J.L. Alonso

Efficient formalism for large-scale ab initio molecular dynamics based on time-dependent density functional theory.

A new on the fly method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schrödinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time scale of the fictitious electronic motion and speeds up the calculations with respect to standard Ehrenfest dynamics. In contrast with other methods, wave function orthogonality needs not be imposed as it is automatically preserved, which is of paramount relevance for large-scale AIMD simulations.

Hybrid Monte Carlo algorithm for the double exchange model

Abstract The Hybrid Monte Carlo algorithm is adapted to the simulation of a system of classical degrees of freedom coupled to non self-interacting lattices fermions. The diagonalization of the Hamiltonian matrix is avoided by introducing a path-integral formulation of the problem, in d+1 Euclidean space–time. A perfect action formulation allows to work on the continuum Euclidean time, without need for a Trotter–Suzuki extrapolation. To demonstrate the feasibility of the method we study the Double Exchange Model in three dimensions. The complexity of the algorithm grows only as the system volume, allowing to simulate in lattices as large as 16 3 on a personal computer. We conclude that the second order paramagnetic–ferromagnetic phase transition of Double Exchange Materials close to half-filling belongs to the Universality Class of the three-dimensional classical Heisenberg model.

A mathematical and computational review of Hartree–Fock SCF methods in quantum chemistry

We present a review of the fundamental topics of Hartree–Fock theory in quantum chemistry. From the molecular Hamiltonian, using and discussing the Born–Oppenheimer approximation, we arrive at the Hartree and Hartree–Fock equations for the electronic problem. Special emphasis is placed on the most relevant mathematical aspects of the theoretical derivation of the final equations, and on the results regarding the existence and uniqueness of their solutions. All Hartree–Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. The discretization of the one-electron orbital space is then reviewed and the Roothaan–Hall formalism introduced. This leads to an exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing on algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (especially those related to the design of linear-scaling methods) are commented on and linked to the issues discussed. The paper is intentionally introductory and rather self-contained, and may be useful for non-experts intending to use quantum chemical methods in interdisciplinary applications. Moreover, much material that can be found scattered in the literature has been put together to facilitate comprehension and to serve as a handy reference.

Enteric calicivirus and rotavirus infections in domestic pigs

We report the prevalence of rotavirus and calicivirus infections, along with their respective association with diarrhoea in the porcine population of the region of northern Spain. A total of 221 samples were collected at random from different farms in the region and from the main slaughterhouse facility in the city of Zaragoza. Faecal samples were scored as diarrhoeic or normal and grouped into five groups to match general farm management and age criteria: group I (suckling 0-4 weeks), group II (weaning >4-8 weeks), group III (transition >8-16 weeks), group IV (fattening >16-24 weeks) and group V (adults >24 weeks). Group A rotavirus detection and caliciviruses were investigated by reverse transcription-polymerase chain reaction (RT-PCR). Conventional RT-PCR was performed using primers designed to detect rotavirus group A, caliciviruses and/or human noroviruses. A real-time RT-PCR was carried out using TaqMan probes for genogroups GI and GII of noroviruses. Rotaviruses and caliciviruses were detected with an overall prevalence of 16.7% and 12.2%, respectively. Rotavirus detection in faecal samples was associated with both age and faecal consistency, being more frequent in piglets aged <8 weeks with odds ratios (ORs) equal to 4.3 and 4.9, respectively. Calicivirus shedding in faecal samples was homogenously distributed in all ages, showing no significant association with age or faecal consistency (OR 0.87 and 0.99, respectively). A selection of rotavirus-positive stools were genotyped by multiplex nested PCR. G10, P[6], G12 P[8], G9 [p8] and G4 P[23] genotype combinations were found. Three isolates showed a G3 genotype, but their VP4 gene could not be amplified. It should be noted that the G9 genotype was the major G genotype circulating during that period in Spain. None of the porcine samples was positive for norovirus by real-time RT-PCR, despite the ability of this technique to detect at least 18 human norovirus genotypes. Our data indicate that human noroviruses are unlikely to be circulating in the porcine population; however, sapoviruses have been found. Contrary to rotavirus infection, Calicivirus infection is asymptomatic. Specific primers to detect porcine noroviruses are needed.

