[ES] Los biosensores son dispositivos analíticos con aplicabilidad en diferentes campos y con numerosas ventajas frente a otros métodos analíticos convencionales, como son el uso de pequeños volúmenes de muestra y reactivos, su sensibilidad y su rápida respuesta, sin necesidad de pretratamiento de la muestra, equipos caros o personal especializado. Sin embargo, se trata de un campo de investigación relativamente nuevo en el que todavía queda mucho camino por andar. Esta Tesis doctoral pretende aportar un granito de arena a este campo de conocimiento mediante el estudio del potencial de diferentes materiales porosos como transductores para el desarrollo de biosensores ópticos con respuesta en tiempo real y sin marcajes. Los materiales propuestos van desde aquellos artificialmente sintetizados, como silicio poroso (SiP), nanofibras (NFs) poliméricas o membranas poliméricas comerciales, hasta materiales naturales con propiedades fotónicas que todavía no habían sido explotadas para el sensado, como son los exoesqueletos de biosílice de diatomeas. Todos ellos tienen en común la simplicidad en su obtención, evitando costosos y laboriosos procesos de nanofabricación. Para su estudio, se analizará su respuesta óptica y, en aquellos casos en los que ésta permita llevar a cabo experimentos de detección, se desarrollarán estrategias para su biofuncionalización y su implementación en experimentos de biosensado. En el caso del SiP y las NFs se han optimizado los parámetros de fabricación para obtener una respuesta óptica adecuada que permita su interrogación. A continuación, se ha llevado a cabo su biofuncionalización empleando métodos covalentes y no covalentes, así como diferentes bioreceptores (aptámeros de ADN y anticuerpos) para estudiar su potencial y sus limitaciones como biosensores. En el caso de las membranas comerciales y el exoesqueleto de sílice de diatomeas, se ha caracterizado su respuesta óptica y se han llevado a cabo experimentos de sensado de índice de refracción para estudiar su sensibilidad. Así mismo, se ha desarrollado un método de funcionalización de la superficie del exoesqueleto de diatomeas basado en el uso de polielectrolitos catiónicos. Como resultado, se ha demostrado el potencial tanto de NFs para el desarrollo de biosensores, como el de membranas comerciales para sensores cuya aplicación no requiera una elevada sensibilidad pero sí un bajo coste. Además, se ha puesto de manifiesto el gran potencial del exoesqueleto de diatomeas para el desarrollo de sensores basados en su respuesta óptica. Por el contrario, las limitaciones encontradas en el desarrollo de biosensores basados en SiP han evidenciado la necesidad de un estudio riguroso y la optimización de la estructura de materiales porosos previamente a ser usados en (bio)sensado. / [CA] Els biosensors són dispositius analítics amb aplicabilitat en diferents camps i amb nombrosos avantatges enfront d'altres mètodes analítics convencionals, com són l'ús de xicotets volums de mostra i reactius, la seua sensibilitat i la seua ràpida resposta, sense necessitat de pretractament de la mostra, equips cars o personal especialitzat. No obstant això, es tracta d'un camp d'investigació relativament nou en el qual encara queda molt camí per fer. Aquesta Tesi doctoral pretén aportar el seu òbol a aquest camp de coneixement mitjançant l'estudi del potencial de diferents materials porosos com a transductors per al desenvolupament de biosensors òptics amb resposta en temps real i sense marcatges. Els materials proposats van des d'aquells artificialment sintetitzats, com a silici porós (SiP), nanofibras (NFs) polimèriques o membranes polimèriques comercials, fins a materials naturals amb propietats fotòniques que encara no havien sigut explotades per al sensat, com són els exoesquelets de biosílice de diatomees. Tots ells tenen en comú la simplicitat en la seua obtenció, evitant costosos i laboriosos processos de nanofabricació. Per al seu estudi, s'analitzarà la seua resposta òptica i, en aquells casos en els quals aquesta permeta dur a terme experiments de detecció, es desenvoluparan estratègies per a la seua biofuncionalizació i la seua implementació en experiments de biosensat. En el cas del SiP i les NFs s'han optimitzat els paràmetres de fabricació per a obtenir una resposta òptica adequada que permeta la seua interrogació. A continuació, s'ha dut a terme la seua biofuncionalizació emprant mètodes covalents