Thesis (M.S. in Systems Engineering)--Naval Postgraduate School, December 2009. / Thesis Advisor(s): Langford, Gary O. ; Franck, Raymond. Second Reader: Rummel, John P. "December 2009." Description based on title screen as viewed on January 27, 2010. Author(s) subject terms: Peer Production, Crowd Sourcing, Collaboration, Web 2.0, Peer to peer, P2P. Includes bibliographical references (p. 139-140). Also available in print.

Up until recently, unsignalized nodes have been either ignored or inadequately represented in Dynamic Traffic Assignment (DTA) models. This is due to the difficult nature of incorporating internal node conflicts into dynamic flow models. It was thought or assumed that these nodes had little impact on overall model results, but evidence from testing in Visual Interactive System for Transportation Algorithms (VISTA), a DTA model, reveals that may not be the case. This paper explores recent attempts at characterizing stop sign effects within DTA flow models. From previous studies, it has been found that incorporating these unsignalized and priority movements internal to the flow model requires large amounts of computational power, are challenging to make efficient, and lead to a multiple or infinite solution space. Based on these findings, a deterministic approach is both impractical and likely impossible in the existing framework of the Cell Transmission (CTM) and Link Transmission (LTM) models commonly used in DTA. Thus, a method of utilizing empirical relationships based on information readily available in these models may be a more acceptable approach. Microsimulation is much more suitable for modeling these types of interactions and is capable of producing results near to reality. For this reason, microsimulation was chosen as a viable method for developing empirical relationships of such complex interactions to then be used as inputs into the macroscopic flow models of DTA. This paper presents a model developed to calculate delays expected by vehicles at stop approaches based on information that can be taken from a dynamic flow model such as CTM and LTM models. This model is validated by video data recorded and analyzed for accuracy. Potential uses and probable implementations of the model are explored to appropriately incorporate unsignalized and priority movements into existing flow models. / text

What materials designers most envy is nature’s building design. It has long been a dream for scientists to mimic and further engineer the behaviors, interactions, and reactions of biomolecules beyond experimental limits. To interpret and facilitate novel materials’ design, a hierarchical approach is presented in this dissertation. With the advent of molecular modeling, many biomolecular interactions can be studied. Using both computational and experimental approaches, we investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dipeptides (which are called “biomimetic materials”) including Fmoc-dialanine (Fmoc-AA) and Fmoc-Alanine-Lactic acid (Fmoc-ALac) molecules. We simulated the assembly of Fmoc-dipeptides and compared with experiments. We illustrated not only the angstrom-scale self-assembled structures, but also a prevalent polyproline II conformation with β-sheet-like hydrogen bonding pattern among short peptides. Further, simulations to calculate the potential of mean force (PMF) and melting temperatures were performed to gain deeper insights into the inter-fibril interaction. An energetic preference for fibril-fibril surface contact was demonstrated for the first time, which arises from a fibril-level amphiphilicity. From our study, a hierarchical self-assembly process mediated by the balance between hydrophobicity and hydrophilicity of fibril structures was unveiled. The next major topic in this dissertation involves the development of a chemically accurate polarizable multipole-based molecular mechanics model with the investigation of a series of chloromethanes. The ability of molecular modeling to make prediction is determined by the accuracy of underlying physical model. The traditional fixed-charge based force field is severely limited when applied to highly charged systems, halogen, phosphate and sulfate compounds. Via a sophisticated electrostatic model, an accurate description of electrostatics in organochlorine compounds and halogen bonds were achieved. Our model demonstrated its advantages by reproducing the experimental density and heat of vaporization; besides, the calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes were all in good agreement with experimental and ab initio data. / text

Before 1971, all the electronics were based on three basic circuit elements. Until a professor from UCBerkeley reasoned that another basic circuit element exists, which he called memristor; characterized bythe relationship between the charge and the flux-linkage. A memristor is essentially a resistor withmemory. The resistance of a memristor (memristance) depends on the amount of current that is passingthrough the device. In 2008, a research group at HP Labs succeeded to build an actual physical memristor. HP's memristorwas a nanometer scale titanium dioxide thin film, composed of two doped and undoped regions,sandwiched between two platinum contacts. After this breakthrough, a huge amount of research startedwith the aim of better realization of the device and discovering more possible applications of thememristor. In this report, it is attempted to cover a proper amount of information about the history, introduction,implementation, modeling and applications of the device. But the main focus of this study is onmemristor modeling. Four papers on modeling of the memristor were considered, and since there wereno cadence models available in the literature at the time, it was decided to develop some cadencemodels. So, cadence models from the mentioned papers were designed and simulated. From the samemodeling papers some veriloga models were written as well. Unfortunately, due to some limitation of thedesign tool, some of the models failed to provide the expected results, but still the functioning modelsshow satisfactory results that can be used in the circuit simulations of memristors.

