The structural optimization of atomic and molecular microclusters using a genetic algorithm in real-valued space-fixed coordinates

This dissertation documents the development and application of the space-fixed modified genetic algorithm, SFMGA. The SFMGA is shown to be both portable and fast for the structural optimization of Lennard-Jones, silicon, water, benzene, naphthalene, and anthracene microclusters. We introduce the SFMGA and apply it to LJ atomic clusters. CPU times needed to obtain the global minimum are compared with similar methods. We then investigate a complicated potential representing silicon atoms. The results show that SFMGA is applicable to non-pairwise additive potentials. We demonstrate the use of SFMGA for clusters where the monomers are molecules. Water clusters are optimized and the relative performance of the genetic operators, for both LJ and H\sb2O clusters, is explored. Finally, we investigate benzene, naphthalene, and anthracene clusters. In these clusters the size and potential surface complexity can be varied independently

Critical incidents in paediatric critical care: who is at risk?

We evaluated the characteristics of children for whom critical incidents (CIs) were reported by performing prospective collection of patient data and retrospective review of reported CIs in a multidisciplinary neonatal-paediatric intensive care unit of a tertiary care university children's hospital. A period of 1year was analysed (January to December 2007; 1,251 admissions). CIs comprised adverse events (actual patient injury), as well as near-misses. The report form of critical incidents was web-based and reporting was voluntary, anonymous and non-punitive. The severity of all CIs was divided into minor, moderate and major. Patients with and without CIs were compared regarding the following characteristics: Paediatric Index of Mortality (PIM2), duration of mechanical ventilation, length of stay in the intensive care, admission mode (surgery, cardiopulmonary bypass, cardiac/non-cardiac unit), age and sex. There were 360 CI reports (83 per 1,000 patient days; 13% major, 26% moderate, 61% minor severity). Of these, 310 CIs could be assigned to 198 specific patients. In the univariate analysis, patient-related risk factors for CIs were higher PIM2 score (p < 0.0001), increased length of stay (p < 0.0001), mechanical ventilation (p < 0.0001), increased ventilator days (p < 0.0001), male gender (p = 0.022) and young age (p < 0.0001). Using a logistic regression model, mechanical ventilation (p < 0.0001), male gender (p = 0.034) and length of stay (p < 0.0001) continued to be associated with the occurrence of CIs. Conclusion CIs often occur in paediatric intensive care. Among the patient-related factors, male gender, mechanical ventilation, and length of stay are independently associated with CIs. Already known at admission to intensive care are male gender and, usually, requirement for mechanical ventilation. Improved knowledge of the risk factors for CIs could help to minimize their frequency and thus improve quality of car

Impact of Chest X-Ray Before Discharge in Asymptomatic Children After Cardiac Surgery—Prospective Evaluation

In many paediatric cardiac units chest radiographs are performed routinely before discharge after cardiac surgery. These radiographs contribute to radiation exposure. To evaluate the diagnostic impact of routine chest X-rays before discharge in children undergoing open heart surgery and to analyze certain risk factors predicting pathologic findings. This was a prospective (6months) single-centre observational clinical study. One hundred twenty-eight consecutive children undergoing heart surgery underwent biplane chest X-ray at a mean of 13days after surgery. Pathologic findings on chest X-rays were defined as infiltrate, atelectasis, pleural effusion, pneumothorax, or signs of fluid overload. One hundred nine asymptomatic children were included in the final analysis. Risk factors, such as age, corrective versus palliative surgery, reoperation, sternotomy versus lateral thoracotomy, and relevant pulmonary events during postoperative paediatric intensive care unit (PICU) stay, were analysed. In only 5.5% (6 of 109) of these asymptomatic patients were pathologic findings on routine chest X-ray before discharge found. In only three of these cases (50%), subsequent noninvasive medical intervention (increasing diuretics) was needed. All six patients had relevant pulmonary events during their PICU stay. Risk factor analysis showed only pulmonary complications during PICU stay to be significantly associated (p=0.005) with pathologic X-ray findings. Routine chest radiographs before discharge after cardiac surgery can be omitted in asymptomatic children with an uneventful and straightforward perioperative course. Chest radiographs before discharge are warrantable if pulmonary complications did occur during their PICU stay, as this is a risk factor for pathologic findings in chest X-rays before discharg

Basin Hopping with Occasional Jumping

Basin-Hopping (BH) or Monte-Carlo Minimization (MCM) is so far the most reliable algorithms in chemical physics to search for the lowest-energy structure of atomic clusters and macromolecular systems. BH transforms the complex energy landscape into a collection of basins, and explores them by hopping, which is achieved by random Monte Carlo moves and acceptance/rejection using the Metropolis criterion. In this report, we introduce the jumping process in addition to the hopping process in BH. Jumping are invoked when the hopping stagnates by reaching the local optima, and are achieved using the Monte Carlo move at the temperature $T=\infty$ without rejection. Our Basin-Hopping with Occasional Jumping (BHOJ) algorithm is applied to the Lennard-Jones clusters of several notoriously difficult sizes. It was found that the probability of locating the true global optima using BHOJ is significantly higher than the original BH

