PhD Positions in Biophotonics and Biomedical Optics

Tyndall National Institute
February 29, 2024
Offerd Salary:$1.4Tril
Working address:N/A
Contract Type:Fixed Term
Working Time:Full time
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SAE-26b PhD Positions in Biophotonics and Biomedical Optics

Contract: Full Time/Fixed Term

Are you interested in a unique opportunity to become a PhD student in a fabulous team at an excellent research centre?

Biophotonics@Tyndall is offering new fully funded PhD positions in an already diverse and dynamic team. You will join an exciting and stimulating environment at one of the world-leading photonics centres - IPIC at Tyndall National Institute in Ireland. This will provide many opportunities for stimulating PhD training in close collaboration with clinicians and industry. The intention is to form an inclusive top-class PhD student cohort of which we would really like you to be part. This cohort of enthusiastic and talented new PhD students from diverse backgrounds will create an amazing environment for inspiring and successful training. Six well-motivated early carrier supervisors and two experienced mentors will support you.

This will all happen within this newly established collaborative Biophotonics@Tyndall research programme led by Professor Stefan Andersson- Engels. The team's focus is to form close collaborations with clinicians, research centres and companies to accelerate biophotonics technology and rapidly deliver breakthrough technologies into the hands of health-care providers. Using photonics as a driver for the faster development and deployment of more accurate, less invasive diagnostic and treatment methods for cancer and other diseases.

The positions will offer great opportunities for learning and to become internationally visible as successful candidates emerging from Biophotonics@Tyndall, which is becoming a key player in the field. The candidate is expected to be creative, self-motivated, and should help to sustain the efficient and friendly atmosphere established within the diverse Biophotonics team and beyond, to all teams at IPIC and Tyndall.

The specific areas of the positions are provided below:

WP2: Project on TOF-GASMAS

The Biophotonics@Tyndall team is working on gas in absorption media scattering spectroscopy (GASMAS) and time of flight (TOF) spectroscopy for non- invasive sensing of oxygen gas and hemodynamics in the lungs of infants. This hybrid technique combines benefits of oxygen gas sensing of GASMAS with blood biomarkers, path length correction from TOF spectroscopy.

The aim of this PhD research will be to design, develop and optimize a hybrid GASMAS-TOF system for neonatal lung application, to investigate and develop data analysis tools to quantify the oxygen and work closely with clinicians to explore hybrid device for neonatal application. This position will provide experience in developing high-performance clinical grade biophotonics system, systematic protocols to characterize and validate the system on phantoms and infants, simulations, data analysis tools to extract gas concentration and optical properties of biological tissues.

For this position, the Desirable Criteria are:

  • Background in optics and programming.
  • Strong experimental skills working with optics, lasers and detectors (aligning complex optical setup, troubleshooting experimental errors).
  • Knowledge of programming with Matlab for
  • communicating with all the instruments to synchronise the data acquisition.
  • processing the data acquired by the experimental setup.
  • Knowledge of programming for simulations (using Matlab or other programming language).
  • WP4: Project on Raman Spectroscopy for molecular fingerprinting

    Biophotonics@Tyndall team is developing advanced Raman systems for clinical applications. Raman spectroscopy is sensitive to molecular composition and structure/conformation and therefore has the potential to provide specific diagnostic information. Our goal is to develop cutting-edge Raman systems that can detect the presence of diseases at an early stage, pushing the boundaries of technological innovation. For these projects, we are seeking two highly motivated, inquisitive, and determined candidates to pursue PhDs in the field of Optical Spectroscopy, specifically with a focus on Diffuse Optics, Raman Spectroscopy, and theoretical modeling.

    Assessment of Bone Quality:

    This project aims to develop an advanced Raman system to extract quantitative information from the bone through scattering media. Inverse spatially offset Raman spectroscopy (iSORS) system and structured beams will be used to acquire bone signals through tissue. Further, optical attenuation parameters obtained using time-resolved diffuse reflectance spectroscopy will be utilized to extract quantitative information. This project will enable enhanced understanding of bone composition, providing insights into bone degeneration and regeneration.

