STEM Summer Research Dublin Courses

You will earn 6 research credits over 8 weeks, conducting faculty-supervised, hands-on, directed study research projects with results that will culminate in the preparation of a research paper.  You will complete a minimum of 240 hours on research in and out of the laboratory.

Faculty mentors will work closely with you to direct your continued growth and knowledge development in the chosen research topic discipline.

  • Please review your project with your academic or study abroad advisor to ensure it will transfer back to your home school and that you are following your home school’s policies.

Choosing Your Research Project

  • Review Project titles and descriptions below.
  • List 3 (in order of preference) in your Academic Preferences Form, using DUBL as the course code.
  • Program is highly individualized, with limited enrollment.
  • You will need to complete a brief Literature Review in consultation with your research supervisor prior to departure before the start of the program. More details here.
  • We encourage you to contact Arcadia’s Associate Dean of Academic Access and Curricular Solutions, Rob Hallworth, to discuss your particular research interests further.
Course ID Title Credits Syllabus
DUBI RSLW 392S International Independent Research in STEM Fields 6 PDF

Summer 2025 Research Projects

Is There Mislabeling of Native Irish Seaweed Products?

Supervisor: Dr Craig Wilding (School of Biology & Environmental Science) 

A number of manufacturers sell purported native Irish seaweed products – typically dried seaweed, e.g. dulce, to the health-food market. But are the products what  they claim? Fish product mislabelling has been a major issue across Europe - is the same true of seaweed products? Here, multi-locus DNA sequencing of commercial samples will be undertaken to identify the species composition and determine if product labeling is applied correctly. 

Relevant majors: Biochemistry, Molecular Biology, Environmental Biology, Genetics, Zoology

 

The Molecular Characterization of Variation at the Hexokinase and Malate Dehydrogenase loci between Color Morphs of the Beadlet Anemone Actinia Equina

Supervisor: Dr Craig Wilding (School of Biology & Environmental Science)

The beadlet anemone Actinia equina (L.) (Cnidaria: Anthozoa: Actiniaria: Actiniidae) is a common intertidal species on European rocky shores and occurs in a variety of color morphs. Previous research has indicated that anemones with red/pink pedal discs (the structure used to attach to the substratum) are genetically differentiated from those with green/gray pedal discs. The initial work that identified genetic differentiation used allozyme electrophoresis of enzymatic proteins, identifying allele frequency differences at  both the Hexokinase (Hk) and Malate dehydrogenase (Mdh) loci. This project will use genomic and transcriptomic data alongside molecular biology techniques (RNA extraction, cDNA construction, primer design, cloning, sequencing, simple bioinformatic analysis of sequences) to examine the genetic basis of these allozyme differences through sequencing of Hk and Mdh cDNAs from multiple anemone color morphs. 

Desired qualifications: the student should be comfortable with (limited) field-work (collection of Actinia), and learning and applying both molecular techniques and basic bioinformatics. 

Relevant majors: Biochemistry, Molecular Biology, Genetics, Zoology

 

The Molecular Characterization and Expression of Heat Shock Proteins in the Stress Response of the Beadlet Anemone Actinia Equina

Supervisor: Dr Craig Wilding (School of Biology & Environmental Science)

The beadlet anemone Actinia equina (L.) (Cnidaria: Anthozoa: Actiniaria: Actiniidae) is a common intertidal species on European rocky shores and occurs in a variety of color morphs. Previous research has indicated that anemones with red/pink pedal discs (the structure used to attach to the substratum) are genetically differentiated from those  with green/gray pedal discs and have different distributions on the intertidal zone (red/pink  pedal disc forms are found predominantly higher on the shore and green/gray forms lower  on the shore). As intertidal organisms, A. equina are subjected to heat stress on both diurnal and seasonal cycles and are particularly prone to the effects of climate change. This  project will study the Heat Shock Protein (HSP) repertoire and response of A. equina. HSPs are an evolutionary conserved family of proteins that act as molecular chaperones, correcting protein folding and/or maintaining protein homeostasis during periods of  environmental stress. In this project, the HSP family members will be identified in the A.  equina genome. Then gene family members previously identified as involved in the stress response in other organisms (e.g. HSP60 and HSP90) will be characterized in heat-stressed anemones using either qPCR or Western blotting, utilizing assays developed in concert with the student. 

