Ligand dynamics in myoglobin: calculation of infrared spectra for photodissociated NO

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Application of the entropy technique and genetic algorithms to construction site layout planning of medium-size projects

Genetic algorithms (GAs) have been introduced into site layout planning as reported in a number of studies. In these studies, the objective functions were defined so as to employ the GAs in searching for the optimal site layout. However, few studies have been carried out to investigate the actual closeness of relationships between site facilities; it is these relationships that ultimately govern the site layout. This study has determined that the underlying factors of site layout planning for medium-size projects include work flow, personnel flow, safety and environment, and personal preferences. By finding the weightings on these factors and the corresponding closeness indices between each facility, a closeness relationship has been deduced. Two contemporary mathematical approaches - fuzzy logic theory and an entropy measure - were adopted in finding these results in order to minimize the uncertainty and vagueness of the collected data and improve the quality of the information. GAs were then applied to searching for the optimal site layout in a medium-size government project using the GeneHunter software. The objective function involved minimizing the total travel distance. An optimal layout was obtained within a short time. This reveals that the application of GA to site layout planning is highly promising and efficient.

Correlation between regioselectivity and site charge in propene polymerisation catalysed by metallocene

The reactions of propene with [Zr(cyclopentadienyl)(2)Me](+) have been investigated using density functional theory in order to study the correlation between regioselectivity and site charge in propene polymerisation. The reaction paths of the 1,2 and 2,1 additions of the methyl group to propene have been established. The geometries and energies of the reactants, transition states and products have been obtained using both PBEPBE/LANL2DZ and B3LYP/LANL2DZ methodologies. The results with both density functionals show that the activation energy for 1,2-insertion is lower than that for 2,1-insertion (Fig. 5) and this is consistent with the experiment results. Also for both density functionals, the difference of the thermal dynamic driving forces between the 2,1 product named 2-21 and the 1,2 product named 2-12 is significantly lower than the difference between the energy barriers. It is noted that in the reactants, the Mulliken partial charge on the central carbon atom C2 is positive and it can be concluded that 1,2-insertion is favoured because it can proceed via a cationic reaction.

Ultra-distal tephra deposits from super-eruptions: examples from Toba, Indonesia and Taupo Volcanic Zone, New Zealand

Voluminous rhyolitic eruptions from Toba, Indonesia, and Taupo Volcanic Zone (TVZ), New Zealand, have dispersed volcanic ash over vast areas in the late Quaternary. The ~74 ka Youngest Toba Tuff (YTT) eruption deposited ash over the Bay of Bengal and the Indian subcontinent to the west. The ~340 ka Whakamaru eruption (TVZ) deposited the widespread Rangitawa Tephra, dominantly to the southeast (in addition to occurrences northwest of vent), extending across the landmass of New Zealand, and the South Pacific Ocean and Tasman Sea, with distal terrestrial exposures on the Chatham Islands. These super-eruptions involved ~2500 km^3 and ~1500 km3 of magma (dense-rock equivalent; DRE), respectively. Ultra-distal terrestrial exposures of YTT at two localities in India, Middle Son Valley, Madhya Pradesh, and Jurreru River Valley, Andhra Pradesh, at distances of >2000 km from the source caldera, show a basal ‘primary’ ashfall unit ~4 cm thick, although deposits containing reworked ash are up to ~3 m in total thickness. Exposures of Rangitawa Tephra on the Chatham Islands, >900 km from the source caldera, are ~15-30 cm thick. At more proximal localities (~200 km from source), Rangitawa Tephra is ~55-70 cm thick and characterized by a crystal-rich basal layer and normal grading. Both distal tephra deposits are characterized by very-fine ash (with high PM10 fractions) and are crystal-poor. Glass chemistry, stratigraphy and grain-size data for these distal tephra deposits are presented with comparisons of their correlation, dispersal and preservation. Using field observations, ash transport and deposition were modeled for both eruptions using a semi-analytical model (HAZMAP), with assumptions concerning average wind direction and strength during eruption, column shape and vent size. Model outputs provide new insights into eruption dynamics and better estimates of eruption volumes associ- ated with tephra fallout. Modeling based on observed YTT distal tephra thicknesses indicate a relatively low (<40 km high), very turbulent eruption column, consistent with deposition from a co-ignimbrite cloud extending over a broad region. Similarly, the Whakamaru eruption was modeled as producing a predominantly Plinian column (~45 km high), with dispersal to the southeast by strong prevailing winds. Significant ash fallout of the main dispersal direction, to the northwest of source, cannot be replicated in this modeling. The widespread dispersal of large volumes of fine ash from both eruptions may have had global environmental consequences, acutely affecting areas up to thousands of kilometers from vent.

Cloud statistics and cloud radiative effect for a low-mountain site

In 2007, the Atmospheric Radiation Measurement (ARM) Mobile Facility (AMF) was operated for a nine-month period in the Murg Valley, Black Forest, Germany, in support of the Convective and Orographically-induced Precipitation Study (COPS). The synergy of AMF and COPS partner instrumentation was exploited to derive a set of high-quality thermodynamic and cloud property profiles with 30 s resolution. In total, clouds were present 72% of the time, with multi-layer mixed phase (28.4%) and single-layer water clouds (11.3%) occurring most frequently. A comparison with the Cloudnet sites Chilbolton and Lindenberg for the same time period revealed that the Murg Valley exhibits lower liquid water paths (LWPs; median = 37.5 g m−2) compared to the two sites located in flat terrain. In order to evaluate the derived thermodynamic and cloud property profiles, a radiative closure study was performed with independent surface radiation measurements. In clear sky, average differences between calculated and observed surface fluxes are less than 2% and 4% for the short wave and long wave part, respectively. In cloudy situations, differences between simulated and observed fluxes, particularly in the short wave part, are much larger, but most of these can be related to broken cloud situations. The daytime cloud radiative effect (CRE), i.e. the difference of cloudy and clear-sky net fluxes, has been analysed for the whole nine-month period. For overcast, single-layer water clouds, sensitivity studies revealed that the CRE uncertainty is likewise determined by uncertainties in liquid water content and effective radius. For low LWP clouds, CRE uncertainty is dominated by LWP uncertainty; therefore refined retrievals, such as using infrared and/or higher microwave frequencies, are needed.

Analysis of pottery samples from Bourewa, the earliest known Lapita site in Fiji

We have carried out a thorough mineralogical analysis of 16 pottery samples from the Lapita site of Bourwera in Fiji, using micromorphological techniques with optical and polarising microscopes. While the overall mineralogy of all of the samples is similar the samples clearly divide into two groups, namely those with or without the mineral calcite. Our findings are backed up by chemical analysis using SEM–EDX and FTIR. SEM–EDX shows the clear presence of inclusions of calcite in some of the samples; FTIR shows bands arising from calcite in these samples. The study suggests that it is likely that more than one clay source was used for production of this pottery, but that most of the pottery comes from a single source. This finding is in line with previous studies which suggest some trading of pottery between the Fijian islands but a single source of clay for most of the pottery found at Bouwera. We found no evidence for the destruction of CaCO3 by heating upon production of the pottery in line with the known technology of the Lapita people who produced earthenware pottery but not high temperature ceramics.