Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

Climate and energy scenarios for Ireland to 2050 using the Irish TIMES energy systems model

Due to growing concerns regarding the anthropogenic interference with the climate system, countries across the world are being challenged to develop effective strategies to mitigate climate change by reducing or preventing greenhouse gas (GHG) emissions. The European Union (EU) is committed to contribute to this challenge by setting a number of climate and energy targets for the years 2020, 2030 and 2050 and then agreeing effort sharing amongst Member States. This thesis focus on one Member State, Ireland, which faces specific challenges and is not on track to meet the targets agreed to date. Before this work commenced, there were no projections of energy demand or supply for Ireland beyond 2020. This thesis uses techno-economic energy modelling instruments to address this knowledge gap. It builds and compares robust, comprehensive policy scenarios, providing a means of assessing the implications of different future energy and emissions pathways for the Irish economy, Ireland’s energy mix and the environment. A central focus of this thesis is to explore the dynamics of the energy system moving towards a low carbon economy. This thesis develops an energy systems model (the Irish TIMES model) to assess the implications of a range of energy and climate policy targets and target years. The thesis also compares the results generated from the least cost scenarios with official projections and target pathways and provides useful metrics and indications to identify key drivers and to support both policy makers and stakeholder in identifying cost optimal strategies. The thesis also extends the functionality of energy system modelling by developing and applying new methodologies to provide additional insights with a focus on particular issues that emerge from the scenario analysis carried out. Firstly, the thesis develops a methodology for soft-linking an energy systems model (Irish TIMES) with a power systems model (PLEXOS) to improve the interpretation of the electricity sector results in the energy system model. The soft-linking enables higher temporal resolution and improved characterisation of power plants and power system operation Secondly, the thesis develops a methodology for the integration of agriculture and energy systems modelling to enable coherent economy wide climate mitigation scenario analysis. This provides a very useful starting point for considering the trade-offs between the energy system and agriculture in the context of a low carbon economy and for enabling analysis of land-use competition. Three specific time scale perspectives are examined in this thesis (2020, 2030, 2050), aligning with key policy target time horizons. The results indicate that Ireland’s short term mandatory emissions reduction target will not be achieved without a significant reassessment of renewable energy policy and that the current dominant policy focus on wind-generated electricity is misplaced. In the medium to long term, the results suggest that energy efficiency is the first cost effective measure to deliver emissions reduction; biomass and biofuels are likely to be the most significant fuel source for Ireland in the context of a low carbon future prompting the need for a detailed assessment of possible implications for sustainability and competition with the agri-food sectors; significant changes are required in infrastructure to deliver deep emissions reductions (to enable the electrification of heat and transport, to accommodate carbon capture and storage facilities (CCS) and for biofuels); competition between energy and agriculture for land-use will become a key issue. The purpose of this thesis is to increase the evidence-based underpinning energy and climate policy decisions in Ireland. The methodology is replicable in other Member States.

Residential consumption of gas and electricity in the U.S.: The role of prices and income

We study the residential demand for electricity and gas, working with nationwide household-level data that cover recent years, namely 1997-2007. Our dataset is a mixed panel/multi-year cross-sections of dwellings/households in the 50 largest metropolitan areas in the United States as of 2008. We estimate static and dynamic models of electricity and gas demand. We find strong household response to energy prices, both in the short and long term. From the static models, we get estimates of the own price elasticity of electricity demand in the -0.860 to -0.667 range, while the own price elasticity of gas demand is -0.693 to -0.566. These results are robust to a variety of checks. Contrary to earlier literature (Metcalf and Hassett, 1999; Reiss and White, 2005), we find no evidence of significantly different elasticities across households with electric and gas heat. The price elasticity of electricity demand declines with income, but the magnitude of this effect is small. These results are in sharp contrast to much of the literature on residential energy consumption in the United States, and with the figures used in current government agency practice. Our results suggest that there might be greater potential for policies which affect energy price than may have been previously appreciated. (C) 2011 Elsevier B.V. All rights reserved.

Can we meet targets for biofuels and renewable energy in transport given the constraints imposed by policy in agriculture and energy?