Relevant majors: Biochemistry, Molecular Biology, Genetics, Zoology

 

Unraveling Cold Stress Responses in Brassica napus L.: Physiological and Molecular Approaches to Enhance Crop Resilience 

Supervisor: Dr Mortaza Khodaeiaminjan

Cold stress is a significant environmental challenge that affects crop productivity and quality. Brassica napus L., commonly known as oilseed rape, is an economically vital crop cultivated for its oil-rich seeds. However, its growth and yield potential are highly sensitive to low temperatures, particularly during early developmental stages such as germination, seedling establishment, and flowering. This research aims to investigate the physiological  and molecular responses of B. napus to cold stress by monitoring plant growth and analyzing gene expression. 

The study will be conducted under controlled glasshouse conditions, where B. napus plants will be subjected to cold stress to assess key physiological responses, including changes in overall plant growth, root development, and yield potential. At the molecular level, RNA will be extracted from different plant tissues to analyze the expression profiles of genes associated with cold response. The findings from this research are expected to contribute to breeding strategies for developing cold-tolerant B. napus varieties, ultimately enhancing crop yield and stability in regions prone to low temperatures. 

Relevant Majors: Plant Biology, Molecular Biology, Environmental Science 

 

Evaluating Waterlogging Stress Responses in Brassica napus L.: A Physiological and Molecular Approach to Enhancing Flood Tolerance 

Supervisor: Dr Mortaza Khodaeiaminjan (School of Biology & Environmental Science)

Waterlogging stress is a major environmental factor that limits crop productivity by restricting oxygen availability to plant roots, which disrupts essential physiological processes. 

Brassica napus L., also known as oilseed rape, is an economically important crop grown for its oil-rich seeds, but it is highly susceptible to waterlogging, especially during early developmental stages like germination and seedling establishment. This research aims to investigate the physiological and molecular responses of B. napus to waterlogging stress by assessing plant growth, root function, and yield characteristics and gene expression under simulated waterlogged conditions. The study will be conducted in a controlled glasshouse environment, where B. napus plants will be subjected to waterlogging stress for varying durations to observe the effects on key physiological parameters such as biomass, root and shoot growth, leaf chlorosis, and yield. At the molecular level, RNA will be extracted from different plant tissues to analyze the expression profiles of genes associated with waterlogging response. 

Data from this research will contribute to identifying physiological traits that could enhance waterlogging tolerance in B. napus. Such insights are valuable for breeding programs aimed at developing resilient varieties with improved performance under waterlogged conditions, thereby enhancing crop yield stability in flood-prone areas. 

Relevant Majors: Plant Biology, Molecular Biology, Environmental Science

 

Using Camera Trap and Acoustic Surveys to Reveal the Dynamics of Deer  “Hotspots” in Ireland 

Supervisors: Dr Simone Cuiti and Dr Colin Brock LAB LINK 

Camera trap and passive acoustic monitoring surveys are important for gathering information  on terrestrial wildlife’s distribution and behavior, providing insights into ecosystem health  and functioning. These methods play a crucial role in informing conservation strategies and  wildlife management decisions. The UCD Laboratory of Wildlife Ecology and Behaviour has  established two major Irish projects monitoring wildlife using non-invasive techniques. The  first one -Snapshot Europe - is a coordinated camera trap effort to collect data on mammals  across Europe. The second one – bioDEERversity – is a govt-funded biodiversity monitoring  program set up in the Wicklow and Dublin mountains. These projects have been gathering  data on wildlife and general biodiversity (soil ecology, plant diversity, and vertebrate  diversity) in a deer hotspot area of Ireland, where Sika deer have been shown to occur at  unsustainable high densities. Camera traps and acoustic recorders have been set up to  capture data in areas with no deer (fenced exclusion zones) as well as in those areas spread  across a gradient of sika deer relative density. Students involved will learn how to use user-friendly deep learning softwares (e.g., DeepFaune and Kaleidoscope Pro) designed to identify species using large numbers of image and audio files. Furthermore, the students will analyze camera trap data and/or acoustic data, and will have the opportunity to tackle a research question that will be defined with the help of the supervisor (e.g.: What is the effect of deer presence on the occurrence and diversity of the other mammal species?). 

