Abstract
Modern biochemical techniques are continuously refined to produce new and improved results. Improvements in the useful power of a biochemical technique can in principle be achieved in two ways. One is the classic trial-and-error approach whereby the parameters of the experimental conditions are varied one by one until a suitable set of conditions is found. The other way of improving or optimizing a technique is theoretical. The desired quality of the outcome of the experiment in question (i.e., the degree of analytical reliability or the desired power of resolution) is considered in physicochemical terms, and the experimental conditions that are needed to achieve this quality are calculated.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Anderson, N. G. (ed.), 1966, The development of zonal centrifuges and ancillary systems for tissue fractionation and analysis, Natl. Cancer Inst. Monogr. 21.
Barber, E. J., 1966, Calculation of density and viscosity of sucrose solutions as a function of concentration and temperature, Natl. Cancer Inst. Monogr. 21:219–239.
Berman, A. S., 1966, Theory of centrifugation: Miscellaneous studies, Natl. Cancer Inst. Monogr. 21:41–76.
Bishop, B. S., 1966, Digital computation of sedimentation coefficients in zonal centrifuges, Natl. Cancer Inst. Monogr. 21:175–188.
Carlson, A. D., and Souček, B., 1975, Computer simulation of firefly flash sequences, J. Theor. Biol. 55:353–370.
Cox, D. J., 1965a, Computer simulation of sedimentation in the ultracentrifuge. I. Diffusion, Arch. Biochem. Biophys. 112:249–258.
Cox, D. J., 1965b, Computer simulation of sedimentation in the ultracentrifuge. II. Concentration-independent sedimentation, Arch. Biochem. Biophys. 112:259–266.
Cox, D. J., 1967, Computer simulation of sedimentation in the ultracentrifuge. III. Concentration-dependent sedimentation, Arch. Biochem. Biophys. 119:230–239.
Cox, D. J., 1969, Computer simulation of sedimentation in the ultracentrifuge. IV. Velocity sedimentation of self-associating solutes, Arch. Biochem. Biophys. 129:106–123.
Eikenberry, E. F., Bickle, T. A., Traut, R. R., and Price, C. A., 1970, Separation of large quantities of ribosomal subunits by zonal centrifugation, Eur. J. Biochem. 12:113–116.
Fisher, É., and Keleti, T., 1975, Sigmoidal substrate saturation curves in Michaelis-Menten mechanism as an artefact, Acta Biochim. Biophys. Acad. Sci. Hung. 10(3):221–227.
Funding, L., 1973, Estimation of equivalent sedimentation coefficients with zonal rotors, in: European Symposium of Zonal Centrifugation in Density Gradient, Spectra 2000 (J.-C. Chermann, ed.), Vol. 4, pp. 45–49, Editions Cité Nouvelle, Paris.
Garfinkel, D., London, J. W., Dzubow, L., and Nicklas, W. J., 1975, Computer simulation of the metabolism of guinea pig brain slices, and how they differ from the intact brain, Brain Res. 92:207–218.
Gilbert, L. M., and Gilbert, G. A., 1973, Sedimentation velocity measurement of protein association, in: Methods in Enzymology (S. P. Colowick and N. O. Kaplan, eds.), Vol. XXVII, pp. 273–296, Academic Press, New York.
Hinton, R. H., 1971, Computational approaches in the processing of zonal results, in: Separations with Zonal Rotors (E. Reid, ed.), pp. Z–5.l–Z–5.10, Wolfson Bioanalytical Centre, University of Surrey, Guildford, England.
Ifft, J. B., Voet, D. H., and Vinograd, J., 1961, The determination of density distributions and density gradients in binary solutions at equilibrium in the ultracentrifuge, J. Phys. Chem. 65:1138–1145.
Johns, P., and Stanworth, D. R., 1976, A simple numerical method for the construction of isokinetic sucrose density gradients, and their application to the characterization of immunoglobulin complexes, J. Immunol. Methods 10:231–252.
Kim, M., and Woo, K. B., 1975, Kinetic analysis of cell size and DNA content distributions during tumor cell proliferation: Erlich ascites tumor study, Cell Tissue Kinet. 8:197–218.
Leach, J. M., 1971, Data processing of zonal centrifuge experiments, in: Separations with Zonal Rotors (E. Reid, ed.), pp. Z–4.l–Z–4.16, Wolfson Bioanalytical Centre, University of Surrey, Guildford, England.
London, J. W., Yarrish, R., Dzubow, L. D., and Garfinkel, D., 1974, Computer simulation and optimization, as exemplified by the enzyme-coupled aminotransferase (transaminase) assays, Clin. Chem. 20(11): 1403–1407.
Ludlum, D. B., and Warner, R. C., 1965, Equilibrium centrifugation in cesium sulfate solutions, J. Biol. Chem. 240:2961–2965.
Martin, R. G., and Ames, B. N., 1961, A method for determining the sedimentation behaviour of enzymes: Application to protein mixtures, J. Biol. Chem. 236:1372–1379.
Meuwissen, J. A. T. P., 1973, Hydrodynamic instability: An explanation of anomalous zone spreading in density gradient methodology, in: European Symposium of Zonal Centrifugation in Density Gradient, Spectra 2000 (J.-C. Chermann, ed.), Vol. 4, pp. 21–31, Editions Cité Nouvelle, Paris.
