graphene nano-ribbon

It is very important to visualize molecular dynamics (MD) trajectories since there are many aspects of MD simulations which are difficult to identify without a proper visualization tool. Improper bounday condition in MD is one of such examples. I use Visual Molecular Dynamics (VMD) to visualize my MD simulations. Some of my movies, created using VMD, are shown below.

In appendix A of my PhD thesis, I share a MATLAB code to get coordinates of carbon atoms in a graphene sheet. The code also generates the data file required for LAMMPS. In addition, I included a sample input and the corresponding output files from LAMMPS. I hope this will be useful for those who would like to learn MD simulations.

I would like to share with you my first paper in a SCI journal: doi:10.1088/0965-0393/21/6/065017

http://iopscience.iop.org/0957-4484/23/38/385702/

We investigate bending behaviors of graphene nanoribbons (GNRs) induced by surface adsorption of hydrogen atoms or molecules. At low adsorption coverage, it is shown that the chemical adsorption of hydrogen atoms causes a GNR to bend away from the adsorbed atoms while the physical adsorption of hydrogen molecules causes it to bend toward the adsorbed molecules. Interestingly, these trends are reversed at high adsorption coverage.