Search results for "Pair potential"
showing 10 items of 27 documents
AMYR 2: A new version of a computer program for pair potential calculation of molecular associations
1998
AMYR is a computer program for the calculation of molecular associations using Fraga's pairwise atom-atom potential. The interaction energy is evaluated through a 1R expansion. The electrostatic energy is calculated through either the one-centre-per atom or the three-centres-per atom model by Hunter and Sanders. A pairwise dispersion energy term is included in the potential and corrected by a damping function. The program carries out energy minimizations through variable metric methods. The new version allows for the stationary point analysis of the intermolecular potential by means of the Hessian eigenvalues. Although using low-gradient thresholds optimization procedures to avoid many stat…
Study of a medium-size biological molecular association by means of a pair potential semiempirical approach: β-carboline-lumiflavin
1985
The molecular association between some substituted β-carbolines and a model flavin, lumiflavin, has been studied by means of a semiempirical approach proposed by Fraga based on a 1/R expansion of atom-atom pair potentials. Only stacked minima have been considered because of their possible biological interest. The calculations characterize 15 different minimum stacked conformations, most of them occurring in the complexes considered. The structural and energetic effects of 1–Me, 6–OH and 7–OH substituents of β-carboline are discussed. An equilibrium conformation involving geometric overlap between the pteridinic portion of flavin and the indole group of β-carboline is predicted to be the mos…
Electronic Properties of Point Defects in Metals
1982
Recent progress in electronic structure and related properties of point defects in metals is reviewed. Topics discussed include transition metal impurities in a non-magnetic host, construction of potential energy surfaces from effective-medium theories, trapping of light interstitials, and pair potential in metals.
Improved AMYR program: an algorithm for the theoretical simulation of molecular associations, including geometrical and topological characterization …
1991
Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility of carrying out energy minimizations through variable metric methods, as well as the optional calculation of geometrical and topological indices. Program AMYR has been adapted also for high-performance computing and vectorization. An interactive version of the program carries out real-time molecular graphics showing simultaneously the energy prof…
Rational computing of energy levels for organic electronics: the case of 2-benzylidene-1,3-indandiones
2016
Device engineering in organic electronics, an active area of research, requires knowledge of the energy levels of organic materials (traditionally but ambiguously denoted as HOMO and LUMO). These can be effectively determined by electrochemical investigation, but yet more effective would be quantum chemical (QC) computation of these quantities. However, there is no consensus on the computational method in the research community. Ongoing discussions often focus on choosing the right density functional method, but neglect other model parameters, in particular, the basis set. This study considers comparison of various methodologies and parameters for predicting ionization energy I and electron…
Monte Carlo investigation of head-tail ordering of CO monolayers on graphite
1994
Abstract Heat capacity measurements recently showed that CO physisorbed on graphite undergoes a head-tail ordering transition at roughly 5 K. The present paper is a detailed Monte Carlo study of this phase transition and the ordered state. The simulations are based on an ab initio pair potential and rely crucially on a thorough finite-size scaling study of various quantities. In agreement with experiments we find that the transition belongs to the universality class of the Ising model in two dimensions. We go beyond experimental knowledge by revealing the particular ferrielectric structure of the ground state, and show that the transition is due to the molecule's shape asymmetry rather than…
BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks
2019
Neural networks (NNs) are employed to predict equations of state from a given isotropic pair potential using the virial expansion of the pressure. The NNs are trained with data from molecular dynamics simulations of monoatomic gases and liquids, sampled in the NVT ensemble at various densities. We find that the NNs provide much more accurate results compared to the analytic low-density limit estimate of the second virial coefficient and the Carnahan-Starling equation of state for hard sphere liquids. Furthermore, we design and train NNs for computing (effective) pair potentials from radial pair distribution functions, g(r), a task that is often performed for inverse design and coarse-graini…
Amorphous silica modeled with truncated and screened Coulomb interactions: A molecular dynamics simulation study
2007
We show that finite-range alternatives to the standard long-range BKS pair potential for silica might be used in molecular dynamics simulations. We study two such models that can be efficiently simulated since no Ewald summation is required. We first consider the Wolf method, where the Coulomb interactions are truncated at a cutoff distance r_c such that the requirement of charge neutrality holds. Various static and dynamic quantities are computed and compared to results from simulations using Ewald summations. We find very good agreement for r_c ~ 10 Angstroms. For lower values of r_c, the long--range structure is affected which is accompanied by a slight acceleration of dynamic properties…
A New Approach to Deriving Interatomic Many-Body Interactions in Metals
1998
An original method of treating the kinetic and exchange-correlation en- ergies functionals in terms of many particle interactions was developed. It is based on utilizing the local density approximation. The total electron density, extracted from the ab initio . band structure calculations, is expressed as a lin- ear superposition of contributions from the individual pseudoions embedded in the uniform background. The explicit expressions for the pair and triplet potentials are presented. The general form for the part of the pair interatomic interactions caused by the kinetic and. the exchange-correlation effects is ob- tained. Relationship between the developing approach and the perturbation…
On the applicability of density dependent effective interactions in cluster-forming systems
2016
We systematically studied the validity and transferability of effective, coarse-grained, pair potentials in ultrasoft colloidal systems. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping particles to minimize the contact area with the surrounding (implicit) solvent. Simulations were performed for both the monomeric and coarse-grained model in the liquid phase at densities ranging from infinite dilution up to values close to the freezing point. For every state point, each macromolecule was mapped onto a single interaction site and the effective pair potential was computed using a coarse-graining technique based on force-matching. We found e…