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Updated: 06 September 2022

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General

Plascencia-Villa, G., Demeler, B., Whetten, RL., Griffith, WP., Alvarez, M., Black, DM., & José-Yacamán, M. (2016). Analytical Characterization of Size-Dependent Properties of Larger Aqueous Gold Nanoclusters. Journal of Physical Chemistry C. 120(16):8950-8958.

Data Analysis Methods

Lawson, C.L., & Hanson, R.J. (1974). Solving Least Squares Problems. Prentice-Hall, Englewood Cliffs, New Jersey.

Brookes, E. H., & Demeler, B. (2010). Performance optimization of large non-negatively constrained least squares problems with an application in biophysics. In Proceedings of the 2010 TeraGrid Conference (TG '10). Association for Computing Machinery, New York, NY, USA, Article 5, 1–9. https://doi.org/10.1145/1838574.1838579

Ruhe, A., & P. Å. Wedin. (1980). Algorithms for separable nonlinear least squares problems. SIAM Review, 22:318-337.

Schuck, P., & Demeler, B. (1999). Direct sedimentation analysis of interference-optical data in analytical ultracentrifugation. Biophysical Journal, 76:2288-2296.

2 Dimensional Spectrum Analysis

Brookes, E., Cao, W., & Demeler, B. (2010). A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape. European Biophysics Journal. Feb;39(3):405-14. https://doi.org/10.1007/s00249-009-0413-5

Kim, H., Brookes, E., Cao, W., & Demeler, B. (2018). Two-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifuge. European Biophysics Journal. Oct;47(7):837-844. https://doi.org/10.1007/s00249-018-1309-z

Finite Element Analysis

Cao, W., & Demeler, B. (2005) Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution of the Lamm equation. Biophysics Journal. 89(3):1589-602.

Demeler, B., & Saber, H. (1998). Determination of Molecular Parameters by Fitting Sedimentation Data to Finite Element Solutions of the Lamm Equation. Biophysical Journal. 74(1):444-454.

Genetic Algorithm

Brookes, E., and& Demeler, B. (2006). Genetic Algorithm Optimization for obtaining accurate Molecular Weight Distributions from Sedimentation Velocity Experiments. Analytical Ultracentrifugation VIII, Progr. Colloid Polym. Sci. 131:78-82. Wandrey, C., & Coelfen H., eds. Springer.

Lamm Equation

Demeler, B., Behlke, J., & Ristau, O. (2000). Determination of molecular parameters from sedimentation velocity experiments: Whole boundary fitting using approximate and numerical solutions of the lamm equation. In Johnson, M. L., & Brand, L., eds, Methods in Enzymology, Numerical Computer Methods, Part C. 321:38-66.

Pametrically Constrained Spectrum Analysis

Van Holde-Weischet Analysis

Demeler, B. and K.E. van Holde. (2004). Sedimentation velocity analysis of highly heterogeneous systems. Analytical Biochemistry. 335(2):279-288.

Demeler, B., Saber, H., & Jansen, J. C. (1997). Identification and Interpretation of Complexity in Sedimentation Velocity Boundaries. Biophysical Journal. 72: 397-407.

Experimental Methods

Multiwavelength

Henrickson, A., Gorbet, G. E., Savelyev, A., Kim, M., Hargreaves, J., Schultz, S. K., Kothe, U., & Demeler, B. (2022). Multi-wavelength analytical ultracentrifugation of biopolymer mixtures and interactions. Analytical Biochemistry. May;21:114728. https://doi.org/10.1016/j.ab.2022.114728

Henrickson, A., Kulkarni, J. A., Zaifman, J., Gorbet, G. E., Cullis, P. R., & Demeler, B. (2021). Density Matching Multi-wavelength Analytical Ultracentrifugation to Measure Drug Loading of Lipid Nanoparticle Formulations. ACS Nano. https://doi.org/10.1021/acsnano.0c10069

Horne, C. R., Henrickson, A., Demeler, B., & Dobson, R. C. J. (20200). Multi-wavelength analytical ultracentrifugation as a tool to characterise protein-DNA interactions in solution. European Biophysics Journal. https://doi.org/10.1007/s00249-020-01481-6

Johnson, C. N., Gorbet, G. E., Ramsower, H., Urquidi, J., Brancaleon, L., & Demeler, B. (2018). Multi-wavelength analytical ultracentrifugation of human serum albumin complexed with porphyrin. European Biophysics Journal. 17;115(2):328-340. https://doi.org/10.1007/s00249-018-1301-7

Zhang, J., Pearson, J.Z., Gorbet, G.E., Coelfen, H., Germann, M. W., Brinton, M. A., & Demeler, B. (2017). Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge. Analytical Chemistry. Jan;89(1):862-870.

Methodology & Protocols

Stoutjesdyk, M., Brookes, E., Henrickson, A., & Demeler, B. (2020). Measuring compressibility in the Optima AUCTM analytical ultracentrifuge. European Biophysics Journal. Dec;49(8):711-718. https://doi.org/10.1007/s00249-020-01482-5

Stoutjesdyk, M., Henrickson, A., Minors, G., & Demeler, B. (2020). A calibration disk for the correction of radial errors from chromatic aberration and rotor stretch in the Optima AUC™ analytical ultracentrifuge. European Biophysics Journal. https://doi.org/0.1007/s00249-020-01434-z

Software

SedAnal

SedFit

UltraScan

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Savelyev, A., Gorbet, G. E., Henrickson, A., & Demeler, B. (2020). Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment. PLoS Computational Biology. Jun;16(6):e1007942. https://doi.org/10.1371/journal.pcbi.1007942

Williams, T. L., Gorbet, G.E., & Demeler, B. (2018). Multi-speed sedimentation velocity simulations with UltraScan-III. European Biophysics Journal. Oct;47(7):815-823. https://doi.org/10.1007/s00249-018-1308-0

Gorbet, G. E., Mohapatra, S., & Demeler, B. (2018). Multi-speed sedimentation velocity implementation in UltraScan-III. European Biophysics Journal. Oct;47(7):825-835. https://doi.org/10.1007/s00249-018-1297-z

Demeler, B. (2005). 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). pp. 210-229.

