DNA-origami-pohjaiset in vitro -kuljettimet

The field of DNA nanotechnology aims to construct artificial nanoscale structures and functionalized materials from DNA. The rapid development of DNA nanotechnology has inspired researchers to develop various DNA-based drug delivery vehicles. One approach to build complex DNA nanostructures is to use the method of DNA origami, which is discussed in more detail in this thesis. This thesis examines the use of a tubular DNA origami as a cellular delivery vehicle for the transport of Streptavidin-Lucia luciferase enzymes into HEK293 cells in vitro. The correct folding of the origamis was evaluated using agarose gel electrophoresis and transmission electron microscopy. The transfection was studied using confocal microscopy and the activity of the delivered enzymes was detected in the cell lysates using a bioluminescence assay. These DNA origami-enzyme complexes were also coated with varying amounts of different cationic block-copolymers, and the effect of these coatings on the enzyme activity was investigated using the bioluminescence assay. According to the results, the DNA origami delivered the enzymes into cells and the enzymes remained active after transfection. The results also suggest that it is possible to control the enzyme kinetics of the complexes by varying the amount of cationic polymers that coat the DNA origamis. However, the enzymes were found to bind nonspecifically to the origamis, and it remains unclear whether the shape of the origami contributed to the transfection. The stability and integrity of the complexes should be studied more carefully.DNA-nanoteknologia tarkoittaa keinotekoisten nanomittakaavan rakenteiden ja funktionaalisten materiaalien muodostamista DNA:sta. DNA-nanorakenteiden nopea kehitys on innostanut tutkijoita kehittämään niistä erilaisia lääkeainekuljettimia kohdennettuun lääkeannosteluun. Monimutkaisia DNA-rakenteita voidaan muodostaa muun muuassa DNA-origami-tekniikalla, jota käsitellään tässä diplomityössä tarkemmin. Tässä diplomityössä tutkitaan putkimaisen DNA-origamin soveltuvuutta kuljettaa Streptavidin-Lucia luciferase -entsyymejä HEK293-solujen sisään in vitro. Transfektiota tutkittiin konfokaalimikroskoopilla, ja entsyymien aktiivisuutta solujen lysaateissa tarkasteltiin mittaamalla bioluminesenssia. Nämä DNA-origami-entsyymi-kompleksit päällystettiin myös kolmella erilaisella kationisella blokkipolymeerilla. Polymeeripeitteiden vaikutusta entsyymin aktiivisuuteen tutkittiin mittaamalla bioluminesenssia. Tulosten perusteella DNA-origamia voidaan käyttää kuljettamaan entsyymit solun sisään, ja entsyymit säilyttivät aktiivisuutensa transfektion jälkeen. Lisäksi kompleksin entsyymikinetiikkaa voidaan mahdollisesti kontrolloida säätämällä polymeerien määrää päällysteessä. Entsyymi ei kuitenkaan sitoutunut spesifisesti origamiin, ja origamin muoto ei näyttänyt vaikuttavan transfektion tehokkuuteen. Kompleksin stabiilisuutta ja eheyttä on tutkittava tarkemmin

Nucleation of Minerals: Precursors, Intermediates and Their Use in Materials Chemistry

Nucleation is the key event in mineralisation, but a general molecular understanding of phase separation mechanisms is still missing, despite more than 100 years of research in this field. In recent years, many studies have highlighted the occurrence of precursors and intermediates, which seem to challenge the assumptions underlying classical theories of nucleation and growth. This is especially true for the field of biomineralisation, where bio-inspired strategies take advantage of the special properties of the precursors and intermediates for the generation of advanced materials. All of this has led to the development of "non-classical" frameworks, which, however, often lack quantitative expressions for the evaluation and prediction of phase separation, growth and ripening processes, and are under considerable debate. It is thus evident that there is a crucial need for research into the early stages of mineral nucleation and growth, designed for the testing, refinement, and expansion of the different existing notions. This Special Issue of Minerals aims to bring together corresponding studies from all these areas, dealing with precursors and intermediates in mineralisation with the hope that it may contribute to the achievement of a better understanding of nucleation precursors and intermediates, and their target-oriented use in materials chemistry

