An implementation of the coupled perturbed Kohn-Sham equations: perturbation due to nuclear displacements

The Coupled Perturbed Kohn-Sham equations have been implemented in the Amsterdam Density Functional program package. Our implementation differs from previous ones in many ways. This program uses density fitting to calculate the Coulomb and exchange integrals. Further, all matrix elements of the Fock type matrix and its derivatives are calculated by numerical integration. The frozen core approximation is also implemented. Our implementation is approximately 10 times faster than a finite difference algorithm, and the absolute CPU times also compare favorably with other reported implementations.     

Adiabatic quantum optimization with qudits

Most realistic solid state devices considered as qubits are not true two-state systems. If the energy separation of the upper energy levels from the lowest two levels is not large, then these upper states may affect the evolution of the ground state over time and therefore cannot be neglected. In this work, we study the effect of energy levels beyond the lowest two energy levels on adiabatic quantum optimization in a device with a double-well potential as the basic logical element. We show that the extra levels can be modeled by adding additional ancilla qubits coupled to the original logical qubits, and that the presence of upper levels has no effect on the final ground state. We also study the influence of upper energy levels on the minimum gap for a set of 8-qubit spin glass instances.     

Design of a performance-oriented workplace e-learning system using ontology

E-learning is emerging as a popular learning approach utilized by many organizations. Despite the ever increasing practices of e-learning in the workplace, most e-learning applications fail to meet learners’ needs or serve organization’s quests for success. Significant gaps exist between organizational interests and individual needs when they come to e-learning, which make e-learning applications less goal-effective. To solve this problem, a performance-oriented approach is presented in this study. Key performance indicators (KPIs) are set up to clarify organizational training needs, and help learners establish rational learning objectives. In addition, ontology is used for constructing formal and machine-understandable conceptualization of the performance-oriented learning environment. Using this approach, a KPI-oriented learning ontology and prototype system have been developed and evaluated to demonstrate the effectiveness of the approach.     

Agent-based negotiation and decision making for dynamic supply chain formation

Modern businesses are facing the challenge of effectively coordinating their supply chains from upstream to downstream services. It is a complex problem to search, schedule, and coordinate a set of services from a large number of service resources under various constraints and uncertainties. Existing approaches to this problem have relied on complete information regarding service requirements and resources, without adequately addressing the dynamics and uncertainties of the environments. The real-world situations are complicated as a result of ambiguity in the requirements of the services, the uncertainty of solutions from service providers, and the interdependencies among the services to be composed. This paper investigates the complexity of supply chain formation and proposes an agent-mediated coordination approach. Each agent works as a broker for each service type, dedicated to selecting solutions for each service as well as interacting with other agents in refining the decision making to achieve compatibility among the solutions. The coordination among agents concerns decision making at strategic, tactical, and operational level. At the strategic level, agents communicate and negotiate for supply chain formation; at the tactical level, argumentation is used by agents to communicate and understand the preferences and constraints of each other; at the operational level, different strategies are used for selecting the preferences. Based on this approach, a prototype has been implemented with simulated experiments highlighting the effectiveness of the approach.     

Performance of QPET, a high-resolution 3D PET imaging system for small volumes

QPET is a positron imaging system developed at Queen's University for high-resolution, 3D imaging of small volumes; it includes a pair of planar gamma-ray detectors 25.4 cm square, which rotate about a central axis with a quasi-cylindrical geometry. The authors describe the performance of this system. Basic characteristics of the detectors are evaluated: a spatial sampling of 1 mm, a quantum efficiency of 9.3% (for 511 keV gamma rays with normal incidence), and a time resolution of 88 ns. Models are developed to characterize the system deadtime and the sensitivity in terms of the noise-equivalent counting rate. With an 8 cm diameter spherical source, the noise-equivalent counting rate reaches a maximum at just over 3 kcps for an activity concentration of 2 muCi/cc; the random coincidence events and the deadtime losses both contribute significantly and the scatter contribution is small. Spatial resolution and uniformity over the field of view are evaluated by imaging short and long line sources; a spatial resolution of 2.7 mm in the transverse directions and 2.0 mm in the axial direction is achieved, with excellent uniformity throughout the field of view. The detector response is amplitude invariant across a 20 cm transverse diameter and a 9 cm axial length with the acceptance angle limited to +/-25 degrees in the axial direction. As an example of the imaging capabilities of QPET, the authors show 3D images of (18)F uptake in the bones of a rat, showing the excellent spatial resolution. This system is best suited to limited-volume applications where high counting rates are not necessary, but where high spatial resolution and uniform detector response are priorities.     

Effects of microbial inhibitors and modified atmosphere packaging on growth of Listeria monocytogenes and Salmonella enterica Typhimurium and on quality attributes of injected pork chops and sliced cured ham

This study was designed to determine the inhibitory effects of modified atmosphere packaging (MAP), both alone and in combination with potassium lactate and sodium diacetate (PLSD), on selected pathogens common to pork products. Effects of the treatments on product quality also were assessed. The hypothesis was that high-CO2 MAP would increase the effectiveness of PLSD for inhibition of pork pathogens. Fresh chops from untreated pork loins and loins that were injected with PLSD were inoculated with Salmonella enterica Typhimurium, and slices of untreated hams and hams that were injected with PLSD were inoculated with Listeria monocytogenes. The samples were subjected to vacuum packaging (VP) or MAP with high concentrations (99.5 to 100%) of CO2. Pathogens were enumerated periodically during storage at 4 and 10 degrees C. Storage of pork chops at 4 degrees C slowed the growth of Salmonella Typhimurium, and there was little difference in pathogen numbers between VP and MAP samples. L. monocytogenes growth on ham slices at 4 degrees C was inhibited for up to 28 days by all of the treatments, but after 28 days, the VP-PLSD treatment had a greater inhibitory effect than did the other treatments. At 10 degrees C, the PLSD and MAP treatments each effectively inhibited the growth of the pathogens on pork chops and ham slices when compared with controls (VP). However, the results obtained with MAP plus PLSD at 10 degrees C were not different from those obtained with either MAP or PLSD alone. Therefore, the hypothesis was not supported; the high-CO2 atmosphere of the MAP did not increase the effectiveness of PLSD for inhibition of pathogens.     

