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 Texas Health Science Center at San Antonio, Department of
Biochemistry. http:/www.ultrascan.uthscsa.edu
(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. Cölfen, 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 Texas at San Antonio
- 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
- García 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.
www contact: Borries Demeler
This document is part of the UltraScan Software
Documentation distribution.
Copyright © notice
The latest version of this document can always be found at:
http://www.ultrascan.uthscsa.edu
Last modified on July 12, 2006.