Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

We demonstrate a chain length dependent crossover in the structural properties of linear hydrocarbon (n-alkane) chains using detailed atomistic simulations in explicit water. We identify a number of exotic structures of the polymer chain through energy minimization of representative snapshots collected from molecular dynamics trajectory. While the collapsed state is ring-like (circular) for small chains (CnH2n+2; n <= 20) and spherical for very long ones (n = 100), we find the emergence of ordered helical structures at intermediate lengths (n similar to 40). We find different types of disordered helices and toroid-like structures at n = 60. We also report a sharp transition in the stability of the collapsed state as a function of the chain length through relevant free energy calculations. While the collapsed state is only marginally metastable for C20H42, a clear bistable free energy surface emerges only when the chain is about 30 monomers long. For n = 30, the polymer exhibits an intermittent oscillation between the collapsed and the coil structures, characteristic of two stable states separated by a small barrier.

Jump Reorientation of Water Molecules Confined in Narrow Carbon Nanotubes

We used molecular dynamics (MD) simulations to study the reorientational dynamics of water molecules confined inside narrow carbon nanotubes immersed in a bath of water. Our simulations show that the confined water molecules exhibit bistability in their reorientational relaxation, which proceeds by angular jumps between the two stable states. The angular jump of a water molecule in the bulk involves the breaking of a hydrogen bond with one of its neighbors and the formation of a hydrogen bond with a different neighbor. In contrast, the angular jump of a confined water molecule corresponds to an interchange of the two hydrogen atoms that can form a hydrogen bond with the same neighbor. The free energy barrier between these two states is a few k(B)T. The analytic solution of a simplified two-state jump model that qualitatively explains the reorientational behavior observed in simulations is also presented.

Nutrient loss and water quality under extensive grazing in the upper Burdekin river catchment, North Queensland

Increased sediment and nutrient losses resulting from unsustainable grazing management in the Burdekin River catchment are major threats to water quality in the Great Barrier Reef Lagoon. To test the effects of grazing management on soil and nutrient loss, five 1 ha mini-catchments were established in 1999 under different grazing strategies on a sedimentary landscape near Charters Towers. Reference samples were also collected from watercourses in the Burdekin catchment during major flow events.Soil and nutrient loss were relatively low across all grazing strategies due to a combination of good cover, low slope and low rainfall intensities. Total soil loss varied from 3 to 20 kg haˉ¹ per event while losses of N and P ranged from 10 to 1900 g haˉ¹ and from 1 to 71 g haˉ¹ per event respectively. Water quality of runoff was considered moderate across all strategies with relatively low levels of total suspended sediment (range: 8-1409 mg lˉ¹), total N (range: 101-4000 ug lˉ¹) and total P (range: 14-609 ug lˉ¹). However, treatment differences are likely to emerge with time as the impacts of the different grazing strategies on land condition become more apparent.Samples collected opportunistically from rivers and creeks during flow events displayed significantly higher levels of total suspended sediment (range: 10-6010 mg lˉ¹), total N (range: 650-6350 ug lˉ¹) and total P (range: 50-1500 ug lˉ¹) than those collected at the grazing trial. These differences can largely be attributed to variation in slope, geology and cover between the grazing trial and different catchments. In particular, watercourses draining hillier, grano-diorite landscapes with low cover had markedly higher sediment and nutrient loads compared to those draining flatter, sedimentary landscapes.These preliminary data suggest that on relatively flat, sedimentary landscapes, extensive cattle grazing is compatible with achieving water quality targets, provided high levels of ground cover are maintained. In contrast, sediment and nutrient loss under grazing on more erodable land types is cause for serious concern. Long-term empirical research and monitoring will be essential to quantify the impacts of changed land management on water quality in the spatially and temporally variable Burdekin River catchment.

Interactions between a Trawl fishery and spatial closures for biodiversity conservation in the Great Barrier Reef World Heritage Area, Australia.

