A Reactive Signaling Approach to Ensure Coexistence Between Molecular Communication and External Biochemical Systems

International audienceIn molecular communication systems operating in a crowded biochemical environment, there is the potential for unintended chemical or physical interactions with external biochemical systems. In order to avoid these interactions, or ensure coexistence, it is necessary to tailor the signaling scheme. In this paper, we propose a signaling strategy exploiting chemical reactions between different transmitted chemical species. While intuitively appealing, the non-linear nature of the governing partial differential equations (PDE) means that selecting the signaling strategy to minimize the probability of error is com-putationally challenging. To reduce this computational burden, we introduce a new proxy metric called the modified signal-to-interference difference (mSID). We show that optimizing the mSID yields low complexity and near-optimal solutions, requiring only deterministic nonlinear programming rather than standard brute force Monte Carlo methods

Robustness of networked systems to unintended interactions with application to engineered genetic circuits

A networked dynamical system is composed of subsystems interconnected through prescribed interactions. In many engineering applications, however, one subsystem can also affect others through "unintended" interactions that can significantly hamper the intended network's behavior. Although unintended interactions can be modeled as disturbance inputs to the subsystems, these disturbances depend on the network's states. As a consequence, a disturbance attenuation property of each isolated subsystem is, alone, insufficient to ensure that the network behavior is robust to unintended interactions. In this paper, we provide sufficient conditions on subsystem dynamics and interaction maps, such that the network's behavior is robust to unintended interactions. These conditions require that each subsystem attenuates constant external disturbances, is monotone or "near-monotone", the unintended interaction map is monotone, and the prescribed interaction map does not contain feedback loops. We employ this result to guide the design of resource-limited genetic circuits. More generally, our result provide conditions under which robustness of constituent subsystems is sufficient to guarantee robustness of the network to unintended interactions

The Effect of Loads in Molecular Communications

© 1963-2012 IEEE. The ability of cells to sense and respond to their environment is encoded in biomolecular reaction networks, in which information travels through processes such as production, modification, and removal of biomolecules. Recent advances in biotechnology have made it possible to reengineer these physical processes to the point where synthetic biomolecular circuits can be inserted into cells to program cell behavior for useful functionalities. These circuits are often designed in a bottom-up fashion with smaller components connected to form complex systems. In a bottom-up approach to design, it is highly desirable that circuit components behave modularly, that is, the input-output behavior of a module characterized in isolation remains unchanged when the context changes. Unfortunately, due to the physical processes by which information is communicated from one biomolecular circuit module to the other, the lack of modularity is often a problem. In fact, the input-output behavior of a module depends on both direct connectivity to other modules, due to loading effects, and indirect connectivity arising from loads applied to shared cellular resources. In this paper, we summarize the published work illustrating how the means of molecular communication lead to these problems. Specifically, we review the concept of retroactivity, which has been proposed to capture loading problems within a 'signals and systems' framework, allowing for engineering solutions that restore modularity