Biological Oscillators in Nanonetworks-Opportunities and Challenges

Computational characterization of recombinase circuits for periodic behaviors

Recombinases are site-specific proteins found in nature that are capable of rearranging DNA. This function has made them promising gene editing tools in synthetic biology, as well as key elements in complex artificial gene circuits implementing Boolean logic. However, since DNA rearrangement is irreversible, it is still unclear how to use recombinases to build dynamic circuits like oscillators. In addition, this goal is challenging because a few molecules of recombinase are enough for promoter inversion, generating inherent stochasticity at low copy number. Here, we propose six different circuit designs for recombinase-based oscillators operating at a single copy number. We model them in a stochastic setting, leveraging the Gillespie algorithm for extensive simulations, and show that they can yield coherent periodic behaviors. Our results support the experimental realization of recombinase-based oscillators and, more generally, the use of recombinases to generate dynamic behaviors in synthetic biology.

A New Impedance Sensor Based on Electronically Implemented Chaotic Coupled van der Pol and Damped Duffing Oscillators

The chaotic behaviour of a system depends on the parameter values, and when the system exhibits such a chaotic behaviour, it is sensitive to the initial conditions. This feature can be used for manufacturing high sensitivity sensors. Sensors based on chaotic circuits have already been used for measuring water salinity, inductive effects, and both noise and weak signals. This article investigates an impedance sensor based on the van der Pol and Duffing damped oscillators. The calibration process is a key point and therefore the folding behaviour of signal periods was also explored. A sensitivity of 0.15 kΩ/Period was estimated over a range from 89.5 to 91.6 kΩ. This range can be adjusted according to the application by varying the gain of the operational amplifier used in this implementation. The development of this type of sensor might be used in medical and biological engineering for skin impedance measurements, for example. This type of chaotic impedance sensor has the advantage of sensing small disturbances and then rapidly detecting small impedance changes within biological materials.

Slot Self-Allocation Based MAC Protocol for Energy Harvesting Nano-Networks

Nano-networks are composed of interconnected nano-nodes and can enable unprecedented applications in various fields. Due to the peculiarities of nano-networks, such as high density, extremely limited energy and computational resources, traditional carrier-sensing based Media Access Control (MAC) protocols are not suitable for nano-networks. In this paper, a Slot Self-Allocation based MAC protocol (SSA-MAC) is proposed for energy harvesting nano-networks. Two transmission schemes for centralized and distributed nano-networks are designed, respectively. In centralized nano-networks, nano-nodes can only send packets to the nano-controller in their Self-Allocation Slots (SASs), while, in distributed nano-networks, nano-nodes can only receive packets from surrounding nano-nodes in their SASs. Extensive simulations were conducted to compare the proposed SSA-MAC with PHysical LAyer aware MAC (PHLAME), Receiver-Initiated Harvesting-aware MAC (RIH-MAC) and Energy Efficient Wireless NanoSensor Network MAC (EEWNSN). From the results, it can be concluded that the proposed SSA-MAC achieves better performance and can reduce the collision probability, while improving the energy efficiency of nano-networks.