6th Annual UltraScan Analytical Ultracentrifugation Workshop

May 1st - May 6th, 2008

Daily Workshop Schedule:

PLEASE NOTE: Participants wishing to have UltraScan installed on their laptops please see Jeremy Mann throughout the course for assistance.

Session 1: Session 2: Session 3: Session 4: Session 5: Session 6:

Introduction to Hydrodynamic Theory and Analytical Ultracentrifugation Sedimentation Velocity (1): Sedimentation Velocity (2): Sedimentation Equilibrium Global Analysis, Software practice Instrument Workshop

8:30 am: Continental Breakfast and Welcome

9:00 am: Setup and UltraScan Overview

Assistance will be provided to help with UltraScan software installations, set up and testing of database connections and network operation. Installation of User Account.

10:00 pm: Coffee Break

10:15 am: Introduction to AUC, Part I (Lecture Slides)

Review of the Basics: First Principles in Hydrodynamic Theory

• Instrumentation
• What can be learned from sedimentation velocity and sedimentation equilibrium experiments?
• Review of transport processes
• Frictional Ratio
• Hydrodynamic Corrections (density, viscosity, partial specific volume)
• What experiments should be conducted?

11:15 pm: Coffee Break

11:30 am: Introduction to AUC, Part II (Lecture Slides)

Review of the Basics: First Principles in Hydrodynamic Theory

• Available optical Systems
• Intensity vs. Absorbance
• Types of experimental Noise
• Overview of analysis approaches:
  • Model-free approaches
  • Parameterized Models
  • Non-interacting vs. reversibly associating systems
• How do we extract parameters from the data?
• Linear vs. non-linear fitting

12:30 pm: Lunch Break

1:30 pm: UltraScan Basics (Lecture Slides)

Introduction to UltraScan (Software Practice Session)

• Basic operations
• Converting intensity data
• UltraScan file utilities

2:30 pm: Coffee Break

2:45 pm: UltraScan Laboratory Information Management System

Managing data and experiments with the UltraScan LIMS and web portal (Software Practice Session)

• Project Tracking
• Committing and retrieving experimental data
• Associating buffer files and peptide sequences
• Managing experiments and multiple investigators
• Editing data
• Uploading all Workshop Sample Data
• HTML reports
• Using the web portal for sharing data

4:30 pm: Adjourn Session 1

8:30 am: Continental Breakfast

9:00 am: Sedimentation Velocity Basics (Lecture Slides)

Experimental Design (Software Practice Session)

• Choice of optical systems
• Speed selection
• Wavelength Considerations
• Sample selection, buffer considerations, sample preparation
• Lamm Equation Models
• Sedimentation Velocity Model Editor
• ASTFEM solution
• Model File Exchange

10:00 pm: Coffee Break

10:15 am: Sedimentation Velocity Data Analysis I (Lecture Slides)

Velocity Analysis Methods: Model-independent Methods (Software Demo)

• Enhanced van Holde - Weischet Analysis
• Second Moment Analysis
• dc/dt Analysis

11:15 pm: Coffee Break

11:30 am: Sedimentation Velocity Data Analysis II (Lecture Slides)

Velocity Analysis Methods: Lamm Equation Modeling (Software Demo)

• Nonlinear fitting of finite element solutions
• C(s) method
• 2-dimensional Spectrum analysis
• Parsimonious regularization with Genetic Algorithms
• Non-linear parameter estimation with Genetic Algorithms

12:30 pm: Lunch Break

1:30 pm: Presentation by Emre Brookes (UTSA)

Parallel computational techniques for the analysis of sedimentation velocity experiments in UltraScan.

2:30 pm: Coffee Break and meet with speaker

3:00 pm: USLIMS submission of HPC jobs

Non-interacting Finite Element Analysis using HPC resources on the USLIMS (software Demo)

• 2DSA Initialization
• Time-invariant Noise removal
• Meniscus Fitting and updating
• Monte Carlo Analysis (2DSA)
• Genetic Algorithm Initialization (linear models)
• Genetic Algorithm
• Monte Carlo Analysis (Genetic Algorithm)

4:30 pm: Adjourn Session 2

8:30 am: Continental Breakfast

9:00 am: Equilibrium Experimental Design (Lecture Slides)

Experimental Design and Data editing

• Speed Determination and run simulation
• Equilibrium Data Simulation
• Editing of absorbance data
• Editing of interference data

10:00 pm: Coffee Break

10:15 am: Global Equilibrium Data Fitting Session 1

Software Demonstration and Practice Session

• Wavelength editing
• Spectrum analysis
• Global Fitting

11:15 pm: Coffee Break

11:30 am: Global Equilibrium Data Fitting Session 2

Software Demonstration and Practice Session, continued...

• Data Modeling
• Monte Carlo Analysis
• Model Comparison
• Data export and presentation

12:30 pm: Lunch Break

1:30 pm: Participant Presentations and Discussion

Topics and speakers to be determined

1. Fang Wei, Rice University: Study of the stability of ABC heterotrimeric collagen-like peptides

2:30 pm: Coffee Break

2:45 pm: Data Analysis of user data

• Individual sessions with tutor
• upload of user provided data
• submission of user data to supercomputer for overnight runs

4:30 pm: Adjourn Session 4

8:30 am: Continental Breakfast (Lecture Slides)

9:00 am: Instrument Basics

• Wavelength calibration
• Radial calibration
• intensity monitoring
• Monochromator Issues
• Interference optics issues
• diagnostic checks

10:00 pm: Coffee Break

10:15 am: Instrument Diagnostics (Lecture Slides)

Examples and discussion of common instrument problems

• Presentation by Virgil Schirf, Center for Analytical Ultracentrifugation of Macromolecular Assemblies (UTHSCSA).

11:15 pm: Coffee Break

11:30 am: Instrument Maintenance

Diagnostics, Tests, and Remedies

• Cleaning of monochromator
• Cleaning of lamp
• Cleaning of slit assembly
• adjusting contrast and timing for interference experiments

12:30 pm: Lunch Break

1:30 pm: CAUMA visit

Hands on Instrument Maintenance, Group 1

• (group 2 has opportunity for more data analysis and individual tutoring)

2:30 pm: Coffee Break

2:45 pm: CAUMA visit

Hands on Instrument Maintenance, Group 2

• (group 1 has opportunity for more data analysis and individual tutoring)

4:30 pm: Adjourn Session 6