A theoretical approach to the engineering of bioinspired systems: design, applications & information management

Premi extraordinari doctorat curs 2010-2011, àmbit d’Enginyeria Enginyeria IndustrialL’enginyeria de sistemes bioinspirats ha crescut en importància i nombre d’aplicacions en el últims anys, atraient l’atenció dels científics sobre els seus usos potencials en camps com ara la bionanotecnologia, la nanomedicina i la ciència de materials. En aquesta tesis, es presenta una aproximació mitjançant mètodes computacionals a l’enginyeria de sistemes biomimètics. Em posat la nostra èmfasi en l’estudi teòric basat en principis fonamentals de sistemes peptídics, això vol dir des de mètodes mecànic quàntics d’alt nivell per als elements més bàsics fins a la simulació de tot o part del sistema en un ambient més realista a partir de diferents aproximacions computacionals. Un altre objectiu del present treball és la recopilació exhaustiva de la informació derivada dels estudis fets així com dels potencials usos en un sistema informàtic orientat a l’usuari d’emmagatzemament de dades. S’han caracteritzat anàlegs conformacionalment restringits de l’arginina, prolina i fenilalanina a través de càlculs mecànic quàntics d’alt nivell. Aquest aminoàcids no codificats (és a dir que no estan entre els 20 aminoàcids naturals) han demostrat la seva capacitat de modulació del perfil conformacional dels pèptids a on són introduïts. A més a més, indueixen resistència a l’acció de les proteases a banda d’introduir noves propietats electròniques i espectroscòpiques útils en aplicacions tals com els sistemes de diagnòstic, alliberadors de fàrmacs i del camp de l’enginyeria de materials. Els aminoàcids obtinguts són emprats per a modificar pèptids de “homing”, blocs proteics autoagregants i superfícies actives recobertes de pèptids. La remarcable quantitat d’informació sobre aminoàcids no codificats accessible en publicacions científiques expressa la necessitat urgent de sistemes que, basant-se en ordinadors recopilin, organitzin i ofereixin aquesta informació de manera intel·ligible per a l’usuari final. Una base de dades ha estat dissenyada, creada i posada en funcionament per tal d’emmagatzemar dades conformacionals teòriques sobre aminoàcids no codificats. La base de dades també conté, en cas que la informació sigui accessible, dades experimentals referents a aplicacions, caracterització estructural i propietats espectroscòpiques. En resum, aquests treball ofereix un nou enfoc a l’enginyeria assistida per ordinador i la gestió de la informació de sistemes bioinspirats des de les seves unitats més elementals fins al disseny de les aplicacions de major complexitatThe engineering of systems inspired by biochemical molecules has grown in importance and number of applications in the recent years, focusing the researchers’ attention in its potential uses in fields such as nanotechnology, bionanotechnology, nanomedicine and material sciencie. A computational approach to engineering of biomimetic systems is presented in this work. Our emphasis is put on theoretical studies of some peptidic systems from scratch, this means from the use high level quantum mechanics studies of their primary building blocks to the simulation using different computational approaches of their behavior as part of an entire system in a more realistic environment. The thorough compilation of the derived information and its potential uses in a proper user-friendly data-storage support is also a question dealt in the thesis. Conformationaly restricted analogues of arginine, proline and phenylalanine amino acids are designed and fully characterized using high level quantum mechanics methods. These new non-coded amino acids (non-naturally occurring amino acids in proteins) demonstrate to modulate the conformational profile of peptides where they are inserted. Furthermore, they induce resistance to proteolysis altogether with new electronic and spectroscopic features useful in diagnostics, drug delivery and material engineering. The developed non-coded amino acids are used to engineer systems such as homing peptides, self-aggregating protein building blocks and peptide-coated active surfaces. The remarkable amount of information available about non-coded amino acids in scientific publications stressed out the dire need of computer-based systems to gather, to organize and to display in a user-friendly way the information about these compounds. A data base has been designed, implemented and run to store theoretically-obtained conformational information on non-coded amino acids. The data bases also contains, if available, experimentallyacquired knowledge such us structural and spectroscopic characterizations and reported applications. To conclude, this thesis offers a successful approach to the computer-aided engineering and information management of bioinspired systems from their basics to high complexity design.Award-winningPostprint (published version

