Basis set effects on the hyperpolarizability of CHCl_3: Gaussian-type orbitals, numerical basis sets and real-space grids

Calculations of the hyperpolarizability are typically much more difficult to converge with basis set size than the linear polarizability. In order to understand these convergence issues and hence obtain accurate ab initio values, we compare calculations of the static hyperpolarizability of the gas-phase chloroform molecule (CHCl_3) using three different kinds of basis sets: Gaussian-type orbitals, numerical basis sets, and real-space grids. Although all of these methods can yield similar results, surprisingly large, diffuse basis sets are needed to achieve convergence to comparable values. These results are interpreted in terms of local polarizability and hyperpolarizability densities. We find that the hyperpolarizability is very sensitive to the molecular structure, and we also assess the significance of vibrational contributions and frequency dispersion

Theoretical X-Ray Absorption Debye-Waller Factors

An approach is presented for theoretical calculations of the Debye-Waller factors in x-ray absorption spectra. These factors are represented in terms of the cumulant expansion up to third order. They account respectively for the net thermal expansion $\sigma^{(1)}(T)$, the mean-square relative displacements $\sigma^2(T)$, and the asymmetry of the pair distribution function $\sigma^{(3)}(T)$. Similarly, we obtain Debye-Waller factors for x-ray and neutron scattering in terms of the mean-square vibrational amplitudes $u^2(T)$. Our method is based on density functional theory calculations of the dynamical matrix, together with an efficient Lanczos algorithm for projected phonon spectra within the quasi-harmonic approximation. Due to anharmonicity in the interatomic forces, the results are highly sensitive to variations in the equilibrium lattice constants, and hence to the choice of exchange-correlation potential. In order to treat this sensitivity, we introduce two prescriptions: one based on the local density approximation, and a second based on a modified generalized gradient approximation. Illustrative results for the leading cumulants are presented for several materials and compared with experiment and with correlated Einstein and Debye models. We also obtain Born-von Karman parameters and corrections due to perpendicular vibrations.Comment: 11 pages, 8 figure

Accuracy of generalized gradient approximation functionals for density functional perturbation theory calculations

We assess the validity of various exchange-correlation functionals for computing the structural, vibrational, dielectric, and thermodynamical properties of materials in the framework of density-functional perturbation theory (DFPT). We consider five generalized-gradient approximation (GGA) functionals (PBE, PBEsol, WC, AM05, and HTBS) as well as the local density approximation (LDA) functional. We investigate a wide variety of materials including a semiconductor (silicon), a metal (copper), and various insulators (SiO$_2$ $\alpha$-quartz and stishovite, ZrSiO$_4$ zircon, and MgO periclase). For the structural properties, we find that PBEsol and WC are the closest to the experiments and AM05 performs only slightly worse. All three functionals actually improve over LDA and PBE in contrast with HTBS, which is shown to fail dramatically for $\alpha$-quartz. For the vibrational and thermodynamical properties, LDA performs surprisingly very good. In the majority of the test cases, it outperforms PBE significantly and also the WC, PBEsol and AM05 functionals though by a smaller margin (and to the detriment of structural parameters). On the other hand, HTBS performs also poorly for vibrational quantities. For the dielectric properties, none of the functionals can be put forward. They all (i) fail to reproduce the electronic dielectric constant due to the well-known band gap problem and (ii) tend to overestimate the oscillator strengths (and hence the static dielectric constant)

Length-weight relationships for 22 crustaceans and cephalopods from the Gulf of Cadiz (SW Spain)

Life history traits are available for many fish species in different regions, but less so for invertebrates such as cephalopods and crustaceans, though, they are increasingly needed for implementing an ecosystem-based approach. Recent food web modelling in the Gulf of Cadiz has identified invertebrates as keystone groups. However, information on life history traits of such groups remains incomplete in this region. To fill this knowledge gap, we report length-weight relationships for 12 cephalopods and 10 crustaceans collected in the Gulf of Cadiz from 2009 to 2013. This study reports, for the first time, life history traits of nine species in the area (Chlorotocus crassicornis, Pasiphaea sivado, Plesionika heterocarpus, Plesionika martia, Processa canaliculata, Solenocera membranacea, Allotheutis media, Sepia orbignyana and Sepietta oweniana). For each species, length-weight relationships, minimum and maximum lengths, mean weights, and depth ranges are presented. Overall, the results revealed that all species showed negative allometric growth (hypoallometry), except P. sivado, the only species showing an isometric growth pattern. We expect that this study will contribute to link sustainable fisheries with biodiversity conservation goals enabling the implementation of operational ecosystem-based management in the Gulf of Cadiz.IEO through FPIinfo:eu-repo/semantics/publishedVersio