Background: The Queensland East Coast Otter Trawl Fishery (ECOTF) for penaeid shrimp fishes within Australia's Great Barrier Reef World Heritage Area (GBRWHA). The past decade has seen the implementation of conservation and fisheries management strategies to reduce the impact of the ECOTF on the seabed and improve biodiversity conservation. New information from electronic vessel location monitoring systems (VMS) provides an opportunity to review the interactions between the ECOTF and spatial closures for biodiversity conservation. Methodology and Results: We used fishing metrics and spatial information on the distribution of closures and modelled VMS data in a geographical information system (GIS) to assess change in effort of the trawl fishery from 2001-2009 and to quantify the exposure of 70 reef, non-reef and deep water bioregions to trawl fishing. The number of trawlers and the number of days fished almost halved between 2001 and 2009 and new spatial closures introduced in 2004 reduced the area zoned available for trawl fishing by 33%. However, we found that there was only a relatively minor change in the spatial footprint of the fishery as a result of new spatial closures. Non-reef bioregions benefited the most from new spatial closures followed by deep and reef bioregions. Conclusions/Significance: Although the catch of non target species remains an issue of concern for fisheries management, the small spatial footprint of the ECOTF relative to the size of the GBRWHA means that the impact on benthic habitats is likely to be negligible. The decline in effort as a result of fishing industry structural adjustment, increasing variable costs and business decisions of fishers is likely to continue a trend to fish only in the most productive areas. This will provide protection for most benthic habitats without any further legislative or management intervention.

Water-wave scattering by two submerged plane vertical barriers-Abel integral-equation approach

The classical problem of surface water-wave scattering by two identical thin vertical barriers submerged in deep water and extending infinitely downwards from the same depth below the mean free surface, is reinvestigated here by an approach leading to the problem of solving a system of Abel integral equations. The reflection and transmission coefficients are obtained in terms of computable integrals. Known results for a single barrier are recovered as a limiting case as the separation distance between the two barriers tends to zero. The coefficients are depicted graphically in a number of figures which are identical with the corresponding figures given by Jarvis (J Inst Math Appl 7:207-215, 1971) who employed a completely different approach involving a Schwarz-Christoffel transformation of complex-variable theory to solve the problem.

Light thresholds derived from seagrass loss in the coastal zone of the northern Great Barrier Reef, Australia

There is a world-wide trend for deteriorating water quality and light levels in the coastal zone, and this has been linked to declines in seagrass abundance. Localized management of seagrass meadow health requires that water quality guidelines for meeting seagrass growth requirements are available. Tropical seagrass meadows are diverse and can be highly dynamic and we have used this dynamism to identify light thresholds in multi-specific meadows dominated by Halodule uninervis in the northern Great Barrier Reef, Australia. Seagrass cover was measured at similar to 3 month intervals from 2008 to 2011 at three sites: Magnetic Island (MI) Dunk Island (DI) and Green Island (GI). Photosynthetically active radiation was continuously measured within the seagrass canopy, and three light metrics were derived. Complete seagrass loss occurred at MI and DI and at these sites changes in seagrass cover were correlated with the three light metrics. Mean daily irradiance (I-d) above 5 and 8.4 mol m(-2) d(-1) was associated with gains in seagrass at MI and DI, however a significant correlation (R = 0.649, p < 0.05) only occurred at MI. The second metric, percent of days below 3 mol m(-2) d(-1), correlated the most strongly (MI, R = -0.714, p < 0.01 and DI, R = -0.859, p = <0.001) with change in seagrass cover with 16-18% of days below 3 mol m(-2) d(-1) being associated with more than 50% seagrass loss. The third metric, the number of hours of light saturated irradiance (H-sat) was calculated using literature-derived data on saturating irradiance (E-k). H-sat correlated well (R = 0.686, p <0.01; and DI, R = 0.704, p < 0.05) with change in seagrass abundance, and was very consistent between the two sites as 4 H-sat was associated with increases in seagrass abundance at both sites, and less than 4 H-sat with more than 50% loss. At the third site (GI), small seasonal losses of seagrass quickly recovered during the growth season and the light metrics did not correlate (p > 0.05) with change in percent cover, except for I-d which was always high, but correlated with change in seagrass cover. Although distinct light thresholds were observed, the departure from threshold values was also important. For example, light levels that are well below the thresholds resulted in more severe loss of seagrass than those just below the threshold. Environmental managers aiming to achieve optimal seagrass growth conditions can use these threshold light metrics as guidelines; however, other environmental conditions, including seasonally varying temperature and nutrient availability, will influence seagrass responses above and below these thresholds. (C) 2012 Published by Elsevier Ltd.