Effects of hydroxyapatite (0001) Ca2+/Mg2+ substitution on adsorbed D-ribose ring puckering

Advanced Molecular Dynamics (MD) simulation protocols have been used to assess the ring puckering of cyclic D-ribose when the sugar is adsorbed on the most stable (0001) facet of calcium hydroxyapatite (HAp). In addition, sugar¿mineral interactions, which are crucial for transfection processes and prebiotic chemistry, have been studied for systems in which the Ca2+ ions of the above mentioned HAp facet were totally or partially replaced by Mg2+. The latter replacement is spatially and quantitatively limited and has been found to cause important alterations in the conformational behavior of D-ribose that are similar to those suffered in hairpin RNA from A to B helical structures. Accordingly, replacement of Ca2+ by Mg2+ has a dramatic effect on the functionality of the nucleic acid. These changes have been related to both the substitution site on the surface and the amount of ions. Our results show that when replacement by Mg2+ occurs in OH--coordinated Ca2+ ions, Mg2+¿D-ribose interactions are strong enough to prevent the interactions between the hydroxyl groups of the sugar and the remaining Ca2+ ions.Peer ReviewedPostprint (published version

Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif

Self-assembly in aqueous solution has been investigated for two Fmoc [Fmoc ¼ N-(fluorenyl)-9-methoxycarbonyl] tetrapeptides comprising the RGDS cell adhesion motif from fibronectin or the scrambled sequence GRDS. The hydrophobic Fmoc unit confers amphiphilicity on the molecules, and introduces aromatic stacking interactions. Circular dichroism and FTIR spectroscopy show that the self-assembly of both peptides at low concentration is dominated by interactions among Fmoc units, although Fmoc-GRDS shows b-sheet features, at lower concentration than Fmoc-RGDS. Fibre X-ray diffraction indicates b-sheet formation by both peptides at sufficiently high concentration. Strong alignment effects are revealed by linear dichroism experiments for Fmoc-GRDS. Cryo-TEM and smallangle X-ray scattering (SAXS) reveal that both samples form fibrils with a diameter of approximately 10 nm. Both Fmoc-tetrapeptides form self-supporting hydrogels at sufficiently high concentration. Dynamic shear rheometry enabled measurements of the moduli for the Fmoc-GRDS hydrogel, however syneresis was observed for the Fmoc-RGDS hydrogel which was significantly less stable to shear. Molecular dynamics computer simulations were carried out considering parallel and antiparallel b-sheet configurations of systems containing 7 and 21 molecules of Fmoc-RGDS or Fmoc-GRDS, the results being analyzed in terms of both intermolecular structural parameters and energy contributions

Permanently polarized hydroxyapatite for selective electrothermal catalytic conversion of carbon dioxide into ethanol

Conversion of CO2 into valuable chemicals is not only a very challenging topic but also a socially demanding issue. In this work, permanently polarized hydroxyapatite obtained using a thermal stimulated polarization process is proposed as a highly selective catalyst for green production of ethanol starting from CO2 and CH4.Peer ReviewedPostprint (author's final draft

Biominerals formed by DNA and calcium oxalate or hydroxyapatite: a comparative study

Biominerals formed by DNA and calcium oxalate (CaOx) or hydroxyapatite (HAp), the most important and stable phase of calcium phosphate) have been examined and compared using a synergistic combination of computer simulation and experimental studies. The interest of this comparison stems from the medical observation that HAp- and CaOx-based microcalcifications are frequently observed in breast cancer tissues, and some of their features are used as part of the diagnosis. Molecular dynamics simulations show that (1) the DNA double helix remains stable when it is adsorbed onto the most stable facet of HAp, whereas it undergoes significant structural distortions when it is adsorbed onto CaOx; (2) DNA acts as a template for the nucleation and growth of HAp but not for the mineralization of CaOx; and (3) the DNA double helix remains stable when it is encapsulated inside HAp nanopores, but it becomes destabilized when the encapsulation occurs into CaOx nanopores. Furthermore, CaOx and HAp minerals containing DNA molecules inside and/or adsorbed on the surface have been prepared in the lab by mixing solutions containing the corresponding ions with fish sperm DNA. Characterization of the formed minerals, which has been focused on the identification of DNA using UV–vis spectroscopy, indicates that the tendency to adsorb and, especially, encapsulate DNA is much smaller for CaOx than for HAp, which is in perfect agreement with results from molecular dynamics simulations. Finally, quantum mechanical calculations have been performed to rationalize these results in terms of molecular interactions, evidencing the high affinity of Ca2+ toward oxalate anions in an aqueous environment.Postprint (author's final draft

