Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, which is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,‘bottom-up’ and ‘top-down’, are illustrated. Preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.     

Multi-scale interactions in a compressible boundary layer

The properties of spectral subranges of scales in a boundary layer at Mach=2.3 and friction Reynolds number Reτ = 570 are investigated by analysing DNS data. One major aim is to examine whether footprinting and modulation of small-scale near-wall motions by outer large structures, observed at high Reynolds numbers, also pertain to this low-Reynolds-number case, or whether the logarithmic layer simply contains a continuous hierarchy of motions without specific outer scales playing a distinctive role. To this end, the spectrum of scales is decomposed into modes by application of the “Empirical Mode Decomposition”. The properties of different scales are then investigated by means of spectra, maps of isotropy/anisotropy parameters, the premultiplied derivative of the second-order structure function, correlation coefficients and joint probability density function (PDF), the last constructed from conditionally sampled data for the small-scale motions within the large-scale footprints. A clear commonality is identified between interactions in high-Reynolds-number channel flow and the present low-Reynolds-number boundary layer.     

Statistical Examination of the <Emphasis Type="Italic">a</Emphasis> and <Emphasis Type="Italic">a</Emphasis> + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions

Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue.

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Negative Ions Enhance Survival of Membrane Protein Complexes

Membrane protein complexes are commonly introduced to the mass spectrometer solubilized in detergent micelles. The collisional activation used to remove the detergent, however, often causes protein unfolding and dissociation. As in the case for soluble proteins, electrospray in the positive ion mode is most commonly used for the study of membrane proteins. Here we show several distinct advantages of employing the negative ion mode. Negative polarity can yield lower average charge states for membrane proteins solubilized in saccharide detergents, with enhanced peak resolution and reduced adduct formation. Most importantly, we demonstrate that negative ion mode electrospray ionization (ESI) minimizes subunit dissociation in the gas phase, allowing access to biologically relevant oligomeric states. Together, these properties mean that intact membrane protein ions can be generated in a greater range of solubilizing detergents. The formation of negative ions, therefore, greatly expands the possibilities of using mass spectrometry on this intractable class of protein.

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Metallization of cyanide-modified Pt(111) electrodes with copper

Journal of Solid State Electrochemistry - The reduction of Cu2+ ions irreversibly attached to the surface of a cyanide-modified Pt(111) electrode via non-covalent or weakly covalent interactions...     

Spatially Extended Networks with Singular Multi-scale Connectivity Patterns

The cortex is a very large network characterized by a complex connectivity including at least two scales: a microscopic scale at which the interconnections are non-specific and very dense, while macroscopic connectivity patterns connecting different regions of the brain at larger scale are extremely sparse. This motivates to analyze the behavior of networks with multiscale coupling, in which a neuron is connected to its \(v(N)\) nearest-neighbors where \(v(N)=o(N)\) , and in which the probability of macroscopic connection between two neurons vanishes. These are called singular multi-scale connectivity patterns. We introduce a class of such networks and derive their continuum limit. We show convergence in law and propagation of chaos in the thermodynamic limit. The limit equation obtained is an intricate non-local McKean–Vlasov equation with delays which is universal with respect to the type of micro-circuits and macro-circuits involved.     

Modifier cation (Ba,Ca, La,Y) field strength effects on aluminum and boron coordination in aluminoborosilicate glasses: the roles of fictive temperature and boron content

The field strength of modifier cations has long been known to have important effects on oxide glass properties, but effects on network structure can be complex. For two series of barium, calcium, lanthanum and yttrium aluminoborosilicates with two different B/Si ratios, we report systematic variations in boron and aluminum coordination determined by NMR, and glass transition and heat capacities from differential scanning calorimetry. Data on glasses with different fictive temperatures allow B and Al speciation to be compared on an isothermal basis, rather than as conventionally done for as-quenched structures. Temperature and compositional effects can thus be isolated. These data and comparison to previous studies on glasses with lower B/Si ratios clearly show that higher modifier cation field strength increases the fraction of five- and six-coordinated Al in all compositions. In contrast, the previously documented trend towards more three-coordinated boron (and hence more non-bridging oxygens, NBO) in low B/Si glasses with higher field strength cations reverses in high B/Si and in high NBO compositions. Al and B coordination numbers both decrease with higher fictive temperature in the glasses studied here, suggesting a simple mechanism of coupled structural change.     

Temperature-induced changes in the EPR spectrum of the magnetic center in kaolin

Studies of kaolin have revealed an effect characterized by an unusual temperature-induced change of the EPR spectrum of the Fe3+ ion, which is the magnetic probe in kaolin-clay. At low temperature (T=4.2 K) a resonance line with an effective g-value g1=4.13 +/- 0.16 is observed. At high temperature (T=288 K) one observes a resonance line with the effective g-value g2=2.15 +/- 0.1. The transition from the low- to high-temperature spectrum is gradual and it is accompanied by a redistribution of the absorption intensity. The observed properties of the temperature dependence of the EPR spectrum are characteristic of systems with a multiminimum potential.