PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

New classes of spatial central configurations for the n+3-body problem

In this paper, we show the existence of new families of spatial central configurations for the n + 3-body problem, n >= 3. We study spatial central configurations where n bodies are at the vertices of a regular n-gon T and the other three bodies are symmetrically located on the straight line that is perpendicular to the plane that contains T and passes through the center of T. The results have simple and analytic proofs. (c) 2010 Elsevier Ltd. All rights reserved.

Stacked central configurations for the spatial six-body problem

In this paper we show the existence of three new families of stacked spatial central configurations for the six-body problem with the following properties: four bodies are at the vertices of a regular tetrahedron and the other two bodies are on a line connecting one vertex of the tetrahedron with the center of the opposite face. (c) 2009 Elsevier B.V. All rights reserved.

Performance Evaluation of Different PV-Array Configurations under Weak Light Conditions and Partial Shadings

The paper analyses empirical performance data of five commercial PV-plants in Germany. The purpose was on one side to investigate the weak light performance of the different PV-modules used. On the other hand it was to quantify and compare the shading losses of different PV-array configurations. The importance of this study relies on the fact that even if the behavior under weak light conditions or the shading losses might seem to be a relatively small percentage of the total yearly output; in projects where a performance guarantee is given, these variation can make the difference between meeting or not the conditions.When analyzing the data, a high dispersion was found. To reduce the optical losses and spectral effects, a series of data filters were applied based on the angle of incidence and absolute Air Mass. To compensate for the temperature effects and translate the values to STC (25°C), five different methods were assessed. At the end, the Procedure 2 of IEC 60891 was selected due to its relative simplicity, usage of mostly standard parameters found in datasheets, good accuracy even with missing values, and its potential to improve the results when the complete set of inputs is available.After analyzing the data, the weak light performance of the modules did not show a clear superiority of a certain technology or technology group over the others. Moreover, the uncertainties in the measurements restrictive the conclusiveness of the results.In the partial shading analysis, the landscape mounting of mc-Si PV-modules in free-field showed a significantly better performance than the portrait one. The cross-table string using CIGS modules did not proved the benefits expected and performed actually poorer than a regular one-string-per-table layout. Parallel substrings with CdTe showed a proper functioning and relatively low losses. Among the two product generations of CdTe analyzed, none showed a significantly better performance under partial shadings.

COMPARISON OF PARTIAL SHADING LOSSES IN FREE FIELD PV-PLANTS WITH DIFFERENT ARRAY CONFIGURATIONS

A common problem when planning large free field PV-plants is optimizing the ground occupation ratio while maintaining low shading losses. Due to the complexity of this task, several PV-plants have been built using various configurations. In order to compare the shading losses of different PV technologies and array designs, empirical performance data of five free field PV-plants operating in Germany was analyzed. The data collected comprised 140 winter days from October 2011 until March 2012. The relative shading losses were estimated by comparing the energy output of selected arrays in the front rows (shading-free) against that of shaded arrays in the back rows of the same plant. The results showed that landscape mounting with mc-Si PV-modules yielded significantly better results than portrait one. With CIGS modules, making cross-table strings using the lower modules was not beneficial as expected and had more losses than a one-string-per-table layout. Parallel substrings with CdTe showed relatively low losses. Among the two CdTe products analyzed, none showed a significantly better performance.

Vortex-Antivortex Dynamics in a Mesoscopic Superconducting Prism with a Centered Antidot

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Vortex dynamics in mesoscopic superconducting square of variable surface

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Vortex state in a mesoscopic flat disk with rough surface

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Vortex-antivortex annihilation dynamics in a square mesoscopic superconducting cylinder

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Irregular satellites of Jupiter: capture configurations of binary-asteroids

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Proposal of an alternative transmission line model for symmetrical and asymmetrical configurations

This article shows a transmission line model for simulation of fast and slow transients, applied to symmetrical or asymmetrical configurations. A transmission line model is developed based on lumped elements representation and state-space techniques. The proposed methodology represents a practical procedure to model three-phase transmission lines directly in time domain, without the explicit or implicit use of inverse transforms. In three-phase representation, analysis modal techniques are applied to decouple the phases in their respective propagation modes, using a correction procedure to set a real and constant matrix for untransposed lines with or without vertical symmetry plane. The proposed methodology takes into account the frequency-dependent parameters of the line and in order to include this effect in the state matrices, a fitting procedure is applied. To verify the accuracy of the proposed state-space model in frequency domain, a simple methodology is described based on line distributed parameters and transfer function associated with input/output signals of the lumped parameters representation. In addition, this article proposes the use of a fast and robust integration procedure to solve the state equations, enabling transient and steady-state simulations. The results obtained by the proposed methodology are compared with several established transmission line models in EMTP, taking into account an asymmetrical three-phase transmission line. The principal contribution of the proposed methodology is to handle a steady fundamental signal mixed with fast and slow transients, including impulsive and oscillatory behavior, by a practical procedure applied directly in time domain for symmetrical or asymmetrical representations. (C) 2011 Elsevier Ltd. All rights reserved.

Change of the vortex lattice symmetry in the vicinity of the macro-to-mesoscopic threshold

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Crossover between macroscopic and mesoscopic regimes of vortex interactions in type-II superconductors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)