Lattice Modeling of Early-Age Behavior of Structural Concrete.

The susceptibility of structural concrete to early-age cracking depends on material composition, methods of processing, structural boundary conditions, and a variety of environmental factors. Computational modeling offers a means for identifying primary factors and strategies for reducing cracking potential. Herein, lattice models are shown to be adept at simulating the thermal-hygral-mechanical phenomena that influence early-age cracking. In particular, this paper presents a lattice-based approach that utilizes a model of cementitious materials hydration to control the development of concrete properties, including stiffness, strength, and creep resistance. The approach is validated and used to simulate early-age cracking in concrete bridge decks. Structural configuration plays a key role in determining the magnitude and distribution of stresses caused by volume instabilities of the concrete material. Under restrained conditions, both thermal and hygral effects are found to be primary contributors to cracking potential

Flooding and Inundation Modeling in the Great Bay Estuary

As part of this research, FVCOM, a finite-volume coastal ocean numerical hydrodynamic model (Chen, et al., 2003), was implemented into the Great Bay estuary. FVCOM is one of several community models that have been developed for coastal regions, and was selected because it utilizes an unstructured grid to discretize the model domain. The unstructured grid provides the ability to have fine scale resolution near the boundary or coastline and decreased resolution away from the boundary where the flow field is less complicated, resulting in greatly reduced computational expense in less dynamic regions allowing model runs to be completed in much shorter time periods. Grid development also requires that bathymetric data is accurately assigned to grid nodes in such a way that the model itself will be numerically stable. This requires significant development time implementing an appropriate grid mesh (Persson and Strang, 2004) with bathymetry data that has been smoothed to limit inherent numerical noise in the computations. FVCOM was implemented on a grid with finest resolution equaling 30 m, and then tested on a 10 day run with offshore forcing determined analytically by the 8 most energetic semi-diurnal (M2, N2, S2, K2) and diurnal (K1, O1, P1, Q1) tidal constituents at Fort Pt., NH (https://tidesandcurrents.noaa.gov/harcon.html?id=8423898), and including fresh water river fluxes from 6 rivers equivalent to 5 times the average daily discharge (Ward and Bub, 2007). The model was further tested utilizing the 100 year tropical storm event estimated from the North Atlantic Coast Comprehensive Study (NACCS; USACE, 2015), and the highest projected sea level rise scenario for year 2100 estimated by NOAA (http://www.corpsclimate.us/ccaceslcurves.cfm). The numerically stable model indicates that the grid can be used to simulate tidal forcing with maximum projected year storm surge and sea level rise in the Great Bay, and – with further development to include finer (10 m) mesh resolution and inclusion of surface waves and wind forcing – may be able to predict future flooding scenarios based on forecasted storm events and sea level rise

Doctor of Philosophy

dissertationConfocal microscopy has become a popular imaging technique in biology research in recent years. It is often used to study three-dimensional (3D) structures of biological samples. Confocal data are commonly multichannel, with each channel resulting from a different fluorescent staining. This technique also results in finely detailed structures in 3D, such as neuron fibers. Despite the plethora of volume rendering techniques that have been available for many years, there is a demand from biologists for a flexible tool that allows interactive visualization and analysis of multichannel confocal data. Together with biologists, we have designed and developed FluoRender. It incorporates volume rendering techniques such as a two-dimensional (2D) transfer function and multichannel intermixing. Rendering results can be enhanced through tone-mappings and overlays. To facilitate analyses of confocal data, FluoRender provides interactive operations for extracting complex structures. Furthermore, we developed the Synthetic Brainbow technique, which takes advantage of the asynchronous behavior in Graphics Processing Unit (GPU) framebuffer loops and generates random colorizations for different structures in single-channel confocal data. The results from our Synthetic Brainbows, when applied to a sequence of developing cells, can then be used for tracking the movements of these cells. Finally, we present an application of FluoRender in the workflow of constructing anatomical atlases

