Research Interests

VMD Development

I'm developing scientific tools for VMD.
Currently my efforts concentrate on developing an interface to quantum chemical simulations. We enabled VMD to compute molecular orbitals with revolutionary speed using graphics processors which makes VMD the first program ever to allow the interactive visualization of orbitals dynamics.

I also wrote the SymmetryTool plugin which provides an easy-to-use graphical interface to the "measure symmetry" command (for which I also developed the algorithm). It determines the symmetry pointgroup of a given selection and displays the symmetry elements. The underlying algorithm is very robust and can handle molecules whose coordinates deviate to a certain extent (controlled by a tolerance parameter) from the ideal symmetry. The closest match with the highest symmetry is returned. Atoms can be snapped into idealized symmetric positions.

Further I'm working on the improvement of the Implicit Ligand Sampling (ILS) method. We achieved significant speedups of ILS up by improving the CPU version of the code and by adding parallel versions that use SSE, multiple CPUs or GPUs. Further, I provided a graphical user interface for setting up ILS calculations. Another goal is to extend the GUI to suport analysis and visualization of ILS results.

Biophysics

One of my main scientific interests are oxygen migration pathways in proteins. The following project was done while I was working at the Charite in Berlin:

Identification of Dynamic Oxygen Access Pathways in 12/15-Lipoxygenase

Figure 1: Distribution of oxygen in lipoxygenase shown in terms of free energy isosurfaces (yellow). Red arrows indicate the energetically most favorable oxygen access route connecting a high affinity region at the protein surface with the catalytic center. Above, the energy profile along this path is projected. The grey line marks the level of the drawn energy isosurface.

General scientific interests:

• Scientific Visualization
• Oxygen Diffusion in Proteins
• Quantum Chemistry
• Force Field Parametrization

Publications

Stone JE, Saam J, Hardy DJ, Vandivort KL, Hwu WW, and Schulten K.
High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. Second Workshop on General-Purpose Computation on Graphics Processing Units, 2009. In press.

Saam J, Ivanov I, Walther M, Holzhütter H, and Kuhn H. (2007)
Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels. Proc. Natl. Acad. Sci., 104(33), 13319-13324 [pdf]

Ivanov I, Saam J, Kühn H, Holzhütter H. (2005)
Dual role of oxygen during lipoxygenase reactions. FEBS Journal 272, 2523-2535 [pdf]

Kühn, H, Saam J, Eibach S, Holzhütter H, Ivanov I, Walther M. (2005)
Structural biology of mammalian lipoxygenases: Enzymatic consequences of targeted alterations of the protein structure Biochem. Biophys. Res. Commun. 338, 93-101 [pdf]

Saam J, Tajkhorshid E, Hayashi S, and Schulten K. (2002)
Molecular Dynamics Investigation of Primary Photoinduced Events in the Activation of Rhodopsin. Biophys. J. 83, 3097-3112 [pdf, PubMed]

Ernsting NP, Kovalenko SA, Senyushkina T, Saam J and Farztdinov V. (2001)
Wave-packet-assisted decomposition of femtosecond transient ultraviolet-visible absorption spectra: Application to excited-state intramolecular proton transfer in solution. J. Phys. Chem. A 105, 3443-3453 [journal]