All-atom level computational study of peptide aggregation into protofibril structures Soonmin Jang and Jungho Shin Department of Chemistry, Sejong University, Gwangjin-Gu Gunja-Dong 98, Seoul 143-747, Korea Aggregation of peptides became intense research topics recently due to its importance in biomedical, biotechnological, and material science. It is important to understand the detailed rules governing the self assembly of peptides, which could be different from that of single protein folding. In many cases, experimental techniques have difficulty in identification of the detailed structure behind the resulting aggregates. Therefore, computer simulations based on reasonable model could be alternative approach to understand the peptide aggregation. We have performed molecular dynamics simulation of peptide aggregation that is known to form amyloid fibril-like structure. Using efficient sampling scheme coupled with all-atom model, we observed direct aggregation of peptides into protofibril structures. The resulting aggregates are investigated to elucidate the stability and the detailed interaction features. Characteristics of those aggregates as well as its temperature dependence will be presented.