Relevant majors: Biology, Ecology, Environmental Science 

 

Investigating a Novel Therapeutic Strategy for Bacterial Meningitis-Related Neuronal Dysfunction 

Project Supervisor: Dr Derek Costello Head of Neuroscience 

Bacterial meningitis (BM) is a severe condition involving inflammation of the protective membranes surrounding the brain and spinal cord, often leading to irreversible neuronal  damage and degeneration. Despite medical advances, BM continues to have a significant  mortality rate and long-term consequences for survivors, with approximately 30%  experiencing issues like seizures, sensory deficits, and cognitive or neurodevelopmental  impairments. These survivors are also at an increased risk of age-related neurodegenerative diseases such as Alzheimer’s disease (AD). The variability in prognosis is exacerbated by regional disparities in vaccine uptake and rising antibiotic resistance, making BM a persistent global health threat. 

Gram-positive bacteria, particularly Streptococcus pneumoniae in adults and Streptococcus agalactiae in neonates, are among the leading causes. The complex pathology is characterized by neuroinflammation, largely due to the activation of microglia. Metal ion imbalance further promotes oxidative stress and excitotoxicity, leading to neuronal death. This damage is especially pronounced in the hippocampus, where atrophy contributes to the  seizures and cognitive deficits common in BM sequelae. 

Our collaborators at TU Dublin have developed a new class of coumarin-derivative chemical agents with metal-chelating and antioxidant properties. Our preliminary evidence shows  that these agents can reduce microglial activation and preserve neuronal health under AD related conditions. This study aims to assess this novel set of multi-functional agents as  potential therapeutics for BM. We will evaluate their effectiveness in ameliorating bacterial induced inflammation and neuronal dysfunction, in cell-based models of AD in vitro and a  zebrafish model of AD in vivo. 

Techniques: Cell culture, cell viability, nitric oxide and protein expression analysis, Western immunoblot/qPCR analysis, in-vivo zebrafish behavioral assays. 

Relevant majors: Neuroscience, Pharmacology, Pre-Med  

The project objectives can be expanded to accommodate two students.

 

CRISPR Base Editing to Treat Inherited Retinal Disease Models in Zebrafish 

Project Supervisors: Professor Breandan Kennedy, Dr. Tess McCann

The Kennedy group uses zebrafish as a model organism to study biological processes relevant to human retinal diseases, many of which arise from single nucleotide mutations in individual genes. Currently, therapeutic options for these conditions are limited. CRISPR base editing offers a promising approach, enabling precise single-base changes in genomic DNA; however, aspects of safety and efficiency still need refinement. At UCD, we have established CRISPR base editing in zebrafish, following protocols by Rosello et al. (2023) and Qin et al. (2024). This project will extend this work to rescue mutations in vision-related genes using zebrafish models. 

The student will design guide RNAs targeting zebrafish that carry single nucleotide mutations in genes, such as emc1 and rab28, which are associated with retinal disease phenotypes. Base editing components will be introduced into single-cell zebrafish embryos via microinjections, using established protocols. To assess whether visual function has been restored, the student will conduct optokinetic and visual motor response assays. Genomic DNA from edited models will then be extracted and analyzed through Sanger sequencing to confirm successful base editing. Finally, retinal cryosections will be prepared to evaluate whether retinal morphology has been restored. 

This project aims to refine CRISPR base editing applications in zebrafish to rescue retinal disease, potentially paving the way for therapeutic approaches targeting single nucleotide mutation-based vision disorders in humans. 

References: Rosello, M., Serafini, M., Concordet, JP. et al. Precise mutagenesis in zebrafish using cytosine base editors. Nat Protoc 18, 2794–2813 (2023). https://doi.org/10.1038/s41596-023-00854-3

Relevant majors: Neuroscience, Genetics, Pharmacology

 

Association of Lipopolysaccharide Binding Protein (LBP) Concentration as a Biomarker of Gut Barrier Function, and LBP Genetic Variation with Colorectal Cancer 

Supervisor: Dr David Hughes - Cancer Biology and Therapeutics Lab, Conway Institute, UCD

