The analysis of a finite element method for the three-species Lotka–Volterra competition-diffusion with Dirichlet boundary conditions

A Galerkin finite element method is developed for the two dimensional/three dimensional nonlinear time-dependent three-species Lotka–Volterra competition-diffusion equations on a bounded domain. The existence and uniqueness of the solution to the numerical formulation are proved. An error estimate for the numerical solution is obtained. Numerical computations are carried out to examine the expected orders of accuracy in the error estimates.     

Surface versus volume emissions in photon–hadron correlations

High-p _T photon–hadron correlations are studied within the next-to-leading order (NLO) perturbative QCD parton model with modified parton-jet fragmentation functions due to jet quenching in high-energy A+A collisions. In central A+A collisions, the away-side hadrons with large z _T=p _T ^h /p _T ^γ are controlled mainly by the surface emission of the gamma-jet events, while a small z _T region will be volume emission bias. In other words, gamma jets for a small-z _T region probe the dense matter deeper than those gamma jets for a large-z _T region, so the small-z _T gamma jets are found to be slightly more sensitive to the properties of the dense matter than the large-z _T gamma jets.     

On the Choice of Nugget in Kriging Modeling for Deterministic Computer Experiments

Kriging is commonly used for developing emulators as surrogates for computationally intensive simulations. One difficulty with kriging is the potential numerical instability in the computation of the inverse of the covariance matrix, which can lead to large variability and poor performance of the kriging predictor. First, we study some causes of ill-conditioning in kriging. We then study the use of nugget in kriging to overcome the numerical instability. Some asymptotic results on its interpolation bias and mean squared prediction errors are presented. Finally, we study the choice of the nugget parameter based on some algebraic lower bounds and use of a regularizing trace. A simulation study is performed to show the differences between kriging with and without nugget and to demonstrate the advantages of the former. This article has supplementary materials online.     

Trends in exchange coupling for trimethylenemethane-type Bis(semiquinone) biradicals and correlation of magnetic exchange with mixed valency for cross-conjugated systems

A magnetostructural correlation (conformational electron spin exchange modulation) within an isostructural series of biradical complexes is presented. X-ray crystal structures, variable-temperature electron paramagnetic resonance spectroscopy, zero-field splitting parameters, and variable-temperature magnetic susceptibility measurements were used to evaluate molecular conformation and electron spin exchange coupling in this series of molecules. Our combined results indicate that the ferromagnetic portion of the exchange couplings occurs via the cross-conjugated pi-systems, while the antiferromagnetic portion occurs through space and is equivalent to incipient bond formation. Thus, molecular conformation controls the relative amounts of ferro- and antiferromagnetic contributions to exchange coupling. In fact, the exchange parameter correlates with average semiquinone ring torsion angles via a Karplus-Conroy-type relation. Because of the natural connection between electron spin exchange coupling and electronic coupling related to electron transfer, we also correlate the exchange parameters in the biradical complexes to mixed valency in the corresponding quinone-semiquinone radical anions. Our results suggest that delocalization in the cross-conjugated, mixed-valent radical anions is proportional to the ferromagnetic contribution to the exchange coupling in the biradical oxidation states.     

A first-principles study of methanol decomposition on Pt(111)

A periodic, self-consistent, Density Functional Theory study of methanol decomposition on Pt(111) is presented. The thermochemistry and activation energy barriers for all the elementary steps, starting with O[bond]H scission and proceeding via sequential hydrogen abstraction from the resulting methoxy intermediate, are presented here. The minimum energy path is represented by a one-dimensional potential energy surface connecting methanol with its final decomposition products, CO and hydrogen gas. It is found that the rate-limiting step for this decomposition pathway is the abstraction of hydroxyl hydrogen from methanol. CO is clearly identified as a strong thermodynamic sink in the reaction pathway while the methoxy, formaldehyde, and formyl intermediates are found to have low barriers to decomposition, leading to very short lifetimes for these intermediates. Stable intermediates and transition states are found to obey gas-phase coordination and bond order rules on the Pt(111) surface.     

