Soft and Biological Matter Xiang-Yang Liu   Editor Frontiers and Progress of Current Soft Matter Research Soft and Biological Matter Series Editors David Andelman, School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel Wenbing Hu, School of Chemistry and Chemical Engineering, Department of Polymer Science and Engineering, Nanjing University, Nanjing, China Shigeyuki Komura, Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan Roland Netz, Department of Physics, Free University of Berlin, Berlin, Berlin, Germany Roberto Piazza, Department of Chemistry, Materials Science, and Chemical Engineering “G. Natta”, Polytechnic University of Milan, Milan, Italy Peter Schall, Van der Waals-Zeeman Institute, University of Amsterdam, Amsterdam, Noord-Holland, The Netherlands Gerard Wong, Department of Bioengineering, California NanoSystems Institute, UCLA, Los Angeles, CA, USA “SoftandBiologicalMatter”isaseriesofauthoritativebookscoveringestablished andemergentareasintherealmofsoftmatterscience,includingbiologicalsystems spanning all relevant length scales from the molecular to the mesoscale. It aims to serve a broad interdisciplinary community of students and researchers in physics, chemistry, biophysics and materials science. Pure research monographs in the series, as well as those of more pedagogical nature, will emphasize topics in fundamental physics, synthesis and design, characterization and new prospective applications of soft and biological matter systems. The series will encompass experimental, theoretical and computational approaches. Topics in the scope of this series include but are not limited to: polymers, biopolymers, polyelectrolytes, liquids, glasses, water, solutions, emul- sions, foams, gels, ionic liquids, liquid crystals, colloids, granular matter, complex fluids, microfluidics, nanofluidics, membranes and interfaces, active matter, cell mechanics and biophysics. Both authored and edited volumes will be considered. More information about this series at http://www.springer.com/series/10783 Xiang-Yang Liu Editor Frontiers and Progress of Current Soft Matter Research 123 Editor Xiang-Yang Liu Research Institution for Biomimetics andSoft Matter Xiamen University Xiamen, China ISSN 2213-1736 ISSN 2213-1744 (electronic) Soft andBiological Matter ISBN978-981-15-9296-6 ISBN978-981-15-9297-3 (eBook) https://doi.org/10.1007/978-981-15-9297-3 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerNatureSingapore PteLtd.2021 Thisworkissubjecttocopyright.AllrightsaresolelyandexclusivelylicensedbythePublisher,whether thewholeorpartofthematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseof illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmissionorinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilar ordissimilarmethodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfrom therelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. 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, expressed or implied, with respect to the material contained hereinorforanyerrorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregard tojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSingaporePteLtd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Preface The soft matter research started more than one hundred years ago. Over a century, the correlated subjects have been examined extensively. People not only keep updating many new soft matter systems, and renewing the knowledge, but also looking into the new applications arising from new demands across areas of phy- sics, biology and chemistry. The systems of soft matter share some common characteristics, such as notable thermal fluctuations, multiple metastable states, mesoscopic multi-scale self-assembled structures, entropy-driven order-disorder transitions, macro flexi- bility. Briefly, these are the systems having “small stimulus, big response” and displaying strong nonlinearities. These characteristics are not so much related to their microstructures (at atomic or molecular levels) but more to their mesoscopic self-assembled structures. These obviously belong to multi-scale complex systems and certainly are good subjects for complex statistic physics research. Within the different types of soft matter systems, flexible materials have been listed as one of the most important materials in recent years, due to the broad applications to big health and related area.In combination with big data and Ai technologies, flexible materials and the correlated flexible