Colorectal cancer is a common cancer with currently alarming increases at younger ages,  making prevention highly important. Although there are complex disease causes, environmental factors, particularly obesity and lifestyle, are known to play a strong role.  Recent evidence suggests that commensal microbial dysregulation and exposures to microbial toxins are involved in its development. We hypothesize that this occurs through inflammatory-induced weakening of the protective gut mucosal barrier by obesity, dietary/lifestyle, and microbiome factors that lead to translation of pathogenic bacteria and their toxins into the epithelial lining of the gastrointestinal tract. To help explore this hypothesis, the student will measure biomarkers of gut-barrier function and bacterial translocation (as biomarkers of microbial dysbiosis) by custom ELISAs, e.g., the human  Lipopolysaccharide Binding Protein (LBP) for bacterially derived lipopolysaccharide – integral to an intact barrier (which modulates the permeability of tight junctions between intestinal  tract cells). This will be done in a series of blood samples from non-disease controls  (n=120) and patients with colorectal cancer (n=120). Secondly, common genetic variants (SNPs; single nucleotide polymorphisms) in human genes within the LPS / LBP pathway (see our related study at doi:10.1093/mutage/geae008) will be genotyped by Taqman genotyping assays from blood DNA samples from these same patients. Together, these findings will illuminate gut-barrier function in colorectal cancer and possible contribution of bacterial toxin exposure from the gut. Note that both Postdoctoral and PhD researchers in the lab will be available to provide support to students who are unfamiliar with these methods. By the end of the project the student will become familiar with several techniques, including ELISA and DNA genotyping assays, and biostatistical packages such as R. 

Relevant majors: Genetics, Biochemistry, Epidemiology, Biology

 

Determining the Host Response to Novel Vaccine Antigens against ESKAPE Pathogens 

Supervisor: Assoc Prof Siobhán McClean 

Antimicrobial resistance is a massive growing problem in the fight against bacterial infections. The number of antibiotics that are effective at treating many bacterial infections is shrinking. In particular the ESKAPE pathogens are a group of highly virulent pathogens that can escape the majority of antibiotics. Vaccines represent one of the best ways to prevent bacterial infections and have also been shown to reduce antimicrobial resistance 1, We focus on discovering candidates in order to prevent these difficult and challenging infections. We use a proteomic approach to identify highly effective vaccine antigens which  prevent infections in mouse models. We have several vaccine projects ongoing in our  laboratory against antibiotic resistant infections such as respiratory infections that impact  the lives of people with cystic fibrosis 2 ; the tropical infection, melioidosis 3, 4 ; O157 E. coli  and three of the ESKAPE pathogens, namely Klebsiella pneumoniae, A.baumannii and P. aeruginosa 5, 6

We recently demonstrated that three P. aeruginosa antigens were very protective in an acute pneumonia mouse model (7) Immunized mice showed 80-times less bacteria after  immunization compared with unimmunized control mice. We are currently examining the protective immunological responses, including antibody responses and cytokine responses in serum or immune cells. This project will focus on investigating the mechanisms of protection of these antigens and investigate how we can maximize the protective response. It will involve using ELISA to determine the levels of antigen specific IgGs in immunized mice. In addition the host response will be further examined by exposing immune cells to antigen and evaluating the profile of cytokines produced using flow cytometry, ELISpot and/ or ELISA. Understanding how the antigens protect against infection is an important stage in progressing the vaccines towards human trials. 

Relevant majors: Immunology, Microbiology, Biochemistry 

References: 

[1] Frost, I., Sati, H., Garcia-Vello, P., Hasso-Agopsowicz, M., Lienhardt, C., Gigante, V.,  and Beyer, P.(2023) The role of bacterial vaccines in the fight against antimicrobial resistance: an analysis of the preclinical and clinical development pipeline, Lancet Microbe 4,  e113-e125. 

[2] McClean, S., Healy, M. E., Collins, C., Carberry, S., O'Shaughnessy, L., Dennehy,  R., Adams, A.,Kennelly, H., Corbett, J. M., Carty, F., Cahill, L. A., Callaghan, M., English, K.,  Mahon, B. P.,Doyle, S., and Shinoy, M. (2016) Linocin and OmpW Are Involved in  Attachment of the Cystic Fibrosis-Associated Pathogen Burkholderia cepacia Complex to  Lung Epithelial Cells and Protect Mice against Infection, Infect Immun 84, 1424-1437. [3] Casey, W. T., and McClean, S. (2015) Exploiting molecular virulence determinants in  burkholderia to develop vaccine antigens, Curr Med Chem 22, 1719-1733. [4] Casey, W. T., Spink, N., Cia, F., Collins, C., Romano, M., Berisio, R., Bancroft, G. J., and  McClean, S.(2016) Identification of an OmpW homologue in Burkholderia pseudomallei, a  protective vaccine antigen against melioidosis, Vaccine 34, 2616-2621. [5] Jurado-Martin, I., Sainz-Mejias, M., and McClean, S. (2021) Pseudomonas aeruginosa:  An Audacious Pathogen with an Adaptable Arsenal of Virulence Factors, Int J Mol Sci 22. [6] Ma, C., and McClean, S. (2021) Mapping Global Prevalence of Acinetobacter baumannii  and Recent Vaccine Development to Tackle It, Vaccines (Basel) 9. 

