Bioengineering

This PhD project aims to delve into the complex mechanisms of mechanobiology and their crucial influence on human embryo development. A growing body of evidence suggests that mechanical forces, alongside biochemical signals, play a significant role in cellular function and organismal development. However, the specific interactions and effects of these forces during the early stages of human development remain largely unexplored due to technical and ethical limitations. This research seeks to bridge this gap by employing state-of-the-art techniques in biomechanics, developmental biology, and computational modeling to examine how mechanobiological forces guide cell differentiation, tissue morphogenesis, and organ development during the first weeks of pregnancy.

The study will focus on three primary objectives: (1) To measure and analyze the mechanical forces exerted on cells in the developing embryo, (2) to assess how these forces influence signaling pathways and gene expression related to cell fate decisions, and (3) to determine the implications of aberrant mechanical forces on developmental anomalies in both embryonic and extraembryonic tissues

The project will utilize advanced microfabricated devices capable of simulating the mechanical environment of the womb. These devices will house cells and be subjected to controlled mechanical stimuli, mimicking the natural stresses and strains experienced during early embryogenesis. Live cell imaging techniques will allow for real-time observation and quantification of mechanical forces at play.

Simultaneously, cutting-edge genetic sequencing technologies will monitor changes in gene expression in response to different mechanical conditions. By integrating these data, the project intends to construct a detailed map of the mechanotransduction pathways that are active during early development.

By focusing on a largely underexploited yet critical area of embryonic development, this research is expected to provide groundbreaking insights into the role of mechanobiological forces in human embryo development. Understanding these interactions will not only refine our fundamental knowledge of developmental biology but could lead to improved clinical protocols in assisted reproduction technologies (ART) and potentially pave the way for novel interventions for developmental disorders.

Location and skills

The project will be carried out at the Institute for Bioengineering (IBioE) at the University of Edinburgh. The student will attain skills in mammalian cell culture, embryo models, microfluidics, materials, optical microscopy, as well as data and image analysis.

Career development

Institutional and Peer Support: you will benefit from an excellent supportive environment at the School of Engineering within the Institute for Bioengineering at The University of Edinburgh.

International Collaboration: the successful student will also have to opportunity visit and interact with our network of international collaborators.

Impactful publications and dissemination: the student will also benefit from strong support towards publications in world class journals and participation in major conferences as well as support to undertake outreach to the wider public.

Teaching and Research Development: the potential student will have the opportunity (once trained and familiar with relevant materials) to become a teaching assistant for courses offered at the School of Engineering.

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity: https://www.ed.ac.uk/equality-diversity

Minimum entry qualification - an Honours degree at 2:1 or above (or International equivalent) in a relevant science or engineering discipline, possibly supported by an MSc Degree. Further information on English language requirements for EU/Overseas applicants.

We welcome applications from self-funded students

Further information and other funding options.

Synthetic genetic circuits are the foundational technology that permit mammalian cells to be transformed into agents, be that for bioproduction, tissue engineering or cell therapies. Given their importance, it is our inconvenient truth that we are yet to achieve sufficient control of their performance1, nor the ability to scale their design beyond a few devices2 or ensure their long-term operation3.

This PhD will dive deep into the parameters that influence synthetic genetic circuits and work to redefine the boundaries of the possible. You’ll become expert in the genetic modification of mammalian cells (from lines to primary and stem cells) using a huge range of different transfection approaches and a host of analytical approaches from advanced imaging and molecular biology. The work benefits from the rich environment of the University of Edinburgh and core facilities such as the Edinburgh Genome Foundry and Edinburgh Genomics.

Engineering Biology is developing rapidly as a preeminent technology for the delivery of much of humankind’s needs and this PhD will equip you to contribute to diverse fields from cultured meat to therapeutic cells. More background is available by contacting Prof. Alistair Elfick.

1. Yeoh et al. (2022) Genetic Circuit Design Principles. In: Thouand, G. (eds) Handbook of Cell Biosensors. Springer, Cham.Shakiba et al. (2021) Context-aware Synthetic Biology by Controller Design: Engineering the Mammalian Cell, Cell Systems, 12(6), 561-592.Cabrera et al. (2022) The sound of silence: Transgene silencing in mammalian cell engineering, Cell Systems, 13(12), 950-973.

