Numerical modelling of flows involving submerged bodies and free surfaces

Kinetic energy extraction devices for ocean and river flows are often located in the vicinity of the fluid free surface. This differs from wind turbines where the atmosphere may be considered to extend to infinity for the purposes of numerical modelling. As most kinetic energy extraction devices are based on lifting surfaces, a numerical model is sought which can model both lifting and free surface flows. One such model is the boundary element method which has been successfully applied to free surface problems and to lifting flows as well as the combined problem. This study seeks to develop a high order boundary element method that is capable of modelling unsteady lifting and free surface flows in three dimensions. Although high order formulations of boundary element methods are common for free surface problems, providing improved accuracy and computational time, their usage for lifting flows is less frequent. This may be due to the hypersingular boundary integral equation (HBIE) which must be solved in order to find the velocity of the vortex wakes behind lifting surfaces. In previous lifting flow studies using high order boundary element methods the wake velocities have been determined at the element centres and then interpolated to the collocation points. Not until the paper of Gray et al. (2004b) has a method been available for the direct solution of the HBIEs at the edges of three dimensional high order elements with C0 continuous interfaces. The solution employs a technique known as the Galerkin boundary element method. This study shows, for the first time, that the Galerkin boundary element method is applicable to the solution of the HBIE on the vortex wake of a lifting body. The application of the technique is then demonstrated as part of the numerical model developed herein. The model is based on the high order boundary element method developed by Xu (1992) for non-linear free surface flows. This formulation is extended to include steady uniform flow throughout the computational domain as well as the presence of lifting and non-lifting bodies. Several verification cases are implemented to test the accuracy of the model

Reducing variability in the cost of energy of ocean energy arrays

Variability in the predicted cost of energy of an ocean energy converter array is more substantial than for other forms of energy generation, due to the combined stochastic action of weather conditions and failures. If the variability is great enough, then this may influence future financial decisions. This paper provides the unique contribution of quantifying variability in the predicted cost of energy and introduces a framework for investigating reduction of variability through investment in components. Following review of existing methodologies for parametric analysis of ocean energy array design, the development of the DTOcean software tool is presented. DTOcean can quantify variability by simulating the design, deployment and operation of arrays with higher complexity than previous models, designing sub-systems at component level. A case study of a theoretical floating wave energy converter array is used to demonstrate that the variability in levelised cost of energy (LCOE) can be greatest for the smallest arrays and that investment in improved component reliability can reduce both the variability and most likely value of LCOE. A hypothetical study of improved electrical cables and connectors shows reductions in LCOE up to 2.51% and reductions in the variability of LCOE of over 50%; these minima occur for different combinations of components.The research leading to this publication is part of the DTOceanPlus project which has received funding from the EuropeanUnion's Horizon 2020 research and innovation programme under grant agreement No 785921. Funding was also received from the European Community's Seventh Framework Programme for the DTOcean Project (grant agreement No. 608597). The contribution of Sandia National Laboratories was funded by the U.S. Department of Energy's Water Power Technologies Office. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy or the United States Government. The image of the RM3 device, in Fig. 7, was reproduced with the permission of Sandia National Laboratorie

Recruitment of a SAP18-HDAC1 Complex into HIV-1 Virions and Its Requirement for Viral Replication

HIV-1 integrase (IN) is a virally encoded protein required for integration of viral cDNA into host chromosomes. INI1/hSNF5 is a component of the SWI/SNF complex that interacts with HIV-1 IN, is selectively incorporated into HIV-1 (but not other retroviral) virions, and modulates multiple steps, including particle production and infectivity. To gain further insight into the role of INI1 in HIV-1 replication, we screened for INI1-interacting proteins using the yeast two-hybrid system. We found that SAP18 (Sin3a associated protein 18 kD), a component of the Sin3a-HDAC1 complex, directly binds to INI1 in yeast, in vitro and in vivo. Interestingly, we found that IN also binds to SAP18 in vitro and in vivo. SAP18 and components of a Sin3A-HDAC1 complex were specifically incorporated into HIV-1 (but not SIV and HTLV-1) virions in an HIV-1 IN–dependent manner. Using a fluorescence-based assay, we found that HIV-1 (but not SIV) virion preparations harbour significant deacetylase activity, indicating the specific recruitment of catalytically active HDAC into the virions. To determine the requirement of virion-associated HDAC1 to HIV-1 replication, an inactive, transdominant negative mutant of HDAC1 (HDAC1H141A) was utilized. Incorporation of HDAC1H141A decreased the virion-associated histone deacetylase activity. Furthermore, incorporation of HDAC1H141A decreased the infectivity of HIV-1 (but not SIV) virions. The block in infectivity due to virion-associated HDAC1H141A occurred specifically at the early reverse transcription stage, while entry of the virions was unaffected. RNA-interference mediated knock-down of HDAC1 in producer cells resulted in decreased virion-associated HDAC1 activity and a reduction in infectivity of these virions. These studies indicate that HIV-1 IN and INI1/hSNF5 bind SAP18 and selectively recruit components of Sin3a-HDAC1 complex into HIV-1 virions. Furthermore, HIV-1 virion-associated HDAC1 is required for efficient early post-entry events, indicating a novel role for HDAC1 during HIV-1 replication