electronics will reshape our living and working styles. In this regard, the research efforts on soft materials are targeting on three main aspects, namely recoverable, multi-functional and biocompatible.Thecurrentmajorattentionfromthecommunityisthenfocusedon theidentificationandfabricationofnewmaterialswithhighperformanceforusein protonic/electronicdevices,environmentfriendlyintelligentbuildingmaterialswith the applications in chemo-catalysis, drug delivery, gene delivery, biological imaging and tissue engineering. remote diagnosis related-fields. In particular, wearable, implantable, bio-degradable/absorbable and injectable flexible devices will exert a huge impact on human health and daily life. Thisbookisbasedonthelecturesdeliveredbyinternationalexpertsinthe2019 International Graduate Summer School on Soft Matter and Non-equilibrium Physics. The school covers some fundamental aspects and frontier in non-equilibrium physics and soft matter research. Apart from the basic knowledge on nonlinear statistic physics, dynamics, computer simulations, and main v vi Preface approachesandemergingsystemsinsoftmatterresearch,theparticularattentionis also devoted to new conceptual flexible functional materials, i.e. silk meso-molecular materials, molecular gels, liquid crystals, and the enriching areas, i.e. flexible electronics, new types of catalysis, etc. One of the intentions of this book is to start with the structure formation dynamics and the correlation between thestructuresandmacroscopicperformance.Thislaysdownthefoundationforthe mesoscopic materials design and functionalization. The book evolves from the lecturing style of the school. Therefore, the basic principlesandtechnologiesofcomputersimulationsandexperimentalmethodsare explained in more detail. Illustrations, tables and videos are included in this text- booktoimprovethereadability.Examplesareaddedtohelpunderstanding.Itcan, therefore, be adopted as a reference book for senior undergraduate students, graduate students, and researchers who are interested in soft matter researches. I am sincerely indebted to the authors for the great efforts in the composition of the respective chapters that combine timely and comprehensive reviews of currentfrontierswiththefundamental principlesto serve thepurpose ofthis book. My appreciation also extends to Dr. Q. L. Huang from Physics, the Xiamen Universityforhergreateffortandkindassistanceinsolicitingthemanuscriptsfrom authors,Dr.M.C.HuangandthewholeeditorialteamofSpringerNaturefortheir professionalismthroughoutthewholeeditingprocess.Finally,itisoursincerewish that this book will further stimulate exciting multilateral collaborations among the international scientific communities. Singapore Xiang-Yang Liu August 2020 State Distinguished Professor Contents 1 Introduction to Nonequilibrium Statistical Physics and Its Foundations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Lamberto Rondoni 2 On the Foundational Principles of Statistical Mechanics. . . . . . . . . . 83 Wei-Mou Zheng 3 Generalized Onsager Principle and It Applications . . . . . . . . . . . . . 101 Qi Wang 4 An Introduction to Emergence Dynamics in Complex Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Zhigang Zheng 5 Basics of Molecular Modeling and Molecular Simulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 Chenyu Tang (唐晨宇) and Yanting Wang (王延颋) 6 Cocoon Silk: From Mesoscopic Materials Design to Engineering Principles and Applications. . . . . . . . . . . . . . . . . . . . 241 Wu Qiu and Xiang-Yang Liu 7 A Primer on Gels (with an Emphasis on Molecular Gels) . . . . . . . . 299 Richard G. Weiss 8 Fréedericksz-Like Positional Transition Triggered by An External Electric Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323 Ke Xiao and Chen-Xu Wu vii Chapter 1 Introduction to Nonequilibrium Statistical Physics and Its Foundations LambertoRondoni Abstract Statistical physics is a subject in which determinism and randomness, probabilitiesandrigorouslawsrelatingmaterialpropertiesofmacroscopicobjects are finely intertwined. This calls for particular care in the interpretation of results. When this is done, statistical physics, and in particular its nonequilbrium branch, appliesverywidelytonaturalphenomena,butalsotootherfields,inwhichastatisti- caltreatmentisappropriate.Inthispaper,thefundamentalelementsandresultsofthis subject,meanttointerpretthethermodynamicpictureofmatterintermsoftheatomic hypothesis,arereviewed.TheseincludetheBrownianmotion;theFluctutationDis- sipationTheorem;theBoltzmannequation;thefluctuationrelations;thelinearand