[7] Jurado-Martin, I., Tomas-Cortazar, J., Hou, Y., Sainz-Mejias, M., Mysior, M. M.,  Sadones, O.,Huebner, J., Romero-Saavedra, F., Simpson, J. C., Baugh, J. A., and McClean,  S. (2024) Proteomic approach to identify host cell attachment proteins provides protective Pseudomonas aeruginosa vaccine antigen FtsZ, NPJ Vaccines 9, 204. 

 

Investigating the Regulation of Cell-Cell Interactions in Chronic Inflammatory Intestinal Diseases 

Supervisor: Dr. Mario Manresa 

The intestinal mucosa is a dynamic environment full of structural cells such as fibroblasts that interact closely with the immune system to maintain a healthy gut and fight infectious pathogens. Alterations of the normal functioning of this environment can lead to abnormal immune responses that are characteristic of chronic inflammation. In the gut, chronic inflammation leads to ulcerative colitis or Crohn's disease, two debilitating conditions that affect millions of people worldwide and can lead to complications requiring surgical removal of gut segments. In recent years, fibroblasts have been identified as an important component of the abnormal mucosal immune response seen in chronic inflammation. These cells are now thought to establish intricate interactions with macrophages and neutrophils that may exacerbate the inflammatory response and lead to tissue damage. As a result, understanding the signals that activate these disease-contributing functions on fibroblasts and uncovering the ways in which they communicate with the immune system is of great therapeutic value. My research lab recently discovered a mediator that drives this cell-cell communication network. Delving further into this concept, we use primary cells and patient biopsies to understand the mechanisms that coordinate fibroblast-immune interaction. In this project, the student will integrate into our team and contribute to one of our CORE research areas, learning techniques such as in vitro cell culture, flow cytometry and western blot to characterize functional changes in fibroblasts and immune cells during inflammatory responses. 

Relevant majors: Biology, Genetics, Biochemistry, Pharmacology

 

Study of the Cross-Talk between SRF and AR in Prostate Cancer 

Supervisor: Dr Maria Prencipe 

Current treatments for prostate cancer mainly target the Androgen Receptor (AR), however despite initial response these treatments fail. Serum response factor (SRF) was previously identified as an important transcription factor in in vitro models of castrate resistant prostate cancer (CRPC) and a cross-talk between AR and SRF was demonstrated.  To further understand this cross-talk, we used mass spectrometry to identify common interactors between these two proteins. The aim of this project is to manipulate the key  common interactors to assess cellular response and to study their signaling pathway in prostate cancer cell lines. 

Objectives: 

  1. Manipulate common interactors of SRF and AR including HSP70, HSP90, PI3K and Akt using small-molecule inhibitors in a panel of prostate cancer cell lines. 
  2. Assess cell proliferation in response to these inhibitors singly and in combination with enzalutamide (current treatment for CRPC).
  3. Assess protein expression and activity of several proteins in the pathway after treatments. 

Techniques: Cell culture, MTT assays (cell viability), colony forming assay (cell  proliferation), Incucyte (cell proliferation for combination treatments), treatment with small  molecule inhibitors, western blotting (protein expression) and luciferase assays (protein  activity). 

Relevant majors: Pharmacology, Genetics, Biochemistry, Molecular Biology 

Two students possible. 

