B is


dr2
m1
exp
c(r, ) = 
.

2
2 (x2 p2 )
2 p2 ) d/2
(x
d
(8)

III. N UMERICAL A NALYSIS

If is specified, c(r, ) is a requirement for amplifier

activation. Then, the number of particles m1 that must be

We now use the model presented above for one- (1D),

two- (2D), and three-dimensional (3D) molecular channels
to numerically evaluate the benefit of deploying an amplifier
between a transmitter and a receiver. A 1D scenario might
correspond to communication in a capillary, networks formed
on membranes and planar nanobiochips can be modeled in 2D,
and communication in cell nuclei or cytoplasm corresponds to
3D networking. We assume that D = 109 m2 s1 , which is
the diffusion coefficient of small molecules in water at 310 K.
For all scenarios considered, the transmitter and the receiver
are separated by 100 m which is an order of magnitude larger
than the size of a typical eukaryotic cell. Note that the estimated
time for particles to diffuse over such a distance is 10 s [5]. The
particle sensing radius of the amplifier is taken as b = 10 m.
First, we show the effect of an amplifier that is placed in the
middle of a line segment joining the transmitter and the receiver
in a 3D space. The numerical analyses were conducted for a
molecule budget M = 105 particles and = 0.01 or = 0.10.
Fig. 2 illustrates the normalized2 concentration at the receiver
as a function of time when the amplifier is activated at the
optimal time according to (5) and the normalized concentration
at the receiver without an amplifier when all the molecules are
placed at the transmitter. It can be seen that the amplifier is
extremely beneficial in enhancing the signal strength in 3D.
In particular, when = 0.10, the gain G is 1.7. We observe
that the maximum concentration at the receiver increases by
59% when is increased from 0.01 to 0.10; such an increase
in signal strength might be significant in practical applications.
In order to highlight the disadvantage of amplifier activation
at a non-optimal time, we repeated our calculations for the
given setup and with an activation time that corresponded to
the peak concentration at the amplifier. The results indicate that
the maximum concentration at the receiver would be 3.5% and
14.1% lower for = 0.01 and = 0.10, respectively.

2 When plotting concentration values, we normalize c(x, t) by M ; the

integral of normalized concentration values over the entire space at any instant
equals 1.

1894

Fig. 2. Normalized concentration at the receiver as a function of time in a 3D

environment with and without an amplifier when M = 105 . The amplifier is
placed in the middle of a line segment joining the transmitter and the receiver
and = 0.01 or 0.10.

IEEE COMMUNICATIONS LETTERS, VOL. 18, NO. 11, NOVEMBER 2014

Fig. 4. Model-predicted and simulation-based normalized concentration values at the receiver as a function of time in a 3D network when M = 105 . The
amplifier is placed in the middle of a line segment joining the transmitter and
the receiver and = 0.10.

IV. C ONCLUSION

Fig. 3. The ratio of number of particles m1 that must be allocated at the

transmitting source to as a function of the amplifiers distance r = r
from the transmitter (plotted on a logarithmic scale).

The analysis presented in this study has an impact on design

of molecular communication systems that employ diffusion for
particle transport. As mentioned before, this mode of communication has an extremely short range. However, biocompatibility
and energy-efficiency features of diffusion-based communication make its use in healthcare applications and nanomedicine
very attractive. By using amplifiers, one can increase the communication range of transmitters to control targets at longer
distances. Our closed-form solutions based on a deterministic
model reveal the functional relationships among different parameters including particle allocations, detection threshold, and
amplifiers distance from the transmitter. Our results may offer
useful insights into the design and deployment of amplifiers in
sensing and actuation applications of nanonetworks.
R EFERENCES

Fig. 3 shows the logarithm of the ratio of the number of

particles m1 that must be allocated at the transmitting source
to as a function of the amplifiers distance r = r from
the source. In this part, we take = 100 for 1D, 2D, and
3D cases. The number of particles m1 required at the source
compared to increases rapidly as the amplifier is deployed
further away from the transmitting source. However, the rate of
increase exhibits different trends in different dimensions.
Finally, the accuracy of the results predicted by our model
was assessed through simulations. A Monte Carlo simulator for
analyzing the 3D random walk of M particles was developed
in MATLAB. The simulation captured 10 s of particle activity
and the simulator had a time resolution of 0.5 ms, which results
in jumps of a maximum size of 1 m in any direction and
is thus sufficiently small for the scenario considered. Fig. 4
illustrates both the model-predicted and simulation-based concentration values at the receiver as a function of time in 3D
when M = 105 . Here, the amplifier activated at the optimal
time is positioned right in the middle of the line segment joining
the transmitter and the receiver, and = 0.10. It can be seen
that simulation and model-based results agree well. The rootmean-square deviation of normalized concentration values was
1 1010 m3 .

[1] I. F. Akyildiz, J. M. Jornet, and M. Pierobon, Nanonetworks: A new

frontier in communications, Commun. ACM, vol. 54, no. 11, pp. 8489,
Nov. 2011.
[2] R. A. Freitas, Jr., Nanomedicine, Volume I: Basic Capabilities. Austin,
TX, USA: Landes Bioscience, 1999.
[3] B. Atakan, O. B. Akan, and S. Balasubramaniam, Body area nanonetworks with molecular communications in nanomedicine, IEEE Commun.
Mag., vol. 50, no. 1, pp. 2834, Feb. 2012.
[4] I. F. Akyildiz, F. Fekri, R. Sivakumar, C. R. Forest, and B. K. Hammer,
MoNaCo: Fundamentals of molecular nano-communication networks,
IEEE Wireless Commun. Mag., vol. 19, no. 5, pp. 1218, Oct. 2012.
[5] H. C. Berg, Random Walks in Biology. Princeton, NJ, USA: Princeton
University Press, 1983.
[6] W. H. Bossert and E. O. Wilson, The analysis of olfactory communication among animals, J. Theoret. Biol., vol. 5, no. 3, pp. 443469, 1963.
[7] N. Garralda, I. Llatser, A. Cabellos-Aparicio, E. Alarcn, and
M. Pierobon, Diffusion-based physical channel identification in molecular nanonetworks, Nano Commun. Netw., vol. 2, no. 4, pp. 196204,
Dec. 2011.
[8] L.-S. Meng, P.-C. Yeh, K.-C. Chen, and I. F. Akyildiz, MIMO communications based on molecular diffusion, in Proc. IEEE GLOBECOM,
Dec. 2012, pp. 53805385.
[9] T. Nakano and J. Shuai, Repeater design and modeling for molecular communication networks, in Proc. IEEE INFOCOM WKSHPS,
Apr. 2012, pp. 501506.
[10] A. Ahmadzadeh, A. Noel, and R. Schober, Analysis and Design of
Two-Hop Diffusion-Based Molecular Communication Networks.
[Online]. Available: http://arxiv.org/abs/1404.5538
[11] M. Pierobon and I. F. Akyildiz, Capacity of a diffusion-based molecular
communication system with channel memory and molecular noise, IEEE
Trans. Inform. Theory, vol. 59, no. 2, pp. 942954, Feb. 2013.