Onset of Convection in Porous Media Induced by Transient Heat Conduction

In this study a computational fluid dynamics (CFD) package – FLUENT/UNS was adopted to simulate the occurrence of convection in an isotropic porous media. The porous layer was homogenous and bounded by two horizontal rigid surfaces. 2-D simulation for steady state and time-dependent were conducted for the bottom surface with two boundary conditions: i) Fixed Surface Temperature – FST, ii) Constant Heat Flux – CHF. The top surface was maintained at FST boundary condition and the vertical wall was adiabatic. The 2-D steady state simulations were carried out to investigate the occurrence of convection as predicted by the linear theory. The 2-D time-dependent were conducted to investigate the possibility of adopting Tan and Thorp’s transient Rayleigh number theory in deep layer of porous media saturated with water. The CFD was successful in modeling the onset of convection in saturated porous media. The range of maximum velocity at the onset of convection and the finger shape of the thermal plume were in agreement with the literatures (Horton and Roger 1949, Elder 1968). The maximum Nusselt number based on кm for the FST and CHF boundary condition were in the range between 3-4, depending on the rate of heat transfer. The steady state and time-dependent simulation results showed no significant difference in the Rayleigh number as predicted by Lapwood (1948) Rac = 39.5, Ribando and Torrance (1976) Rac = 27.1 for the FST and CHF boundary condition. The average Rayleigh numbers based on кm for the steady state simulation were respectively 32.02 and 32.71 for the FST and CHF boundary conditions. The average transient numbers for the time-dependent simulations were respective 30.90 and 30.40 for FST and CHF boundary conditions respectively. The deviation of the Rayleigh number may be due to the complexity of the heat transfer in porous media as wide difference of thermal diffusivity of the solid and liquid that are existing in the saturated porous media. Beside this, large temperature difference ATs or heat flux qº, imposed on the porous media to induce the convection was against the assumption of perturbation theory in which allows only a small disturbance or change in density of the fluid and constant fluid properties

Using Avida to test the effects of natural selection on phylogenetic reconstruction methods

Phylogenetic trees group organisms by their ancestral relationships. There are a number of distinct algorithms used to reconstruct these trees from molecular sequence data, but different methods sometimes give conflicting results. Since there are few precisely known phylogenies, simulations are typically used to test the quality of reconstruction algorithms. These simulations randomly evolve strings of symbols to produce a tree, and then the algorithms are run with the tree leaves as inputs. Here we use Avida to test two widely used reconstruction methods, which gives us the chance to observe the effect of natural selection on tree reconstruction. We find that if the organisms undergo natural selection between branch points, the methods will be successful even on very large time scales. However, these algorithms often falter when selection is absent

Biological and functional relevance of CASP predictions.

Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo-sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo-sites), and ten sites containing important motifs, loops, or key residues with important disease-associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best-ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand-binding sites, most prediction methods have higher performance on apo-sites than holo-sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein-protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein-protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template

On-Bottom Stability Study of Non-Metallic Pipeline Due To Hydrodynamic Loadings

In order to prolong the service life, the integrity and stability of the submarine pipeline always been a concern of the oil and gas industry. However, conventional steel subsea are subjected to corrosion in sour service and even sweet service. Inspection of the subsea pipeline are frequently scheduled to ensure the integrity of the pipeline which is very costly. The non-metallic pipeline are introduced to be replacement of the steel pipeline. The non-metallic properties is known to have highly resistance to corrosion yet it also has lighter weight which lead to on-bottom stability problem. Hence, this project aim to determine the minimum weight of chain per unit length for the subsea non-metallic pipeline to be stabilized. The on-bottom stability study will based of DNV recommended practice with the use of finite element analysis package. This project also will include a finite element analysis of the submarine pipeline by using ABAQUS. The water velocity and acceleration are generated from the sea surface wave and current given the sea state in the South China Sea. The weight of chain is determine from the optimization of the simulation. The simulation’s result by using one year return waves and currents show 32.32kg/m of chain can stabilize the non-metallic pipeline with 0.7654 m lateral displacemen