Circular Materials Bioeconomy Network: From bio-based resources to advanced materials (CIMANET) is an interdisciplinary doctoral education pilot programme designed to meet the competency requirements for a more sustainable future in Finland. The mission is to promote sustainable growth by strengthening the knowledge base required to enhance the bio-based industry with novel solutions unveiling the full potential of biomass.

CIMANET operates in close collaboration with the industry, research organizations, as well as other stakeholders to create economic and societal impact by addressing the major challenges of our century: resource sufficiency, access to clean water, and climate change. CIMANET starts in 2024 and provides altogether 67 doctoral researchers funding for three years. Check out all the open positions at the CIMANET pilot website.

The application is now open (deadline 30 September 2024) and is found here.

Research areas at Åbo Akademi:

• Lignocellulose chemistry
• Advanced lignocellulosic materials for packaging, construction, and electronics
• Advanced characterization methods for biomass and biomolecules

Three new positions open starting 1.1.2025:

• Topic: Novel technologies for chemical modification of biomass derived molecules and materials
  Supervisor: Professor Patrik Eklund
• Topic: Tailoring biopolymers for photo/thermal curable coating applications
  Supervisor: Professor Chunlin Xu
• Topic: Bio-based materials for recyclable electronics
  Supervisor: Professor Martti Toivakka

Photonics involves the generation, detection, and manipulation of light in the form of photons through emission, scattering, and amplification. Photons cover the full frequency range of electromagnetic radiation, but photonic applications typically employ ultraviolet/visible/near-infrared light.

Photonics is a rapidly growing industry sector in Finland with 6000–7500 employees directly working with photonics at Finnish photonics companies, with an annual growth rate of approximately 14% (see pdf-file Photonics industry in Finland 2023).

The doctoral pilot programme Innovative Doctoral Education Ecosystem for Photonics –  I‑DEEP reaches all Finnish universities with research activities in light-based technologies. Furthermore, with Photonics Finland and VTT as I‑DEEP associate members, excellent possibilities for collaboration with the industry exist.

At Åbo Akademi University, we host the following 3 projects within I‑DEEP:

Modelling of signal enhancement and fluorescence imaging in nanowire-based fluorescence biosensors

PI Assoc. Prof. Nicklas Anttu
High refractive-index nanowires could offer considerable signal enhancement in fluorescence-based biodetectors. To understand how light behaves in such applications and how to optimize the device materials and geometry, modelling is an effective approach. Here, we will model with the Maxwell equations the enhancement of excitation light, directionality of emitted photons from the fluorophore marker for enhanced collection of fluorescence signal, and enhanced quantum yield of the fluorophore through the Purcell factor. Furthermore, we will model the image sharpness from fluorophores from the vicinity of the nanowires, in which case the standard point-spread function in optical microscopy breaks down due to the strong diffraction of light by the high refractive-index nanowires.

Optimal nanoparticle deployment for passive cooling skylight day-time performance

PI Prof. Ron Zevenhoven
Passive systems for cooling that do not need external energy input (electricity) are dearly needed in these times of climate change and global warming. Controlling visible and non-visible short wavelenght (SW) thermal radiation at the same time as long wavelength (LW) thermal radiation entering or leaving buidling spaces offers opportunities for passive systems that selectively absorb/emit/reflect/transmit these different wavelength ranges. In this project, we consider passive cooling performance of a building roof skylight window.  The focus is to approach from a material physics viewpoint the photonics-material selection challenges combined with aspects of costs.

Enhancing efficiency and stability of organic and perovskite photovoltaic cells

PI Prof. Ronald Österbacka
Organic semiconductors and metal halide perovskites are two materials showing great promise for future thin-film solar cells. In such devices, the degradation of electrical contacts is a major effect. The aim of this project is to better understand contact degradation processes for increased long-term operation. We will use charge-extraction transient techniques to better understand the degradation processes in organic and perovskite photovoltaic cells. To support the characterization analysis, new models are developed for integrated optical and electrical device simulations, taking the contacts in particular focus.

