Abstract
The current status of the UltraScan-III (US3) data analysis software suite is described. An overview of the US3 concepts, software layout, the data workflows and US3 components is presented, followed by a discussion of the analysis methods and their applications. Also described are visualization modules for analysis results, US3’s utilities and simulation tools, as well as the collaboration environments for online data and result exchange.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bhattacharyya SK et al (2006) Development of fast fiber based UV-vis multiwavelength detector for an ultracentrifuge. Progr Colloid Polym Sci 131:9–22
Brookes EH, Demeler B (2007) Parsimonious regularization using genetic algorithms applied to the analysis of analytical ultracentrifugation experiments. In: GECCO '07 proceedings of the 9th annual conference on genetic and evolutionary computation. ACM, New York, pp 361–368. ISBN: 978-1-59593-697-4. doi:10.1145/1276958.1277035
Brookes EH, Demeler B (2008) Parallel computational techniques for the analysis of sedimentation velocity experiments in UltraScan. Colloid Polym Sci 286:138–148
Brookes EH, Boppana RV, Demeler B (2006) Computing large sparse multivariate optimization problems with an application in biophysics. In: Proceedings of the SC 2006 conference. ACM/IEEE. doi:10.1109/SC.2006.18 E-ISBN: 0-7695-2700-0 Print ISBN: 0-7695-2700-0 INSPEC Accession Number: 9343095
Brookes EH, Cao W, Demeler B (2010a) A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape. Eur Biophys J 39:405–414
Brookes E, Demeler B, Rosano C, Rocco M (2010b) 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 39(3):423–435
Brookes E, Demeler B, Rocco M (2010c) Developments in the US-SOMO bead modeling suite: new features in the direct residue-to-bead method, improved grid routines, and influence of accessible surface area screening. Macromol Biosci 10(7):746–753. doi:10.1002/mabi.200900474
Brookes E, et al (2013) US-SOMO cluster methods: year one perspective. XSEDE ’13. In: Proceedings of the conference on extreme science and engineering discovery environment: gateway to discovery, at San Diego, California 01/2013. doi:10.1145/2484762. 2484815. ISBN: 9781450321709
Cao W, Demeler B (2005) Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution of the Lamm equation. Biophys J 89(3):1589–1602
Cao W, Demeler B (2008) Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution for multi-component reacting systems. Biophys J 95(1):54–65
Cölfen H et al (2010) The open AUC project. Eur Biophys J 39(3):347–359
Demeler B (2009) High-resolution modeling of hydrodynamic experiments with UltraScan. http://www.XSEDE.org/gateways/projects.php?id=77
Demeler B (2010) Methods for the design and analysis of sedimentation velocity and sedimentation equilibrium experiments with proteins. Curr Protoc Protein Sci 07: Unit 7.13. doi:10.1002/0471140864.ps0713s60 PMCID: PMC4547541
Demeler B, Brookes EH (2008) Monte Carlo analysis of sedimentation experiments. Colloid Polym Sci 286:129–137
Demeler B, van Holde KE (2004) Sedimentation velocity analysis of highly heterogeneous systems. Anal Biochem 335:279–288
Demeler B et al (2010) Characterization of reversible associations by sedimentation velocity with UltraScan. Macromol Biosci 10(7):775–782. PMID: 20486142
Demeler B et al (2014) Characterization of size, anisotropy, and density heterogeneity of nanoparticles by sedimentation velocity. Anal Chem 86(15):7688–7695
Gorbet G et al (2014) A parametrically constrained optimization method for fitting sedimentation velocity experiments. Biophys J 106:1741–1750
Laue TM, Shah BD, Ridgeway TM, Pelletier SL (1992) Computer-aided interpretation of analytical sedimentation data for proteins. In: Harding SE, Rowe AJ, Horton JC (eds) Analytical ultracentrifugation in biochemistry and polymer science. Royal Society of Chemistry, Cambridge, pp 90–125
Marru S, et al (2011) Apache Airavata: a framework for distributed applications and computational workflows. In: GCE ’11 Proceedings of the 2011 ACM workshop on Gateway computing environments, pp 21–28, ACM New York, NY, USA. Apache Airavata: http://airavata.apache.org/
Memon S, et al (2013) Improvements of the UltraScan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures. In: XSEDE ’13 Proceedings of the conference on extreme science and engineering discovery environment: gateway to discovery No. 39, ACM New York, ISBN: 978-1-4503-2170-9, doi:10.1145/2484762.2484800
Memon S, et al (2014) Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures. Concurr Computat Pract Exper, Wiley. doi: 10.1002/cpe.3251
Schilling K (2014) A multiwavelength capable detector for the analytical ultracentrifuge (Nanolytics, Potsdam, Germany). Personal Communication
Schuck P, Demeler B (1999) Direct sedimentation analysis of interference optical data in analytical ultracentrifugation. Biophys J 76(4):2288–2296
Stafford WF (1992) Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Anal Biochem 203(2):295–301
UltraScan-III wiki: http://wiki.bcf2.uthscsa.edu/ultrascan3/
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Japan
About this chapter
Cite this chapter
Demeler, B., Gorbet, G.E. (2016). Analytical Ultracentrifugation Data Analysis with UltraScan-III. In: Uchiyama, S., Arisaka, F., Stafford, W., Laue, T. (eds) Analytical Ultracentrifugation. Springer, Tokyo. https://doi.org/10.1007/978-4-431-55985-6_8
Download citation
DOI: https://doi.org/10.1007/978-4-431-55985-6_8
Published:
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-55983-2
Online ISBN: 978-4-431-55985-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)