Numerical Methods for the Life Scientist Binding and Enzyme Kinetics
Enzyme kinetics, binding kinetics and pharmacological dose-response curves are currently analyzed by a few standard methods. Some of these, like Michaelis-Menten enzyme kinetics, use plausible approximations, others, like Hill equations for dose-response
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Heino Prinz
Numerical Methods for the Life Scientist Binding and Enzyme Kinetics Calculated with GNU Octave and MATLAB The source code of all programs is available on extras.springer.com
Dr. Heino Prinz Max-Planck-Institut fu¨r molekulare Physiologie AG Biochemische Analytik Otto-Hahn-Str. 11 44227 Dortmund Germany [email protected]
ISBN 978-3-642-20819-5 e-ISBN 978-3-642-20820-1 DOI 10.1007/978-3-642-20820-1 Springer Heidelberg Dordrecht London New York Library of Congress Control Number: 2011933466 # Springer-Verlag Berlin Heidelberg 2011 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)
Preface
This textbook gives an introduction to numerical methods. They are key tools for the calculation of reaction schemes and for the development of functional models in life sciences. The most exciting of this is model development, but it probably cannot be taught in a book. It is surprisingly personal. I will illustrate some aspects together with an acknowledgment of the scientists who impressed me most. Multiple theoretical approaches: I was fortunate to study physics at Bonn University at a time when Wolfgang Paul gave his main lectures on “Experimentalphysik”. The lectures themselves were spectacular, but the emphasis was laid on the variety of possible interpretations of the same experimental findings. For the topic of gravity, for example, Wolfgang Paul included geocentric astronomy and concluded that one cannot rule out angels carrying planets in retrograde loops around the earth, but that the assumption of gravity is so much simpler. For an experimental physicist the observation itself is the result. Theoretical models are only limited by the creativity of the analyst. All are valid when they can be verified experimentally. Courage and creativity: Friedrich Cramer was my PhD supervisor at the MaxPlanck Institute in Go¨ttingen. He had published a structural model for tRNA based on a map of reactive groups. When I entered his group, this model just had been disproven, so that he was criticized for having published a preliminary model. Model building is part of a scientific discourse, and one sometimes needs cour
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