Maßgeschneiderte Protein Inkapsulierung in einen DNA Käfig mittels geometrisch angeordneter supramolekularer Wechselwirkung

Im Rahmen dieser Dissertation wurden verschiedene Aspekte der DNA-Nanotechnologie, Biologie und der supramolekularen Chemie miteinander verknüpft und zur Anwendung gebracht. Die Arbeit kann in drei Teilbereiche unterteilt werden: (i) Das Designen eines geeigneten hexagonalen turbularen DNA-Käfigs mittels der Software CaDNAno2, dessen räumliche Dimensionen zur Immobilisierung des Proteins DegP in seinen unterschiedlichen Oligomerisierungs-Zuständen entsprechen musste. (ii) (ii) Die Synthese eines Oligonukleotid-Heptapeptid-Konjugates, welches supramolekular an die PDZ1 Domäne des Zielproteins bindet. (iii) (iii) Das Laden des Proteins in den Käfig mit anschließendem Versuch der gerichteten Freisetzung des Proteins. Der DNA-Origami-Käfig wurde mittels der Software CaDNAno2 als einlagiges, turbuläres und hexagonales DNA-Röhrchen mit einem inneren Radius von 20 nm und einem äußeren Radius von 23 nm entworfen und erfolgreich realisiert. Die einzelnen Seitenwände des Käfigs wurden durch jeweils speziell entworfene Oligonukleotide miteinander verknüpft, so dass zum einen die Orientierung der Seitenflächen zum Zentrum der Kavität (6p120 und 6p240) determiniert werden konnte, (vgl. Kapitel 3.2.1 und 3.2.2) und zum anderen durch eine flexible Verbindung der Seitenflächen mittels drei Thyminen eine zufällige Orientierung (6p180) der Seitenflächen zum Zentrum der Kavität vorlag. Zusätzlich wurde jede Seitenfläche mit der Option entworfen, mit null, ein, zwei oder drei (insgesamt 0cA1, 6cA1 oder 18cA1) orthogonal herausragenden Oligonukleotiden (Protruding-Arme), die als Verlängerung von zentral liegenden Oligonukleotiden zu sehen sind, ausgestattet zu werden. Die Protruding-Arme dienen als Träger für die mit Peptiden modifizierten komplementären Oligonukleotid-Liganden (Kapitel 3,3), welche wahlweise mit Fluorescein (Flc-A1-DPMFKLV) oder TAMRA (TAMRA-A1-DPMFKLV) ausgestattet waren. Mittels eines Biotin-modifizierten Liganden konnte durch Zugabe von Streptavidin die korrekte Formation der Konstrukte 6p120, 6p180 und 6p240 durch Gel-Elektrophorese und Raster-Kraft-Mikroskopie (AFM) bestätigt werden. Messungen durch das Transmissions-Elektronen-Mikroskop (durchgeführt von Pascal Lill am MPI in Dortmund im Rahmen seiner Masterarbeit) und der dynamischer Lichtstreuung bestätigten ebenfalls die korrekte Formation in Lösung. Unter Berücksichtigung des antiproportionalen Verhältnisses der Diffusionsrate durch den Käfig zur Größe des Proteins wurde der DNA-Origami-Komplex so geplant, dass das 12-mer des Proteins DegP bevorzugt binden sollte. Die Synthese des Peptidfragmentes der Liganden erfolgte mittels Festphasenpeptidsynthese nach Standardbedingungen. Die N-terminale Aminogruppe der Peptidsequenz konnte direkt in eine Maleimide Funktion überführt werden (Kapitel 6.5.2.8.2). Ohne die Verwendung eines üblichen Crosslinkers konnten Thiol-modifizierte Oligonukleotide über eine kovalente Bindung an das Maleimid gebunden werden. Dieser erfolgreich etablierte Weg stellt somit eine universelle Methode dar, N-terminale Peptide direkt an Thiol-modifizierte Oligonukleotide zu binden. Eine Charakterisierung der Konjugate erfolgte anschließend mittels MALDI-TOF. Das Laden diverser DegP Protein-Varianten (vgl. Kapitel 3.1, Tabelle 1) erfolgte nur in Anwesenheit des Peptid-Liganden (vgl. Kapitel 3.4.3), was die Selektivität der Methode erfolgreich demonstrierte und unspezifische Wechselwirkungen ausschloß. Das spezifische und erfolgreiche Binden an die DNA-Nano-Käfige konnte mittels interner Totalreflexionsfluoreszenzmikroskopie durch Überlagerung der Fluoreszenzsignale in Einzelmolekül-Experimenten bestätigt werden (durchgeführt durch die AG Birkedal, Aarhus Universität). Nach statistischer