BENG/CHEM/PHAR/MATH 276 Numerical Analysis for Multi-Scale Biology, Winter 2017
Week |
Date |
Topic |
Instructor |
Downloads and Links |
1 |
Tu Jan 10 |
Introduction to Multi-Scale Modeling in Biology |
McCammon |
|
1 |
Th Jan 12 |
Atomistic to Molecular Level Models |
McCammon |
|
2 |
Tu Jan 17 |
Poisson-Boltzmann Models of Molecular Electrostatics |
McCammon |
|
2 |
Th Jan 19 |
Introduction to APBS |
Konecny |
|
3 |
Tu Jan 24 |
APBS |
Konecny |
|
3 |
Th Jan 26 |
Brownian Dynamics Modeling with BrownDye |
Huber |
|
4 |
Tu Jan 31 |
Brownian Dynamics Modeling with BrownDye |
Huber |
|
4 |
Th Feb 2 |
|||
5 |
Tu Feb 7 |
Introduction to Monte Carlo Modeling with MCell |
Bartol |
|
5 |
Th Feb 9 |
Subcellular Stochastic Modeling |
Bartol |
|
6 |
Tu Feb 14 |
Monte Carlo Modeling with M-Cell |
Bartol |
|
6 |
Th Feb 16 |
Monte Carlo Modeling with M-Cell |
Sejnowski |
|
7 |
Tu Feb 21 |
Spatially Coupled cell Modeling: Leveraging multiscale computational techniques to understand the fundamental mechanisms of the heartbeat |
Hirakis |
|
7 |
Th Feb 23 |
Modeling Cell Biochemical and Biophysical Networks: Virtual Cell Exercises |
McCulloch/McCabe |
|
8 |
Tu Feb 28 |
VCell Exercises |
McCabe |
|
8 |
Th Mar 2 |
Introduction to Finite Element Modeling with Continuity |
McCulloch |
|
9 |
Tu Mar 7 |
Monodomain Modeling of Action Potential Propagation: Continuity – Electrophysiology Module |
McCulloch |
|
9 |
Th Mar 9 |
Continuity – Electrophysiology Exercises |
McCulloch/Vincent |
|
10 |
Tu Mar 14 |
Continuum Modeling of Cell and Tissue Mechanics: Continuity – Biomechanics Module |
McCulloch |
|
10 |
Th Mar 16 |
Continuity – Biomechanics Exercises |
McCulloch |
|
11 |
TBA |
Project Presentations Examples of Past Projects |
McCulloch |