 

Acyl-Dihydropyridines - A New Class of Type-1 Photoinitiators for Holography 

Supervisor: Dr Bartosz Bieszczad

Acyl-dihydropyridines (acyl-DHPs, Figure 1) are synthetic analogues of nicotinamide adenine  dinucleotides (NADH), important biological co-enzymes. It has been found that upon  irradiation with visible light, acyl-DHPs release highly reactive acyl radicals. Acyl radicals can be trapped and used in organic synthesis in order to attach a carbonyl unit  to a molecule. Although acyl-DHPs are currently used by many groups around the world to  synthesize biologically active molecules, their application to material chemistry is much less  developed. 

Acyl-DHPs can act as type-1 photoinitiators, i.e. they are able to initiate the polymerization  upon irradiation with a visible light, while remaining stable and unreactive towards solvents  and other weak nucleophiles. This is a very rare and beneficial property. 

Acyl-DHPs can be easily prepared from simple starting materials in a single synthetic step.  They are also very tuneable, and many different types are synthetically possible. This project aims to develop new types of acyl-DHPs to act as type-1 photoinitiators for polymerization of methacrylates and other monomers for application in holography. In particular, it is expected that the addition of electron donating groups to the  acyl moiety will cause the red shift in absorbance, allowing the use of longer wavelengths: green and red lights. These types of photoinitiators are highly sought after in material science. The student will be involved in the synthesis and characterization of new acyl-DHPs and will apply them to the photopolymerization of methyl methacrylates. The progress of the polymerization will be monitored by Raman spectroscopy. 

Relevant major: Chemistry 

 

CORE Olefination: Organocatalytic Extension of the Wittig Chemistry 

Supervisor: Dr Kirill Nikitin

The Wittig olefination reaction has gotten a very significant makeover. First, the annoying  phosphine oxide by-product can now be used as the starting material. It can be converted directly to quaternary phosphonium salt, QPS, via new fast and high-yielding “Umpolung quaternization.” We have eliminated the waste problem and olefinations can be run using  phosphine oxide and avoiding phosphines at the interim stages. 

Second, we have developed novel ion-pair carboxylate reagents containing their own (hence  Eigenbase) endogenous anionic base. The Eigenbase reagents work in the absence of added  bases and this process is hinged on the interplay of structure and function of phosphonium  carboxylate ion pairs in different solvents. The olefinations furnish a range of alkenes in high  yields, no protecting groups are needed. 

Third, most Eigenbase reagents can be prepared directly from alcohols as shown in route 1. This variant termed acidic stoichiometric olefination reaction (SORE) avoids use of  halogen derivatives, bases and metal salts altogether. 

Fourth, we went a step further and have achieved a shortcut catalytic cycle 2 and developed  cycle 3. These circular olefination reactions (CORE) are single-step organocatalytic protocols. The venerable Wittig-type olefination is done without phosphorus waste, protecting groups, organic halides, metal salts and bases. Ironically, it is now acid catalyzed. 

Project Aims: identify set of conditions for CORE process and reagents; explore new classes catalyst for example solid acids. You will learn: air-free wet chemistry (O2 and  water); detailed NMR characterisation: 1H, 13C, 31P Isolation and purification; Intro-level  DFT computations. 

Relevant majors: Chemistry, Chemical Engineering 

 

Application of Cinematic Videography for Scientific Communication 

Supervisor: Dr. Fun Man Fung 

Scientific research is a major global investment and changes people’s lives. In 2024, a projected $2.53 trillion is being allocated worldwide to research and development (R&D).  This substantial figure demonstrates the increasing recognition of the importance of scientific innovation in addressing global challenges and driving economic growth. Scientific research is funded by taxpayer’s money. However, science is deemed difficult to comprehend by the public as most of them are not scientists by training. Therefore, there is a need to leverage the technology of videography to bridge the gap between scientists and the public, making scientific research more accessible and engaging. 

This study aims to provide empirical evidence for the benefits of using cinematic videography as an accessible tool for scientific communication, potentially contributing to a  more informed and scientifically literate society. 

Researchers on this project will create and employ cinematic videography as a technique to conduct the research. The person will be assigned to combine visually engaging imagery with clear and concise explanations in order to captivate audiences and facilitate a deeper  understanding of complex scientific processes. This work is important and could lead to the next stage of a longitudinal research – Using a mixed-methods approach to investigate the  effectiveness of cinematic videography. 

