Developing numerical libraries in Java

The rapid and widespread adoption of Java has created a demand for reliable and reusable mathematical software components to support the growing number of compute-intensive applications now under development, particularly in science and engineering. In this paper we address practical issues of the Java language and environment which have an effect on numerical library design and development. Benchmarks which illustrate the current levels of performance of key numerical kernels on a variety of Java platforms are presented. Finally, a strategy for the development of a fundamental numerical toolkit for Java is proposed and its current status is described.Comment: 11 pages. Revised version of paper presented to the 1998 ACM Conference on Java for High Performance Network Computing. To appear in Concurrency: Practice and Experienc

Rigidity analysis of HIV-1 protease

We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes significantly in the presence of an inhibitor. Our study shows that the action of the inhibitors is to restrict the flexibility of the beta-hairpin flaps which allow access to the active site. The results are discussed in the context of full molecular dynamics simulations as well as data from NMR experiments.Comment: 4 pages, 3 figures. Conference proceedings for CMMP conference 2010 which was held at the University of Warwic

Comparative analysis of rigidity across protein families

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks

Adatom Bonding Sites in a Nickel-Fe₃O₄(001) Single-Atom Model Catalyst and O₂ Reactivity Unveiled by Surface Action Spectroscopy with Infrared Free-Electron Laser Light

Single-atom (SA) catalysis presently receives much attention with its promise to decrease the cost of the active material while increasing the catalyst’s performance. However, key details such as the exact location of SA species and their stability are often unclear due to a lack of atomic level information. Here, we show how vibrational spectra measured with surface action spectroscopy (SAS) and density functional theory (DFT) simulations can differentiate between different adatom binding sites and determine the location of Ni and Au single atoms on Fe3O4. We reveal that Ni and Au adatoms selectively bind to surface oxygen ions which are octahedrally coordinated to Fe ions. In addition, we find that the Ni adatoms can activate O2 to superoxide in contrast to the bare surface and Ni in subsurface positions. Overall, we unveil the advantages of combining SAS and DFT for improving the understanding of single-atom catalysts

Tracking heterogeneous structural motifs and the redox behaviour of copper-zinc nanocatalysts for the electrocatalytic CO₂ reduction using operando time resolved spectroscopy and machine learning

Copper-based catalysts are established catalytic systems for the electrocatalytic CO2 reduction reaction (CO2RR), where wasteful CO2 is converted into valuable industrial resources, such as energy-dense C2+ products, using energy from renewable sources. However, better control over the catalyst selectivity, especially at industrially relevant high current density conditions is needed to expedite the economically viability of the CO2RR. For this purpose, bimetallic materials, where copper is combined with a secondary metal, comprise a promising and a highly tunable catalyst for CO2RR. However, the synergy between copper and the selected secondary metal species, the evolution of the bimetallic structural motifs under working conditions and the effect of the secondary metal on the kinetics of the Cu redox behavior require careful investigation. Here, we employ operando quick X-ray absorption spectroscopy (QXAFS), coupled with machine-learning based data analsysis and surface-enhanced Raman spectroscopy (SERS) to investigate the time-dependent chemical and structural changes in catalysts derived from shape-selected Zn/Cu2O nanocubes under CO2RR conditions at current densities up to -500 mA/cm2. We furthermore relate the transformation observed under working conditions to the catalytic activity and selectivity and correlate potential-dependent surface and subsurface processes. We report that the addition of Zn to a Cu-based catalyst has crucial impact on the kinetics of subsurface processes, while redox processes of the Cu surface layer remain largely unaffected. Interestingly, the presence of Zn was found to contribute to the stabilization of cationic Cu(I) species, which is of catalytic relevance since Cu(0)/Cu(I) interfaces have been reported beneficial for the efficient CO2 conversion to complex multicarbon products. At the same time, we attribute the increase of the C2+ product selectivity to the formation of Cu-rich CuZn alloys in samples with low Zn content, while Zn-rich alloy phases result in an increased formation of CO paralleled by an increase of the parasitic hydrogen evolution reaction

Adatom Bonding Sites in a Nickel-Fe₃O₄(001) Single-Atom Model Catalyst and O₂ Reactivity Unveiled by Surface Action Spectroscopy with Infrared Free-Electron Laser Light

Single-atom (SA) catalysis presently receives much attention with its promise to decrease the cost of the active material while increasing the catalyst’s performance. However, key details such as the exact location of SA species and their stability are often unclear due to a lack of atomic level information. Here, we show how vibrational spectra measured with surface action spectroscopy (SAS) and density functional theory (DFT) simulations can differentiate between different adatom binding sites and determine the location of Ni and Au single atoms on Fe3O4. We reveal that Ni and Au adatoms selectively bind to surface oxygen ions which are octahedrally coordinated to Fe ions. In addition, we find that the Ni adatoms can activate O2 to superoxide in contrast to the bare surface and Ni in subsurface positions. Overall, we unveil the advantages of combining SAS and DFT for improving the understanding of single-atom catalysts

Surface oxygen Vacancies on Reduced Co₃O₄(100): Superoxide Formation and Ultra-Low-Temperature CO Oxidation

The activation of molecular oxygen is a fundamental step in almost all catalytic oxidation reactions.We have studied this topic and the role of surface vacancies for Co3O4(100) films with a synergistic combination of experimental and theoretical methods. We show that the as-prepared surface is Blayer terminated and that mild reduction produces oxygen single and double vacancies in this layer. Oxygen adsorption experiments clearly reveal different superoxide species below room temperature. The superoxide desorbs below ca. 120 K from a vacancy-free surface and is not active for CO oxidation while superoxide on a surface with oxygen vacancies is stable up to ca. 270 K and can oxidize CO already at the low temperature of 120 K. The vacancies are not refilled by oxygen from the superoxide, which makes them suitable for long-term operation. Our joint experimental/theoretical effort highlights the relevance of surface vacancies in catalytic oxidation reactions

Surface oxygen Vacancies on Reduced Co₃O₄(100): Superoxide Formation and Ultra-Low-Temperature CO Oxidation

The activation of molecular oxygen is a fundamental step in almost all catalytic oxidation reactions.We have studied this topic and the role of surface vacancies for Co3O4(100) films with a synergistic combination of experimental and theoretical methods. We show that the as-prepared surface is Blayer terminated and that mild reduction produces oxygen single and double vacancies in this layer. Oxygen adsorption experiments clearly reveal different superoxide species below room temperature. The superoxide desorbs below ca. 120 K from a vacancy-free surface and is not active for CO oxidation while superoxide on a surface with oxygen vacancies is stable up to ca. 270 K and can oxidize CO already at the low temperature of 120 K. The vacancies are not refilled by oxygen from the superoxide, which makes them suitable for long-term operation. Our joint experimental/theoretical effort highlights the relevance of surface vacancies in catalytic oxidation reactions