Software engineering is a discipline and research field that entails designing, developing, maintaining, and managing software systems. Its role is essential in most areas of business and society, and a high level of software engineering knowledge and expertise is needed for success. The Software Pilot invests in doctoral education in software engineering, aligns it with real-world industry needs, and promotes academic-industry collaboration. The initiative gathers all nine universities that offer doctoral education in software engineering in Finland and creates a national environment for high quality academic work with industrial relevance. Åbo Akademi  offers four doctoral researcher positions in this pilot at the department of Information Technologies.

The application is now open (deadline 30 September 2024) and is found here.

Research areas: Software Engineering
Application period: 3.9.2024 – 30.9.2024
Doctoral researcher positions start 1 January 2025
Åbo Akademi University contact: Professor Ivan Porres

The Finnish Doctoral Program Network in Artificial Intelligence (AI-DOC) will educate 100 doctoral researchers across 10 universities. The program is an essential building block for our wider initiative of strengthening Finland’s position as an internationally attractive AI hub. The program’s main target is to educate new high-quality talent to bring AI expertise to advance a wide range of fields and to address the huge need for AI expertise in Finnish society and industry. It also contributes towards developing doctoral education by testing new practices that utilize the synergy in the wide consortium and consolidating the current effective practices. The program will boost collaboration among research organizations and Finnish industry through close links during the program and for the next career steps of the new PhDs. The program rests on two interlinked pillars: (1) strong fundamental research in AI as a necessary condition for applying AI responsibly and competitively, and (2) a set of application areas of high scientific quality and wide impact in industry and society. The program takes a broad view of AI, covering not only its technical fundamentals and applications, but also its broader societal implications. The main topical areas within the program are Fundamental AI, AI in Communications and Signal Processing, AI in Health, AI in Engineering, AI in Language and Speech Technology, and AI in Society and Business. The program pilots a joint call for applicants and their selection, and a high degree of cross-institute co-supervision, to provide each doctoral researcher with the best set of resources for their success.

Research areas at Åbo Akademi University:  AI in Health, AI in Engineering, and AI in Society and Business

Application period: 6 March – 2 April 2024 (tentative schedule, see FCAI site for more information)
Doctoral researcher positions start 1 August 2024 or 1 January 2025.
Åbo Akademi University contact: Professor Ivan Porres

The FCAI doctoral pilot is coordinated by Aalto University.

Digital Waters – Securing water resources with digital twins

The DIWA flagship is a leading research and innovation ecosystem, using research to support decision-making and pave the way for the next revolution in the water sector – digitally.

The duration of the DIWA doctoral researcher positions is three years, from 1 January 2025, to 31 December 2027. Two doctoral researchers recruited to the Department of Environmental and Marine Biology and one doctoral researcher recruited to the Department of Geology are expected to apply the right to study a doctoral degree at the Doctoral Programme in the Faculty of Science and Engineering. More information about researcher positions at other Digital Waters universities can be found here.

The application is now open (deadline 31 October 2024).

Available projects with positions starting 1 January 2025:

Projects (2): Ecological impact of ferry traffic waves on littoral biodiversity and ecological processes in an archipelago seascape

Supervisor: Associate Professor Christoffer Boström

Apply here!

Project (1): Geochemical processes related to gypsum treatment on farmland soils along the Baltic Sea

Supervisor: Professor Peter Österholm

Apply here!

For more information see the Digital Waters site.

The ImmuDocs consortia is coordinated by the University of Turku and the InFLAMES Flagship. Funding was applied for a total of 81 doctoral researcher positions for three years. These positions are divided between universities, of which Åbo Akademi University receives 6 of positions.

The application is now open (deadline 30 September 2024). More information is found here.

