== 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 ||[attachment:McCammonDay1.pdf PDF] ||
||1 ||Th Jan 12 ||Atomistic to Molecular Level Models ||!McCammon ||[attachment:McCammonDay2.pdf PDF] ||
||2 ||Tu Jan 17 ||Poisson-Boltzmann Models of Molecular Electrostatics ||!McCammon ||[attachment:McCammonDay3.pdf PDF] ||
||2 ||Th Jan 19 ||Introduction to APBS ||Konecny ||[attachment:Konecky_elstat_2017.pdf PDF] ||
||3 ||Tu Jan 24 ||APBS ||Konecny ||[attachment:APBStutorials.pdf PDF] ||
||3 ||Th Jan 26 ||Brownian Dynamics Modeling with !BrownDye ||Huber ||[http://browndye.ucsd.edu BrownDye website] ||
||4 ||Tu Jan 31 ||Brownian Dynamics Modeling with !BrownDye ||Huber ||[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994412/ BrownDye article in Comp Phys Commun] ||
||4 ||Th Feb 2 ||
||5 ||Tu Feb 7 ||Introduction to Monte Carlo Modeling with MCell ||Bartol||[attachment:Mcell_tutorial.pdf Mcell tutorial] ||
||5 ||Th Feb 9 ||Subcellular Stochastic Modeling ||Bartol ||[attachment:Monte_Carlo_sim.pdf 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||[attachment:Virtual_Cell_Lecture_1.pptx PPT2] [attachment:276HW2VC2017.pdf HW2] ||
||8 ||Tu Feb 28 ||VCell Exercises ||!McCabe||[attachment:Virtual_Cell_Lecture_3_KM.ppt PPT] [attachment:276HW3VC2017.pdf HW3]||
||8 ||Th Mar 2 ||Introduction to Finite Element Modeling with Continuity ||!McCulloch ||[attachment:FEM_intro_2017.pptx PPT] [attachment:FEM_intro_2017.pdf PDF] [https://www.youtube.com/watch?v=Vz9wYkXFM7c Video Tutorial] ||
||9 ||Tu Mar 7 ||Monodomain Modeling of Action Potential Propagation: Continuity - Electrophysiology Module ||!McCulloch ||[attachment:Monodomain_2017.pptx PPT] [attachment:Monodomain_2017.pdf PDF] [attachment:EP_Atria_example.zip EP Atria example]||
||9 ||Th Mar 9 ||Continuity - Electrophysiology Exercises ||!McCulloch/Vincent|| [http://www.youtube.com/watch?v=tOXZCdZvfOk 2DRing Tutorial] [http://continuity.ucsd.edu/Continuity/Documentation/Tutorials/2Dsheet Continuity tutorial] [http://www.youtube.com/watch?v=zZPTjzepsLs YouTube Version] [attachment:Project_HW.pdf HW] ||
||10 ||Tu Mar 14 ||Continuum Modeling of Cell and Tissue Mechanics: Continuity - Biomechanics Module ||!McCulloch ||[attachment:Lecture17_2013March5.ppt PPT] [attachment:Lecture17_2013March5.pdf PDF] ||
||10 ||Th Mar 16 ||Continuity - Biomechanics Exercises ||!McCulloch || [attachment:Biomechanics_Exercises.pptx PPT] [attachment:Models_BM.zip Models] [attachment:nodes.xls Nodes]||
||11 ||TBA ||Project Presentations [:Courses/be276/Topics/PastProjects:Examples of Past Projects] ||!McCulloch || ||