An improved potential mean force (PMF) scoring function, named KScore, has been developed by using 23 redefined ligand atom types and 17 protein atom types, as well as 28 newly introduced atom types for nucleic acids (DNA and RNA). Metal ions and water molecules embedded in the binding sites of receptors are considered explicitly by two newly defined atom types. The individual potential terms w...

Single-electron pumps based on isolated impurity atoms have recently been experimentally demonstrated. In these devices the Coulomb potential of an atom creates a localised electron state with a large charging energy and considerable orbital level spacings, enabling robust charge capturing processes. In contrast to the frequently used gate-defined quantum dot pumps, which experience a strongly ...

The development of a new tailor-made scoring function to predict binding affinities of protein-ligand complexes is described. Knowledge-based pair-potentials are specifically adapted to a particular protein by considering additional ligand-based information. The formalism applied to derive the new function is similar to the well-known CoMFA approach, however, the fields used in the approach ori...

A quantitative comparison between experimental and Monte Carlo simulation results for the epitaxial growth of Cu/Cu~001! in the submonolayer regime is presented. The simulations take into account a complete set of hopping processes whose activation energies are derived from semiempirical calculations using the embedded-atom method. The island separation is measured as a function of the incoming...

Static calculation and preliminary kinetic Monte Carlo simulation studies are undertaken for the nucleation and growth on a model system which follows a Frank-van der Merwe mechanism. In the present case, we consider the deposition of Ag on Au(100) and Au(111) surfaces. The interactions were calculated using the embedded atom model. The process of formation and growth of 2D Ag structures on Au(...

The elastic moduli of polymer-carbon nanotube composites are examined by molecular dynamics simulations of a single-walled carbon nanotube embedded in polyethylene. The overall system is modeled with a many-body bond order potential due to Brenner. Alternatively, only the carbon nanotube is modeled with Brenner’s potential and the polyethylene matrix is modeled by a united-atom potential. For t...

Our computational study presents embedded cluster models of the hydrated electron focusing on its reactivity with the hydrated proton and the nitrous oxide molecule leading to formation of a hydrogen atom in the former case and a nitrogen molecule plus hydroxyl radical and hydroxide anion in the latter case. We show using ab initio calculations combined with the nudged elastic band method for d...

In this research, the effects of B, O and B&O−doped on the SO2 gas adsorption on the surface of the (4, 4) armchair AlNNTs are investigated by using DFT method. From optimized structures the geometrical and electrical properties, adsorption energy, gap energy, global hardness, electrical potential, HOMO−LUMO orbitals, density of states (DOS) plots, electrostatic potential (ESP) plots and NMR pa...

A new potential smoothing method, the shifted-tophat (or stophat) is presented. This method uses a tophat function as the smoothing kernel, instead of the gaussian used in conventional methods. Stophat smoothing is applied, as part of the Potential Smoothing and Search (PSS) procedure for global optimization, to several biomolecular problems, including polyalanine helices, united-atom and all-a...

Structural optimization for heteronuclear clusters consisting of one alkali-metal ion and of up to 79 neutral rare gas atoms has been carried out. The basin-hopping Monte Carlo minimization method of Wales and Doye is used. Rare gas atoms interact with the Lennard–Jones potential, whereas the interaction between a neutral atom and an ion impurity is given by the Mason–Schamp potential. Starting...