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity: https://www.ed.ac.uk/equality-diversity

Minimum entry qualification - an Honours degree at 2:1 or above (or International equivalent) in a relevant science or engineering discipline, possibly supported by an MSc Degree. Further information on English language requirements for EU/Overseas applicants.

Applications are welcomed from self-funded students, or students who are applying for scholarships from the University of Edinburgh* or elsewhere.

Further information and other funding options.

*A number of scholarships are available through a competitive process. Applicants are encouraged to contact the project’s supervisor, Professor Elfick, to discuss their interest in applying for the project, and scholarships.

The notion of artificial electromagnetic materials (AEMs) was conceived over a century ago; fabricating arrays of conducting objects within a nonconducting matrix can result in a composite material that achieves bespoke electromagnetic properties. The vital prerequisite for the macroscopic composite is that it possesses a periodic structure with active features of dimensions and lattice spacing much smaller than the length of the electromagnetic wave (Figure 4a). Indeed, if the size of the active features is sufficiently small, then these may act as an effective medium; i.e., the electromagnetic wave will experience the material as a monolithic entity. Examples of AEMs include, among other examples, materials with negative refractive indices and photonic crystals. The 1940s–1970s saw the accelerated development of AEMs in the microwave region (wavelengths of 30–0.1 cm), but until recently AEMs in the optical regime (400–700 nm), also known as optical metamaterials, were unmanufacturable. However, such materials are of considerable interest as they open the door to new ways of manipulating light, providing functions such as enhanced imaging capability or invisibility cloaks.

DNA nanotechnology has a plethora of applications in photonics which draw upon the nanoscale patterning and precise spatial arrangement of EM active features that can be achieved. Your PhD will straddle biophysics and electromagnetics, you will achieve experimental excellence across DNA nanotechnologies, AFM, optical characterization, and even EM modelling.

More background is available by contacting Prof. Alistair Elfick.

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity. Please see details here: https://www.ed.ac.uk/equality-diversity

Minimum entry qualification - an Honours degree at 2:1 or above (or International equivalent) in a relevant science or engineering discipline, possibly supported by an MSc Degree.

Further information on English language requirements for EU/Overseas applicants.

Applications are welcomed from self-funded students, or students who are applying for scholarships from the University of Edinburgh* or elsewhere.

Further information and other funding options.

*A number of scholarships are available through a competitive process. Applicants are encouraged to contact the project’s supervisor, Prof Elfick, to discuss their interest in applying for the project, and scholarships.

Organ-on-chip (OoC) technologies have become increasingly important in the study of disease aetiology and the development of drugs to intervene in disease processes. These miniaturized flow devices sustain cell cultures, often with multiple cell types and in 3-dimensions over extended periods in order to model tissue structure and behaviour in the body more accurately. However, they regularly present challenges to the researcher, not least the paucity of tools for multiparametric, real-time measurement of cell behaviour and response to stimuli during an OoC experiment.

A significant opportunity exists in the application of artificial intelligence and machine learning approaches to harness the true experimental power of OoC platforms. But a gap needs bridged between the data-intensive requirements of AI approaches and the data-sparse outputs of existing OoC technologies. OoC platforms needs instrumented to generate the massive datasets needed to power AI.

This PhD will explore the available technologies to enable high-content analysis of OoC systems. Three discrete, yet multiplexable, approaches to achieve this will be considered in parallel: Engineering of the cells to enable reporting of phenotype (e.g., Tx/Tl); Decoration of the chip with sensor technologies for in situ monitoring (e.g., pH, pO, temperature, cell impedance, biomarkers); and, stand-off, trans-chip measurement (e.g., microscopy & spectroscopy).

This cross-institutional collaboration benefits from the expertise and joint infrastructure of the University of Edinburgh and Heriot-Watt University, creating a world-class environment to pursue a project which promises great impact and reach in engineering for healthcare.

