Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: Preserved folding energy drives fiber formation

Most gram-negative pathogens express fibrous adhesive virulence organelles that mediate targeting to the sites of infection. The F1 capsular antigen from the plague pathogen Yersinia pestis consists of linear fibers of a single subunit (Caf1) and serves as a prototype for nonpilus organelles assembled via the chaperone/usher pathway. Genetic data together with high-resolution X-ray structures corresponding to snapshots of the assembly process reveal the structural basis of fiber formation. Comparison of chaperone bound Caf1 subunit with the subunit in the fiber reveals a novel type of conformational change involving the entire hydrophobic core of the protein. The observed conformational change suggests that the chaperone traps a high-energy folding intermediate of Caf1. A model is proposed in which release of the subunit allows folding to be completed, driving fiber formation.

An investigation of the germylene addition reaction, GeH2+C2H2: Time-resolved gas-phase kinetic studies and quantum chemical calculations of the reaction energy surface

Time resolved studies of germylene, GeH2, generated by laser flash photolysis of 3,4-dimethylgermacyclopentene-3, have been carried out to obtain rate constants for its bimolecular reaction with acetylene, C2H2. The reaction was studied in the gas-phase over the pressure range 1-100 Tort, with SF6 as bath gas, at 5 temperatures in the range 297-553 K. The reaction showed a very slight pressure dependence at higher temperatures. The high pressure rate constants (obtained by extrapolation at the three higher temperatures) gave the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) (-10.94 +/- 0.05) + (6.10 +/- 0.36 kJ mol(-1))/RTln10. These Arrhenius parameters are consistent with a fast reaction occurring at approximately 30% of the collision rate at 298 K. Quantum chemical calculations (both DFT and ab initio G2//B3LYP and G2//QCISD) of the GeC2H4 potential energy surface (PES), show that GeH2 + C2H2 react initially to form germirene which can isomerise to vinylgermylene with a relatively low barrier. RRKM modelling, based on a loose association transition state, but assuming vinylgermylene is the end product (used in combination with a weak collisional deactivation model) predicts a strong pressure dependence using the calculated energies, in conflict with the experimental evidence. The detailed GeC2H4 PES shows considerable complexity with ten other accessible stable minima (B3LYP level), the three most stable of which are all germylenes. Routes through this complex surface were examined in detail. The only product combination which appears capable of satisfying the (P-3) + C2H4.C2H4 was confirmed as a product by GC observed lack of a strong pressure dependence is Ge(P-3) + C2H4. C2H4 was confirmed as a product by GC analysis. Although the formation of these products are shown to be possible by singlet-triplet curve crossing during dissociation of 1-germiranylidene (1-germacyclopropylidene), it seems more likely (on thermochernical grounds) that the triplet biradical, (GeCH2CH2.)-Ge-., is the immediate product precursor. Comparisons are made with the reaction of SiH2 with C2H2.

Self assembly of a model amphiphilic phenylalanine peptide/polyethylene glycol block copolymer in aqueous solution

There has been great interest recently in peptide amphiphiles and block copolymers containing biomimetic peptide sequences due to applications in bionanotechnology. We investigate the self-assembly of the peptide-PEG amphiphile FFFF-PEG5000 containing the hydrophobic sequence of four phenylalanine residues conjugated to PEG of molar mass 5000. This serves as a simple model peptide amphiphile. At very low concentration, association of hydrophobic aromatic phenylalanine residues occurs, as revealed by circular dichroism and UV/vis fluorescence experiments. A critical aggregation concentration associated with the formation of hydrophobic domains is determined through pyrene fluorescence assays. At higher concentration, defined beta-sheets develop as revealed by FTIR spectroscopy and X-ray diffraction. Transmission electron microscopy reveals self-assembled straight fibril structures. These are much shorter than those observed for amyloid peptides, the finite length may be set by the end cap energy due to the hydrophobicity of phenylalanine. The combination of these techniques points to different aggregation processes depending on concentration. Hydrophobic association into irregular aggregates occurs at low concentration, well-developed beta-sheets only developing at higher concentration. Drying of FFFF-PEG5000 solutions leads to crystallization of PEG, as confirmed by polarized optical microscopy (POM), FTIR and X-ray diffraction (XRD). PEG crystallization does not disrupt local beta-sheet structure (as indicated by FTIR and XRD). However on longer lengthscales the beta-sheet fibrillar structure is perturbed because spheruilites from PEG crystallization are observed by POM. (C) 2009 Elsevier B.V. All rights reserved.

