In recent years, the unique optical properties supported by noble metal nanostructures have fostered great interest in the field of biosensing. Studies have concluded that incident light can excite collective electron oscillations, called surface plasmon polaritons (SPP), which propagate as waves along planar metal film surfaces. When confined to sub-wavelength physical features, these waves resonate and produce tremendous, localized electric fields that significantly enhance optical phenomenon. Surface-enhanced Raman spectroscopy (SERS) arises from the concentrated electric fields supported by irradiated nanostructured noble metal films. Due to its chemical specificity, and extraordinary Raman signal intensification, SERS has emerged as powerful tool for chemical and biological sensing applications. Our group utilizes lithographic techniques to manufacture arrays of quasi three-dimensional (Q3D) nanostructured patterns with precise geometric dimensions. The physical dimensions of Q3D nanostructures may be tuned such that incident light selectively induces electric field enhancement on the top, continuous gold surface that contains nanoholes, or in the bottom, discontinuous phase comprised of gold nanodisks. As a consequence, Q3D nanostructured arrays may be specifically designed to detect larger analytes (e.g. microorganisms) that contact the top continuous phase, or molecular species capable of passing through nanoholes to contact the nanodisks. In this study, Q3D nanostructures designed for nanodisk enhancement are utilized to detect pesticide molecules at low concentrations in aqueous solution. Results from this research may aid in the development of a microfluidic device for on-site environmental monitoring of river systems. 

Ozone in surface air is toxic to both humans and plants, and has negative implications to human health and crop yields. Surface ozone is enhanced by anthropogenic emissions of nitrogen oxides and hydrocarbons, which are a direct result of fuel combustion and other industrial activities. Yet, the highest concentrations of ozone in California are often observed in the foothills of the Sierra Nevadas, some 50-100 kilometers from the urban plumes of the Sacramento and San Joaquin valleys. How anthropogenic emissions affect ozone in areas strongly influenced by biogenic emissions remains a critical question in our understanding of air quality, with implications for control strategies. To examine these issues we are using data from two multi-year atmospheric chemistry field measurement campaigns: CALNEX SJV and BEARPEX. CALNEX SJV took place in 2010 near Bakersfield, CA, an area heavily influenced by urban and agricultural emissions. The BEARPEX 2007 and 2009 campaigns took place in Blodgett Forest, CA, a rural forested area primarily influenced by biogenic emissions. We are quantifying the extent to which anthropogenic emissions of hydrocarbons affect ozone production in these two regimes by performing a statistical analysis of a unique set of chemical indicators, acyl peroxynitrates, or APN. APN are produced in the atmosphere during the photochemical degredation of hydrocarbons that leads to ozone production. APN carry a fingerprint of an anthropogenic or biogenic hydrocarbon precursor. Through linear combination modeling of ozone using various APN compounds and trend analysis along independent axes such as temperature and day of week, we estimate the relative importance of anthropogenic and biogenic hydrocarbons. Moreover, by comparing data from these two sites, we provide a much broader understanding of such effects in both rural and urban areas.

The glass transition temperature is a feature of polymer systems that dictates the transition between glassy and molten-like states in amorphous solids. Glassy polymers have many advantageous properties and are highly desirable for commercial and industrial uses. However, the conditions that lead to glass formation are usually well above room temperature, making implementation of most polymer glasses unfeasible. In a recent discovery, ultra-stable poly(methyl methacrylate) (PMMA) glasses were formed using a technique known as matrix assisted pulsed laser evaporation (MAPLE). These results showed a significant decrease in the polymer’s density, while maintaining chemical stability under normal conditions. The exciting experimental discoveries hold great promise for future technological developments. However, there is much to understand about the underling atomic scale features that arise from MAPLE deposited glassy polymer films. To help answer some of these questions, molecular dynamics (MD) computer simulations were used to understand the mechanisms behind the ultra-stable polymer formation. Previous studies include observing the collapse of the polymer PMMA from an extended to a globular-like state under various solvent and temperature conditions. This poster will show how we track formation of the globular state using different order parameters (e.g., radius of gyration) and also show our generalized strategy for quickly building new polymer simulations. Understanding the fundamentals behind ultra-stable glass formation can unlock discoveries in the development and implementation of new materials.

