Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Applied biomaterials from sustainable sources

If we look back in time at the history of humanity, we can state that our generation is living an era of outstanding efficiency and progress because of globalization and global competition, even if this is resulting in the rapid depletion of energy sources and raw materials. The environmental impact of non-biodegradable plastic wastes is of increasing global concern: nowadays, imagining a world without synthetic plastics seems impossible, though their large-scale production and their extensive use have only spread since the end of the World War II. In recent years, the demand for sustainable materials has increased significantly and, with a view to circular economy, research has also focused on the enhancement and subsequent reuse of waste materials produced by industrial processing, intensive farming and the agricultural sector. Plastic polymers have been the most practical and economical solution for decades due to their low cost, prompt availability and excellent optical, mechanical and barrier properties. Biodegradable polymers could replace them in many applications, thus reducing the problems of traditional plastics disposability and the dependence on petroleum. Natural biopolymers are in fact characterized by a high biocompatibility and biodegradability and have already prompted research in the field of regenerative medicine. During my PhD, my goal was to use natural polymers from sustainable sources as raw materials to produce biomaterials, which are materials designed to interface with biological systems to evaluate, support or replace any tissue, organ, or function of the body. I focused on the use of the most abundant biopolymers in nature to produce biomaterials in the form of films, scaffolds and cements. After a complete characterization, the materials were proposed for suitable applications in different fields, from tissue engineering to cosmetics and food packaging. Some of the obtained results were published on international scientific and peer-reviewed journals.

A novel hybrid thermochemical-biological refinery integrated with power-to-X approach for obtaining biopolymers

In this study, a novel hybrid thermochemical-biological refinery integrated with power-to-x approach was developed for obtaining biopolymers (namely polyhydroxyalkanoates, PHA). Within this concept, a trilogy process schema comprising of, (i) thermochemical conversion via integrated pyrolysis-gasification technologies, (ii) anaerobic fermentation of the bioavailable products obtained through either thermochemistry or water-electrolysis for volatile fatty acids (VFA) production, (iii) and VFA-to-PHA bioconversion via an original microaerophilic-aerobic process was developed. During the first stage of proposed biorefinery where lignocellulosic (wooden) biomass was converted into, theoretically fermentable products (i.e. bioavailables) which were defined as syngas and water-soluble fraction of pyrolytic liquid (WS); biochar as a biocatalyst material; and a dense-oil as a liquid fuel. Within integrated pyrolysis - gasification process, biomass was efficiently converted into fermentable intermediates representing up to 66% of biomass chemical energy content in chemical oxygen demand (COD) basis. In the secondary stage, namely anaerobic fermentation for obtaining VFA rich streams, three different downstream process were investigated. First fermentation test was acidogenic bioconversion of WS materials obtained through pyrolysis of biomass within an original biochar-packed bioreactor, it was sustained up to 0.6 gCOD/L-day volumetric productivity (VP). Second, C1 rich syngas materials as the gaseous fraction of pyrolysis-gasification stage, was fermented within a novel char-based biofilm sparger reactor (CBSR), where up to 9.8 gCOD/L-day VP was detected. Third was homoacetogenic bioconversion within the innovative power-to-x pathway for obtaining commodities via renewable energy sources. More specifically, water-electrolysis derived H2 and CO2 as a primary greenhouse gas was successfully bio-utilized by anaerobic mixed cultures into VFA within CBSR system (VP: 18.2 gCOD/L-day). In the last stage of the developed biorefinery schema, VFA is converted into biopolymers within a new continuous microaerophilic-aerobic microplant, where up to 60% of PHA containing sludges was obtained.