    Desirable Criteria

  • Background in physics, physical chemistry, optics, and related area
  • Experience in Optical Alignment
  • Familiarity with Monte Carlo simulations, Machine Learning
  • WP5: Up-Converting Nano Particles

    Project A: Implantable Biosensor for Long-term Treatment Surveillance of Chronic Conditions

    The total global cost of Chronic Diseases (CDs) amounts up to about $1.4Trillion annually due to our ageing population. CDs not only are detrimental to the quality of life, but also pose a significant economic burden to our society due to the increased healthcare expenditure and productivity losses. Many often, the treatment for CDs is long-term and under an outpatient setting. To this end, an implantable biosensor will be desirable to facilitate remote monitoring, patient adherence as well as self-management. In this project, you will be involved in a very exciting research programme developing an implantable nanophotonic biosensor based on Up-conversion Nanoparticles (UCNP). This is really a multidisciplinary project, but with more emphasis on numerical modelling as well as electromagnetic theory. Specifically, you will be studying how the luminescent dynamics of UCNP grafted with molecule-capturing receptor, can be rendered sensitive to the binding of its target molecule. As such, we will look at two effects: a) fluorescence resonance energy transfer (FRET), which occurs when photon energy is transferred non-radiatively out of an excited UCNP upon binding; b) lifetime changes due to local increases in the refractive index surrounding an excited UPLN as a result of binding. Computational optimization (including the use of Machine learning) technique will be used to assist sensor design and to augment detection sensitivity and accuracy. In addition to theoretical study, you will also be required to perform experiments to validate your simulation outputs. This will include fabrication of the nanosensor as well as designing optical setups for experiments. If time permits, you will also be involved in developing miniaturized photonic platform. We are mostly interested in medical conditions among older patients; these include chronic pain, adverse drug effects, Alzheimer disease. Additionally, the project will also provide you with first-hand experience in healthcare, as we will be working closely with physicians.

    Desirable Criteria

  • Preferably a bioengineering background.
  • Be well versed in optical physics, electromagnetic theory, engineering mathematics, numerical calculations (MATLAB).
  • Preferably with some knowledge of material science.
  • Ability to construct a miniaturized device.
  • You must have some basic understanding of chemistry and also be willing to carry out surface chemistry experiments among other tasks and be comfortable working with biological samples (e.g., animal blood or cells).
  • Project B: Light Triggerable Drug Delivery with Luminescent Nanomaterials

    Globally, 1 in 3 adults suffer from some form of chronic conditions, which are responsible for about 3 in 4 deaths. Unfortunately, traditional therapeutic treatments are usually associated with poor efficacy or undesirable side effects. Developing new medicine unfortunately has increasingly become a financially unsustainable option. Here, we employ on an ‘old-drug-new-trick' approach to address such challenges by allowing doctors to augment traditional treatment methodology in a novel way through the use of nanophotonics. Specifically, we want to be able to direct drugs only to a targeted site in order to avoid unwanted toxic effects, and be able to time precisely its release via optical means, which would provide physician with an unprecedented control over the treatment outcome. Here, you will investigate the use of Upconversion Nanoparticles (UCNPs) for such purposes. Our UCNPs will be coated with a layer of light-responsive drug releasing polymer layer. To this end, you will perform computational modelling of luminescence dynamics from the UCNP against various excitation laser pulse shapes. This is then followed by modelling of drug release and intracellular diffusion kinetics. You will then need to design an optical-fibre based setup to verify your simulation results. Once a reliable light-triggering mechanism is successfully attained and well understood, you will then proceed to perform timed drug-delivery with cell culture. Here, you will need to use image analysis techniques to reveal insights into the treatment outcomes. As this is a multidisciplinary project, you should be willing to adopt and develop various approaches to research. Additionally, the project will also provide you with first-hand experience in healthcare, as we will be working closely with physicians.

    Desirable Criteria

  • Preferably a bioengineering background.
  • Be well versed in optical physics, electromagnetic theory, engineering mathematics, numerical calculations (MATLAB).
  • Preferably with some knowledge of material science.
  • Ability to construct a miniaturized device.
  • You must have some basic understanding of chemistry, and also be willing to carry out surface chemistry experiments among other tasks and be comfortable working with biological samples (e.g., cell culture).
  • WP6: PhD in Embedded Systems Hardware/Firmware Co-Design for Medical Devices

    The Biophotonics group at Tyndall National Institute invites applications for a challenging and exciting PhD position in embedded systems hardware/firmware co-design for sensorised medical devices.

