Poster Presentation - UD Undergraduate Studies

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					               3D Visualization of Macromolecules for Effective Instruction of
                   Protein Structure/Function and Biochemical Evolution
                                                                  Adam Marsh, College of Marine Studies
                                                                  Brian Bahnson, Dept. of Chemistry Biochemistry

    Hardware:                                                                                                   Software:                                                                               Mind-ware
     A cluster of 9 LINUX workstations                                              State of the art molecular visualization and modeling tools                                     Integrating biochemistry and marine biolo

                                                                                                                                 The biochemical intuition that can be
                                                                                                                                 obtained by the visualization of molecular
                                                                                                                                 3D structures has traditionally been one of
                                                                                                                                 the most difficult areas to teach in
                                                                                                                                 biochemistry. Both PIs have utilized 3D
                                                                                                                                 modeling and display programs in teaching
Computer room setup for project in Brown Laboratory. A total of
six machines were located in this space for student access.                                                                      biochemistry courses at UD. However, the
                                                                                                                                 limitations on computer hardware and
    We have setup nine high-end graphics                                                                                         software that were accessible to students
workstations with 21” high-resolution video                                                                                      led us to propose developing a cluster of
monitors. Six of the computers are located in                                                                                    graphical workstations for molecular
Newark (Biochem) and three are located in                                                                                        modeling. We are using these machines
                                                                                                                                 for cross-college instruction in Marine           The interaction between the PIs brings two groups
Lewes (Marine Studies). The computers have                        Workstation screen-shot of LINUX desktop. Using a unix-based                                                     of students together with very different perspectives
been configured with a LINUX operating system                     OS provides tight security for a system, while the LINUX x-    Studies and Biochemistry using 3D
                                                                  windows provide a familiar GUI for students.                   molecular modeling and visualization              on protein structure and function: marine biologists
(RH 8.0) for tight user management and back-                                                                                                                                       interested in evolutionary adaptations (MAST
up options to restore hard-disk configurations if                                                                                software tools. This approach has been
                                                                                                                                 effective in 2002-2003 by providing the use       634/434) and biochemists interested in molecular
inadvertently altered by students. The LINUX                                                                                                                                       interactions (CHEM 641/667). Integrating these
OS provides us with excellent system security to                                                                                 of dedicated PC workstations, which
                                                                                                                                 greatly simplifies issues of program              different perspectives is important for understanding
manage course-related files and to limit the use                                                                                                                                   how subtle changes at a molecular level can have
of the computers to the applications that are                                                                                    installation, file security, software licensing
                                                                                                                                 and user access.                                  profound influences at an evolutionary scale. This
necessary for the course project assignments.                                                                                                                                      program is designed to bridge the interface between
    All the hard-drives are managed from one                                                                                                                                       Molecules and Life and develop a new educational
image. The workstations are “plug-n-play” in                                                                                                                                       focus within our biochemistry courses at UD.
that they can be configured for different courses
in a matter of seconds just by swapping out the
hard drives.

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