Coupling CAD and CFD codes within a virtual integration platform

The Virtual Integration Platform (VIP) is an essential component of the VIRTUE project. It provides a system for combining disparate numerical analysis methods into a simulation environment. The platform allows for defining process chains, allocating of which tools to be used, and assigning users to perform the individual tasks. The platform also manages the data that are imported into or generated within a process, so that a version history of input and output can be evaluated. Within the VIP, a re-usable template for a given process chain can be created. A process chain is composed of one or more smaller tasks. For each of these tasks, a selection of available tools can be allocated. The advanced scripting methods in the VIP use wrappers for managing the individual tools. A wrapper allows communication between the platform and the tool, and passes input and output data as necessary, in most cases without modifying the tool in any way. In this way, third-party tools may also be used without the need for access to source code or special modifications. The included case study demonstrates several advantages of using the integration platform. A parametric propeller design process couples CAD and CFD codes to adapt the propeller to given operating constraints. The VIP template helped eliminate common user errors, and captured enough expert knowledge so that the casual user could perform the given tasks with minimal guidance. Areas of improvements to in-house codes and to the overall process were identified while using the integration platform. Additionally, the process chain was designed to facilitate formal optimisation methods

Virtual integration platform for computational fluid dynamics

Computational Fluid Dynamics (CFD) tools used in shipbuilding industry involve multiple disciplines, such as resistance, manoeuvring, and cavitation. Traditionally, the analysis was performed separately and sequentially in each discipline, which often resulted in conflict and inconsistency of hydrodynamic prediction. In an effort to solve such problems for future CFD computations, a Virtual Integration Platform (VIP) has been developed in the University of Strathclyde within two EU FP6 projects - VIRTUE and SAFEDOR1. The VIP provides a holistic collaborative environment for designers with features such as Project/Process Management, Distributed Tools Integration, Global Optimisation, Version Management, and Knowledge Management. These features enhance collaboration among customers, ship design companies, shipyards, and consultancies not least because they bring together the best expertise and resources around the world. The platform has been tested in seven European ship design companies including consultancies. Its main functionalities along with advances are presented in this paper with two industrial applications

The State of Health Insurance in California: Findings From the 2003 California Health Interview Survey

Provides an overview of the shift from job-based health insurance to enrollment in public insurance programs, and discusses the advantages and disadvantages of key public policy options to extend coverage to California's uninsured residents

A collaborative platform for integrating and optimising Computational Fluid Dynamics analysis requests

A Virtual Integration Platform (VIP) is described which provides support for the integration of Computer-Aided Design (CAD) and Computational Fluid Dynamics (CFD) analysis tools into an environment that supports the use of these tools in a distributed collaborative manner. The VIP has evolved through previous EU research conducted within the VRShips-ROPAX 2000 (VRShips) project and the current version discussed here was developed predominantly within the VIRTUE project but also within the SAFEDOR project. The VIP is described with respect to the support it provides to designers and analysts in coordinating and optimising CFD analysis requests. Two case studies are provided that illustrate the application of the VIP within HSVA: the use of a panel code for the evaluation of geometry variations in order to improve propeller efficiency; and, the use of a dedicated maritime RANS code (FreSCo) to improve the wake distribution for the VIRTUE tanker. A discussion is included detailing the background, application and results from the use of the VIP within these two case studies as well as how the platform was of benefit during the development and a consideration of how it can benefit HSVA in the future

Field evaluation of passive capillary samplers for estimating groundwater recharge

Passive capillary samplers (PCAPS), which sample water from the vadose zone via a hanging water column in a fiberglass wick, have shown potential to provide superior estimates of soil water flux compared to alternative methods. The objectives of this study were to evaluate the performance of PCAPS under natural rain-fed conditions concerning (1) their operational characteristics and (2) their ability to estimate soil water flux. Forty-two PCAPS were installed in 21 commercial agricultural fields in Lane County, Oregon. Monthly measurements of soil water flux and precipitation were recorded at each site for the 4-year project duration. Of the 42 installed PCAPS, 12 samplers at six sites were inoperable or did not operate efficiently: 10 samplers were consistently below the water table, which overflowed the collection vessels rendering the samplers inoperable. Only two of the PCAPS exhibited technical failure resulting in unusually low collection efficiencies, thought to be due to a collapse of the collection vessel from oversuction during sample retrieval. On average, the 30 remaining PCAPS measured soil water flux 25% greater than that obtained from a water balance estimate. This discrepancy represents ∼8% of the total annual precipitation and irrigation each site received. PCAPS collection efficiency was found to be significantly correlated (R2 = 0.75) to the water balance yearly estimated recharge. The difference between PCAPS measured and water balance estimated percolation could be the result of inaccuracy in water balance evapotranspiration estimates and/or oversampling in the presence of high water tables. To estimate the mean yearly recharge at each site with a 30% bound on the mean at the 0.05 confidence level, eight PCAPS are required. This number corresponds closely to the results of Brandi-Dohrn et al. [1996a] and is thought to be due to intrinsic variability of percolation