Relevant majors: Chemistry, Biology, Physics, Geology

 

Fundamentals and Applications of Nanopore Chemistry 

Supervisor: Dr Robert Johnson 

The Johnson group has expertise in the fabrication of nanopore structures and is interested in investigating the confinement of molecules within these structures. The transport of ions, as well as other fundamental chemical properties, can be quite different when confined to the nanoscale as opposed to the bulk. Typical projects will involve the fabrication of nanopores and their characterization, followed by the development of a sensing system for trace analytes of interest. Target analytes range from chemical and biological contaminants in foods and medicine through to toxic ions in the environment. Our research is highly interdisciplinary, with past students in biology, chemistry, physics and chemical engineering all enjoying successful placements within the research group. Projects are tailored to the student’s interests, but typically involve learning/developing some of the following methodologies: 

  • Electrochemical characterization (e.g. cyclic voltammetry, impedance  spectroscopy)
  • Nanoscale imaging (SEM, TEM) 
  • Surface chemistry measurements (e.g., QCM, contact angle) 
  • Surface modification chemistry (“solid-state synthesis”) 
  • Mathematical modeling with Finite Element Analysis 
  • Microbiology (PCR, cell culturing etc.) 

Relevant majors: Chemistry, Physics, Chemical Engineering, Biology 

Can host up to two students. 

 

Phosphorus-Based Cations as Main Group Catalysts 

Supervisor: Dr. Tom Hooper

Catalysis produces over $500 billion worth of products worldwide each year and homogeneous catalysts are used to produce a huge range of compounds, from large quantities of feedstock chemicals to complex drug molecules. Many of these catalysts are based on rare and expensive transition metals, the supplies of which are limited. Developing catalysts based on main-group elements will make catalytic processes less expensive and more sustainable. Phosphorus is an excellent candidate as a catalytic center because it can adopt different coordination numbers and oxidation states and its NMR active nucleus provides an excellent handle to directly interrogate reactions. Phosphenium cations have 2 substituents and phosphorus can interact with substrate molecules in a similar way to metals. 

The aim of this project is to synthesize and characterize a range of phosphenium cations with varying steric and electronic properties. This is done by manipulation of the ligand backbone through organic synthetic methods with the phosphenium center introduced using standard air sensitive methods (Schlenk line and glove box techniques). These potential catalysts will be tested for reactivity towards small molecules (H2, NH3, CO2 etc.) and organic substrates (alkenes, alkynes, furans, carbonyls etc.) with emphasis on reversible binding and reactivity. Onward reactivity towards the functionalization of these substrates will be targeted with the aim of regeneration of the catalytic center. In situ analysis of these reactions will be performed by multinuclear NMR spectroscopy, mass spectrometry and reaction kinetics studies. 

Relevant majors: Chemistry

 

WebXR Visualization of the Aqueducts of the Greater Iraklio Area (AGIA) 

Supervisor: Dr. Abraham Campbell 

The student will collaborate with the School of Archaeology to develop a visualization of the  Aqueducts of the Greater Iraklio Area (AGIA). The project’s primary goal is to explore how  models can be generated and experienced by users online with varying levels of computer  hardware, such as additional notes on the models, to provide users with more historical details. The student will be part of a team working on the project, so they could either come from a Computer Science background to help with that side of the project or come from an Archaeology background to help more with the Archaeology side as one area of research is to see if using the 3D models alone can provide real-world archaeology insights. The models will be generated in multiple ways such as photogrammetry, Neural Radiance  Fields (NeRF) and techniques like Gaussian Splatting for presentation. 

Relevant majors: Computer Science, Archaeology 

 

Can an LLM Help Shape and Improve an Existing Mobile App? 

Supervisor: Dr. Abraham Campbell 

The student will join an existing project exploring the use of LLM in app development. The  project explores whether Large Language Models (LLMs) can assist non-experts in improving an existing app, specifically focusing on transforming the "Pruritus Severity Scale" (PSS) for burn patients into a mobile application. The goal is to create an accessible, user-friendly app that allows patients to record their experiences daily. Given the unique challenges faced by burn patients, the project will emphasize accessibility and usability  while exploring the potential of LLMs in refining the app’s features. 

