Method publications/references related to UltraScan:

1. Monte Carlo Analysis:

1. Demeler, B. and E. Brookes. Monte Carlo analysis of sedimentation experiments. Colloid Polym Sci (2008) 286(2) 129-137
2. Parallel Computational Techniques:

1. Brookes, E. and B. Demeler. Parallel computational techniques for the analysis of sedimentation velocity experiments in UltraScan. Colloid Polym Sci (2008) 286(2) 138-148
2. Demeler, B., E. Brookes, L. Nagel-Steger. Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing. Methods in Enzymology (pre-print).
3. Genetic Algorithm Publications:

1. Brookes, E and B. Demeler. Parsimonious Regularization using Genetic Algorithms Applied to the Analysis of Analytical Ultracentrifugation Experiments. GECCO ACM Proceedings 978-1-59593-697-4/07/0007 (2007)
2. Brookes, E, and B. Demeler.Genetic Algorithm Optimization for obtaining accurate Molecolar Weight Distributions from Sedimentation Velocity Experiments. Analytical Ultracentrifugation VIII, Progr. Colloid Polym. Sci. 131:78-82. C. Wandrey and H. Cölfen, Eds. Springer (2006)
4. 2-Dimensional Spectrum Analysis:

1. Brookes, E., W. Cao, B. Demeler.A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape. Eur. Biophys. J, (in press)
2. Brookes, E., Boppana, R.V., and B. Demeler. (2006) Computing Large Sparse Multivariate Optimization Problems with an Application in Biophysics. ACM Proceedings 0-7695-2700-0/06 Supercomputing 2006.
5. Finite Element Models:

1. Cao W, Demeler B. Modeling Analytical Ultracentrifugation Experiments with an Adaptive Space-Time Finite Element Solution for Multi-Component Reacting Systems. (2008) Biophys. J. 95(1):54-65
2. Cao W, Demeler B. Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution of the Lamm equation. (2005) Biophys J. 89(3):1589-602
3. Demeler, B. and H. Saber. Determination of Molecolar Parameters by Fitting Sedimentation Data to Finite Element Solutions of the Lamm Equation. Biophysical Journal. 74, 444-454 (1998)
6. Bead Modeling:

1. Brookes, E., B. Demeler, C. Rosano, and M. Rocco. The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. Eur. Biophys. J. (in press)
7. van Holde - Weischet analysis:

1. Demeler, B. and K.E. van Holde. Sedimentation velocity analysis of highly heterogeneous systems. (2004). Anal. Biochem. Vol 335(2):279-288
2. Demeler B, Saber H, Hansen JC.Identification and interpretation of complexity in sedimentation velocity boundaries. Biophys J. 1997 Jan;72(1):397-407.
8. UltraScan Software References:

1. Demeler, B. UltraScan (current version), A comprehensive software package for the analysis of sedimentation experiments. Dept. of Biochemistry, The University of Texas Health Science Center, http://www.ultrascan.uthscsa.edu
2. Demeler, B. UltraScan - A Comprehensive Data Analysis Software Package for Analytical Ultracentrifugation Experiments. Modern Analytical Ultracentrifugation: Techniques and Methods. D. J. Scott, S.E. Harding and A.J. Rowe. Eds. Royal Society of Chemistry (UK) (2005) 210-229
9. Noise processing:

1. Demeler, B. and E. Brookes. Monte Carlo analysis of sedimentation experiments. Colloid Polym Sci (2008) 286(2) 129-137
2. Schuck, P and B. Demeler. Direct Sedimentation Boundary Analysis of Interference Optical Data in Analytical Ultracentrifugation. Biophysical Journal, 76:2288-2296 (1999)
10. Posters:

1. Demeler, B, Brookes, E. Characterization of shape, mass and reversible interactions in complex protein mixtures by analytical ultracentrifugation. Lorne Protein Conference, Australia, 2009.
2. Brookes, E, Demeler, B. Parsimonious Regularization using Genetic Algorithms Applied to the Analysis of Analytical Ultracentrifugation Experiments. GECCO Conference, London, UK 2007
3. Brookes, E, Demeler, B. A Grid-Enabled Supercomputer Implementation for Fitting Sedimentation Velocity Experiments. 16th Intl. AUC Conference in Hannover, Germany, 2007.
4. Nagel-Steger, L., Demeler, B. Willbold D. Aggregate size and shape distributions in amyloid-beta solutions. Computational Biophysics Meeting, Jülich, Germany 2007
5. Brookes, E, Demeler, B. Globular or end-to-end? A two dimensional Spectrum Analysis for Assessing Modes of Aggregation from Sedimentation Velocity Experiments. UTHSCSA, 2006.