Selected configuration interaction with truncation energy error and application to the Ne atom

Selected configuration interaction (SCI) for atomic and molecular electronic structure calculations is reformulated in a general framework encompassing all CI methods. The linked cluster expansion is used as an intermediate device to approximate CI coefficients BK of disconnected configurations (those that can be expressed as products of combinations of singly and doubly excited ones) in terms of CI coefficients of lower-excited configurations where each K is a linear combination of configuration-state-functions (CSFs) over all degenerate elements of K. Disconnected configurations up to sextuply excited ones are selected by Brown's energy formula, ΔEK=(E-HKK)BK2/(1-BK2), with BK determined from coefficients of singly and doubly excited configurations. The truncation energy error from disconnected configurations, Δdis, is approximated by the sum of ΔEKS of all discarded Ks. The remaining (connected) configurations are selected by thresholds based on natural orbital concepts. Given a model CI space M, a usual upper bound ES is computed by CI in a selected space S, and EM=E S+ΔEdis+δE, where δE is a residual error which can be calculated by well-defined sensitivity analyses. An SCI calculation on Ne ground state featuring 1077 orbitals is presented. Convergence to within near spectroscopic accuracy (0.5 cm-1) is achieved in a model space M of 1.4× 109 CSFs (1.1 × 1012 determinants) containing up to quadruply excited CSFs. Accurate energy contributions of quintuples and sextuples in a model space of 6.5 × 1012 CSFs are obtained. The impact of SCI on various orbital methods is discussed. Since ΔEdis can readily be calculated for very large basis sets without the need of a CI calculation, it can be used to estimate the orbital basis incompleteness error. A method for precise and efficient evaluation of ES is taken up in a companion paper

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.

Gas phase kinetic and quantum chemical studies of the reactions of silylene with the methylsilanes. Absolute rate constants, temperature dependences, RRKM modelling and potential energy surfaces

Time resolved studies of silylene, SiH2, generated by the 193 nm laser. ash photolysis of phenylsilane, have been carried out to obtain rate coefficients for its bimolecular reactions with methyl-, dimethyl- and trimethyl-silanes in the gas phase. The reactions were studied over the pressure range 3 - 100 Torr with SF6 as bath gas and at five temperatures in the range 300 - 625 K. Only slight pressure dependences were found for SiH2 + MeSiH3 ( 485 and 602 K) and for SiH2 + Me2SiH2 ( 600 K). The high pressure rate constants gave the following Arrhenius parameters: [GRAPHICS] These are consistent with fast, near to collision-controlled, association processes. RRKM modelling calculations are consistent with the observed pressure dependences ( and also the lack of them for SiH2 + Me3SiH). Ab initio calculations at both second order perturbation theory (MP2) and coupled cluster (CCSD(T)) levels, showed the presence of weakly-bound complexes along the reaction pathways. In the case of SiH2 + MeSiH3 two complexes, with different geometries, were obtained consistent with earlier studies of SiH2 + SiH4. These complexes were stabilised by methyl substitution in the substrate silane, but all had exceedingly low barriers to rearrangement to product disilanes. Although methyl groups in the substrate silane enhance the intrinsic SiH2 insertion rates, it is doubtful whether the intermediate complexes have a significant effect on the kinetics. A further calculation on the reaction MeSiH + SiH4 shows that the methyl substitution in the silylene should have a much more significant kinetic effect ( as observed in other studies).

Quantum mechanics studies of the tautomers of dlhydrodiacetylformoin, an important Maillard intermediate and the synthesis of furaneol

Conformational analyses have been carried out on the acyclic and cyclic forms of dihydrodiacetylformoin, an important Maillard intermediate and precursor for furaneol. For the acyclic forms, the 2,5-dicarbonyl isomers have the lowest energy, while for the cyclic forms, the 3-carbonyl are favoured over the 4-carbonyl isomers. The likely path for cyclisation is investigated and it is shown that the favoured path is dependent upon the relative chiralities of the carbon atoms and in particular that the reaction proceeds more readily if C2 and C3 have different chiralities. After cyclisation, the reaction path to produce furaneol proceeds via the loss of a water molecule. This reaction has been studied with a model including two water molecules and a hydroxide anion and shows relatively low-energy barriers. (C) 2008 Published by Elsevier B.V.

