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Structure, Mechanical Properties, and Self-Assembly of Viral Capsids

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Structure, Mechanical Properties, and Self-Assembly of Viral Capsids Structure, Mechanical Properties, and Self-Assembly of Viral Capsids Antoni Luque Santolaria ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tdx.cat) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tdx.cat) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR. No se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora. WARNING. On having consulted this thesis you’re accepting the following use conditions: Spreading this thesis by the TDX (www.tdx.cat) service has been authorized by the titular of the intellectual property rights only for private uses placed in investigation and teaching activities. Reproduction with lucrative aims is not authorized neither its spreading and availability from a site foreign to the TDX service. Introducing its content in a window or frame foreign to the TDX service is not authorized (framing). This rights affect to the presentation summary of the thesis as well as to its contents. In the using or citation of parts of the thesis it’s obliged to indicate the name of the author. Structure, Mechanical Properties, and Self-Assembly of Viral Capsids Antoni Luque Santolaria Departament de F´ısica Fonamental Facultat de F´ısica Universitat de Barcelona Facultat de F´ısica Departament de F´ısica Fonamental Structure, Mechanical Properties, and Self-Assembly of Viral Capsids Programa de doctorat: F´ısica L´ınia d’investigaci´o: F´ısica de la mat`eria condensada Director de tesi: David Reguera L´opez Memoria presentada per Antoni Luque Santolaria per a optar al t´ıtol de Doctor en F´ısica (8 de Juny de 2011). Agra¨ıments Probablement, aquestes siguin les l´ınies m´es complicades d’escriure de tota la tesi. Fer el doctorat ha estat una etapa d’una significaci´o molt important per a mi, i sortosament l’he poguda compartir amb gent molt especial, tant a dins com aforadelauniversitat. El meu primer agra¨ıment va inevitablement dirigit cap al David Reguera. De la seva m`a he tingut el privilegi d’iniciar-me en el m´on de la recerca i cr`eixer dia a dia com a investigador, gaudint d’una llibertat envejable, i a l’hora d’una atenci´o i disponibilitat per part seva excepcionals. A m´es vull donar-li les gr`acies per tot el suport que m’ha donat durant tot el doctorat, especialment en aquesta darrera etapa de la tesi. Dono les gr`acies tamb´e a tot el personal del departament, per la seva actitud i cordialitat al llarg d’aquest per´ıode. En particular volia agrair a tots aquells doctorands, postdocts i professors (tant del Departament de F´ısica Fonamental com del d’Estructura i Constituents de la Mat`eria) que, a partir del seu inter´es i participaci´o, han fet possible els Condensed Matter Seminars.S´e que a vegades he estat una mica pesat amb els anuncis de les xerrades, per`o crec que ha valgut la pena i ha estat una activitat enriquidora. Tamb´e volia destacar els valuosos consells que he rebut en diferents moments per part del F`elix Ritort, la Marta Iba˜nes, el Jordi Ort´ın, el Javier Buceta i l’Ignasi Pagonabarraga. Gr`acies tamb´e a l’Eduard, l’Helena, l’Olga, i, en especial, a la Bea, per la paci`encia i atenci´o que sempre han tingut amb mi quan he hagut de fer gestions al departament. Aix´ı mateix, vull destacar el gran record que guardo de la meva experi`encia a Los Angeles al grup d’en Robijn Bruisnma. Gr`acies Robijn per la teva gen- erositat. I gr`acies tamb´e Joseph Rudnick, Howard Reiss, Will Klug, i el “virus research groupˆa de UCLA (en particular: Bill Gelbart, Chuck Knobler, Ajay Gopal, Walter, i Mauricio Comas) per la vostra gran acollida. Tots vosaltres vau contribuir a que la meva estada cient´ıfica a UCLA fos excepcional. Gr`acies tamb´e al grup de