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

PDF

1

Th Jan 12

Atomistic to Molecular Level Models

McCammon

PDF

2

Tu Jan 17

Poisson-Boltzmann Models of Molecular Electrostatics

McCammon

PDF

2

Th Jan 19

Introduction to APBS

Konecny

PDF

3

Tu Jan 24

APBS

Konecny

PDF

3

Th Jan 26

Brownian Dynamics Modeling with BrownDye

Huber

BrownDye website

4

Tu Jan 31

Brownian Dynamics Modeling with BrownDye

Huber

BrownDye article in Comp Phys Commun

4

Th Feb 2

5

Tu Feb 7

Introduction to Monte Carlo Modeling with MCell

Bartol

Mcell tutorial

5

Th Feb 9

Subcellular Stochastic Modeling

Bartol

Fast Monte Carlo Simulation

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

PPT2 HW2

8

Tu Feb 28

VCell Exercises

McCabe

PPT HW3

8

Th Mar 2

Introduction to Finite Element Modeling with Continuity

McCulloch

PPT PDF Video Tutorial

9

Tu Mar 7

Monodomain Modeling of Action Potential Propagation: Continuity - Electrophysiology Module

McCulloch

PPT PDF EP Atria example

9

Th Mar 9

Continuity - Electrophysiology Exercises

McCulloch/Vincent

2DRing Tutorial Continuity tutorial YouTube Version HW

10

Tu Mar 14

Continuum Modeling of Cell and Tissue Mechanics: Continuity - Biomechanics Module

McCulloch

PPT PDF

10

Th Mar 16

Continuity - Biomechanics Exercises

McCulloch

PPT Models Nodes

11

TBA

Project Presentations Examples of Past Projects

McCulloch