Analysis of nitrogen fixation by a catalyst capable of transforming N2, CO2 and CH4 into amino acids under mild reactions conditions

The processes related to the fixation of nitrogen ina catalyst able to produce glycine and alanine from a N2, CO2and CH4gas mixture at mild reaction conditions have been studied by combining experimental and theoretical investigations.Results have allowed to understand the role of different elements of the catalyst, which is constituted by permanently polarized hydroxyapatite (p-HAp), zirconia, and aminotris(methylenephosphonic acid)(ATMP). ATMP attractsN2moleculestowards the surface,maintainingthem close to the zirconiaand p-HAp componentsthatare the most active from a catalytic point of view. On the other hand, the associative mechanismisthermodynamicallyfavouredunder mild reaction conditionswith respect to the dissociative one,whichis limited by the barrier associated to the N–Nbondcleavage. Because this reaction mechanism is similar to that employed in the nitrogen fixation bynitrogenase enzymes, thesefindingsprovide an opportunity to designnew bioinspired catalystsPostprint (author's final draft

Dissolving hydroxyolite: a DNA molecule into its hydroxyapatite mold

In spite of the clinical importance of hydroxyapatite (HAp), the mechanism that controls its dissolution in acidic environments remains unclear. Knowledge of such a process is highly desirable to provide better understanding of different pathologies, as for example osteoporosis, and of the HAp potential as vehicle for gene delivery to replace damaged DNA. In this work, the mechanism of dissolution in acid conditions of HAp nanoparticles encapsulating double-stranded DNA has been investigated at the atomistic level using computer simulations. For this purpose, four consecutive (multi-step) molecular dynamics simulations, involving different temperatures and proton transfer processes, have been carried out. Results are consistent with a polynuclear decalcification mechanism in which proton transfer processes, from the surface to the internal regions of the particle, play a crucial role. In addition, the DNA remains protected by the mineral mold and transferred proton from both temperature and chemicals. These results, which indicate that biomineralization imparts very effective protection to DNA, also have important implications in other biomedical fields, as for example in the design of artificial bones or in the fight against osteoporosis by promoting the fixation of Ca2+ ions.Peer ReviewedPostprint (published version

Mineralization of DNA into nanoparticles of hydroxyapatite

Encapsulation of DNA into hydroxyapatite (HAp) has been investigated using a rational approach that involves computer simulation and experimental techniques. The temporal evolution of the radial distribution functions derived from atomistic molecular dynamics simulations of Ca2+, PO4 3− and OH−-containing aqueous solutions in the presence and absence of B-DNA has been used to conclude that the backbone of the double helix acts as a template for HAp growth. More specifically, results reveal the formation of calcium phosphate clusters at the first stages of the simulations, which subsequently reorganize to nucleate HAp. This effect is produced in the absence and, especially, presence, of DNA indicating that the biomolecules do not inhibit but even promote mineral growth. Furthermore, computer simulations suggest that the diffusion of the OH− anions through the inorganic solution is the limiting step for the nucleation of the biomineral. Nanocapsules and crystalline nanorods of HAp containing DNA molecules inside have been prepared by mixing solutions containing Ca2+ and PO4 3− ions with fish sperm DNA at high pH. The dimensions and morphology of such nanostructures have been examined by transmission electron microscopy, while the characterization of the biomineral has been focused on the identification of DNA inside HAp using infrared, X-ray photoelectron and UV-vis spectroscopies, as well as gel electrophoresis. The biominerals reported in this work are important for biomedical applications requiring the protection of DNA from aggressive environmental conditionsPostprint (published version

