In this thesis, we study the problem of what microscopic thermodynamic driving forces can stabilize target macroscopic structures. First, we demonstrate that inverse statistical mechanical optimization can be used to rationally design inter-particle interactions that display target open structures as ground states over a wide range of thermodynamic conditions. We focus on designing simple interactions (e.g., isotropic, convex-repulsive) that drive the spontaneous assembly of material constituents to low-coordinated ground states of diamond and simple cubic lattices. This is significant because these types of phases are typically accessible given more complex systems (e.g., particles with orientation-dependent attractive interactions) and for a narrow range of conditions. We subject the optimal interactions to stringent stability tests and also observe assembly of the target structures from disordered fluid states. We then use extensive free energy based Monte Carlo simulation techniques to construct the equilibrium phase diagrams for the model materials with interactions designed to feature diamond and simple cubic ground states, i.e., at zero temperatures. We find that both model materials, despite the largely featureless interaction form, display rich polymorphic phase behavior featuring not only thermally stable target ground state structures, but also a variety of other crystalline (e.g., hexagonal and body-centered cubic) phases. Next, we investigate whether isotropic interactions designed to stabilize given two-dimensional (2D) lattices (e.g., honeycomb or square) will favor their analogous three-dimensional (3D) structures (e.g., diamond or simple cubic), and vice versa. We find a remarkable transferability of isotropic potentials designed to stabilize analogous morphologies in 2D and 3D, irrespective of the exact interaction form, and we discuss the basis of this cross-dimensional behavior. Our results suggest that computationally inexpensive 2D material optimizations can assist in isolating rare isotropic interactions that drive the assembly of materials into 3D open lattice structures. / text

Colloidal nanocrystal assemblies offer an attractive opportunity for designer metamaterials. The ability to permute chemical composition, size, shape, and arrangement of nanocrystals leads to an astounding number of unique materials properties that find use in an extensive array of applications---ranging from solar cells to medicine. However, to take full advantage of these materials in useful applications, the nature of their assembly and their behavior under external stimuli must be well understood. Additionally, the assembly of colloidal nanocrystals into thin films provides a promising pathway to the solution-processing of inorganic materials that are prohibitively too expensive and/or difficult to deposit by conventional methods. Nanocrystal superlattices (NCSLs) of sterically stabilized nanocrystals were assembled by slow evaporation of colloidal dispersions on various substrates. Detailed analysis of the NCSL structures was carried out using transmission and scanning electron microscopy (TEM and SEM) and small-angle x-ray scattering (SAXS). Body-centered cubic (bcc) NCSLs, in particular, were studied in detail and ligand packing frustration was proposed as a significant driving force for their assembly. The behavior of NCSLs was also studied by SAXS under mild heating and solvent vapor exposure revealing several remarkable order-order, order-disorder, and amorphous-crystalline structural transitions. Colloidal Cu(In [subscript 1-x] Ga [subscript x])Se₂ (CIGS) nanocrystals were synthesized by arrested precipitation and formulated into inks. These inks were spray deposited into thin films under ambient conditions to serve as the active light absorbing material in printed low-cost photovoltaic (PV) devices. These devices, which were fabricated without the need for high temperature processes, have achieved power conversion efficiencies above 3 % under AM1.5 illumination. While the efficiencies of these devices are still too low for commercial viability, this work does provide a proof of concept that reasonable efficient solar cells can be created with a low-cost printable process using nanocrystal inks. Since high temperatures are not used to form the light-absorbing layer, nanocrystal-based solar cells were built on flexible light weight plastic substrates. The main obstacle to achieving high power conversation efficiencies was found to be the ability to extract the photo induced charge carriers. Nanocrystal films suffer from poor transport that leads to high recombination rates in thicker films. To date, the best efficiencies have been achieved with thin light absorber layers that only absorb a fraction of the incident light. / text