Strategies for the management and treatment of coal seam gas associated water

Coal seam gas (CSG) is a growing industry in Queensland and represents a potential major employer and deliverer of financial prosperity for years to come. CSG is a natural gas composed primarily of methane and is found trapped underground in coal beds. During the gas extraction process, significant volumes of associated water are also produced. This associated water could be a valuable resource, however, the associated water comprises of various salt constituents that make it problematic for beneficial use. Consequently, there is a need to implement various water treatment strategies to purify the associated water to comply with Queensland’s strict guidelines and to mitigate environmental risks. The resultant brine is also of importance as ultimately it also has to be dealt with in an economical manner. In some ways it can be considered that the CSG industry does not face a water problem, as this has inherent value to society, but rather has a “salt issue” to solve. This study analyzes the options involved in both the water treatment and salt recovery processes. A brief overview of the constituents present in Queensland CS water is made to illustrate the challenges involved and a range of treatment technologies discussed. Water treatment technologies examined include clarification (ballasted flocculation, dissolved air flotation, electrocoagulation), membrane filtration (ultrafiltration), ion exchange softening and desalination (ion exchange, reverse osmosis desalination and capacitance deionization). In terms of brine management we highlighted reinjection, brine concentration ponds, membrane techniques (membrane distillation, forward osmosis), thermal methods, electrodialysis, electrodialysis reversal, bipolar membrane electrodialysis, wind assisted intensive evaporation, membrane crystallization, eutectic freeze crystallization and vapor compression. As an entirety this investigation is designed to be an important tool in developing CS water treatment management strategies for effective management in Queensland and worldwide.

A Paddock to reef monitoring and modelling framework for the Great Barrier Reef: Paddock and catchment component

Targets for improvements in water quality entering the Great Barrier Reef (GBR) have been set through the Reef Water Quality Protection Plan (Reef Plan). To measure and report on progress towards the targets set a program has been established that combines monitoring and modelling at paddock through to catchment and reef scales; the Paddock to Reef Integrated Monitoring, Modelling and Reporting Program (Paddock to Reef Program). This program aims to provide evidence of links between land management activities, water quality and reef health. Five lines of evidence are used: the effectiveness of management practices to improve water quality; the prevalence of management practice adoption and change in catchment indicators; long-term monitoring of catchment water quality; paddock & catchment modelling to provide a relative assessment of progress towards meeting targets; and finally marine monitoring of GBR water quality and reef ecosystem health. This paper outlines the first four lines of evidence. (C) 2011 Elsevier Ltd. All rights reserved.

Combined effect of double antireflection coating and reversible molecular doping on performance of few-layer graphene/n-silicon Schottky barrier solar cells

Few-layer graphene films were grown by chemical vapor deposition and transferred onto n-type crystalline silicon wafers to fabricate graphene/n-silicon Schottky barrier solar cells. In order to increase the power conversion efficiency of such cells the graphene films were doped with nitric acid vapor and an antireflection treatment was implemented to reduce the sunlight reflection on the top of the device. The doping process increased the work function of the graphene film and had a beneficial effect on its conductivity. The deposition of a double antireflection coating led to an external quantum efficiency up to 90% across the visible and near infrared region, the highest ever reported for this type of devices. The combined effect of graphene doping and antireflection treatment allowed to reach a power conversion efficiency of 8.5% exceeding the pristine (undoped and uncoated) device performance by a factor of 4. The optical properties of the antireflection coating were found to be not affected by the exposure to nitric acid vapor and to remain stable over time.