Relevant majors: Computer Science 

 

Large Language Models (e.g., ChatGPT/BERT/LLaMA) for Digital Forensic Investigation

Project Supervisor: Assoc. Prof. Mark Scanlon 

A large language model (LLM) is a type of artificial neural network designed for understanding and generating human-like text. It is a subset of models within the broader domain of natural language processing (NLP), which focuses on enabling machines to interpret, generate, and respond to human language. This project aims to develop a novel approach for digital forensic investigation using language models, such as ChatGPT/BERT/LLaMa, to generate forensically sound solutions for discovering and analyzing digital evidence. The proposed method will evaluate the potential for LLMs to enable digital investigators to analyze and interpret digital evidence from a variety of digital data sources and devices. Specifically, the project will look at the prospect of natural language digital forensic query being taken as an input, a step by step process being defined to answer the query, automating the evidence discovery through generated scripting, interpreting the results and presenting this interpretation back using natural language. The solution will be benchmarked using a framework designed in my group. 

The work of the student would involve working in a team of researchers in the creation of  end-to-end tests to assess the viability of LLM-aided digital forensic investigation. Working with this ongoing project in my research group will expose the research intern to the full research lifecycle from research design, development, experimentation with devices and datasets, and dissemination/discussion of results at UCD Forensics and Security Research Group meetings. 

Relevant majors: Computer Science, Computer Engineering, Data Science, Software Engineering 

 

Computer Vision Based Indoor Multimedia Geolocation 

Project Supervisor: Assoc. Prof. Mark Scanlon 

The task of multimedia geolocation is becoming an increasingly essential component to  effectively combat human trafficking and other illegal acts. While text-based metadata can  easily provide geolocation information with access to the original media, this metadata is  stripped when shared via social media and common chat applications. Geolocating, geotagging, or finding geographical clues in the multimedia content itself is a complex tax.  While there are numerous manual/crowdsourcing approaches to this, recent research has shown that computer vision is one viable avenue for research. 

The work of the intern would involve working in a team in the creation of novel datasets for  multimedia geolocation and developing computer vision-based techniques for indoor multimedia geolocation. The aim is to develop powerful methods for image geolocation that enable more efficient investigations in the field of human trafficking. Color values serve here as a key component to describe specific characteristics of an image and color-based descriptors will be used for Content-Based Image Retrieval. The performance of the developed methods will be evaluated using the Hotels-50K dataset as a foundation. Working with this ongoing project in my research group will expose the research intern to the full research lifecycle from research design, development, experimentation with devices and  datasets, international collaboration, and dissemination/discussion of results at UCD  Forensics and Security Research Group meetings 

Relevant majors: Computer Science, Computer Engineering, Data Science, Cybersecurity

 

Large Language Model Powered Password Cracking to Overcome Encryption  for Law Enforcement 

Project Supervisor: Assoc. Prof. Mark Scanlon 

Passwords have been and still remain the most common method of authentication in computer systems. From accessing your smartphone, to setting up your online banking  account or social identification, there is a plethora of passwords that users are required to set and remember in hundreds of websites. Complex passwords make the job of law enforcement engaged in a digital investigation more difficult, especially since time is often of the essence. 

This project aims to provide insights into the password selection process of users and the  impact of contextual information in it. Additionally, the ways that this contextual information  can be leveraged in order to assist with the lawful password cracking process will be explored. Large Language Models (LLMs) will be trained to generate password candidate dictionaries. To this end, intelligent, community-targeted dictionaries will be assembled. For  example, when targeting a community of superhero enthusiasts, we assume and want to  prove that a larger proportion of passwords would be contextually relevant to that  community than not.

The work of the intern would involve contributing to the benchmarking process through a  framework for evaluating different password cracking methods, as well as evaluating existing and newly created “smart” dictionaries against existing password datasets. The tools and dictionaries will be evaluated for different metrics and for varying degrees of contextualization, with the aim of establishing the impact of context in passwords.  Additionally, the intern can contribute to the dictionary creating process and be able to test their own dictionaries with this framework. 

Relevant majors: Computer Science, Computer Engineering, Data Science, Cybersecurity


The following information is vetted and provided by the American Association of Collegiate Registrars and Admissions Officers (AACRAO) on the Electronic Database for Global Education (EDGE).

Letter Grade Percentage Ranking U.S. Equivalent
A+/A/A- 70 - 100% First Class Honours A
B+/B/B- 60 - 69% Second Class Honours Upper B+
C+/C/C- 50 - 59% Second Class Honours Lower B
D+ 45 - 49% Third Class Honours C+
D/D- 40 - 44% Pass C
F 0 - 39% Fail F
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