The deployment of biofuels is significantly affected by policy in energy and agriculture. In the energy arena, concerns regarding the sustainability of biofuel systems and their impact on food prices led to a set of sustainability criteria in EU Directive 2009/28/EC on Renewable Energy. In addition, the 10% biofuels target by 2020 was replaced with a 10% renewable energy in transport target. This allows the share of renewable electricity used by electric vehicles to contribute to the mix in achieving the 2020 target. Furthermore, only biofuel systems that effect a 60% reduction in greenhouse gas emissions by 2020 compared with the fuel they replace are allowed to contribute to meeting the target. In the agricultural arena, cross-compliance (which is part of EU Common Agricultural Policy) dictates the allowable ratio of grassland to total agricultural land, and has a significant impact on which biofuels may be supported. This paper outlines the impact of these policy areas and their implications for the production and use of biofuels in terms of the 2020 target for 10% renewable transport energy, focusing on Ireland. The policies effectively impose constraints on many conventional energy crop biofuels and reinforce the merits of using biomethane, a gaseous biofuel. The analysis shows that Ireland can potentially satisfy 15% of renewable energy in transport by 2020 (allowing for double credit for biofuels from residues and ligno-cellulosic materials, as per Directive 2009/28/EC) through the use of indigenous biofuels: grass biomethane, waste and residue derived biofuels, electric vehicles and rapeseed biodiesel. © 2010 Elsevier Ltd. All rights reserved.

Dynamic Modeling and Interaction of Hybrid Natural Gas and Electricity Supply System in Microgrid

Natural gas (NG) network and electric network are becoming tightly integrated by microturbines in the microgrid. Interactions between these two networks are not well captured by the traditional microturbine (MT) models. To address this issue, two improved models for single-shaft MT and split-shaft MT are proposed in this paper. In addition, dynamic models of the hybrid natural gas and electricity system (HGES) are developed for the analysis of their interactions. Dynamic behaviors of natural gas in pipes are described by partial differential equations (PDEs), while the electric network is described by differential algebraic equations (DAEs). So the overall network is a typical two-time scale dynamic system. Numerical studies indicate that the two-time scale algorithm is faster and can capture the interactions between the two networks. The results also show the HGES with a single-shaft MT is a weakly coupled system in which disturbances in the two networks mainly influence the dc link voltage of the MT, while the split-shaft MT is a strongly coupled system where the impact of an event will affect both networks.

Delocalization of a hole in van der Waals clusters: Ionization potential of rare-gas and small Hg_n clusters

The size dependence of the ionization potential I_p(n) of van der Waals (vdW) bound clusters has been calculated by using a model Hamiltonian, which includes electron hopping, vdW interactions, and charge-dipole interactions. The charge-density and dipole-density distributions for both neutral and ionized n-atom clusters are determined self-consistently. The competition between the polarization energy of the neutral atoms surrounding a partially localized hole and the tendency toward hole delocalization in the ionized clusters is found to dominate the size dependence of I_p(n). To test our theory, we culculate I_p(Xe_n) and I_p(Kr_n) for n \le 300. Good quantitative agreement with experiment is obtained. The theory is also applied to calculate I_p(Hg_n). Comparison with experiments suggests that in Hg_n^+ clusters with n \le 20 the positive charge is mainly distributed within a trimer which is situated at the center of the cluster and which polarizes the n - 3 surrounding neutral atoms.

Impact of sward type, cutting date and conditioning temperature on mass and energy flows in the integrated generation of solid fuel and biogas from semi-natural grassland