i no covalents, així com diferents bioreceptors (aptàmers d'ADN i anticossos) per a estudiar el seu potencial i les seues limitacions com a biosensors. En el cas de les membranes comercials i l'exoesquelet de sílice de diatomees, s'ha caracteritzat la seua resposta òptica i s'han dut a terme experiments de sensat d'índex de refracció per a estudiar la seua sensibilitat. Així mateix, s'ha desenvolupat un mètode de funcionalizació de la superfície de l'exoesquelet de diatomees basat en l'ús de polielectròlits catiònics. Com a resultat, s'ha demostrat el potencial tant de NFs per al desenvolupament de biosensors, com el de membranes comercials per a sensors amb una aplicació que no requerisca una elevada sensibilitat però sí un baix cost. A més, s'ha posat de manifest el gran potencial de l'exoesquelet de diatomees per al desenvolupament de sensors basats en la seua resposta òptica. Per contra, les limitacions trobades en el desenvolupament de biosensors basats en SiP han evidenciat la necessitat d'un estudi rigorós i l'optimització de l'estructura dels materials porosos prèviament a ser usats en (bio)sensat. / [EN] Biosensors are analytical devices with application in diverse fields and with several advantages relative to other conventional methods, such as the use of small volumes of sample and reagents, their sensitivity and their fast response, without the need of the sample pretreatment, expensive equipments or specialised technicians. Nevertheless, this is a relatively new research field in which there is a long way to go yet. This doctoral Thesis aims at doing its bit to this field of knowledge by studying the potential of different porous materials as transducers for the development of real-time and label-free optical biosensors. The proposed materials range from those artificially synthesised, such as porous silicon (pSi), polymeric nanofibres (NFs) or commercial polymeric membranes, to natural materials with photonic properties that had not been exploited for sensing yet, such as biosilica exoskeletons of diatoms. All of them have in common its simple production, avoiding expensive and laborious nanofabrication processes. For their study, their optical response will be analysed and, in those cases in which such optical response allows performing detection experiments, strategies for their biofunctionalisation and their implementation in biosensing experiments will be developed as well. Regarding pSi and NFs, the fabrication parameters were optimised to get a suitable optical response for their interrogation. Afterwards, their surface functionalisation was carried out by covalent and non-covalent methods, as well as different bioreceptors (DNA aptamers and antibodies), to study their potential and their constraints as biosensors. Concerning commercial membranes and the biosilica exoskeleton of diatoms, their optical response was characterised and refractive index sensing experiments were carried out to study their sensitivity. Additionally, a biofunctionalisation method for the surface of the diatoms exoskeleton was developed based on the use of cationic polyelectrolytes. As a result, it was demonstrated the potential of NFs for the development of biosensors, as well as the potential of commercial membranes for developing sensors for an application that does not require a high sensitivity but a low cost. Furthermore, the great potential of biosilica exoskeleton of diatoms for the development of sensors based on their optical response has been revealed. By contrast, the constraints found in the development of pSi illustrate the importance of an accurate study and optimisation of porous materials structure before using them for (bio)sensing. / Martínez Pérez, P. (2021). Development and Optimization of Experimental Biosensing Protocols Using Porous Optical Transducers [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172541 / TESIS

