Dipped adcluster model for chemisorptions and catalytic reactions on a metal surface: Image force correction and applications to Pd–O2 adclusters

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

We have developed a new docking method to consider receptor flexibility, a hybrid method of molecular dynamics and harmonic dynamics. The global motions of the whole receptor were approximately introduced into those of the receptor in the docking simulation as harmonic dynamics. On the other hand, the local flexibility of the side chains was also considered by conventional molecular dynamics. We confirmed that this new method can reproduce the fluctuations of the whole receptor by making a comparison of the directions and amplitudes of the global fluctuations. Then this method was applied to the docking of HIV-1 protease and its ligand. As a result, we observed a docking process where the ligand enters into the binding pocket well, which implies that this method is effective enough to reproduce a molecular complex formation.

Models for the treatment of crystalline solids and surfaces

Crystalline solids and surfaces have become a subject of growing interest. The difficulty of a comprehensive description of a variety of phenomena by a single method has led to the development of many models. These models can be classified as nonperiodic and periodic models. The former include free clusters, saturated clusters, and embedded clusters. The latter two models serve to remove the boundary effects of the free clusters. No perfect avoidance of such effects can be achieved in this way. The cyclic cluster model overcomes this difficulty in a natural way. It is periodic with a finite periodicity. An embedding can take into account a long-range effect in ionic crystals. Previous periodic approaches relied on the large unit cell model, which is related to the supercell approach. For perfect crystals the conventional unit cell approach is a well-known standard. However, its disadvantage is the unphysical periodicity of defects, which is avoided in the cyclic cluster model. The present article presents a description of these models together with selective applications to solid-state systems and surfaces.