A hybrid approach to Fermi operator expansion

In a recent paper we have suggested that the finite temperature density matrix can be computed efficiently by a combination of polynomial expansion and iterative inversion techniques. We present here significant improvements over this scheme. The original complex-valued formalism is turned into a purely real one. In addition, we use Chebyshev polynomials expansion and fast summation techniques. This drastically reduces the scaling of the algorithm with the width of the Hamiltonian spectrum, which is now of the order of the cubic root of such parameter. This makes our method very competitive for applications to ab-initio simulations, when high energy resolution is required.Comment: preprint of ICCMSE08 proceeding

Evolution of the structure of amorphous ice - from low-density amorphous (LDA) through high-density amorphous (HDA) to very high-density amorphous (VHDA) ice

We report results of molecular dynamics simulations of amorphous ice for pressures up to 22.5 kbar. The high-density amorphous ice (HDA) as prepared by pressure-induced amorphization of Ih ice at T=80 K is annealed to T=170 K at various pressures to allow for relaxation. Upon increase of pressure, relaxed amorphous ice undergoes a pronounced change of structure, ranging from the low-density amorphous ice (LDA) at p=0, through a continuum of HDA states to the limiting very high-density amorphous ice (VHDA) regime above 10 kbar. The main part of the overall structural change takes place within the HDA megabasin, which includes a variety of structures with quite different local and medium-range order as well as network topology and spans a broad range of densities. The VHDA represents the limit to densification by adapting the hydrogen-bonded network topology, without creating interpenetrating networks. The connection between structure and metastability of various forms upon decompression and heating is studied and discussed. We also discuss the analogy with amorphous and crystalline silica. Finally, some conclusions concerning the relation between amorphous ice and supercooled water are drawn.Comment: 11 pages, 12 postscript figures. To be published in The Journal of Chemical Physic

An Efficient and Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics

We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab-initio simulations. Depending on the system a gain in efficiency of one to two orders of magnitude has been observed, which allows ab-initio molecular dynamics of much larger time and length scales than previously thought feasible. It will be demonstrated that the dynamics is correctly reproduced and that high accuracy can be maintained throughout for systems ranging from insulators to semiconductors and even to metals in condensed phases. This development considerably extends the scope of ab-initio simulations.Comment: 4 pages, 3 figures; Accepted by Phys. Rev. Lett. for publicatio

Taxonomy and palaeobiogeography of the Cenozoic Euro-Mediterranean rissoid gastropod Galeodinopsis and its relationship with close genera

The investigation of the Late Paleogene to Late Neogene species of rissoid gastropod Galeodinopsis in the Euro-Mediterranean area has supported the hypothesis that this genus is an intermediate form between two well-known rissoids, Alvinia and Manzonia. We recognized four species of Galeodinopsis: G. biangulata, G. germanica sp. nov., G. semperi (new name for Rissoa duboisii), and G. tiberiana. The oldest (very Late Eocene/Oligocene) representatives of Galeodinopsis, G. biangulata, and G. semperi, share similar shell shape and microsculpture with Alvinia. This suggests that Galeodinopsis originated from some Eocene species related to Alvinia. The new species represents the first occurrence within Galeodinopsis of a combination of characters very close to those of Manzonia, above all the typical pitted microsculpture. We hypothesize that Manzonia evolved from Galeodinopsis rather than from the genera Alvania or Alvinia, as previously supposed. Galeodinopsis originated during the very Late Eocene/Oligocene in the North Sea Basin. Afterwards it underwent a strong southward shift to the mid-high east Atlantic and the Mediterranean area, during the Mio-Pliocene, and to the Recent tropical eastern Atlantic coasts, where the type species G. tiberiana still lives. The shift likely was due to a combination of climate cooling and palaeogeographical changes. The distribution of G. biangulata suggests that connections between the North Sea Basin and the Atlantic domain opened through the Channel area at least during the Early Oligocene, earlier than indicated previously. The distribution of Manzonia moulinsi supports the idea of a southern connection to the Atlantic Aquitaine Basin via the Rhine Graben during the Late Oligocene. From a palaeoecological point of view, Galeodinopsis includes warm species with planktotrophic larval development that are typical of the shelf environment in fully marine conditions

Ciona intestinalis galectin (CiLgals-a and CiLgals-b) genes are differentially expressed in endostyle zones and challenged by LPS

Immunohistochemical and in situ hybridization assays were performed to answer the question whether the endostyle, that is the initial gastro-intestinal trait of Ciona intestinalis pharynx, is involved in galectin (CiLgals-a and CiLgals-b) production during the pharynx inflammatory response to LPS inoculation. Specific anti-CiLgal-a and anti-CiLgals-b antibodies, and oligonucleotide probes, that mark inflammatory hemocytes inside the pharynx vessels and vessel epithelium as shown by a previous paper, were assayed on endostyle histological sections. For the first time, we show that galectins are produced by endostyle zones, and both CiLgals-a and eb genes are upregulated by LPS. CiLgals-a and CiLgals-b are constitutively expressed in the endostyle zone 2 and 3, respectively, both genes are upregulated by LPS in the zone 2, and CiLgals-b in the zone 3 and 4. The antibody-reacting material contained in intracellular and extracellular large vesicles suggest an unexpected vesicle-dependent transporting mechanism of galectins not provided with signal peptide. Differential expression and gene upregulation in not-treated and LPStreated specimens, support the role of endostyle galectins both in filter feeding and defense responses

Displaced path integral formulation for the momentum distribution of quantum particles

The proton momentum distribution, accessible by deep inelastic neutron scattering, is a very sensitive probe of the potential of mean force experienced by the protons in hydrogen-bonded systems. In this work we introduce a novel estimator for the end to end distribution of the Feynman paths, i.e. the Fourier transform of the momentum distribution. In this formulation, free particle and environmental contributions factorize. Moreover, the environmental contribution has a natural analogy to a free energy surface in statistical mechanics, facilitating the interpretation of experiments. The new formulation is not only conceptually but also computationally advantageous. We illustrate the method with applications to an empirical water model, ab-initio ice, and one dimensional model systems