ImmuDocs to train immunology specialists

In 2024–2027, the Ministry of Education and Culture will provide funding for a national doctoral training pilot which tests new doctoral training practices in Finland. The pilot also aims to promote the employment of doctors widely in different sectors of society. To this end, the Research Council of Finland organised a call for pilot projects in November, in which the universities that are part of the Finnish Flagship Programme and consortia formed by these universities applied for funding for pilot project costs.

The ImmuDocs consortia is coordinated by the University of Turku and the InFLAMES Flagship. Funding was applied for a total of 81 doctoral researcher positions for three years. These positions are divided between universities as follows: University of Turku: 59, Åbo Akademi University: 6, University of Helsinki: 10, University of Oulu: 2, University of Eastern Finland: 2 and University of Tampere: 2. In addition, ImmuDocs’ consortium partners include the wellbeing services county of Southwest Finland and Finnish Vaccine Research, which contribute to doctoral training with their own extensive experience.

There is a constant and growing need for immunology expertise

Infections, autoimmune diseases and inflammatory diseases are major challenges for healthcare in the future. These diseases are caused by abnormal immune responses and consequently, influencing the immune system is at the core of the prevention, diagnosis and treatment of diseases. Therefore, healthcare urgently needs specialists who understand the possibilities and costs of immunological treatments.

The business world also needs immunologists. Already more than a hundred companies operating in the rapidly growing field of life sciences in the Turku region have a major, constant need for immunological expertise. This need is not limited to Turku only: the situation is the same in other life science companies operating in Finland. The majority of Finnish universities participate in the ImmuDocs pilot, and thus Turku’s strong immunological expertise benefits the whole country.

Doctoral researchers are supported in many ways

The aim of ImmuDocs is to renew doctoral training with measures that will enable doctoral researchers to complete their dissertations in 3–4 years. These measures include the careful advance assessment and planning of the doctoral dissertation project. In addition, doctoral researchers will be offered a clear, personal, scheduled and structured study plan. Researchers can benefit from enhanced motivation and support activities, their work will be closely monitored and the administrative processes related to studies will be streamlined. When applying for the participation in the programme, doctoral researchers and their supervisors must commit to new practices.

Half of the positions of ImmuDocs doctoral researchers will be filled from the beginning of August 2024 and half from the beginning of January 2025. There will therefore be two application processes during 2024.

The application process has two stages. In the first stage, research groups submit their doctoral dissertation research plans to the ImmuDocs Board, which selects the plans to be advanced. The selected doctoral dissertation projects and their descriptions will be published on the ImmuDocs pilot website and an open application process will be launched for doctoral researchers to participate in them.

Contact information:

For further information about the ImmuDoc doctoral researcher positions regarding the Subject of Cell Biology, please contact Professor Cecilia Sahlgren.

Projects starting in January 2025

Deciphering the interaction of Circulating Cell with Endothelial Cells using computer vision

PI: Guillaume Jacquemet

This PhD project aims to unravel the complex interactions between circulating cells (including immune and cancer cells) and endothelial cells, which are crucial for health maintenance and misregulated in various diseases. The candidate will develop and utilize Python-based, open-source imaging tools to establish a comprehensive analysis pipeline, drawing upon lab-developed software like ZeroCostDL4Mic, TrackMate, and CellTracksColab. This will enable the study of cell attachment and transmigration under various conditions, such as inflammation, and employ single-cell image-based profiling to identify endothelial cell traits predictive of circulating cell attachment. This research holds the potential to significantly advance our understanding of cellular mechanisms in cell adhesion and migration, offering insights into novel therapeutic strategies for inflammation and cancer. The project provides extensive training in imaging analysis, machine learning, AI, and drug screening, equipping the candidate for a successful career in the intersecting fields of cell biology, immunology and computational biology. With the support of existing lab resources and expert mentorship, this strategic approach is designed to fulfil the project’s ambitious goals and contribute essential findings to the scientific community.

Utilizing PNA/MNAzymes to generate precision immunodiagnostic tools for Epstein-Barr virus and CAR-T cell detection.