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Colloids are promising building blocks in material synthesis because of their controllability of size and surface properties. The synthesis of chemically and/or geometrically anisotropic colloidal particles has received attentions with the expectation of building blocks for complex structures. However, the synthesis of anisotropic colloidal particles is by far more difficult than the synthesis of spherical colloidal particles. Lack of monodispersity and productivity of many anisotropic particles often limits their applications as a building block for complex structures. Thus, it is highly desirable to develop methods which can produce a large amount of monodisperse non-spherical particles with controllable asymmetric surface properties. This dissertation details the work for developing such a method. The major result of this dissertation is a synthetic method to produce monodisperse non-spherical colloids with anisotropic surface property in a large quantity. The anisotropic colloid, which we call it as Dimer particle, has two fused lobes like a dumbbell and each lobe’s size can be independently controlled. We present a novel method to synthesize sub-micron size Dimer particles. This method can produce a large amount of submicron-sized Dimer particles with good monodispersity and well-controlled shape. Submicron-sized Dimer particles have been highly desired since they can be used as a building block for self assembly using Brownian motion, colloidal surfactant for Pickering emulsion, and photonic materials. To fully take advantage of the anisotropy of the particles, we develop a facile method to tailor the surface property of each lobe independently by asymmetrically coating the particles with gold nanoparticles. This method doesn’t need the arrangement of particles onto any type of interfaces. Asymmetric coating of gold nanoparticles can be carried out simply by mixing Dimer particles with gold nanoparticles. The formation mechanism of the submicron-sized Dimer particles is explained with evidences. Finally, we illustrate that Dimer particles show rich phase behavior under electric fields and explain the behavior by considering various interactions involved in the system. Our investigation shows that electric field can effectively control the orientation and assembled structure of Dimer particles. In conclusion, these asymmetrically functionalized Dimer particles are promising building blocks to generate suprastructures that will be useful in photonic, electronic and diagnostic applications. / Engineering and Applied Sciences

Native vascular tissue functions are highly dependent on structural organization at the super-cellular, cellular, and sub-cellular spatial scales. We hypothesized that the structure-function relationship of vascular tissues in vivo can be leveraged to engineer vascular tissues in vitro by prescribing the shape of constituent cells and their assembly into organized three-dimensional structures. To this end, we first asked if vascular smooth muscle cell shape influences cellular contractility. We engineered human vascular smooth muscle cells to assume similar shapes to those in elastic and muscular arteries and then measured their contraction while stimulating with endothelin-1. We found that vascular smooth muscle cells with elongated shapes exhibited lower contractile strength but a greater percentage increase in contraction after endothelin-1 stimulation, suggesting that elongated vascular smooth muscle cell shape endows the muscular artery with greater dynamic contractile range. Next, we sought to assemble cells into tissues by employing a three-dimensional cellular patterning strategy based on the folding of porous, thin polymer films. We assembled different three-dimensional endothelial and vascular smooth muscle organizations by patterning two-dimensional poly(lactic-co-glycolic) acid and collagen thin films with cell suspensions at prescribed locations. The films were subsequently folded following Miura-ori geometry guidelines and the matrices were embedded subcutaneously in immunodeficient mice in order to assess the vascularization of the implanted constructs. We found that spatial organization that allowed endothelial and vascular smooth muscle cells to interact adjacent to each other laterally in the same folding plane created the densest vascularized network, suggesting that three-dimensional structural organization of vascular cells can influence the formation of vascularized networks. Taken together, our result shows that functional vascular tissues in vitro can be engineered by encoding structure cues in their design and assembly. / Engineering and Applied Sciences

In many habitats, species’ traits correspond strongly to local environmental conditions. The cause of this pattern may be in-situ evolution, where initially mal-adapted resident species evolved traits that increased their fitness. Alternatively, species with suitable traits may have colonized the focal habitat and replaced resident species. Since theories in the fields of evolutionary biology and community ecology developed independently, few guidelines tell us when to expect evolutionary adaptation or ecological species replacement as the primary driver of species and trait composition in a given habitat. The goal of my dissertation research was to explain how evolutionary adaptation and ecological species replacement together determine the composition of pond zooplankton communities. I combined theoretical models with thorough surveys of natural pond communities and manipulative experiments. I discovered that one particular zooplankton species, Daphnia pulex, evolved to have different trait values in ponds with different environments. The evolutionary divergence within D. pulex profoundly affected its ecological interactions with other zooplankton species. D. pulex populations diverged from one another so much that they differed in their ability to successfully colonize ponds full of competing zooplankton species. I also used a computer simulation model to determine when a community’s trait changes were explained by evolutionary adaptation or ecological species replacement. The dispersal rate of species among habitats and the amount of genetic variance within these species both influenced adaptive trait change in a community. The group of research studies that indicate evolutionary and ecological processes operate on a similar time scale is small but growing. My dissertation research provides another crucial demonstration that evolution within individual species, such as D. pulex, influences their community ecological interactions with other species. I also identified key parameters (dispersal rate among and genetic variance within species) that may help biologists predict whether evolution or ecological species replacement explained adaptive trait change. My projects mostly concern the community and trait distributions that result from the assembly of species in new habitats. However, this framework may inform studies of community response to environmental changes such as invasive species or habitat destruction. / text

