Non-quantized minimum free energy in untranslated region exons

In an attempt to improve automated gene prediction in the untranslated region of a gene, we completed an in-depth analysis of the minimum free energy for 8,689 sub-genetic DNA sequences. We expanded Zhang's classification model and classified each sub-genetic sequence into one of 27 possible motifs. We calculated the minimum free energy for each motif to explore statistical features that correlate to biologically relevant sub-genetic sequences. If biologically relevant sub-genetic sequences fall into distinct free energy quanta it may be possible to characterize a motif based on its minimum free energy. Proper characterization of motifs can lead to greater understanding in automated genefinding, gene variability and the role DNA structure plays in gene network regulation.

Our analysis determined: (1) the average free energy value for exons, introns and other biologically relevant sub-genetic sequences, (2) that these subsequences do not exist in distinct energy quanta, (3) that introns exist however in a tightly coupled average minimum free energy quantum compared to all other biologically relevant sub-genetic sequence types, (4) that single exon genes demonstrate a higher stability than exons which span the entire coding sequence as part of a multi-exon gene and (5) that all motif types contain a free energy global minimum at approximately nucleotide position 1,000 before reaching a plateau. These results should be relevant to the biochemist and bioinformatician seeking to understand the relationship between sub-genetic sequences and the information behind them.

Embodied energy in buildings : wood versus concrete - reply to Börjesson and Gustavsson

We analyse the wood and concrete designs of the Wälludden building described by Börjesson et al. (Energy Policy 28 (2000) 575) in terms of their embodied energy, employing an environmentally extended input–output framework in a tiered hybrid life-cycle assessment, and in a structural path analysis. We illustrate the complexity of the inter-industry supply chains underlying the upstream energy requirements for the building options, and demonstrate that higher-order inputs are difficult to capture in a conventional process analysis. Our calculations show that Börjesson and Gustavsson's estimates of energy requirements and greenhouse gas emissions are underestimated by a factor of about 2, and that corresponding greenhouse gas balances are positive at about 30 t C-eq. Nevertheless, Börjesson and Gustavsson's general result—the concrete-framed building causing higher emissions—still holds.

The 'caffeine-sweetness' effect; potential reduction of energy in caffeinated sugar-sweetened soft drinks

Background – Excessive consumption of sugar sweetened beverages (SSB) is a contributing factor in the occurrence of overweight and obesity. The high energy intake, low satiation, high glycemic index, and intense marketing are all thought to contribute to their over consumption. In addition, the role of the mildly-addictive chemical caffeine in SSB has been questioned (Griffiths and Vernotica, 2000, Keast and Riddell, 2007). We have previously shown that low concentrations of caffeine may decrease sweetness of sugars and thereby result in excess energy in SSB formulations (Ebbeling et al., 2006).
Objective – Without noticeably affecting flavour, to determine potential energy reduction when decreasing sucrose concentration from caffeinated and de-caffeinated SSB.
Design – Human psychophysical taste evaluations in water, sucrose and model SSB. Triangle forced-choice ascending method of limits was used to determine caffeine taste threshold in water and sucrose (n= 62). Directional paired comparison tests to determine 1/ the influence of caffeine on sweetness of sucrose (n= 23), and 2/ the nonperceivable difference when decreasing the sucrose and caffeine concentrations in a model SSB (n= 30).
Outcomes – Caffeine, at sub-threshold concentrations in common SSB (0.67mM) can be perceived in sucrose solutions because it significantly inhibits sweetness (p<0.001), the ‘caffeine sweetness effect’. Presumably coremoval of caffeine and sucrose could be achieved without affecting the sweetness of the SSB. Removing caffeine from the model SSB allowed an energy reduction of 137.4 KJ per 500 ml serving (12.6% sucrose reduction) without noticeably affecting flavour for 80% of the population. The energy reduction possible without co-removal of caffeine was a more modest 32 KJ per 500 ml serving (3.5% sucrose reduction).
Conclusion – Sub-threshold concentrations of caffeine suppress sweetness resulting in higher concentrations of sugars in SSB. Excessive consumption of SSB is linked to the obesity epidemic, and we suggest the removal of caffeine and subsequent removal of 137.4 KJ energy will have long term public health benefits.

The potential to reduce the embodied energy in construction through the use of renewable materials

The threat of dangerous levels of global warming demand that we significantly reduce carbon emissions over the coming decades. Globally, carbon emissions from all energy end-uses in buildings in 2004 were estimated to be 8.6 Gt CO2 or almost one quarter of total CO2 emissions (IPCC 2007). In Australia, nearly ten per cent of greenhouse gases come from the residential sector (DCCEE 2012). However, it is not merely the operation of the buildings that contributes to their CO2 emissions, but the energy used over their entire life cycle. Research has demonstrated that the embodied energy of the construction materials used in a building can sometimes equal the operational energy over the building’s entire lifetime (Crawford 2011). Therefore the materials used in construction need to be carefully considered. Conventional building materials not only represent high levels of embodied energy but also use resources that are finite and are being depleted. Renewable building materials are those materials that can be regenerated quickly enough to remove the threat of depletion and in theory their production could be carbon-neutral. To assess the potential for renewable building materials to reduce the embodied energy content of residential construction, the embodied energy of a small residential building has been determined. Wherever possible, the conventional construction materials were then replaced by commercially-available renewable building materials. The embodied energy of the building was then recalculated. The analysis showed that the embodied energy of the building could be reduced from 7.5 GJ per m2 to 5.4 GJ per m2 i.e. by 28%. The commercial availability of renewable materials, however, was a limiting factor and indicated that the industry is not yet well positioned to embrace this strategy to reduce embodied energy of construction. While some conventional building materials could readily be replaced, in many instances a renewable substitute could not be found.