A growing number of applications seek to use electrostatic effects in non-polar media. However, the science behind particle charging in such systems is not fully understood. Previous work has suggested that the presence of surface hydroxyl groups, when combined with certain surfactants, can induce charging on particles. These surfactants also serve to prevent particle aggregation through steric stabilization. However, dispersing these particles typically requires extended sonication or some other dispersive technique. One possible solution for decreasing the dispersion time is to first hydrophobically surface-treat the particles. Unfortunately, this process has the potential to remove the hydroxyl groups necessary for particle charging. Therefore, our group has investigated the effects of surface modification on particle hydrophobicity and chargeability. Silica particles on the micron and submicron scale were surface treated with tri-methoxy(octyl)silane and methoxy(dimethyl)octylsilane in order to create hydrophobic silica particles with varying amounts of hydroxide groups on their surfaces. The resulting surface energy and acid/base characteristics of these particles were then tested using Inverse Gas Chromatography, with the intent of comparing these properties to the particles' chargeability. This was assessed by measuring their electrophoretic mobilities using a Zeta Potential Analyzer. Our results indicated that particles could both be made hydrophobic and chargeable after surface treatments. However, further investigation is required in order to better understand the mechanism behind this charging. If the surface modification of these particles can preserve their chargeability while adding a steric barrier, this process could be used to reduce dispersion time for charged particles in non-polar media.

The acid-catalyzed dehydration of 4-methylcyclohexanol yields a mixture of several isomeric methylcyclohexene products. The major product of this elimination reaction, 4-methylcyclohexene, is produced through the E2 mechanism. However, mechanisms for the formation of the minor methylcyclohexene products are not predicted by the traditional textbook explanations of carbocation rearrangements. 1-methylcyclohexene is thought to be produced by means of an E1 mechanism in which rearrangement of a carbocation intermediate takes place. This experiment was designed to classify the hydride shifts by observing the products of this reaction using 1,2-²H-4-methylcyclohexanol. The deuterated starting materials for this reaction were prepared in our lab. Gas chromatography-mass spectroscopy and nuclear magnetic resonance analysis were used in the characterization of the products and for the classification of the pair of 1,2 hydryde shifts in tendem and of the single 1,3 di-axial hydride shift, leading to the formation of the 1-methylcyclohexene product. This is useful to know when trying to predict the products of reactions in which intermolecular rearrangements occur during carbocation intermediates.

 The ability to resist nonspecific protein adsorption, low fouling, is an essential surface property necessary for medical implants and biosensors. Mixed-charge surfaces with net neutral uniformly distributed charged amino acid residues have been shown experimentally to highly resistant to nonspecific protein adsorption, and thus have become a new field for biomaterial design. These mixed-charge surfaces have analogues in nature: The interior surfaces, or cavities, of molecular chaperone protein complexes. In addition to assisting hundreds of proteins folding through nonspecific interaction, the cavities usually show transition between a more charged residues state when assisting protein folding and a less charged residues state when actively unfolding proteins. Thus if these interior cavities are well studied, they can be mimicked to create new surface designs. In this study, GroEL-GroES, one of the most well characterized chaperon complexes, is used along with 528 substrate proteins found in Escherichia coli (E.coli). We hypothesized that the interior surface of GroEL-GroES will interact nonspecifically and assist the substrate proteins in folding by lowering their folding free energy. In order to quantitatively calculate these values, we have extended entropic models by introducing a new enthalpy term derived from the knowledge of the residues on the cavity surface. The model not only includes entropic confinement effects but also accounts for energetic interactions between residues found on GroEL-GroES and the substrate protein. Applied to the substrate proteins, our model presents results that match the experimentally observed changes in folding free energies. Furthermore, the optimization of the surface residues distribution of the cavity suggested by this model shows which residues contribute most to stabilized folding. This study provides a better understanding of GroEL-GroES’s ability to nonspecifically assist protein folding. Finally, it also gives insight into the mixed-charge surface design projects where low fouling materials are used as medical devices or sensors.

Diluted magnetic semiconductor (DMS) technology combines the properties of a semiconductor with ferromagnetism. Nanoparticles doped with magnetic elements such as Manganese offer a prime example of this type of material. Our specific task was to analyze the effects of p-type doping with nitrogen in ZnO quantum dots (QD) of 2.4 nm in diameter. p-type doping in this material involves the replacement of an O^2- ion with an N^2- ion, which has one less electron resulting in a hole due to an empty N^2- p-orbital. We hypothesize that when p-type doping is combined with paramagnetic Mn²⁺ doping, the unpaired 3d electrons of two Mn²⁺ ions separated by an N^2- ion will adopt a ferromagnetic orientation as opposed to their traditional antiferromagnetic state. Testing for this experiment was done with the development version of Gaussian. Energy calculations within this program and further data analysis reveal information such as the total energy of each state of the system, molecular orbital data, and energy diagrams concerning the semiconductor properties of these materials. Results show that the lowest energy state occurs when the Mn²⁺ ions adopt a ferromagnetic arrangement with the N^2- hole sharing this alignment. The potential for this QD and others with similar properties is extreme as many semiconductor applications could be revolutionized by DMS's. New applications such as solar cells made of DMS's are also under consideration.

