Stacking of oligo and polythiophenes cations in solution: surface tension and dielectric saturation

The stacking of positively charged (or doped) terthiophene oligomers and quaterthiophene polymers in solution is investigated applying a recently developed unified electrostatic and cavitation model for first-principles calculations in a continuum solvent. The thermodynamic and structural patterns of the dimerization are explored in different solvents, and the distinctive roles of polarity and surface tension are characterized and analyzed. Interestingly, we discover a saturation in the stabilization effect of the dielectric screening that takes place at rather small values of $\epsilon_0$. Moreover, we address the interactions in trimers of terthiophene cations, with the aim of generalizing the results obtained for the dimers to the case of higher-order stacks and nanoaggregates

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon

Estimating wild boar ( Sus scrofa ) abundance and density using capture-resights in Canton of Geneva, Switzerland

We estimated wild boar abundance and density using capture-resight methods in the western part of the Canton of Geneva (Switzerland) in the early summer from 2004 to 2006. Ear-tag numbers and transmitter frequencies enabled us to identify individuals during each of the counting sessions. We used resights generated by self-triggered camera traps as recaptures. Program Noremark provided Minta-Mangel and Bowden's estimators to assess the size of the marked population. The minimum numbers of wild boars belonging to the unmarked population (juveniles and/or piglets) were added to the respective estimates to assess total population size. Over the 3years, both estimators showed a stable population with a slight diminishing tendency. We used mean home range size determined by telemetry to assess the sampled areas and densities. Mean wild boar population densities calculated were 10.6individuals/km2 ± 0.8 standard deviation (SD) and 10.0ind/km2 ± 0.6 SD with both estimators, respectively, and are among the highest reported from Western Europe. Because of the low proportion of marked animals and, to a lesser extent, of technical failures, our estimates showed poor precision, although they displayed similar population trends compared to the culling bag statistics. Reported densities were consistent with the ecological conditions of the study are

MIKA: a multigrid-based program package for electronic structure calculations

A general real-space multigrid algorithm MIKA (Multigrid Instead of the K-spAce) for the self-consistent solution of the Kohn-Sham equations appearing in the state-of-the-art electronic-structure calculations is described. The most important part of the method is the multigrid solver for the Schr\"odinger equation. Our choice is the Rayleigh quotient multigrid method (RQMG), which applies directly to the minimization of the Rayleigh quotient on the finest level. Very coarse correction grids can be used, because there is in principle no need to represent the states on the coarse levels. The RQMG method is generalized for the simultaneous solution of all the states of the system using a penalty functional to keep the states orthogonal. Special care has been taken to optimize the iterations towards the self-consistency and to run the code in parallel computer architectures. The scheme has been implemented in multiple geometries. We show examples from electronic structure calculations employing nonlocal pseudopotentials and/or the jellium model. The RQMG solver is also applied for the calculation of positron states in solids.Comment: To appear in a special issue of Int J. Quant. Chem. devoted to the conference proceedings of 9th International Conference on the Applications of the Density Functional Theory in Chemistry and Physic

Recent progress with large-scale ab initio calculations: the CONQUEST code

While the success of density functional theory (DFT) has led to its use in a wide variety of fields such as physics, chemistry, materials science and biochemistry, it has long been recognised that conventional methods are very inefficient for large complex systems, because the memory requirements scale as $N^2$ and the cpu requirements as $N^3$ (where $N$ is the number of atoms). The principles necessary to develop methods with linear scaling of the cpu and memory requirements with system size ($\mathcal{O}(N)$ methods) have been established for more than ten years, but only recently have practical codes showing this scaling for DFT started to appear. We report recent progress in the development of the \textsc{Conquest} code, which performs $\mathcal{O}(N)$ DFT calculations on parallel computers, and has a demonstrated ability to handle systems of over 10,000 atoms. The code can be run at different levels of precision, ranging from empirical tight-binding, through \textit{ab initio} tight-binding, to full \textit{ab initio}, and techniques for calculating ionic forces in a consistent way at all levels of precision will be presented. Illustrations are given of practical \textsc{Conquest} calculations in the strained Ge/Si(001) system.Comment: 12 pages, 7 figures, accepted by phys. stat. sol.

A novel multigrid method for electronic structure calculations

A general real-space multigrid algorithm for the self-consistent solution of the Kohn-Sham equations appearing in the state-of-the-art electronic-structure calculations is described. The most important part of the method is the multigrid solver for the Schroedinger equation. Our choice is the Rayleigh quotient multigrid method (RQMG), which applies directly to the minimization of the Rayleigh quotient on the finest level. Very coarse correction grids can be used, because there is no need to be able to represent the states on the coarse levels. The RQMG method is generalized for the simultaneous solution of all the states of the system using a penalty functional to keep the states orthogonal. The performance of the scheme is demonstrated by applying it in a few molecular and solid-state systems described by non-local norm-conserving pseudopotentials.Comment: 9 pages, 3 figure

Real-space grid representation of momentum and kinetic energy operators for electronic structure calculations

We show that the central finite difference formula for the first and the second derivative of a function can be derived, in the context of quantum mechanics, as matrix elements of the momentum and kinetic energy operators using, as a basis set, the discrete coordinate eigenkets $\vert x_n\rangle$ defined on the uniform grid $x_n=na$. Simple closed form expressions of the matrix elements are obtained starting from integrals involving the canonical commutation rule. A detailed analysis of the convergence toward the continuum limit with respect to both the grid spacing and the approximation order is presented. It is shown that the convergence from below of the eigenvalues in electronic structure calculations is an intrinsic feature of the finite difference method

Three real-space discretization techniques in electronic structure calculations

A characteristic feature of the state-of-the-art of real-space methods in electronic structure calculations is the diversity of the techniques used in the discretization of the relevant partial differential equations. In this context, the main approaches include finite-difference methods, various types of finite-elements and wavelets. This paper reports on the results of several code development projects that approach problems related to the electronic structure using these three different discretization methods. We review the ideas behind these methods, give examples of their applications, and discuss their similarities and differences.Comment: 39 pages, 10 figures, accepted to a special issue of "physica status solidi (b) - basic solid state physics" devoted to the CECAM workshop "State of the art developments and perspectives of real-space electronic structure techniques in condensed matter and molecular physics". v2: Minor stylistic and typographical changes, partly inspired by referee comment