Computational Electrostatics for Biological Applications Geometric a
This book presents established and new approaches to perform calculations of electrostatic interactions at the nanoscale, with particular focus on molecular biology applications. It is based on the proceedings of the Computational Electrostatics for Biolo
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mputational Electrostatics for Biological Applications Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules
Computational Electrostatics for Biological Applications
Walter Rocchia Michela Spagnuolo •
Editors
Computational Electrostatics for Biological Applications Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules
123
Editors Walter Rocchia CONCEPT Lab—CompuNet Istituto Italiano di Tecnologia Genova Italy
ISBN 978-3-319-12210-6 DOI 10.1007/978-3-319-12211-3
Michela Spagnuolo Institute of Applied Mathematics and Information Technologies National Research Council Genova Italy
ISBN 978-3-319-12211-3
(eBook)
Library of Congress Control Number: 2014956206 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, 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. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com)
Foreword
Electrostatic interactions manifest themselves under a wide range of situations in biomolecular systems. While certainly approximate, simple models based on macroscopic continuum dielectric media can be extremely useful to capture the dominant physical effects associated with electrostatics. Classic approaches treating the solvent as a continuum rely on the finite-difference Poisson–Boltzmann (PB) equation or on finite-element methods. Numerical solutions to the PB equation can then be used to calculate a wide range of properties, including the solvation free energy of a biomolecule, pKa shift of ionizable residues, changes in redox potential, or the gating charge of a voltage-activated ion channel. Obviously, a number of technical aspects must be taken into consideration to advance the field and continue to make progress with this methodology. The present monograph offers a broad panoramic view of the field, which can
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