The present Doctoral Thesis focuses on the investigation, characterization and influence of polyacrylic materials in different scientific and technological disciplines via a detailed computer simulation using the Molecular Dynamics (MD) technique, in conjunction with the very accurate, all-atom Dreiding force-field. The main research concepts and objectives are discussed and analyzed in three separate parts. In the first part, atomistic configurations of two model pressure-sensitive acrylic adhesives (PSAs), the atactic homopolymer poly(n-BA) [poly(n-butyl acrylate)] and the atactic copolymer poly(n-BA-co-AA) [poly(n-butyl acrylate-co-acrylic acid)] in the bulk phase or confined between two selected substrates, glassy silica (SiO2) and metallic α-ferrite (α-Fe), were built and simulated by MD in the NPT statistical ensemble. First, an equilibration cycle consisting of temperature annealings and coolings was followed, in order to generate well-equilibrated configurations of the PSA systems. Detailed results from the atomistic simulations are presented concerning their volumetric behavior, glass transition temperature, conformational, structural, viscoelastic and dynamic properties. Particular emphasis was given to the analysis and characterization of the hydrogen bonds that form in the poly(n-BA-co-AA) system. By analyzing the MD trajectories, poly(n-BA-co-AA) was found to exhibit a higher density than poly(n-BA) by about 7% at all temperatures, to be characterized by smaller-size chains for a given molecular weight (MW), to exhibit significantly slower terminal and segmental dynamics properties, and to be characterized by a glass transition temperature that was approximately 40% higher than that of poly(n-BA). We also examined the type and degree of adsorption of the two acrylic systems on the selected substrates by analyzing the MD results for the local mass density as a function of distance from the solid plane and the distribution of adsorbed chain segments in train, loop, and tail conformations, and by computing the work of adhesion at the two substrates. The results revealed a stronger adsorption for both acrylics on the SiO2 surface due to highly attractive interactions between polymer molecules and substrate atoms, and as a consequence a higher value for the work of adhesion compared to that on the α-Fe surface. Furthermore, we have developed a generalized non-equilibrium molecular dynamics (NEMD) algorithm to simulate the mechanical response of the two adhesives under a uniaxial stretching deformation. In the second part of the Thesis, results have been obtained from a hierarchical simulation methodology that led to the prediction of the thermodynamic, conformational, structural, dynamic and mechanical properties of two polymer nanocomposites based on syndiotactic poly(methyl methacrylate) or sPMMA. The first was reinforced with uniformly dispersed graphene sheets and the second with fullerene particles. How graphene functionalization affects the elastic constants of the resulting nanocomposite has also been examined. The phase behavior of the nanocomposite (in particular as we varied the relative size between the sPMMA chains and the diameter of fullerene molecules) has also been studied as a function of fullerene volume fraction. The simulation strategy entailed three steps: 1) Generation of an initial structure, which was then subjected to potential energy minimization and detailed molecular dynamics (MD) simulations at T = 500K and P = 1atm to obtain well relaxed melt configurations of the nanocomposite. 2) Gradual cooling of selected configurations down to room temperature to obtain a good number of structures representative of the glassy phase of the polymer nanocomposite. 3) Molecular mechanics (MM) calculations of its mechanical properties following the method originally proposed by Theodorou and Suter. By analyzing the results under constant temperature and pressure, all nanocomposite systems were found to exhibit slower terminal and segmental relaxation dynamics than the pure polymer matrices. The addition of a small fraction of graphene sheets led in all cases to the enhancement of the elastic constants; this was significantly more pronounced in the case of functionalized graphene sheets. We further mention that, for all polymer/fullerene nanocomposites addressed here, no phase separation or variation of polymer chain dimensions was observed as a function of fullerene size and/or fullerene volume fraction. In the third part of the Thesis, and motivated by the use of acrylic polymers for the design of membranes with aligned carbon nanotubes (CNTs) for several separation technologies (such as water desalination and wastewater treatment), we report results from a detailed computer simulation study for the nano-sorption and mobility of four different small molecules (water, tyrosol, vanillic acid, and p-coumaric acid) inside smooth single-wall CNTs (SWCNTs). Most of