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

Numerical modelling of flows involving submerged bodies and free surfaces

Kinetic energy extraction devices for ocean and river flows are often located in the vicinity of the fluid free surface. This differs from wind turbines where the atmosphere may be considered to extend to infinity for the purposes of numerical modelling. As most kinetic energy extraction devices are based on lifting surfaces, a numerical model is sought which can model both lifting and free surface flows. One such model is the boundary element method which has been successfully applied to free surface problems and to lifting flows as well as the combined problem. This study seeks to develop a high order boundary element method that is capable of modelling unsteady lifting and free surface flows in three dimensions. Although high order formulations of boundary element methods are common for free surface problems, providing improved accuracy and computational time, their usage for lifting flows is less frequent. This may be due to the hypersingular boundary integral equation (HBIE) which must be solved in order to find the velocity of the vortex wakes behind lifting surfaces. In previous lifting flow studies using high order boundary element methods the wake velocities have been determined at the element centres and then interpolated to the collocation points. Not until the paper of Gray et al. (2004b) has a method been available for the direct solution of the HBIEs at the edges of three dimensional high order elements with C0 continuous interfaces. The solution employs a technique known as the Galerkin boundary element method. This study shows, for the first time, that the Galerkin boundary element method is applicable to the solution of the HBIE on the vortex wake of a lifting body. The application of the technique is then demonstrated as part of the numerical model developed herein. The model is based on the high order boundary element method developed by Xu (1992) for non-linear free surface flows. This formulation is extended to include steady uniform flow throughout the computational domain as well as the presence of lifting and non-lifting bodies. Several verification cases are implemented to test the accuracy of the model.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