A framework for local terrain deformation based on diffusion theory

Terrains have a key role in making outdoor virtual scenes believable and immersive as they form the support for every other natural element in the scene. Although important, terrains are often given limited interactivity in real-time applications. However, in nature, terrains are dynamic and interact with the rest of the environment changing shape on different levels, from tracks left by a person running on a gravel soil (micro-scale), to avalanches on the side of a mountain (macro-scale). The challenge in representing dynamic terrains correctly is that the soil that forms them is vastly heterogeneous and behaves differently depending on its composition. This heterogeneity introduces difficulties at different levels in dynamic terrains simulations, from modelling the large amount of different elements that compose the oil to simulating their dynamic behaviour. This work presents a novel framework to simulate multi-material dynamic terrains by taking into account the soil composition and its heterogeneity. In the proposed framework soil information is obtained from a material description map applied to the terrain mesh. This information is used to compute deformations in the area of interaction using a novel mathematical model based on diffusion theory. The deformations are applied to the terrain mesh in different ways depending on the distance of the area of interaction from the camera and the soil material. Deformations away from the camera are simulated by dynamically displacing normals. While deformations in a neighbourhood of the camera are represented by displacing the terrain mesh, which is locally tessellated to better fit the displacement. For gravel based soils the terrain details are added near the camera by reconstructing the meshes of the small rocks from the texture image, thus simulating both micro and macro-structure of the terrain. The outcome of the framework is a realistic interactive dynamic terrain animation in real-time

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: 1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. 2) The highly different accessibility in the membrane and water regions are addressed with a two-step, two-probe grid labeling procedure, and 3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 {\AA} for globular proteins is a very reasonable default value for membrane protein simulations. It gives an overall minimum number of inconsistencies between the continuum and explicit representations of water distributions in membrane channel proteins, at least in the water accessible pore/channel regions that we focus on. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe a good agreement with experiment results.Comment: 40 pages, 6 figures, 5 table

Memristors for the Curious Outsiders

We present both an overview and a perspective of recent experimental advances and proposed new approaches to performing computation using memristors. A memristor is a 2-terminal passive component with a dynamic resistance depending on an internal parameter. We provide an brief historical introduction, as well as an overview over the physical mechanism that lead to memristive behavior. This review is meant to guide nonpractitioners in the field of memristive circuits and their connection to machine learning and neural computation.Comment: Perpective paper for MDPI Technologies; 43 page

High-Performance Integrated Window and Façade Solutions for California

The researchers developed a new generation of high-performance façade systems and supporting design and management tools to support industry in meeting California’s greenhouse gas reduction targets, reduce energy consumption, and enable an adaptable response to minimize real-time demands on the electricity grid. The project resulted in five outcomes: (1) The research team developed an R-5, 1-inch thick, triplepane, insulating glass unit with a novel low-conductance aluminum frame. This technology can help significantly reduce residential cooling and heating loads, particularly during the evening. (2) The team developed a prototype of a windowintegrated local ventilation and energy recovery device that provides clean, dry fresh air through the façade with minimal energy requirements. (3) A daylight-redirecting louver system was prototyped to redirect sunlight 15–40 feet from the window. Simulations estimated that lighting energy use could be reduced by 35–54 percent without glare. (4) A control system incorporating physics-based equations and a mathematical solver was prototyped and field tested to demonstrate feasibility. Simulations estimated that total electricity costs could be reduced by 9-28 percent on sunny summer days through adaptive control of operable shading and daylighting components and the thermostat compared to state-of-the-art automatic façade controls in commercial building perimeter zones. (5) Supporting models and tools needed by industry for technology R&D and market transformation activities were validated. Attaining California’s clean energy goals require making a fundamental shift from today’s ad-hoc assemblages of static components to turnkey, intelligent, responsive, integrated building façade systems. These systems offered significant reductions in energy use, peak demand, and operating cost in California