Energetics and stability of vacancies in carbon nanotubes

In this work we present ab initio calculations of the formation energies and stability of different types of multi-vacancies in carbon nanotubes. We demonstrate that, as in the case of graphene, the reconstruction of the defects has drastic effects on the energetics of the tubes. In particular, the formation of pentagons eliminates the dangling bonds thus lowering the formation energy. This competition leads to vacancies having an even number of carbon atoms removed to be more stable. Finally the appearance of magic numbers indicating more stable defects can be represented by a model for the formation energies that is based on the number of dangling bonds of the unreconstructed system, the pentagons and the relaxation of the final form of the defect formed after the relaxation. (C) 2011 Elsevier Ltd. All rights reserved.

Furan interaction with the Si(001)-(2 x 2) surface: structural, energetics, and vibrational spectra from first-principles

In this work we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of furan on the silicon (001) surface. A direct comparison of different adsorption structures with x-ray photoelectron spectroscopy (XPS), ultra-violet photoelectron spectroscopy (UPS), high resolution electron energy loss spectroscopy (HREELS), near edge x-ray absorption fine structure (NEXAFS), and high resolution spectroscopy experimental data allows us to identify the [4 + 2] cycloaddition reaction as the most probable adsorbate. In addition, theoretical scanning tunnelling microscopy (STM) images are presented, with a view to contributing to further experimental investigations.

Exploring new molecular species on the (1)[H, Se, F] singlet potential energy surface: Energetics, structures, IR spectra, and heats of formation

Structural, energetic, and vibrational properties of new molecular species, HSeF and HFSe, the associated transition state, and dissociation fragments are investigated using a state-of-the-art theoretical approach, CCSD(T)/CBS. HSeF is a normal covalently bonded molecule 38.98 kcal mol (1) more stable than the complex HF-Se, which shows an unusual structure with a central fluorine atom and a bond angle of 101.8 degrees.A barrier (Delta G(#)) of 49.01 kcal mol (1) separates the two species. Vibrational frequencies are also quite distinct. Heats of formation are evaluated for the diatomic fragments and HSeF. Final Delta(f)H values depend on the experimental accuracy of those of Se(g) and H(2)Se. (c) 2009 Elsevier B.V. All rights reserved.

Temperature and meal size effects on the postprandial metabolism and energetics in a boid snake

We investigated the combined effect of meal size and temperature on the aerobic metabolism and energetics of digestion in Boa constrictor amarali. Oxygen uptake rates ((V) over dot o(2)) and the. duration of the digestion were determined in snakes fed with meals equaling to 5%, 10%, 20%, and 40% of the snake's body mass at 25degrees and 30 degreesC. The maximum (V) over dot o(2) values attained during digestion were greater at 30 degreesC than at 25 degreesC. Both maximal (V) over dot (o2) values and the duration of the specific dynamic action. (SDA) were attained sooner at 30 degreesC than at 25 degreesC. Therefore, the temperature effect on digestion in Boa is characterized by the shortening of the SDA duration at the expense of increased. Energy allocated to SDA was not affected by meal size but. was greater at 25 degreesC compared to 30 degreesC. This indicates that a postprandial thermophilic response can be advantageous not only by decreasing the duration of digestion but also by improving digestive efficiency. Maximal (V) over dot o(2) and SDA duration. increased with meal size at both temperatures.

Nonmodal energetics of resistive drift waves

The modal and nonmodal linear properties of the Hasegawa-Wakatani system are examined. This linear model for plasma drift waves is nonnormal in the sense of not having a complete set of orthogonal eigenvectors. A consequence of nonnormality is that finite-time nonmodal growth rates can be larger than modal growth rates. In this system, the nonmodal time-dependent behavior depends strongly on the adiabatic parameter and the time scale of interest. For small values of the adiabatic parameter and short time scales, the nonmodal growth rates, wave number, and phase shifts (between the density and potential fluctuations) are time dependent and differ from those obtained by normal mode analysis. On a given time scale, when the adiabatic parameter is less than a critical value, the drift waves are dominated by nonmodal effects while for values of the adiabatic parameter greater than the critical value, the behavior is that given by normal mode analysis. The critical adiabatic parameter decreases with time and modal behavior eventually dominates. The nonmodal linear properties of the Hasegawa-Wakatani system may help to explain features of the full system previously attributed to nonlinearity.

