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==Introduction==
This is a test!
==1 Introduction to Molecular Biophysics==
'''1.1 Introduction to Macromolecular Structure; Inter-atomic Forces & Force Fields (4.5 hr)'''
1.1.1 Primary Through Quaternary Structure
1.1.2 Covalent Bonding
1.1.3 Non-bonded Interactions (hydrophobic effect covered later)
1.1.4 Forces/Fields Used to Model Interactions Computationally
'''1.2 Thermodynamics & Kinetics (7.5 hr)'''
Illustrated with applications to Membrane Transport.
1.2.1 Energy, Entropy, Free Energy
1.2.1.1 Hydrophobic effect
1.2.2 Statistical mechanics & determinism
1.2.3 Equilibria
1.2.3.1 Reactions
1.2.3.2 Binding
1.2.3.3 Calorimetry
1.2.3.4 Conformation
1.2.4 Transport & Diffusion
1.2.4.1 Membranes / Proteins
1.2.4.2 Ion channels & pumps
1.2.4.3 Action potentials / measurement / synapses
'''1.3 Theory of Crystallography (6 hr)'''
1.3.1 Diffraction theory
1.3.2 Phasing methods
1.3.3 Maps, Models & Refinement
1.3.4 Quality assessment
'''1.4 Spectroscopy - Visible & UV (6 hr)'''
1.4.1 Absorption
1.4.2 Polarization spectroscopy
1.4.3 Fluorescence
1.4.3.1 Fluorescence anisotropy
1.4.3.2 FRET
'''1.5 Introduction to Magnetic Resonance (7.5 hr)'''
1.5.1 Spin Physics & 2-state models
1.5.2 Magentic Resonance Imaging
1.5.3 Biomolecular Structure determination (Introduction)
==2 Advanced Molecular Biophysics==
'''2.1 Avanced Magnetic Resonance (7.5 hr):'''
2.1.1 Methods of Biomolecular Structure Determination
2.1.2 Probing the dynamics of macromolecules
2.1.3 Special topics: Paramagnetic NMR & ESR, spin labeling & Solid-state NMR
'''2.2 Visible & Electron Microscopy (4 hr)'''
2.2.1 Theory of Light Microscopy (1 hr)
2.2.2 Fluorescence, Confocal & Correlative Microscopy (0.5 hr)
2.2.3 Transmission EM – theory
2.2.2 Biological samples
2.2.3 3D reconstruction
'''2.3 Practical Crystallography (8 hr)'''
2.3.1 Crystallization (+ lab)
2.3.2 Data collection (+ lab?)
2.3.3 Phasing by molecular replacement (+ computer exercise?)
2.3.4 Model-building & Refinement (+ computer exercise)
'''2.4 Interpretation of Structure (5.5 hr)'''
2.4.1 Databases & their use
2.4.2 Homology modeling
2.4.3 Docking
2.4.4 Electrostatics – Potentials & pKs
'''2.5 Molecular Dynamics (2.5 hr)'''
2.5.1 Simulated annealing
2.5.2 Normal modes
2.5.3 Accelerated methods / enhanced sampling
'''2.6 Mass spectrometry in biomolecular structure / interactions (2 hr)'''
2.6.1 Footprinting
2.6.2 Dynamics
'''2.7 Single Molecule Methods (time available, or reading)'''
2.7.1 Fluorescence
2.7.2 AFM
'''2.9 Case Studies to be woven in:'''
(a) Molecular Motors
(b) Protein Mis-folding & Disease
'''2.10 Topics to be covered in reading (only)'''
(a) Surface Plasmon Resonance
==3 Sources==
[http://www.med.upenn.edu/bmbgrad/Program/course_descriptions/course_descriptions.html UPenn Biochemistry and Molecular Biology Graduate Program]
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