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Published by
World Scientific Publishing Co. Pte. Ltd.
5 Toh Tuck Link, Singapore 596224
USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601
UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE
Library of Congress Cataloging-in-Publication Data
Allemand, Jean-François.
[Physique et biologie. English]
Physics and biology : from molecules to life / Jean-François Allemand (école Normale
Supérieure, France), Pierre Desbiolles (Université Pierre et Marie Curie, France).
pages cm
Translation of French title: Physique et biologie : de la molécule au vivant, 2012.
Includes bibliographical references.
ISBN 978-9814618922 (hardcover : alk. paper)
1. Biophysics. I. Desbiolles, Pierre. II. Title.
QH505.A4713 2014
571.4--dc23
2014013887
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library.
Originally published in French as “Physique et Biologie: de la molécule an vivant” by EDP Sciences.
Copyright © EDP Sciences 2012. A co-publication with EDP Sciences, 17, av. du Hoggar F-91944 Les Ulis, France.
This edition is distributed worldwide by World Scientific Publishing Co. Pte. Ltd., except France.
Copyright © 2015 by World Scientific Publishing Co. Pte. Ltd.
All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or
mechanical, including photocopying, recording or any information storage and retrieval system now known or to
be invented, without written permission from the publisher.
For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center,
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the publisher.
Copyedited by Christopher Teo Qiang Long
Typeset by Stallion Press
Email: [email protected]
Printed in Singapore
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Coordinators and contributors
Thisbookisacollectivework.Adozenpeopledidcontributetoitswriting.
Coordinators
Jean-FrançoisAllemandisprofessorattheÉcolenormalesupérieure(ENS).He
is a former student of the École normale supérieure de Cachan, with a doctorate
fromPierreandMarieCurieuniversity.Hetaughtbiophysicsatthebachelorsand
masterslevelbutalsoatthe graduatelevelfor physicists,chemistsandbiologists.
His research activity takes place in the Statistical Physics laboratory of the ENS
whichfocusesonthetopics:DNAelasticproperties,DNAmolecularmotorsboth
invitroandinvivowithmicromanipulationandfluorescencetechniques.
v
September11,2014 9:32 PhysicsandBiology:FromMoleculestoLife 9.75inx6.5in b1845-fm pagevi
vi Coordinatorsandcontributors
PierreDesbiollesisageneralinspectoroftheFrenchministryofeducation.He
was professor at Pierre et Marie Curie University in Paris. His research activities
wereledintheKastlerlaboratoryattheÉcolenormalesupérieure.HegotaPhDin
cold atoms physics, and in particular on Bose–Einstein condensation;he directed
experiments,usingfluorescencemicroscopy,tostudyDNA/proteinsinteractionsat
thesinglemoleculelevel.
Contributors
— Olivier Benichou is a CNRS researcher working at Laboratoire de Physique
Théorique de la Matière Condenséein Université Pierre and Marie Curie. His
researchistheoreticalandfocusesonstatisticalphysicsandrandomprocesses,
andtheirapplicationstolivingsystems.
— David Bensimon graduated with L. Kadanoff in the University of Chicago
researching Chaos and non-linear phenomena. In 1986, he joined Bell Labo-
ratories for a post-doctoralperiod studyingconvectionin binary fluids. There,
he met Vincent Croquette and together they established a research group at
the École normale supérieure in Paris that moved towards more biologically
inspiredproblems.Initiallyhestudiedtheshapeofmembranesandvesiclesand
thentogetherwithV.Croquetteandtheirstudentsthemechanicalpropertiesof
single DNA molecules, DNA/protein interactions at the single molecule level.
Recently, D. Bensimon has diversified his interest developing means to con-
trolopticallytheactivityofproteinsin singlecellofazebrafishembryo.Heis
using that technique to study problems in developmentand cancer. He is also
interestedintheevolutionandecologyofbacterialcolonies.
— Yves Boubenecreceived the Biology master’s degree from the École normale
supérieure (ENS), Paris, France, in 2008 and the doctorate degree in Neuro-
sciencesfromtheENSandUPMC,Paris,France,in2013.From2013,hejoined
September11,2014 9:32 PhysicsandBiology:FromMoleculestoLife 9.75inx6.5in b1845-fm pagevii
PhysicsandBiology:FromMoleculestoLife vii
the UNIC in Gif-sur-Yvette, France with research interests including whisker
mechanics and tactile texture perception in rats. His focus is now on sound
texturesintheferretauditorysystem.
— Laurent Bourdieu is a 44 year old CNRS researcher. After a PhD in soft con-
densed matter at the Institut Curie (Paris) and a postdoc in biophysics at The
RockefellerUniversity(NewYork),heworkedattheUniversityofStrasbourg
andnowattheÉcolenormalesupérieureinParis,intheIBENSlaboratory.
— Jean-FrançoisLégerisa40-yearoldCNRSresearcher.AfteraPhDinbiophysics
at the University of Strasbourg, he did a postdoc in neurophysiology at the
UniversityofFreiburg.HeiscurrentlyworkingattheÉcolenormalesupérieure
inParis,intheIBENSlaboratory.