Demeler, B. (2005) Hydrodynamic Methods. Bioinformatics Basics: Applications in Biological Science and Medicine. 2nd Edition. H. Rashidi and L. Buehler, Eds. CRC Press LLC. 226-255

Demeler, B. UltraScan version XXX. A Comprehensive Data Analysis Software Package for Analytical Ultracentrifugation Experiments. The University of Lethbridge, Department of Chemistry and Biochemistry. http:/www.ultrascan.aucsolutions.com

Optical Systems

Bhattacharyya, S. (2006). Development of detectors for the analytical ultracentrifuge. PhD Thesis, University of Potsdam, Potsdam.

Laue, T. M., Austin, J. B., & Rau, D. A. (2006). A light intensity measurement system for the analytical ultracentrifuge. Prog Colloid Polym Sci. 131:1–8. https://doi.org/10.1007/2882_001

Lloyd, P. H. (1974). Optical methods in ultracentrifugation, electrophoresis and diffusion: with a guide to the interpretation of records. Oxford: Clarendon Press.

Absorbance

Giebeler, R. (1992). The optima XL-A: a new analytical ultracentrifuge with a novel precision absorption optical system. In: Harding SE, Rowe AJ, Horton JC, editors. Analytical ultracentrifugation in biochemistry and polymer science. Cambridge: Royal Society of Chemistry; pp. 16–25.

Fluorescence

MacGregor, I. K. (2000). Fluorescence optics for the analytical ultracentrifuge. MS Thesis, University of New Hampshire, Durham

MacGregor, I. K., Anderson, A. L., & Laue, T. M. (2004). Fluorescence detection for the XLI ultracentrifuge. Biophys Chem. 108:165–185. https://doi.org/10.1016/j.bpc.2003.10.018

Schmidt, B., &am; Riesner, B. (1992). A fluorescence detection system for the analytical ultracentrifuge and its application to proteins, nucleic acids, viroids and viruses. In: Harding SE, Rowe AJ, Horton JC, editors. Analytical ultracentrifugation in biochemistry and polymer science. Cambridge: The Royal Society of Chemistry; pp. 176–207.

Interference

Laue, T. M., Yphantis, D.A., Rhodes, D.G. (1984). Rapid precision interferometry for the analytical ultracentrifuge. III. Determination of period of rotation, frequency of rotation and elapsed time. Anal Biochem. 143:103–112. https://doi.org/10.1016/0003-2697(84)90563-3

Lavrenko, P., Lavrenko, V., & Tsvetkov. V.(1999). Shift interferometry in analytical ultracentrifugation of polymer solutions. Prog Colloid Polym Sci. 113:14–22. https://doi.org/https://doi.org/10.1007/2882_002

Yphantis, D. A., Lary, J. W., Stafford, W. F., Liu, S., Olsen, P. H., Hayes, D. B., Moody, T. P., Ridgeway, T. M., Lyons, D. A., & Laue, T. M. (1994). On line data acquisition for the Rayleigh interference optical system of the analytical ultracentrifuge. In: Schuster TM, Laue TM, editors. Modern analytical ultracentrifugation. Boston: Birkhäuser; pp. 209–226.

Multiwavelength

Bhattacharyya, S. K., Maciejewska, P., Börger, L., Stadler, M., Gülsün, A. M., Cicek, H. B., & Cölfen, H. (2006). Development of fast fiber based UV-Vis multiwavelength detector for an ultracentrifuge. Prog Colloid Polym Science. 131:9–22. https://doi.org/10.1007/2882_002

Strauss, H. M., Karabudak, E., Bhattacharyya, S., Kretzschmar, A., Wohlleben, W., & Cölfen, H. (2008) Performance of a fast fiber based UV/Vis multi-wavelength detector for the analytical ultracentrifuge. Prog Colloid Polym Sci. 286:121–128.

Schlieren

Börger, L., Lechner, M. D., & Stadler, M. (2004). Development of a new digital camera setup for the online recording of schlieren optical pictures in a modified Beckman optima XL analytical ultracentrifuge. Prog Colloid Polym Sci. 127:19–25.

Cölfen, H., Borchard, W., et al. (1994). Ultrasensitive Schlieren optical system. In: Bonner RF, et al., editors. Progress in biomedical optics. Washington: SPIE Bellingham; p. 307.

https://publishup.uni-potsdam.de/opus4-ubp/frontdoor/deliver/index/docId/3828/file/karabudak_diss.pdf

https://www.biophysics.org/Portals/0/BPSAssets/Articles/vbloomfield.pdf

https://www.mcgill.ca/biochemistry/files/biochemistry/404_silvius_15.pdf

file:///tmp/mozilla_marielle0/1-s2.0-S0076687915004024-main.pdf

https://doi.org/10.1016/S0065-3233(08)60191-6

[Analysis for Systematic Noise])(https://sedfitsedphat.github.io/systematic_noise_analysis.htm)