Pedro de Pablo i la gent del CNB de Madrid (JR, Daniel, Carmen, i companyia) per la vostra hospitalitat i col·laboraci´o durant la iii tesi. He de remarcar que la recerca duta a terme en aquesta tesi no hauria estat possible sense el suport econ`omic que he rebut al llarg d’aquests anys per part de la Generalitat de Catalunya a trav´es de l’AGAUR, que sempre m’ha ofert, a m´es, un tracte excel·lent. No puc oblidar tampoc aquells que no nom´es hem caminat plegats durant el doctorat, sin´oque,am´es, vam comen¸car la singladura d’aquest cim el primer dia de la llicenciatura: el David “ay” L´opez, el Camps, el Pau, la Bel´en, el Tavi, el Capde, el Ricard, l’Alvaro,´ l’Escart´ın, l’Albert talladit, el Richi, el Tarr´us. sens dubte aquesta ha estat una promoci´o, i sobretot, un grup hum`a excepcional. Ha estat un plaer haver passat aquests anys amb vosaltres, i ´es una ll`astima que no h`agim tornat a visitar Berl´ın! Em perdonareu, per`o al Pau, l’hi he dedicar unes paraules a part. No exagero si dic que ell ´es un dels responsables que jo ara estigui escrivint aquestes l´ınies. La seva amistat a l’institut va ser un punt d’inflexi´o no nom´es en el pla personal, sin´otamb´e en el vocacional. I aix´ıhem acabat: parlant de gens i prote¨ınes entre “hamiltonians”. A la Noela, el Ricard, el Silvio, el Paolo, i el recent emigrat Dr. Camps, us he de donar les gr`acies per tots els bons moments que hem compartit al 3.45, itamb´e demanar perd´o per totes les hores de feina que us he robat parlant del Bar¸ca, d’scripts de linux, o de qualsevol an`ecdota no excessivament transcendent. Moltsanims ` Noela en aquest tram final de l’escriptura! Espero que ben aviat puguis tornar gaudir relaxadament del sol i un bon llibre al balc´odeGr`acia. Per cert, Ricard, aix`o s’acaba i al final no hem aconseguit muntar cap empresa. Vull mencionar tamb´e als recentment doctorats Alvaro´ i David que tantes hores de tert´ulia hem compartit a les escales, aix´ı com als “cafeters” Nico, Martin, Mar´ıa i companyia per tots els dinars que hem passat al “ranxo”. De fet, la Mar´ıa mereix una menci´o especial perqu`e m’ha d’aguantar als “groups meetings”, i tot i que em posi pesat quan treballem plegats (com en l’estudi del Cap´ıtol 4 d’aquesta tesi), sempre est`a de bon humor i ambanims ` de fer una canya! Xavi, perdona, la tesi no m’ha deixat venir a Flor`encia, sempre em passa igual. Javier, gr`acies de nou per la teva generositat oferint-me la teva habitaci´o “santuari” de Madrid, imolts`anims en aquesta nova etapa com a divulgador. Doro i Jan, gr`acies per la vostra amistat, i tots els consells i el suport que m’heu donat els pocs dies que ens hem pogut veure aquests mesos. No vull oblidar tampoc a la Lynne, el Jesse, la Sasha i el Marshall que em van adoptar a la seva fam´ılia durant la meva estada a Los Angeles, i que juntament amb el Mauricio, la Veta, la Charlotte, l’Ashley, el Peter, el Noah, l’Allegra, la Shellie, el Jon, la Laura, el Joan i la penya cul´e del Busby’s em van fer sentir iv com a casa, i viure uns mesos fabulosos. Una abra¸cada gegant als de sempre: Albert, Joan, Diego, Alex` i Tolo. Espero que brindem aviat fent un vermut a la Barceloneta, en un concert d’en Jortx el “r´afagas”, o en el “dancefloor” de la Gaviota amb el Nacho, el Txepe, els peluts, i la penya de les Corts, si cal. Aquests darrers mesos us he trobat a faltar. I don’t like you, I love you! Gr`acies papa i Montse per aquest regal anomenat Aitana. Gr`acies iaia, Laura i mama pel vostre suport incondicional durant tota la vida. I gr`acies my Butzie pel present i el futur que tenim entre mans. v Amamare Contents Introduction 1 Scope..................................... 8 References................................... 13 I Structure of Viral Capsids 17 1 Geometrical Construction of Viral Capsids 19 1.1Introduction..............................
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