A case of four-coordinate silver(I) adopting a high energy planar geometry. Experiment and theory

The ligands PhL and MeL are obtained by condensing 2-formylpyridine with benzil dihydrazone and diacetyl dihydrazone, respectively, in 2: 1 molar proportion. With silver( I), PhL yields a double-stranded dinuclear cationic helicate 1 in which the metal is tetrahedral but MeL gives a cationic one-dimensional polymeric complex 2 where silver( I) is distorted square planar and the ligand backbone is nearly planar. In both complexes, metal: ligand ratio is 1: 1. Ab initio calculations on the ligands at the HF/6-31+G* level reveal that while PhL strongly prefers a helical conformation, MeL has a natural inclination to remain in a planar conformation. Density functional theory calculations on model silver( I) complexes show that formation of the linear polymer in the case of MeL is also an important factor in imposing the planar geometry of Ag(I) in 2.

Inelastic neutron scattering in spectroscopic studies of hydrogen on carbon-supported catalysts-experimental spectra and computed spectra of model systems

Inelastic neutron scattering spectroscopy has been used to observe and characterise hydrogen on the carbon component of a Pt/C catalyst. INS provides the complete vibration spectrum of coronene, regarded as a molecular model of a graphite layer. The vibrational modes are assigned with the aid of ab initio density functional theory calculations and the INS spectra by the a-CLIMAX program. A spectrum for which the H modes of coronene have been computationally suppressed, a carbon-only coronene spectrum, is a better representation of the spectrum of a graphite layer than is coronene itself. Dihydrogen dosing of a Pt/C catalyst caused amplification of the surface modes of carbon, an effect described as H riding on carbon. From the enhancement of the low energy carbon modes (100-600 cm(-1)) it is concluded that spillover hydrogen becomes attached to dangling bonds at the edges of graphitic regions of the carbon support. (C) 2003 Elsevier Science B.V. All rights reserved.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively. (C) 2008 American Institute of Physics.

Model for calculating the sustainable building index (SBI) in the kingdom of Bahrain

We have developed a model that allows players in the building and construction sector and the energy policy makers on energy strategies to be able to perceive the interest of investors in the kingdom of Bahrain in conducting Building Integrated Photovoltaic (BIPV) or Building integrated wind turbines (BIWT) projects, i.e. a partial sustainable or green buildings. The model allows the calculation of the Sustainable building index (SBI), which ranges from 0.1 (lowest) to 1.0 (highest); the higher figure the more chance for launching BIPV or BIWT. This model was tested in Bahrain and the calculated SBI was found 0.47. This means that an extensive effort must be made through policies on renewable energy, renewable energy education, and incentives to BIPV and BIWT projects, environmental awareness and promotion to clean and sustainable energy for building and construction projects. Our model can be used internationally to create a "Global SBI" database. The Sustainable building and construction initiative (SBCI), United Nation, can take the task for establishing such task using this model.

A multicriteria lifespan energy efficiency approach to intelligent building assessment

This paper presents a multicriteria decision-making model for lifespan energy efficiency assessment of intelligent buildings (IBs). The decision-making model called IBAssessor is developed using an analytic network process (ANP) method and a set of lifespan performance indicators for IBs selected by a new quantitative approach called energy-time consumption index (ETI). In order to improve the quality of decision-making, the authors of this paper make use of previous research achievements including a lifespan sustainable business model, the Asian IB Index, and a number of relevant publications. Practitioners can use the IBAssessor ANP model at different stages of an IB lifespan for either engineering or business oriented assessments. Finally, this paper presents an experimental case study to demonstrate how to use IBAssessor ANP model to solve real-world design tasks.

