The effects of ionizing particles on sensitive microelectronics is an important component of the design of systems as diverse as satellites and space probes, detectors for high energy physics experiments and even internet server farms. Understanding the effects of radiation on human cells is an equally important endeavor directed towards future manned missions in space and towards cancer therapy. At the 88-Inch Cyclotron at the Berkeley Laboratory, facilities are available for radiation effects testing (RET) with heavy ions and with protons. The techniques for doing these measurements and the advantages of using a cyclotron will be discussed, and the Cyclotron facilities will be compared with other facilities worldwide. RET of the same part at several facilities of varying beam energy can provide tests of the simple models used in this field and elucidate the relative importance of atomic and nuclear effects. The results and implications of such measurements will be discussed.

The dissertation presents results on control and state estimation for a physics-based ``Stefan" model of phase change. Design procedures, theoretical analysis, applications to industrial processes, and experimental validation are addressed. The Stefan model describes a time-evolution of a material's temperature profile during melting/solidification phenomena along with the dynamics of the liquid-solid interface position. The mathematical description comprises a parabolic Partial Differential Equation (PDE), defined on a time-varying spatial domain, whose boundary position dynamics are governed by an Ordinary Differential Equation (ODE) driven by the PDE's state. None of the existing systematic and theoretical control are applicable to this problem due to the system's geometric nonlinearity as well as the infinite dimensionality. We design a boundary heat control to promote the melting so that the liquid-solid interface position is driven to a desired setpoint position. Our design is an extension of the ``PDE backstepping" method to the Stefan system. The closed-loop stability is proven by Lyapunov analysis. The constraints of the temperature state and the heat input are guaranteed by virtue of the maximum principle. Analogous results for the state estimation are also developed to estimate the entire temperature profile from available measurements of the surface temperature and the liquid-solid interface position.

The latter half of the dissertation is devoted to the application of the designed method to several practical problems. First, we introduce a Stefan model of ``sea ice", which has been studied intensively due to the recent rapid melting of sea ice. We verify the desired robust performance of the designed estimator in a numerical simulation, which incorporates further complexity in the model and uncertainties. Second, we focus on ``lithium-ion batteries", which have become ubiquitous in electronic devices, such as laptops and smartphones, and in electric vehicles. The model is described by a Stefan system of the lithium-ion concentration due to a solid-solid phase change in the electrodes during the charging and discharging cycles. Our estimator achieves accurate State-of-Charge estimation in simulation. Third, we apply the designed control method to ``polymer 3D-printing" via screw extrusion for the sake of stabilizing the filament production under a fast printing, by extending the design to deal with the convection and heat loss. Fourth, we focus on ``metal 3D-printing" which has a high impact on products and supply chains in industries. The proposed control method is applied for generating the desired shape of the melt pool, which shows the robust performance with respect to a radiation effect and sensor noise in numerical study. Finally, we conduct experiments of melting paraffin wax as an energy storage material, which shows the successful performance of our PDE-based control algorithm.

Stomatopoda, otherwise known as mantis shrimp, are a diverse group of marine crustaceans with some notable features. They have enlarged second maxillipeds encompassing the raptorial claw that distinguishes them into two groups: smashers and spearers. Previous studies have focused on morphology or a few gene trees, but only recently have there been whole mitochondrial genome-based phylogenies of mantis shrimp. However, there is only a small set of mantis shrimp taxa with their mitogenomes sequenced. Nine new mitochondrial genomes were generated from genome skimming with a conserved gene order and a combined phylogenetic analysis with available data of the mitochondrial 13 protein coding genes, 12S, 16S, and nuclear 18S. Species from three out of the seven superfamilies were used in this study. Two different rooting options were used: 1) Euphausia pacifica (krill) and 2) Hemisquilla californiensis based on the current hypothesis that Hemisquilla is the sister group to the rest of Stomatopoda. The H. californiensis outgroup datasets had the same tree topology as the E. pacifica outgroup datasets with slight variation at low supported nodes. Squilloidea was found to be highly supported as monophyletic while Gonodactyloidea was non-monophyletic. The position of H. californiensis was found inside its superfamily, Gonodactyloidea, and grouped in a low supported clade containing Odontodactylus havanensis and Lysiosquillina maculata for the E. pacifica datasets. An ancestral state reconstruction was performed on the raptorial claw form to determine the evolution of one of its most characteristic features. The results exhibited spearers as the ancestral state with smashing evolving after.