To simulate molecular Communication (MC) using NS2, which is a novel communication paradigm that comprises the transmission and reception of data using molecules, frequently in biological environments or micro/nano-scale systems. NS2 (Network Simulator 2) was not originally created to replicate Molecular Communication that contains communication mechanisms rather distinct from traditional wireless or wired networks. But, researchers have improved methods to replicate communication, typically through custom models and extensions to the NS2 framework.
Even though NS2 does not deliver a built-in module for Molecular Communication, we can replicate the behaviour by changing or extending NS2 to make a molecular-based nodes, communication channels, and transport mechanisms. As well, molecular communication projects within NS2 may involve:
- Emitter (Transmitter): A node that emits molecules into a medium.
- Receiver: A node that detects the presence of molecules.
- Diffusion/Propagation Medium: The medium via which molecules travel (normally modelled using random walks or diffusion equations).
Steps to Simulate Molecular Communication Projects in NS2:
- Basic Concepts in Molecular Communication
In Molecular Communication, the transmission of data is modelled by the release of molecules that propagate via a fluid medium (e.g., air, water, or a biological fluid) to attain the receiver. The following elements are critical to replicating molecular communication:
- Diffusion-based propagation: Molecules diffuse via the medium and arbitrarily propagate based on the diffusion laws.
- Emitter and Receiver: The Emitter releases molecules, and the Receiver identifies them according to the particular thresholds (e.g., the number of molecules received).
- Channel Model: The molecular channel can be influenced by factors like medium viscosity, temperature, and molecule types.
- Extending NS2 for Molecular Communication Simulation
Since NS2 was not designed for Molecular Communication, we can prolong it by:
- Describing new nodes for the Emitter and Receiver.
- Replicating molecular diffusion using custom diffusion models.
- Utilizing timing and counting mechanisms to denote the emission and detection of molecules.
- Basic Molecular Communication Simulation in NS2
Example: Simulating Molecular Communication with Simplified Diffusion Model
In this instance, we will be made a basic molecular communication system in which an Emitter releases molecules, and a Receiver identifies them after they propagate via the environment utilizing a simple diffusion-based model.
# Create NS2 simulator instance
set ns [new Simulator]
# Define the molecular communication channel (a simple diffusion model)
set channel [new Channel/WirelessChannel]
# Define a new node type for Molecular Communication Emitter
set emitter [$ns node]
$emitter set X_ 0.0
$emitter set Y_ 0.0
$emitter set Z_ 0.0
# Define a new node type for Molecular Communication Receiver
set receiver [$ns node]
$receiver set X_ 50.0 ;# Place the receiver 50 units away from the emitter
$receiver set Y_ 0.0
$receiver set Z_ 0.0
# Set up a custom agent to simulate molecular emission (Emitter)
set mol_emission [new Agent/UDP]
$ns attach-agent $emitter $mol_emission
# Set up a custom agent for molecule reception (Receiver)
set mol_reception [new Agent/Null]
$ns attach-agent $receiver $mol_reception
# Connect the emission and reception agents
$ns connect $mol_emission $mol_reception
# Define a simple molecular diffusion mechanism
proc molecular_diffusion {} {
global ns mol_emission mol_reception emitter receiver
# Simulate molecule diffusion from emitter to receiver
puts “Emitter: Releasing molecules at time [$ns now]”
# Introduce a delay to emulate diffusion time (based on distance)
set distance 50.0
set diffusion_speed 10.0 ;# Assume diffusion speed of 10 units/second
set diffusion_delay [expr $distance / $diffusion_speed]
# Schedule the molecules to arrive at the receiver after the diffusion delay
$ns at $diffusion_delay “receiver_detected_molecules”
}
# Define a procedure for the receiver to detect molecules
proc receiver_detected_molecules {} {
puts “Receiver: Molecules detected at time [$ns now]”
}
# Schedule molecular emission to start at time 1.0
$ns at 1.0 “molecular_diffusion”
# Enable tracing
set tracefile [open molecular_trace.tr w]
$ns trace-all $tracefile
# Finish procedure to end the simulation
proc finish {} {
global ns tracefile
$ns flush-trace
close $tracefile
exit 0
}
# End simulation after 5 seconds
$ns at 5.0 “finish”
$ns run
Explanation:
- Emitter and Receiver: We describe two nodes: the Emitter that releases molecules, and the Receiver that identifies molecules.