A study of the atmospherically relevant reaction between molecular chlorine and dimethylsulfide (DMS): establishing the reaction intermediate and measurement of absolute photoionization cross-sections

In a study using UV photoelectron spectroscopy (PES) of the atmospherically relevant reaction CH3SCH3 + Cl2 → CH3SCH2Cl + HCl bands associated with a reaction intermediate have been observed. These have been assigned to ionization of the covalently bound molecule (CH3)2SCl2 on the basis of the intensity of the observed bands as a function of reaction time, molecular orbital calculations of vertical ionization energies and evidence from infrared spectroscopy. A method has also been developed, with the flow-tube/PE spectrometer combination used, to measure photoionization cross-sections of the reagents and products at the photon energy utilized and this has allowed the photoionization cross-section of the intermediate to be estimated. This work augments an earlier study in which the rate constant of the reaction between CH3SCH3 (DMS) and Cl2 has been measured at room temperature.

Unusual isotope effect in the reaction of chlorosilylene with trimethylsilane-1-d: Absolute rate studies and quantum chemical and Rice–Ramsperger–Kassel–Marcus calculations provide strong evidence for the involvement of an intermediate complex

Time-resolved studies of chlorosilylene, ClSiH, generated by the 193 nm laser flash photolysis of 1-chloro-1- silacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with trimethylsilane-1-d, Me3SiD, in the gas phase. The reaction was studied at total pressures up to 100 Torr (with and without added SF6) over the temperature range of 295−407 K. The rate constants were found to be pressure independent and gave the following Arrhenius equation: log[(k/(cm3 molecule−1 s−1)] = (−13.22 ± 0.15) + [(13.20 ± 1.00) kJ mol−1]/(RT ln 10). When compared with previously published kinetic data for the reaction of ClSiH with Me3SiH, kinetic isotope effects, kD/kH, in the range from 7.4 (297 K) to 6.4 (407 K) were obtained. These far exceed values of 0.4−0.5 estimated for a single-step insertion process. Quantum chemical calculations (G3MP2B3 level) confirm not only the involvement of an intermediate complex, but also the existence of a low-energy internal isomerization pathway which can scramble the D and H atom labels. By means of Rice−Ramsperger−Kassel−Marcus modeling and a necessary (but small) refinement of the energy surface, we have shown that this mechanism can reproduce closely the experimental isotope effects. These findings provide the first experimental evidence for the isomerization pathway and thereby offer the most concrete evidence to date for the existence of intermediate complexes in the insertion reactions of silylenes.

Enrichment and stability: a phenomenological coupling of energy value and carrying capacity

Simple predator–prey models with a prey-dependent functional response predict that enrichment (increased carrying capacity) destabilizes community dynamics: this is the ‘paradox of enrichment’. However, the energy value of prey is very important in this context. The intraspecific chemical composition of prey species determines its energy value as a food for the potential predator. Theoretical and experimental studies establish that variable chemical composition of prey affects the predator–prey dynamics. Recently, experimental and theoretical approaches have been made to incorporate explicitly the stoichiometric heterogeneity of simple predator–prey systems. Following the results of the previous experimental and theoretical advances, in this article we propose a simple phenomenological formulation of the variation of energy value at increased level of carrying capacity. Results of our study demonstrate that coupling the parameters representing the phenomenological energy value and carrying capacity in a realistic way, may avoid destabilization of community dynamics following enrichment. Additionally, under such coupling the producer–grazer system persists for only an intermediate zone of production—a result consistent with recent studies. We suggest that, while addressing the issue of enrichment in a general predator–prey model, the phenomenological relationship that we propose here might be applicable to avoid Rosenzweig’s paradox.

Solvent assisted decomposition of the tetrahedral intermediate of the transesterification reaction to biodiesel production. A density functional study

B3LYP/6-31 + G(d) calculations were employed to investigate the mechanism of the transesterification reaction between a model monoglyceride and the methoxide and ethoxide anions. The gas-phase results reveal that both reactions have essentially the same activation energy (5.9 kcal mol(-1)) for decomposition of the key tetrahedral intermediate. Solvent effects were included by means of both microsolvation and the polarizable continuum solvation model CPCM. Both solvent approaches reduce the activation energy, however, only the microsolvation model is able to introduce some differentiation between methanol and ethanol, yielding a lower activation energy for decomposition of the tetrahedral intermediate in the reaction with methanol (1.1 kcal mol(-1)) than for the corresponding reaction with ethanol (2.8 kcal mol(-1)), in line with experimental evidences. Analysis of the individual energy components within the CPCM approach reveals that electrostatic interactions are the main contribution to stabilization of the transition state. (C) 2009 Elsevier Ltd. All rights reserved.