Impact of nanodiffusion on the stacking fault energy in high-strength steels

A key requirement of modern steels – the combination of high strength and high deformability – can best be achieved by enabling a local adaptation of the microstructure during deformation. A local hardening is most efficiently obtained by a modification of the stacking sequence of atomic layers, resulting in the formation of twins or martensite. Combining ab initio calculations with in situ transmission electron microscopy, we show that the ability of a material to incorporate such stacking faults depends on its overall chemical composition and, importantly, the local composition near the defect, which is controlled by nanodiffusion. Specifically, the role of carbon for the stacking fault energy in high-Mn steels is investigated. Consequences for the long-term mechanical properties and the characterisation of these materials are discussed.

Potentialities of renewable energy in Victoria, Australia

In utility power system, electricity demand is being covered largely by fossil fueled power generation, which contributes high level of GHG (greenhouse gas) emission and causes global warming worldwide. In order to reduce GHG emission level, most of the countries in the world targeting towards green energy that is power generation from RE (renewable energy) sources. In this paper, it is considered to study prospects of RE sources in particular, solar and wind in Victoria State which are abundant as compared to other sources of renewable. The wind and solar energy feasibility study and sensitivity analysis has been done for Victoria with the aid of HOMER (hybrid optimization model of electric renewable) simulation software. From the study, it has clearly evicted that wind energy combinational HPS (hybrid power system) has more contribution, and high potential than solar PV (photovoltaic) systems for a particular location. This study also investigates the influences of energy storage in the proposed HPS.

Prospects of renewable energy in semi-arid region

Continuous usage of fossil fuels and other conventional resources to meet the growing demand has resulted in in-creased energy crisis and greenhouse gas emissions. Hence, it is essential to use renewable energy sources for more reliable, effective, sustainable and pollution free transmission and distribution networks. Therefore, to facilitate large-scale integration of renewable energy in particular wind and solar photovoltaic (PV) energy, this paper presents the feasibility analysis for semi-arid climate and finds the most suitable places in North East region of Victoria for re-newable energy generation. For economic and environmental analysis, Hybrid Optimization Model for Electric Re-newables (HOMER) has used to investigate the prospects of wind and solar energy considering the Net Present Cost (NPC), Cost of Energy (COE) and Renewable fraction (RF). Six locations are selected from North East region of Victo-ria and simulations are performed. From the feasibility analysis, it can be concluded that Mount Hotham is one of the most suitable locations for wind energy generation while Wangaratta is the most suitable location for solar energy generation. Mount Hotham is also the best suitable locations in North East region for hybrid power systems i.e., com-bination of both wind and solar energy generation.

Net Energy Analysis of Double Glazing for Residential Buildings in Temperate Climates

Energy used in buildings is a major contributor to Australia’s energy consumption and associated environmental impacts. The advent of complex glazing systems such as double glazing, particularly in northern America and Europe, has partially closed a weak thermal link in the building envelope. In milder climates, however, building envelope features may not be as effective in life cycle energy terms, i.e. including the embodied energy of their manufacture. A net energy analysis compares the savings in operational energy to the additional requirements for embodied energy, in terms of the energy payback period and energy return on investment. The effectiveness of double glazing is determined for an Australian residential building. A wide range of building operation regimes was simulated. These results support the principle of installing double glazing in residential buildings in Melbourne, Australia, at least in terms of net primary energy savings.

Solar energy use for energy savings in dairy processing plants

New Zealand is one of the world’s largest producers of dairy products and has a climate with high levels of solar radiation; however, the use of solar energy in the dairy processing industry has received limited attention. An examination of historical records found that the annual peak in New Zealand milk production and processing occurs at a time when solar radiation levels are increasing markedly. An F-Chart analysis was used to simulate the performance of large-area arrays of solar collectors and to determine their suitability for heating and cooling in a dairy processing environment. For the study four types of solar collectors were analysed: glazed flat plates, evacuated tubes, evacuated tubes with CPC reflectors and a building-integrated solar collector under development at the University of Waikato (UoW). It was found that of these echnologies, both flat plate and evacuated tubes with CPC reflectors could make useful heating and cooling contributions. Furthermore, the solar fraction was determined mainly by the collector area to storage volume ratio. Finally, it was found that the UoW building-integrated solar collector could make a significant contribution to energy use in dairies and may be an attractive future technology for the industry.

Numerical investigation of the turbulent energy budget in the wake of freely oscillating elastically mounted cylinder at low reduced velocities

We present a numerical study of the turbulent kinetic energy budget in the wake of cylinders undergoing Vortex-Induced Vibration (VIV). We show three-dimensional Large Eddy Simulations (LES) of an elastically mounted circular cylinder in the synchronization regime at Reynolds number of Re=8000. The Immersed Boundary Method (IBM) is used to account for the presence of the cylinder. The flow field in the wake is decomposed using the triple decomposition splitting the flow variables in mean, coherent and stochastic components. The energy transfer between these scales of motions are then studied and the results of the free oscillation are compared to those of a forced oscillation. The turbulent kinetic energy budget shows that the maximum amplitude of VIV is defined by the ability of the mean flow to feed energy to the coherent structures in the wake. At amplitudes above this maximum amplitude, the energy of the coherent structures needs to be fed additionally by small scale, stochastic energy in form of backscatter to sustain its motion. Furthermore, we demonstrate that the maximum amplitude of the VIV is defined by the integral length scale of the turbulence in the wake