Nonmodal energetics of electromagnetic drift waves

The linear properties of an electromagnetic drift-wave model are examined. The linear system is non-normal in that its eigenvectors are not orthogonal with respect to the energy inner product. The non-normality of the linear evolution operator can lead to enhanced finite-time growth rates compared to modal growth rates. Previous work with an electrostatic drift-wave model found that nonmodal behavior is important in the hydrodynamic limit. Here, similar behavior is seen in the hydrodynamic regime even with the addition of magnetic fluctuations. However, unlike the results for the electrostatic drift-wave model, nonmodal behavior is also important in the adiabatic regime with moderate to strong magnetic fluctuations. © 2000 American Institute of Physics.

Kinematics and Energetics of Nut-Cracking in Wild Capuchin Monkeys (Cebus libidinosus) in Piaui, Brazil

Wild bearded capuchins (Cebus libidinosus, quadrupedal, medium-sized monkeys) crack nuts using large stones. We examined the kinematics and energetics of the nut-cracking action of two adult males and two adult females. From a bipedal stance, the monkeys raised a heavy hammer stone (1.46 and 1.32 kg, from 33 to 77% of their body weight) to an average height of 0.33 m, 60% of body length. Then, they rapidly lowered the stone by flexing the lower extremities and the trunk until the stone contacted the nut. A hit consisting of an upward phase and a downward phase averaged 0.74 s in duration. The upward phase lasted 69% of hit duration. All subjects added discernable energy to the stone in the downward phase. The monkeys exhibited individualized kinematic strategies, similar to those of human weight lifters. Capuchins illustrate that human-like bipedal stance and large body size are unnecessary to break tough objects from a bipedal position. The phenomenon of bipedal nut-cracking by capuchins provides a new comparative reference point for discussions of percussive tool use and bipedality in primates. Am J Phys Anthropol 138:210-220, 2009. (C) 2008 Wiley-Liss, Inc.

Structural properties and energetics of diffuse Rb-87 clusters in three-dimension

A correlated two-body basis function is used to describe the three-dimensional bosonic clusters interacting via two-body van der Waals potential. We calculate the ground state and the zero orbital angular momentum excited states for Rb-N clusters with up to N = 40. We solve the many-particle Schrodinger equation by potential harmonics expansion method, which keeps all possible two-body correlations in the calculation and determines the lowest effective many-body potential. We study energetics and structural properties for such diffuse clusters both at dimer and tuned scattering length. The motivation of the present study is to investigate the possibility of formation of N-body clusters interacting through the van der Waals interaction. We also compare the system with the well studied He, Ne, and Ar clusters. We also calculate correlation properties and observe the generalised Tjon line for large cluster. We test the validity of the shape-independent potential in the calculation of the ground state energy of such diffuse cluster. These are the first such calculations reported for Rb clusters. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4730972]

Charge transfer reactions of organic ions containing oxygen: Correlation between reaction energetics and cross sections

Cross sections for charge transfer reactions of organic ions containing oxygen have been obtained using time-of-flight techniques. Charge transfer cross sections have been determined for reactions of 2.0 to 3.4 keV ions produced by electron impact ionization of oxygen containing molecules such as methanol, ethanal and ethanol. Experimental cross section magnitudes have been correlated with reaction energy defects computed from ion recombination energies and target ionization energies. Large cross sections are observed for reacting systems with small energy defects.

Structures, energetics and fragmentation pathways of CnH22+ carbodications

Potential energy curves have been calculated for CnH22+ (n = 2−9) ions and results have been compared with data on unimolecular charge-separation reactions obtained by Rabrenović and Beynon. Geometry-optimized, minimum energy, linear CnH22+ structures have been computed for ground and low-lying excited states. These carbodications exist in stable configurations with well depths greater than 3 eV. Decomposition pathways into singly charged fragment ions lead to products with computed kinetic energies in excess of 1 eV. A high degree of correlation exists between experimental information and results computed for linear CnH22+ structures having hydrogen atoms on each end. The exception involves C4H22+reactions where a low-lying doubly charged isomer must be invoked to rationalize the experimental data.

Energetics of byssus attachment and feeding in the green-lipped mussel Perna canaliculus.

In most animals, significant increases in metabolic rate are due to activity and to feeding (known as apparent specific dynamic action). We determined the energetic costs of activity and feeding in adult green-lipped mussels (Perna canaliculus). Maximal metabolic rate was determined, using closed-chamber respirometry, during byssus re-attachment, during specific dynamic action after 16 h of feeding with Isochrysis galbana, and for the two activities combined, in 23 mussels. Metabolic rate was significantly elevated above rest by about 1.9-fold during byssus attachment (17.1 ± 1.53 μg O(2) h(-1) g(-1) whole mussel wet weight at rest, increased to 27.9 ± 0.91 μg O(2) h(-1) g(-1)), and by 2.2-fold after feeding (31.4 ± 1.20 μg O(2) h(-1) g(-1)). Combined feeding and byssus attachment led to a still higher metabolic rate (34.0 ± 1.23 μg O(2) h(-1) g(-1)). Behavior was also significantly altered, with mussels being almost continuously open during attachment and after feeding (90%-99% of the time); however, the time spent open during the day decreased, reaching a minimum of 52% ± 9% 3 days after feeding, and remained low (67%-82%) for the following 45-day starvation period. Significant diurnal differences were observed, with mussels continuously (92%-100%) open at night. The key findings from this study are that green-lipped mussels (1) have an aerobic scope of approximately 2-fold; (2) reach a higher metabolic rate during feeding than during activity, and the two combined can raise the metabolic rate higher still; (3) display a marked diurnal behavior.

