Defining Communication at the Bottom

Bush, Stephen F.; Paluh, Janet L.; Piro, Giuseppe; Rao, Vijay S.; Prasad, Ramjee; Eckford, Andrew W.

doi:10.1109/tmbmc.2015.2465513

Cited by 43 publications

(16 citation statements)

References 12 publications

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“…As a communication network, the model provides spatiotemporal information and makes predictions on efficiencies in various steps of intracellular neuronal signaling. We have defined the underlying communication system in neuronal cells regarding message, message carrier, receiver, transmitter, and medium, concepts developed in the 6,54 The NEMo platform is ideal for modeling intracellular nano-molecular events and has not previously been applied to neurons. It uses a physical layer protocol framework to map communication systems.…”

Section: Discussionmentioning

confidence: 99%

“…The IEEE p1906.1-2015 standard applies Shannon's rules of communication theory for systems with nanoscale components even if they operate multiscale from nanoscale over larger scales. 6,54 The NEMo software is designed to apply the IEEE standard framework. Some of the current limitations of the model relate to the need for more detailed information and as such may help to drive this type of experimental discovery.…”

Section: Discussionmentioning

confidence: 99%

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Modeling the neuron as a nanocommunication system to identify spatiotemporal molecular events in neurodegenerative disease

Banerjee

Paluh

Mukherjee

et al. 2018

IJN

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AimIn tauopathies such as Alzheimer’s disease (AD), molecular changes spanning multiple subcellular compartments of the neuron contribute to neurodegeneration and altered axonal signaling. Computational modeling of end-to-end linked events benefit mechanistic analysis and can be informative to understand disease progression and accelerate development of effective therapies. In the calcium-amyloid beta model of AD, calcium ions that are an important regulator of neuronal function undergo dysregulated homeostasis that disrupts cargo loading for neurotrophic signaling along axonal microtubules (MTs). The aim of the present study was to develop a computational model of the neuron using a layered architecture simulation that enables us to evaluate the functionalities of several interlinked components in the calcium-amyloid beta model.MethodsThe elevation of intracellular calcium levels is modeled upon binding of amyloid beta oligomers (AβOs) to calcium channels or as a result of membrane insertion of oligomeric Aβ1-42 to form pores/channels. The resulting subsequent Ca2+ disruption of dense core vesicle (DCV)-kinesin cargo loading and transport of brain-derived neurotrophic factor (BDNF) on axonal MTs are then evaluated. Our model applies published experimental data on calcium channel manipulation of DCV-BDNF and incorporates organizational complexity of the axon as bundled polar and discontinuous MTs. The interoperability simulation is based on the Institute of Electrical and Electronics Engineers standard association P1906.1 framework for nanoscale and molecular communication.ResultsOur analysis provides new spatiotemporal insights into the end-to-end signaling events linking calcium dysregulation and BDNF transport and by simulation compares the relative impact of dysregulation of calcium levels by AβO-channel interactions, oligomeric Aβ1-42 pores/channel formation, and release of calcium by internal stores. The flexible platform of our model allows continued expansion of molecular details including mechanistic and morphological parameters of axonal cytoskeleton networks as they become available to test disease and treatment predictions.ConclusionThe present model will benefit future drug studies on calcium homeostasis and dysregulation linked to measurable neural functional outcomes. The algorithms used can also link to other multiscale multi-cellular modeling platforms to fill in molecular gaps that we believe will assist in broadening and refining multiscale computational maps of neurodegeneration.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Modeling the neuron as a nanocommunication system to identify spatiotemporal molecular events in neurodegenerative disease

Banerjee

Paluh

Mukherjee

et al. 2018

IJN

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“…It also includes design, analysis, and computer simulations of higherlayer mechanisms of molecular communication (Lio and Balasubramaniam 2012;Felicetti et al 2014). It further includes standardization efforts to establish molecular communication as a standard framework and to develop simulation tools (Bush et al 2015).…”

Section: Historical Backgroundmentioning

confidence: 99%

AODV Protocol with Trust Based Mechanism

2020

Encyclopedia of Wireless Networks

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“…Not only are there numerous physical layers to accommodate, but there are likely to be different requirements in the data and control aspects at each stage, some of which will be well-defined, but others will not. For example, the TCP/IP of the internet, or one of the numerous IEEE802.x Wi-Fi standards, are not up for negotiation, whilst the protocols required for the links between nanoand macro-devices, are still at the debate stage within the literature [5] [6], [7], [8], [9].…”

Section: Introductionmentioning

confidence: 99%

Energy requirements of error correction codes in diffusion-based molecular communication systems

Wang

Higgins

et al. 2017

Nano Communication Networks

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Permanent WRAP URL:http://wrap.warwick.ac.uk/81742 Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-for-profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP URL' above for details on accessing the published version and note that access may require a subscription. AbstractMolecular Communications is a promising area with significant potential applications. To enhance the reliability of the transmission process, self-orthogonal convolutional codes (SOCCs) are proposed and investigated with respect to both bit error rate (BER) and energy efficiency. The codes are compared to both an un-coded system and one that employs Hamming codes to show that they can provide a benefit for molecular communication systems. The influence of the channel memory is also analysed in this paper. In addition, taking into account the extra energy required to implement the coding, the critical distance is investigated as another performance metric for nano-to-nano device communication, nano-to-macro device communication and macro-to-nano device communication. Considering the transmission distance and the operating BER of the designed system, the designer can determine whether the use of coding is beneficial or which code better suits the system.

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Defining Communication at the Bottom

Cited by 43 publications

References 12 publications

Modeling the neuron as a nanocommunication system to identify spatiotemporal molecular events in neurodegenerative disease

Modeling the neuron as a nanocommunication system to identify spatiotemporal molecular events in neurodegenerative disease

AODV Protocol with Trust Based Mechanism

Energy requirements of error correction codes in diffusion-based molecular communication systems

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