Auswertung der AFM-Bilder konnte gezeigt werden, dass eine Präferenz zur Immobilisierung von 12-meren im Verhältnis 1 : 2.2 : 1.3 für DegP6, DegP12 und DegP24 vorlag, was der Zielsetzung bezüglich der Selektivtät entsprach. Durch das Assemblieren eines 6p120 Käfigs mit einer unterschiedlichen Anzahl an Protruding-Armen (vgl. Kapitel 3.4.3.5) und dementsprechend mit einer unterschiedlichen Anzahl von Liganden konnte gezeigt werden, dass zum einen ein Ligand ausreicht, um ein Protein (DegP6) erfolgreich zu immobilisieren und zum anderen ein proportionales Verhältnis zwischen Ladungseffiziens und der Anzahl der Protruding-Arme besteht. Um den positiven Effekt einer hohen lokalen Konzentration der Peptid-Liganden auf die Bindeeffiziens der Proteine zu zeigen, wurden die DNA-Käfige mit den jeweiligen Ausrichtungen der Protruding-Arme (6p120, 6p180 und 6p240, vgl. Kapitel 3.4.3.4) und gleicher Anzahl der Liganden mit DegP12/24A488SA versetzt und mittels eines Vergleiches der Intensität des Fluorescein-Signals die höchste Bindeeffiziens im Verhältnis 8 : 1.4 : 1 (6p120: 6p180 : 6p240) für die Käfige mit nach innen-orientierten Liganden bestimmt. Nach dem erfolgreichen Immobilisieren des Proteins innerhalb der Kavität des Käfigs wurde anschließend eine Freisetzung des Proteins durch einen Austausch des zum Protruding-Arm nicht vollständig komplementären, mit Fluorophoren markierten Peptid-Liganden durch ein vollständig komplementäres Oligonukleotid versucht. Der erfolgreiche Austausch der markierten Liganden konnte mittels Gel-Elektrophorese gezeigt werden, jedoch nicht unter vollständiger Freisetzung des Proteins. Eine verbesserte Freisetzung konnte trotz Änderung der Nettoladung des Proteins ebenfalls nicht erreicht werden (vgl. Kapitel 3.4.3.8). Zusammenfassend kann festgehalten werden, dass zum ersten Mal ein Protein durch schwache supramolekulare Interaktionen innerhalb einer DNA-Origamistruktur immobilisiert werden konnte. Diese Proteine konnten ohne chemische Veränderung nur aufgrund der räumlichen Nähe der Peptid-Liganden, die an die PDZ1-Domänen der Proteine bindeten, und der hohen lokalen Konzentration innerhalb der Kavität durch multivalente Wechselwirkungen mit geringer Reichweite im Käfig gehalten werden. Die Bedeutung der Oberflächenladung der Proteine für die Immobilisierung innerhalb der Kavität bedarf noch weiterer Untersuchungen. Ein Indiz für diese Bedeutung liefern die Versuche mit dem molekularen Tweezer, welche an die Lysine an der Oberfläche der Proteine bindet und deren positive Ladung abschirmt. Folglich führt dies zur Abschwächung der unspezifischen Wechselwirkungen zwischen den Proteinen und dem Käfig, so dass diese erfolgreich geladen werden konnten. Die analogen Ergebnisse der Experimente mit einer weiteren Struktur eines offenen Prismas im HoneyComb-Design (vgl. Kapitel 1.2.3) werden in Kapitel 8 gezeigt, da diese keine neuen, bzw. nur die bisherigen Ergebnisse bestätigende Resultate erbracht haben.During this PhD project, aspects of DNA nanotechnology, biology and supramolecular chemistry have been merged. This work can be divided into three main parts: (i) the design of a suitable tubular DNA cage, which is able to encapsulate all different oligomers of DegP; (ii) the synthesis of a DNA-hepta-peptide conjugate, which binds non-covalently to the PDZ1 domain of the target protein and (iii) the loading of the protein. The DNA origami cage was successfully designed and realized as a single-layer hexagonal DNA prism with an inner radius of 20 nm and an outer radius of 23 nm. Using special spatial staples strands for the face-to-face connections, the orientation of the faces towards the cavity could be programmed (6p120 and 6p240). Alternatively, stochastically oriented faces (6p180) were obtained using three thymines as flexible hinges (see chapter 