About the Course
Largely hands-on, independent work
Free access to the computers
Exercises and projects: no exams
Develop projects related to your research
Cooperation encouraged
Goals
Learn the basics of the Linux operating system
Learn to use some of the basic modeling software
Learn what kinds of things can be computed, and which tools to use
Learn how to formulate problems so they can be solved by computation
Why Linux ?
True multi-user, multi-tasking operating system for PC hardware
Flexible and powerful
Stable; no blue screen of death
Free; much free software
What is Modeling ?
Construction of a virtual 3-D molecule
Computation of some properties expected to be associated with a real molecule, of which this is a representation
A virtual, microscopic experiment
Modeling has been described as a "computational spectrometer"
Kinds of Models
"Model: anything of a particular form, shape, size, quality, construction, or the like, intended for imitation; a copy in miniature..."
Webster's New World Dictionary, 1938
Bond-based: bonds between atoms and properties of the bonds are part of the model
methodologies are molecular mechanics, molecular dynamics, docking
Atom-based: positions of the atoms and their electronic structures are input
Methodologies are quantum mechanical
What Can We Learn ?
What does it look like ?
What do its neighbors look like ?
What does the neighborhood (the potential energy surface) look like ?
How do we get from one neighborhood to another ? (transition states)
How do the structure and its neighborhood change with time ?
How do two molecules interact with each other?
Computable Physical Properties
Vibrational spectrum
Chemical shift: nuclear shielding tensors, NICS
Properties relating to molecular orbital energies:
Electronic spectrum
Electron affinity and ionization potential
How do these properties depend on structure ?
bioChemical Applications
Protein folding landscapes
Interactions, such as: enzyme-substrate, drug-DNA
Interpretation of X-ray diffraction patterns, NOE spectra
Site-directed mutagenesis the easy way
Homology modeling
Solvation models
This page last modified
10:02 AM on Wednesday May 17th, 2006.
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, Department of Chemistry, University of Maine, Orono, ME 04469