Molecular Dynamics Simulations of Warm Dense Carbon

We present classical and DFT‐based molecular dynamics (MD) simulations of carbon in the warm dense matter regime (? = 3.7 g/cc, 0.86 eV < T < 8.62 eV [T < 100 eV for classical MD]). Two different classical interatomic potentials are used: 1. LCBOP, designed to simulate condensed (e.g. solid) phases of C, and 2. linearly screened Coulomb (Yukawa) potentials. It is shown that LCBOP over‐predicts minima and maxima in the pair correlation functions of liquid‐C in this regime when compared to the DFT‐MD results. The screened Coulomb model, while under‐correlating at low‐T, seems to produce the correct qualitative features in the static ionic pair distributions at the highest‐T. However, both approaches predict the decay in the ionic contribution of the specific heat as T → ∞ to be much slower than that predicted by a model based on DFT‐MD. These differences in the MD‐derived equations of state in warm dense regimes could have important consequences when using classical inter‐ionic forces such as these in large‐scale MD simulations aimed at studying, for instance, processes of relevance to inertial confinement fusion when C is used as an ablator material. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Evaluation of the sensitivity of the ‘Wiley registry of tandem mass spectral data,MSforID’ with MS/MS data of the ‘NIST/NIH/EPA mass spectral library’

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the ‘NIST/NIH/EPA Mass Spectral Library’ (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross‐validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.     

Revisiting the big valley search space structure in the TSP

The solution space of the travelling salesman problem under 2-opt moves has been characterized as having a big-valley structure, in which the evaluation of a tour is positively correlated to the distance of the tour from the global optimum. We examine the big-valley hypothesis more closely and show that while the big-valley structure does appear in much of the solution space, it breaks down around local optima that have solutions whose evaluation is very close to that of the global optimum; multiple funnels appear around local optima with evaluations close to the global optimum. The appearance of multiple funnels explains why certain iterated local search heuristics can quickly find high-quality solutions, but fail to consistently find the global optimum. We then investigate a novel search operator, which is demonstrated to have the ability to escape funnels at evaluations close to the global optimum.     

Effect of high-dose irradiation on the optically stimulated luminescence of Al2O3:C

This paper examines the effect of high-dose irradiation on the optically stimulated luminescence (OSL) of Al2O3:C, principally on the shape of the OSL decay curve and on the OSL sensitivity. The effect of the degree of deep trap filling on the OSL was also studied by monitoring the sensitivity changes after doses of beta irradiation and after step-annealing of samples previously irradiated with high doses. The OSL response to dose shows a linear-supralinear-saturation behavior, with a decrease in the response for doses higher than those required for saturation. This behavior correlates with the sensitivity changes observed in the samples annealed only to 773 K, which show sensitization for doses up to 20-50 Gy and desensitization for higher doses. Data from the step-annealing study leads to the suggestion that the sensitization is caused by the filling of deep electron traps, which become thermally unstable at 1100-1200 K, whereas the desensitization is caused by the filling of deep hole traps, which become thermally unstable at 800-875 K, along with a concomitant decrease in the concentration of recombination centers (F+ -centers). Changes in the shape of the OSL decay curves are also observed at high doses, the decay becoming faster as the dose increases. These changes in the OSL decay curves are discussed in terms of multiple overlapping components, each characterized by different photoionization cross-sections. However, using numerical solutions of the rate equations for a simple model consisting of a main trap and a recombination center, it is shown that the kinetics of OSL process may also be partially responsible for the changes in the OSL curves at high doses in Al2O3:C. Finally, the implication of these results for the dosimetry of heavy charged particles is discussed.     

Metalation of o-methylanisole (o-MA); an optional-site selectivity reassessment

‘Deficiency catalysis’ is the concept applied to metalation chemistry that increments of TMEDA or an equivalent or two of an ether activate alkyllithiums in hydrocarbon media. Amplification of this concept to conflicting reports of α- and ortho-metalation of ortho-methylanisole (o-MA) is explored. Both regioselective metalations were realized in selectivity ratios of >7:1 for the desired isomers. Some rationale is provided for the various selectivities. These results are at variance with prior results and interpretations thereof found in the literature.     