Design of New Dispersants Using Machine Learning and Visual Analytics

Artificial intelligence (AI) is an emerging technology that is revolutionizing the discovery of new materials. One key application of AI is virtual screening of chemical libraries, which enables the accelerated discovery of materials with desired properties. In this study, we developed computational models to predict the dispersancy efficiency of oil and lubricant additives, a critical property in their design that can be estimated through a quantity named blotter spot. We propose a comprehensive approach that combines machine learning techniques with visual analytics strategies in an interactive tool that supports domain experts’ decision-making. We evaluated the proposed models quantitatively and illustrated their benefits through a case study. Specifically, we analyzed a series of virtual polyisobutylene succinimide (PIBSI) molecules derived from a known reference substrate. Our best-performing probabilistic model was Bayesian Additive Regression Trees (BART), which achieved a mean absolute error of (Formula presented.) and a root mean square error of (Formula presented.), as estimated through 5-fold cross-validation. To facilitate future research, we have made the dataset, including the potential dispersants used for modeling, publicly available. Our approach can help accelerate the discovery of new oil and lubricant additives, and our interactive tool can aid domain experts in making informed decisions based on blotter spot and other key propertie

Taking the pulse of Earth's tropical forests using networks of highly distributed plots

Tropical forests are the most diverse and productive ecosystems on Earth. While better understanding of these forests is critical for our collective future, until quite recently efforts to measure and monitor them have been largely disconnected. Networking is essential to discover the answers to questions that transcend borders and the horizons of funding agencies. Here we show how a global community is responding to the challenges of tropical ecosystem research with diverse teams measuring forests tree-by-tree in thousands of long-term plots. We review the major scientific discoveries of this work and show how this process is changing tropical forest science. Our core approach involves linking long-term grassroots initiatives with standardized protocols and data management to generate robust scaled-up results. By connecting tropical researchers and elevating their status, our Social Research Network model recognises the key role of the data originator in scientific discovery. Conceived in 1999 with RAINFOR (South America), our permanent plot networks have been adapted to Africa (AfriTRON) and Southeast Asia (T-FORCES) and widely emulated worldwide. Now these multiple initiatives are integrated via ForestPlots.net cyber-infrastructure, linking colleagues from 54 countries across 24 plot networks. Collectively these are transforming understanding of tropical forests and their biospheric role. Together we have discovered how, where and why forest carbon and biodiversity are responding to climate change, and how they feedback on it. This long-term pan-tropical collaboration has revealed a large long-term carbon sink and its trends, as well as making clear which drivers are most important, which forest processes are affected, where they are changing, what the lags are, and the likely future responses of tropical forests as the climate continues to change. By leveraging a remarkably old technology, plot networks are sparking a very modern revolution in tropical forest science. In the future, humanity can benefit greatly by nurturing the grassroots communities now collectively capable of generating unique, long-term understanding of Earth's most precious forests. Resumen Los bosques tropicales son los ecosistemas más diversos y productivos del mundo y entender su funcionamiento es crítico para nuestro futuro colectivo. Sin embargo, hasta hace muy poco, los esfuerzos para medirlos y monitorearlos han estado muy desconectados. El trabajo en redes es esencial para descubrir las respuestas a preguntas que trascienden las fronteras y los plazos de las agencias de financiamiento. Aquí mostramos cómo una comunidad global está respondiendo a los desafíos de la investigación en ecosistemas tropicales a través de diversos equipos realizando mediciones árbol por árbol en miles de parcelas permanentes de largo plazo. Revisamos los descubrimientos más importantes de este trabajo y discutimos cómo este proceso está cambiando la ciencia relacionada a los bosques tropicales. El enfoque central de nuestro esfuerzo implica la conexión de iniciativas locales de largo plazo