Method publications/references related to UltraScan:

  1. Experimental Design:

    1. Demeler, B. Methods for the Design and Analysis of Sedimentation Velocity and Sedimentation Equilibrium Experiments with Proteins. Curr Protoc Protein Sci. 2010 Apr;Chapter 7:Unit 7.13.

  2. Calibration and Measurement:

    1. 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

    2. 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

  3. Good Manufacturing Processes (GMP):

    1. 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

  4. Multi-Wavelength Analysis:

    1. Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun. 2021 Mar 31;12(1):1988. doi: 10.1038/s41467-021-22253-6. PMID: 33790291; PMCID: PMC8012715.

    2. 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.

    3. 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 Oct;47(7):789-797. doi: 10.1007/s00249-018-1301-7. Epub 2018 Apr 19.

    4. 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

    5. Zhang J, Pearson JZ, Gorbet GE, Cölfen H, Germann MW, Brinton MA, Demeler B. Anal Chem. 2017 Jan 3;89(1):862-870. doi: 10.1021/acs.analchem.6b03926. Epub 2016 Dec 15. Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge.

    6. Karabudak E, Brookes E, Lesnyak V, Gaponik N, Eychmüller A, Walter J, Segets D, Peukert W, Wohlleben W, Demeler B, Cölfen H. Simultaneous Identification of Spectral Properties and Sizes of Multiple Particles in Solution with Subnanometer Resolution. Angew Chem Int Ed Engl. 2016 Sep 19;55(39):11770-4. doi: 10.1002/anie.201603844. Epub 2016 Jul 27.

    7. Gorbet GE, Pearson JZ, Demeler AK, Cölfen H, Demeler B. Next-Generation AUC: Analysis of Multiwavelength Analytical Ultracentrifugation Data. Methods Enzymol. 2015;562:27-47. doi: 10.1016/bs.mie.2015.04.013. Epub 2015 Aug 21.

    8. Pearson JZ, Krause F, Haffke D, Demeler B, Schilling K, Cölfen H. Next-Generation AUC Adds a Spectral Dimension: Development of Multiwavelength Detectors for the Analytical Ultracentrifuge. Methods Enzymol. 2015;562:1-26. doi: 10.1016/bs.mie.2015.06.033. Epub 2015 Aug 3.

  5. Multi-Speed Analysis:

    1. 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. Epub 2018 May 10.

    2. 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. Epub 2018 Apr 2.

  6. Monte Carlo Analysis:

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

  7. 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).

  8. Reversible Associations:

    1. Demeler B, Brookes E, Wang R, Schirf V, Kim CA. Characterization of Reversible Associations by Sedimentation Velocity with UltraScan. Macromol. Biosci. Macromol Biosci. 2010 Jul 7;10(7):775-82.PMID: 20486142

  9. 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 Molecular Weight Distributions from Sedimentation Velocity Experiments. Analytical Ultracentrifugation VIII, Progr. Colloid Polym. Sci. 131:78-82. C. Wandrey and H. Cölfen, Eds. Springer (2006)

  10. 2-Dimensional Spectrum Analysis (2DSA):

    1. Brookes EH, Demeler B. Performance optimization of large non-negatively constrained least squares problems with an application in biophysics. Proceedings of the 2010 TeraGrid Conference, ACM New York, NY, USA 2010

    2. 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. Epub 2018 May 17.

    3. 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, (2009)

    4. 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.

  11. Custom Grid Analysis:

    1. Demeler B, Nguyen TL, Gorbet GE, Schirf V, Brookes EH, Mulvaney P, El-Ballouli AO, Pan J, Bakr OM, Demeler AK, Hernandez Uribe BI, Bhattarai N, Whetten RL. Characterization of size, anisotropy, and density heterogeneity of nanoparticles by sedimentation velocity. Anal Chem. 2014 Aug 5;86(15):7688-95.

  12. Parametrically Constrained Spectrum Analysis (PCSA):

    1. Gorbet G, Devlin T, Hernandez Uribe BI, Demeler AK, Lindsey ZL, Ganji S, Breton S, Weise-Cross L, Lafer EM, Brookes EH, Demeler B. A parametrically constrained optimization method for fitting sedimentation velocity experiments. Biophys J. 2014 Apr 15;106(8):1741-50.

    2. Walter J, Gorbet G, Akdas T, Segets D, Demeler B, Peukert W. 2D analysis of polydisperse core-shell nanoparticles using analytical ultracentrifugation. Analyst. 2016 Dec 19;142(1):206-217.~

  13. 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)

  14. Bead Modeling:

    1. Brookes E, Singh R, Pierce M, Marru S, Demeler B, Rocco M. UltraScan Solution Modeler: Integrated Hydrodynamic Parameter and Small Angle Scattering Computation and Fitting Tool. Published in: Proceeding XSEDE '12 Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond Article No. 42 ACM New York, NY, USA 2012

    2. 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. 2010 39(3):423-35.

    3. Brookes E, Demeler B, Rocco M. 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. 2010 Jul 7;10(7):746-53.

  15. 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.

  16. UltraScan Software References:

    1. Demeler B., and G. Gorbet. Analytical Ultracentrifugation Data Analysis with UltraScan-III. Ch. 8, In Analytical Ultracentrifugation: Instrumentation, Software, and Applications. Eds: Uchiyama S., Stafford W. F. and T. Laue. Springer, 2016; 119-143

    2. 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

    3. 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

    4. Cölfen H, Laue TM, Wohlleben W, Schilling K, Karabudak E, Langhorst BW, Brookes E, Dubbs B, Zollars D, Rocco M, Demeler B. The Open AUC Project. Eur Biophys J (2010) 39:347-359

  17. 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)

  18. 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.

    6. Brookes E , Cao W , Schirf V , Wang R , Zhuo Y , Lafer EM , Kim CA and Demeler, B, Characterization of Kinetic Rates and Equilibrium Constants for Reversible Associations using Sedimentation Velocity. Biochemistry Retreat 2010

    7. Brookes E , Demeler B and Rocco M The UltraScan SOlution MOdeler (US-SOMO) Software Suite and its application to the modeling of integrin alpha2b-beta3.

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