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SAE-26 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 10 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 10 positions are provided below:
WP1: A - Project on acousto-optic tomography
The Biophotonics@Tyndall team is currently investigating Acousto-Optic Tomography (AOT), which is a technique combining light with ultrasound to retrieve optical information deep within optically turbid media such as biological tissue. Since AOT uses both light and ultrasound, the signal of interest carries both optical information and mechanical/ultrasonic information.
The aim of this PhD research will be to investigate and quantify the contributions of the different tissue properties (optical properties and mechanical properties) on the acousto-optic signal. This is a necessary step to be able to decouple the information provided by both light and ultrasound and quantify the changes of optical absorption and optical scattering of the medium. This will help move AOT towards a quantitative imaging method and bring it closer to clinical applications.
For this position, the desirable criteria are:
WP1: B - Project on wavefront shaping
The Biophotonics@Tyndall team is currently investigating wavefront shaping to control light propagation in turbid medium such as biological tissue. Controlling the propagation of light in tissue is of great interest for multiple application such as local photo-activation or imaging for example.
This PhD research position will consist in investigating wavefront shaping in multiple scattering media both theoretically and experimentally. The goal will be to develop novel methods to focus light in tissue and improve the excitation of photosensitive targets like luminescent molecules with the aim of applying these methods to other projects within the Biophotonics@Tyndall team to increase performance.
For this position, the desirable criteria are:
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:
WP3: A - Project 1
Biophotonics@Tyndall team is developing multimodal systems for clinical in vivo applications. Diffuse reflectance (DRS) and fluorescence are simple and sensitive techniques providing important information about tissue. The overall aim is to develop real-time diagnostic systems based on those complementary techniques that can be easily integrated into the surgical workflow and provide clinicians with information aiding the decision-making process. Such systems can be well suited for both intraoperative diagnostic tools (e.g. identifying tissue types and disease states) and surgical guidance (e.g. navigation during surgery, delineating tumour margins).
The specific aim of this project is to design and build real-time diagnostic system based on DRS and fluorescence (and possibly other non-invasive optical modalities providing complementary information) to identify tissue in-vivo during gastrointestinal (GI) and orthopaedic procedures. This project provides exciting opportunity to work closely with clinical partners and multidisciplinary team of researchers to address current unmet clinical needs and translate lab-based prototypes into clinical setting. The candidate should be enthusiastic and motivated to push the envelope of current non-invasive optical diagnostic systems leveraging from multidisciplinary expertise of the Biophotonics@Tyndlal team.
Desirable criteria:
WP3: B - Project 2
Biophotonics@Tyndall team is developing multimodal systems for multiple clinical in vivo applications. These systems employ several non-invasive optical techniques (e.g. diffuse reflectance, fluorescence), which provide complementary information about tissue. The overall aim is to employ machine learning techniques to extract important information about tissue state from abundance of spectroscopic data to improve tissue classification and aid real-time diagnostics. Faster and more accurate algorithms, combined with improved understanding of physical features can not only help designing simpler and more compact instrumentation, but also extract previously hidden information.
The specific aim of this project is to develop data collection and processing algorithms for feature extraction and tissue classification for applications in surgical guidance and intraoperative diagnostics. This project provides exciting opportunity to work closely with clinical partners and multidisciplinary team of researchers to address current unmet clinical needs by developing the next generation of diagnostic tools.
Desirable criteria:
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, Nanotechnology, and Multivariate Data Analysis.
A: Early diagnosis of Oral Cancer: This project aims to develop a novel screening method based on salivary biomarkers characterized using surface-enhanced Raman spectroscopy (SERS) in photonic crystal fibres (PCFs) followed by spectral signatures guided biopsy of the oral lesions in-vivo. Optical fibre probe will be utilized to acquire in-vivo Raman and multispectral imaging data. Artificial intelligence-based methods will be developed to identify/extract spectral markers enabling automatic classification of unknown samples. This comprehensive platform will assist early detection and classification of oral cancer.
For this position the Desirable Criteria are:
B: 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:
WP5: Up-Converting Nano Particles
Project A: Long-term Continuous Biosensor for Real-Time In-vivo Monitoring of Biomolecules for Chronic-Pain Management.