con protocolos estandarizados y manejo de datos para producir resultados que se puedan trasladar a múltiples escalas. Conectando investigadores tropicales, elevando su posición y estatus, nuestro modelo de Red Social de Investigación reconoce el rol fundamental que tienen, para el descubrimiento científico, quienes generan o producen los datos. Concebida en 1999 con RAINFOR (Suramérica), nuestras redes de parcelas permanentes han sido adaptadas en África (AfriTRON) y el sureste asiático (T-FORCES) y ampliamente replicadas en el mundo. Actualmente todas estas iniciativas están integradas a través de la ciber-infraestructura de ForestPlots.net, conectando colegas de 54 países en 24 redes diferentes de parcelas. Colectivamente, estas redes están transformando nuestro conocimiento sobre los bosques tropicales y el rol de éstos en la biósfera. Juntos hemos descubierto cómo, dónde y porqué el carbono y la biodiversidad de los bosques tropicales está respondiendo al cambio climático y cómo se retroalimentan. Esta colaboración pan-tropical de largo plazo ha expuesto un gran sumidero de carbono y sus tendencias, mostrando claramente cuáles son los factores más importantes, qué procesos se ven afectados, dónde ocurren los cambios, los tiempos de reacción y las probables respuestas futuras mientras el clima continúa cambiando. Apalancando lo que realmente es una tecnología antigua, las redes de parcelas están generando una verdadera y moderna revolución en la ciencia tropical. En el futuro, la humanidad puede beneficiarse enormemente si se nutren y cultivan comunidades de investigadores de base, actualmente con la capacidad de generar información única y de largo plazo para entender los que probablemente son los bosques más preciados de la tierra. Resumo Florestas tropicais são os ecossistemas mais diversos e produtivos da Terra. Embora uma boa compreensão destas florestas seja crucial para o nosso futuro coletivo, até muito recentemente os esforços de medições e monitoramento foram amplamente desconexos. É essencial formarmos redes para obtermos respostas que transcendem fronteiras e horizontes de agências financiadoras. Neste estudo nós mostramos como uma comunidade global está respondendo aos desafios da pesquisa de ecossistemas tropicais, com equipes diversas medindo florestas, árvore por árvore, em milhares de parcelas monitoradas à longo prazo. Nós revisamos as maiores descobertas científicas deste trabalho, e mostramos também como este processo está mudando a ciência de florestas tropicais. Nossa abordagem principal envolve unir iniciativas de base a protocolos padronizados e gerenciamento de dados a fim de gerar resultados robustos em escalas ampliadas. Ao conectar pesquisadores tropicais e elevar seus status, nosso modelo de Rede de Pesquisa Social reconhece o papel-chave do produtor dos dados na descoberta científica. Concebida em 1999 com o RAINFOR (América do Sul), nossa rede de parcelas permanentes foi adaptada para África (AfriTRON) e Sudeste asiático (T-FORCES), e tem sido extensamente reproduzida em todo o mundo. Agora estas múltiplas iniciativas estão integradas através de uma infraestrutura cibernética do ForestPlots.net, conectando colegas de 54 países de 24 redes de parcelas. Estas iniciativas estão transformando coletivamente o entendimento das florestas tropicais e seus papéis na biosfera. Juntos nós descobrimos como, onde e por que o carbono e a biodiversidade da floresta estão respondendo às mudanças climáticas, e seus efeitos de retroalimentação. Esta duradoura colaboração pantropical revelou um grande sumidouro de carbono persistente e suas tendências, assim como tem evidenciado quais direcionadores são mais importantes, quais processos florestais são mais afetados, onde eles estão mudando, seus atrasos no tempo de resposta, e as prováveis respostas das florestas tropicais conforme o clima continua a mudar. Dessa forma, aproveitando uma notável tecnologia antiga, redes de parcelas acendem faíscas de uma moderna revolução na ciência das florestas tropicais. No futuro a humanidade pode se beneficiar incentivando estas comunidades basais que agora são coletivamente capazes de gerar conhecimentos únicos e duradouros sobre as florestas mais preciosas da Terra. Résume Les forêts tropicales sont les écosystèmes les plus diversifiés et les plus productifs de la planète. Si une meilleure compréhension de ces forêts est essentielle pour notre avenir collectif, jusqu'à tout récemment, les efforts déployés pour les mesurer et les surveiller ont été largement déconnectés. La mise en réseau est essentielle pour découvrir les réponses à des questions qui dépassent les frontières et les horizons des organismes de financement. Nous montrons ici comment une