A simulation tool for nanoscale biological networks

Felicetti, Luca; Femminella, Mauro; Reali, Gianluca

doi:10.1016/j.nancom.2011.09.002

Cited by 60 publications

(41 citation statements)

References 11 publications

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“…Another interesting simulator [34] models a generic set of nanomachines in a given environment. Communication may occur by means of a number of techniques, such as electromagnetic waves or calcium ions.…”

Section: Related Workmentioning

confidence: 99%

N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks

Llátser

Demiray

Cabellos‐Aparicio

et al. 2014

Simulation Modelling Practice and Theory

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Diffusion-based molecular communication is a promising bio-inspired paradigm to implement nanonetworks, i.e., the interconnection of nanomachines. The peculiarities of the physical channel in diffusion-based molecular communication require the development of novel models, architectures and protocols for this new scenario, which need to be validated by simulation. N3Sim is a simulation framework for nanonetworks with transmitter, receiver, and harvester nodes using Diffusion-based Molecular Communication (DMC). In DMC, transmitters encode the information by releasing molecules into the medium, thus varying their local concentration. N3Sim models the movement of these molecules according to Brownian dynamics, and it also takes into account their inertia and the interactions among them. Harvesters collect molecules from the environment to reuse them for later transmissions. Receivers decode the information by sensing the particle concentration in their neighborhood. The benefits of N3Sim are multiple: the validation of channel models for DMC and the evaluation of novel modulation schemes are just a few examples.

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Section: Related Workmentioning

confidence: 99%

N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks

Llátser

Demiray

Cabellos‐Aparicio

et al. 2014

Simulation Modelling Practice and Theory

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“…In [7], a Java package designed to simulate nanoscale communications, Biological and Nanoscale communication simulator (BiNS), is presented. The approach of BiNS, further improved in [23], [24], is fine grained in that the position of each element is evaluated at each simulation step, and collisions are managed according to an elastic model.…”

Section: A Related Work In Biological Nanoscale Communicationsmentioning

confidence: 99%

“…These investigations could either make use of both the estimated numerical value of parameters for determining other unknowns by analyzing experimental results, or analyze the effect of both drugs or any other countermeasure affecting the generation of adhesion molecules. The newly developed Markov chain model of the receiver, together with other enhancements described in Section IV, was incorporated into an extensive simulation package for biological communications developed in the Networking Laboratory of the University of Perugia called BiNS [7]. One objective of this simulator is essentially medical, and consists of implementing a simulation-based method for assessing the risk of cardiovascular diseases per single patient.…”

Section: Introductionmentioning

confidence: 99%

Modeling CD40-Based Molecular Communications in Blood Vessels

Felicetti

Femminella

Reali

et al. 2014

IEEE Trans.on Nanobioscience

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This paper presents a mathematical characterization of the main features of the molecular communication between platelets and endothelial cells via CD40 signaling during the initial phases of atherosclerosis, known also as atherogenesis. We demonstrate through laboratory experimentation that the release of soluble CD40L molecules from platelets in a fluid medium is enough to trigger expression of adhesion molecules on endothelial cell's surface; that is, physical contact between the platelets and the endothelial cells is not necessary. We also propose the mathematical model of this communication, and we quantify the model parameters by matching the experiment results to the model. In addition, this mathematical model of platelet-endothelium interaction, along with propagation models typical of blood vessels, is incorporated into a simulation platform. Analysis of the simulation results indicates that these enhancements render the simulator a useful tool upon which to base discussion for planning research, and has the potential to be an important step in the understanding, diagnosis, and treatment of cardiovascular diseases.

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“…The sensing of the local concentration is used for the reception model [15]. In [9], a simulation platform for modeling information exchange at the nano-scale is introduced. A Java based software library is created using object oriented concepts.…”

Section: Introductionmentioning

confidence: 99%

Understanding Communication via Diffusion: Simulation Design and Intricacies

Acar

Akkaya

Genc

et al. 2017

Modeling, Methodologies and Tools for Molecular and Nano-Scale Communications

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Understanding Communication via Diffusion (CvD) is key to molecular communications research since it dominates the movement at the nano-scale. The researcher needs to properly understand the random diffusion of the molecules for the analysis of a molecular communication system. This chapter aims explaining the dynamics of diffusion from a communication engineer's perspective as well as providing useful hints for an effective simulation design by discussing some key intricacies. The chapter starts with a brief survey of simulators for molecular communications, followed by the basics of the simulation of Brownian motion and CvD. Several intricacies are addressed to help the researcher in simulation design, such as the number of replications required in terms of movement and bit sequence. We utilize this information further by discussing the design of more complex CvD systems such as tunnel-based approach that utilizes destroyer molecules and distributed simulator design based on HLA. Introduction of more complex CvD systems provides significant improvements in data rate and communications in general, bridging the gap between human-scale and nano-scale systems and enabling nanonetworking as a viable technology.

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A simulation tool for nanoscale biological networks

Cited by 60 publications

References 11 publications

N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks

N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks

Modeling CD40-Based Molecular Communications in Blood Vessels

Understanding Communication via Diffusion: Simulation Design and Intricacies

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