The influence of leaf characteristics on epiphyllic cover : a test of hypotheses with artificial leaves

Studies of epiphyll ecology have been hindered by the biochemical and morphological variability of the leaf substrate. The use of artificial (plastic ribbon tape) leaves solved that problem in a study done at the Braulio Carrillo National Park, Costa Rica. It showed that after nine months of field exposure, relative epiphyll cover was similar in five leaf shapes and two sizes. Driptips do not affect epiphyll cover, which was four times higher under a clearing than in the shaded understory, for all leaf shapes and sizes

The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of Lennard-Jones fluids

We propose a general approach for determining the entropy and free energy of complex systems as a function of temperature and pressure. In this method the Fourier transform of the velocity autocorrelation function, obtained from a short (20 ps) molecular dynamics trajectory is used to obtain the vibrational density of states (DoS) which is then used to calculate the thermodynamic properties by applying quantum statistics assuming each mode is a harmonic oscillator. This approach is quite accurate for solids, but leads to significant errors for liquids where the DoS at zero frequency, S(0), remains finite. We show that this problem can be resolved for liquids by using a two phase model consisting of a solid phase for which the DoS goes to zero smoothly at zero frequency, as in a Debye solid; and a gas phase (highly fluidic), described as a gas of hard spheres. The gas phase component has a DoS that decreases monotonically from S(0) and can be characterized with two parameters: S(0) and 3Ng, the total number of gas phase modes [3Ng0 for a solid and 3Ng3(N–1) for temperatures and pressures for which the system is a gas]. To validate this two phase model for the thermodynamics of liquids, we applied it to pure Lennard-Jones systems for a range of reduced temperatures from 0.9 to 1.8 and reduced densities from 0.05 to 1.10. These conditions cover the gas, liquid, crystal, metastable, and unstable states in the phase diagram. Our results compare quite well with accurate Monte Carlo calculations of the phase diagram for classical Lennard-Jones particles throughout the entire phase diagram. Thus the two-phase thermodynamics approach provides an efficient means for extracting thermodynamic properties of liquids (and gases and solids)

Elucidation of the dynamics for hot-spot initiation at nonuniform interfaces of highly shocked materials

The fundamental processes in shock-induced instabilities of materials remain obscure, particularly for detonation of energetic materials. We simulated these processes at the atomic scale on a realistic model of a polymer-bonded explosive (3,695,375 atoms/cell) and observed that a hot spot forms at the nonuniform interface, arising from shear relaxation that results in shear along the interface that leads to a large temperature increase that persists long after the shock front has passed the interface. For energetic materials this temperature increase is coupled to chemical reactions that lead to detonation. We show that decreasing the density of the binder eliminates the hot spot

Aristolochia quiricoana (Aristolochiaceae), a new species from southern Costa Rica

Background and Aims: Aristolochia is the largest genus in Aristolochiaceae and is widely distributed in the world. A recent synopsis of Aristolochia in Costa Rica recognized 19 species; nevertheless, recent botanical exploration in southwestern Costa Rica has revealed yet another new species of this genus. Methods: The new species resulted from fieldwork in Buenos Aires, Puntarenas Province. Specimens from several herbaria were examined, as well as the type material of the most morphologically similar species. Comments about its distribution, habitat, phenology, conservation status and morphological distinction from related species are provided. Key results: Aristolochia quiricoana, a member of Aristolochia series Thyrsicae, is described and illustrated from the southern Pacific region of Costa Rica, where it is apparently endemic. It is similar to A. ornithorhyncha, from which it is distinguished by its shorter pedicels, wider, oblong perigone limbs with a shorter appendix, and a different floral color pattern. Conclusions: The new taxon described here represents the 22nd species documented in Aristolochia series Thyrsicae, as well as the 20th species of the genus from Costa Rica

Secondary Organic Aerosol Formation by Heterogeneous Reactions of Aldehydes and Ketones: A Quantum Mechanical Study