A sensor based intelligent building assessment model

While building provides shelter for human being, the previous models for assessing the intelligence of a building seldom consider the responses of occupants. In addition, the assessment is usually conducted by an authority organization on a yearly basis, thus can seldom provide timely assistance for facility manager to improve his daily facility maintenance performance. By the extending the law of entropy into the area of intelligent building, this paper demonstrate that both energy consumption and the response of occupants are important when partially assessing the intelligence of a building. This study then develops a sensor based real time building intelligence (BI) assessment model. An experimental case study demonstrates how the model can be implemented. The developed model can address the two demerits of the previous BI assessment model.

A conceptual design of a wireless sensor actuator system for optimising energy and well-being in a building

This article presents a prototype model based on a wireless sensor actuator network (WSAN) aimed at optimizing both energy consumption of environmental systems and well-being of occupants in buildings. The model is a system consisting of the following components: a wireless sensor network, `sense diaries', environmental systems such as heating, ventilation and air-conditioning systems, and a central computer. A multi-agent system (MAS) is used to derive and act on the preferences of the occupants. Each occupant is represented by a personal agent in the MAS. The sense diary is a new device designed to elicit feedback from occupants about their satisfaction with the environment. The roles of the components are: the WSAN collects data about physical parameters such as temperature and humidity from an indoor environment; the central computer processes the collected data; the sense diaries leverage trade-offs between energy consumption and well-being, in conjunction with the agent system; and the environmental systems control the indoor environment.

LIPGENE food-exchange model for alteration of dietary fat quantity and quality in free-living participants from eight European countries

Controlled human intervention trials are required to confirm the hypothesis that dietary fat quality may influence insulin action. The aim was to develop a food-exchange model, suitable for use in free-living volunteers, to investigate the effects of four experimental diets distinct in fat quantity and quality: high SFA (HSFA); high MUFA (HMUFA) and two low-fat (LF) diets, one supplemented with 1.24g EPA and DHA/d (LFn-3). A theoretical food-exchange model was developed. The average quantity of exchangeable fat was calculated as the sum of fat provided by added fats (spreads and oils), milk, cheese, biscuits, cakes, buns and pastries using data from the National Diet and Nutrition Survey of UK adults. Most of the exchangeable fat was replaced by specifically designed study foods. Also critical to the model was the use of carbohydrate exchanges to ensure the diets were isoenergetic. Volunteers from eight centres across Europe completed the dietary intervention. Results indicated that compositional targets were largely achieved with significant differences in fat quantity between the high-fat diets (39.9 (SEM 0.6) and 38.9 (SEM 0.51) percentage energy (%E) from fat for the HSFA and HMUFA diets respectively) and the low-fat diets (29.6 (SEM 0.6) and 29.1 (SEM 0.5) %E from fat for the LF and LFn-3 diets respectively) and fat quality (17.5 (SEM 0.3) and 10.4 (SEM 0.2) %E front SFA and 12.7 (SEM 0.3) and 18.7 (SEM 0.4) %E MUFA for the HSFA and HMUFA diets respectively). In conclusion, a robust, flexible food-exchange model was developed and implemented successfully in the LIPGENE dietary intervention trial.

Successful manipulation of the quality and quantity of fat and carbohydrate consumed by free-living individuals using a food exchange model

Our objective in this study was to develop and implement an effective intervention strategy to manipulate the amount and composition of dietary fat and carbohydrate (CHO) in free-living individuals in the RISCK study. The study was a randomized, controlled dietary intervention study that was conducted in 720 participants identified as higher risk for or with metabolic syndrome. All followed a 4-wk run-in reference diet [high saturated fatty acids (SF)/high glycemic index (GI)]. Volunteers were randomized to continue this diet for a further 24 wk or to I of 4 isoenergetic prescriptions [high monounsaturated fatty acids (MUFA)/high GI; high MUFA/low GI; low fat (LF)/high GI; and LF/low GI]. We developed a food exchange model to implement each diet. Dietary records and plasma phospholipid fatty acids were used to assess the effectiveness of the intervention strategy. Reported fat intake from the LF diets was significantly reduced to 28% of energy (%E) compared with 38% E from the HM and LF diets. SF intake was successfully decreased in the HM and LF diets was similar to 10% E compared with 17% E in the reference diet (P = 0.001). Dietary MUFA in the HIM diets was similar to 17% E, significantly higher than in the reference (12% E) and LF diets (10% E) (P = 0.001). Changes in plasma phospholipid fatty acids provided further evidence for the successful manipulation of fat intake. The GI of the HGI and LGI arms differed by similar to 9 points (P = 0.001). The food exchange model provided an effective dietary strategy for the design and implementation across multiple sites of 5 experimental diets with specific targets for the proportion of fat and CHO. J. Nutr. 139: 1534-1540, 2009.