    Working closely with our multidisciplinary research team, clinical and industry collaborators, the successful PhD candidate will take a lead on the research and development of the next generation of Biophotonics based sensor electronics and embedded systems for smart implantable devices and for smart devices integrated onto surgical tools.

    The project will leverage other research activities within the Biophotonics team to drive the development of impactful sensorised medical devices, such as biopsy devices with embedded fibre optics for tissue classification and navigation and image sensors for in-vivo tumour monitoring.

    The Biophotonics group have 45 researchers and conduct excellent research in the area of Biophotonics, Medical device research and translation. Our work is translated to the clinics with support from clinicians and the medical device industry. Many of our graduates go on to work in industry (Ireland has the second largest MedTech sector in Europe), industry facing research and others continue to do post-doctoral research in our group or collaborating research groups. Our group is multidisciplinary and this position is for an Engineer with embedded systems expertise looking to begin a research and design career in medical devices.

    Essential Criteria

  • Honours primary degree or MSc in Electrical/Electronic/Instrumentation Engineering (or equivalent).
  • A good understanding of hardware and firmware co-design for embedded systems.
  • Demonstrable expertise in embedded system from previous project.
  • Programming experience in C, Python or similar
  • Strong interest in medical device research.
  • Good teamwork skills and communications skills
  • If you are interested in this position and or completing your studies this year, please contact the researchers below for more information of an informal discussion with regard to this position.

    Dr Simon Sorensen [email protected] or Mr Ray Burke [email protected]

    Essential Criteria for all Projects:

  • MSc or BSc with first honors in one of the following disciplines: Physics, Applied Physics, Biomedical engineering, Electronics, Embedded systems engineering, Chemistry or related fields.
  • A good understanding of Biophotonics and light propagation in turbid media.
  • Demonstrate an academic record of scientific excellence and independent research.
  • Good communication, writing, organization, and interpersonal skills. Proficiency in English.
  • Highly self-motivated and able to demonstrate initiative.
  • Capable of working within a project team to achieve results.
  • A commitment to personal development.
  • Desirable Criteria in addition to those specific to the individual projects:

  • An appetite to learn and develop the understanding of biophotonics and light propagation in turbid media.
  • Passionate about pushing the boundaries of biophotonics sensor technology and system development.
  • Experience of relevance for the fields of biomedical optics is highly desired.
  • Good project management skills.
  • Demonstrate a capability to conduct specified programmes of research and participate in developing future research initiatives within the group.
  • Appropriate research experience.
  • Ability to engage in the wider research and scholarly activities of the research group.
  • An ambition to help create a friendly and inclusive work environment.
  • Good communication, writing, organization, and interpersonal skills.
  • Appropriate technical competence and accomplishment.
  • Highly self-motivated and able to demonstrate initiative.
  • A capability of working within a project team to achieve results.
  • A commitment to personal development.
  • Participate in Education and Public Engagement activities, as required.
  • Carry out any additional duties as may reasonably be required within the general scope and level of the post.
  • The annual stipend is €22,000 pa. In addition, yearly University academic fees will paid by the Tyndall National Institute.

    Informal enquiries can be made in confidence to Stefan Andersson-Engels at [email protected]

    Please indicate which WP you are applying for in your application.

    The closing date for applications is 29th February, 2024.

    Application Instructions

    Clickhere to Apply

    Postgraduate applicants whose first language is not English must provide evidence of English language proficiency as per UCC regulations (https: // www. Certificates should be valid (usually less than 2 years old) and should be uploaded with their application.

    Please note that Garda vetting and/or an international police clearance check may form part of the selection process.

    The University, at its discretion, may undertake to make an additional appointment(s) from this competition following the conclusion of the process.

    Please note that an appointment to posts advertised will be dependent on University approval, together with the terms of the employment control framework for the higher education sector.

    At this time, Tyndall National Institute does not require the assistance of recruitment agencies.

    Tyndall National Institute at University College, Cork is an Equal Opportunities Employer.

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