Biomedical subjects

Arnaldo Rapallo

Publications and source records attributed to Arnaldo Rapallo.

4 recordsLinked to original sources

PubMed2006

An algorithm for the uniform sampling of iso-energy surfaces and for the calculation of microcanonical averages.

In this article an algorithm is proposed to efficiently perform the uniform sampling of an iso-energy surface corresponding to a fixed potential energy U of a molecular system, and for calculating averages of certain quantities over microstates having this energy (microcanonical averages). The developed sampling technique is based upon the combination of a recently proposed method for performing constant potential energy molecular dynamics simulations [Rapallo, A. J Chem Phys 2004, 121, 4033] with well-established thermostatting techniques used in the framework of standard molecular dynamics simulations, such as the Andersen thermostat, and the Nose-Hoover chain thermostat. The proposed strategy leads to very accurate and drift-free potential energy conservation during the whole sampling process, and, very important, specially when dealing with high-dimensional or complicated potential functions, it does not require the calculation of the potential energy function hessian. The technique proved to be very reliable for sampling both low- and high-dimensional surfaces.

Algorithms↗

PubMed2005

Global optimization of bimetallic cluster structures. I. Size-mismatched Ag-Cu, Ag-Ni, and Au-Cu systems.

A genetic algorithm approach is applied to the optimization of the potential energy of a wide range of binary metallic nanoclusters, Ag-Cu, Ag-Ni, Au-Cu, Ag-Pd, Ag-Au, and Pd-Pt, modeled by a semiempirical potential. The aim of this work is to single out the driving forces that make different structural motifs the most favorable at different sizes and chemical compositions. Paper I is devoted to the analysis of size-mismatched systems, namely, Ag-Cu, Ag-Ni, and Au-Cu clusters. In Ag-Cu and Ag-Ni clusters, the large size mismatch and the tendency of Ag to segregate at the surface of Cu and Ni lead to the location of core-shell polyicosahedral minimum structures. Particularly stable polyicosahedral clusters are located at size N = 34 (at the composition with 27 Ag atoms) and N = 38 (at the composition with 32 and 30 Ag atoms). In Ag-Ni clusters, Ag32Ni13 is also shown to be a good energetic configuration. For Au-Cu clusters, these core-shell polyicosahedra are less common, because size mismatch is not reinforced by a strong tendency to segregation of Au at the surface of Cu, and Au atoms are not well accommodated upon the strained polyicosahedral surface.

Journal Article↗

PubMed2005

Global optimization of bimetallic cluster structures. II. Size-matched Ag-Pd, Ag-Au, and Pd-Pt systems.

Genetic algorithm global optimization of Ag-Pd, Ag-Au, and Pd-Pt clusters is performed. The 34- and 38-atom clusters are optimized for all compositions. The atom-atom interactions are modeled by a semiempirical potential. All three systems are characterized by a small size mismatch and a weak tendency of the larger atoms to segregate at the surface of the smaller ones. As a result, the global minimum structures exhibit a larger mixing than in Ag-Cu and Ag-Ni clusters. Polyicosahedral structures present generally favorable energetic configurations, even though they are less favorable than in the case of the size-mismatched systems. A comparison between all the systems studied here and in the previous paper (on size-mismatched systems) is presented.

Journal Article↗

PubMed2004

Potential energy constrained molecular dynamics simulations.

A method for carrying out molecular dynamics simulations in which the potential energy U of the molecular system is constrained at its initial value is developed and thoroughly tested. The constraint is not introduced within the framework of the Lagrange multipliers technique, rather it is fulfilled in a natural way by carrying out the simulations in terms of suitable sets of delocalized coordinates. Such coordinates are defined by an appropriate tuning of the Baker, Kessi, and Delley internal delocalized nonredundant coordinates technique [J. Chem. Phys. 105, 192 (1996)]. The proposed method requires multiple evaluations of energy and gradients in each step of the molecular dynamics simulation, so that constant U simulations suffer some overhead compared to ordinary simulations. But the particular formulation of the delocalized coordinates and of the equations of motion greatly simplifies all the various steps required by the Baker's technique, thus allowing for the efficient implementation of the method itself. The technique is reliable and allows for very high accuracy in the potential energy conservation during the whole simulation. Moreover, it proved to be free of drift troubles which can occur when standard constraint methods are straightforwardly implemented without the application of appropriate correcting techniques.

Journal Article↗