Scanning Probe Investigations of the Surface Self-Assembly of Organothiols and Organosilanes Using Nanoscale Lithography

Particle lithography and scanning probe lithography were applied to study the kinetics and mechanisms of surface self-assembly processes. Organothiols on Au(111) and organosilane on Si(111) were chosen as model systems for investigations at the nanoscale using atomic force microscopy (AFM). Fundamental insight of structure/property interrelationships and understanding the properties of novel materials are critical for developments with molecular devices. Methods using an AFM probe for nanofabrication have been applied successfully to prepare sophisticated molecular architectures with high reproducibility and spatial precision. The established capabilities of AFM-based nanografting were reviewed for inscribing patterns of diverse composition, to generate complicated surface designs with well-defined chemistries. Nanografting provides a versatile tool for generating nanostructures of organic and biological molecules, as well as nanoparticles. Protocols of nanografting are accomplished in liquid media, providing a mechanism for introducing new reagents for successive in situ steps for 3-D fabrication of designed nanopatterns. Because so many chemical reactions can be accomplished in solution, there are rich possibilities for chemists to design studies of other surface reactions. Surface assembly and self-polymerization of chloromethylphenyltrichlorosilane (CMPS) were investigated using test platforms of organosilanes fabricated with particle lithography. A thin film of octadecyltrichlorosilane (OTS) with well-defined nanopores was prepared on Si(111) to spatially confine the surface assembly of CMPS within nanopores of OTS. Time-dependent changes during the self-polymerization of CMPS was visualized ex situ using AFM. Molecular-level details of CMPS nanostructures were obtained from high resolution AFM images to track the growth of organosilanes on Si(111). Measurements of the heights and diameters of CMPS nanostructures provided quantitative information of the kinetics of CMPS self-polymerization. Scanning probe-based methods of nanolithography were applied to investigate the self-assembly of a tridentate organothiol, 1,1,1-tris(mercaptomethyl)heptadecane (TMMH). Multidentate adsorbates can address problems with long-term stability to oxidation observed with monothiolated n-alkylthiols. Multidentate thiol ligands demonstrate improved resistance to oxidation, thermal desorption and UV exposure. Progressive changes in surface morphology for TMMH assembly onto Au(111) was studied in situ with time-lapse AFM, monitoring changes in surface coverage at different time intervals. Nanoshaving and nanografting were used as molecular rulers to evaluate the thickness of films of TMMH

Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by biology's fantastic ability to assemble biomolecules that form systems with complicated structure and dynamics, from molecular motors that walk on rigid tracks and proteins that dynamically alter the structure of the cell during mitosis, to embryonic development where large-scale complicated organisms efficiently grow from a single cell. Using this active self-assembly model, we show how to efficiently self-assemble shapes and patterns from simple monomers. For example, we show how to grow a line of monomers in time and number of monomer states that is merely logarithmic in the length of the line. Our main results show how to grow arbitrary connected two-dimensional geometric shapes and patterns in expected time that is polylogarithmic in the size of the shape, plus roughly the time required to run a Turing machine deciding whether or not a given pixel is in the shape. We do this while keeping the number of monomer types logarithmic in shape size, plus those monomers required by the Kolmogorov complexity of the shape or pattern. This work thus highlights the efficiency advantages of active self-assembly over passive self-assembly and motivates experimental effort to construct general-purpose active molecular self-assembly systems

Investigations of Structure / Property Interrelationships of Organic Thin Films Using Scanning Probe Microscopy and Nanolithography

Studies of the surface assembly and molecular organization of organic thin films were studied using scanning probe microscopy (SPM) and scanning probe lithography (SPL). Systems of organic thin films such as n-alkanethiols and pyridyl functionalized porphyrins were characterized at the molecular level, and measurements of the conductive properties of polythiophenes containing in-chain cobaltabisdicarbollides were accomplished. Understanding the self-organization and mechanisms of self-assembly of organic molecules provides fundamental insight for structure/property interrelationships. Investigations of the surface assembly of 5,10-diphenyl-15,20-di-pyridin-4-yl-porphyrin (DPP) on Au(111) were done using SPL methods of nanoshaving and nanografting. Automated computer designs were developed for nanofabrication to provide local characterizations of the thickness of DPP films and nanostructures. Nanolithography was accomplished using DPP films as either matrix self-assembled monolayers (SAMs) or as molecules for nanofabrication. Results presented in this dissertation demonstrate that DPP forms compact layers on Au(111), which can be used for inscribing nanopatterns of n-alkanethiols. Arrays of DPP nanopatterns with precise geometries and alignment were fabricated within n-alkanethiols by nanografting, demonstrating nanoscale lithography with pyridyl porphyrins can be accomplished to produce an upright surface orientation on Au(111) mediated by nitrogen-gold chemisorption. Beyond research investigations, the applicability of atomic force microscopy (AFM) and advancements with automated SPL were applied for teaching undergraduate chemistry laboratories to introduce the fundamentals of surface chemistry and molecular manipulation. New classroom activities were developed for the Chemistry 3493 Physical Chemistry laboratory to give students “hands-on” training with AFM. Undergraduates were trained to prepare nanopatterns of n-alkanethiols using software to control the position, force and speed of the AFM tip for nanolithography experiments. The sensitivity and nanoscale resolution of current sensing AFM was applied for studies of the conductive properties of electropolymerized thin films of polythiophenes with cobaltabisdicarbollide moieties. Images acquired with AFM furnished views of the morphology of different polymers prepared on gold surfaces. Surface maps of the conductivity of electropolymerized films were acquired with AFM current images. These studies provide new insight of the effects of the bound cobaltabisdicarbollide moiety and coordinated metal centers for the electronic properties of the resulting conducting materials