Experimental studies have provided convincing evidence that aerosol-phase heterogeneous chemical reactions (possibly acid-catalyzed) are involved to some extent in the formation of secondary organic aerosol (SOA). We present a stepwise procedure to determine physical properties such as heats of formation, standard entropies, Gibbs free energies of formation, and solvation energies from quantum mechanics (QM), for various short-chain aldehydes and ketones. We show that quantum mechanical gas-phase Gibbs free energies of formation compare reasonably well with the literature values with a root-mean-square (RMS) value of 1.83 kcal/mol for the selected compounds. These QM results are then used to determine the equilibrium constants (reported as log K) of aerosol-phase chemical reactions, including hydration reactions and aldol condensation for formaldehyde, acetaldehyde, acetone, butanal, hexanal, and glyoxal. Results are in qualitatively agreement with previous studies. In addition, the QM results for glyoxal reactions are consistent with experimental observations. To our knowledge, this is the first QM study that supports observations of atmospheric particle-phase reactions. Despite the significant uncertainties in the absolute values from the QM calculations, the results are potentially useful in determining the relative thermodynamic tendency for atmospheric aerosol-phase reactions

Wax Inhibition by Comb-like Polymers: Support of the Incorporation−Perturbation Mechanism from Molecular Dynamics Simulations

Deposition of wax on a cold surface is a serious problem in oil production. Progress in developing more effective wax inhibitors has been impeded by the lack of an established mechanism connecting the molecular structure to inhibitor efficiency. Some comb-like polymers having long alkyl side chains are known to decrease the rate of wax formation. Among several possible mechanisms, we investigate here the incorporation−perturbation mechanism. According to this mechanism, the inhibitor molecules in oil are preferentially partitioned (incorporation) toward the wax-rich (amorphous) wax deposits (soft wax), which then serves as a perturbation to slow down the ordering transition of soft amorphous wax into more stable but problematic hard wax crystals. Indeed, molecular dynamics simulations on an effective inhibitor molecule in both the oil phase and in the amorphous wax phase support the idea that the oil-to-wax partition of the inhibitor is energetically favorable. With the inhibitor molecule embedded, the structure of wax crystal is disturbed, significantly decreasing the order and significantly lowering the cohesive energy density relative to that of the pure wax crystal, supporting the slower transition from soft wax to hard wax. Thus, in the presence of an effective wax inhibitor, crystallization (formation of hard wax) is slowed dramatically, so that there is time to flush out the soft wax with a high-pressure flow inside the pipeline. This suggests design principles for developing improved wax inhibitors

Linking Molecular Switches to Platinum Electrodes Studied with DFT

Density functional theory (DFT) with the B3LYP exchange−correlation functional was used to study new linkages between electrodes and molecular switches (alligator-clip compounds) for molecular electronics using Pt electrodes. Starting with the commonly used molecule 3-methyl-1,2-dithiolane (MDTL), which forms a five-membered ring structure in the gas phase, we found the most stable structure of the adsorbed MDTL to be the ring-opened molecule (32.44 kcal/mol) with each S atom bound to a surface bridge position. Afterward we calculated binding energies and geometries for a variety of different compounds:  S/O-based (oxathiolanes), O-based (methanol), N-based (imidazole, 1,2,3-triazole, purine, 2,4-diazapentane), and P-based molecules (methylphosphino, PCH_3, 3-methyl-1,2-diphospholane before (MDPL) and after H dissociation (H_(diss)-MDPL)). Among these alternative linkage molecules we find that only the P-based compounds lead to much higher binding energies than MDTL. The best compromise between strong surface attachment and mechanical stability provide the MDPL molecules. For the cis-ring-closed structure of MDPL a binding energy of 47.72 kcal/mol was calculated and even 54.88 kcal/mol for the ring-opened molecule. In the case of H-dissociative adsorption, which leads to H_(diss)-MDPL, both binding energies increase to 53.74 (ring-closed) and 74.99 kcal/mol (ring-opened). Thus, MDPL provides a much more stable link to the metal surface and might increase the conductance between molecular switch and electrode. In addition, the minor differences in charge and spin-density distribution between MDTL and MDPL might indicate similar properties for the attachment of the molecular switch to either of both alligator-clip compounds