Organic photovoltaics (OPVs) are a promising low-cost option in developing renewable energies. OPVs are solar cells made from organic semiconductors instead of the more traditionally used inorganic semiconductors such as silicon. OPVs have several advantages including: low cost, ease of processing, physical flexibility, and highly tunable properties. Therefore, if the efficiency of OPVs can be increased, they could become a major, inexpensive renewable energy source. Electron-accepting materials used in OPVs have traditionally been fullerene-based due to their high electron mobility. However, fullerenes contribute little to light harvesting in an OPV as they have negligible absorption in the solar spectrum. Thus, our goal was to develop new electron-accepting materials for OPVs that absorb significantly in the solar spectrum as a means to increase light harvesting and therefore OPV efficiency. A series of novel oligomers with an oligothiophene-naphthalene diimide (NDI) structure was synthesized. All oligomers exhibited absorption in the visible region with band gaps ranging from 1.39 eV to 2.06 eV, and could therefore contribute to light harvesting in an OPV. Solution-processed solar cells using the new oligomers as the electron-acceptors showed power conversion efficiencies up to 1.5%. Overall, these new materials exhibited that non-fullerenes can function as the electron-accepting material in OPVs while contributing to light harvesting. This approach therefore shows promise for increasing OPV efficiency to make OPVs a viable, cost-effective renewable energy source.

In recent years, nanoscience has become a major focus: from technologies in solar cell coatings, to developments in biomolecular detection methods. Utilization of unique optical absorption properties of noble metals, such as gold or silver, opens the door for harnessing photons in new and innovative ways. For these reasons, great emphasis has been placed on the synthesis and characterization of nanostructures. The Pozzo Group has recently shown that structured gold clusters can be formed in solution by exploiting the hydrophobic and steric interactions in self-assembling nanoparticles. Hydrophilic polyethylene-glycol (PEG) chains control long-range steric interactions, while hydrophobic alkane-thiol chains induce clustering through short-range attraction. This simple method has the potential to be a cheap and viable option for nanoscale fabrication; starting from the molecular level and building up. This method of nanoclustering yields multi-particle aggregates in solution. Clusters of different geometries and sizes are formed based on the number of consistuent gold particles in each aggregate. It has been shown that the total amount of PEG adhered to the surface of the gold particle impacts the extent of clustering. At lower PEG concentrations, more diverse populations of nanoclusters are observed. In this project, size-exclusion chromatography (SEC) is being utilized for separating cluster populations. A cluster dispersion is pumped through a column that is packed with a porous stationary phase. By size-exclusion, the largest clusters exit the bottom of the column first, while the smaller clusters have a higher retention time as they navigate the pores of the matrix. The viability of SEC for controlled separation of cluster populations is being investigated on different systems, with the goal of isolating populations of similar aggregation types. Population analysis with SEC is simple and can be used to identify the fundamental parameters that lead to polydispersity in cluster size and shape.

Domoic acid (DA) is a toxin that accumulates in edible shellfish through filter feeding and is the causing agent of a serious neurological condition known as amnesic shellfish poisoning. The increasing intensity and frequency of DA-producing algal blooms has drawn more attention to develop fast and effective ways to detect and quantify DA. At Yu Lab, we developed an effective method for the fast detection and quantification of DA using a surface plasmon resonance coupler and disperser (SPRCD) sensor. The SPRCD sensor is an optical instrument based on the coupling of light to electronic oscillations at the interface between a gold surface and a dielectric material. The sensor measures changes in the optical properties of the interface caused by the binding of a specific molecule to the gold surface. By modifying the gold surface such that only the molecule of interest adsorbs, we are able to detect and quantify low concentrations of the toxin in a sample. Using our method, we can detect concentrations of DA as low as 0.1ng/ml and quantify DA in concentrations ranging from 5ng/ml to 10ug/ml.