PIs: Hongbo Zhang and Silvia Gramolelli

Current methods for monitoring viral loads rely on PCR-based techniques, which can be time-consuming, labor-intensive, and require specialized personnel and equipment. This project aims to develop PCR-free diagnostic methods for detecting specific viral sequences in patient samples by exploiting the catalytic properties of PNA/MNAzymes nanotechnology. Our technology has already been modified to enable the detection of double-stranded DNA, hence we will use this approach to identify specific DNA sequences for virological and immunotherapeutic applications. By completing this project, the candidate will gain expertise in a range of fields, including nanotechnology, precision medicine, viral infection, and viral technologies.

Dysregulation of keratins in intestinal inflammation as expression inducers with biomarker potential

PIs: Diana Toivola and Lauri Polari

Gut diseases and disorders affect the life of over a billion people globally. Their severity varies greatly from minor discomfort to disabling diseases. Inflammatory bowel disease (IBD) is among the most serious ones, but it shares several symptoms with other gut diseases and disorders, which makes the initial diagnosis challenging. This PhD project will focus on a recently identified IBD biomarker, cytoskeletal keratin 7 (K7), that is not expressed in the healthy colon but occurs de-novo in the colonic epithelium of patients with IBD. The project will develop K7-based non-invasive assays to detect IBD and characterize the potential of K7 as an IBD biomarker. The specificity of the K7 expression in IBD compared to other gut diseases will also be established. In addition to diagnostic challenges, the complex molecular factors that contribute to IBD and K7 induction are poorly known. This PhD project also aims to characterize immunological and other molecular mediators affecting K7 regulation in the colon.

Projects started in August 2024

Development of targeted assays to measure lysosomal dysfunction and infectious pathogenic signatures as primary sources of immune system dysfunction in Parkinson’s disease.

PI: Eleanor Coffey

A growing body of evidence underscores the role of immune dysfunction in the early pathogenesis of Parkinson’s disease. Specifically, disturbances in lysosomal degradation and autophagy are observed in immune cells in Parkinson’s disease, particularly associated with gain-of-function mutations in LRRK2 and loss-of-function mutations in GBA, which play a pivotal role in this process. Moreover, dysfunctions in protein degradation via these pathways are believed to be triggered by pathogen infections. Consequently, the accumulation of protein aggregates originating from the gut and systemic immune system eventually infiltrates the brain, leading to the loss of dopaminergic neurons. This project will develop a molecular assay capable of assessing lysosomal dysfunction from immune cell proteomic data for the purpose of patient stratification and monitoring. In addition, the project will analyse data from over 6000 patient samples. Transdiagnostic modular analysis of these cohorts will be applied to identify disease associated networks.

Development of ubiquitin-based biomarkers for inflammation and cancer

PI: Annika Meinander

This PhD project focuses on developing ubiquitin-based biomarkers for inflammation and cancer, crucial for early diagnosis and treatment initiation. Chronic inflammation, linked to diseases like inflammatory bowel disease (IBD), heightens the risk of colorectal cancer. Met1Ub chains, associated with NF-κB pathway activation, serve as indicators of inflammation and cancer in cellular and murine models. Aptamers and antibodies facilitate highly sensitive detection methods for Met1Ub chains, applicable in both research and diagnostics. Collaboration with various experts ensures the project’s success, promising significant advancements in understanding and diagnosing inflammation-related conditions and cancers.

Expanding Toolbox for Targeted Oncotherapy: Intercepting Clever-1

PI: Tiina A. Salminen

Novel cancer treatments complementary to the immune checkpoint targeting therapies are urgently needed to combat currently non-treatable cancers. Macrophage-targeted therapies, which break the immune-tolerance of tumors and assist activating host immune defense mechanisms, belong to these innovative treatments. Targeting Clever-1 with anti-Clever-1 antibody bexamarilimab interferes with the immunosuppressive properties of macrophages and slows the spread of cancer. As part of a larger interdisciplinary effort towards developing Clever-1-targeted immunotherapy, we will determine the 3D structure for Clever-1 and elucidate its interactions with bexmarilimab at the atomic level to uncover inhibitory epitope. The obtained results will enable structure-based drug design of small molecular inhibitors expanding the toolbox for Clever-1-targeted oncotherapy.