Energy production from biomass and the conservation of ecologically valuable grassland habitats are two important issues of agriculture today. The combination of a bioenergy production, which minimises environmental impacts and competition with food production for land with a conversion of semi-natural grasslands through new utilization alternatives for the biomass, led to the development of the IFBB process. Its basic principle is the separation of biomass into a liquid fraction (press fluid, PF) for the production of electric and thermal energy after anaerobic digestion to biogas and a solid fraction (press cake, PC) for the production of thermal energy through combustion. This study was undertaken to explore mass and energy flows as well as quality aspects of energy carriers within the IFBB process and determine their dependency on biomass-related and technical parameters. Two experiments were conducted, in which biomass from semi-natural grassland was conserved as silage and subjected to a hydrothermal conditioning and a subsequent mechanical dehydration with a screw press. Methane yield of the PF and the untreated silage was determined in anaerobic digestion experiments in batch fermenters at 37°C with a fermentation time of 13-15 and 27-35 days for the PF and the silage, respectively. Concentrations of dry matter (DM), ash, crude protein (CP), crude fibre (CF), ether extract (EE), neutral detergent fibre (NDF), acid detergent fibre (ADF), acid detergent ligning (ADL) and elements (K, Mg, Ca, Cl, N, S, P, C, H, N) were determined in the untreated biomass and the PC. Higher heating value (HHV) and ash softening temperature (AST) were calculated based on elemental concentration. Chemical composition of the PF and mass flows of all plant compounds into the PF were calculated. In the first experiment, biomass from five different semi-natural grassland swards (Arrhenaterion I and II, Caricion fuscae, Filipendulion ulmariae, Polygono-Trisetion) was harvested at one late sampling (19 July or 31 August) and ensiled. Each silage was subjected to three different temperature treatments (5°C, 60°C, 80°C) during hydrothermal conditioning. Based on observed methane yields and HHV as energy output parameters as well as literature-based and observed energy input parameters, energy and green house gas (GHG) balances were calculated for IFBB and two reference conversion processes, whole-crop digestion of untreated silage (WCD) and combustion of hay (CH). In the second experiment, biomass from one single semi-natural grassland sward (Arrhenaterion) was harvested at eight consecutive dates (27/04, 02/05, 09/05, 16/05, 24/05, 31/05, 11/06, 21/06) and ensiled. Each silage was subjected to six different treatments (no hydrothermal conditioning and hydrothermal conditioning at 10°C, 30°C, 50°C, 70°C, 90°C). Energy balance was calculated for IFBB and WCD. Multiple regression models were developed to predict mass flows, concentrations of elements in the PC, concentration of organic compounds in the PF and energy conversion efficiency of the IFBB process from temperature of hydrothermal conditioning as well as NDF and DM concentration in the silage. Results showed a relative reduction of ash and all elements detrimental for combustion in the PC compared to the untreated biomass of 20-90%. Reduction was highest for K and Cl and lowest for N. HHV of PC and untreated biomass were in a comparable range (17.8-19.5 MJ kg-1 DM), but AST of PC was higher (1156-1254°C). Methane yields of PF were higher compared to those of WCD when the biomass was harvested late (end of May and later) and in a comparable range when the biomass was harvested early and ranged from 332 to 458 LN kg-1 VS. Regarding energy and GHG balances, IFBB, with a net energy yield of 11.9-14.1 MWh ha-1, a conversion efficiency of 0.43-0.51, and GHG mitigation of 3.6-4.4 t CO2eq ha-1, performed better than WCD, but worse than CH. WCD produces thermal and electric energy with low efficiency, CH produces only thermal energy with a low quality solid fuel with high efficiency, IFBB produces thermal and electric energy with a solid fuel of high quality with medium efficiency. Regression models were able to predict target parameters with high accuracy (R2=0.70-0.99). The influence of increasing temperature of hydrothermal conditioning was an increase of mass flows, a decrease of element concentrations in the PC and a differing effect on energy conversion efficiency. The influence of increasing NDF concentration of the silage was a differing effect on mass flows, a decrease of element concentrations in the PC and an increase of energy conversion efficiency. The influence of increasing DM concentration of the silage was a decrease of mass flows, an increase of element concentrations in the PC and an increase of energy conversion efficiency. Based on the models an optimised IFBB process would be obtained with a medium temperature of hydrothermal conditioning (50°C), high NDF concentrations in the silage and medium DM concentrations of the silage.

Perfil de exposición ocupacional a polvo de cemento y sílice cristalina en procesos de cementación y Fracturamiento hidráulico en el sector Oil & Gas en Colombia: un estudio retrospectivo (2009 – 2013).