Our laboratory has used the 1,4,5,8 Naphthalenetetracarboxylic diimine (NDI) unit to develop threading polyintercalators that bind DNA with the NDI units intercalated in between GpG steps and two different peptide linkers, which connect the NDI units, situated in either the major or minor grooves. The first generation bisintercalators, G₃K and [beta]Ala₃K, were shown to bind two different sequences of DNA, where the peptide linkers reside in the major and minor grooves respectively. These binding modules were then combined to generate threading polyintercalators that bound different DNA sequences with simultaneous occupation of both grooves. In particular, a cyclic bisintercalator was designed and DNAse I footprinting revealed a strong preference for the sequence 5'-GGTACC-3'. NMR structural studies of the complex with d(CGGTACCG)₂ verified a pseudocatenane structure in which the NDI units reside four base pairs apart, with one linker located in the minor groove and the other in the major groove. This was the first structurally well-characterized pseudocatenane complex between a sequence-specific cyclic bisintercalator and its preferred binding sequence. The ability to simultaneously occupy both groves of the same sequence is interesting for several reasons. Most significantly, it raises questions about a complex DNA intercalator's ability to locate its preferred sequence within a long strand of DNA. In order to directly assess this, the intercalator was modified (CBI-Cys) to incorporate a gold nanoparticle probe to allow for the direct visualization of the intercalator locating its preferred sequence within a long DNA strand. The appropriate protocols to visualize DNA using electron and atomic force microscopy were unsuccessful; however, the foundation has been set for future work to develop the appropriate method to determine the mechanism by which the cyclic bisintercalator locates its preferred sequence. Additionally, the bisintercalators developed in our laboratory offered a unique opportunity to exploit their sequence specificity for controlled nanoparticle assembly. Over the past decade, nanoparticles and DNA have been used to develop novel nanoparticle assembly systems with the goal of developing electronic devices and nanomaterials. The G₃K bisintercalator was synthetically modified to incorporate a gold nanoparticle probe. This intercalator-nanoparticle conjugate, BisKC·Au, maintained its binding specificity (5'-GGTACC-3') to a modified DNA fragment containing multiple G₃K binding sites. The atomic force microscope has become the most promising tool in visualizing individual DNA molecules. A modified procedure utilized APS to allow for the direct visualizing of plasmid DNA. The framework is now in place to confirm the controlled assembly of the gold nanoparticles. This protocol can then be used for the [beta]Ala₃K bisintercalator to lead to the development of a nanoparticle assembly system that can precisely control the organization of multiple types of nanoparticles. / text

published_or_final_version / abstract / toc / Mechanical Engineering / Doctoral / Doctor of Philosophy