sphinx-contrib/matlabdomain: 0.20.1

A Sphinx extension for documenting Matlab cod

sphinx-contrib/matlabdomain: 0.20.0

A Sphinx extension for documenting Matlab cod

sphinx-contrib/matlabdomain: 0.21.4rc2

A Sphinx extension for documenting Matlab cod

WEC-Sim/WEC-Sim: v6.0

<h2>New Features</h2> <ul> <li>initial commit largeXYDispOption by @dforbush2 in https://github.com/WEC-Sim/WEC-Sim/pull/877</li> <li>Update coordinate system figure by @JiaMiGit in https://github.com/WEC-Sim/WEC-Sim/pull/931</li> <li>Property validation for WEC-Sim objects by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/904</li> <li>Dev: adding ampSpectraForWS function by @dforbush2 in https://github.com/WEC-Sim/WEC-Sim/pull/907</li> <li>Customizable DOFs for plotBEMIO by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/944</li> <li>Calculation_of_Ainf_using_radiationIRF.m by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/946</li> <li>Update citation names by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/954</li> <li>Update getDofNames() by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/957</li> <li>included readCAPYTAINE() argument to explicitly define KH.dat & Hydro… by @dav-og in https://github.com/WEC-Sim/WEC-Sim/pull/962</li> <li>Extract mask variable by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/958</li> <li>Add tests to check that SLX file versions do not exceed R2020b by @H0R5E in https://github.com/WEC-Sim/WEC-Sim/pull/919</li> <li>Products of Inertia in WEC-Sim by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/981</li> <li>Pull bug fixes #954, #999, #1002 from master into dev by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/1011</li> <li>updating readNEMOH based on #983 by @kmruehl in https://github.com/WEC-Sim/WEC-Sim/pull/990</li> <li>Remove 'fixed' mass option from OSWEC input file by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1022 and https://github.com/WEC-Sim/WEC-Sim/pull/1024</li> <li>Save the applied added mass time series by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/1023</li> <li>Update tutorials by @kmruehl in https://github.com/WEC-Sim/WEC-Sim/pull/1030</li> <li>Control applications docs by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1018</li> <li>Update read- and writeBEMIOH5 to allow for pressure integration for mean drift by @nathanmtom in https://github.com/WEC-Sim/WEC-Sim/pull/1046</li> <li>Add function to read h5 file to hydro data structure by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1048</li> <li>Update radiationIRF.m by @nathanmtom in https://github.com/WEC-Sim/WEC-Sim/pull/1045</li> <li>Normalize quaternion to increase simulation robustness by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/1049</li> <li>Plot bemio features by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1034</li> <li>Updates to Morison Element Implementation by @nathanmtom in https://github.com/WEC-Sim/WEC-Sim/pull/1052</li> <li>Moving PTO-Sim to main WEC-Sim library by @jleonqu in https://github.com/WEC-Sim/WEC-Sim/pull/1057</li> <li>Add windows runner to dev branch unit test workflow by @H0R5E in https://github.com/WEC-Sim/WEC-Sim/pull/1061</li> <li>Update docs dependencies by @H0R5E in https://github.com/WEC-Sim/WEC-Sim/pull/1080</li> <li>Type property pto sim by @jleonqu in https://github.com/WEC-Sim/WEC-Sim/pull/1064</li> <li>Added mass updates by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/1058</li> <li>Feature paraview by @agmoore4 in https://github.com/WEC-Sim/WEC-Sim/pull/1081</li> <li>Paraview documentation hyperlink fix by @agmoore4 in https://github.com/WEC-Sim/WEC-Sim/pull/1093</li> <li>use capytaine v2 to compute hydrostatics by @dav-og in https://github.com/WEC-Sim/WEC-Sim/pull/1092</li> <li>Update paraview doc images by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1098</li> <li>readNEMOH update to be compatible with v3.0.0 release (but not QTF) by @nathanmtom in https://github.com/WEC-Sim/WEC-Sim/pull/1087</li> <li>Add simple direct drive PTO model by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1106</li> <li>Control+pto docs by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1108</li> <li>MOST Capabilities - Continuation by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/1127</li> <li>Implement an FIR filter to calculate radiation forces by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/1071</li> <li>Updating documentation to include links for the Advanced Features Web… by @jleonqu in https://github.com/WEC-Sim/WEC-Sim/pull/1126</li> <li>Multiple Wave Spectra by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/1130</li> <li>Update WECSim_Lib_Body_Elements.slx for N Waves Applications by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/1133</li> <li>Update to MoorDyn v2 by @RyanDavies19 in https://github.com/WEC-Sim/WEC-Sim/pull/1134</li> <li>Updating WEC-Sim tests for dev branch by @kmruehl in https://github.com/WEC-Sim/WEC-Sim/pull/1142</li> </ul> <h2>Bug Fixes</h2> <ul> <li>Remove fixed mass option by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/856</li> <li>Move run('stopWecSim') to wecSim.m by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/885</li> <li>Pull bug fixes into dev by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/900</li> <li>Save slx files in 2020b fixes #920 by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/923</li> <li>Fix readCAPYTAINE by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/884</li> <li>Fixes saveViz feature for elevation import by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/929</li> <li>Fix wave elevation import with rampTime = 0 by @jtgrasb in https://github.com/WEC-Sim/WEC-Sim/pull/917</li> <li>readCapytaine_fixes_for_reading_dataformats_correctly by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/947</li> <li>Pull #954 into dev by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/955</li> <li>Bug fix for direction in readCapytaine by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/999</li> <li>Fix sign bug reported on issue #993 by @jleonqu in https://github.com/WEC-Sim/WEC-Sim/pull/1002</li> <li>Dev: reverts PR 910, fixing error in nonLinearBuoyancy by @dforbush2 in https://github.com/WEC-Sim/WEC-Sim/pull/1017</li> <li>Fix the transpose of linear restoring matrix to make roll mode rows to be 0 by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/1032</li> <li>Bugfix resolving documentation build error by @kmruehl in https://github.com/WEC-Sim/WEC-Sim/pull/1059</li> <li>fix_readWAMIT_and_writeBEMIOh5 by @salhus in https://github.com/WEC-Sim/WEC-Sim/pull/1065</li> <li>Pulling master bugfixes into dev by @kmruehl in https://github.com/WEC-Sim/WEC-Sim/pull/1101</li> <li>Bug fixes for v6.0 by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/1136</li> <li>Path fix for BEMIO example by @akeeste in https://github.com/WEC-Sim/WEC-Sim/pull/1144</li> </ul> <h2>New Contributors</h2> <ul> <li>@JiaMiGit made their first contribution in https://github.com/WEC-Sim/WEC-Sim/pull/931</li> <li>@agmoore4 made their first contribution in https://github.com/WEC-Sim/WEC-Sim/pull/1081</li> <li>@RyanDavies19 made their first contribution in https://github.com/WEC-Sim/WEC-Sim/pull/1134</li> </ul> <h2>Issues and Pull Reqeusts</h2> <ul> <li>>130 issues closed since v5.0.1</li> <li>>74 PRs merged since v5.0.1</li> <li><strong>v6.0 Changelog</strong>: https://github.com/WEC-Sim/WEC-Sim/compare/v5.0.1...v6.0</li> </ul&gt