Strain rate effects on the energy absorption of rapidly manufactured composite tubes

As a result of recent increases in fuel prices and the growing number of accident fatalities, the two major concerns of the automotive industry and their customers are now occupant safety and fuel economy {1, 2]. Increasing the amount of energy and optimizing the manner in which energy is absorbed within vehicle crush zones can improve occupant survivability in the event of a crash, while fuel economy is improved through a reduction in weight.  Axial crush tests were conducted on tubular specimens of Carbon/Epoxy (Toray T700/G83C) and Glass/Polypropylene (Twintex). This paper presents results from the tests conducted at quasi-static rates at Deakin Unniversity, Victoria Australia, and intermediate rate tests performed at the Oak Ridge National Laboratory, Tennessee  USA.   The quasi-static tests were conducted at 10mm/min (1.67x10-4m/s) using 5 different forms of initiation. Tests at intermediate rates were performed at speeds of 0.25m/s, 0.5m/s, 0.75m/s 1m/s, 2m/s and 4m/s. Quasi-static tests of tubular specimens showed high specific energy absorption (SEA) values with 86 kJ/kg for Carbon/Epoxy specimens. The SEA of the Glass/Polypropylene specimens was measured to be 29 kJ/kg. Results from the intermediate test rates showed that SEA values did not fall below 55kJ/kg for carbon specimens or 35kJ/kg for the Glass/Polypropylene specimens. When compared with typical steel and aluminium, SEA values of 15 kJ/kg and 30kJ/kg respectively, the benefits of using composite materials in crash structures is apparent.                                                                     

Strain rate effects on the energy absorption of rapidly manufactured composite tubes

Quasi-static and intermediate rate axial crush tests were conducted on tubular specimens of Carbon/Epoxy (Toray T700/G83C) and Glass/Polypropylene (Twintex). The quasi-static tests were conducted at 10 mm/min (1.67 x 10¯⁴ m/s); five different crush initiators were used. Tests at intermediate rates were performed at speeds of 0.25, 0.5, 0.75, 1, 2, and 4m/s. Modes of failure and specific energy absorption (SEA) values were studied. The highest SEA measured was 86 kJ/kg. This value was observed using Carbon/Epoxy samples at quasi static rates with a 45° chamfer initiator. The highest energy absorption for Twintex tubes was observed to be 57.56 kJ/kg during 45° chamfer initiated tests at 0.25 m/s. Compared with steel and aluminium, SEA values of 15 and 30 kJ/kg, respectively, the benefits of using composite materials in crash structures become apparent.

Step Counting and Energy Expenditure Estimation in Patients With Chronic Obstructive Pulmonary Disease and Healthy Elderly: Accuracy of 2 Motion Sensors

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Ultra peripheral heavy ion collisions and the energy dependence of the nuclear radius

To estimate realistic cross sections in ultra peripheral heavy ion collisions we must remove effects of strong absorption. One method to eliminate these effects make use of a Glauber model calculation, where the nucleon-nucleon energy dependent cross sections at small impact parameter are suppressed. In another method we impose a geometrical cut on the minimal impact parameter of the nuclear collision ((b)min > R-1 + R-2, where R-i is the radius of ion 'i'). In this last case the effect of a possible nuclear radius dependence with the energy has not been considered in detail up to now. Here we introduce this effect showing that for final states with small invariant mass the effect is negligible. However when the final state has a relatively large invariant mass, e.g., an intermediate mass Higgs boson, the cross section can decrease up to 50%. (C) 2003 Published by Elsevier B.V.

Comments on energy confinement in non-periodic structures

In this study, we investigate the possibility of mode localization occurrence in a non-periodic Pfluger's column model of a rocket with an intermediate concentrated mass at its middle point. We discuss the effects of varying the intermediate mass magnitude and its position and the resulting energy confinement for two cases. Free vibration analysis and the severity of mode localization are appraised, without decoupling the system, by considering as a solution basis the fundamental free response or dynamical solution. This allows for the reduction of the dimension of the algebraic modal equation that arises from satisfying the boundary and continuity conditions. By using the same methodology, we also consider the case of a cantilevered Pluger's column with rotational stiffness at the middle support instead of an intermediate concentrated mass. (c) 2008 Elsevier Ltd. All rights reserved.