thenon-perturbativeresponsetheory.Furthemore,recentapplicationsrangingfrom active matter to the detection of gravitational waves and to machine learning are brieflysummarized.Theliteraturecitedinsupportofthetextissupplementedbya list of further readings, meant to fill some of the very many inevitable gaps in the presentationofthissubject. · · · · Keywords Physicallaws Materialproperties Determinism Stochasticity · · · Probability Emergence Responsetoperturbations Fluctuations 1.1 Prologue:TheRealmofTheoriesandMeasurements PrepareacupofItaliancoffee,whichmeansquiteasmallamountofhotwaterand coffee.Layitonawoodentableinadininghallinacity,whichisonEarth,whichis intheSolarsystem,intheMilkyWayetc.Leavethecuponthetableforawhile;our sensesperceivethatitstemperaturechanges.Inlessthanhalfanhour,werealizethe coffee has reached the room temperature. After a few days, the coffee is not there B L.Rondoni( ) DipartimentodiMatematica,PolitecnicodiTorino, corsoDucadegliAbruzzi24,10129Torino,Italy e-mail:[email protected] SezionediTorino,INFN,ViaP.Giuria1,10125Torino,Italy ©TheAuthor(s),underexclusivelicensetoSpringerNatureSingaporePteLtd.2021 1 X.-Y.Liu(ed.),FrontiersandProgressofCurrentSoftMatterResearch, SoftandBiologicalMatter,https://doi.org/10.1007/978-981-15-9297-3_1 2 L.Rondoni anymore: although nobody drunk it, it evaporated, leaving only dark stains in the cup.Letsomethousandyearspass;eventhetablehasdeteriorated,andmaybethe cuplikeourcityhaveundergonemassivedestruction,becauseofwar,earthquakes, hurricanesetc.Severalbillionyearslater,theEarthisvaporisedbytheexplosionof theSun,andstilllatertheMilkyWayhasundergoneadestructivecollisionwiththe Andromedagalaxy. Has our coffee ever reached a stationary state? A state in which its physical properties do not change in time? Has any of the small or large objects that we mentionedeverbeeninathermodynamicstationarystate?Dostationarystatesexist? Whyisthermodynamicsomuchconcernedwithequilibriumstates,aspecialkind ofstationarystates? ThermodynamicsisamostsuccessfulbranchofPhysicsdescribingmacroscopic objects, and Physics is the realm of quantitative—hence mathematical—theories meanttodescribeandpredictthebeingandbecomingofnaturalphenomena.They aremotivatedbytheirresistiblehumandrivetounderstandtheexistentandgivelifeto newrealities.Theformulationofacorrecttheoryrequiresandinspiresexperiments (not just experiences) that involve measurements of relevant quantities, in order to test its validity. Measurements should then provide objective data, that become intelligible within the mathematical framework constituting the theory. Objective means that they do not depend on the observer, i.e. their significance stands for a passer-bywhetherthatpersonisawareorisnotawareofthemeasurement:ifwater inapotis90◦Chot,thoseimmersingahandinitwillbeburned,whethertheyknew or did not know that a temperature measurement had previously been performed; whetherameasurementhadbeenperformedornotperformed. The goal of thermodynamics is to investigate the consequences of fundamental principlessuchastheconservationofenergy,theimpossibilityofperpetualmotion, etc.ItssecondlawhasbeendescribedbyLiebandYngvason[1]asfollows: The second lawof thermodynamics is, without adoubt, one of themost perfect laws in physics.Anyreproducibleviolationofit,howeversmall,wouldbringthediscoverergreat richesaswellasatriptoStockholm.Theworld’senergyproblemswouldbesolvedatone stroke.Itisnotpossibletofindanyotherlaw(except,perhaps,forsuperselectionrules suchaschargeconservation)forwhichaproposedviolationwouldbringmoreskepticism thanthisone.NotevenMaxwell’slawsofelectricityorNewton’slawofgravitationareso sacrosanct,foreachhasmeasurablecorrectionscomingfromquantumeffectsorgeneral relativity.Thelawhascaughttheattentionofpoetsandphilosophersandhasbeencalled thegreatestscientificachievementofthenineteenthcentury. Describingthebehaviourofmatteratthescaleofourdailylife—whatwecallthe macroscopicworld—notallkindsofmeasurementsareofthermodynamicconcern; onlymeasurementsthatcanbeperformedwithcertaintools,followingcertainpro- tocols are considered. This should be understood, because measurement tools and protocolsnecessarilyaffectthepictureofrealityonegets.Indeed,differentmeasure- ment tools probe different properties of reality, and yield different descriptions of eventheverysameobjects.Wearingglassesthatallowonlyradiationaround510– 530THzmakesthewholeworldlookeitheryelloworblack.Otherglassesyielda differentpicture.