Our research interests focus on how to apply fundamental disciplines in Robotics (e.g., Kinematics and Dynamics) to Bio- and Nano-technology such as Computational Structural Biology, Bioinformatics, Protein Folding Theory, and Nanoscale Material Science. As the first step, we have successfully done harmonic/anharmonic analysis using coarse-grained elastic network models to infer the relationship between structures and functions in various biological macromolecules such as proteins and nucleic acids. The results will be opened to the public through KOrea SKKU MOrph Server(KOSMOS). This unique methodology is extensively applied to the study of multiscale (micro and nano) polymer composites. We also initiate the study of protein folding based on Robot Kinematics.
To reduce the computational burden with the increased size of a macromulecule, coarse-grained elastic network models have been developed and used. For example, only C-alpha atoms in a protein structure represent residues as illustrated in right side picture and a simplified harmonic potential function is used for considering internal interactions between neighboring residues. Such models are suitable to describe the global behaviors of large macromolecules because the collective motions are usually insensitive to atomic details.
1. Protein Simulation
Elastic network model based Protein simulation can elucidate the relationship between protein structure and function which might be one of the most fundamental techniques for next generation drug design, so we developed an automated online server for protein dynamics. Using this server, we not only construct a database including dynamic features of the whole known protein structure but also elucidate the misfolding mechanism of human inherited disease proteins such as antithrombin and amyroid beta protein. In the future, this server and database will be a corner stone of protein structure based drug design.
2. DNA Simulation
DNA simulation reveals its self-assembly mechanism. Multiple physical insights on DNA nanostructure are derived from this kind of simulation based engineering. For example, DX tile which is one of DNA nanostructures is self-assembled as circular shape when DX tile synthesize because bending is dominant motion of DX tile that is result of simulation based on elastic network model. For now, we simulate DNA hairpin nanostructure for constructing dynamic database of various DNA hairpin nanostructures. This database will be useful for applications of DNA nanostructure.
3. Lithium Ion Battery
Introducing a multi-scale simulation platform from atomistic to meso, marcro-scale, we can optimize Lithium ion battery’s material and its structure. This study can improve the competitiveness of lithium ion battery industries. The final goal of this project is, making a web based massive parallel computation platform to simulate all kinds of materials that need multi-scale simulation. We will demonstrate a specific example of lithium ion, the most common energy nano material.
4. Seismic Design for Nuclear Power Plant
Ever since the nuclear power plant was built, it was necessary to evaluate its safety from breakout. From the latest event of Fukushima, people around the world saw how vulnerable a nuclear power plant can be, to severe earthquakes. The term ‘seismic design’ means a study on the validity of piping interface design under base isolation system versus non-base isolation system. These simulation results can be helpful to secure safety of nuclear power plant when natural disasters occur.
For a seismic analysis, we have developed a 3D piping model of APR-1400 reactor. The seismic simulation includes earthquake wave modal spectral analysis, limit load analysis, and fatigue analysis. To verify the simulation results, we are also planning to build a scaled down nuclear reactor model for a earthquake test.
5. Thermal Barrier Coating (TBC)
The thermal barrier coating (TBC) system is one of the most important technologies to improve the durability of hot components operated under extreme environment. The goal of this TBC simulation is to develop core technologies for the TBC system such as optimal design, performance evaluation and residual life prediction.