Adaptive smoothing techniques for 3-D unstructured meshes

To correctly capture the behavior of deforming material volumes in 3-D, the Los Alamos unstructured grid code X3D has access to a variety of moving mesh algorithms. The authors present two such algorithms which markedly differ in their computational complexity. The first algorithm, Moving finite Elements for Surfaces, has only 2-D computational complexity, in that they only solve for interface motions and obtain volume point motions through interpolation. The second algorithm, Minimum Error Gradient Adaption, has 3-D complexity, since the volume tetrahedral deformations must be computed. Naturally, the 3-D complexity algorithm can model realistically a larger class of physical problems than the lower complexity approach. They present examples in metallic grain growth and semiconductor process modeling

3D modeling of metallic grain growth

This paper will describe simulating metallic grain growth using the Gradient Weighted Moving Finite Elements code, GRAIN3D. The authors also describe the set of mesh topology change operations developed to respond to changes in the physical topology such as the collapse of grains and to maintain uniform calculational mesh quality. Validation of the method is demonstrated by comparison to analytic calculations. The authors present results of multigrain simulations where grain boundaries evolve by mean curvature motion and include results which incorporate grain boundary orientation dependence

Capacitance extraction from complex 3D interconnect structures

A new tool has been developed for calculating the capacitance matrix for complex 3D interconnect structures involving multiple layers of irregularly shaped interconnect, imbedded in different dielectric materials. This method utilizes a new 3D adaptive unstructured grid capability, and a linear finite element algorithm. The capacitance is determined from the minimum in the total system energy as the nodes are varied to minimize the error in the electric field in the dielectric(s)

Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp.

This is the final version. Available on open access from Frontiers Media via the DOI in this recordData Availability Statement: The atomic coordinates and structure factors for the crystal structures of TsLI and its complexes have been deposited in the Protein Data Bank with the following codes: 7NZO for the native structure, 7NZP for the D-fructose bound structure, 7NZQ for the D-mannose bound structure.A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases. This is the most thermoactive and thermostable lyxose isomerase reported to date, showing activity above 95°C and retaining 60% of its activity after 60 min incubation at 80°C. This lyxose isomerase is stable in the presence of 50% (v/v) of solvents ethanol, methanol, acetonitrile and DMSO. The crystal structure of the enzyme has been resolved to 1.4–1.7 A. resolution in the ligand-free form and in complexes with both of the slowly reacting sugar substrates mannose and fructose. This thermophilic lyxose isomerase is stabilised by a disulfide bond between the two monomers of the dimeric enzyme and increased hydrophobicity at the dimer interface. These overall properties of high substrate specificity, thermostability and solvent tolerance make this lyxose isomerase enzyme a good candidate for potential industrial applications.European UnionBMBFUniversity of KielBiotechnology and Biological Sciences Research Council (BBSRC)University of Exete

EMSL and Institute for Integrated Catalysis (IIC) Catalysis Workshop

Within the context of significantly accelerating scientific progress in research areas that address important societal problems, a workshop was held in November 2010 at EMSL to identify specific and topically important areas of research and capability needs in catalysis-related science

Artificial boundaries and formulations for the incompressible Navier-Stokes equations. Applications to air and blood flows.

International audienceWe deal with numerical simulations of incompressible Navier-Stokes equations in truncated domain. In this context, the formulation of these equations has to be selected carefully in order to guarantee that their associated artificial boundary conditions are relevant for the considered problem. In this paper, we review some of the formulations proposed in the literature, and their associated boundary conditions. Some numerical results linked to each formulation are also presented. We compare different schemes, giving successful computations as well as problematic ones, in order to better understand the difference between these schemes and their behaviours dealing with systems involving Neumann boundary conditions. We also review two stabilization methods which aim at suppressing the instabilities linked to these natural boundary conditions

Maintaining tetrahedral mesh quality in response to time-dependent topological and geometrical deformation

When modeling deformation of geometrically complex regions, unstructured tetrahedral meshes provide the flexibility necessary to track interfaces as they change geometrically and topologically. In the class of time-dependent simulations considered in this paper, multimaterial interfaces are represented by sets of triangular facets, and motion of the interfaces is controlled by physical considerations. The motion of interior points in the conforming tetrahedral mesh (i.e., points not on interfaces) is arbitrary and may be chosen to produce good element shapes. In the context of specified boundary motion driven by physical considerations, they have found that a rather large glossary of mesh changes is required to allow the simulation to survive all the transitions of interface geometry and topology that occur during time evolution. This paper will describe mesh changes required to maintain good element quality as the geometry evolves, as well as mesh changes required to capture changes i n topology that occur when material regions collapse or pinch off. This paper will present a detailed description of mesh changes necessary for capturing the aforementioned geometrical and topological changes, as implemented in the code GRAIN3D, and will provide examples from a metallic grain growth simulation in which the normal velocity of the grain boundary is proportional to mean curvature

Bridging simulations and experiments in microstructure evolution

We demonstrate the importance of anisotropic interface properties in microstructure evolution by comparing computed evolved microstructures to final experimental microstructures of 5170 grains in 19 thin aluminum foil samples. This is the first time that a direct experimental validation of simulation has been performed at the level of individual grains. We observe that simulated microstructures using curvature-driven grain boundary motion and anisotropic interface properties agree well with experimentally evolved microstructures, whereas agreement is poor when isotropic properties are used. DOI: 10.1103/PhysRevLett.90.016106 PACS numbers: 68.35.-p, 68.37.Hk, 68.55.Jk, 81.40.-z This paper seeks to extend previous statistical comparisons of predicted and experimentally observed grain boundary network evolution by demonstrating agreement at the scale of individual grains, provided that the anisotropy of interfacial energy and mobility is included. With very few exceptions [1], only statistical comparisons have been made such as determining the exponent in the power-law relationship between average radius and time. In addition to this general aim, we consider coarsening in networks of low angle grain boundaries (subgrains), which has been the subject of some controversy. Some authors have postulated that the interfaces are essentially sessile because they are themselves networks of lattice dislocations and that coarsening occurs by rotation of individual subgrains We have previously shown a strong agreement between small-scale grain growth experiments and anisotropic three-dimensional simulations [5] obtained from electron backscatter diffraction (EBSD) measurements Our simulation model uses curvature-driven motion implemented by GRAIN3D ( ). The grain boundary mobility is low for small misorientations but undergoes a sharp transition to high mobilities between 10 and 15 in misorientation which is in agreement with the literature [12 -14]. For our simulations, we assume that all high angle grain boundaries (> 15 ) have the same values of energy and mobility. The occurrence of high angle boundaries is very low in this material, which means that only a small error is introduced by this assumption. This experiment permitted a verification of curvature-driven interface motio

X3D moving grid methods for semiconductor applications

The Los Alamos 3D grid toolbox handles grid maintenance chores and provides access to a sophisticated set of optimization algorithms for unstructured grids. The application of these tools to semiconductor problems is illustrated in three examples: grain growth, topographic deposition and electrostatics. These examples demonstrate adaptive smoothing, front tracking, and automatic, adaptive refinement/derefinement