Monte Carlo Simulations of Molecular Clusters in Nucleation

A better understanding of the limiting step in a first order phase transition, the nucleation process, is of major importance to a variety of scientific fields ranging from atmospheric sciences to nanotechnology and even to cosmology. This is due to the fact that in most phase transitions the new phase is separated from the mother phase by a free energy barrier. This barrier is crossed in a process called nucleation. Nowadays it is considered that a significant fraction of all atmospheric particles is produced by vapor-to liquid nucleation. In atmospheric sciences, as well as in other scientific fields, the theoretical treatment of nucleation is mostly based on a theory known as the Classical Nucleation Theory. However, the Classical Nucleation Theory is known to have only a limited success in predicting the rate at which vapor-to-liquid nucleation takes place at given conditions. This thesis studies the unary homogeneous vapor-to-liquid nucleation from a statistical mechanics viewpoint. We apply Monte Carlo simulations of molecular clusters to calculate the free energy barrier separating the vapor and liquid phases and compare our results against the laboratory measurements and Classical Nucleation Theory predictions. According to our results, the work of adding a monomer to a cluster in equilibrium vapour is accurately described by the liquid drop model applied by the Classical Nucleation Theory, once the clusters are larger than some threshold size. The threshold cluster sizes contain only a few or some tens of molecules depending on the interaction potential and temperature. However, the error made in modeling the smallest of clusters as liquid drops results in an erroneous absolute value for the cluster work of formation throughout the size range, as predicted by the McGraw-Laaksonen scaling law. By calculating correction factors to Classical Nucleation Theory predictions for the nucleation barriers of argon and water, we show that the corrected predictions produce nucleation rates that are in good comparison with experiments. For the smallest clusters, the deviation between the simulation results and the liquid drop values are accurately modelled by the low order virial coefficients at modest temperatures and vapour densities, or in other words, in the validity range of the non-interacting cluster theory by Frenkel, Band and Bilj. Our results do not indicate a need for a size dependent replacement free energy correction. The results also indicate that Classical Nucleation Theory predicts the size of the critical cluster correctly. We also presents a new method for the calculation of the equilibrium vapour density, surface tension size dependence and planar surface tension directly from cluster simulations. We also show how the size dependence of the cluster surface tension in equimolar surface is a function of virial coefficients, a result confirmed by our cluster simulations.

Tribology of steel/steel interaction in oil-in-water mulsion; a rationale for lubricity

Oil droplets are dispersed in water by an anionic urfactant to form an emulsion. The lubricity of this emulsion in steel/steel interaction is explored in a ball on flat nanotribometer. The droplet size and charge are measured using dynamic light scattering, while the substrate charge density is estimated using the pH titration method. These data are combined to calculate the DLVO forces for the droplets generated for a range of surfactant concentration and two oil to water volume ratios. The droplets have a clear bi-modal size distribution. The study shows that the smaller droplets which experience weak repulsion are situated (at the highest DLVO barrier) much closer to the substrate than thebigger droplets, which experience the same DLVO force, are. We suggest that the smaller droplets thus play a more important role in lubricity than what the bigger droplets do. The largest volume of such small droplets occurs in the 0.5 mM-1 mM range of surfactant concentration and 1% oil to water volume ratio, where the coefficient of friction is also observed to be the least. (C) 2010 Elsevier Inc. All rights reserved.

Structure of the hydrogen-bonded water molecule in crystals

A correlation of the structural data on IS hydrates obtained by x-ray diffraction, neutron diffraction, and proton magnetic resonance reveals that when a water molecule is hydrogen bonded into a crystal structure and the angle subtended at the donor water oxygen by the acceptor atoms deviates from the vapor H-O-H angle, bent hydrogen bonds are formed in preference to distortion of the H-O-H angle. Theoretical justification for this result is obtained from energy considerations by calculating the energy of formation of bent hydrogen bonds on the basis of the Lippincott-Schroeder potential function model for the hydrogen bond and the energy of deformation of the H-O-H angle from spectroscopic force constants.

