Synthetic biology: advancing biological frontiers by building synthetic systems

Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field

What constitutes a nanoswitch? A Perspective

Progress in the last two decades has effectively integrated spintronics and nanomagnetics into a single field, creating a new class of spin-based devices that are now being used both to Read (R) information from magnets and to Write (W) information onto magnets. Many other new phenomena are being investigated for nano-electronic memory as described in Part II of this book. It seems natural to ask whether these advances in memory devices could also translate into a new class of logic devices. What makes logic devices different from memory is the need for one device to drive another and this calls for gain, directionality and input-output isolation as exemplified by the transistor. With this in mind we will try to present our perspective on how W and R devices in general, spintronic or otherwise, could be integrated into transistor-like switches that can be interconnected to build complex circuits without external amplifiers or clocks. We will argue that the most common switch used to implement digital logic based on complementary metal oxide semiconductor (CMOS) transistors can be viewed as an integrated W-R unit having an input-output asymmetry that give it gain and directionality. Such a viewpoint is not intended to provide any insight into the operation of CMOS switches, but rather as an aid to understanding how W and R units based on spins and magnets can be combined to build transistor-like switches. Next we will discuss the standard W and R units used for magnetic memory devices and present one way to integrate them into a single unit with the input electrically isolated from the output. But we argue that this integrated W-R unit would not provide the key property of gain. We will then show that the recently discovered giant spin Hall effect could be used to construct a W-R unit with gain and suggest other possibilities for spin switches with gain.Comment: 27 pages. To appear in Emerging Nanoelectronic Devices, Editors: An Chen, James Hutchby, Victor Zhirnov and George Bourianoff, John Wiley & Sons (to be published

Computing Nash Equilibrium in Wireless Ad Hoc Networks: A Simulation-Based Approach

This paper studies the problem of computing Nash equilibrium in wireless networks modeled by Weighted Timed Automata. Such formalism comes together with a logic that can be used to describe complex features such as timed energy constraints. Our contribution is a method for solving this problem using Statistical Model Checking. The method has been implemented in UPPAAL model checker and has been applied to the analysis of Aloha CSMA/CD and IEEE 802.15.4 CSMA/CA protocols.Comment: In Proceedings IWIGP 2012, arXiv:1202.422

A population-based microbial oscillator

Genetic oscillators are a major theme of interest in the emerging field of synthetic biology. Until recently, most work has been carried out using intra-cellular oscillators, but this approach restricts the broader applicability of such systems. Motivated by a desire to develop large-scale, spatially-distributed cell-based computational systems, we present an initial design for a population-level oscillator which uses three different bacterial strains. Our system is based on the client-server model familiar to computer science, and uses quorum sensing for communication between nodes. We present the results of extensive in silico simulation tests, which confirm that our design is both feasible and robust.Comment: Submitte

A temporal switch model for estimating transcriptional activity in gene expression

Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription–polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states. Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation

Self-Synchronization in Duty-cycled Internet of Things (IoT) Applications

In recent years, the networks of low-power devices have gained popularity. Typically these devices are wireless and interact to form large networks such as the Machine to Machine (M2M) networks, Internet of Things (IoT), Wearable Computing, and Wireless Sensor Networks. The collaboration among these devices is a key to achieving the full potential of these networks. A major problem in this field is to guarantee robust communication between elements while keeping the whole network energy efficient. In this paper, we introduce an extended and improved emergent broadcast slot (EBS) scheme, which facilitates collaboration for robust communication and is energy efficient. In the EBS, nodes communication unit remains in sleeping mode and are awake just to communicate. The EBS scheme is fully decentralized, that is, nodes coordinate their wake-up window in partially overlapped manner within each duty-cycle to avoid message collisions. We show the theoretical convergence behavior of the scheme, which is confirmed through real test-bed experimentation.Comment: 12 Pages, 11 Figures, Journa