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)

https://sedfitsedphat.github.io/systematic_noise_analysis.htm

General

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

Data Analysis Methods

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

Emre H. Brookes and Borries Demeler. 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., and P. Å. Wedin. (1980) Algorithms for separable nonlinear least squares problems. SIAM Review. 22:318-337.

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

2DSA

Brookes E, Cao W, Demeler B. A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape. Eur Biophys J. 2010 Feb;39(3):405-14. doi: 10.1007/s00249-009-0413-5. Epub 2009 Feb 27. PMID: 19247646.

Kim H, Brookes E, Cao W, Demeler B. Two-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifuge. Eur Biophys J. 2018 Oct;47(7):837-844. doi: 10.1007/s00249-018-1309-z. PMID: 29777290 4

Finite Element Analysis

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.

Demeler, B. and H. Saber. Determination of Molecular Parameters by Fitting Sedimentation Data to Finite Element Solutions of the Lamm Equation. Biophysical Journal (1998) 74 (1) 444-54

Genetic Algorithms

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

Lamm Equation

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

PSCA

A Parametrically Contrainsed Optimization Method for Fitting Sedimentation Velocity Experiments. Gary Gorbet et al. 201

Van Holde-Weischet Analysis

Enhanced van Holde - Weischet method: Demeler, B. and K.E. van Holde. Sedimentation velocity analysis of highly heterogeneous systems. (2004). Anal. Biochem. Vol 335(2):279-288

Interpretation of van Holde - Weischet Results: Borries Demeler, Hashim Saber and Jeffrey C. Hansen. Identification and Interpretation of Complexity in Sedimentation Velocity Boundaries. Biophysical Journal 72, 397-407 (1997)

Experimental Methods

Sedimentation Velocity

Characterization of Size, Anisotropy, and Density Heterogeneity of Nanoparticles by Sedimentatin Velocity. Borries Demeler et al. 2014

Multiwavelength

Henrickson A, Gorbet GE, Savelyev A, Kim M, Hargreaves J, Schultz SK, Kothe U, Demeler B. Multi-wavelength analytical ultracentrifugation of biopolymer mixtures and interactions. Anal Biochem. 2022 May 21:114728. doi: 10.1016/j.ab.2022.114728. Epub ahead of print. PMID: 35609686.

Henrickson A, Kulkarni JA, Zaifman J, Gorbet GE, Cullis PR, Demeler B. Density Matching Multi-wavelength Analytical Ultracentrifugation to Measure Drug Loading of Lipid Nanoparticle Formulations. ACS Nano. 2021 Feb 22. doi: 10.1021/acsnano.0c10069. Epub ahead of print. PMID: 33617224

Horne CR, Henrickson A, Demeler B, Dobson RCJ. Multi-wavelength analytical ultracentrifugation as a tool to characterise protein-DNA interactions in solution Eur Biophys J. 2020 Nov 21. doi: 10.1007/s00249-020-01481-6. Online ahead of print. PMID: 33219833

Johnson CN, Gorbet GE, Ramsower H, Urquidi J, Brancaleon L, Demeler B. Multi-wavelength analytical ultracentrifugation of human serum albumin complexed with porphyrin. Eur Biophys J. 2018 Jul 17;115(2):328-340. doi: 10.1007/s00249-018-1301-7.

Zhang J, Pearson JZ, Gorbet GE, Cölfen H, Germann MW, Brinton MA, Demeler B. Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge. Anal Chem. 2017 Jan 3;89(1):862-870. PMID: 27977168

Methodology

Stoutjesdyk M, Brookes E, Henrickson A, Demeler B. Measuring compressibility in the Optima AUCTM analytical ultracentrifuge. Eur Biophys J. 2020 Dec;49(8):711-718. doi: 10.1007/s00249-020-01482-5. Epub 2020 Nov 24. PMID: 33236172

Stoutjesdyk M, Henrickson A, Minors G, Demeler B. A calibration disk for the correction of radial errors from chromatic aberration and rotor stretch in the Optima AUC™ analytical ultracentrifuge. Eur Biophys J. 2020 May 9. doi: 10.1007/s00249-020-01434-z. Online ahead of print. PMID: 32388675

Software

UltraScan

Click here for more.

Savelyev A, Gorbet GE, Henrickson A, Demeler B. Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment. PLoS Comput Biol. 2020 Jun 19;16(6):e1007942. doi: 10.1371/journal.pcbi.1007942. PMID: 32559250

Williams TL, Gorbet GE, Demeler B. Multi-speed sedimentation velocity simulations with UltraScan-III. Eur Biophys J. 2018 Oct;47(7):815-823. doi: 10.1007/s00249-018-1308-0. PMID: 29748855

Gorbet GE, Mohapatra S, Demeler B. Multi-speed sedimentation velocity implementation in UltraScan-III. Eur Biophys J. 2018 Oct;47(7):825-835. doi: 10.1007/s00249-018-1297-z.

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 (includes description of applications, sedimentation velocity and equilibrium analysis methods (up to version 6.2), UltraScan utilities, and a description of the UltraScan Laboratory Information Management Database System (LIMS))

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

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 (the actual website for downloading the program)

Optical Systems

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

Laue TM, Austin JB, Rau DA. A light intensity measurement system for the analytical ultracentrifuge. Prog Colloid Polym Sci. 2006;131:1–8. doi: 10.1007/2882_001

Lloyd PH. Optical methods in ultracentrifugation, electrophoresis and diffusion: with a guide to the interpretation of records. Oxford: Clarendon Press; 1974.

Absorbance

Giebeler R. 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; 1992. pp. 16–25.

Fluorecence

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

MacGregor IK, Anderson AL, Laue TM. Fluorescence detection for the XLI ultracentrifuge. Biophys Chem. 2004;108:165–185. doi: 10.1016/j.bpc.2003.10.018.

Schmidt B, Riesner B. 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; 1992. pp. 176–207.

Interference

Laue TM, Yphantis DA, Rhodes DG. Rapid precision interferometry for the analytical ultracentrifuge. III. Determination of period of rotation, frequency of rotation and elapsed time. Anal Biochem. 1984;143:103–112. doi: 10.1016/0003-2697(84)90563-3.

Lavrenko P, Lavrenko V, Tsvetkov V. Shift interferometry in analytical ultracentrifugation of polymer solutions. Prog Colloid Polym Sci. 1999;113:14–22. doi: 10.1007/3-540-48703-4_3.

Yphantis DA, Lary JW, Stafford WF, Liu S, Olsen PH, Hayes DB, Moody TP, Ridgeway TM, Lyons DA, Laue TM. 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; 1994. pp. 209–226

Multiwavelength

Bhattacharyya SK, Maciejewska P, Börger L, Stadler M, Gülsün AM, Cicek HB, Cölfen H. Development of fast fiber based UV-Vis multiwavelength detector for an ultracentrifuge. Prog Colloid Polym Sci. 2006;131:9–22. doi: 10.1007/2882_002

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

Schlieren

Börger L, Lechner MD, Stadler M. 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. 2004;127:19–25.

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