Projects

Each faculty member in charge of a project has experience with and is committed to, mentoring REU participants and undergraduates. The seven weeks spent in each faculty mentor's lab prove to be an insightful and singular experience that allows participants to witness the reality of academic research.

These projects are important parts of larger research programs funded by the NSF, DOD, DOE, NASA, NIH, and other federal and private funding agencies. All projects contain microscopy- and microanalysis-related investigations with sustainability-driven objectives (whether by direct investigation of climate change and ecology or material studies with applications in solar or fuel cell technologies).

Biology | Chemistry | Civil and Environmental Engineering | Electrical & Computer Engineering | Mechanical & Materials Engineering |  Physics 

Biology and Environmental Science

Ken Stedman – Viruses from Extremophiles

This work concentrates on the characterization of novel viruses from extreme environments, particularly an acidic hot lake (Boiling Springs Lake) in Lassen Volcanic National Park. This unique ecosystem is completely microbial and viruses are predicted to be the only "predators." This work uses TEM, SEM, and EDS, together with light microscopy and molecular biology. This research project may involve field work. These viruses are different from other known viruses, both in their structures and genome sequences. New viruses and virus-like particles that we discover have unique ultrastructures and may offer insights into the thermal and acid stability of natural and engineered nanostructures. In order to fully characterize these viruses and to determine their structures and chemical composition, we use high-resolution TEM, SEM, and EDS. REU students will work together with graduate students, other undergraduate students, and postdocs. Their work will focus on a few aspects of these investigations. We also have REU projects working on vaccine stabilization and diagnosis of intestinal parasites.

Jeffrey Singer – Ubiquitin Degradation System

Research in the Singer lab centers on ubiquitin signaling and how it affects proliferation. In order to gain a better understanding of how ubiquitin-signaling is regulated focus has been placed on the structure and function of an E3 ligase that we identified as a regulator of a cyclin called cyclin E. This cyclin is an important mediator of entrance into the cell cycle and thus is important in normal proliferative processes such as wound healing and liver regeneration as well as abnormal processes such as cancer. We have taken a broad approach that encompasses biochemical methods and proteomics, as well as mouse disease models, to determine how E3 ligases work. In doing so, we have uncovered unique in vivo roles for this E3 ligase as well as new molecular details regarding the structure of the active complex. For further investigation, REU students will work with graduate students and learn the necessary cell biology experimental procedures first. He/she will then take on one or two aspects of this project and conduct them independently.

Chemistry

Andrea Goforth – Functional, Inorganic Nanomaterials for Biomedical Imaging & Nanoscale Electronics Applications

My lab’s overarching goals are to synthesize uniform, colloidal nanomaterials, optimize the physical properties that allow for imaging, and tune the surface properties and colloidal stability appropriately for biological imaging applications. My work emphasizes understanding the physical and biological properties of nanoscale materials in order to rationally develop optimal imaging agents for use in biomedicine. Thus, my lab uses chemical, microscopic, spectroscopic, and medical imaging techniques, as well as biological feedback (e.g., cytotoxicity studies), to guide nanomaterial synthesis goals. My work also emphasizes developing synthetic methods using biocompatible elements and reagents, promoting the higher likelihood of environmentally friendly and biocompatible nanoparticle products, suitable for use in medicine.

My lab is expert in the synthesis of size-controlled, uniform nanomaterials of diverse kinds, with emphasis on photoluminescent, elemental silicon and X-ray opaque, elemental bismuth nanoparticles, since these elements are biologically well tolerated. We are also expert in nanomaterials characterization, using a large suite of techniques, including: TEM (HR-TEM, EDX spectroscopy), SEM, dynamic light scattering (DLS), surface charge measurement, various materials characterizations by X-ray diffraction and scattering, UV-visible spectroscopy, photoluminescence spectroscopy, FT-IR, Raman, XPS and NMR spectroscopies. Not only do we use these techniques to characterize the materials that we synthesize, we also use them to follow dynamic changes to the nanoparticles in aqueous and biological environments, and thus are developing nanoparticles not only as imaging agents but also as sensing agents and reaction catalysts, as we better understand and exploit their properties. In general, we apply solution syntheses, aqueous workups and purifications, and accomplish biological and proof-of-principle imaging assays in high-impact collaborations.

Marilyn Mackiewicz – Designing Nanostructured Materials for Biomedical Applications

The Mackiewicz lab consists of modern-day explorers of the molecular world and architects of nanoscale materials. The research in the laboratory of nanostructured materials bridges concepts in inorganic, analytical, and nanomaterials chemistry. Our research has focused the development of nanostructured materials for applications that relate to human health and the environment. Our major projects are centered on 1) the design of nanoscale materials using green synthetic approaches for biosensing, drug delivery and imaging, 2) studying nanoparticle-biological interactions in vitro and in vivo, 3) development of diagnostic assays and imaging agents to monitor disease states and therapeutic response, and 4) systems for targeted drug delivery for cancer therapy, and 5) nanoparticle-based optical agents to monitor the repair process in age-related macular degeneration. Our long-term goal is to advance our bench side chemistry into translational applications.

We envision that the fundamental chemistry developed in our lab will also help improve our understanding of major diseases that impact the quality of human life. As the only all undergraduate funded research lab in the chemistry department, we aim to strengthen the problem-solving and critical thinking skills of each developing scientist. Each mentored student will learn valuable synthetic, analytical, spectroscopic, and transferable techniques for a rewarding research career.

Reuben Simoyi –  Kinetics and Mechanism of S-Nitrosation of Proteins, Peptides, and Biologically-Active Thiols

Nitric oxide (NO) has a crucial and extensive role in human physiology. NO, which is synthesized in-vivo via the oxidation of L-arginine to citrulline by the enzyme NO synthase1 acts as a messenger molecule effecting muscle relaxation2, a cytotoxic agent in the non-specific immune system3, a carcinogen4, and as a neurotransmitter in the brain and peripheral nervous system5. This rather modest molecule is also known to inhibit platelet aggregation6 and is also involved in host defense7, among other diverse physiological roles. Many workers have come up with results and mechanistic propositions that are controversial and exhibit the complex biological roles of this simple molecule in the mammalian body. A number of reviews have tried to outline the physiological and pathophysiological roles of NO8,9. Excessive production of nitric oxide has thus been linked to so many cytotoxic activities such as septic shock and liver injury 10.  It is necessary to have processes that can reduce NO concentrations to beneficial levels in the physiological environment. Such processes would include its reaction with thiols to form S-nitrosothiols (RSNO). For example, RSNO has been shown to improve end-organ recovery in models of ischemia/reperfusion injury in the heart and liver 11,12. Biological nitrosothiol formation is a post-translational modification of biological thiols that is subsequently linked to all those functions that are attributed to nitric oxide.  Possible roles of S-nitrosation include the regulation of apoptosis through glyceraldehyde-3-phosphate dehydrogenase modification 13 as well as involvement in the pathogenesis of Parkinson’s Disease 14. Despite the potential benefits of the relevance of the mechanistic basis of nitrosations (both S- and N-nitrosations), very few studies have been directed at elucidating these mechanisms. This REU work on S-nitrosation of active biological thiols has been funded by the NSF since 2006 up to CHE 1056366 for which a renewal is being sought.  The REU students work on the mechanistic aspects of NO interactions with biologically-active thiols. Specifically, while NO is accepted to be endothelial-derived relaxation factor, S-Nitrosothiols sometimes as act as same. Thus, the conjecture is that thiols are carriers of NO from point of production.

Theresa McCormick – Solar Energy Storage

The McCormick lab is interested in ways to store solar energy in the form of chemical bonds. The ability to store solar energy is critical to sustainably meet future energy demands. We use a combination of experimental and computational chemistry to develop new catalysts for water splitting reactions that allow for the production of hydrogen gas. We are also interested in photochemical reactions that will allow for oxygen gas from the atmosphere to be used in oxidation reactions as a green approach to organic synthesis. REU students working in our lab will synthesize new catalysts and characterize the properties of the compounds. Students interested in learning how to run DFT calculations will be given instructions on how to use the supercomputer and how to apply their calculations to their research projects. No prior computational experience is needed.

Civil and Environmental Engineering

Miguel Figliozzi – Drones, Connected Vehicles, Public Transportation, and Bike/Ped. Safety

There are several active projects in the Transportation Technology and People (TTP) lab. The following is a quick sample of active projects: (i) There is a lot of hype regarding the potential of drones or unmanned aerial vehicles (UAVs) to improve the efficiency of supply chains and freight transportation. REU students will review and analyze recent advances in UAV technologies, capabilities, and applications. (ii) Delivery robots are coming and government agencies are struggling to cope with the potential implications of automated delivery vehicles on roads and sidewalks. REU students will analyze recent trends and applications of delivery robots. (iii) TTP lab members are working with TriMet (Portland’s public transportation agency) to identify routes with low performance and slow travel times. REU students will help analyze TriMet’s data (GPS bus data and stop level data) and it may be possible to extend the work to an economic analysis. (iv) TTP lab members are working with the Oregon Department of Transportation on a project that is developing a methodology to establish speed limits in urban areas with a high number of cyclist and pedestrians. Field data collection and analysis are part of this project. Other topics involving modeling and optimization of transportation systems are available; please contact Prof. Figliozzi to know more about the TTP lab and potential projects. In all the projects, REU students will work together with graduate students and/or a TTP lab faculty.

Thomas Schumacher – Carbon Nanotube-based Sensing Composites for Civil Infrastructure Applications

Nationwide, civil infrastructure systems are aging and deteriorating. Due to the limited funds available for repair, informed decisions need to be made by infrastructure owners. Carbon nanotube (CNT)-based composites have proven versatile and robust in this important task. This research focuses on the integration of CNT-based sensing technology into structural health monitoring (SHM) systems. CNT sensing layers consist of a conductive network structure that enables nerve-like distributed sensing capabilities. The sensing concept is based on utilizing electrically conductive nanotube networks integrated into the polymer matrix of a textile composite. CNT-based sensors have a number of unique characteristics as compared to traditional SHM sensors, such as strain gages, accelerometers, or displacement sensors, and are extremely well suited for distributed sensing. Additionally, they can be readily integrated with structural fabrics to form a self-sensing reinforcement. Selected REU students will work with faculty and graduate students to advance these sensors under laboratory and real world conditions. Work may include the characterization of sensing layers by use of electron microscopes, sensor response characterization under mechanical and environmental loadings, and processing, analysis, and interpretation of monitoring data.

Electrical & Computer Engineering

Christof Teuscher – 3D FPGA Cell Matrix by Self-assembly

To overcome physical size limitations in Moore’s law scaling of transistors in inherently two-dimensional geometries, efforts are being directed at wafer stacking to implement more quasi three dimensional (3D) architectures. However, significant and unprecedented gains in terms of packing and speed can be achieved if CMOS components can be integrated in truly 3D cellular porous architectures. This project combines cross-disciplinary expertise in software and hardware to create prototype 3D cellular computational devices by self-assembly. The interdisciplinary approach combines cutting-edge chemistry with CMOS technology and novel communication and computing paradigms. The student will first study the creation of electronic devices based on the paradigm of self-assembling smart modules in 3D crystals. We are interested to explore several research directions that the student can choose from. For example, a specific research goal is to investigate the influence of different 3D topologies and their influence on the overall system performance. Other possible research directions include the design and validation of new 3D Cell Matrix architectures, 3D visualization by means of Virtual Reality, and the investigation of defect- and fault-tolerance. The project is very interdisciplinary and allows a student to learn to solve problems related to software, hardware architectures, devices, self-assembly, and visualization.

Biomolecular Computation

Molecular computing is a promising computational paradigm, in which computational functions are evaluated at the nanoscale, with potential applications in smart molecular diagnostics and therapeutics. Drawing on a combination of experimental, theoretical, and computational tools, molecular computing systems will be developed. The student will first design, model, and simulate simple biomolecular circuits by either using existing tools or writing his/her own code. Later, more advanced molecular circuit architectures capable of adaptive, bio-inspired behavior, such as dynamic learning and adaptation, will be designed and simulated.

Geology

Andrew G. Fountain – Changing Glaciers of the American West

Glaciers are an important high alpine water resource in the western US. They melt most during the hottest and driest periods of the summer when the water is needed most. Furthermore, they are important agents of erosion, slowly carving into the bedrock. Tracking how the glaciers are changing over time and across the West are tasks important to assessing the effect of climate warming and the changing hydrological picture. At Portland State University we are tracking these changes using remote imagery and GIS, using the results for research papers and making them available to the general public via our website. Students will be engaged in digitizing the glacier outlines using Google Earth and/or ArcView depending on their experience. Making web pages to host the results may be an option. They may also be involved with field or laboratory work, if they so choose and if field/lab  work is being conducted that summer.

Mechanical & Materials Engineering

Jun Jiao – Low Temperature Growth of Graphene Films for Graphene-Based Silicon-CMOS Applications

Currently, the complementary metal-oxide-semiconductor (CMOS) based integrated circuits (ICs) scaling toward single-digit nanometer dimensions are facing tremendous challenges caused by the quantum limit, current leakage, thermal constraints, signal/power integrity, and device parameter variability. Graphene is predicted to have the greatest impact on geometric scaling due to its high mobility, which is desirable in CMOS field effect transistor (MOSFET) channels. In this Intel-funded project, we strive to develop a scalable technique for low-temperature (within 400–600C) growth of graphene with controlled properties by a chemical vapor deposition (CVD) process. A systematic experimental investigation will be carried out. The results will be comparatively analyzed, and the correlations of the synergistic effects among the growth parameters will be established. This will lead to the identification of optimal parameters for direct deposition of graphene films that could be readily integrated with the silicon-CMOS process for nanoscaled electronic fabrication. This project creates unique opportunities for the REU students who will be involved in growing graphene and participating in design, fabrication and measurement of related nanodevices. The REU students will also learn how to operate the electron microscopes for imaging, and the probe station for electrical measurements.

Elliot Gall  Passive Reduction of Human Exposures to Air Pollution Through Multifunctional Building Envelopes

Ozone is a ubiquitous outdoor air pollutant; over 120,000,000 Americans live in ‘nonattainment’ areas based on EPA regulatory levels. However, much of human exposure to ozone and ozone reaction byproducts occurs inside buildings, particularly inside homes where people spend most of their time. In residential dwellings, outdoor ozone typically transports into buildings via large openings like windows or by infiltration through cracks and gaps in building enclosures. While infiltrating through residential building enclosures, ozone can react with building materials and reduce the fraction that transports indoors. While this reaction suppresses indoor ozone concentrations, such reactions may result in the formation of oxidized byproducts, including aldehydes, ketones, carboxylic acids that may be more harmful and/or irritating than ozone itself. In this project, students will investigate the kinetics and byproducts of ozone surface reactions with a variety of typical building envelope materials. Surface treatments that encourage rapid decomposition of ozone will be investigated and assessed for inclusion in building envelope design based on an understanding of flow paths of infiltrating air crossing the building envelope, baseline material reactivity, kinetics of surface-treated components of building materials, and byproduct formation. Reactor models will be used to develop parameterizations that enabling scaling analyses to predict the implications of multifunctional, pollutant removing building envelope designs on human exposures to ozone and ozone reaction byproducts.

Alexander Hunt – Biologically Inspired Control Systems 

Robots and automation are moving beyond the manufacturing world and becoming an increasingly significant part of our lives. However, developing a robot or system which can work with and respond to people and demands in unstructured environments is extremely difficult. It is impossible to program a controller from scratch which can robustly respond to all possible situations. This is where machine learning comes in. By developing controllers which are able to learn from data and experience, we are able to build systems which are more adaptable and capable of changing situations than traditional control systems. In much of machine learning, a black box approach is taken where an artificial network of neurons is set up and then trained to produce the proper input-output relationships for problems such as image and speech recognition, game playing, or even robot locomotion. These work well for accomplishing specific tasks; however when a new demand is in place, a new network must be created and trained. In the Hunt lab, we work to build functional networks based on direct biology and neuroscience research and then train them to accomplish their tasks. This approach allows for increased transparency and the ability to grow the network to add functionality without needed to create a new one. REU participants will have the opportunity to apply the basics of computational neuroscience, optimization, and learning techniques to the field of robotics to solve a variety of different problems.

Tae-Kyu Lee – Enhancement of Reliability in Automobile Application Electronic Components with Conformal Coating Materials

From personal electronic devices to massive information traffic in and out of a "Cloud," we are in an Internet-dominated era. A good example of the ubiquity of electronic components and devices in our daily life can be found in the automobile sector. With the introduction of in-car instrumentation, navigation capabilities, and safety features, vehicle electronic systems become increasingly complex. As a result, the challenge to assure the reliability performance of automotive electronics is greater than ever, including self-driving vehicles -- which demand a very high level of reliability to assure safety for all vehicles on the road. Electronic components experience various end-use conditions, including cases of extreme heat, low temperatures, and corrosive environments. To assure the performance of these components, protection layers like conformal coating layer materials are applied; these layers protect the component, but can also potentially degrade its lifetime because of thermo-mechanical stress. Identifying the degradation mechanism is the goal of the project, since knowing the failure mechanism will give us a solution for improving component lifetime. Students will learn various electronic component types and structures, related materials sets and conformal coating options, and will participate in the process of testing the components and completing microstructure analysis.

Raúl Bayoán Cal – Fluid Mechanics/Turbulence

A common thread found between volcanic plumes, wind farms, urban canopies, and forests is their interaction with the atmospheric boundary layer. These flows possess a wide range of time and length scales with embedded non-linearities which give rise to the turbulence phenomena. In pursuit of understanding, it is beneficial to recreate the problem in a control environment such as a wind tunnel. Via laser-based non-intrusive techniques, quantitative observations are made on the physical/transport processes primarily driven by the equations of motion. In other instances, numerical simulations are required to represent the problem. Data analytics are continually employed to extract relevant information as to elucidate the flow physics. The work has direct consequences on efficiency increase in wind energy, prediction of ash dispersion from an eruption, building efficiency to name a few. Participants are provided with numerous options for possibilities of topics.

Zhiqiang Chen – Development of Advance Interconnect for Wearable Electronic Application

Wearable electronics have emerged as a new form of electronics that combine sensors and wireless communication. The applications for wearable electronics include health monitoring and disease detection, robotics, robotic surgery, implantable electronics, driverless cars, structural monitoring, and virtual reality and augmented reality.To construct a wearable electronic system for transporting electrical signals effectively, flexible and stretchable interconnect arrays that are capable of making conformal contacts on the curvilinear, soft, and dynamic surfaces of the target have been extensively researched. Among many strategies, the most representative approach is to fabricate interconnect arrays on plastic substrates to achieve more intimate and conformal contact with the target. Our research is focused on the optimization of electrical performance and mechanical compliance as well as manufacturability of compliant interconnects to provide an effective way of attaching sensors, device, or interconnects to the flexible substrate via surface modification on substrate and nano inks. The ultimate goal is to improve the electrical performance and mechanical compliance of the elastic interconnects through understanding the links between interconnect performance and surface and interface microstructure determined by number of electron microscopy and spectroscopy techniques. The REU students will be involved in experiment design for nano thin film and ink fabrication and learning how to operate the electron microscopes for imaging and spectroscopy.

Physics 

Erik Sánchez – Development of Ultra-high-resolution Near-field Microscopes

The research in Prof. Sánchez’s group focuses on the development of novel imaging and spectroscopic techniques utilizing field enhancement concepts [5–6] for the study of biological and semiconductor systems. Recently, other non-optical microscopes have been developed utilizing neutral atoms. The optical microscopes developed in Prof. Sánchez’s group are used for imaging samples using nano-Raman, nano-fluorescence, and magnetic domain techniques. He utilizes computational modeling of electromagnetic fields in order to design probes for generating a high field enhancement for imaging. Once a probe design has been determined, the group uses both high-resolution SEMs and FIBs to assist in the design and modification of these novel near-field probes. Apertureless probes typically require milling by a FIB system, which is then followed by inspection with a high-resolution SEM. The recent non-optical microscope development involves the usage of neutrally charged helium atoms projected to a sample and scattering off the surface, which allows the user to look at magnets, insulators and other materials difficult or impossible to see in an electron or ion microscope. So far, the resolution is roughly 250 nm but can be better with more development. REU students will take part in the design and fabrication of key components of these instruments.

Jay Nadeau – Encapsulation of Probiotic Bacteria for Food and Cosmetic Applications

A tremendous number of food and cosmetic products are marketed as “probiotics.” However, studies have shown that the bacteria in these products are largely dead. Micro-encapsulation may be a way to preserve bacterial cells in products stored in the refrigerator or at room temperature, in both oil-based and water-based matrices. In this industry-funded project, we aim to encapsulate beneficial bacteria in chitosan, cellulose, or other biocompatible polymer microcapsules and study their growth and viability by light and electron microscopy. Time-lapse videos under light microscopy will enable visualization of bacterial growth inside the capsules, and electron microscopy will be used to study the microstructure of the capsules and determine bacterial packing rates and morphology. The REU students will team up with a senior staff member and will be involved with making microcapsules, fixing and dehydrating them, using critical point drying (CPD), and embedding/sectioning the capsules for TEM. The students will learn to operate the SEM and TEM instruments independently for imaging of capsules and cells.