Do you want to be part of developing the school of the future and tackle the core issues of learning using the latest technologies and methods?

The positions are part of the EDUCA-doc doctoral education pilot, which commences on August 1, 2024, and is financially supported by the Ministry of Education and Culture. The University of Jyväskylä leads the coordination of the project, with Åbo Akademi University playing a key role as one of the responsible implementers. In total, 78 doctoral researchers will be employed within the EDUCA-doc doctoral education pilot, collaborating closely with researchers, supervisors, and partner organisations of the EDUCA Flagship.

The mission of the EDUCA – The Education for the Future Flagship is to generate new knowledge and understanding of why learning outcomes decline, why the educational dropout rate increases, and how technology is used in teaching. The goal of the EDUCA-doc doctoral education pilot is to promote the development of education through research-based knowledge and to support evidence-based leadership. The Flagship and doctoral education pilot project aim to strengthen the research basis of educational policy decisions and experiments, as well as the expertise of teachers and principals. The research will increase understanding of the variation in individual and social learning processes, as well as factors explaining differences between schools. The research aims to identify optimal learning situations for students, as well as problems with engagement in education and reasons for increased school absenteeism. In addition, the goal is to create scalable digital solutions for everyday teaching and to utilise timely technology in learning contexts where it has been shown to produce better result.

Research areas:  education, psychology or other relevant field
Åbo Akademi University contact: Professor Johan Korhonen

EDUCA-doc

The EDUCA-doc doctoral training pilot aims to promote the development of education through research-based knowledge and to support evidence-based leadership. The flagship and the doctoral training pilot will strengthen the research basis of the educational policy decisions and experiments and the expertise of teachers and principals. The research will increase understanding of the variation in individual and social learning processes, as well as the factors explaining differences between schools. It will help to identify optimal learning situations for students, problems with engagement in education and the reasons for increased school absenteeism. In addition, it aims to create scalable digital solutions for everyday teaching and to utilise timely technology in learning contexts where it has been shown to produce better results.

The main themes of the EDUCA-Doc project are:

1. Educational experiments, reforms, and interventions (especially educational policy reforms and the impact of RCT interventions),
2. Variation in learning and support for learning (individual, group, kindergarten/school, municipal, and regional perspectives),
3. Scalable digital solutions for learning and teaching (especially variations in learning and learning analytics to support learning during early childhood education and compulsory education),
4. Strengthening the competence of teachers and principals and,
5. Data infrastructure as part of the EDUCA ecosystem.

EDUCA-Doc collaborates with non-university work-life partners who are already committed themselves to offer co-supervision, training events, and secondment positions to the doctoral researchers. EDUCA-Doc non-university partners present private sector, public sector, nonprofit sector, and research institutions.

Examples of organisations committed to EDUCA-Doc:

• Opetushallitus / EduFi
• Kansallinen koulutuksen arviointikeskus KARVI / The Finnish Education Evaluation Centre (FINEEC)
• Eduten Oy
• Niilo Mäki Institute
• KELA
• Finnish Institute of Occupational Health (acronym TTL in Finnish)
• Finnish Institute for Health and Welfare (acronym THL in Finnish)
• Itsenäisyyden juhlavuoden lastensäätiö (ITLA)
• Hyvinvointialueyhtiö Hyvil Oy
• Kuntien Tiera Oy
• City of Helsinki
• City of Kuopio
• City of Tampere
• VATT Institute for Economic Research
• ETLA Economic Research
• Työn ja talouden tutkimus LABORE
• Headai
• 3dbear
• Lingsoft Group Oy
• Qridi Oy
• Valamis Group Oy
• Suomen Ilmailuopisto Oy