3.2.1 and 3.2.2). Additionally, each face was equipped with zero, one, two or three orthogonal protruding arms (for a total of 0cA1, 6cA1 or 18cA1 arms, respectively). These arms were used for hybridization with DNA-peptide conjugates equipped with optional fluorophores (chapter 3.3). Correct formation of the different designs (6p120, 6p180 and 6p240) was proven by AFM and gel electrophoresis, after adding streptavidin to the biotinylated ligands. TEM characterization (performed by Pascal Lill at the MPI in Dortmund) and dynamic light scattering confirmed the correct dimensions of the DNA structures in solution. The peptide sequence DPMFKLV was synthesized via solid phase peptide synthesis under standard coupling conditions. Transforming the N-terminal amino group of the peptide directly into a maleimide function allowed reaction with the thiol group of an oligonucleotide without the use of any crosslinking agents. This successful method represents a general method to link the terminal amino-group of a peptide to a thiol bearing oligonucleotide. Purification via HPLC allowed characterization of the DNA-DPMFKLV ligands per MALDI-TOF. Loading of diverse DegP proteins (compare chapter 3.1, table 1) only took place in the presence of the A1-DPMFKLV ligands, demonstrating the validity of the encapsulation strategy (compare chapter 3.4.3). Successful and specific binding was shown at the single-molecule level using total internal reflection fluorescence (TIRF) microscopy, (performed by AG Birkedal, Aarhus University). Statistical evaluation of AFM images revealed preferential encapsulation of the DegP12 protein, with a ratio of 1.3 : 2.2 : 1 for the DegP6, DegP12 and DegP24, respectively. Loading experiments performed with DegP6A633SA and cages with a different number of PAs (see chapter 3.4.3.5) and a correspondingly different number of A1-peptide ligands, showed that one A1-DPMFKLV ligand is sufficient for encapsulation of the protein, with a loading efficiency proportional to the number of ligands. DNA origami cages with identical number of ligands but different orientations of the PAs (6p120, 6p180 and 6p240, see chapter 3.4.3.4) were loaded with DegP12/24A488SA. Gel electrophoresis analysis showed a highest binding efficiency for the 6p120 design in a ratio of 8 : 1.4 : 1 for the 6p120-, 6p180- and 6p240-designs, respectively, thus indicating the importance of a high local concentration of peptide ligands. After successful encapsulation of the protein, experiments to release the protein from the cage were performed, using single strand displacement reactions. Disappearance of the fluorophore signals from the cage sample showed successful displacement of the ligands; however, without releasing the protein. Variation of the pH of the solution and its ionic strength did not result in any beneficial effects (see chapter 3.4.3.8). To sum up, it could be shown that a protein can be encapsulated within a DNA origami cage by weak non-covalent supramolecular interactions without any previous chemical treatment of the protein. The arrangement of a distinct number of peptide ligands in the vicinity of the corresponding binding sites on the protein surface allowed modulation of local concentration effects and multivalent short-range interactions in a single system. The importance of the net charge of the protein for encapsulation within the cavity of the DNA nanochamber and the different binding efficiencies observed for distinct fluorophores, require further investigation. Evidence for the important role of the net charge is the successful loading of the DegP12 protein in presence of molecular tweezers, targeting the lysine residues on the surface of the protein. Results of analogue experiments performed with a second DNA cage, (HoneyComb design, see chapter 1.2.3) are shown in chapter 8