On the Encapsulation of Nickel Clusters by Molecular Nitrogen

The structures and energetic effects of molecular nitrogen adsorbates on nickel clusters are investigated using an extended Hückel model coupled with two models of the adsorbate–nickel interaction. The potential parameters for the adsorbates are chosen to mimic experimental information about the binding strength of nitrogen on both cluster and bulk surface phases of nickel. The first model potential is a simple Lennard-Jones interaction that leads to binding sites in holes defined by sets of near-neighbor nickel atoms. The second model potential has a simple three-body form that forces the model nitrogen adsorbates to bind directly to single nickel atoms. Significant rearrangement of the core nickel structures are found in both models. A disconnectivity graph analysis of the potential energy surfaces implies that the rearrangements arise from low transition state barriers and the small differences between available isomers in the nickel core

Expanded sampling of New Zealand glass sponges (Porifera: Hexactinellida) provides new insights into biodiversity, chemodiversity, and phylogeny of the class

Glass sponges (Hexactinellida) constitute important parts of ecosystems on the deep-sea floor worldwide. However, they are still an understudied group in terms of their diversity and systematics. Here, we report on new specimens collected during RV Sonne expedition SO254 to the New Zealand region, which has recently emerged as a biodiversity hotspot for hexactinellids. Examination of the material revealed several species new to science or so far unknown from this area. While formal taxonomic descriptions of a fraction of these were published earlier, we here briefly report on the morphology of the remaining new species and use the collection to greatly expand the molecular phylogeny of the group as established with ribosomal DNA and cytochrome oxidase subunit I markers. In addition, we provide a chemical fingerprinting analysis on a subset of the specimens to investigate if the metabolome of glass sponges contains phylogenetic signal that could be used to supplement morphological and DNA-based approaches

New Tetrahedral Global Minimum for the 98-atom Lennard-Jones Cluster

A new atomic cluster structure corresponding to the global minimum of the 98-atom Lennard-Jones cluster has been found using a variant of the basin-hopping global optimization algorithm. The new structure has an unusual tetrahedral symmetry with an energy of -543.665361, which is 0.022404 lower than the previous putative global minimum. The new LJ_98 structure is of particular interest because its tetrahedral symmetry establishes it as one of only three types of exceptions to the general pattern of icosahedral structural motifs for optimal LJ microclusters. Similar to the other exceptions the global minimum is difficult to find because it is at the bottom of a narrow funnel which only becomes thermodynamically most stable at low temperature.Comment: 3 pages, 2 figures, revte

Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms

We describe a global optimization technique using `basin-hopping' in which the potential energy surface is transformed into a collection of interpenetrating staircases. This method has been designed to exploit the features which recent work suggests must be present in an energy landscape for efficient relaxation to the global minimum. The transformation associates any point in configuration space with the local minimum obtained by a geometry optimization started from that point, effectively removing transition state regions from the problem. However, unlike other methods based upon hypersurface deformation, this transformation does not change the global minimum. The lowest known structures are located for all Lennard-Jones clusters up to 110 atoms, including a number that have never been found before in unbiased searches.Comment: 8 pages, 3 figures, revte

CALYPSO: a method for crystal structure prediction

We have developed a software package CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) to predict the energetically stable/metastable crystal structures of materials at given chemical compositions and external conditions (e.g., pressure). The CALYPSO method is based on several major techniques (e.g. particle-swarm optimization algorithm, symmetry constraints on structural generation, bond characterization matrix on elimination of similar structures, partial random structures per generation on enhancing structural diversity, and penalty function, etc) for global structural minimization from scratch. All of these techniques have been demonstrated to be critical to the prediction of global stable structure. We have implemented these techniques into the CALYPSO code. Testing of the code on many known and unknown systems shows high efficiency and high successful rate of this CALYPSO method [Wang et al., Phys. Rev. B 82 (2010) 094116][1]. In this paper, we focus on descriptions of the implementation of CALYPSO code and why it works.Comment: accepted in Computer Physics Communication

Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management

The objectives of this research were to identify alternatives to glyphosate for intra- row (under-trellis) vineyard floor management and to evaluate the potential for intra- row and inter-row (alleyway) groundcovers to reduce vegetative vigor of `Marquette\u27 grapevines (Vitis spp.) in a southeast Nebraska vineyard. The experiment was a randomized factorial design with five intra-row treatments (crushed glass mulch [CG], distillers\u27 grain mulch [DG], creeping red fescue [CRF], non-sprayed control [NSC], and glyphosate [GLY]) and three inter-row treatments (creeping red fescue [CRF], Kentucky bluegrass [KB], and resident vegetation [RV]). Treatments were established in 2010-2011 and measurements were conducted during 2012 and 2013 on 5- and 6-year- old vines. Soil temperatures were mostly higher under mulches and lower under intra- row groundcovers, compared to GLY. Weed cover in CG, DG, and CRF treatments was the same or less than GLY. At most sampling dates, inter-row soil moisture was lowest under KB. Intra-row soil moisture was highest under DG mulch and lowest under CRF and NSC; CG had the same or lower soil moisture than GLY. Surprisingly, we did not detect differences in mid-day photosynthetically active radiation (PAR) reflectance, despite visual differences among the intra-row treatments. Mid-day vine water potential did not differ among treatments. We concluded it is not necessary to maintain a bare soil strip under established vines in this region, where soil fertility and moisture are non-limiting