The Earth’s magnetic field deflects most of the energetic particles contained in solar wind, but some are captured and trapped in regions called radiation belts. Sometimes, high-energy particles migrate from the radiation belts into Earth’s upper atmosphere, where they interact with matter to produce X-rays. Our project focuses on attempting to understand radiation belt loss processes by analyzing the X-ray data. Professor Michael McCarthy and I modeled an existing X-ray detector on the computer and simulated electron populations (having various energy distributions) as they move through the upper atmosphere. We recorded the energy distribution of X-rays captured in the detector. We then compared this distribution with the actual X-ray energy distribution recorded by real experiments. This method of working backwards limits what the energy distribution of the original charged particles may have been. This is significant, because knowing the energy distribution of charged particles in radiation belts and understanding how they move into the upper atmosphere will allow engineers to design spacecraft and satellites that are more resistant to damage from high-energy particles and X-rays. It is also an interesting research question that will teach us about the radiation belts of other planets in the universe that have magnetic fields. Our project will be applied to more experiments; in December 2012, the research team will return to Antarctica to release more balloons equipped with X-ray detectors into the upper atmosphere. Another extension of this work is to model the effects of high-energy protons from solar wind on Earth’s upper atmosphere.

The ability of the semiconductor FeS₂, or iron pyrite, to absorb sunlight makes it a cheap and abundant potential material for use in solar cells. Current photovoltaic studies using nanocrystalline pyrite rely on the synthesis of small, uniform crystals. However, pyrite naturally takes different crystal shapes depending on the conditions of its formation. Even the same shapes can have different surface chemistry, which directly impacts crystal growth direction. The mechanisms behind pyrite synthesis are not fully understood and are difficult to discern out of the complexity of real reaction mixtures. Density functional theory (DFT), a method for simplifying and calculating the quantum mechanics behind a physical system, allows for the numerical approximation of pyrite’s material properties. Our group performed DFT calculations of two common pyrite surfaces using the supercell approach. Slabs of pyrite separated by artificial vacuums were allowed to come to energy minimums. We hypothesized that the energetic and electronic properties of real pyrite surfaces would match those of the DFT-optimized supercells. Preliminary results agreed with published experimental data. After ensuring that our computations could reproduce physical properties, we put small molecules that could be found in reaction mixtures into contact with the lowest-energy pyrite surface and optimized using the same methods. The most-favorable interaction sites between pyrite and the reactants needed to make it are key components to the mechanisms of pyrite growth. Once these mechanisms are known, synthesis conditions can be controlled to produce only crystals fit for use in photovoltaic cells.

Self-assembling silver nanoparticles have been of great interest to the scientific community due to their unique optical properties and potential use in areas such as cancer therapy and semiconductors. This research explores using a simple one-pot technique to produce self-assembling silver nanoparticles with controllable geometries based on steric interactions. The core advantage of this method is that it employs a bottom-up approach using commonly available and relatively inexpensive materials. Successive doping of long hydrophilic polyethylene glycol (PEG) chains followed by a short hydrophobic alkane-thiol renders the nanoparticles amphiphilic. Clusters of different sizes self-assemble depending on the concentration of PEG added to the silver dispersion. As PEG concentration increases, the extent of clustering decreases as the long chained PEG molecules create a corona around the silver particles and inhibit functionalization with alkane-thiol. This synthesis method is analyzed with Dynamic Light Scattering (DLS), Small Angle X-ray Scattering (SAXS), and Transmission Electron Microscopy (TEM). While the samples follow the expected clustering size trends, data indicates that monodisperse silver is critical to the reproducibility of the technique.

A strong understanding of the intricacies of blood coagulation is essential for proper treatment of coagulopathies such as hemophilia, hemorrhage, Von Willebrand’s disease, and numerous thrombosis related conditions. The coagulation behavior of blood is directly related to the structure of the supporting protein networks. Fibrinogen is a protein found in human blood that, upon polymerization into cross-linked fibers, forms the scaffold-like support structure of a blood clot. Based on the observation that emergency room patients with traumatic injuries experience a greater extent of hemorrhage and abnormal hemostasis, our group has investigated the effect of acidic oxidation on the structure and mechanical properties of fibrin gels. Purified fibrinogen was oxidized using hypochlorous acid to simulate the acidification of blood during trauma and shock. Rheological, x-ray scattering, and turbidity studies were performed to characterize the structural and mechanical differences between oxidized and normal fibrin gels. Preliminary results from these studies indicate the oxidation causes a delay in fibrin gelation as well as a decrease in the elastic modulus of the fiber network. Additionally, evidence from turbidity studies suggests that oxidation prevents lateral aggregation between protofibrils leading to an overall reduction in fiber diameter.