Inkjet bioprinting and 3D culture of human MSC-laden binary starPEG-heparin hydrogels for cartilage tissue engineering

Articular cartilage is a highly specialized, hierarchically organized tissue covering the articular surfaces of diarthrodial joints that absorbs and distributes forces upon mechanical loading and enables low-friction movement between opposing bone ends. Despite a strong resilience towards mechanical stress, once damaged cartilage is generally not regenerated due to a limited repair potential of the residing cells (chondrocytes) and the local absence of vascularized blood vessels and nerves. Eventually, this may lead to osteoarthritis, a chronic degenerative disorder of the synovial joints which has a strongly growing prevalence worldwide. Modern regenerative therapies that aim to rebuild cartilage tissue in vivo and in vitro using chondrocyte- and stem cell-based methods are still not able to produce tissue constructs with desired biomechanical properties and organization for long-term repair. Therefore, cartilage tissue engineering seeks for new ways to solve these problems. In this regard, the application of hydrogel-based scaffolding materials as artificial matrix environments to support the chondrogenesis of embedded cells and the implementation of appropriate biofabrication techniques that help to reconstitute the zonal structure of articular cartilage are considered as promising strategies for sophisticated cartilage regeneration approaches. In this thesis, a modular starPEG-heparin hydrogel platform as cell-instructive hydrogel scaffold was used in combination with a custom-designed 3D inkjet bioprinting method with the intention to develop a printable 3D in vitro culture system that promotes the chondrogenic differentiation of human mesenchymal stromal cells (hMSC) in printed cell-laden hydrogels with layered architectures in order to fabricate cartilage-like tissue constructs with hierarchical organization. Firstly, the successful bioprinting of horizontally and vertically structured, cell-free and -laden hydrogel scaffolds that exhibit layer thicknesses in the range of the superficial zone, the thinnest articular cartilage layer is demonstrated. The long-term integrity of the printed constructs and the cellular functionality of the plotted cells that generally had a high viability after the printing process are shown by a successful PDGF-BB-mediated hMSC migration assay in a printed multilayered hydrogel construct over a culture period of 4 weeks. Secondly, when the established printing procedures were applied for the chondrogenic differentiation of hMSCs, it was found that the printed cell-laden constructs showed a limited potential for in vitro chondrogenesis as indicated by a weaker immunostaining for cartilage-specific markers compared to casted hydrogel controls. In order to increase the post-printing cell density to tackle the limited printable cell concentration which was regarded as the primary reason for the impaired performance of the printed scaffolds, different conditions with varying culture medium and hydrogel compositions were tested to stimulate 3D cell proliferation. However, a significant 3D cell number increase could not be achieved which ultimately resulted in shifting the further focus to casted hMSC-laden starPEG-heparin hydrogels. Thirdly, the chondrogenic differentiation of hMSCs in casted hydrogels proved to be successful which was indicated by a uniform deposition of cartilage-specific ECM molecules comparable with the outcomes of scaffold-free MSC micromass cultures used as reference system. However, the quantitative analysis of biochemical and physical properties of the engineered hydrogel constructs yielded still significant lower values in relation to native articular cartilage tissue. Fourthly, in order to improve these properties and to enhance the chondrogenesis in starPEGheparin hydrogels, a dualistic strategy was followed. In the first part, specific externally supplied stimulatory cues including a triple growth factor supply strategy and macromolecular crowding were applied. As second part, intrinsic properties of the modular hydrogel system such as the crosslinking degree, the enzymatic degradability and the heparin content were systematically and independently altered. It was found that while the external cues showed no supportive benefits for the chondrogenic differentiation, the reduction of the heparin content in the hydrogel proved to be a key trigger that resulted in a significantly increased cartilage-like ECM deposition and gel stiffness of engineered constructs with low and no heparin content. In conclusion, this work yielded important experiences with regards to the application of inkjet bioprinting for hMSC-based cartilage tissue engineering approaches. Furthermore, the obtained data provided valuable insights into the interaction of MSCs and a surrounding hydrogel-based microenvironment that can be used for the further development of chondrosupportive scaffolding materials which may facilitate the fabrication of cartilage-like tissue constructs

