Summer School 2008
From CTBP wiki
Coarse-Grained Physical Modeling of Biological Systems: Advanced Theory and Methods
August 11-15, 2008 at UCSD campus in La Jolla, CA
Contents |
Information & Update
The Summer school participants can use this wiki page for any feedback, questions, suggestions, etc.
Housing, Meals & Travel Information
Schedule
Monday, August 11: Electrostatics
A.M. Lectures (1205 Natural Sciences Building (NSB)
- 8:00 - 8:10 - Andy McCammon – Introductory Overview
- 8:10 - 9:10 - David Sept (Wash. U) – Poisson-Boltzmann Theory
- 9:10 - 9:30 - Break
- 9:30 - 10:40 - Mike Holst – Introduction to FEtk
- 10:40 - 11:00 - Break
- 11:00 - 12:10 - Robert Konecny – Introduction to APBS
- 12:10 - 1:45 - Lunch
P.M. Computer Lab (Engineering Building II (EBU2), Rm 239)
- 2 - 5pm - APBS and FEtk (Robert, Dave)
Tuesday, August 12: Advanced Solvation Models
A.M. Lectures (1205 Natural Sciences Building (NSB)
- 8:00 - 9:10 - Joe Dzubiella (Munich) – Variational Theory of Solvation
- 9:10 - 9:30 - Break
- 9:30 - 10:40 - Bo Li – Level Set Methods
- 10:40 - 11:00 - Break
- 11:00 - 12:10 - Herbie Levine/Wouter-Jan Rappel – Phase Field Methods
- 12:10 - 1:45 - Lunch
P.M. Computer Lab (Engineering Building II (EBU2), Rm 239)
- 2 - 5pm - APBS and FEtk / variational methods (Robert, Dave)
Wednesday, August 13: Brownian Dynamics
A.M. Lectures (1205 Natural Sciences Building (NSB)
- 8:00 - 9:10 - Gary Huber – Overview
- 9:10 - 9:30 - Break
- 9:30 - 10:40 - David Sept (Wash. U) – Modeling the Cytoskeleton
- 10:40 - 11:00 - Break
- 11:00 - 12:10 - Ady Elcock (Iowa) – Crowded Systems
- 12:10 - 1:45 - Lunch
P.M. Computer Lab (Engineering Building II (EBU2), Rm 239)
- 2 - 5pm - Brownian Dynamics (Gary, Ady)
Thursday, August 14: Fully-continuum Diffusion
A.M. Lectures (1205 Natural Sciences Building (NSB)
- 8:00 - 9:10 - Yuhui Cheng – Overview
- 9:10 - 9:30 - Break
- 9:30 - 10:40 - Steve Bond (U. Illinois) – Time-dependent Methods
- 10:40 - 11:00 - Break
- 11:00 - 12:10 - Benzhou Lu – Poisson-Nernst-Planck
- 12:10 - 1:45 - Lunch
P.M. Computer Lab (Engineering Building II (EBU2), Rm 239)
- 2 - 5pm - SMOL (Yuhui, Gary, Steve, Ben)
Friday, August 15: Emerging Topics
A.M. Lectures (1205 Natural Sciences Building (NSB)
- 8:00 - 9:10 - Valentina Tozzini (Pisa) – One-Bead Coarse Grained models: the balance between accuracy and predictive power
- 9:10 - 9:30 - Break
- 9:30 - 10:40 - Joanna Trylska (Warsaw) – Association of aminoglycosidic antibiotics with the ribosome. Molecular and Brownian dynamics studies
- 10:40 - 11:00 - Break
- 11:00 - 12:10 - Frank Brown (UCSB) – Modeling Membranes
- 12:10 - 1:45 - Lunch
P.M. Computer Lab (Engineering Building II (EBU2), Rm 239)
- 2 - 5pm - Individual Projects (with help of faculty as needed). Introduction to coarse grained MD - RedMD (Joanna).
Lab material
Monday: APBS and FEtk
User Guides:
Tutorials:
CTBP Summer School 2008 tutorial 1
Tuesday: APBS and FEtk
For this lab session please bring continuum solvation/electrostatics projects (or just problems) that are of interest to you. We will spend the majority of the time focusing on the application of these tools to your projects.
CTBP Summer School 2008 tutorial 2
Wednesday: Brownian Dynamics: BrownDye
Thursday: SMOL
Friday: Individual Projects
Coarse-grained MD tutorial using RedMD (Reduced Molecular Dynamics) (Joanna).
Computer lab instructions
The hands-on tutorials will take place in EBU2, room 239, Building 610 on UCSD campus. Every participant will have a Linux desktop available and also access to CTBP high performance computational cluster. You will receive login information at the begining of the first lab on Monday.
- After you log in you need to initialize software environment by executing the following in your terminal window before starting the tutorials (this needs to be done in every new terminal window):
. /home/linux/ieng6/nbcr08/public/CTBP/paths.sh
- Available software:
- Applications available on-line:
- PDB2PQR web service.
- Opal dashboard.
- PDB2PQR/APBS Opal integrated web service (beta): server1 and server2.
