Logical Nano-Computation in Enzymatic Reaction Networks

Stetter,; Schurmann,; Hofstetter,

doi:10.1109/bimnics.2006.361813

Cited by 6 publications

(10 citation statements)

References 5 publications

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“…Many other known cellular signaling pathways which include autophagy pathways, adenosine monophosphateactivated protein kinase (AMPK) pathways, mammalian target of rapamycin (mTOR) pathways, and protein kinase B pathways can also be mimicked to perform dedicated tasks that are ordinarily associated to them. The whole or part of the biocircuit can also be some molecular computing circuit like the enzymatic circuits [68][69][70]. In this form of enzymatic computing a flip-flop switch can be created.…”

Section: Biocircuit Modelmentioning

confidence: 99%

Bio-inspired physical layered device architectures for diffusion-based molecular communication: Design Issues and suggestions

Chude-Okonkwo

Malekian

Mharaj

et al. 2015

2015 IEEE 13th International Conference on Industrial Informatics (INDIN)

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The aim of molecular communication (MC) is to develop communication systems for biochemical information interchange among nano devices. While there have been research efforts to model, design and analyze various MC network and devices, a lot still have to be done before we can develop and deploy such systems. Following the traditional physical layered architecture of communication networks, this paper presents design initiatives, open research issues and proffer suggestion towards modeling and designing diffusion-based MC devices.Specifically, we present biologically inspired modular theoretical design approach to modeling and designing MC devices. We also discussed various issues that should be considered in developing an accurate system-theoretic model of an MC system.

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Section: Biocircuit Modelmentioning

confidence: 99%

Bio-inspired physical layered device architectures for diffusion-based molecular communication: Design Issues and suggestions

Chude-Okonkwo

Malekian

Mharaj

et al. 2015

2015 IEEE 13th International Conference on Industrial Informatics (INDIN)

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“…In doing so, the author demonstrates the use of ultra-sensitive cell-based enzyme signaling pathways to perform digital logic computation. Similarly, in [5] Stetter et al uses the bistable nature of biochemical enzymatic reactions to create a reusable, "easy to engineer" architecture that forms the basis of several Boolean logic functions such as AND, and OR gates. This small enzyme-based circuit can act as a sub-component in composing more complex functions.…”

Section: Enzyme Based Computingmentioning

confidence: 99%

“…In our case, instead of oligonucleotides, we diffuse our encoded ssDNA from the previous section. In this study, interface selection is achieved using the "real world" implementation of the logical recurrent architecture as described by Stetter et al in [5]. The switching circuit releases/alters a corresponding chemical signal that "switches" the ssDNA to the correct interface.…”

Section: Molecular Interface Controlmentioning

confidence: 99%

Hybrid DNA and Enzyme Based Computing for Address Encoding, Link Switching and Error Correction in Molecular Communication

Walsh

Balasubramaniam

Botvich

et al. 2009

Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering

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Abstract. This paper proposes a biological cell-based communication protocol to enable communication between biological nanodevices. Inspired by existing communication network protocols, our solution combines two molecular computing techniques (DNA and enzyme computing), to design a protocol stack for molecular communication networks. Based on computational requirements of each layer of the stack, our solution specifies biomolecule address encoding/decoding, error correction and link switching mechanisms for molecular communication networks.

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“…Stetter et al [4] developed a mechanism to allow logical nano computation to be performed by manipulating the concentration of enzyme molecules. Manipulation of enzymes includes mechanism of kinase activation to allow an enzyme to be active, while de-activation is performed through phosphorylation of the enzymes.…”

Section: Molecular Computingmentioning

confidence: 99%

“…Similar to the encoding process, the transmission error-recovery process is also based on using molecular computing techniques. Our solution is based on the solution proposed by Stetter et al [4]. The solution is based on defining a finite state machine that defines transmission and error-recovery at the transport layer (since we only have two layers, the transmission layer is also in charge of propagating the molecule at the physical layer where solutions of Enomoto et al [2] or Nakano et al [3] can be used.…”

Section: Transmission and Error Recoverymentioning

confidence: 99%

Development of Molecular based Communication Protocols for Nanomachines

Walsh

Balasubramaniam

Botvich

et al. 2007

Proceedings of the Second International Conference on Nano-Networks

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Communication between nanomachines (e.g. biological nanoscale devices) has the potential to open up new opportunities and applications, especially in areas such as health care and information processing. Inspired by current data communication protocols, we propose a molecular-based communication protocol to enable reliable communication between nanomachines. In this paper, we present a protocol stack which enables nanomachine communication through the encoding and transmission of data as biomolecules. Extending previous work in logical nanocomputation, we define an error-recovery process through the use of a chemical state machine based on nano-logic circuit. Finally, we present initial results of simulation of nanomachine communication in the presence of both channel and chemical instability and demonstrate the performance of the nano-circuit in such conditions. Enomoto et al [2] have proposed a molecular communication solution for nano-scale communication for nano-devices. The molecular communication allows devices to encode and decode information into molecules and to transport this information to peer nano-devices. The solution is inspired by biological systems that communicate using molecules, where molecular communication using molecular motors was observed within a biological cell. The authors seek to develop an engineered molecular communication system employing various processes (encoding, sending, propagating, receiving, and decoding) and components (sender and receiver). The solution proposed by the authors uses molecular motors (e.g. kinesin, dynein), which are used to transport materials in eukaryotic cells along filaments referred to as rail molecules (e.g. microtubles), for controlled nanomachine communication. Nakano et al [3] proposed a mechanism to allow intercellular communication between distant nanodevices using induced calcium signalling. The solution proposed by the authors exploits the current calcium signalling between cells, by modifying the frequency and amplitude of the calcium concentration. Through this mechanism, calcium wave propagation occurs which allows controlled intercellular communication. By interfacing a nanodevice to a specific cell, calcium communication can be formed by controlling the calcium production in the event the device has access to the cytosol of the cell. In the event that cell has no access to the cytosol, then the nanodevice can emit substances that can bind to specific receptor of the cell that can induce calcium production. The challenges relating to describing accurately a communication channel for the transmission of messages in 'wet' techniques are highlighted by Alfano et al [5] who state the 'most urgent question' for molecular communications is the characterization of the 'wet' communication channel. The authors point to the challenge posed by non-linear nature of the channel and the necessity for experimentation and computer simulation to address this.

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Logical Nano-Computation in Enzymatic Reaction Networks

Cited by 6 publications

References 5 publications

Bio-inspired physical layered device architectures for diffusion-based molecular communication: Design Issues and suggestions

Bio-inspired physical layered device architectures for diffusion-based molecular communication: Design Issues and suggestions

Hybrid DNA and Enzyme Based Computing for Address Encoding, Link Switching and Error Correction in Molecular Communication

Development of Molecular based Communication Protocols for Nanomachines

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