the results have been obtained with the molecular dynamics (MD) method, but especially for the most narrow of the CNTs considered, the results for water molecule were further confirmed through an additional Grand Canonical (μVT) Monte Carlo (GCMC) simulation using a value for the water chemical potential μ pre-computed with the particle deletion method. Issues addressed in the Thesis include molecular packing and ordering inside the nanotube for the four molecules, average number of sorbed molecules per unit length of the tube, and mean residence time and effective axial diffusivities, all as a function of tube diameter and tube length. In all cases, a strong dependence of the results on carbon nanotube diameter was observed, especially in the way the different molecules are packed and organized inside the CNT. For water for which predictions of properties such as local structure and packing were computed with both methods (MD and GCMC), the two sets of results were found to be fully self-consistent for all types of SWCNTs considered. Water diffusivity inside the CNT (although, strongly dependent on the CNT diameter) was computed with two different methods, both of which gave identical results. For large enough CNT diameters (larger than about 13 Å), this was found to be higher than the corresponding experimental value in the bulk by about 55%. Surprisingly enough, for the rest of the (phenolic) molecules simulated in this Thesis, the simulations revealed no signs of mobility inside nanotubes with a diameter smaller than the (20, 20) tube. This has been attributed to strong phenyl-phenyl attractive interactions, also to favorable interactions of these molecules with the CNT walls, which cause them to form highly ordered, very stable structures inside the nanotube, especially under strong confinement. The interaction, in particular, of the methyl group (present in tyrosol, vanillic acid, and p-coumaric acid) with the CNT walls seems to play a key role in all these compounds causing them to remain practically immobile inside nanotubes characterized by diameters smaller than about 26 Å. It was only for larger-diameter CNTs that tyrosol, vanillic acid, and p-coumaric acid were observed to demonstrate appreciable mobility. / Η παρούσα Διδακτορική Διατριβή εστιάζει στη μελέτη της σχέσης μεταξύ δομής και μακροσκοπικών φυσικών ιδιοτήτων υλικών από πολυακρυλικά μέσω μίας λεπτομερούς προσομοίωσης στον υπολογιστή με τη μέθοδο της Μοριακής Δυναμικής (ΜΔ), σε συνδυασμό με ένα πολύ επακριβές πεδίο δυνάμεων (το Dreiding) σε ατομιστική λεπτομέρεια. Οι κύριες ερευνητικές έννοιες καθώς και οι στόχοι συζητιούνται και αναλύονται σε τρία ξεχωριστά μέρη. Στο πρώτο μέρος, ατομιστικές απεικονίσεις δύο προτύπων πίεσο-ευαίσθητων συγκολλητικών υλικών (acrylic pressure sensitive adhesives ή PSAs), του ατακτικού πολυ-βουτυλικού-ακρυλικού εστέρα (poly(n-BA)) και του συμπολυμερούς του με ακρυλικό οξύ (poly(n-BA-co-AA)), τόσο μακριά όσο και κοντά σε υποστρώματα σίλικας (SiO2) και α-φερρίτη (α-Fe), μελετήθηκαν στη βάση ενός φάσματος ιδιοτήτων (θερμοδυναμικές, δομικές, ιξωδοελαστικές, δυναμικές, και συγκολλητικές), όπως και η μηχανική τους απόκριση υπό συνθήκες μονοαξονικής εκτατικής παραμόρφωσης. Στο δεύτερο μέρος παρουσιάζονται τα αποτελέσματα που εξήχθησαν από μία ιεραρχική μεθοδολογία προσομοίωσης που οδήγησε στην πρόβλεψη της φασικής συμπεριφοράς και των μηχανικών ιδιοτήτων νανοσύνθετων πολυμερικών υλικών (polymer nanocomposites ή PNCs) βασισμένων στο συνδιοτατκτικό πολυ-μεθακρυλικό μεθυλεστέρα (syndiotactic poly(methyl methacrylate) ή sPMMA), ενισχυμένο με ομοιόμορφα διεσπαρμένα φύλλα γραφενίου (graphene sheets) ή σωματίδια φουλερενίου (fullerene particles). Στο τρίτο μέρος, υποκινούμενοι από τη χρήση των ακρυλικών πολυμερών στο σχεδιασμό μεμβρανών με ενσωματωμένους ευθυγραμμισμένους νανοσωλήνες άνθρακα (ΝΑ, carbon nanotubes ή CNTs) σε διάφορες τεχνολογίες διαχωρισμού μορίων (με έμφαση στον καθαρισμό του νερού), παρουσιάζουμε αποτελέσματα από προσομοιώσεις, για τη νανο-ρόφηση και την κινητικότητα τεσσάρων διαφορετικών μικρών μορίων (water, tyrosol, vanilic acid, και p-coumaric acid) στο εσωτερικό λείων μονο-στρωματικών ΝΑ (single-wall CNTs ή SWCNTs). Τα θέματα που εξετάζονται περιλαμβάνουν τη μοριακή διευθέτηση και τη διάταξη στο εσωτερικό Ν.Α. των τεσσάρων μορίων, το μέσο χρόνο παραμονής τους, καθώς και τους αξονικούς συντελεστές διάχυσής του, συναρτήσει της διαμέτρου και του μήκους των ΝΑ.