Molecular simulations of the pressure, temperature, and chemical potential dependencies of clay swelling

A new method for the determination of clay swelling thermodynamics from computer simulation is discussed and evaluated. This method allows for the determination of temperature, pressure, and water chemical potential dependence of clay swelling from simulations at a single thermodynamic state point. The temperature dependence and pressure dependence of clay swelling are shown to be directly related to the composite system entropy and volume change, respectively, that accompany swelling. Expressions for the chemical potential dependence of clay swelling are used to determine constant pressure layer spacing and adsorption isotherms, quantities that are well suited for comparison with experimental measurements. This method is evaluated through grand isoshear ensemble simulations of Na-montmorillonite, a prototypical swelling clay. Approximations associated with all expressions are discussed with explicit calculations used to demonstrate their regimes of validity.     

The effects of deep trap population on the thermoluminescence of Al2O3:C

The influence of deep traps on the 450 K thermoluminescence (TL) peak of Al₂O₃:C is studied. Depending upon the sample and on the degree of deep trap filling, features such as the TL width, area and height can vary considerably. These effects are interpreted to be due to: (a) sensitivity changes introduced by competition mechanisms involving deep electron and hole traps, and (b) the multiple component nature of the 450 K TL peak. The influence of the deep traps on the TL was studied using different excitation sources (beta irradiation or UV illumination), and step annealing procedures. Optical absorption measurements were used to monitor the concentration of F- and F⁺-centers. The data lead to the suggestion that the competing deep traps which become unstable at 800–875 K are hole traps, and that the competing deep traps which become unstable at 1100–1200 K are electron traps. Both the dose response of the TL signal and the TL sensitivity are shown to be influenced by sensitization and desensitization processes caused by the filling of deep electron and hole traps, respectively. Changes in the TL peak at low doses were also shown to be connected to the degree of filling of deep traps, emphasizing the influence of deep trap concentration and dose history of each sample in determining the TL properties of the material. Implications of these results for the optically stimulated luminescence properties are also discussed.     

A determinate model of thrust-augmenting ejectors

A theoretical analysis of the compressible flow through a constant-area jet-engine ejector in which a primary jet mixes with ambient fluid from a uniform free stream is pursued. The problem is reduced to a determinate mathematical one by prescribing the ratios of stagnation properties between the primary and secondary flows. For some selections of properties and parameters more than one solution is possible and the meaning of these solutions is discussed by means of asymptotic expansions. Our results further show that while under stationary conditions the thrust-augmentation ratio assumes a value of 2 in the large area-ratio limit, for a free-stream Mach number greater than 0.6 very little thrust augmentation is left. Due to the assumptions made, the analysis provides idealized values for the thrust-augmentation ratio and the mass flux entrainment factor.     

Ion-exchange equilibria of lysozyme, myoglobin and bovine serum albumin. Effective valence and exchanger capacity

A series of ion-exchange equilibrium experiments were completed and analyzed by a mass action model. The isotherms at various counter-ion concentrations are regressed to determine the average number of binding sites, Z, the mass action constant, K, and the effective capacity of the exchanger, Pm. The estimates for Pm are 1-10 mmol of protein adsorbed per liter of packed Sepharose exchanger, in agreement with values determined from fitting the Langmuir isotherms. A geometric model, developed to relate the charge distribution of the exchanger and the size of the protein to the protein capacity, also confirms the estimates of Pm. The Z values estimated (and confirmed with an independent slope method) range from 0.8 to 3.6, indicating that most of the ionized sites on the protein do not undergo ion exchange. Geometric model estimates of exchanger sites covered by a protein at maximum surface coverage show that only 1-32% of the sites actually undergo ion exchange. This result indicates that adsorbed protein molecules "block" many exchanger sites, preventing other molecules from ion exchanging at those sites. This high degree of blocking by proteins also indicates that there is an excess of exchanger sites, as evidenced by Z showing no dependence on charge separation distance over the range 6-10 A. Scatchard pots of the equilibrium data indicate that there is competition between at least two different binding forms of each protein studied. For the high-affinity systems, cooperative binding was observed at low exchanger loading; the character then changed to heterogeneous competitive binding as the exchanger loading increased. The effect on an isotherm plot is a subtle but systematic deviation from the Langmuir and mass action models. More important, the competition means that Z represents an average for competing binding forms and, as such, Z can be fractional.