Extended X-Ray Absorption Fine Structure of ZrW2O8: Theory vs. Experiment

Extended x-ray absorption fine structure (EXAFS) is well-suited for investigations of structure and disorder of complex materials. Recently, experimental measurements and analysis of EXAFS have been carried out to elucidate the mechanisms responsible for the negative thermal expansion (NTE) in zirconium tungstate (ZrW2O8). In contrast to previous work suggesting that transverse O-displacements are largely responsible, the EXAFS analysis suggested that correlated rotations and translations of octahedra and tetrahedra within the structure are a major source. In an effort to resolve this controversy, we have carried out ab initio calculations of the structure, lattice vibrations, and EXAFS of ZrW2O8 based on real-space multiple-scattering calculations using the FEFF9 code and auxiliary calculations of structure and Debye-Waller factors. We find that the theoretical simulations are consistent with observed EXAFS, and show that both of the above mechanisms contribute to the dynamical structure of ZrW2O8

Biotechnological applications of bacteriophages: state of the art

Bacteriophage particles are the most abundant biological entities on our planet, infecting specific bacterial hosts in every known environment and being major drivers of bacterial adaptive evolution. The study of bacteriophage particles potentially sheds light on the development of new biotechnology products. Bacteriophage therapy, although not new, makes use of strictly lytic phage particles as an alternative in the antimicrobial treatment of resistant bacterial infections and is being rediscovered as a safe method due to the fact that these biological entities devoid of any metabolic machinery do not have affinity to eukaryotic cells. Furthermore, bacteriophage-based vaccination is emerging as one of the most promising preventive strategies. This review paper discusses the biological nature of bacteriophage particles, their mode(s) of action and potential exploitation in modern biotechnology. Topics covered in detail include the potential of bacteriophage particles in human infections (bacteriophage therapy), nanocages for gene delivery, food biopreservation and safety, biocontrol of plant pathogens, phage display, bacterial biosensing devices, vaccines and vaccine carriers, biofilm and bacterial growth control, surface disinfection, corrosion control, together with structural and functional stabilization issues.Project funding by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, São Paulo, Brazil) (FAPESP Refs. No. 2016/08884- 3 (Project PneumoPhageColor) and 2016/12234-4 (Project TransAppIL)), is hereby gratefully acknowledged. Funding by Fundação de Amparo à Pesquisa do Estado de São Paulo(FAPESP Ref. No. 2016/ 16641-3) in the form of an M.Sc. fellowship granted to Liliam Harada is hereby gratefully acknowledged. This work also received support from CNPq, National Council for Scientific and Technological Development Brazil, in the form of Research Productivity (PQ) fellowships granted to Victor M. Balcão (Refs. No. 306113/2014-7 and 308208/2017-0). Financial support to Krystyna Dąbrowska by the National Science Centre in Poland (Grant UMO-2012/05/E/NZ6/03314) is also gratefully acknowledged. The authors have no conflicts of interest whatsoever to declare.info:eu-repo/semantics/publishedVersio

The global threat of antimicrobial resistance: science for intervention

In the last decade we have witnessed a dramatic increase in the proportion and absolute number of bacterial pathogens resistant to multiple antibacterial agents. Multidrug-resistant bacteria are currently considered as an emergent global disease and a major public health problem. The B-Debate meeting brought together renowned experts representing the main stakeholders (i.e. policy makers, public health authorities, regulatory agencies, pharmaceutical companies and the scientific community at large) to review the global threat of antibiotic resistance and come up with a coordinated set of strategies to fight antimicrobial resistance in a multifaceted approach. We summarize the views of the B-Debate participants regarding the current situation of antimicrobial resistance in animals and the food chain, within the community and the healthcare setting as well as the role of the environment and the development of novel diagnostic and therapeutic strategies, providing expert recommendations to tackle the global threat of antimicrobial resistance

Intensity oscillations in the carbon 1s ionization cross sections of 2-butyne

Carbon 1s photoelectron spectra for 2-butyne (CH3C CCH3) measured in the photon energy range from threshold to 150 eV above threshold show oscillations in the intensity ratio C2,3/C1,4. Similar oscillations have been seen in chloroethanes, where the effect has been attributed to EXAFS-type scattering from the substituent chlorine atoms. In 2-butyne, however, there is no high-Z atom to provide a scattering center and, hence, oscillations of the magnitude observed are surprising. The results have been analyzed in terms of two different theoretical models: a density-functional model with B-spline atom-centered functions to represent the continuum electrons and a multiple-scattering model using muffin-tin potentials to represent the scattering centers. Both methods give a reasonable description of the energy dependence of the intensity ratios. (C) 2013 AIP Publishing LLC.Copyright 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. This is the publisher’s final pdf. The published article is copyrighted by American Physical Society and can be found at: http://www.aps.org/.Keywords: Photoelectron, Energies, Absorption fine structure, PhotoionizationKeywords: Photoelectron, Energies, Absorption fine structure, Photoionizatio