Comment on “The diatomic dication CuZn2+ in the gas phase” [J. Chem. Phys. 135, 034306 (2011)]

In this Comment, the density functional theory (DFT) calculations carried out by Diez et al. [J. Chem. Phys. 135, 034306 (2011)10.1063/1.3613624] are revised within the framework of the coupled-cluster single double triple method. These more sophisticated calculations allow us to show that the 2Σ+ electronic ground state of CuZn2+, characterized as the metastable ground state by DFT calculations, is a repulsive state instead. The 2Δ and 2Π metastable states of CuZn2+, on the other hand, should be responsible for the formation mechanism of the dication through the near-resonant electron transfer CuZn+ + Ar+ → CuZn2+ + Ar reaction.Fil: Pis Diez, Reinaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Química Inorgánica "Dr. Pedro J. Aymonino". Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Química Inorgánica "Dr. Pedro J. Aymonino"; ArgentinaFil: Franzreb, Klaus. Arizona State University; Estados UnidosFil: Alonso, Julio A.. Universidad de Valladolid; Españ

Time relaxation of interacting single--molecule magnets

We study the relaxation of interacting single--molecule magnets (SMMs) in both spatially ordered and disordered systems. The tunneling window is assumed to be, as in Fe8, much narrower than the dipolar field spread. We show that relaxation in disordered systems differs qualitatively from relaxation in fully occupied cubic and Fe_8 lattices. We also study how line shapes that develop in ''hole--digging'' experiments evolve with time t in these fully occupied lattices. We show (1) that the dipolar field h scales as t^p in these hole line shapes and show (2) how p varies with lattice structure. Line shapes are not, in general, Lorentzian. More specifically, in the lower portion of the hole, they behave as (h/t^p)^{(1/p)-1} if h is outside the tunnel window. This is in agreement with experiment and with our own Monte Carlo results.Comment: 21 LaTeX pages, 6 eps figures. Submitted to PRB on 15 June 2005. Accepted on 13 August 200

Orbital-Free Molecular Dynamics Simulations of Melting in Na8 and Na20: Melting in Steps

The melting-like transitions of Na8 and Na20 are investigated by ab initio constant energy molecular dynamics simulations, using a variant of the Car-Parrinello method which employs an explicit electronic kinetic energy functional of the density, thus avoiding the use of one-particle orbitals. Several melting indicators are evaluated in order to determine the nature of the various transitions, and compared with other simulations. Both Na8 and Na20 melt over a wide temperature range. For Na8, a transition is observed to begin at approx. 110 K, between a rigid phase and a phase involving isomerizations between the different permutational isomers of the ground state structure. The ``liquid'' phase is completely established at approx. 220 K. For Na20, two transitions are observed: the first, at approx. 110 K, is associated with isomerization transitions between those permutational isomers of the ground state structure which are obtained by interchanging the positions of the surface-like atoms; the second, at approx. 160 K, involves a structural transition from the ground state isomer to a new set of isomers with the surface molten. The cluster is completely ``liquid'' at approx. 220 K.Comment: Revised version, accepted for publication in J. Chem. Phys. The changes include longer simulations for the Na20 microcluster, a more complete comparison to previous theoretical results, and the discussion of some technical details of the method applie

Can optical spectroscopy directly elucidate the ground state of C20?

The optical response of the lowest energy members of the C20 family is calculated using time-dependent density functional theory within a real-space, real-time scheme. Significant differences are found among the spectra of the different isomers, and thus we propose optical spectroscopy as a tool for experimental investigation of the structure of these important clusters.Comment: 11 pages, 2 figures. To be published in J. Chem. Phy

Inference of complex biological networks: distinguishability issues and optimization-based solutions

<p>Abstract</p> <p>Background</p> <p>The inference of biological networks from high-throughput data has received huge attention during the last decade and can be considered an important problem class in systems biology. However, it has been recognized that reliable network inference remains an unsolved problem. Most authors have identified lack of data and deficiencies in the inference algorithms as the main reasons for this situation.</p> <p>Results</p> <p>We claim that another major difficulty for solving these inference problems is the frequent lack of uniqueness of many of these networks, especially when prior assumptions have not been taken properly into account. Our contributions aid the distinguishability analysis of chemical reaction network (CRN) models with mass action dynamics. The novel methods are based on linear programming (LP), therefore they allow the efficient analysis of CRNs containing several hundred complexes and reactions. Using these new tools and also previously published ones to obtain the network structure of biological systems from the literature, we find that, often, a unique topology cannot be determined, even if the structure of the corresponding mathematical model is assumed to be known and all dynamical variables are measurable. In other words, certain mechanisms may remain undetected (or they are falsely detected) while the inferred model is fully consistent with the measured data. It is also shown that sparsity enforcing approaches for determining 'true' reaction structures are generally not enough without additional prior information.</p> <p>Conclusions</p> <p>The inference of biological networks can be an extremely challenging problem even in the utopian case of perfect experimental information. Unfortunately, the practical situation is often more complex than that, since the measurements are typically incomplete, noisy and sometimes dynamically not rich enough, introducing further obstacles to the structure/parameter estimation process. In this paper, we show how the structural uniqueness and identifiability of the models can be guaranteed by carefully adding extra constraints, and that these important properties can be checked through appropriate computation methods.</p

Magnetization Process of Single Molecule Magnets at Low Temperatures

We show that correlations established before quenching to very low temperatures, later drive the magnetization process of systems of single molecule magnets, after a magnetic field is applied at t=0. We also show that in SC lattices, m \propto sqrt(t), as observed in Fe_8, but only for 1+2*log_10(h_d/h_w) time decades, where h_d is a nearest neighbor dipolar magnetic field and a spin reversal can occur only if the field on it is within (-h_w,h_w). However, the sqrt(t) behavior is not universal. For BCC and FCC lattices, m \propto t^p, but p \simeq 0.7. The value to which m finally levels off is also given.Comment: 5 LaTeX pages, 2 figures. Submitted to Phys. Rev. Lett. on 26 January 2003, accepted on 24 July 200