DOI: 10.1016/j.bpj.2014.02.022. A Parametrically Constrained Optimization Method for Fitting Sedimentation Velocity Experiments

A Parametrically Constrained Optimization Method for Fitting Sedimentation Velocity Experiments

10.1016/j.bpj.2014.02.022

Crossref journal-article

Elsevier BV

Biophysical Journal (78)

Bibliography

Gorbet, G., Devlin, T., HernandezÂ Uribe, B. I., Demeler, A. K., Lindsey, Z. L., Ganji, S., Breton, S., Weise-Cross, L., Lafer, E. M., Brookes, E. H., & Demeler, B. (2014). A Parametrically Constrained Optimization Method for Fitting Sedimentation Velocity Experiments. Biophysical Journal, 106(8), 1741â1750.

Authors 11

Gary Gorbet (first)
Taylor Devlin (additional)
Blanca I. Hernandez Uribe (additional)
Aysha K. Demeler (additional)
Zachary L. Lindsey (additional)
Suma Ganji (additional)
Sabrah Breton (additional)
Laura Weise-Cross (additional)
Eileen M. Lafer (additional)
Emre H. Brookes (additional)
Borries Demeler (additional)

References 26 Referenced 65

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10.1002/mabi.200900481 / Macromol. Biosci. / Characterization of reversible associations by sedimentation velocity with ULTRASCAN by Demeler (2010)
Brookes, E. H., Boppana, R. V., and Demeler, B. 2006. Computing large sparse multivariate optimization problems with an application in biophysics. Supercomputing ‘06 ACM. 0–7695–2700–0/06. (10.1109/SC.2006.18)
10.1007/s00249-009-0413-5 / Eur. Biophys. J. / A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape by Brookes (2010)
{'key': '10.1016/j.bpj.2014.02.022_bib5', 'series-title': 'Solving Least Squares Problems', 'author': 'Lawson', 'year': '1974'} / Solving Least Squares Problems by Lawson (1974)
Brookes, E. H., and B. Demeler. 2007. Parsimonious regularization using genetic algorithms applied to the analysis of analytical ultracentrifugation experiments. GECCO Proc. ACM. 978–1-59593–697–4/07/0007. (10.1145/1276958.1277035)
10.1007/s00396-007-1699-4 / Colloid Polym. Sci. / Monte Carlo analysis of sedimentation experiments by Demeler (2008)
10.1529/biophysj.105.061135 / Biophys. J. / Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution of the Lamm equation by Cao (2005)
10.1529/biophysj.107.123950 / Biophys. J. / Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution for multicomponent reacting systems by Cao (2008)
10.1016/S0006-3495(00)76713-0 / Biophys. J. / Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling by Schuck (2000)
10.1090/qam/10666 / Q. Appl. Math. / A Method for the solution of certain non-linear problems in least squares by Levenberg (1944)
10.1137/0111030 / SIAM J. Appl. Math. / An algorithm for least-squares estimation of nonlinear parameters by Marquardt (1963)
10.1002/0471140864.ps0713s60 / Cur. Protoc. Prot. Sci. / Methods for the design and analysis of sedimentation velocity and sedimentation equilibrium experiments with proteins by Demeler (2010)
10.1016/j.ab.2004.08.039 / Anal. Biochem. / Sedimentation velocity analysis of highly heterogeneous systems by Demeler (2004)
{'key': '10.1016/j.bpj.2014.02.022_bib15', 'series-title': 'Parameter Estimation and Inverse Problems', 'author': 'Aster', 'year': '2005'} / Parameter Estimation and Inverse Problems by Aster (2005)
10.1137/1034115 / SIAM Rev. / Analysis of discrete ill-posed problems by means of the L-curve by Hansen (1992)
10.1214/aoms/1177706645 / Ann. Math. Stat. / A note on the generation of random normal deviates by Box (1958)
Demeler, B., G. Gorbet, …, B. Dubbs. 2013. ULTRASCAN-III Ver. 2.0: a comprehensive data analysis software package for analytical ultracentrifugation experiments. http://www.ultrascan3.uthscsa.edu/.
The Extreme Science and Engineering Discovery Environment (XSEDE) Scientific Gateway Portal, National Science Foundation, Arlington, VA. https://www.xsede.org/gateways-listing.
10.1016/S0021-9258(18)53946-6 / J. Biol. Chem. / Binding of the RNA polymerase I transcription complex to its promoter can modify positioning of downstream nucleosomes assembled in vitro by Georgel (1993)
{'key': '10.1016/j.bpj.2014.02.022_bib21', 'series-title': 'Molecular Cloning', 'author': 'Maniatis', 'year': '1982'} / Molecular Cloning by Maniatis (1982)
10.1523/JNEUROSCI.19-23-10201.1999 / J. Neurosci. / A role for the clathrin assembly domain of AP180 in synaptic vesicle endocytosis by Morgan (1999)
10.1002/bip.1975.360140811 / Biopolymers / Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations by Claverie (1975)
10.1021/bi802205g / Biochemistry / Crystal structure of human fibrinogen by Kollman (2009)
10.1007/s00249-009-0418-0 / Eur. Biophys. J. / 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 by Brookes (2010)
10.1002/mabi.200900474 / Macromol. Biosci. / 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 by Brookes (2010)

Dates

Type	When
Created	11 years, 4 months ago (April 15, 2014, 11:45 a.m.)
Deposited	3 years, 5 months ago (April 1, 2022, 1:59 p.m.)
Indexed	1 month, 1 week ago (July 23, 2025, 8:18 a.m.)
Issued	11 years, 5 months ago (April 1, 2014)
Published	11 years, 5 months ago (April 1, 2014)
Published Print	11 years, 5 months ago (April 1, 2014)

Funders 0

None

BibTeX

@article{Gorbet_2014, title={A Parametrically Constrained Optimization Method for Fitting Sedimentation Velocity Experiments}, volume={106}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2014.02.022}, DOI={10.1016/j.bpj.2014.02.022}, number={8}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Gorbet, Gary and Devlin, Taylor and Hernandez Uribe, Blanca I. and Demeler, Aysha K. and Lindsey, Zachary L. and Ganji, Suma and Breton, Sabrah and Weise-Cross, Laura and Lafer, Eileen M. and Brookes, Emre H. and Demeler, Borries}, year={2014}, month=apr, pages={1741–1750} }

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