La exposición a polvo de cemento y sílice ha sido estudiada por años en países como Estados Unidos y Canadá, cuando el polvo de cemento se inhala durante diferentes actividades, se puede ocasionar afectación del tracto respiratorio de las personas expuestas. El estudio “Perfil de exposición ocupacional a polvo de cemento y sílice cristalina en procesos de cementación y Fracturamiento hidráulico en el sector Oil & Gas en Colombia: un estudio retrospectivo (2009 – 2013).” Permitió identificar las actividades funcionales que representan un riesgo potencial por la presencia de partículas aerosuspendidas, analizar una base de datos que reúne cerca de 18298 registros de evaluaciones higiénicas en el sector Oil & Gas, realizar posteriormente el cálculo de material particulado en la fracción respirable y sílice cristalina aplicables para cada proceso y el procesamiento de los datos estadísticamente, confrontar estos estimadores estadísticos con los valores límites permisibles definidos por el gobierno nacional, los resultados incluyeron la caracterización de un perfil de exposición ocupacional por actividad funcional para el proceso de cementación, la identificación de los trabajadores más expuestos según las condiciones de exposición y cuáles de estos perfiles superan los límites máximos permisibles para un turno de trabajo de 12 horas, esta información permitirá a los profesionales de la salud e higiene laboral orientar actividades de seguimiento, vigilancia y control en los grupos de exposición similar específicos. Para el proceso de fracturamiento hidráulico los datos encontrados no fueron estadísticamente significativos.

Shale Gas and the EU Internal Gas Market: Beyond the Hype and Hysteria. CEPS Working Document No. 369, September 2012

This paper analyses the interplay between shale gas and the EU internal gas market. Drawing on data presented in the 2012 International Energy Agency’s report on unconventional gas and additional scenario analyses performed by the Joint Research Centre, the paper is based on the assumption that shale gas will not fundamentally change the EU’s dependence on foreign gas supplies. It argues that attention should be shifted away from hyping shale gas to completing the internal gas market. Two main reasons are given for this. First, the internal gas market is needed to enable shale gas development in countries where there is political support for shale gas extraction. And second, a well-functioning internal gas market would, arguably, contribute much more to Europe’s security of supply than domestic shale gas exploitation. This has important implications for the shale gas industry. As it is hard to see how subsidies or exemptions from environmental legislation could be justified, shale gas development in Europe will only go ahead if it proves to be both economically and environmentally viable. It is thus up to the energy industry to demonstrate that this is the case.

Revisiting the Earth's sea-level and energy budgets from 1961 to 2008

We review the sea-level and energy budgets together from 1961, using recent and updated estimates of all terms. From 1972 to 2008, the observed sea-level rise (1.8 ± 0.2 mm yr−1 from tide gauges alone and 2.1 ± 0.2 mm yr−1 from a combination of tide gauges and altimeter observations) agrees well with the sum of contributions (1.8 ± 0.4 mm yr−1) in magnitude and with both having similar increases in the rate of rise during the period. The largest contributions come from ocean thermal expansion (0.8 mm yr−1) and the melting of glaciers and ice caps (0.7 mm yr−1), with Greenland and Antarctica contributing about 0.4 mm yr−1. The cryospheric contributions increase through the period (particularly in the 1990s) but the thermosteric contribution increases less rapidly. We include an improved estimate of aquifer depletion (0.3 mm yr−1), partially offsetting the retention of water in dams and giving a total terrestrial storage contribution of −0.1 mm yr−1. Ocean warming (90% of the total of the Earth's energy increase) continues through to the end of the record, in agreement with continued greenhouse gas forcing. The aerosol forcing, inferred as a residual in the atmospheric energy balance, is estimated as −0.8 ± 0.4 W m−2 for the 1980s and early 1990s. It increases in the late 1990s, as is required for consistency with little surface warming over the last decade. This increase is likely at least partially related to substantial increases in aerosol emissions from developing nations and moderate volcanic activity

Waste cooking oil as an energy resource: review of Chinese policies

Converting waste cooking oil into biofuel represents a three-win solution, dealing simultaneously with food security, pollution, and energy security. In this paper, we encode the policy documents of waste cooking oil refining biofuel in China based on content analysis, and explore the related policies from the two dimensions as basic policy tools and enterprises supply chain. Research indicates the weak institution coordination of policy issuing entities. Also, the findings show that tools of regulatory control and goal planning are overused. Policies of government procurement, outsourcing and biofuel consumption are relatively scarce. Generally, government focuses more on formulating policies from the strategic, administrative and regulatory aspects, while less on market-oriented initiatives as funding input and financial support.

Does fertilizer type and method of application cause significant differences in essential oil yield and composition in rosemary (Rosmarinus officinalis L.)?