Reversible binding of the HPLC6 isoform of type I antifreeze proteins to ice surfaces and the antifreeze mechanism studied by multiple quantum filtering-spin exchange NMR experiment

Antifreeze proteins (AFPs) protect organisms from freezing damage by inhibiting the growth of seed-ice crystals. It has long been hypothesized that irreversible binding of AFPs to ice surfaces is responsible for inhibiting the growth of seed-ice crystals as such a mechanism supports the popularly accepted Kelvin effect for the explanation of local freezing-point depression. However, whether the binding is reversible or irreversible is still under debate due to the lack of direct experimental evidence. Here, we report the first direct experimental result, by using the newly developed multiple quantum (MQ) filtering-spin exchange NMR experiment, that shows that the binding of HPLC6 peptides to ice surfaces is reversible. It was found that the reversible process can be explained by the model of monolayer adsorption. These results suggest that the Kelvin effect is not suitable for explaining the antifreeze mechanism, and direct interactions between the peptides and the ice-surface binding sites are the driving forces for the binding of AFPs to ice surfaces. We propose that there exists a concentration gradient of AFP from an ice-binding surface to the solution due to the affinity of ice surfaces to AFPs. This concentration gradient creates a dense layer of AFP in contact with the ice-binding surface, which depresses the local freezing point because of the colligative property, but not the Kelvin effect.     

Synthesis of molybdenum nitrido complexes for triple-bond metathesis of alkynes and nitriles

Complexes of the type N≡Mo(OR)(3) (R = tertiary alkyl, tertiary silyl, bulky aryl) have been synthesized in the search for molybdenum-based nitrile-alkyne cross-metathesis (NACM) catalysts. Protonolysis of known N≡Mo(NMe(2))(3) led to the formation of N≡Mo(O-2,6-(i)Pr(2)C(6)H(3))(3)(NHMe(2)) (12), N≡Mo(OSiPh(3))(3)(NHMe(2)) (5-NHMe(2)), and N≡Mo(OCPh(2)Me)(3)(NHMe(2)) (17-NHMe(2)). The X-ray structure of 12 revealed an NHMe(2) ligand bound cis to the nitrido ligand, while 5-NHMe(2) possessed an NHMe(2) bound trans to the nitride ligand. Consequently, 17-NHMe(2) readily lost its amine ligand to form N≡Mo(OCPh(2)Me)(3) (17), while 12 and 5-NHMe(2) retained their amine ligands in solution. Starting from bulkier tris-anilide complexes, N≡Mo(N[R]Ar)(3) (R = isopropyl, tert-butyl; Ar = 3,5-dimethylphenyl) allowed for the formation of base-free complexes N≡Mo(OSiPh(3))(3) (5) and N≡Mo(OSiPh(2)(t)Bu)(3) (16). Achievement of a NACM cycle requires the nitride complex to react with alkynes to form alkylidyne complexes; therefore the alkyne cross-metathesis (ACM) activity of the complexes was tested. Complex 5 was found to be an efficient catalyst for the ACM of 1-phenyl-1-butyne at room temperature. Complexes 12 and 5-NHMe(2) were also active for ACM at 75 °C, while 17-NHMe(2) and 16 did not show ACM activity. Only 5 proved to be active for the NACM of anisonitrile, which is a reactive substrate in NACM catalyzed by tungsten. NACM with 5 required a reaction temperature of 180 °C in order to initiate the requisite alkylidyne-to-nitride conversion, with slightly more than two turnovers achieved prior to catalyst deactivation. Known molybdenum nitrido complexes were screened for NACM activity under similar conditions, and only N≡Mo(OSiPh(3))(3)(py) (5-py) displayed any trace of NACM activity.     

