This study proposed a finite element procedure for protein normal mode analysis (NMA). The finite element model adopted the protein solvent-excluded surface to generate a homogeneous and isotropic volume. A simplified triangular approximation of coarse molecular surface was generated from the original surface model by using the Gaussian-based blurring technique. Similar to the widely adopted elastic network model, the finite element model holds a major advantage over standard all-atom normal mode analysis: the computationally expensive process of energy minimization that may distort the initial protein structure has been eliminated. This modification significantly increases the efficiency of normal mode analysis. In addition, the finite element model successfully brings out the capability of normal mode analysis in low-frequency/high collectivity molecular motion by capturing protein shape properties. Fair results from six protein models in this study have fortified the capability of the finite element model in protein normal mode analysis.

Analyses of heat and mass transfer between different materials and phases are essential in numerous fundamental scientific problems and practical engineering applications, such as thermal and chemical transport in porous media, design of heat exchangers, dendritic growth during solidification, and thermal/mechanical analysis of additive manufacturing processes. In the numerical simulation, interface treatment can be further divided into sharp interface schemes and diffuse interface schemes according to the morphological features of the interface. This work focuses on the following subjects through computational studies: (1) critical evaluation of the various sharp interface schemes in the literature for conjugate heat and mass transfer modeling with the lattice Boltzmann method (LBM), (2) development of a novel sharp interface scheme in the LBM for conjugate heat and mass transfer between materials/phases with very high transport property ratios, and (3) development of a new diffuse-interface phase-field-lattice Boltzmann method (PFM/LBM) for dendritic growth and solidification modeling. For comparison of the previous sharp interface schemes in the LBM, the numerical accuracy and convergence orders are scrutinized with representative test cases involving both straight and curved geometries. The proposed novel sharp interface scheme in the LBM is validated with both published results in the literature as well as in-house experimental measurements for the effective thermal conductivity (ETC) of porous lattice structures. Furthermore, analytical correlations for the normalized ETC are proposed for various material pairs and over the entire range of porosity based on the detailed LBM simulations. In addition, we provide a modified correlation based on the SS420-air and SS316L-air metal pairs and the high porosity range for specific application. The present PFM/LBM model has several improved features compared to those in the literature and is capable of modeling dendritic growth with fully coupled melt flow and thermosolutal convection-diffusion. The applicability and accuracy of the PFM/LBM model is verified with numerical tests including isothermal, iso-solutal and thermosolutal convection-diffusion problems in both 2D and 3D. Furthermore, the effects of natural convection on the growth of multiple crystals are numerically investigated.

High temperature hydrogen attack (HTHA) is a damage mechanism that only affects carbon steel and low alloy material. Most of the data regarding HTHA are experimental-driven. Even though this approach has been successful, there are still much more things that the oil and gas industry does not understand about HTHA. The regions that were considered safe (below the Nelson curves) have experienced catastrophic failure. Our research consists of performing Molecular Dynamics (MD) and the Nudge Elastic Band (NEB) calculation of HTHA to better understand the atomistic behavior of this damage mechanism.

Artificial Neural Network (ANN) ensemble and Response Surface Method (RSM) surrogate models were generated from Finite Element (FE) simulations to predict the overpressure load and vehicle impact response of a novel rapidly deployable protective structure. A Non-dominated Sorting Genetic Algorithm-II (NSGA-II) was used in conjunction with the surrogate models to determine structure topology input variable configurations which were suited to produce the optimal balance of minimum mass, minimum rotation angle, minimum displacement, and maximum total length of the deployable structure. The structure was designed to retract into a container, be lightweight to facilitate transportation, and be able to adapt to varying terrain slopes. This research demonstrates that, in comparison to the RSM, ANN ensembles can more accurately and efficiently be used for identifying optimal design solutions for multi-objective design problems when two surrogate models from the same method corresponding to separate FE models are used simultaneously in a NSGA-II.

Defrosting in the refrigeration industry is used to remove the frost layer accumulated on the evaporators after a period of running time. It is one way to improve the energy efficiency of refrigeration systems. There are many studies about the defrosting process but none of them use computational fluid dynamics (CFD) simulation. The purpose of this thesis is (1) to develop a defrost model using the commercial CFD solver FLUENT to simulate numerically the melting of frost coupled with the heat and mass transfer taking place during defrosting, and (2) to investigate the thermal response of the evaporator and the defrost time for different hot gas temperatures and frost densities. A 3D geometry of a finned tube evaporator is developed and meshed using Gambit 2.4.6, while numerical computations were conducted using FLUENT 12.1. The solidification and melting model is used to simulate the melting of frost and the Volume of Fluid (VOF) model is used to render the surface between the frost and melted frost during defrosting. A user-defined-function in C programming language was written to model the frost evaporation and sublimation taking place on the free surface between frost and air. The model was run under different hot gas temperatures and frost densities and the results were analyzed to show the effects of these parameters on defrosting time, input energy and stored energy in the metal mass of the evaporator. The analyses demonstrate that an optimal hot gas temperature can be identified so that the defrosting process takes place at the shortest possible melting time and with the lowest possible input energy.