Morphology and dynamics of ice crystals and the effect of proteins

286 p.La tesis "Morfología y dinámica de los cristales de hielo y su efecto en las proteínas" se basa en una amplia gama de temas que abarcan el fundamento de la estructura del hielo (tanto su superficie como su morfología), la interacción de las proteínas con el hielo y las ciencias ambientales (formación de las nubes y la dinámica de los glaciares). El enfoque se centra en las interfaces hielo/vapor e hielo/agua.Mediante el microscopio electrónico de barrido ambiental (ESEM) a temperaturas inusualmente bajas, se ha logrado acceder a estudiar la morfología del hielo in-situ en diversas áreas del diagrama de fases (presión-temperatura). Además de reproducir las morfologías ya conocidas de cristales individuales e hielo poli-cristalino, se han observado formas ya conocidas de hielo, así como hielo poli-cristalino. Nuevas geometrías llamadas ¿pools¿, formas circulares de ¿m de diámetro, fueron encontradas en los límites del grano de la superficie del hielo poli-cristalino durante procesos de sublimación lento.Además, se estudiaron ocho soluciones diferentes de proteínas en condiciones de súper-enfriamiento mediante las técnicas de congelación de gota (drop freezing technique) y calorimetría diferencial de barrido (DSC). Únicamente, la (apo)ferritina y la ferritina han mostrado buenas características para la nucleación de hielo, es decir, la congelación bajo pequeño súper-enfriamiento (solo algunos grados debajo de 0 ºC), mientras que la mayoría de las soluciones de proteínas estudiadas se congelan por debajo de -15 ºC, como el agua pura.CIC NanoGUNE:nanoscience cooperative research center CFM: materials physics center ETH Zürich: Institute for Atmospheric and Climate Scienc

Informative potential of multiscale observations in archaeological biominerals down to the nanoscale

International audienceHumans have intentionally used biological materials such as bone, ivory and shells since prehistoric times due to their particular physical and chemical properties. The composite nature of biological materials at the nanoscale combined with an important structural hierarchy up to the macroscopic level is responsible for these exceptional properties. In this chapter we discuss the relation of the structural features of different biological materials within their archaeological and historical contexts along with their anthropological use and function. Amid the wealth of biological materials of archaeological interest, a special attention is paid to carbonate-based materials such as corals and shells and phosphate-based ones, including bone, teeth, ivory and antler. The structural features of these archaeobiominerals at different length scales down to the nanoscopic scale are highlighted in this chapter as they allow drawing conclusions on ancient working techniques, the provision and circulation of raw materials, anthropological heat processes, and, last but not least, on diagenetic changes and authentication purposes. The informative potential of observations of archaeological biological materials at different length scales is finally illustrated by some study cases

