Electronic structure benchmark calculations of CO2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach.

Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO2 ) fixation in the biosphere. This enzyme catalyzes a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD, and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions. However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing, and potentially adding to modeling of enzyme reaction mechanisms with DFT methods.

Adding fuel to the fire: the impacts of non-native grass invasion on fire management at a regional scale.

BACKGROUND: Widespread invasion by non-native plants has resulted in substantial change in fire-fuel characteristics and fire-behaviour in many of the world's ecosystems, with a subsequent increase in the risk of fire damage to human life, property and the environment. Models used by fire management agencies to assess fire risk are dependent on accurate assessments of fuel characteristics but there is little evidence that they have been modified to reflect landscape-scale invasions. There is also a paucity of information documenting other changes in fire management activities that have occurred to mitigate changed fire regimes. This represents an important limitation in information for both fire and weed risk management. METHODOLOGY/PRINCIPAL FINDINGS: We undertook an aerial survey to estimate changes to landscape fuel loads in northern Australia resulting from invasion by Andropogon gayanus (gamba grass). Fuel load within the most densely invaded area had increased from 6 to 10 t ha(-1) in the past two decades. Assessment of the effect of calculating the Grassland Fire Danger Index (GFDI) for the 2008 and 2009 fire seasons demonstrated that an increase from 6 to 10 t ha(-1) resulted in an increase from five to 38 days with fire risk in the 'severe' category in 2008 and from 11 to 67 days in 2009. The season of severe fire weather increased by six weeks. Our assessment of the effect of increased fuel load on fire management practices showed that fire management costs in the region have increased markedly (∼9 times) in the past decade due primarily to A. gayanus invasion. CONCLUSIONS/SIGNIFICANCE: This study demonstrated the high economic cost of mitigating fire impacts of an invasive grass. This study demonstrates the need to quantify direct and indirect invasion costs to assess the risk of further invasion and to appropriately fund fire and weed management strategies.

Dynamic properties of unstable motion of swirling premixed flames generated by a change in gravitational orientation.

The dynamic behavior of swirling premixed flames generated by the effect of the gravitational orientation has been experimentally and numerically investigated. When the gravitational direction relative to the flame front is changed, i.e., in inverted gravity (-1G), an unstable flame is formed in a limited domain of equivalence ratio and swirl number. The time history of flame front fluctuation shows that high-energy chaotic motion is superimposed on a periodic oscillation generated by unstable vortex motion in the combustion products. This results in the dynamic motion of the unstable flame becoming deterministically chaotic. This is clearly demonstrated by sophisticated nonlinear time series analysis, which has not been widely applied to the investigation of combustion phenomena.

Are we setting about improving the safety of computerised prescribing in the right way? A workshop report.

BACKGROUND: Prescribing errors are common and costly. Technology should enable safer prescribing. The two main current methods of doing so are computer initiated clinical support software (CDSS) and the user initiated information retrieval (IR) systems. However, despite the near universal availability of computerised prescribing support in the UK, errors continue. OBJECTIVE: To evaluate the experience of UK primary health care professionals using CDSS and to consolidate current technical opinion and literature in this area with the aim of creating useful hypotheses for guiding future academic investigation and industrial development. STUDY DESIGN: The study was a synthesis, drawing together a literature review and views from experts in the field to explore from a qualitative perspective where and how CDSS and IR could be used to improve prescribing safety in primary care. We conducted a literature review, held a workshop to explore issues in practice and had a follow-up expert panel meeting to confirm the findings. The workshop was recorded, transcribed verbatim and analysed thematically. PARTICIPANTS AND SETTING: The study involved primary care practitioners, system developers, information suppliers and academics. OUTCOMES: Although CDSS is incorporated into primary care electronic patient record systems there does not appear to be an associated marked reduction in prescribing errors. Clinicians are frustrated with current systems, and are concerned these may have a negative impact on patients. There is an unhelpful signal-noise ratio with too many clinically irrelevant alerts and insufficient recognition of the potential downsides of over alerting - possibly making compliance less likely, having a negative impact on the doctor-patient relationship and overloading clinicians. A preferred way forward would be alerts based on quantitative risk assessment of interaction at the level of the preparations being prescribed, rather than theoretical possibilities of interactions between classes of drugs. CONCLUSION: Prescribing errors remain a major source of unnecessary morbidity and mortality and current systems do not appear to have significantly reduced this problem; nor has the extensive literature about how to reduce unnecessary alerts been taken into account. We need a new and more rational basis for the selection and presentation of alerts that would help, not hinder, the clinician's performance.

Modeling light scattering from Diesel soot particles.

The Mie model is widely used to analyze light scattering from particulate aerosols. The Diesel particle scatterometer, for example, determines the size and optical properties of Diesel exhaust particles that are characterized by the measurement of three angle-dependent elements of the Mueller scattering matrix. These elements are then fitted by Mie calculations with a Levenburg-Marquardt optimization program. This approach has achieved good fits for most experimental data. However, in many cases, the predicted complex index of refraction was smaller than that for solid carbon. To understand this result and explain the experimental data, we present an assessment of the Mie model by use of a light-scattering model based on the coupled-dipole approximation. The results indicate that the Mie calculation can be used to determine the largest dimension of irregularly shaped particles at sizes characteristic of Diesel soot and, for particles of known refractive index, tables can be constructed to determine the average porosity of the particles from the predicted index of refraction.