This thesis details the design and optimization of a buoy used to collect renewable energy from ocean waves. The proposed buoy is a point absorber—a device that transforms the kinetic energy of the vertical motion of surface waves into electrical energy. The focus of the research is on the mechanical system used to collect the energy, and methods to improve it for eventual use in an actual wave energy harvester. A flywheel energy storage system was utilized in order to provide an improved power output from the system, even with the intermittent input of force exerted by ocean waves. A series of laboratory prototypes were developed to analyze parameters that are important to the success of the point absorb mechanical system. By introducing a velocity-based load control scheme in conjunction with flywheel energy storage, it was seen that the average power output by the prototype was increased. The generator load is controlled via a relay switch that removes electrical resistance from the generator—this sacrifices time during which power is drawn from the system, but also allows the buoy to move with less resistance. A simulation model was developed in order to analyze the theoretical wave absorber system and optimize the velocity threshold parameters used in the load control. Results indicate that the power output by the system can be substantially improved through the use of a flywheel energy storage control scheme that engages and disengages the electrical load based on the rotational velocity of the flywheel system. The results of the optimization are given for varying-sized generator systems input into the simulation in order to observe the associated trends.

Football is a much loved sport in the United States. Unfortunately, it is also hard on the players and puts them at very high risk of concussion. To combat this an inventor in Santa Barbara brought a new design to Cal Poly to be tested. The design was tested in small scale first in order to make some preliminary conclusions about the design. In order to fully test the helmet design; however, full scale testing was required. In order to carry out this testing a drop tower was built based on National Operating Committee on Standards for Athletic Equipment, NOCSAE, specification. The drop tower designed for Cal Poly is a lower cost and highly portable version of the standard NOCSAE design. Using this drop tower and a 3D printed prototype the new design was tested in full scale.

This study investigated possible solutions to the current wartime problem of junctional hemorrhaging, or massive traumatic hemorrhaging in non-tourinquetable areas such as the neck, groin, or armpit. Junctional hemorrhaging has been identified as a major contributor to potentially survivable deaths seen on the battlefield today and therefore is a priority for the U.S. armed and coalition forces (Kragh et al., 2011a; Bozeman, 2011). Common tourniquets today are standard issue and carried by soldiers in the military, but are limited to distal extremity trauma. As the battlefield has changes however, trauma has transformed from commonly seen gunshot wounds to more extreme trauma such as dismounted complex blast injuries which typically includes loss of one or more appendages. These newly found situations render the traditional tourniquet ineffective. Thus, the development of a new tourniquet to control hemorrhaging from regions such as the neck, armpit, and groin has been deemed necessary. The development of a new tourniquet for hemorrhage control included market research, preliminary testing to determine design restraints, design ideation, finite element analysis, manufacturing a prototype, and prototype testing. Research and comparisons were done of the strengths and weaknesses of tourniquets already approved by the Food and Drug Administration (FDA). Next, design limitations were found using preliminary testing on a blood-flow replicate model developed by Tracey Cheung. The results from this testing provided a framework for designing a new tourniquet. A new approach to control junction hemorrhaging was then designed, built, and tested on the Cheung model. To verify the design, simplified models were analyzed using finite element analysis. The prototype was then tested and compared against the FDA approved tourniquets, listing the advantages and possible shortcomings.

Ceramic manufacturing is an expensive process with long lead times between the initial design and final manufactured part. This limits the use of ceramic as a viable material unless there is a large project budget or high production volume associated with the part. Ceramic stereolithography is an alternative to producing low cost parts through the mixing of a photo curable resin and ceramic particles. This is an additive manufacturing process in which each layer is built upon the previous to produce a green body that can be sintered for a fully dense ceramic part. This thesis introduces a new approach to ceramic stereolithography with a top mask projection light source which is much more economical compared to current vector scanning methods. The research goes through the design and development of a stereolithography printer prototype capable of handling ceramics and the testing of different mixtures to provide the best printing results with varying viscosities. The initial testing of this printer has created a starting point for top mask projection as an economical alternative to current ceramic manufacturing techniques.

This thesis investigates the feasibility and usability of the finite element method approach in the design of crack arresting devices. Current design and manufacturing practices are improving structures' susceptibility to fracture, in particular brittle fracture; however, cracks in structures are still observed within their lifespans due to severe unexpected service conditions, poor designs, or faulty manufacturing. Crack arrester systems can be added during service to prolong the longevity of structures with sub-critical or critical flaws. Fracture properties of different specific structures under specific services can be obtained experimentally, however, experiments are expensive and of high complexity. Alternatively, the finite element method can reduce these factors and provide reliable solutions. Finite element analysis conducted provides insight into the modeling process and the effectiveness of the simulation of fracture problems. Fracture mechanics technology in conjunction with the finite element method allows for the evaluation of the effectiveness of introducing crack arresters to a flawed structure. Additionally, the simulation of recorded crack arrester experiments alongside analytic methods are used to verify the finite element analysis results. The work in this thesis verifies the validity of using the finite element approach in designing crack arrester systems for flawed structures and suggests further investigation be done with variation in crack arrester types.