English Language Proficiency and Geographical Proximity to a Safety Net Clinic as a Predictor of Health Care Access

Studies suggest that proximity to a safety net clinic (SNC) promotes access to care among the uninsured. Distance-based barriers to care may be greater for people with limited English proficiency (LEP), compared to those who are English proficient (EP), but this has not been explored. We assessed the relationship between distance to the nearest SNC and access in non-rural uninsured adults in California, and examined whether this relationship differs by language proficiency. Using the 2005 California Health Interview Survey and a list we compiled of California’s SNCs, we calculated distance between uninsured interviewee residence and the exact address of the nearest SNC. Using multivariate regression to adjust for other relevant characteristics, we examined associations between this distance and interviewee’s probability of having a usual source of health care (USOC) and having visited a physician in the prior 12 months. To examine differences by language proficiency, we included interactions between distance and language proficiency. Uninsured LEP adults living within 2 miles of a SNC were 9.3% less likely than their EP counterparts to have a USOC (P = 0.046). Further, distance to the nearest SNC was inversely associated with the probability of having a USOC among LEP, but not among EP; consequently, the difference between LEP and EP in the probability of having a USOC widened with increasing distance to the nearest SNC. There was no difference between LEP and EP adults living within 2 miles of a SNC in likelihood of having a physician visit; however, as with USOC, distance to the nearest SNC was inversely associated with the probability of having a physician visit among LEP but not EP. The effect sizes diminished, but remained significant, when we included county fixed effects in the models. Having LEP is a barrier to health care access, which compounds when combined with increased distance to the nearest SNC, among uninsured adults. Future studies should explore potential mechanisms so that appropriate interventions can be implemented

Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots

<p>Abstract</p> <p>Background</p> <p>Knottins are small, diverse and stable proteins with important drug design potential. They can be classified in 30 families which cover a wide range of sequences (1621 sequenced), three-dimensional structures (155 solved) and functions (> 10). Inter knottin similarity lies mainly between 15% and 40% sequence identity and 1.5 to 4.5 Å backbone deviations although they all share a tightly knotted disulfide core. This important variability is likely to arise from the highly diverse loops which connect the successive knotted cysteines. The prediction of structural models for all knottin sequences would open new directions for the analysis of interaction sites and to provide a better understanding of the structural and functional organization of proteins sharing this scaffold.</p> <p>Results</p> <p>We have designed an automated modeling procedure for predicting the three-dimensionnal structure of knottins. The different steps of the homology modeling pipeline were carefully optimized relatively to a test set of knottins with known structures: template selection and alignment, extraction of structural constraints and model building, model evaluation and refinement. After optimization, the accuracy of predicted models was shown to lie between 1.50 and 1.96 Å from native structures at 50% and 10% maximum sequence identity levels, respectively. These average model deviations represent an improvement varying between 0.74 and 1.17 Å over a basic homology modeling derived from a unique template. A database of 1621 structural models for all known knottin sequences was generated and is freely accessible from our web server at <url>http://knottin.cbs.cnrs.fr</url>. Models can also be interactively constructed from any knottin sequence using the structure prediction module Knoter1D3D available from our protein analysis toolkit PAT at <url>http://pat.cbs.cnrs.fr</url>.</p> <p>Conclusions</p> <p>This work explores different directions for a systematic homology modeling of a diverse family of protein sequences. In particular, we have shown that the accuracy of the models constructed at a low level of sequence identity can be improved by 1) a careful optimization of the modeling procedure, 2) the combination of multiple structural templates and 3) the use of conserved structural features as modeling restraints.</p

Local Alignment Refinement Using Structural Assessment

Homology modeling is the most commonly used technique to build a three-dimensional model for a protein sequence. It heavily relies on the quality of the sequence alignment between the protein to model and related proteins with a known three dimensional structure. Alignment quality can be assessed according to the physico-chemical properties of the three dimensional models it produces