(214y) Mechanical Deformation of dsDNA: Molecular Modeling Approach Conference: AIChE Annual MeetingYear: 2013Proceeding: 2013 AIChE Annual MeetingGroup: Computational Molecular Science and Engineering ForumSession: Poster Session: Computational Molecular Science and Engineering Forum (CoMSEF) Time: Monday, November 4, 2013 - 6:00pm-8:00pm Authors: Hwang, H. H., Georgia Institute of Technology Chun, B. J., Georgia Institute of Technology Jang, S. S., Georgia Institute of Technology Kim, H. D., Georgia Institution of Technology Mechanical Deformation of dsDNA: Molecular Modeling Approach Hyea Hennim Hwang, Byeong Jae Chun and Seung Soon Jang School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive, Atlanta, GA 30332-0245 Harold D. Kim School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430 Studying sequence-dependent DNA dynamics is crucial for understanding the relationship between DNA sequence and genome function, which is one of the holy grails of biology. For this purpose, molecular dynamics (MD) simulation can provide detailed information on structural changes of DNA at resolution not yet accessible to current experimental techniques. In this study, we use MD simulation to investigate the structural changes that double-stranded DNA (dsDNA) undergoes during mechanical deformation and measure how stress is distributed in this process. In our simulations, a 9 base pair B-DNA duplex is tethered at two H-terminated Si (111) surfaces through spacers, and is extended by pulling these surfaces apart at a constant rate. The change of stress required for extension is monitored as a function of strain. During the extension, the structural change is analyzed in terms of the hydrogen bonding geometry in each base pair, the torsion angles along backbone, diameter of double helical structure. Transition state from double helix to a novel ladder structure is also analyzed, in which base pairs of one strand are stacked on those of the other strand. By designing the base sequence for simulations, the sequence-dependency of mechanical deformation is elucidated.