MSC Projects Outline

Materials and Molecular Simulation Center
California Institute of Technology
Mail Stop 139-74
Pasadena, CA 91125, USA

Visit on: 19-OCT-95


(Projects are accented by white balls, but those with a lot of graphical processing have black bullets.)


  • RNA Virus (Rh14):
    Vaidehi, Ben R., Jim K., and Ruth Ann

  • Includes: video and .ps files
    o SAMS (monolayer structure):
    jjg, cff

    Includes: video and .ps files
  • DNA/RNA:

  • NEIMO torsion dynamics:
    Ruth Ann, Ben R., Jim K.

    Includes: video with voice over, .ps files
    Applications: Protein folding
  • Surface properties:

    o Protein Folding:
    jing (?) and Matt Carlson


    Includes: video and .ps files
    Shaoyi Jiang

  • Diffusion
    Siddharth, Michael, Sechi, Gao

    Ben Ramirez

    o DFT
    xec, xinlei


    Mamadou Diallo

    If there is a project leader, their name is in bold. That is the main person to ask questions about a project.


  • Blowups: Mario has volunteered to make blowups of pictures. Submit .ps files to him by the end of the first week of Oct.

    Group: Remember to start a home-page so it can be linked to the main list.

    Mail corrections and info to jjg.

    Summary of activities outlined on Sept. 20 group meeting:

    1. Massive Materials Simulations (MSim) program system. T. Cagin, M. Iotov, G. Gao. Get timing tests on scaling with number of processors and number of atoms on all available supercomputers (Cray T3D, Intel Paragon, IBM SP2, SGI PC, KSR, Cray C90). (MI) Update GUI for easy use (M. Carlson). Put into production mode on as many computers as possible (MI, TC) Prepare plan for incorporation of all features and a timeline (TC, GG). Future computer science developments (S. Taylor, TC).
    2. NEIMO (Vaidehi, A. Jain, MI, TC) Incorporate into KSR version of MSim. (MI, VN, TC). Use for grand challenge applications (VN, TC).
    3. Quantum Chemistry Get timing tests on scaling with processors and atoms. (S. Dasgupta) PS-GVB (R. Friesner will send material for Columbia efforts, R. Murphy, M. Ringnalda, J.-M. Langlois) GVB-RCI-SCF. F. Faglioni R-GVB. R. Muller, T. Takeuchi
    4. Density Functional Theory (X. Chen, X. Hua, J.-M. Langlois) Get scaling with number of atoms and with processors (XEC). Periodic Boundary Conditions (XEC) Finite systems (JML)
    5. Monte Carlo Simulations Boltzmann Biased-Continuous Conformation (BB-CC) Method (D. Lu) Protein folding (MJC, DL) Polymer thermodynamics (DL, VN, GG)
    Applications 6. Virus Rhv14 using MSim. (VN, B. Ramirez, R. Bertch) Simulations of virus opening (500,000 atoms) (VN) Graphics and Videos (BR, VN, RB). Include model of membrane and receptor
    7. Gas Diffusion (SDG, S. Kashihara, MI, GG, M. Belmares) Graphics (SDG, SK, J. Kendall)
    8. DNA-RNA-proteins, drugs. K. Brameld, SDG, BER Graphics
    9. Nanomachinery. J. Hu, TC Graphics. JH, DL
    10. SAM. JJG, CFF
    11. Corrosion project. S. Ramachandran, B. Tsai, M. Blanco,
    12. Wear project. S. Jiang, MB
    13. Demulsifier project. M. Diallo, MB.
    14. Protein design. BER, SDG, JK
    15. Alpha Helix folding. RB, VN
    16. VPO Catalysis. FF, JK(graphics)
    17. HgCdTe project. JH, BLT, A. Mintz,
    18. MSC computer network including outside supercomputers. (DLW, JK)
    19. GaN project. (SDG, XEC, JH, Eli Jacobson)
    20. ROMP polymerization. C. Kankel, JK
    21. Polymer simulations: MPB, GG, TC, SDG,
    22. Organic superconductors. E. Demiralp
    23. Amorphos metals M. Li, TC
    24. Refinery Project. J. Perry.
    25. Scale project. MB.
    26. Nylon project. SDG, Upchurch
    If I should have assigned you to a project but forgot, please send email correcting it. If I left off a project, please add it. Also suggest any neat videos that we can do. Wherever possible we should have applications that are outstanding in terms or size or complexity and which indicate the power of the methods and programs developed here. For each project we should have good visual aids to explain the project (color prints or view graphs, video where appropriate) We should also have a good story on the importance of the applications -- why is it important. I would like for everyone in the group to volunteer wherever possible to help others put together a nice story. We will get together at 1pm on Thursday Sept. 28 to see where everything is. Please have specific plans by then. wherever possible bring draft of figures or videos you recommend that we use.