OptCircuit: An optimization based method for computational design of genetic circuits

<p>Abstract</p> <p>Background</p> <p>Recent years has witnessed an increasing number of studies on constructing simple synthetic genetic circuits that exhibit desired properties such as oscillatory behavior, inducer specific activation/repression, etc. It has been widely acknowledged that that task of building circuits to meet multiple inducer-specific requirements is a challenging one. This is because of the incomplete description of component interactions compounded by the fact that the number of ways in which one can chose and interconnect components, increases exponentially with the number of components.</p> <p>Results</p> <p>In this paper we introduce OptCircuit, an optimization based framework that automatically identifies the circuit components from a list and connectivity that brings about the desired functionality. Multiple literature sources are used to compile a comprehensive compilation of kinetic descriptions of promoter-protein pairs. The dynamics that govern the interactions between the elements of the genetic circuit are currently modeled using deterministic ordinary differential equations but the framework is general enough to accommodate stochastic simulations. The desired circuit response is abstracted as the maximization/minimization of an appropriately constructed objective function. Computational results for a toggle switch example demonstrate the ability of the framework to generate the complete list of circuit designs of varying complexity that exhibit the desired response. Designs identified for a genetic decoder highlight the ability of OptCircuit to suggest circuit configurations that go beyond the ones compatible with digital logic-based design principles. Finally, the results obtained from the concentration band detector example demonstrate the ability of OptCircuit to design circuits whose responses are contingent on the level of external inducer as well as pinpoint parameters for modification to rectify an existing (non-functional) biological circuit and restore functionality.</p> <p>Conclusion</p> <p>Our results demonstrate that OptCircuit framework can serve as a design platform to aid in the construction and finetuning of integrated biological circuits.</p

Optimization and control of offshore wind systems with energy storage

Wind energy is widely exploited as a promising renewable energy source worldwide. In this article, an optimization method for the control and operation of the offshore wind farm as an integrated system considering its operational, economic and environmental impacts is proposed. The state of the offshore wind farm development, and the challenges faced by the offshore wind farms, including the challenges of economic costs, operational reliability, and environmental impacts are reviewed and summarized. A systematic methodology is proposed to optimize the costs of an offshore wind farm system based on a framework that extends from the supervisory level dispatch strategies to individual pitch control for load reduction and fatigue mitigation. This holistic approach is able to improve the efficiency and economic performance of a wind farm through overall system optimization, while explicitly operating each wind turbine using a formally designed control framework leading to an extension of their service lifespan. This work provides thorough introduction and innovative solutions for many economic and environmental issues in offshore wind farm development and has strong application potential