UltraScan Citations and References:

NOTE:
If you have a publication that used UltraScan for hydrodynamic data analysis please enter the reference for your publication in the UltraScan Reference Database

You can search the UltraScan Reference Database for author, title keyword, system studied, and method employed by visiting the UltraScan Reference Database Search Form

If you have used UltraScan for a research publication we would also appreciate if you could cite the most relevant publication(s) from the list below:

The latest Methods Publications can be found online available as PDF files.

General UltraScan References:

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)

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)

Finite Element Analysis and Genetic Algorithms:

ASTFEM Solution, Version 7.0+
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.
Composition Analysis:
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)
Finite Element Analysis
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
Review of Whole Boundary Methods:
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

Other References

The UltraScan software was developed by drawing from the work and research of numerous people who have either directly or indirectly contributed to this software. Below is a partial list of references representing work on which UltraScan development is based.

Sedimentation Analysis:

van Holde, K. E. (1985) Physical Biochemistry, 2nd. Edition. Prentice Hall.
Schachman, H.K. (1992) in Analytical Ultracentrifugation in Biochemistry and Polymer Science (Harding, S. E., Rowe, A. J., and Horton, J. C., Eds.) pp. 3-15, Royal Society for Chemistry, Cambridge, U.K.

van Holde - Weischet Analysis:

van Holde, K. E. and W. O. Weischet. (1978). Boundary Analysis of Sedimentation Velocity Experiments with Monodisperse and Paucidisperse Solutes. Biopolymers, 17:1387-1403
van Holde, K. E. Oregon State University. Personal Communication.

Genetic Algorithms:

Holland, J. H. Adaption in Natural and Artificial Systems. (1975). U. of Michigan Press
Koza, J. R. Genetic Programming: On the Programming of Computers by Means of Natural Selection, 1992, MIT Press, Cambridge, MA.
Goldberg, D.E. (1989). Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley.

Finite Element Analysis:

Lamm, O. (1929) Die Differentialgleichung der Ultrazentrifugierung. Ark. Mat. Astron. Fys. 21B, 1-4
Claverie, J.-M. (1976). Sedimentation of Generalized Systems of Interacting Particles. III. Concentration Dependent Sedimentation and Extension to Other Transport Methods. Biopolymers 15:843-857
Claverie, J.-M., Dreux, H., and R. Cohen (1975). Sedimentation of Generalized Systems of Interacting Particles. I. Solutions of Systems of Complete Lamm Equations. Biopolymers 14:1685-1700
Todd, G. P., and R. H. Haschemeyer. (1981). General Solution to the Inverse Problem of the Differential Equation of the Ultracentrifuge. Proc. Natl. Acad. Sci. 78-11:6739-6743
Zienkiewicz, O. C. (1971) The Finite-element Method in Engineering Science, McGraw- Hill, London.
Schuck, Peter. National Institutes of Health. Personal Communication.
Dishon, M., Weiss, G.H., and Yphantis, D.A. (1969) Numerical Solutions of the Lamm Equation. V. Band Centrifugation. Ann. New York Acad. Sci. 164, 33- 51

Treatment of Interference Data:

Schuck, P. and Demeler, B. (1999). Direct Sedimentation Boundary Analysis of Interference Optical Data in Analytical Ultracentrifugation. Biophysical Journal 76 2288-2296
Thomas M. Laue. Choosing Which Optical System of the Optima XL-I Analytical Ultracentrifuge to Use. Beckman-Coulter Application Information Letter A-1821A.
Thomas M. Laue. University of New Hampshire. Personal Communication.

Global Equilibrium Analysis

Johnson, M. L., Correia, J. J., Yphantis, D. A. and Halvorson, H. R. (1981) Analysis of Data from the Analytical Ultracentrifuge by Nonlinear Least Squares Techniques. Biophysical Journal, Vol. 36, 575-588
McRorie, D. K., Voelker, P. J. Self-Associating Systems in the Analytical Ultracentrifuge. Fullerton, CA, Beckman Instruments, Inc., 1993.