Parameters of population dynamics and energetics of ctenophore Mnemiopsis leidyi in Sevastopol Bay from January 1995 to March 1996

Population dynamics of abundance and biomass were studied and specific production of population of ctenophore Mnemiopsis leidyi was estimated in the Sevastopol Bay from January 1995 to March 1996. The ctenophores achieved maximum abundance and biomass in July during period of intensive reproduction. Young specimens (<5 mm) contributed during that period as much as 50-87% to total abundance of population. Annually averaged daily specific growth rate was 0.039. Growth, food consumption, and rate of filtration were measured in a laboratory under two concentrations of food (Acartia clausi and Moina micrura: 60 and 100 specimens per liter, 0.35 and 0.60 mg wet weight/l). Both concentrations sustained growth of animals with dry weight less than 20 mg. However these concentrations were insufficient to sustain growth of larger ctenophores. Specific growth rate of the ctenophores with dry weight <20 mg under favorable food conditions was 0.20-0.30 l/day. Specific growth rate of the ctenophores in the Sevastopol Bay never exceeded 0.093 l/day, mean biomass of fodder zooplankton in the bay being 90 mg/m**3 in terms of wet weight. Hence a conclusion was made that population of M. leidyi in the bay was limited by lack of food.

Impact of medium-term exposure to elevated pCO2 levels on the physiological energetics of the mussel Mytilus chilensis

This study evaluated the impact of medium-term exposure to elevated pCO2 levels (750-1200 ppm) on the physiological processes of juvenile Mytilus chilensis mussels over a period of 70 d in a mesocosm system. Three equilibration tanks filled with filtered seawater were adjusted to three pCO2 levels: 380 (control), 750 and 1200 ppm by bubbling air or an air-CO2 mixture through the water. For the control, atmospheric air (with aprox. 380 ppm CO2) was bubbled into the tank; for the 750 and 1200 ppm treatments, dry air and pure CO2 were blended to each target concentration using mass flow controllers for air and CO2. No impact on feeding activity was observed at the beginning of the experiment, but a significant reduction in clearance rate was observed after 35 d of exposure to highly acidified seawater. Absorption rate and absorption efficiency were reduced at high pCO2 levels. In addition, oxygen uptake fell significantly under these conditions, indicating a metabolic depression. These physiological responses of the mussels resulted in a significant reduction of energy available for growth (scope for growth) with important consequences for the aquaculture of this species during medium-term exposure to acid conditions. The results of this study clearly indicate that high pCO2 levels in the seawater have a negative effect on the health of M. chilensis. Therefore, the predicted acidification of seawater associated with global climate change could be harmful to this ecologically and commercially important mussel.

Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities

The alanine helix provides a model system for studying the energetics of interaction between water and the helical peptide group, a possible major factor in the energetics of protein folding. Helix formation is enthalpy-driven (−1.0 kcal/mol per residue). Experimental transfer data (vapor phase to aqueous) for amides give the enthalpy of interaction with water of the amide group as ≈−11.5 kcal/mol. The enthalpy of the helical peptide hydrogen bond, computed for the gas phase by quantum mechanics, is −4.9 kcal/mol. These numbers give an enthalpy deficit for helix formation of −7.6 kcal/mol. To study this problem, we calculate the electrostatic solvation free energy (ESF) of the peptide groups in the helical and β-strand conformations, by using the delphi program and parse parameter set. Experimental data show that the ESF values of amides are almost entirely enthalpic. Two key results are: in the β-strand conformation, the ESF value of an interior alanine peptide group is −7.9 kcal/mol, substantially less than that of N-methylacetamide (−12.2 kcal/mol), and the helical peptide group is solvated with an ESF of −2.5 kcal/mol. These results reduce the enthalpy deficit to −1.5 kcal/mol, and desolvation of peptide groups through partial burial in the random coil may account for the remainder. Mutant peptides in the helical conformation show ESF differences among nonpolar amino acids that are comparable to observed helix propensity differences, but the ESF differences in the random coil conformation still must be subtracted.