Chronic Pain (CP) affects at least 10% of the world’s population. It not only is detrimental to the quality of life of the sufferer, but also poses a significant economic burden to our society, costing about $1T inclusive of productivity losses. The ability to monitor, in real-time in-vivo, pain-related biomolecules, such as cytokines, endocannabinoids, and/or circulating analgesics over an extended period of time is of tremendous significance for both fundamental study and intervention development. Existing biosensing technologies have not met this requirement. Up-conversion Nanoparticles (UCNP) have recently attracted much attention for its unique features such as ultra-photo-stability as well as the ability to circumvent optical interferences from the body’s background fluorescence. In this project, we will question how such unique properties can be exploited for long-term bio-sensing in the body. More specifically, we will look at how the luminescent lifetime of UCNP grafted with molecule-capturing receptor would be modulated upon binding to its target molecules. Two lifetime-modulating schemes will be looked at: 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. We will also investigate whether the use of UCNP-metallic-nanoparticles hybrid in place of UCNP could result in electromagnetic field enhancements that lead to increased detection sensitivity. Finally, by working in tandem with experts at IPIC, you will be tasked to build a miniaturized bio-sensing prototype. Due to the interdisciplinary nature of this project, you should be willing to adopt and develop a multidisciplinary approach to research.
Desirable Criteria:
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. A chronic condition is normally multi-faceted in nature and can evolve during treatments. To tackle such a challenge, there is a need to be able to deliver drugs on demand at the site of the disease so that treatment can be adjusted adaptively according to the disease state while minimizing off-target side-effects. More importantly, one must also be able to achieve this deep within the tissue. Unfortunately, light-responsive biomaterials that are commonly used for light-controlled drug-release only response to poor tissue-penetrating UV light. Upconversion nanoparticles (UCNP) that convert tissue-penetrating near-infrared (NIR) to UV light could effectively bridge this gap. By coupling light-responsive polymer to UCNP, one would in principle be able to implement deep-tissue drug release. Here in this project, we will explore this unique feature of UCNP, particularly its nonlinear luminescent responses to light switching speed, i.e. pulse-width. Here, through simulation, you will acquire a deep understanding of the energy-transfer upconversion process that is responsible for such a unique property. We will then study how the UV luminescence intensity, hence drug-release triggering, can be modulated in a switch-like manner using NIR pulse-width modulation. 2The benefit of such a scheme is that it permits one to perform NIR imaging and drug-release independently, thereby allowing us to deliver drug on demand in accordance to local disease state. In this project, we expect you to collaborate with many researchers from the University College Cork to develop a protocol to graft the luminescent nanomaterials with photo-responsive polymers for drug release. Due to the interdisciplinary nature of this project, you should be willing to adopt and develop a multidisciplinary approach to research.
Desirable Criteria:
WP6: “Embedded Biophotonics Sensors and Systems for Personal Medical Devices “
The overarching goal of this project is to develop the next generation of Biophotonics specific sensor electronics and embedded systems for smart implantable devices and integration onto surgical tools. Implantable devices can enable surgical navigation and tumour or disease state monitoring in vivo using photonics technology. Surgical tools, on the other hand, can provide guidance and classification of tissue through a multimodal sensing approach, differentiating between tumour and healthy tissue intraoperatively.
The successful candidate will work on the research, design and development of sensor interface electronics and embedded systems for medical devices applications, such as implantable and wearable devices. The candidate will collaborate with a diverse team of experts within the Biophotonics@Tyndall team, alongside other academic partners and clinicians, to understand the system requirements. The sensor electronics and embedded system will be developed to address these research needs.
This project will leverage other activities within the Biophotonics@Tyndall team, such as miniaturisation of multispectral sources, design and integration of highly sensitive detectors, micro spectrometers, and time-of-flight systems. Advanced machine learning and artificial intelligence algorithms will be employed to support the data analysis and interpretation process.
Desirable Criteria:
Essential Criteria for all Projects:
Desirable Criteria in addition to those specific to the individual projects:
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 Stefan.andersson-engels@tyndall.ie
Please indicate which WP you are applying for in your application.
Application Instructions
Step 1 - Click here to download the Application form and indicate the Job Reference SAE-26
Step 2 - Return the completed Application form, together with your CV and motivation letter to careers@tyndall.ie.
Postgraduate applicants whose first language is not English must provide evidence of English language proficiency as per UCC regulations (https://www.ucc.ie/en/study/comparison/english/postgraduate/). Certificates should be valid (usually less than 2 years old) and should be uploaded with their application. In special circumstances the panel may consider a prior degree in English (e.g. Master thesis written in English) as evidence of English language proficiency.
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.
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.