- Molecular Diffusion: A basic diffusion mechanism is mimicked by launching a delay rely on the distance among the Emitter and Receiver and a predefined diffusion speed. After the delay, molecules are “detected” by the receiver.
- Molecular Emission: The emission of molecules is scheduled at time 1.0 seconds, and the diffusion delay is computed rely on the distance and speed.
- Trace File: A trace file records the events of the molecular emission and detection for analysis.
- Advanced Diffusion Models in NS2
For a more exact molecular diffusion model, we can execute more complex diffusion mechanisms, like random walks or Fick’s laws of diffusion. It needs replicating the probabilistic movement of molecules in the medium.
Example: Random Walk Diffusion Model
We can be mimicked molecular diffusion using a random walk model in which molecules propagate in random directions step by step.
# Define a procedure for random walk diffusion
proc random_walk_diffusion {node steps step_size} {
global ns
for {set i 0} {$i < $steps} {incr i} {
# Generate random movements in X, Y, and Z directions
set deltaX [expr rand() * $step_size]
set deltaY [expr rand() * $step_size]
set deltaZ [expr rand() * $step_size]
# Update the node position
set oldX [$node set X_]
set oldY [$node set Y_]
set oldZ [$node set Z_]
$node set X_ [expr $oldX + $deltaX]
$node set Y_ [expr $oldY + $deltaY]
$node set Z_ [expr $oldZ + $deltaZ]
# Simulate the time between steps
$ns at [expr $i * 0.1] “puts \”Molecule at: [$node set X_] [$node set Y_] [$node set Z_]\””
}
}
This random walk diffusion model replicates how molecules are randomly move in 3D space with a step size and number of steps. We can incorporate it into the overall molecular communication system to replicate how molecules diffuse via the medium.
- Detection Mechanism at the Receiver
In molecular communication, the receiver normally identifies the molecules according to a threshold (e.g., a certain number of molecules must arrive to trigger a detection event). We can model this in NS2 by inserting logic to calculate the number of received molecules and activate an event once the threshold is attained.
Example: Detection Based on Molecule Count
# Define a procedure to detect molecules based on a threshold
proc receiver_detect_molecules {molecule_count} {
global mol_reception
# Set a detection threshold
set detection_threshold 100
if {$molecule_count >= $detection_threshold} {
puts “Receiver: Detection threshold reached. Molecules detected at time [ns now]”
} else {
puts “Receiver: Insufficient molecules. No detection.”
}
}
# Simulate molecules arriving at the receiver
set molecule_count 120 ;# Example: 120 molecules received
receiver_detect_molecules $molecule_count
In this example, the receiver detects molecules only if the number of molecules exceeds a detection threshold.
- Analysing Molecular Communication Metrics
After running the simulation, we can investigate numerous performance parameters:
- Propagation Delay: The time taken for molecules to propagate from the emitter to the receiver.
- Molecule Detection Rate: The amount of molecules are identified at the receiver compared to the number emitted by the emitter.
- Communication Success Rate: The percentage of successful transmissions in which the receiver identified enough molecules to interpret the information.
- Visualizing Molecular Communication
We can envision the molecular communication process utilizing NAM (Network Animator) by allowing NAM tracing:
# Enable NAM trace for visualization
set namfile [open molecular_comm.nam w]
$ns namtrace-all $namfile
Through these projects, we clearly learnt the basic concepts, and how to detect, analyse and visualize the Molecular Communication within NS2 simulation environment. If required, we can explore this project further and offer comprehensive informations.
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