Tracer monitored titrations: measurement of total alkalinity

We introduce a new titration methodology, tracer monitored titration (TMT), in which analyses are free of volumetric and gravimetric measurements and insensitive to pump precision and reproducibility. Spectrophotometric monitoring of titrant dilution, rather than volume increment, lays the burden of analytical performance solely on the spectrophotometer. In the method described here, the titrant is a standardized mixture of acid-base indicator and strong acid. Dilution of a pulse of titrant in a titration vessel is tracked using the total indicator concentration measured spectrophotometrically. The concentrations of reacted and unreacted indicator species, derived from Beer's law, are used to calculate the relative proportions of titrant and sample in addition to the equilibrium position (pH) of the titration mixture. Because the method does not require volumetric or gravimetric additions of titrant, simple low-precision pumps can be used. Here, we demonstrate application of TMT for analysis of total alkalinity (A(T)). High-precision, high-accuracy seawater A(T) measurements are crucial for understanding, for example, the marine CaCO3 budget and saturation state, anthropogenic CO2 penetration into the oceans, calcareous phytoplankton blooms, and coral reef dynamics. We present data from 286 titrations on three types of total alkalinity standards: Na2CO3 in 0.7 mol kg x soln(-1) NaCl, NaOH in 0.7 mol kg x soln(-1) NaCl, and a seawater Certified Reference Material (CRM). Based on Na2CO3 standards, the accuracy and precision are +/-0.2 and +/-0.1% (4 and 2 micromol kg x soln(-1) for A(T) approximately 2100-2500 micromol kg x soln(-1), n = 242), using low-precision solenoid pumps to introduce sample and titrant. Similar accuracy and precision were found for analyses run 42 days after the initial experiments. Excellent performance is achieved by optimizing the spectrophotometric detection system and relying upon basic chemical thermodynamics for calculating the equivalence point. Although applied to acid-base titrations in this paper, the approach should be generally applicable to other types of titrations.     

Survival and recovery of viable but nonculturable Listeria monocytogenes cells in a nutritionally depleted medium

Survival of a desiccated five-strain Listeria monocytogenes mixture during storage in sand at 4 degrees C for 2 months was determined using the acridine orange direct count method with novobiocin and plate counts. Samples of inoculated sand were taken every 2 weeks, incubated at 37 degrees C for 6 h, stained with acridine orange, and then examined with a fluorescence microscope. Elongated viable but nonculturable cells were most frequently observed during weeks 2 and 4. At weeks 6 and 8, most of the cells either remained viable or were dead. In each microscopic field, only one or two viable but nonculturable cells were observed among hundreds of other viable culturable cells, indicating that L. monocytogenes does not generally become viable but nonculturable. Therefore, viable but nonculturable cells are not a concern when plating environmental samples or desiccated L. monocytogenes cells on nonselective media. Tryptic soy agar with 0.6% (wt/vol) yeast extract (TSAYE) and Columbia agar were used as nonselective plate count media. Modified Oxford agar and TSAYE + 5% (wt/vol) sodium chloride were used as the selective plate count media. The effects of aerobic or anaerobic incubation and media supplementation with 0.1% or 1% (wt/vol) sodium pyruvate were tested to optimize recovery of desiccated cells. Nonselective media showed better recovery when TSAYE and Columbia agar contained 0.1% (wt/vol) pyruvate and were incubated aerobically. These two culture methods were equally effective (P > 0.05) for recovering desiccated L. monocytogenes cells.     

Survival of Listeria monocytogenes and Escherichia coli O157:H7 during sauerkraut fermentation

Sauerkraut was produced from shredded cabbage, as is typical in the United States, and from whole head cabbages, which is a traditional process in parts of Eastern Europe. The sauerkraut was inoculated with five strain mixtures of Escherichia coli O157:H7 and Listeria monocytogenes, and the populations of these bacteria, as well as lactic acid bacteria, pH, and titratable acidity, were monitored over the course of fermentation. Fermentation variables were temperature (18 and 22 degrees C) and salt concentration (1.8, 2.25, and 3%). For most of the analyses, the type of cabbage processing was a significant factor, although within cabbage type, neither salt nor fermentation temperature had significant effects. The final pH of the whole-head sauerkraut was lower than the shredded sauerkraut, but the titratable acidity was significantly higher in the shredded sauerkraut. E. coli O157:H7 and L. monocytogenes persisted in the brines for most of the fermentation, although at the end of the fermentations (15 days for shredded, 28 days for whole head), neither pathogen had detectable populations. E. coli populations decreased more rapidly in the shredded sauerkraut even though the pH was higher because of the higher total acidity in the shredded sauerkraut. Acid-tolerant strains of E. coli and L. monocytogenes were isolated from both shredded and whole-head sauerkraut at different salt concentrations and temperatures after 15 days of fermentation and could be detected at 35 days in the wholehead sauerkraut.