Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation

Directed self-assembly of block copolymers for sub-10nm fabrication

Directed self-assembly of block copolymers, based on microphase separation, is a promising strategy for high-volume and cost-effective nanofabrication. Over the past decades, manufacturing techniques have been made huge progress that it is now possible to engineer complex systems of heterogeneous materials around a few tens of nanometers (Such as 193i lithography). Further evolution of these techniques, however, is faced with difficult challenges not only because of diffraction limit, but also in prohibitively high capital equipment costs. Materials that self-assemble, on the other hand, spontaneously form nanostructures down to length scales at the molecular scale, but the micrometer areas or volumes over which the materials self-assemble with adequate perfection in structure is incommensurate with the macroscopic dimensions of devices and systems of devices of industrial relevance. Directed Self-Assembly (DSA) refers to the integration of self-assembling materials with traditional manufacturing processes. The key concept of DSA is to take advantage of the self-assembling properties of materials and at the same time meet the constraints of manufacturing. Technically DSA is similar to the double patterning in terms of resolution enhancement. In this report we will discuss the use of lithographically-defined chemically patterned surfaces to direct the assembly of block copolymer films for semiconductor manufacturing

Chirality Effects on Peptide Self-Assembly Unraveled from Molecules to Materials

Self-assembling short peptides are attractive minimal systems for mimicking the constituents of living systems and building (bio)materials. The combination of both D- and L-amino acids into heterochiral sequences is a versatile strategy for building durable supramolecular architectures, especially when their homochiral analogs do not self-assemble. The reasons for this divergent behavior have remained obscure until now. Here, we elucidate how and why homochiral and heterochiral peptides behave differently. We identify a key spectroscopy signature and its corresponding molecular conformation, whereby an amphiphilic structure is uniquely enabled by the peptide stereochemistry. Importantly, we unravel the self-assembly process as a continuum from the conformation of single molecules to their organization into nano- and microstructures and through to macroscopic hydrogels, which are probed for cytotoxicity in fibroblast cell culture. In this way, (bio)material properties at the macro-scale can be linked to the chemical structure of their building blocks at the angstrom scale. Nature makes pervasive use of homochirality (e.g., D-sugars and L-peptides) to assemble biomolecules, whose interactions determine life processes. D-amino acids rarely occur, and their effects are not yet completely understood. For a long time, structural complexity (e.g., polypeptides and constrained molecules) was considered a requirement for achieving defined conformations that ultimately allow biomolecule recognition and function. Here, we detail how minimalist building blocks can adopt conformations with a characteristic spectroscopic signature, whereby substitution of just one L-amino acid for its D mirror image leads to a divergent path for assembly in water. Subtle molecular variations are amplified through increasing size scale all the way to macroscopic differences that are visible to the eye. Ultimately, the design of heterochiral (bio)molecules thus provides an alternative approach to shed new light on the supramolecular interactions that define life as we know it. This work explains why and how heterochiral and homochiral tripeptides differ in their assembly in water. A characteristic spectroscopic signature is assigned to molecular conformation. We monitor the process as a continuum from the molecular scale to the macroscopic biomaterials so that the final properties are linked to chemical structure of the building blocks. This work lays the foundation for the design of supramolecular hydrogel biomaterials based on short sequences of hydrophobic D- and L-amino acids

Çoklu ölçekte kendiliğinden oluşan üç boyutlu eşyösüz rastgele silisyum kuvantum nokta ağı.

The most important problem limiting the impact of nanotechnology is probably the difficulty in effectively linking nanoscale materials and processes to the macroscopic world. Topology and material properties are intricately coupled and conditions that pertain to atomic, microscopic and macroscopic scales are often seemingly mutually exclusive. This thesis introduces a state-of-the-art nanostructure that hierarchically builds itself from the atomic to the microscopic scales, which can connect to the macroscopic world without detracting from its nanoscale properties. The three dimensional anisotropic random network of silicon quantum dots is largely isotropic in the atomic scale but it grows to become anisotropic in the microscopic scale. We show that quantum confinement is preserved and the current flows through the network without relying on inefficient tunnelling currents. Former pertains to the atomic scale and latter manifesting at the microscale; these two scale-dependent features were thought to be mutually exclusive prior to this thesis. The structure is self-assembled from a silicon-rich silicon oxide thin film. Microscale self-assembly is kinetically driven under nonequilibrium conditions established by magnetron sputter deposition and relies on control of surface diffusion through a surface temperature gradient. Atomic scale self-assembly is chemically driven under local nonequilibrium conditions provided by fast stochastic deposition and relies on control of phase separation by stabilizing nominally unstable suboxides. We show that our fabrication methodology is inherently modular, material-independent, and is not affected substantially by the initial conditions, as self-assembly under nonequilibrium conditions and nonlinear dynamics sweeps aside a large number of factors that influence the details of thin-film growth, but provides simple a couple of “rules” with clearly identifiable corresponding experimental conditions to determine the final morphology.Ph.D. - Doctoral Progra

Molecular engineering of chiral colloidal liquid crystals using DNA origami

Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, 1D supramolecular twisted ribbons and 2D colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of 1D twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials

On the Nature and Shape of Tubulin Trails: Implications on Microtubule Self-Organization

Microtubules, major elements of the cell skeleton are, most of the time, well organized in vivo, but they can also show self-organizing behaviors in time and/or space in purified solutions in vitro. Theoretical studies and models based on the concepts of collective dynamics in complex systems, reaction-diffusion processes and emergent phenomena were proposed to explain some of these behaviors. In the particular case of microtubule spatial self-organization, it has been advanced that microtubules could behave like ants, self-organizing by 'talking to each other' by way of hypothetic (because never observed) concentrated chemical trails of tubulin that are expected to be released by their disassembling ends. Deterministic models based on this idea yielded indeed like-looking spatio-temporal self-organizing behaviors. Nevertheless the question remains of whether microscopic tubulin trails produced by individual or bundles of several microtubules are intense enough to allow microtubule self-organization at a macroscopic level. In the present work, by simulating the diffusion of tubulin in microtubule solutions at the microscopic scale, we measure the shape and intensity of tubulin trails and discuss about the assumption of microtubule self-organization due to the production of chemical trails by disassembling microtubules. We show that the tubulin trails produced by individual microtubules or small microtubule arrays are very weak and not elongated even at very high reactive rates. Although the variations of concentration due to such trails are not significant compared to natural fluctuations of the concentration of tubuline in the chemical environment, the study shows that heterogeneities of biochemical composition can form due to microtubule disassembly. They could become significant when produced by numerous microtubule ends located in the same place. Their possible formation could play a role in certain conditions of reaction. In particular, it gives a mesoscopic basis to explain the collective dynamics observed in excitable microtubule solutions showing the propagation of concentration waves of microtubules at the millimeter scale, although we doubt that individual microtubules or bundles can behave like molecular ants