The Research Scope of Lee Group

    Molecular dynamics studies of lipid bilayers interacting with mutant peptides

   Antimicrobial, cytolytic peptides are amphipathic peptides that bind to cell membrane. They are known to be an important part of defense mechanism in eukaryotic organism. Although numerous mechanisms of membrane penetration by antimicrobial peptides have been proposed, no apparent peptide sequence has been found responsible for specific functions of peptides. Recently, Prof. Almeida at UNCW proposed that the cell-penetration mechanism and efficiency are directly related to the Gibbs free energy of insertion into the bilayer: If free energy change is smaller than ~20kcal/mol, peptides disrupt the bilayer by translocating accross membranes. On the other hand, the peptides that require more than ~20kcal/mol of free energy change cannot translocate, but they will accumulate until a pore forms. To investigate the validity of such hypothesis, molecular dynamics simulations are currently underway for POPC lipid bilayers interacting with various peptides with designed sequences. These mutant peptides are designed to convert translocating peptides into non-translocating peptides visa versa.

    Catalytic effect of platinum doped carbon nanotube (Pt/CNT)
 
            
        (picture from DOE website)

The proton exchange membrane fuel cell (PEMFC) is one of the most tantalizing future energy technology. However, wide-spread use of FC has been hampered by the high cost of metal catalyst. To develop cost-effective FC systems, it is highly desirable to maximize the efficiency of expensive Pt catalyst. Recently, a number of research groups have used Pt-doped CNT as an alternative catalyzing/supporting material in FC electrodes and reported superior performance of Pt/CNT electrodes over that of  conventional carbon black based system. In this project, density functional theory (DFT) electronic structure calculation and ab initio molecular dynamics (AIMD) methods will be used to  charaterize the nature of Pt-CNT interaction and understand the catalytic role of Pt/CNT in oxidation/reduction reactions.

  Ab initio molecula dynamics (AIMD) based on real-space basis

       
 Currently, AIMD calculations are most commonly performed in plane-wave basis set. Indeed, the most popular AIMD code in the community, CPMD, is based on this technique. However, localized basis set techniques have been increasingly popular in recent years for improving scaling with system size. Recently, a discrete variable representation (DVR) based approach was introduced as an alternative real-space method for the electronic structure calculation in AIMD simulation (see paper #20). DVR basis has excellent convergence properties, can be used in linear scaling approach and can be easily adapted for massively parallel applications. Car-Parrinello AIMD based on DVR basis was used in our recent study of neat water and protonated water, which showed a significant improvement on structural and dynamical properties (see paper #21 and 22).  This method was recently extended to non-periodic (cluster) system as well (see paper #24). We are currently extending the AIMD/DVR approach to path integral simulation for full nuclear quantum dynamics, as well as simulations with 1D (wire) and 2D (surface) periodic boundary conditiions.