Monitoring trace anion contamination in disk drive components

Ion chromatography was used to determine trace anionic contamination on the surface of hard disk drive components. These contaminants can have a detrimental effect on device reliability and yield. Disk drive components were soaked in deionized water and these extracts were analyzed for anions. The anions fluoride, acetate, formate, acrylate, methacrylate, chloride, nitrite, bromide, nitrate, benzoate, sulfate, oxalate, phthalate and phosphate were separated on a high-performance anion-exchange column and determined at concentrations less than 1 microg/l with suppressed conductivity detection. The extract solutions were analyzed either by injecting 1 ml or by preconcentrating 5 ml. We evaluated the performance of both methods.     

Intermolecular interactions in pi-stacked conjugated molecules. Synthesis,structure, and spectral characterization of alkyl bithiazole oligomers

Syntheses are reported of new 4,4'-dialkyl-2,2'-bithiazole oligomers that have alkenoxy side chains that are capable of easy conversion to oligomers with functionalized side chains, e.g., terminally substituted hydroxy chains. The crystal structures of two representative oligomers (4,4',4' ',4' "-tetra-(2-propenoxymethyl)-2,2',5',5' ',2' ',2' "-quaterthiazole (3P2) and 4,4',4' ',4' "-tetra-(3-hydroxypropyloxymethyl)-2,2',5',5' ',2' ',2' "-quaterthiazole (3H2)) were determined; 3P2 crystallizes in a pi-stacked motif with two molecules per unit cell, whereas 3H2 forms pi-stacks that are linked with hydrogen bonds to form infinite two-dimensional sheets with one molecule per unit cell. A comparison of the UV-vis spectra of the compounds in solution and in the solid state provides unequivocal evidence for the presence of a Davydov splitting, W(D) approximately 0.2 eV, in solid 3P2. The spectra are interpreted in the framework of molecular exciton theory to extract a value of the intermolecular transfer integral, J approximately 0.2 eV, for a total exciton bandwidth of ca. 0.8 eV. Monte Carlo calculations were used to determine the density of states of the exciton band and the absorption and emission line shapes of the 0 <-- 0 transition. It is suggested that the "three-humped" absorption profile typical of partially crystalline, regioregular polymers is the "optical signature" of pi-stacking.     

Factors influencing the DNA nuclease activity of iron, cobalt, nickel, and copper chelates

A library of complexes that included iron, cobalt, nickel, and copper chelates of cyclam, cyclen, DOTA, DTPA, EDTA, tripeptide GGH, tetrapeptide KGHK, NTA, and TACN was evaluated for DNA nuclease activity, ascorbate consumption, superoxide and hydroxyl radical generation, and reduction potential under physiologically relevant conditions. Plasmid DNA cleavage rates demonstrated by combinations of each complex and biological co-reactants were quantified by gel electrophoresis, yielding second-order rate constants for DNA(supercoiled) to DNA(nicked) conversion up to 2.5 × 10(6) M(-1) min(-1), and for DNA(nicked) to DNA(linear) up to 7 × 10(5) M(-1) min(-1). Relative rates of radical generation and characterization of radical species were determined by reaction with the fluorescent radical probes TEMPO-9-AC and rhodamine B. Ascorbate turnover rate constants ranging from 3 × 10(-4) to 0.13 min(-1) were determined, although many complexes demonstrated no measurable activity. Inhibition and Freifelder-Trumbo analysis of DNA cleavage supported concerted cleavage of dsDNA by a metal-associated reactive oxygen species (ROS) in the case of Cu(2+)(aq), Cu-KGHK, Co-KGHK, and Cu-NTA and stepwise cleavage for Fe(2+)(aq), Cu-cyclam, Cu-cyclen, Co-cyclen, Cu-EDTA, Ni-EDTA, Co-EDTA, Cu-GGH, and Co-NTA. Reduction potentials varied over the range from -362 to +1111 mV versus NHE, and complexes demonstrated optimal catalytic activity in the range of the physiological redox co-reactants ascorbate and peroxide (-66 to +380 mV).