Modelling energy consumption of relay-enabled MAC protocols in ad hoc networks

To enhance the throughput of ad hoc networks, dual-hop relay-enabled transmission schemes have recently been proposed. Since in ad hoc networks throughput is normally related to their energy consumption, it is important to examine the impact of using relay-enabled transmissions on energy consumption. In this paper, we present an analytical energy consumption model for dual-hop relay-enabled medium access control (MAC) protocols. Based on the recently reported relay-enabled distributed coordination function (rDCF), we have shown the efficacy of the proposed analytical model. This is a generalized model and can be used to predict energy consumption in saturated relay-enabled ad hoc networks via energy decomposition. This is helpful in designing MAC protocols for cooperative communications and it is shown that using a relay results not only in a better throughput but also better energy efficiency.

Modeling energy consumption of dual-hop relay based MAC protocols in ad hoc networks

Given that the next and current generation networks will coexist for a considerable period of time, it is important to improve the performance of existing networks. One such improvement recently proposed is to enhance the throughput of ad hoc networks by using dual-hop relay-based transmission schemes. Since in ad hoc networks throughput is normally related to their energy consumption, it is important to examine the impact of using relay-based transmissions on energy consumption. In this paper, we present an analytical energy consumption model for dual-hop relay-based medium access control (MAC) protocols. Based on the recently reported relay-enabled Distributed Coordination Function (rDCF), we have shown the efficacy of the proposed analytical model. This is a generalized model and can be used to predict energy consumption in saturated relay-based ad hoc networks. This model can predict energy consumption in ideal environment and with transmission errors. It is shown that using a relay results in not only better throughput but also better energy efficiency. Copyright (C) 2009 Rizwan Ahmad et al.

A neurofuzzy network knowledge extraction and extended gram-Schmidt algorithm for model subspace decomposition

This paper introduces a new neurofuzzy model construction and parameter estimation algorithm from observed finite data sets, based on a Takagi and Sugeno (T-S) inference mechanism and a new extended Gram-Schmidt orthogonal decomposition algorithm, for the modeling of a priori unknown dynamical systems in the form of a set of fuzzy rules. The first contribution of the paper is the introduction of a one to one mapping between a fuzzy rule-base and a model matrix feature subspace using the T-S inference mechanism. This link enables the numerical properties associated with a rule-based matrix subspace, the relationships amongst these matrix subspaces, and the correlation between the output vector and a rule-base matrix subspace, to be investigated and extracted as rule-based knowledge to enhance model transparency. The matrix subspace spanned by a fuzzy rule is initially derived as the input regression matrix multiplied by a weighting matrix that consists of the corresponding fuzzy membership functions over the training data set. Model transparency is explored by the derivation of an equivalence between an A-optimality experimental design criterion of the weighting matrix and the average model output sensitivity to the fuzzy rule, so that rule-bases can be effectively measured by their identifiability via the A-optimality experimental design criterion. The A-optimality experimental design criterion of the weighting matrices of fuzzy rules is used to construct an initial model rule-base. An extended Gram-Schmidt algorithm is then developed to estimate the parameter vector for each rule. This new algorithm decomposes the model rule-bases via an orthogonal subspace decomposition approach, so as to enhance model transparency with the capability of interpreting the derived rule-base energy level. This new approach is computationally simpler than the conventional Gram-Schmidt algorithm for resolving high dimensional regression problems, whereby it is computationally desirable to decompose complex models into a few submodels rather than a single model with large number of input variables and the associated curse of dimensionality problem. Numerical examples are included to demonstrate the effectiveness of the proposed new algorithm.