Mathematical methods for biochemistry and biophysics (BIO 5329)Fall 2009Please see Telesis.Fall 2007Fall 2005Fall 2004Summer 2004Chemistry and physics of biological molecules (BIO 5357)Fall 2009Lecture: PDFBiomedical applications of nanotechnology (BIO 5145)Fall 2009Lecture: PDFCCPB workshop on computational electrostatics, York, UKSpring 2009BII workshop on computational electrostatics, SingaporeSpring 2009Modeling biomolecular systems I (BIO 5476)Fall 2008Lecture: PDFLabs:
Spring 2006Lecture: Introduction (PDF)Lecture: Docking (PDF) Lab: Docking (HTML) Lecture: Binding energies (PDF) Lab: Binding energies (HTML) Lecture: Binding kinetics (PDF) Lecture: Optional binding kinetics tutorials (HTML) Spring 2005Lecture: Introduction (PDF)Lecture: Docking (PDF) Lab: Docking (HTML) Lecture: Binding energies (PDF) Lab: Binding energies (HTML) Lecture: Binding kinetics (PDF) Lab: Optional binding kinetics tutorials (HTML) Spring 2004Lecture: Simulation. Basic Ideas from Statistical Mechanics. PDF (6.4 MB)Lecture: Simulation. Structural and Thermodynamic Properties. PDF (4.4 MB) Lecture: Simulation. Boundaries, Neighbors, and Long Range Forces. PDF (4.0 kB) Lecture: Protein databases. Sequence and function. PDF (4.8 MB) Lecture: Protein databases. Structure. PDF Introduction to biomedical engineering (BME 140)Fall 2008Lecture: Multiscale modeling in biology. Molecular to continuum. PDFFall 2007Lecture: Multiscale modeling in biology. Molecular to continuum. PDFFall 2006Lecture: Multiscale modeling in biology. Molecular to continuum. PDFFall 2005Lecture: Multiscale modeling in biology. Molecular to continuum. PDFFall 2004Lecture: PDFFall 2003Lecture: PowerpointCenter for Theoretical Biological Physics summer workshopSummer 2008Lecture: ZIP fileModeling biomolecular systems II (BME 540)Spring 2008Lecture: PDFLabs:
Fall 2005Lecture: Biomolecular solvation and electrostatics. PDFLab: APBS software overview. Tutorial (HTML), Other documentation (HTML), Home page (HTML) Lab: pKa calculations Lab: MM/PBSA calculations Fall 2004Lecture: The Monte Carlo method (Powerpoint)Lecture: NVT simulations (Powerpoint) Lecture: Simulations in other ensembles (Powerpoint) Lecture: Implicit solvent simulations (Powerpoint) Macromolecular interactions (BIO 5312)Spring 2008Lecture: Electrostatics handouts (figures, PDF format)Spring 2007Lecture: Electrostatics (PDF)Spring 2006Lecture: PDFSpring 2005Lecture: PowerpointSpring 2004Lecture: PDFLab: HTML, Examples archive Spring 2003Lecture: PowerpointNBCR Summer InstituteSummer 2007Summer 2006 Protein structure and function (BIO 5325)Fall 2006Lecture: PDFFall 2005Lecture: PDFSpecial topics in computational biology (BIO 5497)Fall 2006Lecture: Linear algebra in computational biology. PDFFall 2005Lecture: Linear algebra in computational biology. PDFFall 2004Lecture: PDFIntro to biomolecular statistical thermodynamics (BME 531)Spring 2005Lecture: Chapter 20. PowerpointLecture: Chapter 21. Powerpoint Lecture: Chapter 22-23. Powerpoint Modeling biomolecular systems (BME 590N)Fall 2003Lecture: PowerpointLab: Powerpoint, Examples diectory |