In vitro screening of interspecific hybrids (Malus spp.) for resistance to apple proliferation

A breeding programme was set up six years ago in Trentino as part of the Project “Scopazzi del Melo - Apple Proliferation” (SMAP) in order to obtain AP resistant apple rootstocks.Twenty-six hybrids generated from the crossings (Malus sieboldii, second generation, x Malus domestica) were micropropagated and studied in standardised conditions. An in vitro screening system for AP resistance previously set for the parents of the crosses was adopted and modified. Specific symptoms of the disease, as well as height and basal proliferation of the shoot and size of the leaves, were recorded in vitro at 3 months post-inoculation. At the same time, phytoplasma concentration was determined in the whole shoot by quantitative RT-PCR. An in vitro disease index taking into account all the above-mentioned parameters was developed.Each healthy genotype was graft-inoculated in triplicate with two different phytoplasma strains after plant rooting and acclimatisation. Phenotype and phytoplasma titre were evaluated in the roots the year after infection.Preliminary results indicated that the resistance trait segregates in the progenies. The resistant genotypes had lower phytoplasma concentrations than the susceptible controls, did not show AP-specific symptoms and their growth was not affected by infection. By comparing the resistant behaviour of the same genotypes, the in vitro screening allows for a quick selection of genotypes that are worth evaluating in the field for agronomic traits.Keywords: Apple Proliferation, Malus sieboldii, resistance screening, quantitative real-time PCR, disease inde

Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and non-trivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.Comment: 23 pages, 12 figure

Real-time observation of non-equilibrium liquid condensate confined at tensile crack tips in oxide glasses

Since crack propagation in oxide materials at low crack velocities is partly determined by chemical corrosion, proper knowledge of the crack tip chemistry is crucial for understanding fracture in these materials. Such knowledge can be obtained only from in situ studies because the processes that occur in the highly confined environment of the crack tip are very different from those that take place at free surfaces, or that can be traced post mortem. We report the occurrence of hydrous liquid condensate between the two fracture surfaces in the vicinity of the tip of tensile cracks in silica. Observations are performed in real-time by means of atomic force microscopy (AFM) at continuously controlled crack velocities in the regime of stress corrosion. Condensate formation and changes in extent and shape are demonstrated for a wide range of macroscopic humidity at different crack speeds. Its liquid character is confirmed by the study of AFM phase-contrast data. It is believed that this evidence of a nanoscale liquid hydrous phase at the crack tip will enable novel insights in the chemistry of failure of oxide materials.Comment: 13 pages, 4 figures, to be published on J. Am. Cer. So

Evaluation of environmental quality of mediterranean coastal lagoons using persistent organic pollutants and metals in thick-lipped grey mullet

The evaluation of past and present anthropogenic impacts affecting the ecological quality status of transitional ecosystems is crucial from the perspective of protecting them from further deterioration, and to evaluate remediation and restoration measures. Contamination patterns of thick-lipped grey mullet from two Mediterranean coastal lagoons within a protected area in Italy were assessed and compared in order to evaluate their overall quality status and to collect information that can provide useful feedback on management choices aimed at enhancing environmental quality and biodiversity conservation. The quality status of the two lagoons was evaluated by an environmental assessment methodology based on indicators of direct and indirect human pressures, while a broad range of analyses were carried out to determine the presence and concentration of persistent organic pollutants (POPs) and metals in fish muscle tissue. A good quality status resulted for both lagoons, and an overall limited anthropogenic impact in the surrounding area. This could account for POPs and metal contamination levels found in mullet, although limited, and relating to their patterns. The overlap of results achieved with the two evaluation approaches can provide support for management choices in Mediterranean lagoon environments, especially for those committed to the protection and conservation of biodiversity

Molecular dynamics simulation of polymer helix formation using rigid-link methods

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under gradual cooling are followed until each reaches a state from which no further change is possible. The interactions are chosen so that the true ground state is a helix, and a high proportion of simulation runs succeed in reaching this state; the fraction that manage to form defect-free helices is a function of both chain length and cooling rate. In order to demonstrate behavior analogous to the formation of protein tertiary structure, additional attractive interactions are introduced into the model, leading to the appearance of aligned, antiparallel helix pairs. The simulations employ a computational approach that deals directly with the internal coordinates in a recursive manner; this representation is able to maintain constant bond lengths and angles without the necessity of treating them as an algebraic constraint problem supplementary to the equations of motion.Comment: 15 pages, 14 figure