Monte Carlo simulations of molecular clusters in nucleation

A better understanding of the limiting step in a first order phase transition, the nucleation process, is of major importance to a variety of scientific fields ranging from atmospheric sciences to nanotechnology and even to cosmology. This is due to the fact that in most phase transitions the new phase is separated from the mother phase by a free energy barrier. This barrier is crossed in a process called nucleation. Nowadays it is considered that a significant fraction of all atmospheric particles is produced by vapor-to liquid nucleation. In atmospheric sciences, as well as in other scientific fields, the theoretical treatment of nucleation is mostly based on a theory known as the Classical Nucleation Theory. However, the Classical Nucleation Theory is known to have only a limited success in predicting the rate at which vapor-to-liquid nucleation takes place at given conditions. This thesis studies the unary homogeneous vapor-to-liquid nucleation from a statistical mechanics viewpoint. We apply Monte Carlo simulations of molecular clusters to calculate the free energy barrier separating the vapor and liquid phases and compare our results against the laboratory measurements and Classical Nucleation Theory predictions. According to our results, the work of adding a monomer to a cluster in equilibrium vapour is accurately described by the liquid drop model applied by the Classical Nucleation Theory, once the clusters are larger than some threshold size. The threshold cluster sizes contain only a few or some tens of molecules depending on the interaction potential and temperature. However, the error made in modeling the smallest of clusters as liquid drops results in an erroneous absolute value for the cluster work of formation throughout the size range, as predicted by the McGraw-Laaksonen scaling law. By calculating correction factors to Classical Nucleation Theory predictions for the nucleation barriers of argon and water, we show that the corrected predictions produce nucleation rates that are in good comparison with experiments. For the smallest clusters, the deviation between the simulation results and the liquid drop values are accurately modelled by the low order virial coefficients at modest temperatures and vapour densities, or in other words, in the validity range of the non-interacting cluster theory by Frenkel, Band and Bilj. Our results do not indicate a need for a size dependent replacement free energy correction. The results also indicate that Classical Nucleation Theory predicts the size of the critical cluster correctly. We also presents a new method for the calculation of the equilibrium vapour density, surface tension size dependence and planar surface tension directly from cluster simulations. We also show how the size dependence of the cluster surface tension in equimolar surface is a function of virial coefficients, a result confirmed by our cluster simulations.

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Contribution of different physical forces to the disjoining pressure of a thin water film being pressed by an oil droplet

With an objective to understand the nature of forces which contribute to the disjoining pressure of a thin water film on a steel substrate being pressed by an oil droplet, two independent sets of experiments were done. (i) A spherical silica probe approaches the three substrates; mica, PTFE and steel, in a 10 mM electrolyte solution at two different pHs (3 and 10). (ii) The silica probe with and without a smeared oil film approaches the same three substrates in water (pH = 6). The surface potential of the oil film/water was measured using a dynamic light scattering experiment. Assuming the capacity of a substrate for ion exchange the total interaction force for each experiment was estimated to include the Derjaguin-Landau-Verwey-Overbeek (DLVO) force, hydration repulsion, hydrophobic attraction and oil-capillary attraction. The best fit of these estimates to the force-displacement characteristics obtained from the two sets of experiment gives the appropriate surface potentials of the substrates. The procedure allows an assessment of the relevance of a specific physical interaction to an experimental configuration. Two of the principal observations of this work are: (i) The presence of a surface at constant charge, as in the presence of an oil film on the probe, significantly enhances the counterion density over what is achieved when both the surfaces allow ion exchange. This raises the corresponding repulsion barrier greatly. (ii) When the substrate surface is wettable by oil, oil-capillary attraction contributes substantially to the total interaction. If it is not wettable the oil film is deformed and squeezed out. (C) 2010 Elsevier Inc. All rights reserved.