Phase diagram and influence of defects in the double perovskites

The phase diagram of the double perovskites of the type Sr_(2-x)La_(x)FeMoO_(6) is analyzed, with and without disorder due to antisites. In addition to an homogeneous half metallic ferrimagnetic phase in the absence of doping and disorder, we find antiferromagnetic phases at large dopings, and other ferrimagnetic phases with lower saturation magnetization, in the presence of disorder.

Interplay between double-exchange, superexchange, and Lifshitz localization in doped manganites

Considering the disorder caused in manganites by the substitution Mn→Fe or Ga, we accomplish a systematic study of doped manganites begun in previous papers. To this end, a disordered model is formulated and solved using the variational mean-field technique. The subtle interplay between double exchange, superexchange, and disorder causes similar effects on the dependence of T_(C) on the percentage of Mn substitution in the cases considered. Yet, in La_(2/3)Ca_(1/3)Mn_(1-y)Ga_(y)O_(3) our results suggest a quantum critical point (QCP) for y ≈ 0.1–0.2, associated to the localization of the electronic states of the conduction band. In the case of La_(x)Ca_(x)Mn_(1-y)Fe_(y)O_(3) (with x = 1/3,3/8) no such QCP is expected.

Variational mean-field approach to the double-exchange model

It has been recently shown that the double exchange Hamiltonian, with weak antiferromagnetic interactions, has a richer variety of first- and second-order transitions than previously anticipated, and that such transitions are consistent with the magnetic properties of manganites. Here we present a thorough discussion of the variational mean-field approach that leads to these results. We also show that the effect of the Berry phase turns out to be crucial to produce first-order paramagnetic-ferromagnetic transitions near half filling with transition temperatures compatible with the experimental situation. The computation relies on two crucial facts: the use of a mean-field ansatz that retains the complexity of a system of electrons with off-diagonal disorder, not fully taken into account by the mean-field techniques, and the small but significant antiferromagnetic superexchange interaction between the localized spins.

Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the alanine dipeptide

If constraints are imposed on a macromolecule, two inequivalent classical models may be used: the stiff and the rigid one. This work studies the effects of such constraints on the conformational equilibrium distribution (CED) of the model dipeptide HCO‐L‐Ala‐NH2without any simplifying assumption. We use ab initio quantum mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of all the correcting terms to the naive CED based in the potential energy surface that appear when the constraints are considered. These terms are related to mass‐metric tensors determinants and also occur in the Fixmans compensating potential. We show that some of the corrections are non‐negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.

Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split-valence basis sets

We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO‐L‐Ala‐NH2. The model chemistries (MCs) investigated are constructed as homo‐ and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 representants from Poples split‐valence families, ranging from the small 3‐21G to the large 6‐311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6‐311++G(2df,2pd) homolevel, which, as far as we are aware, is the most accurate PES in the literature. All data sets have been analyzed according to a general framework, which can be extended to other complex problems and which captures the nearness concept in the space of MCs. The great number of MCs evaluated has allowed us to significantly explore this space and show that the correlation between accuracy and computational cost of the methods is imperfect, thus justifying a systematic search for the combination of features in a MC that is optimal to deal with peptides. Regarding the particular MCs studied, the most important conclusion is that the potentially very cost‐saving heterolevel approximation is a very efficient one to describe the whole PES of HCO‐L‐Ala‐NH2. Finally, we show that, although RHF may be used to calculate the geometry if a MP2 single‐point energy calculation follows, pure RHF//RHF homolevels are not recommendable for this problem.

Discontinuous transitions in double-exchange materials

It is shown that the double-exchange Hamiltonian, with weak antiferromagnetic interactions, has a rich variety of first-order transitions between phases with different electronic densities and/or magnetizations. The paramagnetic-ferromagnetic transition moves towards lower temperatures, and becomes discontinuous as the relative strength of the double-exchange mechanism and antiferromagnetic coupling is changed. This trend is consistent with the observed differences between compounds with the same nominal doping, such as La_(2/3)Sr_(1/3)MnO_(3) and La_(2/3)Ca_(1/3)MnO_(3). Our results suggest that, in the low doping regime, a simple magnetic mechanism suffices to explain the main features of the phase diagram.