TheLaurentBourdieuandJean-FrançoisLégerresearchesfocusonstudyof
the cellularand network mechanismsunderlyingsensoryintegration in rodent
cortexusingadvancedtwo-photonmicroscopy.
— VincentCroquette followed the ESPCIengineerschoolin Paris;he passedhis
PhD in 1986 on Non-linear physics studying hydrodynamicsand transition to
chaosindynamicalsystems.AfterenteringCNRSandaPostdocinBellLabs,
he joined ENS with D. Bensimon to pursue Non-linear dynamics. In 1992,
both of them changedtheir research interests to biophysics.Since then he has
pioneered single molecule micromanipulation to investigate molecular motors
usingmagnetictweezers.
— As a graduate student, Maxime Dahan was trained in quantum physics in
Pr. Cohen-Tannoudji’s lab at École normale supérieure. After a post-doctoral
visit atBerkeleyunderthe supervisionon Dr. ShimonWeiss,he wasrecruited
asaCNRSscientist.From2000to2012,heworkedasagroupleaderatÉcole
normale on the developmentand application of single molecule assaysin cell
biology,usingacombinationofopticaltoolsandnewnanotechnologies.Since
2013,hehasbeenheadoftheLaboratoirePhysico-ChimieattheInstitutCurie.
— GeorgesDebrégeasisaDirectorofResearchattheCNRS.Hecurrentlyworks
in the Laboratoire Jean Perrin, within the University Pierre and Marie Curie
in Paris. His background is in statistical physics and mechanics. In the last
5years,hehasworkedonthebiomechanicalandneuronalsubstratesunderlying
mechanosensation.
— PascalMartiniscurrentlyDirectorofResearchatCNRS.Hedidhisundergrad-
uatestudiesinPhysicsandChemistry atthe “ÉcoleSupérieuredePhysiqueet
ChimieIndustriellesdelavilledeParis(ESPCI)”andobtainedin1997aPhDin
PhysicsfromtheUniversityPierreandMarieCurie(Paris).Heleadsaresearch
teamattheLaboratoirePhysico-ChimieCurieintheCurieInstitute(Paris)that
September11,2014 9:32 PhysicsandBiology:FromMoleculestoLife 9.75inx6.5in b1845-fm pageviii
viii Coordinatorsandcontributors
works on the active mechanosensitivityof hair cells from the inner ear and of
purifiedmolecular-motorassembliesininvitromotility assays.
— Lia Giuseppewas a researcherat the Centre de GénétiqueMoléculaire (CGM
institute)attheCNRSinGif-sur-Yvette. HeisaformerstudentoftheUniver-
sita degliStudidiMilano in Italy, anddoctoratefromDenis Diderot-Paris VII
universityFrance.
— Sylvie Hénon is professor at University Paris Diderot. Her background is in
softmatterphysics.Shehasbeenworkingoncellularmechanicsandmechano-
transductionfor about15 years,mostlybymicromanipulationscoupledtoflu-
orescencemicroscopy.
— Terence Strick studied physics as an undergraduate at Princeton and obtained
hisPhDinBiologywhileworkinginthegroupofDavidBensimonandVincent
CroquetteattheStatisticalPhysicsLaboratoryoftheÉcolenormalesupérieure
inParis.Hismaininterestisthestudyofprotein-DNAinteractionsinvolvedin
DNAtranscription,replication,repairandchromosomestructure.
— Cécile Sykes was trained as a solid state physicist (PhD in Semiconductor
Physics),andgotinterestedgraduallyinSoftMatterPhysicsandinBiophysics.
Shefoundedagroupin2001attheCurieInstituteinParisnamed“Biomimetism
of Cellular Movements” that aims at designing and studying biomimetic sys-
tems for a better understanding of cell motility and cell shape changes. The
motivationofherworkistounderstandhowcellsmoveandchangeshapeina
diseaselikecancer.
— Raphael Voituriez is a CNRS researcher working at “Laboratoire Jean Perrin
andLaboratoiredePhysiqueThéoriquedelaMatièreCondensée”inUniversité
Pierre and Marie Curie. His research is theoretical and focuses on statistical
physicsandrandomprocesses,andtheirapplicationstolivingsystems.
September11,2014 14:56 PhysicsandBiology:FromMoleculestoLife 9.75inx6.5in b1845-fm pageix
Table of contents
Coordinatorsandcontributors v
Preface xiii
1 Somebiologybasicprinciples 1
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2 Atthecellularlevel . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
3 Atthemolecularscale . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2 Fluorescencemicroscopyforbiologicalimaging 31
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2 Fluorescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3 Fluorescencemicroscopy . . . . . . . . . . . . . . . . . . . . . . . . 37
4 Singlemoleculeimaging . . . . . . . . . . . . . . . . . . . . . . . . 42
5 Conclusionandperspectives . . . . . . . . . . . . . . . . . . . . . . 47
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3 Mechanicalstudiesonsinglemolecules:
generalconsiderations 49
1 Elementsofmolecularbiology . . . . . . . . . . . . . . . . . . . . . 49
2 Advantagesanddrawbacksofsinglemoleculestudies . . . . . . . . . 53
3 Orderofmagnitudeoftherelevantparametersatthesingle
moleculelevel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
ix