Organic fertilizers based on seaweed extract potentially have beneficial effects on many crop plants. Herewe investigate the impact of organic fertilizer on Rosmarinus officinalis measured by both yield and oilquality. Plants grown in a temperature-controlled greenhouse with a natural photoperiod and a controlledirrigation system were treated with seaweed fertilizer and an inorganic fertilizer of matching mineralcomposition but with no organic content. Treatments were either by spraying on to the foliage or wateringdirect to the compost. The essential oil was extracted by hydro-distillation with a Clevenger apparatusand analysed by gas-chromatography mass-spectrometry (GC–MS) and NMR. The chemical composi-tions of the plants were compared, and qualitative differences were found between fertilizer treatmentsand application methods. Thus sprayed seaweed fertilizer showed a significantly higher percentage of�-pinene, �-phellandrene, �-terpinene (monoterpenes) and 3-methylenecycloheptene than other treat-ments. Italicene, �-bisabolol (sesquiterpenes), �-thujene, and E-isocitral (monoterpenes) occurred insignificantly higher percentages for plants watered with the seaweed extract. Each was significantly dif-ferent to the inorganic fertilizer and to controls. The seaweed treatments caused a significant increasein oil amount and leaf area as compared with both inorganic treatments and the control regardless ofapplication method.

Context dependency of comfort and energy performance in mixed mode offices

This article investigates the context dependency of comfort and energy performance in mixed-mode offices in the climate of Athens, Greece. It is based on a parametric study using the simulation software EnergyPlus. Context refers to different building design priorities on the real estate market (prestige, low cost and green), occupant behaviour scenarios (ideal and worst case) and cooling strategies (fixed and adaptive set points). Results are evaluated according to energy consumption and related greenhouse gas emissions, daylight autonomy, view and percentage of working time when heating and cooling are operating. The results indicate that a holistic approach to comfort and energy performance evaluation focused on the specific context of a building and its occupants is necessary to develop appropriate optimization strategies. In early design stages, such specific information is not yet available and ideal/worst-case scenarios can indicate the magnitude of influence of occupants compared to building design.

Differential effects of natural palm oil, chemically and enzymatically-modified palm oil on weight gain, blood lipid metabolites and fat deposition in a pediatric pig model

Background: Increasing prevalence of obesity and overweight in the Western world, continue to be a major health threat and is responsible for increased health care costs. Dietary intervention studies show a strong positive association between saturated fat intake and the development of obesity and cardiovascular disease. This study investigated the effect of positional distribution of palmitic acid (Sn-1, 2 & 3) of palm oil on cardiovascular health and development of obesity, using weaner pigs as a model for young children.

Methods: Male and female weaner piglets were randomly allocated to 4 dietary treatment groups: 1) pork lard (LRD); 2) natural palm olein (NPO); 3) chemically inter-esterified PO (CPO) and 4) enzymatically inter-esterified PO (EnPO) as the fat source. Diets were formulated with 11% lard or with palm olein in order to provide 31% of digestible energy from fat in the diet and were balanced for cholesterol, protein and energy across treatments.

Results: From 8 weeks onwards, pigs on EnPO diet gained (P < 0.05) more weight than all other groups. Feed conversion efficiency (feed to gain) over the 12 week experimental period did not vary between treatment groups. Plasma LDL-C content and LDL-C/HDL-C ratio in pigs fed natural PO tended to be lower compared to all other diets. The natural PO lowered (P < 0.02) the plasma triglyceride (TG) content relative to the lard or EnPO diets, but was not different from the CPO diet. The natural PO diet was associated with lower (P < 0.05) saturated fat levels in subcutaneous adipose tissue than the CPO and EnPO diets that had lower saturated fat levels than the lard diet. Female pigs had lower lean and higher fat and fat:lean ratio in the body compared with male pigs. No difference in weight gain or blood lipid parameters was observed between sexes.

Conclusions: The observations on plasma TG, muscle and adipose tissue saturated fatty acid contents and back fat (subcutaneous) thickness suggest that natural palm oil may reduce deposition of body fat. In addition, dietary supplementation with natural palm oil containing palmitic acid at different positions in meat producing animals may lead to the production of meat and meat products with lower saturated fats. An increase in fat content and a decrease in lean content in female pigs resulted in an increased body fat:lean ratio but gender had no effect on blood lipid parameters or insulin concentrations.