Monte Carlo Analysis:

Efron, B. (1982) The Jackknife, the Bootstrap, and other Resampling Plans. Regional Conference Series in Applied Mathematics. SIAM, Philadelphia, PA

Hydrodynamic Correction of Sedimentation Data:

John Philo, Alliance Protein Laboratories, Thousand Oaks, CA. Personal Communication.
Laue, T. M., Shah, B. D., Ridgeway, T. M., Pelletier, S. L. (1992) Computer-aided interpretation of analytical sedimentation data for proteins. Analytical Ultracentrifugation in Biochemistry and Polymer Science.90-125. Edited by S. E. Harding, A. J. Rowe and J. C. Horton. Cambridge, Royal Society of Chemistry
Sober, H. (1968) The Handbook of Biochemistry and Molecular Biology, Chemical Rubber Co., Cleveland, OH.
CRC Handbook of Chemistry and Physics. CRC Press (http://www.crcpress.com/us).
Durschlag, H. (1986) Specific Volumes of biological macromolecules and some other molecules of biological interest. Thermodynamic Data for Biochemistry and Biotechnology. 45-128. Edited by H.-J. Hinz, Berlin, Springer Verlag.
Cohn, E. J., and Edsall, J. T. (1943) Proteins, Amino Acids, and Peptides as Ions and Dipolar Ions. New York, Reinhold.
Harpaz Y, Gerstein M, Chotia C (1994): "Volume changes on protein folding", Structure 2, 641-649

DNA/RNA Molecular Weight Calculations:

Steve Hardies, University of Texas Health Science Center. Personal Communication.

Extinction Coefficient Calculation:

Gill and von Hippel (1989) Anal. Biochem. 182:319-326

Linear and Nonlinear Least Squares Analysis:

Lawson, C. L., and R. J. Hanson. 1974. Solving Least Squares Problems. Prentice-Hall, Englewood Cliffs, New Jersey.
Ralston, M.L. and Jennrich, R.I. (1978). DUD, a Derivative-Free Algorithm for Nonlinear Least Squares. Technometrics 20, 7-14
Johnson, M.L., and Faunt, L.M. (1992) Parameter Estimation by Least-Squares Methods, Meth. in Enzym. 210, 1-37
Hashim Saber. University of Montana. Personal Communication.
Griewank, A. Evaluating Derivatives Principles and Techniques of Algorithmic Differentiation. SIAM.
Andreas Griewank. Technische Universität, Dresden, Germany. Personal Communication.

Time-differencing Analysis:

Stafford, W. (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, 295-301
Stafford, W. Boston Biomedical Research Institute, Boston MA. Personal Communication.

Parallel Processing:

Donald Morton, University of Montana, Personal Communication
Gang Wu, University of Montana, Personal Communication
Emre Brookes, University of Montana
Raj Boppana, University of Texas at San Antonio

SOMO References:

Rai et al., Structure 13:723-734, 2005
Spotorno et al., Eur. Biophys. J. 25, 373-384; 26, 417
Tsodikov, O. V., Record, M. T. Jr. and Sergeev, Y. V. (2002). A novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem., 23, 600-609.
Byron, Biophys. J. 72, 408-415
Byron, Hydrodynamic bead modeling of biological macromolecules, Methods Enzymol. 321, 278-304, 2000
Abola et al., Nat Struct Biol. 7, 973-977, 2000
Garcia de la Torre et al., Biophys. J. 78, 719-730, 2000
Garcia de la Torre and Bloomfield, Q. Rev. Biophys. 14:81-139, 1981

Software Development:

Stroustrup, B. The C++ Programming Language, Special Edition (2000) Addison Wesley
Lippman, S. B., and Lajoie, J. C++ Primer, 3rd Edition, Addison Wesley.
Satir, G. and Brown, D. C++, the core language. O'Reilly & Associates.
Qualline, S. Practical C++ Programming. O'Reilly & Associates.
Slackware Linux (http://www.slackware.com) and the Linux Documentation Project.