We define a new method for global optimization, the Homotopy Optimization Method (HOM). This method differs from previous homotopy and continuation methods in that its aim is to find a minimizer for each of a set of values of the homotopy parameter, rather than to follow a path of minimizers. We define a second method, called HOPE, by allowing HOM to follow an ensemble of points obtained by perturbation of previous ones. We relate this new method to standard methods such as simulated annealing and show under what circumstances it is superior. We present results of extensive numerical experiments demonstrating performance of HOM and HOPE.
We performed molecular dynamics simulations of beta-amyloid (A{beta}) protein and A{beta} fragment(31-42) in bulk water and near hydrated lipids to study the mechanism of neurotoxicity associated with the aggregation of the protein. We constructed full atomistic models using Cerius2 and ran simulations using LAMMPS. MD simulations with different conformations and positions of the protein fragment were performed. Thermodynamic properties were compared with previous literature and the results were analyzed. Longer simulations and data analyses based on the free energy profiles along the distance between the protein and the interface are ongoing.
Over the past several years, techniques have been developed for clustering very large segments of the technical literature using sources such as Thomson ISI's Science Citation Index. The primary objective of this work has been to develop indicators of potential impact at the paper level to enhance planning and evaluation of research. These indicators can also be aggregated at different levels to enable profiling of departments, institutions, agencies, etc. Results of this work are presented as maps of science and technology with various overlays corresponding to the indicators associated with a particular search or question.
This report investigates the feasibility of applying Adaptive Mesh Refinement (AMR) techniques to a vector finite element formulation for the wave equation in three dimensions. Possible error estimators are considered first. Next, approaches for refining tetrahedral elements are reviewed. AMR capabilities within the Nevada framework are then evaluated. We summarize our conclusions on the feasibility of AMR for time-domain vector finite elements and identify a path forward.
GaN-based microwave power amplifiers have been identified as critical components in Sandia's next generation micro-Synthetic-Aperture-Radar (SAR) operating at X-band and Ku-band (10-18 GHz). To miniaturize SAR, GaN-based amplifiers are necessary to replace bulky traveling wave tubes. Specifically, for micro-SAR development, highly reliable GaN high electron mobility transistors (HEMTs), which have delivered a factor of 10 times improvement in power performance compared to GaAs, need to be developed. Despite the great promise of GaN HEMTs, problems associated with nitride materials growth currently limit gain, linearity, power-added-efficiency, reproducibility, and reliability. These material quality issues are primarily due to heteroepitaxial growth of GaN on lattice mismatched substrates. Because SiC provides the best lattice match and thermal conductivity, SiC is currently the substrate of choice for GaN-based microwave amplifiers. Obviously for GaN-based HEMTs to fully realize their tremendous promise, several challenges related to GaN heteroepitaxy on SiC must be solved. For this LDRD, we conducted a concerted effort to resolve materials issues through in-depth research on GaN/AlGaN growth on SiC. Repeatable growth processes were developed which enabled basic studies of these device layers as well as full fabrication of microwave amplifiers. Detailed studies of the GaN and AlGaN growth of SiC were conducted and techniques to measure the structural and electrical properties of the layers were developed. Problems that limit device performance were investigated, including electron traps, dislocations, the quality of semi-insulating GaN, the GaN/AlGaN interface roughness, and surface pinning of the AlGaN gate. Surface charge was reduced by developing silicon nitride passivation. Constant feedback between material properties, physical understanding, and device performance enabled rapid progress which eventually led to the successful fabrication of state of the art HEMT transistors and amplifiers.
Thiolated cyclodextrins have been shown to be useful as modifiers of electrode surfaces for application in electrochemical sensing. The adsorption of three different thiolated {beta}-cyclodextrin ({beta}-CD) derivatives onto gold (Au) electrodes was studied by monitoring ferricyanide reduction and ferrocene carboxylic acid (FCA) oxidation at the electrode surface using cyclic voltammetry. Electrodes modified with the {beta}-CD MJF-69 derivative bound FCA within the CD cavity. The monolayer acted as a conducting layer with an increase in the oxidation current. On the other hand, the {beta}-CD layer inhibited the reduction of ferricyanide at the electrode surface since ferricyanide is larger than the cavity of the {beta}-CD derivative and thus unable to form an inclusion complex.
Due to the grave public health implications and economic impact possible with the emergence of the highly pathogenic avian influenza A isolate, H5N1, currently circulating in Asia we have evaluated the efficacy of various disinfectant chemistries against surrogate influenza A strains. Chemistries included in the tests were household bleach, ethanol, Virkon S{reg_sign}, and a modified version of the Sandia National Laboratories developed DF-200 (DF-200d, a diluted version of the standard DF-200 formulation). Validation efforts followed EPA guidelines for evaluating chemical disinfectants against viruses. The efficacy of the various chemistries was determined by infectivity, quantitative RNA, and qualitative protein assays. Additionally, organic challenges using combined poultry feces and litter material were included in the experiments to simulate environments in which decontamination and remediation will likely occur. In all assays, 10% bleach and Sandia DF-200d were the most efficacious treatments against two influenza A isolates (mammalian and avian) as they provided the most rapid and complete inactivation of influenza A viruses.
We present the initial stages of development of new agent-based computational methods to generate and test hypotheses about linkages between environmental change and international instability. This report summarizes the first year's effort of an originally proposed three-year Laboratory Directed Research and Development (LDRD) project. The preliminary work focused on a set of simple agent-based models and benefited from lessons learned in previous related projects and case studies of human response to climate change and environmental scarcity. Our approach was to define a qualitative model using extremely simple cellular agent models akin to Lovelock's Daisyworld and Schelling's segregation model. Such models do not require significant computing resources, and users can modify behavior rules to gain insights. One of the difficulties in agent-based modeling is finding the right balance between model simplicity and real-world representation. Our approach was to keep agent behaviors as simple as possible during the development stage (described herein) and to ground them with a realistic geospatial Earth system model in subsequent years. This work is directed toward incorporating projected climate data--including various C02 scenarios from the Intergovernmental Panel on Climate Change (IPCC) Third Assessment Report--and ultimately toward coupling a useful agent-based model to a general circulation model.3