Synthesizing and tuning chemical reaction networks with specified behaviours

We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First, we identify candidate CRNs that have the possibility to produce correct computations for a given finite set of inputs. We then optimise the reaction rates of each CRN using a combination of stochastic search techniques applied to the chemical master equation, simultaneously improving the of correct behaviour and ruling out spurious solutions. In addition, we use techniques from continuous time Markov chain theory to study the expected termination time for each CRN. We illustrate our approach by identifying CRNs for majority decision-making and division computation, which includes the identification of both known and unknown networks.Comment: 17 pages, 6 figures, appeared the proceedings of the 21st conference on DNA Computing and Molecular Programming, 201

Development of a conceptual design tool for mechanism design

Engineering design can be seen as a problem solving process in which engineers and designers convert their thoughts and ideas into real-life designs satisfying market and customer needs. The conceptual design process is crucial in engineering product design since it determines fundamental design features with respect to design requirements. Any decisions made at this stage have a significant impact on later stages of design. However, connection between system functional requirements and selection of actual mechanical components in mechanism designs is severely lacking. With the purpose filling this gap and assisting engineers and designers to obtain in-depth understanding on commonly seen mechanisms and machine elements a database (MMET) was established and programmed containing detail information of these components including technical functional attributes, movement attributes, pictures/drawings and merit analysis. A conceptual design tool built on MMET was then developed aiming to help the user to explore a broad range of mechanical components regarding system requirements. The database and conceptual design tool were validated and improved through industrial case studies which suggest the addition of Function Means tree and Functional Analysis Diagram. The value of MMET and the new conceptual design tool are indicated via positive outcomes of case studies, asserting their capability of offering assistance in understanding engineering product functions and how these functions are achieved, enabling comparisons regarding same functional requirements and finally providing opportunities for conceptual design improvements based on a cyclic process containing detail functional analysis, function-means tree construction and design optimisation.Open Acces

Functional Analysis of Large-scale DNA Strand Displacement Circuits

Abstract. We present a method for the analysis of functional properties of large-scale DNA strand displacement (DSD) circuits based on Satisfiability Modulo Theories that enables us to prove the functional correctness of DNA circuit designs for arbitrary inputs, and provides significantly improved scalability and expressivity over existing methods. We implement this method as an extension to the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root circuit, together with the components used for its construction. We show that our method successfully verifies that certain designs function as required and identifies erroneous computations in others, even when millions of copies of a circuit are interacting with each other in parallel. Our method is also applicable in the verification of properties for more general chemical reaction networks.