Reaction systems are a formal framework for modeling processes driven by biochemical reactions. They are based on the mechanisms of facilitation and inhibition. A main assumption is that if a resource is available, then it is present in sufficient amounts and as such, several reactions using the same resource will not compete concurrently against each other; this makes reaction systems very different as a modeling framework than traditional frameworks such as ODEs or continuous time Markov chains. We demonstrate in this paper that reaction systems are rich enough to capture the essential characteristics of ODE-based models. We construct a reaction system model for the heat shock response in such a way that its qualitative behavior correlates well with the quantitative behavior of the corresponding ODE model. We construct our reaction system model based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We conclude with a discussion on the expressivity of reaction systems as compared to that of ODE-based models.

The use of digital twins for the development of Autonomous Maritime Surface Vessels (AMSVs) has enormous potential to resolve the increasing need for water-based navigation and safety at the sea. Aiming at the problem of lack of broad and integrated digital twin implementations with live data along with the absence of a digital twin-driven framework for AMSV design and development, an application framework for the development of a fully autonomous vessel using an integrated digital twin in a 3D simulation environment has been presented. Our framework has 4 layers which ensure that simulation and real-world vessel and the environment are as close as possible. Åboat, an in-house, experimental research platform for maritime automation and autonomous surface vessel applications, equipped with two trolling electric motors, cameras, LiDARs, IMU and GPS has been used as the case study to provide a proof of concept. Åboat, its sensors, and the environment have been replicated in a commercial, 3D simulation environment, AILiveSim. Using the proposed application framework, we develop obstacle detection and path planning systems based on machine learning which leverage live data from a 3D simulation environment to mirror the complex dynamics of the real world. Exploiting the proposed application framework, the rewards across training episodes of a Deep Reinforcement Learning model are evaluated for live simulated data in AILiveSim.

We present the EVONANO platform for the evolution of nanomedicines with application to anti-cancer treatments. Our work aims to decrease both the time and cost required to develop nanoparticle designs. EVONANO includes a simulator to grow tumours, extract representative scenarios, and simulate nanoparticle transport through these scenarios in order to predict nanoparticle distribution. The nanoparticle designs are optimised using machine learning to efficiently find the most effective anti-cancer treatments. We demonstrate EVONANO with two examples optimising the properties of nanoparticles and treatment to selectively kill cancer cells over a range of tumour environments. Our platform shows how in silico models that capture both tumour and tissue-scale dynamics can be combined with machine learning to optimise nanomedicine.