This dissertation addresses the development of integrative modeling strategies capable of combining deterministic and stochastic, discrete and continuous, as well as multi-scale features. The first set of studies combines the purely deterministic modeling methodology of Biochemical Systems Theory (BST) with a hybrid approach, using Functional Petri Nets, which permits the account of discrete features or events, stochasticity, and different types of delays. The efficiency and significance of this combination is demonstrated with several examples, including generic biochemical networks with feedback controls, gene regulatory modules, and dopamine based neuronal signal transduction. A study expanding the use of stochasticity toward systems with small numbers of molecules proposes a rather general strategy for converting a deterministic process model into a corresponding stochastic model. The strategy characterizes the mathematical connection between a stochastic framework and the deterministic analog. The deterministic framework is assumed to be a generalized mass action system and the stochastic analogue is in the format of the chemical master equation. The analysis identifies situations where internal noise affecting the system needs to be taken into account for a valid conversion from a deterministic to a stochastic model. The conversion procedure is illustrated with several representative examples, including elemental reactions, Michaelis-Menten enzyme kinetics, a genetic regulatory motif, and stochastic focusing. The last study establishes two novel, particle-based methods to simulate biochemical diffusion-reaction systems within crowded environments. These simulation methods effectively simulate and quantify crowding effects, including reduced reaction volumes, reduced diffusion rates, and reduced accessibility between potentially reacting particles. The proposed methods account for fractal-like kinetics, where the reaction rate depends on the local concentrations of the molecules undergoing the reaction. Rooted in an agent based modeling framework, this aspect of the methods offers the capacity to address sophisticated intracellular spatial effects, such as macromolecular crowding, active transport along cytoskeleton structures, and reactions on heterogeneous surfaces, as well as in porous media. Taken together, the work in this dissertation successfully developed theories and simulation methods which extend the deterministic, continuous framework of Biochemical Systems Theory to allow the account of delays, stochasticity, discrete features or events, and spatial effects for the modeling of biological systems, which are hybrid and multiscale by nature.

There is currently a high demand for electric power from renewablesources. One source that remains relatively untapped is the motionof ocean waves. Anders Hagnestål has been developing a uniquelyefficient and simplified design for a point-absorb buoy generator byconverting its linear motion directly into alternating electric power usinga linear PM engine. To test this method, a smaller prototype isbuilt. Its characteristics present some unusual challenges in the designand construction of its winding.Devices of this type typically use relatively low voltage (690V typicallyfor a wind turbine, compared to the 10kV range of traditionalpower plants). To achieve high power, they need high current, whichin turn requires splitting the conductors in the winding into isolatedparallel strands to avoid losses due to eddy currents and current crowding.However, new losses from circulating currents can then arise. Inorder to reduce said losses, the parallel conductors should be transposedin such a way that the aggregate electromotive force the circuitsthat each pair of them forms is minimized.This research and prototyping was performed in absence of advancedindustrial means of construction, with limited space, budget,materials, manpower, know-how, and technology. Manual ingenuityand empirical experimentation were required to find a practical implementationfor: laying the cables, fixing them in place, transferringthem to the machine, stripping their coating at the ends and establishinga reliable connection to the current source.Using theoretical derivations and FEM simulation, a sufficientlygood transposition scheme is proposed for the specific machine thatthe winding is built for. A bobbin replicating the shape of the enginecore is built to lay down the strands.The parallel strands are then organized each into their respectivebobbin, with a bobbin rack and conductor funneling device being designedand constructed to gather them together into a strictly-organizedbundle. An adhesive is found to set the cables in place.Problems with maintaining the orientation and configuration of thecables in the face of repeated torsion are met and solved. A chemicalsolution is used to strip the ends of the conductors, and a reliableconnection is established by crimping the conductors into a bi-metalCu-Al lug.ivIn conclusion, the ideal transposition schemes required to cancelout circulating currents due to magnetic flux leakage are impossibleto put in practice without appropriate technological means. The feasibletransposition scheme turns out to be a simple mirroring of conductors’positions, implemented by building each half of the windingseparately around replicas of the core and then connecting them usingcrimping lugs. / Efterfrågan på el från förnybara källor är hög och inget tyder på att det kommer ändras den närmsta tiden. En källa till förnybar el som än idag står relativt orörd är den där man använder energin från havsvå- gor. Det är denna förnybara källa Anders Hagnestål haft i åtanke när han nu bygger en unikt effektiv generator med syftet att i ett senare skede utvinna el med hjälp av flytande punktabsorberande vågkraft- system. Generatorn är av den linjära typen och omvandlar det punk- tabsorberande systemet rörelse till el. För att testa denna generator- modell så påbörjades bygget av två fullskaliga prototyper 2017. Denna uppsats behandlar specifikt arbetet med generatorlindningen till pro- totyperna och innefattar processen från design till själva byggnatio- nen. Lindingen består av flertalet mindre och isolerade lindningsleda- re med uppgift att bland annat minska skinneffekt och virvelströms- förluster. När man använder denna metod så uppkommer dock ett nytt problem vilket härstammar från att lindningsledarna är samman- kopplade i vardera ända och bildar på så sätt n slutna strömkretsar. Konsekvensen kan vara stora förluster från cirkulerande strömmar på grund av det magnetiska ströflöde som finns runt järnkärnan som lindningen omsluter. Utgångspunkten för att minimera dessa cirkule- rande strömmar är att transponera alla lindningsledare på ett sätt så att den resulterande elektromotoriska spänningen för varje strömkrets blir så liten som möjligt. Med hjälp av förenklade modeller samt FEM simuleringar så bestämdes ett lämpligt sätt att transponera lindningstrådarna utifrån oli- ka kriterier. Lösningen blev att lindningstrådarna endast transponera- des en gång med en så kallad 180 grader transponering. Detta ger en tillräckligt god minimering av de cirkulerande ström- marna, men den stora fördelen med denna lösning är att det är möjligt att linda maskinen med de små resurser projektet hade tillgång till, dock var detta till en stor nackdel då väldigt mycket tid gick till att hitta egna tillvägagångsätt för att utföra byggandet av lindningen på ibland okonventionella sätt.