Melting of Lennard-Jones rare gas clusters doped with a single impurity atom

Single impurity effect on the melting process of magic number Lennard-Jones, rare gas, clusters of up to 309 atoms is studied on the basis of Parallel Tempering Monte Carlo simulations in the canonical ensemble. A decrease on the melting temperature range is prevalent, although such effect is dependent on the size of the impurity atom relative to the cluster size. Additionally, the difference between the atomic sizes of the impurity and the main component of the cluster should be considered. We demonstrate that solid-solid transitions due to migrations of the impurity become apparent and are clearly differentiated from the melting up to cluster sizes of 147 atoms

Interpolated potential energy surface and classical dynamics for H₃⁺+HD and H₃⁺+D₂

A potential energy surface for H₅⁺ has been constructed by a modified Shepard interpolation on a sparse set of data points, using second order Möller–Plesset perturbation theory. An improved version of the surface was also obtained by substituting the energy values at the data points with values evaluated using a coupled cluster treatment (with single and double excitations, and perturbative treatment of triple excitations). Classical simulations for the collisions between H₃⁺+HD and H₃⁺+D2 were carried out in order to calculate the total integral cross sections and rate coefficients for these systems. There is good agreement with earlier experimental data for rate coefficients at temperatures between 80 and 300 K, but the predicted rate coefficient for the reaction of H₃⁺+HD at 10 K deviates from the most recent experimental measurement, suggesting that quantum rather than classical reactiondynamics are necessary

Molecular potential energy surfaces by interpolation: Strategies for faster convergence

A method for interpolating molecular potential energy surfaces introduced [Ischtwan and Collins, J. Chem. Phys. 100, 8080 (1994)] and developed as an iterative scheme has been improved by different criteria for the selection of the data points. Refinements in the selection procedure are based on the variance of the interpolation and the direct exploration of the interpolation error, and produce more accurate surfaces than the previously established scheme for the same number of data points

Interpolated potential energy surfaces and dynamics for atom exchange between H and H⁺₃, and D and H⁺₃

Two ab initio interpolated potential energy surfaces have been constructed to study the dynamics of atomic hydrogen/deuterium exchange in collisions of H(3)(+) with H (D). One of the surfaces is based on energy calculations using quadratic configuration interaction with single and double excitations. The second includes a perturbative treatment of the triple excitations and an additive correction for basis set deficiency. Results from classical dynamics simulation of the exchange reaction on these surfaces are presented and discussed

Ab initio interpolated potential energy surface and classical reaction dynamics for HCO⁺+H, HOC⁺+H, and deuterated analogues

Classical simulations of the reactions between HCO⁺/COH⁺ and hydrogen atoms, as well as their deuterated variants, have been carried out on an ab initio interpolated potential energy surface. The surface is constructed at the quadratic configuration interaction with single and double excitation level of ab initio calculation. At low energies we observe reaction channels associated with the isomerization of the cation, hydrogen/deuterium exchange, and the combination of isomerization with exchange. The HCO⁺/DCO⁺ ions only undergo exchange, and deuteration is more facile than the release of deuterium. The COH⁺/COD⁺ ions undergo isomerization or isomerization combined with exchange, the latter being the dominant reaction channel. Deuteration is again more facile than the release of deuterium, in combination with isomerization. These results are consistent with experimental measurements and with hypotheses on the deuteration of molecules in the interstellar medium

Downregulation of NAC transcription factors modifies cell wall composition and increases strawberry fruit firmness

The strawberry is a soft fruit with a very short post-harvest shelf life. The changes in texture during fruit ripening are mainly due to the dissolution of the middle lamellae, reducing cell-to-cell adhesion, and the weakening of parenchymal cell walls as result of the action of cell wall modifying enzymes. At present, no master regulator of this process has been discovered yet. NAC transcription factors have been involved in numerous physiological processes, including fruit ripening. In strawberry, the NAC family comprises more than 110 genes, and at least 6 of them are expressed during fruit development. In this research, we performed a functional analysis of two ripening-related NAC genes, FaNAC2 and FaNAC3, in Fragaria x ananassa Duch. cv. Chandler. Several RNAi transgenic lines showing low FaNAC2 or FaNAC3 mRNA levels in fruit were obtained through Agrobacterium-mediated transformation. These lines produced fruits significantly firmer than control at the ripe stage, being the increase in firmness higher in FaNAC2 silenced plants. Cell walls were extracted from ripe transgenic fruits and characterized by ELISA and Epitope Detection Chromatography (EDC), using monoclonal antibodies against different polysaccharide epitopes. FaNAC2 transgenic lines showed more extensive changes than FaNAC3; these modifications involved increased amounts of demethylated pectins (LM19) in water and CDTA fractions and an alteration of the lateral branches of RG-I, decreasing the amount of arabinan epitopes and increasing galactan epitopes detected by LM6 and LM5, respectively. The amount of arabinogalactan proteins recognized by the JIM13 antibody was also affected, decreasing in the Na2CO3 fraction and increasing in the 4M KOH and cellulase fraction of the transgenic lines.The results obtained indicate that NAC genes could be involved in the regulation of cell wall disassembly associated to strawberry fruit softening.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type–specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type–specific transcription factor (TF)–target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF–target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks