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STEM Foundry

STEM Foundry Programs


    STEM Pack

    Undergraduate research communities consisting of authentic, interdisciplinary research experiences in a mentored research community structure.

    STEM Neighborhood

    Community-based research teams that collaboratively work on local problems in partnership with communities and local organizations in Southern Colorado.

    STEM Works

    Paid internship and field experience opportunities for undergraduates with companies, non-profits, and governmental agencies both locally and regionally.

    STEM Founder

    Structured incubator to help students generate and launch their own STEM ideas. Mentorship support with patent and startup process.

The STEM Foundry delivers hands-on opportunities to STEM undergraduate students, including exciting, engaged, local research opportunities, internships, and entrepreneurial training. Explore the four Foundry programs below. For any questions on the STEM Foundry, please contact Foundry Director Dr. Jim Carsella.

STEM FOUNDRY Research Projects


    STEM PACK Biology Projects

    Projects in Virology, Microbiology and Bioinformatics
    Amaya Garcia Costas
    Project Description

    Students in my lab will be able to choose from within a variety of projects. In one project we are aiming to characterize the molecular basis of bacteriophage-host interactions, including the bacteriophage lifestyle. A different project seeks to identify microorganisms with high tolerance or resistance to UV radiation and reactive oxygen species. We aim to evaluate this resistance and characterize possible mechanisms of resistance. A third microbiology project involves the development of biosensors (eg. bacteria) to sense pollutants in the environment such as metals or inorganic pollutants such as nitrates. Lastly, a solely bioinformatic project uses comparative genomics to annotate genes in the insulin signaling pathway of Drosophila species as part of a large collaboration. This project aims to better understand the evolution and function of metabolic pathways in eukaryotic organisms.

    Conservation of Migratory Song Birds
    Claire Ramos
    Project Description

    Conservation of migratory songbirds can be particularly challenging as it these animals require three distinct habitats for successful completion of their life cycle: breeding habitat, wintering habitat, and migratory habitat. The migratory phase of the life cycle of these animals may be the most critical as migratory behavior is physiologically stressful and dangerous. This was clearly demonstrated by a mass migratory songbird die-off that occurred in early Sept. 2020 the southwestern United States. Thousands of dead migrating birds were found over the span of just a few days. It is thought that this die-off was a result of a lethal combination of drought conditions reducing food availability, poor air quality caused by wildfires, and a freak snow storm. Migratory banding stations can provide valuable information to better understand the threats that migratory birds face on route to and from their breeding grounds. Migratory songbirds will be captured from field sites in areas heavily used by migrating birds in the area. We will use mist-nets to capture the birds and take various measurements to determine overall physiological condition of the birds. Birds will then be released to continue their migration.

    Colorado Checkered Whiptail Lizards in Urban-Natural Areas
    Dr. Fran Sandmeier
    Project Description

    This project focuses on mapping the local distribution of a rare lizard, the Colorado Checkered Whiptail (Aspidoscelis neotesselatus), as well as quantifying possible threats to its local persistence. The species is considered a species of conservation priority by the Colorado State Parks and Wildlife department, despite high levels of abundance within urban areas in Pueblo County. Because these urban populations have not previously been documented or studied, potential benefits and threats of urbanization have not been quantified for the persistence of lizard populations. A. neotesselatus is a parthenogenetic, asexually reproducing species. Like many similar, asexual species within the genus Aspidoscelis, it appears to thrive in disturbed areas. However, animals living in disturbed areas which are also highly urban may also be susceptible to anthropogenic stressors, including high levels of mesopredators. Increased predator-pressure in Pueblo County is most likely caused by feral cats, but could also include higher densities of natural predators such as raccoons, ravens, and coyotes that are known to aggregate around areas with increased irrigation and increased food sources. Here, we will quantify numbers of lizards across a gradient of urban-natural areas while also quantifying tail drops as a measure of predator attacks. Similarly, we will quantify external and internal parasite loads and differences in white blood cell profiles, as measures of stress. We hypothesize that the lizards in the most urban areas will exhibit higher levels of predator attacks and physiological stress than lizards in natural areas.


    STEM PACK Chemistry Projects

    Synthesis of New Organofluorine Compounds of Biological Interest from Phenols and Alkenes
    Dr. David Dillon and Dr. Melvin Druelinger
    Project Description

    The objectives of this proposal are two-fold. First, to explore the synthetic generation of new organofluorine compounds from two important classes of naturally occurring materials, phenols and alkenes and more specifically using resorcinol and limonene and derivatives. The approach will use electrophilic fluorinations to explore these reactions. It is anticipated that these new compounds will be biologically active; this aspect will be explored as appropriate. Secondly, the project will engage two students doing research in the summer and fall semesters. The students will be fully engaged in all aspects of the research including synthesis, isolation, purification, and structural identification. They will make use of many instrumental spectroscopic and chromatographic techniques. Ultimately it is anticipated that the research will lead to professional presentations and publications.

    Development of new methods in organic synthesis: transforming crude oil into medicines via transition metal catalysis
    Dr. Samuel Gockel
    Project Description

    The treatment of human diseases is a major public health concern that relies heavily on the existence of effective and safe medicines. However, the rate at which successful drugs are discovered is often constrained by the availability of synthetic methods capable of generating novel molecular scaffolds. Given this challenge, one of the primary goals of modern organic chemistry is to develop innovative reactions that can be applied in drug discovery. An important consideration in the design of new transformations is the ability to turn inexpensive building blocks into value-added products. Hydrocarbons derived from crude oil, such as alkenes, alkynes, are one such class of building blocks; however, they often lack the requisite polar functional groups that typically dominate interactions between pharmaceutical agents and their biological targets. The primary objective of the proposed research is to develop new carbon–boron (C–B) bond-forming carboboration reactions of alkenes and alkynes. C–B bonds are versatile functional handles that serve as a gateway to polar functional groups commonly found in medicines, such as amines and ethers. Central to the proposal will be the application of transition metal catalysis to achieve the desired transformations. A secondary goal is to study the mechanisms of the new reactions we develop to further our understanding of the underlying catalysis and to provide insight that will be of broad interest in the field. Students joining on this project can expect to learn the fundamentals of organic synthesis and method development, the foundations of catalysis, and key principles in transition metal reactivity. Students will also gain experience with cutting edge instrumentation and lab techniques. It is anticipated that this research will lead to publications in peer-reviewed scientific journals.

    DBF: The solution to preventing or reducing cataracts without surgery?
    Dr. Cassidy Dobson
    Project Description

    The overall scientific goal of this proposal is to investigate if a protein, Disulfide Bond Forming Enzyme (DBF) has the ability to rearrange incorrectly made disulfide bonds within γ-crystallin protein aggregates, the causative agent of cataracts. Cataracts are the leading cause of blindness worldwide and account for over 51% of all visual impairments1. γ-crystallins are the primary structural proteins in the eye lens. Normally these proteins exist as single entities called monomers that have a size of ~20 kDa. However, they can assemble into larger complexes such as dimers (2 proteins, ~40 kDa) or larger complexes known as γ-crystallin aggregates. Cataracts are ultimately caused when these larger protein complexes cannot be reverted back to their monomeric components. One example of the irreversibility of the γ-crystallin proteins are when strong disulfide bonds are formed between different proteins. These intermolecular disulfide bonds are covalent, irreversible interactions between different proteins, that inhibit their ability to disassemble back to their monomeric form. This type of disulfide-mediated aggregation is not unique to cataracts but has also been observed in other diseases such as Alzheimer’s, Amyotrophic lateral sclerosis (ALS), Parkinson’s as well as certain cancers2.

    1. Khairallah, M. et al. Number of People Blind or Visually Impaired by Cataract and in World Regions, 1990 to 2010. Invest Ophth & Vis Scie. 2015, 56: 6762-6769.
        2. Bechtel, T., Weerapan, E., From structure to redox: the diverse functional roles of disulfides and implications in disease. Proteomics. 2017, 17: pmic.201600391.

    Relationships Between In-Class Behavior and Laboratory Tasks
    Dr. Jonathan Velasco
    Project Description

    The broad objective of this project is to find relationships between instructors' as well as students' behaviors and the specific tasks provided by laboratory activities. In addition, the project's specific aims include finding the usefulness of task analysis to create profiles of laboratory activities. Students' involvement in the research will involve becoming familiar with the analytical instruments used to investigate in-class behavior as well as task analyses, and mentoring will include introducing STEM students to chemistry and/or STEM education research regardless of experience in the area, where they will use their subject matter expertise and experience to provide insight into the data. They will also be trained on the use of statistical software as necessary as well as introduced to theoretical frameworks used for the analysis. Their products will include presentations in symposia (in-campus or out-campus as possible) as well as authorship credit in a future publication.

    Investigation of exoskeletal composition, and the surface characteristics Penicillium fellutanum
    Dr. Jim Carsella
    Project Description

    Treatment of Penicillium fellutanum with different metals and sugars changes the expression of enzymes in P. fellutanum. These enzymes are part of a system of energy regulation and storage. The enzymes are also suspected to act on the remodeling of the surface of P. fellutanum. This project uses Atomic Force Imaging and Bioanalytical techniques to determine which enzymes are increased by which metals and sugars. Correlations and models will be developed in the process of determining which factors have the greatest influence on the surface remodeling of the fungus.

    The effects of cadmium and selenium on the formation of cadmium/selenium complexes regulation of gene expression in the model species and Saccharomyces cerevisiae
    Dr. Jim Carsella
    Project Description

    Treatment of Saccharomyces cerevisiae with cadmium and selenite results in the formation of fluorescent complexes in the yeast cells. The mechanism for this formation of "quantum dots" is poorly understood. This research aims to look at the formation of these complexes and determine which enzymes are responsible for the creation of the complexes.



    STEM PACK Civil Engineering Technology Projects

    Improving prediction of longitudinal cracking in asphalt pavement
    Dr. MD Islam
    Project Description

    Fatigue damage in Asphalt Concrete (AC) can be defined by a decrease in the stiffness of AC under repeated traffic loading. For each cycle of traffic loading, tensile strain develops at the bottom of the AC layer and at the surface of an asphalt pavement. Some localized damages occur in the material at minute- scale due to this developed tensile strain. These damages cause a decrease in the stiffness of AC. Damage caused by a single vehicle is small. However, the accumulated damage is not small if a large number of vehicles are considered over the design life of an asphalt pavement. After a certain level of damage accumulation, bottom-up fatigue cracking and longitudinal top-down cracking initiate and form cracking at the surface. Like traffic loading, repeated day-night temperature cycle causes damage to AC. Damage due to a single day-night temperature fluctuation may be small. However, the accumulated damage due to a large number of day-night temperature cycles may not be small. In this study, fatigue damage due to traffic loading is termed traffic-induced fatigue damage, and fatigue damage due to temperature is termed as temperature-induced fatigue damage. The recently developed AASHTOWare Pavement Mechanistic-Empirical (ME) Design Guide predicts the fatigue performance of AC based on repeated traffic-induced tensile strain at the top of AC layer. Cyclic thermal strain due to day-night temperature fluctuation is not considered due to the fact that there is no closed-form solution or model available for calculating thermal fatigue damage.


    STEM PACK Engineering Projects

    VTOL Octocopter for heavy payloads (200lbs)
    Dr. Nebojsa Jaksic, Dr. Bahaa Ansaf, Dr. Jude Depalma, Dr. Trung Duong
    Project Description

    This project is the continuation of the already established project with a final goal of human flight. At this stage, the octocopter is built and most of the hardware is created and installed. Our last flight attempt was not successful due to calibration problems with our control system. We are planning to upgrade the control system and test the flight characteristics of this octocopter (time in the air, maneuverability, actual maximum payload, etc.) We are also planning to increase the safety measures and design safety hardware. Also, we will be pursuing FAA permissions for outdoor flights.

    Lower Extremities Exoskeleton for Humans
    Dr. Nebojsa Jaksic, Dr. Bahaa Ansaf, Dr. Jude Depalma, Dr. Trung Duong
    Project Description

    Creating a viable low-cost alternative to existing lower extremities exoskeletons. Namely, such commercially available exoskeletons cost from $80K to $180K. We are trying to create such devices for much less. We have a first prototype that may need to be fully redesigned. There are a few directions that this project can take. Including dealing with the hardware design, control system, and AI in decision making and how long and fast the next step is.

    Effect of Fluid Polarity on IPMC performance
    Dr. Bahaa Ansaf, Dr. Jude Depalma, Dr. Nebojsa Jaksic, Dr. Trung Duong
    Project Description

    The Ionic Polymer Metal Composite (IPMC) is a synthetic composite material that can exhibit extreme part deformation under a low electric field. The applications of these artificial muscles range from robotics and biomedical to environmental sciences. These polymeric muscles work in air, underwater, or any polar fluid such as blood. The proposed work is to study the response of IPMC in different work environments (Examples of polar molecules include):

    • Water - H2O
    • Ammonia - NH3
    • Sulfur dioxide - SO2
    • Hydrogen sulfide - H2S 
    • Ethanol - C2H6O

    This work includes an experimentally studying the effect of work environment polarity on the IPMC strip deflection. In addition, this study will also consider the effect of the concertation of polar fluids.

    Deep learning-based semantic segmentation and applications
    Dr. Trung Duong, Dr. Jude DePalma, Dr. Bahaa Ansaf, and Dr. Nebojsa Jaksic
    Project Description

    In the field of computer vision, semantic segmentation is one of the key problems to understanding the scene at a high-level. Inferring knowledge from imagery has many applications, such as autonomous driving, human-computer interaction, virtual reality, etc. In this project, a special deep learning architecture based on the state-of-the-art semantic segmentation algorithm U-net is developed. One application will be the detection, localization, and classification of (asphalt paving or concrete) road cracks. Other applications of image segmentation will be investigated.

    AI-Based Forest Fire Alert System Using Satellite Imagery
    Dr. Bahaa Ansaf
    Project Description

    This project suggests developing an AI-based model to recognize fire in the forest using Satellite imagery. A supervised Convolutional Neural Network (CNN) will be designed and trained to classify images into two classes (Fire and NoFire). The training patterns (Images) will be created using the imagery captured by satellite forest images with superimposed synthetic fire images to create an adequate number of training patterns (examples). To more accurately depict the behavior of potential fires, we need to study wind patterns, fire behavior, and seasonal changes in selected test areas along with gathering the base images.


    SETM PACK Math Projects

    The Science, Mathematics and Context of the Struve Geodetic Arc Survey of 1816-1855
    Dr. Bruce Lundberg
    Project Description

    his project will explore the scientific and mathematical determination of the shape of the earth, still ongoing. It will focus on the data collection and analysis in the Struve Geodetic Arc Survey. This Survey was led by astronomer Frederick Wilhelm Struve over the years 1816-1855 and over 2820 kilometers through 10 countries from Ukraine to Norway. Thirty-four of the 265 station points in 258 main measured triangles are designated as UNESCO World Heritage Sites. These sites honor the outstanding international cooperation leading to great advances in knowledge of the earth's shape and size and topographical mapping techniques. The mentor visited two of these sites in 2021-22.


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