Growth of (110) Diamond using pure Dicarbon

We use a density-functional based tight-binding method to study diamond growth steps by depositing dicarbon species onto a hydrogen-free diamond (110) surface. Subsequent C_2 molecules are deposited on an initially clean surface, in the vicinity of a growing adsorbate cluster, and finally, near vacancies just before completion of a full new monolayer. The preferred growth stages arise from C_2n clusters in near ideal lattice positions forming zigzag chains running along the [-110] direction parallel to the surface. The adsorption energies are consistently exothermic by 8--10 eV per C_2, depending on the size of the cluster. The deposition barriers for these processes are in the range of 0.0--0.6 eV. For deposition sites above C_2n clusters the adsorption energies are smaller by 3 eV, but diffusion to more stable positions is feasible. We also perform simulations of the diffusion of C_2 molecules on the surface in the vicinity of existing adsorbate clusters using an augmented Lagrangian penalty method. We find migration barriers in excess of 3 eV on the clean surface, and 0.6--1.0 eV on top of graphene-like adsorbates. The barrier heights and pathways indicate that the growth from gaseous dicarbons proceeds either by direct adsorption onto clean sites or after migration on top of the existing C_2n chains.Comment: 8 Pages, 7 figure

How a spin-glass remembers. Memory and rejuvenation from intermittency data: an analysis of temperature shifts

The memory and rejuvenation aspects of intermittent heat transport are explored theoretically and by numerical simulation for Ising spin glasses with short-ranged interactions. The theoretical part develops a picture of non-equilibrium glassy dynamics recently introduced by the authors. Invoking the concept of marginal stability, this theory links irreversible `intermittent' events, or `quakes' to thermal fluctuations of record magnitude. The pivotal idea is that the largest energy barrier $b(t_w,T)$ surmounted prior to $t_w$ by thermal fluctuations at temperature $T$ determines the rate $r_q \propto 1/t_w$ of the intermittent events occurring near $t_w$. The idea leads to a rate of intermittent events after a negative temperature shift given by $r_q \propto 1/t_w^{eff}$, where the `effective age' $t_w^{eff} \geq t_w$ has an algebraic dependence on $t_w$, whose exponent contains the temperatures before and after the shift. The analytical expression is verified by numerical simulations. Marginal stability suggests that a positive temperature shift $T \to T'$ could erase the memory of the barrier $b(t_w,T)$. The simulations show that the barrier $b(t_w,T') \geq b(t_w,T)$ controls the intermittent dynamics, whose rate is hence $r_q \propto 1/t_w$. Additional `rejuvenation' effects are also identified in the intermittency data for shifts of both signs.Comment: Revised introduction and discussion. Final version to appear in Journal of Statistical Mechanics: Theory and Experimen

Surface diffusion coefficients by thermodynamic integration: Cu on Cu(100)

The rate of diffusion of a Cu adatom on the Cu(100) surface is calculated using thermodynamic integration within the transition state theory. The results are found to be in excellent agreement with the essentially exact values from molecular-dynamics simulations. The activation energy and related entropy are shown to be effectively independent of temperature, thus establishing the validity of the Arrhenius law over a wide range of temperatures. Our study demonstrates the equivalence of diffusion rates calculated using thermodynamic integration within the transition state theory and direct molecular-dynamics simulations.Comment: 4 pages (revtex), two figures (postscript

A weak characterization of slow variables in stochastic dynamical systems

We present a novel characterization of slow variables for continuous Markov processes that provably preserve the slow timescales. These slow variables are known as reaction coordinates in molecular dynamical applications, where they play a key role in system analysis and coarse graining. The defining characteristics of these slow variables is that they parametrize a so-called transition manifold, a low-dimensional manifold in a certain density function space that emerges with progressive equilibration of the system's fast variables. The existence of said manifold was previously predicted for certain classes of metastable and slow-fast systems. However, in the original work, the existence of the manifold hinges on the pointwise convergence of the system's transition density functions towards it. We show in this work that a convergence in average with respect to the system's stationary measure is sufficient to yield reaction coordinates with the same key qualities. This allows one to accurately predict the timescale preservation in systems where the old theory is not applicable or would give overly pessimistic results. Moreover, the new characterization is still constructive, in that it allows for the algorithmic identification of a good slow variable. The improved characterization, the error prediction and the variable construction are demonstrated by a small metastable system

Properties of the energy landscape of network models for covalent glasses

We investigate the energy landscape of two dimensional network models for covalent glasses by means of the lid algorithm. For three different particle densities and for a range of network sizes, we exhaustively analyse many configuration space regions enclosing deep-lying energy minima. We extract the local densities of states and of minima, and the number of states and minima accessible below a certain energy barrier, the 'lid'. These quantities show on average a close to exponential growth as a function of their respective arguments. We calculate the configurational entropy for these pockets of states and find that the excess specific heat exhibits a peak at a critical temperature associated with the exponential growth in the local density of states, a feature of the specific heat also observed in real glasses at the glass transition.Comment: RevTeX, 19 pages, 7 figure