Spatial and spatiotemporal variation in metapopulation structure affects population dynamics in a passively dispersing arthropod

The spatial and temporal variation in the availability of suitable habitat within metapopulations determines colonization-extinction events, regulates local population sizes and eventually affects local population and metapopulation stability. Insights into the impact of such a spatiotemporal variation on the local population and metapopulation dynamics are principally derived from classical metapopulation theory and have not been experimentally validated. By manipulating spatial structure in artificial metapopulations of the spider mite Tetranychus urticae, we test to which degree spatial (mainland-island metapopulations) and spatiotemporal variation (classical metapopulations) in habitat availability affects the dynamics of the metapopulations relative to systems where habitat is constantly available in time and space (patchy metapopulations). Our experiment demonstrates that (i) spatial variation in habitat availability decreases variance in metapopulation size and decreases density-dependent dispersal at the metapopulation level, while (ii) spatiotemporal variation in habitat availability increases patch extinction rates, decreases local population and metapopulation sizes and decreases density dependence in population growth rates. We found dispersal to be negatively density dependent and overall low in the spatial variable mainland-island metapopulation. This demographic variation subsequently impacts local and regional population dynamics and determines patterns of metapopulation stability. Both local and metapopulation-level variabilities are minimized in mainland-island metapopulations relative to classical and patchy ones

Optimization of supply diversity for the self-assembly of simple objects in two and three dimensions

The field of algorithmic self-assembly is concerned with the design and analysis of self-assembly systems from a computational perspective, that is, from the perspective of mathematical problems whose study may give insight into the natural processes through which elementary objects self-assemble into more complex ones. One of the main problems of algorithmic self-assembly is the minimum tile set problem (MTSP), which asks for a collection of types of elementary objects (called tiles) to be found for the self-assembly of an object having a pre-established shape. Such a collection is to be as concise as possible, thus minimizing supply diversity, while satisfying a set of stringent constraints having to do with the termination and other properties of the self-assembly process from its tile types. We present a study of what we think is the first practical approach to MTSP. Our study starts with the introduction of an evolutionary heuristic to tackle MTSP and includes results from extensive experimentation with the heuristic on the self-assembly of simple objects in two and three dimensions. The heuristic we introduce combines classic elements from the field of evolutionary computation with a problem-specific variant of Pareto dominance into a multi-objective approach to MTSP.Comment: Minor typos correcte

Emerging Approaches to DNA Data Storage: Challenges and Prospects

With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 1014GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 103GB/mm3. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies

Design Automation of Polyomino Set That Self-Assembles into a Desired Shape

The problem of finding the smallest DNA tile set that self-assembles into a desired pattern or shape is a research focus that has been investigated by many researchers. In this paper, we take a polyomino, which is a non-square element composed of several connected square units, as an element of assembly and consider the design problem of the minimal set of polyominoes that self-assembles into a desired shape. We developed a self-assembly simulator of polyominoes based on the agent-based Monte Carlo method, in which the potential energy among the polyominoes is evaluated and the simulation state is updated toward the direction to decrease the total potential. Aggregated polyominoes are represented as an agent, which can move, merge, and split during the simulation. In order to search the minimal set of polyominoes, two-step evaluation strategy is adopted, because of enormous search space including many parameters such as the shape, the size, and the glue types attached to the polyominoes. The feasibility of the proposed method is shown through three examples with different size and complexity

Purification of DNA Origami Nanostructures Using Capillary Electrophoresis

DNA origami are nanostructures designed based on Watson-Crick base-pairing that fold a scaffold into non-arbitrary morphologies using an excess of linear single-stranded DNA staples . As an engineered nanomaterial (ENM) with great customizability, DNA origami also enjoys the benefit of naturally encoded and well-studied structural and functional properties. The flexibility of different folding patterns allows for construction of a wide variety of shapes and sizes of DNA origami, showing potential applications in fields such as medicine, biocomputing, biomedical engineering , and measurement science. Despite the successes as a functional nanomaterial, a major barrier to the applicability of DNA origami rests in the lack of pure, well-folded structures. As such, the development of different purification techniques is essential to support the rapid development of the material toward a vast scope of applications. Current techniques to purify DNA origami from excess precursors (staples), misfolded structures and other impurities have shown low yields, low scalability, tendency for aggregated samples, and lack optimization for automation. Capillary electrophoresis (CE) has previously shown effective separation of single-stranded DNA based on differences of size and charge in a manner similar to gel electrophoresis, but with the added benefit of automation and more substantial control and detection throughout the separation. The development of CE as a purification technique for DNA origami is investigated in this study, where a highly reproducible separation between folded DNA origami from excess DNA staples was achieved by manipulating and understanding the effect of buffer conditions , capillary specifications , and injection parameters on the electropherogram profile. Specifically , CE was investigated under both capillary zone electrophoresis (CZE) and capillary transient isotachophoresis (ctITP) modes, and optimization of both systems yielded baseline resolved separations of DNA origami from the staple strands. The ctITP system demonstrated superior performance in terms of decreasing band broadening, improving resolution, and improving the Gaussian character of migration peaks. Further, the optimized ctITP separation was used in a fraction collection procedure, where the resulting fractions were imaged by atomic force microscopy (AFM) for offline validation of purified structures. However, issues with the intercalating dye and origami aggregation were suspected to impede the imaging process. The reproducibility of the fraction collection procedure was validated to show a highly linear relationship between the peak area of a reinjection of pooled sample and the number of pooled fractions. An approach to calculating the percent yield of CE-based purification was attempt ed but requires further validation. Continued exploration and analysis of CE for the purification of DNA origami could thus lead to a novel , promising, and efficient tool to advance the field as a whole