Noll, H., 1967, Characterization of macromolecules by constant velocity sedimentation, Nature (London) 215:360–363.
Norman, M. R., 1971, Simple equations for relating volume to radius in “B” type zonal rotors, in: Separations with Zonal Rotors (E. Reid, ed.), pp. Z–3.1–Z–3.4, Wolfson Bioanalytical Centre, University of Surrey, Guildford, England.
Pollack, M. S., and Price, C. A., 1971, Equivolumetric gradients for zonal rotors: Separation of ribosomes, Anal. Biochem. 42:38–47.
Pretlow, T. G., 1971, Estimation of experimental conditions that permit cell separations by velocity sedimentation on isokinetic gradients of Ficoll in tissue culture medium, Anal. Biochem. 41:248–255.
Pretlow, T. G., Boone, C. W., Shrager, R. I., and Weiss, G. H., 1969, Rate zonal centrifugation in a Ficoll gradient, Anal. Biochem. 29:230–237.
Price, C. A., 1973, Equivolumetric gradients: Apparent limits on resolution and capacity imposed by gradient-induced zone narrowing, in: European Symposium of Zonal Centrifugation in Density Gradient, Spectra 2000 (J.-C. Chermann, ed.), Vol. 4, pp. 71–81, Editions Cité Nouvelle, Paris.
Rickwood, D., 1976, Metrizamide—A gradient medium for centrifugation studies, Nyegaard & Co., Oslo, Norway.
Sartory, W. K., Halsall, H. B., and Breillat, J. P., 1976, Simulation of gradient and band propagation in the centrifuge, Biophys. Chem. 5:107–135.
Schumaker, V. N., 1967, Zone centrifugation, in: Advances in Biological and Medical Physics (C. A. Tobias and J. H. Lawrence, eds.), pp. 245–339, Academic Press, New York.
Spragg, S. P., Morrod, R. S., and Rankin, C. T., Jr., 1969, The optimization of density gradients for zonal centrifugation, Sep. Sci. 4:467–479.
Steensgaard, J., 1970, Construction of isokinetic sucrose gradients for rate-zonal centrifugation, Eur. J. Biochem. 16:66–70.
Steensgaard, J., and Funding, L., 1974, Computer simulation of rate-zonal centrifugation, in: Methodological Developments in Biochemistry (E. Reid, ed.), Vol. 4, pp. 55–65, Longman, London.
Steensgaard, J., and Hill, R., 1970, Separation and analysis of soluble immune complexes by rate-zonal ultracentrifugation, Anal. Biochem. 34:485–493.
Steensgaard, J., Funding, L., and Meuwissen, J. A. T. P., 1973, Simulation of rate-zonal centrifugation on a digital computer, Eur. J. Biochem. 39:481–491.
Steensgaard, J., Funding, L., and Meuwissen, J. A. T. P., 1974, A FORTRAN program for simulation of zonal centrifugation, in: Methodological Developments in Biochemistry (E. Reid, ed.), Vol. 4, pp. 67–80, Longman, London.
Steensgaard, J., Johansen, H. K. W., and Møller, N. P. H., 1975, Computer simulation of immunochemical interactions, Immunology 29:571–579.
Steensgaard, J., Maw Liu, B., Cline, G. B., and Möller, N. P. H., 1977. The properties of immune complex-forming systems—a new theoretical approach, Immunology 32:445–456.
Steensgaard, J., Møller, N. P. H., and Funding, L., 1978, Rate zonal centrifugation: Quantitative aspects, in: Centrifugal Separations in Molecular and Cell Biology (G. B. Birnie and D. Rickwood, eds.), pp. 115–168, Butterworths, London.
Stewart, J., 1975, Urea handling by the renal countercurrent system: Insights from computer simulation, Pfluegers Arch. 356:133–151.
Svedberg, T., and Pedersen, K. O., 1940, The ultracentrifuge, Oxford University Press, Oxford.
Svensson, H., Hagdahl, L., and Lerner, K.-D., 1957, Zone electrophoresis in a density gradient: Stability conditions and separation of serum proteins, 5c. Tools 4:1–10.
Taketomi, H., Ueda, Y., and Gō, N., 1975, Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions, Int. J. Peptide Protein Res. 7:445–459.
Vinograd, J., and Hearst, J. E., 1962, Equilibrium sedimentation of macromolecules and viruses in a density gradient, Fortschr. Chem. Org. Naturst. 20:372–379.
Walsh, G. R., 1975, Methods of Optimization, J. Wiley & Sons, London.
Wright, R. R., Pappas, W. S., Carter, J. A., and Weber, C. W., 1966, Preparation and recovery of cesium compounds for density gradient solutions, Natl. Cancer Inst. Monogr. 21:241–249.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1979 Plenum Press, New York
About this chapter
Cite this chapter
Steensgaard, J., Møller, N.P.H. (1979). Computer Simulation of Density-Gradient Centrifugation. In: Roodyn, D.B. (eds) Subcellular Biochemistry. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-7945-8_2
Download citation
DOI: https://doi.org/10.1007/978-1-4615-7945-8_2
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4615-7947-2
Online ISBN: 978-1-4615-7945-8
eBook Packages: Springer Book Archive