communauté mondiale relève les défis de la recherche sur les écosystèmes tropicaux avec diverses équipes qui mesurent les forêts arbre après arbre dans de milliers de parcelles permanentes. Nous passons en revue les principales découvertes scientifiques de ces travaux et montrons comment ce processus modifie la science des forêts tropicales. Notre approche principale consiste à relier les initiatives de base à long terme à des protocoles standardisés et une gestion de données afin de générer des résultats solides à grande échelle. En reliant les chercheurs tropicaux et en élevant leur statut, notre modèle de réseau de recherche sociale reconnaît le rôle clé de l'auteur des données dans la découverte scientifique. Conçus en 1999 avec RAINFOR (Amérique du Sud), nos réseaux de parcelles permanentes ont été adaptés à l'Afrique (AfriTRON) et à l'Asie du Sud-Est (T-FORCES) et largement imités dans le monde entier. Ces multiples initiatives sont désormais intégrées via l'infrastructure ForestPlots.net, qui relie des collègues de 54 pays à travers 24 réseaux de parcelles. Ensemble, elles transforment la compréhension des forêts tropicales et de leur rôle biosphérique. Ensemble, nous avons découvert comment, où et pourquoi le carbone forestier et la biodiversité réagissent au changement climatique, et comment ils y réagissent. Cette collaboration pan-tropicale à long terme a révélé un important puits de carbone à long terme et ses tendances, tout en mettant en évidence les facteurs les plus importants, les processus forestiers qui sont affectés, les endroits où ils changent, les décalages et les réactions futures probables des forêts tropicales à mesure que le climat continue de changer. En tirant parti d'une technologie remarquablement ancienne, les réseaux de parcelles déclenchent une révolution très moderne dans la science des forêts tropicales. À l'avenir, l'humanité pourra grandement bénéficier du soutien des communautés de base qui sont maintenant collectivement capables de générer une compréhension unique et à long terme des forêts les plus précieuses de la Terre. Abstrak Hutan tropika adalah di antara ekosistem yang paling produktif dan mempunyai kepelbagaian biodiversiti yang tinggi di seluruh dunia. Walaupun pemahaman mengenai hutan tropika amat penting untuk masa depan kita, usaha-usaha untuk mengkaji dan mengawas hutah-hutan tersebut baru sekarang menjadi lebih diperhubungkan. Perangkaian adalah sangat penting untuk mencari jawapan kepada soalan-soalan yang menjangkaui sempadan dan batasan agensi pendanaan. Di sini kami menunjukkan bagaimana sebuah komuniti global bertindak balas terhadap cabaran penyelidikan ekosistem tropika melalui penglibatan pelbagai kumpulan yang mengukur hutan secara pokok demi pokok dalam beribu-ribu plot jangka panjang. Kami meninjau semula penemuan saintifik utama daripada kerja ini dan menunjukkan bagaimana proses ini sedang mengubah bidang sains hutan tropika. Teras pendekatan kami memberi tumpuan terhadap penghubungan inisiatif akar umbi jangka panjang dengan protokol standar serta pengurusan data untuk mendapatkan hasil skala besar yang kukuh. Dengan menghubungkan penyelidik-penyelidik tropika dan meningkatkan status mereka, model Rangkaian Penyelidikan Sosial kami mengiktiraf kepentingan peranan pengasas data dalam penemuan saintifik. Bermula dengan pengasasan RAINFOR (Amerika Selatan) pada tahun 1999, rangkaian-rangkaian plot kekal kami kemudian disesuaikan untuk Afrika (AfriTRON) dan Asia Tenggara (T-FORCES) dan selanjutnya telah banyak dicontohi di seluruh dunia. Kini, inisiatif-inisiatif tersebut disepadukan melalui infrastruktur siber ForestPlots.net yang menghubungkan rakan sekerja dari 54 negara di 24 buah rangkaian plot. Secara kolektif, rangkaian ini sedang mengubah pemahaman tentang hutan tropika dan peranannya dalam biosfera. Kami telah bekerjasama untuk menemukan bagaimana, di mana dan mengapa karbon serta biodiversiti hutan bertindak balas terhadap perubahan iklim dan juga bagaimana mereka saling bermaklum balas. Kolaborasi pan-tropika jangka panjang ini telah mendedahkan sebuah sinki karbon jangka panjang serta arah alirannya dan juga menjelaskan pemandu-pemandu perubahan yang terpenting, di mana dan bagaimana proses hutan terjejas, masa susul yang ada dan kemungkinan tindakbalas hutan tropika pada perubahan iklim secara berterusan di masa depan. Dengan memanfaatkan pendekatan lama, rangkaian plot sedang menyalakan revolusi yang amat moden dalam sains hutan tropika. Pada masa akan datang, manusia sejagat akan banyak mendapat manfaat jika memupuk komuniti-komuniti akar umbi yang kini berkemampuan secara kolektif menghasilkan pemahaman unik dan jangka panjang mengenai hutan-hutan yang paling berharga di dunia