Energy and protein requirements for maintenance and growth of Boer crossbred kids

Meat production by goats has become an important livestock enterprise in several parts of the world. Nonetheless, energy and protein requirements of meat goats have not been defined thoroughly. The objective of this study was to determine the energy and protein requirements for maintenance and growth of 34 3/4 Boer x 1/4 Saanen crossbred, intact male kids (20.5 +/- 0.24 kg of initial BW). The baseline group was 7 randomly selected kids, averaging 21.2 +/- 0.36 kg of BW. An intermediate group consisted of 6 randomly selected kids, fed for ad libitum intake, that were slaughtered when they reached an average BW of 28.2 +/- 0.39 kg. The remaining kids (n = 21) were allocated randomly on d 0 to 3 levels of DMI (treatments were ad libitum or restricted to 70 or 40% of the ad libitum intake) within 7 slaughter groups. A slaughter group contained 1 kid from each treatment, and kids were slaughtered when the ad libitum treatment kid reached 35 kg of BW. Individual body components (head plus feet, hide, internal organs plus blood, and carcass) were weighed, ground, mixed, and subsampled for chemical analyses. Initial body composition was determined using equations developed from the composition of the baseline kids. The calculated daily maintenance requirement for NE was 77.3 +/- 1.05 kcal/kg(0.75) of empty BW (EBW) or 67.4 +/- 1.04 kcal/kg(0.75) of shrunk BW. The daily ME requirement for maintenance (118.1 kcal/g(0.75) of EBW or 103.0 kcal/kg(0.75) of shrunk BW) was calculated by iteration, assuming that the heat produced was equal to the ME intake at maintenance. The partial efficiency of use of ME for NE below maintenance was 0.65. A value of 2.44 +/- 0.4 g of net protein/kg(0.75) of EBW for daily maintenance was determined. Net energy requirements for growth ranged from 2.55 to 3.0 Mcal/kg of EBW gain at 20 and 35 kg of BW, and net protein requirements for growth ranged from 178.8 to 185.2 g/kg of EBW gain. These results suggest that NE and net protein requirements for growing meat goats exceed the requirements previously published for dairy goats. Moreover, results from this study suggest that the N requirement for maintenance for growing goats is greater than the established recommendations.

Fiber fermentability effects on energy and macronutrient digestibility, fecal traits, postprandial metabolite responses, and colon histology of overweight cats

Considering the different potential benefits of divergent fiber ingredients, the effect of 3 fiber sources on energy and macronutrient digestibility, fermentation product formation, postprandial metabolite responses, and colon histology of overweight cats (Felis catus) fed kibble diets was compared. Twenty-four healthy adult cats were assigned in a complete randomized block design to 2 groups of 12 animals, and 3 animals from each group were fed 1 of 4 of the following kibble diets: control (CO; 11.5% dietary fiber), beet pulp (BP; 26% dietary fiber), wheat bran (WB; 24% dietary fiber), and sugarcane fiber (SF; 28% dietary fiber). Digestibility was measured by the total collection of feces. After 16 d of diet adaptation and an overnight period without food, blood glucose, cholesterol, and triglyceride postprandial responses were evaluated for 16 h after continued exposure to food. on d 20, colon biopsies of the cats were collected under general anesthesia. Fiber addition reduced food energy and nutrient digestibility. of all the fiber sources, SF had the least dietary fiber digestibility (P < 0.05), causing the largest reduction of dietary energy digestibility (P < 0.05). The greater fermentability of BP resulted in reduced fecal DM and pH, greater fecal production [g/(cat x d); as-is], and greater fecal concentration of acetate, propionate, and lactate (P < 0.05). For most fecal variables, WB was intermediate between BP and SF, and SF was similar to the control diet except for an increased fecal DM and firmer feces production for the SF diet (P < 0.05). Postprandial evaluations indicated reduced mean glucose concentration and area under the glucose curve in cats fed the SF diet (P < 0.05). Colon mucosa thickness, crypt area, lamina propria area, goblet cell area, crypt mean size, and crypt in bifurcation did not vary among the diets. According to the fiber solubility and fermentation rates, fiber sources can induce different physiological responses in cats, reduce energy digestibility, and favor glucose metabolism (SF), or improve gut health (BP).