Fractional Extended Diffusion Theory to capture anomalous relaxation from biased/accelerated molecular simulations.

Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A.

Extended diffusion theory: Recovering dynamics from biased/accelerated molecular simulations.

Dynamical properties are of great importance in determining the behavior of synthetic and natural molecules, but capturing them by computational methods is a nontrivial task. Very often the time scales of the relevant phenomena are far beyond the typical time windows accessible by classical Molecular Dynamics (MD) simulations, currently limited to the order of microseconds on standard laboratory workstations. On the other hand, biased and accelerated simulations allow for fast and thorough exploration of the molecular conformational space, but they lose the dynamic information.

Influence of the Ion Coordination Number on Cation Exchange Reactions with Copper Telluride Nanocrystals.

Cu2-xTe nanocubes were used as starting seeds to access metal telluride nanocrystals by cation exchanges at room temperature. The coordination number of the entering cations was found to play an important role in dictating the reaction pathways. The exchanges with tetrahedrally coordinated cations (i.

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets.

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J.

Development of a semiempirical potential for simulations of thiol-gold interfaces. Application to thiol-protected gold nanoparticles.

A new semiempirical potential, based on density functional calculations and a bond-order Morse-like potential, is developed to simulate the adsorption behavior of thiolate molecules on non-planar gold surfaces, including relaxing effects, in a more realistic way. The potential functions include as variables the metal-molecule separation, vibrational frequencies, bending and torsion angles between several pairs of atom types and the coordination number of both the metal (Au) and thiolate groups. The potential was parameterized based on a set of density functional calculations of molecular adsorption in several surface sites (i.

Clusters in strong polyelectrolyte solutions in the condensation theory approach.

The interaction free energy of parallel clusters of like-charged rod polyelectrolytes in solution is calculated in the framework of the extended condensation theory. For sufficiently high linear charge density of the polyelectrolyte, clustering takes place. The greater is the number of polyelectrolytes participating to the cluster, the smaller is the equilibrium interpolyelectrolyte distance, and the deeper is the corresponding free energy minimum.

VARICELLA: a variable-cell direct space method for structure determination from powder diffraction data.

A direct space method for structure determination from powder diffraction data is proposed. Employing a hybrid Monte Carlo algorithm for generating the random conformations of a flexible molecular model, and sampling in a modified multicanonical statistical ensemble, it allows for variable cell parameters during an iterative search process. The acceptance-rejection criterion involves both a disagreement factor between the calculated and the experimental diffraction profiles and a modified crystal energy so that the space of tentative solutions can be widely explored while maintaining some physical meaningfulness of the proposals.

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP.

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.

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.

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.

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.