Atomic simulation algorithm

Atomic simulation algorithm

Mining the Protein Data Bank to improve prediction of changes in protein-protein binding

Predicting the effect of mutations on protein-protein interactions is important for relating structure to function, as well as for in silico affinity maturation. The effect of mutations on protein-protein binding energy (ΔΔG) can be predicted by a variety of atomic simulation methods involving full or limited flexibility, and explicit or implicit solvent. Methods which consider only limited flexibility are naturally more economical, and many of them are quite accurate, however results are dependent on the atomic coordinate set used. In this work we perform a sequence and structure based search of the Protein Data Bank to find additional coordinate sets and repeat the calculation on each. The method increases precision and Positive Predictive Value, and decreases Root Mean Square Error, compared to using single structures. Given the ongoing growth of near-redundant structures in the Protein Data Bank, our method will only increase in applicability and accuracy.

Atomic Simulation of the Melting and Mechanical Behaviors of Silicon Nanowires

Molecular dynamics simulations using a three-body potential show that the melting and mechanical behaviors of silicon nanowires are strongly dependent on their cross-section area. For the wire with a small cross-section area, rearrangements of surface atoms greatly affect thermal stability in a relatively low temperature regime. For these wires with a relatively large area, while some surface atoms adjust their positions, most of the interior atoms hold their tetrahedra packing patterns. At a high temperature, the accumulation of structural disorder can quickly extend into the entire wire, which resembles the melting of the bulk phase. By applying the uniaxial tensile, these silicon nanowires present the typical mechanical behavior of plastic materials. The atomic local stress in the necking region is apparently larger than that outside of the necking region. As the cross-section area becomes large, both the yield strength and tensile strength increase. With the increasing temperature, the elasticity decreases significantly.