Thesis (M.S. in Operations Research)--Naval Postgraduate School, June 2008. / Thesis Advisor(s): Brown, Gerald. "June 2008." Description based on title screen as viewed on August 26, 2008. Includes bibliographical references (p.79-82). Also available in print.

Thesis (M.S. in Operations Research)--Naval Postgraduate School, June 2008. / Thesis Advisor(s): Brown, Gerald. "June 2008." Includes bibliographical references (p.79-82). Also available in print.

The purpose of this research was to identify the forcing factors and processes of sediment transport in Perdido Bay. Data were collected from Perdido Bay in July 2011 and used in the development of a three-dimensional sediment transport model using EFDC as well as in the estimation of a sediment budget. Water and bed samples, water quality readings for salinity, temperature, dissolved oxygen, turbidity, depth, and pH, and velocity measurements were collected. Using field and historical data, an EFDC model was created to simulate the processes of salinity and sediment transport. The model successfully demonstrated the movement of sediment through the bay and proved the existence of a turbidity maximum in the northern bay. From this research, it was determined that freshwater inflow is the primary forcing factor in sedimentation and is the main contributor to sediment entering the bay.

Peripheral neuropathies, affect approximately 20 million people in the United States and are often a complication of conditions such as diabetes that can result in amputation of affected areas such as the feet and toes. In vitro methodologies to facilitate the understanding and treatment of these disorders often lack the cellular and functional complexity required to accurately model peripheral neuropathies. In particular, they are often 2-D and functional readouts, such as electrical activity, are limited to cell bodies thereby limiting the understanding of axonopathy which often characterizes these disorders. We have developed a functional 3-D model of peripheral nerves using a capillary alginate gel (Capgel™), as a scaffold. We hypothesize that: 1) The unique microcapillary structure of Capgel™ allows for the modeling of the 3-D microstructure of the peripheral nerve, and 2) That axon bundling in the capillary allows for the detection of axonal electrical activity. In our initial studies, we demonstrate that culturing embryonic dorsal root ganglia (DRG) within the Capgel™ environment allows for the separation of cell bodies from axons and recreates many of the features of an in vivo peripheral nerve fascicle including myelinated axons and the formation of a rudimentary perineurium. To develop functionality for this model we have integrated the DRG Capgel™ culture with a microelectrode array to examine spontaneous activity in axon bundles, which we find demonstrates superiority to other widely used 2-D models of the same tissue. Furthermore, by analyzing the activity on individual electrodes, we were able to record action potentials from multiple axons within the same bundle indicating a functional complexity comparable to that observed in fascicles in vivo. This 3D model of the peripheral nerve can be used to study the functional complexities of peripheral neuropathies and nerve regeneration as well as being utilized in the development of novel therapeutics.

This research includes a sensitivity analysis of channel geometry and model assumptions in 1 dimensional (1D) dam break analysis. The specific modeling assumptions that are analyzed include, breach development time, breach width, and breach side-slopes. The question always arises when doing 1D dam break modeling of how detailed does the geometry data need to be to answer the subject question within an acceptable tolerance. LIDAR data and bathymetric data used for channel characteristic add significant detail to the model geometry as opposed to using course gridded data such as the USGS 10 meter Digital Elevation Models (DEMs). However, as geometry detail increases so does model development time, model run time, and cost to retrieve data. This research analyzes the level of error introduced in model results from accuracy of channel geometry as compared to the level of error introduced from assumption made in breach characteristic.

This thesis presents the modeling approaches and the challenges involved in electromagnetic modeling of packaging layout. It discusses the methodologies that are being used today. It then applies these methodologies to analyze, model and characterize three packaging technologies: (i) the wirebond technology, (ii) The Metal Post Interconnected Parallel Plate Structure, and the (iii) Multi Layer Structure. The model developed is validated through experimentation. These models are then used in simulation in order to compare the electrical performance of the packaging technologies. Finally some problems with the existing designs are pointed out, and suggestions (both local and generic) are given to improve the layout design. / Master of Science