Development of Molecular based Communication Protocols for Nanomachines

Abstract

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.

Simulating the performance of SW-ARQ schemes within molecular communications

“…14 and Fig. 15, by introducing a new variable k, the time cost for a complete transmission has been reduced significantly due to the increase of the probability of a successful transmission given by (6). However, the increase of such probability will not lead to the decrease of the energy consumption because the energy cost for sending excess ACKs also contribute to the overall energy consumption.…”

“…1, the procedure of this protocol abstraction is as follows. First, the molecules, or bio-molecules, which have been encoded with both the message and the index [6,7] (represented as S1), are emitted by the transmitting (Tx) nanomachine and propagate to the receiving (Rx) nanomachine. Upon reception, the S1 molecules stimulate Rx to release another type of molecules or bio-molecules, known as ACKnowledgements or ACKs (represented as S2).…”

“…Further work on the Assured State Transfer protocol abstraction was carried out in [6,8] where simulations on a molecular based reliable communication protocol with nano-logic computation were discussed. In [9], we expanded the idea and investigated three schemes, schemes 1 through 3 in this paper, but most results were simulated with only two fixed values of the pre-designed waiting time (T r ), and averaged after only 5000 retrails.…”

Molecular communication: Harnessing biochemical materials to engineer biomimetic communication systems

“…Other examples include an information theoretic model of molecular communication based on cellular signaling [56], calculating the maximum capacity for the molecular communication channel between a sender and a receiver [3][4][5][6] and mathematical modeling of molecular communication among floating nanomachines that act as senders/receivers in the aqueous environment based on probabilistic timed finite state automata [102]. The design of a protocol stack, address encoding/decoding, link switching and error correction mechanisms for molecular communication networks are discussed in [98][99][100].…”