Water dynamics, coherent domains and the origin of life

The aim of this thesis is to deploy and develop quantum physics to account for the role of fast electronic dynamics on water’s characteristics, in particular, for water under confinement, and to explore some of its implications in the context of the origin of life. There are unexplained observations of proton synchronization in waterfilled carbon nanotubes, that point at a qualitatively different behavior of water to that predicted by existing theories. A novel study of water as a complex system is proposed and advanced, that combines quantum electrodynamics and quantum chemistry approaches and simulation methods. Several water scales and representations are explored, that aim at the development of a QED-QC multi-scale simulation framework potentially well-adapted for simulation in a biological environment. A multi-scale ontology for water is proposed, with representations at the micro, meso and macroscopic scale, that encode certain properties of the water system. In particular, a polaron model is used at the macroscopic scale, to obtain the size of the polarons that accounts for the observed kinetic energy difference of nanotube water, based on the relationship between radius and number of polarons for kinetic energy value. At the mesoscopic scale, the system is captured through the exciton wave function, using Quantum exciton Hamiltonian, to obtain water quantum dynamics and synchronization. It is argued that the nanotube water molecular dispositions promote quantum electronic synchronization and thus possibly proton synchronization. At the microscopic scale, water is represented as a point charges nuclei, and electron density in 3D space, system. The electron density plots are obtained using linear response, with softening of the potential for the protons. Also, exact Shrödinger equation in the grid is solved using Discrete Variable Representation, in this case for the electron density in 1D, and the time-evolution of the electron density is derived. We show that water molecule’s electronic interaction with a common electromagnetic degree of freedom and synchronization provides a mechanism for proton synchronization. The question of water collective behavior possible role for life is tackled in a model for the origin of life based on our findings. The significance of this study is that it offers a plausible explanation of the observed nanotube water behavior, and several avenues of development of QED-QC study of water, contributing to the development of a QED-QC simulation framework in which to simulate water in biology with potential future applications for biology and medicine.O objetivo desta tese é desenvolver a física quântica para dar conta do papel da dinâmica eletrônica rápida nas características da água, em particular, para a água sob confinamento, e explorar algumas de suas implicações no contexto da origem da água. vida. Existem observações inexplicáveis de sincronização de prótons em nanotubos de carbono cheios de água, que apontam para um comportamento qualitativamente diferente da água ao previsto pelas teorias existentes. Um novo estudo da água como um sistema complexo é proposto e avançado, que combina abordagens de eletrodinâmica quântica e química quântica e métodos de simulação. Várias escalas de água e representações são exploradas, que visam ao desenvolvimento de uma estrutura de simulação multi-escala QED-QC potencialmente bem adaptada para simulação em um ambiente biológico. Uma ontologia multi-escala para a água é proposta, com representações nas escalas micro, meso e macroscópica, que codificam certas propriedades do sistema hídrico. Em particular, um modelo de polaron é usado na escala macroscópica, para obter o tamanho dos polarons que é responsável pela diferença de energia cinética observada da água do nanotubo, com base na relação entre o raio e o número de polarons para o valor da energia cinética. Na escala mesoscópica, o sistema é capturado por meio da função de onda de exciton, usando o Hamiltoniano do exciton quântico, para obter a dinâmica e a sincronização quântica da água. Argumenta-se que as disposições moleculares da água do nanotubo promovem a sincronização eletrônica quântica e, portanto, possivelmente a sincronização de prótons. Na escala microscópica, a água é representada como um núcleo de carga pontual e densidade eletrônica no espaço 3D, sistema. Os gráficos de densidade de elétrons são obtidos usando resposta linear, com amolecimento do potencial para os prótons. Além disso, a equação exata de Shrödinger na grade é resolvida usando Representação de Variável Discreta, neste caso para a densidade de elétrons em 1D, e a evolução temporal da densidade de elétrons é derivada. Mostramos que a interação eletrônica da molécula de água com um grau eletromagnético comum de liberdade e sincronização fornece um mecanismo para a sincronização de prótons. A questão do possível papel do comportamento coletivo da água para a vida é abordada em um modelo para a origem da vida baseado em nossas descobertas. A significância deste estudo é que ele oferece uma explicação plausível do comportamento da água do nanotubo observado, e várias vias de desenvolvimento do estudo QED-QC da água, contribuindo para o desenvolvimento de uma estrutura de simulação QED-QC na qual simular a água na biologia com potenciais aplicações futuras para biologia e medicina

Biomineralization

This open access book is the proceedings of the 14th International Symposium on Biomineralization (BIOMIN XIV) held in 2017 at Tsukuba. Over the past 45 years, biomineralization research has unveiled details of the characteristics of the nano-structure of various biominerals; the formation mechanism of this nano-structure, including the initial stage of crystallization; and the function of organic matrices in biominerals, and this knowledge has been applied to dental, medical, pharmaceutical, materials, agricultural and environmental sciences and paleontology. As such, biomineralization is an important interdisciplinary research area, and further advances are expected in both fundamental and applied research