Molecular Biophysics II – Spring, 2005   (revised 1/3/04 by DMZ)

Interactions and Equilibria in Biomolecules
Mon, Weds, Fri – 1pm – Crawford Hall 343

Course organized by:
Profs. Xiao-lun Wu (Physics) and Daniel Zuckerman (Computational Biology)

Course Links:  Syllabus (.doc),  Statistical Mechanics Notes

 

SECTION 1: FUNDAMENTALS

Date  Topic   Instructor
Jan 5 (W) Overview: interactions & equilibrium Zuckerman
Jan 7 (F) Essential probability theory & statistics  Zuckerman
Jan 10 (M) Probability theory – cont’d Zuckerman
Jan 12 (W) Basic statistical mechanics
 HW1: Statistical thermodynamics I		 Zuckerman
Jan 14 (F) Statistical mechanics – cont’d Zuckerman
Jan 17 (M) NO CLASS – M. L. KING HOLIDAY  
Jan 19 (W) Statistical thermodynamics Zuckerman
Jan 21 (F) Molecular statistical mechanics Zuckerman
Jan 24 (M) Solvation and binding free energy (principles) 
 HW2: Statistical thermodynamics II		 Zuckerman
Jan 26 (W) Protein-DNA interactions – structural aspects Rosenberg
Jan 28 (F) Protein-DNA Interactions  Benos
Jan 31 (M) Structural aspects of protein-protein interactions Camacho
Feb 2 (W) Protein-protein interactions in signaling Smithgall
Feb 4 (F) Protein-ligand interactions in pharmacology
 HW3: Molecular Binding		 Lazo


SECTION 2: EXPERIMENTAL TECHNIQUES

Date Topic Instructor
Feb 7 Optical techniques Watkins
Feb 14 Optical techniques   Watkins
Feb 21 Optical tweezers Leuba
Feb 28 Optical tweezers Leuba
 Mar 7  Spring break – no classes  
Mar 14  Interactions via NMR Y. Xu
Mar 21  Calorimetry  Jen-Jacobson
Mar 28 Calorimetry (1 lecture) Jen-Jacobson
Mar 28 Scattering techniques (2 lectures) X.L. Wu
Apr 4 Midterm on Section 2 (1 lecture)  


SECTION 3: SIMULATION TECHNIQUES

Date Topic Instructor
Apr 6 (W) All-atom forcefields; minimization Zuckerman
Apr 8 (F) … continued  Zuckerman
Apr 11 (M) Equilibrium & Monte Carlo sampling  Swendsen
Apr 13 (W) (basic and advanced)  Swendsen
Apr 15 (F) … continued 
HW: Monte Carlo sampling		 Swendsen
Apr 18  (M) Free energy calculations Swendsen
Apr 20 (W) Virtual (drug) screening Zuckerman
Apr 22 (F) Protein-protein docking Camacho
Apr 25 (M) Coarse-grained & knowledge-based models Zuckerman
Apr 27 (W) … continued   Zuckerman
Apr 29 (F) FINAL EXAM  

University of Pittsburgh ---------- School of Medicine
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Tel : (412) 648-6671,  Fax: (412) 648-6676