National Center for Design of
Biomimetic Nanoconductors

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• Overview
• Meeting and Summer School
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• Agenda

Scientific Meeting:

Experimental and Computational Approaches to Understanding Membrane Assemblies and Permeation

Dates: July 30-31, 2007
At: National Center for Supercomputing Applications (NCSA), University of Illinois at Urbana-Champaign

Scientific Meeting Agenda

Monday, July 30		Membrane Structure and Function
8:15 - 9:00		Registration and Continental Breakfast
9:00 - 9:30 AM		Welcome and Overview of the Functional Protocell Concept: Eric Jakobsson, University of Illinois
9:30-10:30		Jeff Brinker, Sandia National Laboratories/University of New Mexico:Self-Assembly approaches to supported membranes, protocells, and membrane associated bio/nano interfaces
10:30-10:45		Break
10:45-11:45		Mary Kraft, Stanford University/University of Illinois: Using mass spectrometry to understand membrane organization
11:45-12:45		Lunch at NCSA
12:45-1:45		Jennifer Hovis, Purdue University: Controlling Membrane Organization with pH, electrolyte composition, and membrane chemical composition.
1:45-2:45		H. Larry Scott, Illinois Institute of Technology: Multiscale Methods to Simulate and Predict Membrane Organization: Atomistic Molecular Dynamics to Mean Field Langevin Dynamics
2:45-3:15		Break
3:15-4:15		Emad Tajkhorshid, University of Illinois: Multiscale Methods to Simulate Membrane Organization: Combining all-atom and coarse-grained models to simulate transport across lipid bilayers
4:15-5:00		Yong Jiang, Emory University: Molecular modeling of lipid bilayer edge and hybrid-MCMD method: Implementation and application
5:00-6:00		Discussion and volunteer contributions (Audience members will be invited to show a couple of relevant slides)
6:00-8:00		Joint Reception (at NCSA) with the Center for Cellular Mechanics (CCM) Summer Course on Cell Mechano-sensitivity
Tuesday, July 31		Permeation and Transport
8:15 - 9:00		Registration and Continental Breakfast
9:00-9:15		Announcements, etc.
9:15-10:15		Patrick Barth, University of Washington: Prediction of Membrane Protein Structure
10:15-10:45		Break
10:45-11:45		Vishwanath Jogini, University of Chicago: Spectroscopy And Modeling To Infer Channel Structure And Function
11:45-12:45		Lunch
12:45-1:45		Mike Colvin, University of California-Merced: Unstructured Proteins and Transport
1:45-2:45		Susan Rempe, Sandia National Laboratories: Ionic Selectivity in Synthetic and Natural Channels
2:45-3:15		Break
3:15-4:00		Jay Mashl, University of Illinois: Simulating Large Scale Motions in Ion Channels
4:00-5:15		Discussion and volunteer contributions (Audience members will be invited to show a couple of relevant slides)

Summer School:

Multiscale Theory, Simulation, and Reality at the Nano-Bio Interface

nanoHUB.org – reaching thousands of users with scientific simulations

Dates: August 1-10, 2007
At: National Center for Supercomputing Applications (NCSA), University of Illinois at Urbana-Champaign

Agenda Summary

The following is a tentative agenda. The agenda will be finalized near the beginning of the summer.

Date	Activity
Wednesday, August 1	Introduction of Participants (optional sharing of current work and expectations) Hierarchy of simulation models Implicit water particle simulation Monte Carlo model Prototype systems: ionic channels Simulation examples The bioMOCA code nanoHUB demo Structure of input and output files How to create new input structures Lab experiences on sets of results: simplified pores, gramicidin, porin, MscS
Thursday-Friday August 2-3	Molecular dynamics nanoGROMACS Force field calculations Lipid membranes pK calculations
Saturday, August 4	12noon: Picnic Lunch at Illini Grove (Those wishing to make a day or weekend trip to Chicago or other local attractions can do so on your own. For ideas and assistance, please talk to Dave.)
Sunday, August 5	Free Day
Monday, August 6	AM Overview of tool development process Using Subversion for Source Code Control Using nanoHUB workspaces -- PM Introducing the Rappture Toolkit Rappture with Fortran Rappture with Matlab
Tuesday, August 7	AM Rappture Data Objects Advanced Rappture Concepts -- PM Object-oriented programming in Python Rappture with Python
Wednesday, August 8	AM Using Python and SciPy Accessing web resources from Python -- PM Hands-on: Add Rappture to your own tool
Thursday, August 9	AM Using "submit" to launch grid jobs -- PM Hands-on: Add Rappture to your own tool
Friday, August 10	AM Hands-on: Finish up your own tool The summer school will end with a box lunch at noon on Friday. Participants are free to take lunch with them or stay and continue collaboration depending on travel schedule.

 

Sponsors:

• Network for Computational Nanotechnology (NCN@UIUC)
• National Center for Design of Biomimetic Nanoconductors (NCDBN)
• National Center for Supercomputing Applications (NCSA)
• Materials Computation Center (MCC)
• SCCNE-UIUC
• Center for Cellular Mechanics (CCM)

 

The National Center for Design of Biomimetic Nanoconductors is funded by Grant Number PHS 2 PN2 EY016570B from the National Institutes of Health through the NIH Roadmap for Medical Research and is based at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. Partner institutions include University of Chicago, Illinois Institute of Technology, Sandia National Laboratories, Wabash College, University of California, Davis, and the University of New Mexico, University of Illinois at Chicago, Weill Cornell Medical College, and the National Institute of Standards and Technology.