Colloidal semiconductor nanoparticles (NPs) contain hundreds to thousands of atoms in a roughly spherical shape with diameters in the range of 1-10 nm. The extremely small particle size confines electron transitions and creates size tunable bandgaps, giving rise to the name quantum dots (QDs). The unique optoelectronic properties of QDs enable a broad range of applications in optical and biological sensors, solar cells, and light emitting diodes. The most common compound semiconductor combination is chalcogenide II-VI materials, such as ZnSe, CdSe, and CdTe. But III-V and group IV as well as more complicated ternary materials have been demonstrated. Coordinating organic ligands are used to cap the NP surface during the synthesis, as a mean of protecting, confining, and separating individual particles. This study investigated the impact of the ligand on particle growth and self-assembly into hierarchical structures. ZnSe QDs were synthesized using an aqueous route with four different thiol ligands, including 3-mercaptopropionic acid (MPA), thioglycolic acid (TGA), methyl thioglycolate (MTG), and thiolactic acid (TLA). The particle growth was monitored as a function of reaction time by converting the band gaps measured using UV-vis spectroscopy into particle sizes. A kinetic model based on a diffusion-reaction mechanism was developed to simulate the growth process. The growth data were fit to this model, yielding the binding strength in the order TLA < MTG ≈ TGA < MPA. This result showed the relationship between the QD growth rates and the chemical structures of the ligands. Ligands containing electron-withdrawing groups closer to the anchoring S atom and branching promoted growth, whereas longer, possibly bidendate, ligands retarded it. Removing TGA ligands from the surface of CdTe QDs in a controlled manner yielded new superstructures that were composed of either intact or fused particles. Purifying as-synthesized QDs by precipitating them using an anti-solvent removed most of the free ligand in solution. Aging this purified QD suspension for a week caused self-assembly of QDs into nanoribbons. The long time needed for self-assembly was due to the slow equilibrium between the ligands on QD surface and in solution. Accelerating the approach to equilibrium by diluting purifed CdTe QDs with organic solvents triggered rapid self-assembly of superstructures within a day, forming various nanostructures from nanoribbons to nanoflowers. The type of nanostructures that formed was determined by the solvation of TGA in the trigger solvent. Extracting the smallest portion of TGA in methanol promoted vectorial growth into ribbons consistent with dipole-dipole attractive and charge-charge repulsive interactions. Removing more of the TGA layer in IPA caused the dots to fuse into webs containing clustered ribbons and branches, and the directional nature of the superstructure was lost. Completely deprotecting the surface in acetone promoted photochemical etching and dissolved the QDs, yielding ower-like structures composed of CdS. Nanocrystal (NC) growth mediated by a ligand was also studied in the organic synthesis of FeS₂ nanocubes. Oleylamine was used not only as the ligand but also the solvent and reductant during the reaction. A one hour reaction between iron (II) chloride and elemental sulfur in oleylamine at 200 ℃ and a S to Fe ratio of 6 yielded phase pure pyrite cubes with dimensions of 87.9±14.1 nm. X-ray diffraction (XRD) spectra and Raman peaks for pyrite at 340, 375, and 426 cm⁻¹ confirmed phase purity. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) results showed that the oleylamine remained on the FeS₂ surface as a ligand. The reaction mechanism includes the production of pyrrhotite Fe₁₋ᵪS (0≤x<0.5) via reduction of S⁰ to S²⁻ by oleylamine and the oxidation of pyrrhotite to pyrite with remaining S⁰.

Ongoing efforts to improve the efficiency of organic photovoltaic cells emphasize the significance of the architecture of molecular assemblies in thin films, at nanometer and micron length scales, to enhance both exciton diffusion and charge transport, in donor and acceptor layers. Controlled growth of molecules via self-assembly techniques presents new opportunities to develop nano-structured organic thin films for electronic devices. This thesis is focused on controlling the orientation of phthalocyanine molecular assemblies in thin films in order to demonstrate the impact of microscopic control of molecular order on electrical properties and organic solar cell device performance.The studies performed here provide insights into the self-assembling behavior, film morphology, nanoscale electrical conductivity, and photovoltaic properties of a disk-shaped peripherally substituted phthalocyanine (Pc) molecule possessing amide functional groups in the side chains. Amide functionality was integrated in the side chains of this phthalocyanine molecule with the purpose of increasing the intra-columnar interaction through formation of a hydrogen bonding network between molecules, and to guide columnar orientation in a preferred direction via specific surface-molecule interactions. It is realized that molecule-substrate interactions must dominate over molecule-molecule interactions to achieve control over the deposition of molecules in a preferred direction for organic solar cell applications. Microscopic imaging and spectroscopic studies confirm the formation of flat-lying, well ordered, layered phthalocyanine films as anticipated.The remarkable electrical conductivity of the flat-lying phthalocyanine molecules, as studied by Conducting tip Atomic Force Microscopy (C-AFM) provide the impetus for the formation of organic solar cells based on layers of these hydrogen bonding phthalocyanine molecules. The photocurrent from devices that are made with the ordered Pc molecules and disordered Pc molecules as the primary photoactive donor layer, and vacuum deposited C60 as the acceptor material, were evaluated. The results presented here demonstrate the feasibility of increasing the photogenerated current by controlling the molecular organization in the photo active layer.