For further information please contact Prof. Alistair Elfick (University of Edinburgh) or Dr Sally Peyman (Heriot-Watt University).

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity. Please see details here: https://www.ed.ac.uk/equality-diversity

Minimum entry qualification - an Honours degree at 2:1 or above (or International equivalent) in a relevant science or engineering discipline, possibly supported by an MSc Degree. Further information on English language requirements for EU/Overseas applicants.

Applications are welcomed from self-funded students, or students who are applying for scholarships from the University of Edinburgh* or elsewhere

*A number of scholarships are available through a competitive process. Applicants are encouraged to contact the project’s supervisor, Prof Elfick, to discuss their interest in applying for the project, and scholarships.

Further information and other funding options.

This PhD project proposes an innovative exploration of how sex-specific differences in hormonal profiles and blood flow dynamics impact liver function, utilizing cutting-edge techniques involving liver organoids and microfluidic technology. Males and females differ significantly in their liver function and pathology, thought to be largely due to variations in hormonal environment and hemodynamics. Despite these observations, current approaches to elucidating these effects are limited, and rely heavily on expensive, time-consuming, and ethically challenging animal models and clinical trials. This project aims to fill this critical gap by developing and leveraging organoid-based models coupled with microfluidic systems to simulate and study the effects of these variables on liver behavior.

The overarching aims of the project will be:

1. Develop and Characterize Sex-Specific Liver Organoids: Generate male and female liver organoids using cells derived from human pluripotent stem cells. These organoids will provide a 3D cellular architecture that mimics the microenvironment of the human liver.
2. Integrate Liver Organoids into a Microfluidic Platform: Deploy these organoids within a microfluidic device designed to mimic blood flow characteristics. This integration will allow for the precise control and measurement of fluid shear stress and oscillating hormone profiles, mimicking the physiological conditions of male and female circulatory systems.
3. Investigate Hormonal Impact: Examine how exposure to different levels and types of hormones, such as estrogen and testosterone, influences liver function within this controlled setting. Focus will be on key functional metrics like metabolism, bile production, and response to injury.

The project aims to reveal critical insights into the sex-specific regulatory mechanisms of liver function influenced by hormonal and hemodynamic conditions. By elucidating these differences, the research will contribute to a more nuanced understanding of liver disease pathogenesis across sexes, potentially guiding more personalized medical treatments.

Location and skills: The project will be carried out at the Institute for Bioengineering (IBioE) at the University of Edinburgh. The student will attain skills in mammalian cell culture, microfluidics, materials, optical microscopy, as well as data and image analysis.

Career development -

Institutional and Peer Support: you will benefit from an excellent supportive environment at the School of Engineering within the Institute for Bioengineering at The University of Edinburgh.

International Collaboration: the successful student will also have to opportunity visit and interact with our network of international collaborators.

Impactful publications and dissemination: the student will also benefit from strong support towards publications in world class journals and participation in major conferences as well as support to undertake outreach to the wider public.

Teaching and Research Development: the potential student will have the opportunity (once trained and familiar with relevant materials) to become a teaching assistant for courses offered at the School of Engineering.

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity. Please see details here: https://www.ed.ac.uk/equality-diversity

Applicants applying for an MRC DTP in Precision Medicine studentship must have obtained, or will soon obtain, a first or upper-second class UK honours degree or equivalent non-UK qualification, in an appropriate science/technology area.

Further information on English language requirements for EU/Overseas applicants.

We welcome applications from self-funded students

Further information and other funding options.

Zinc-ion batteries (ZIBs) are emerging as a promising alternative to lithium-ion batteries (LIBs) due to their inherent safety, low cost, and environmental friendliness. As the demand for efficient, sustainable, and cost-effective energy storage solutions grows, ZIBs present a viable option for large-scale applications such as grid storage and electric vehicles. One of the key components determining the performance of ZIBs is the electrolyte, which plays a crucial role in ion transport, electrochemical stability, and overall battery efficiency.

This project focuses on the development and optimization of advanced electrolytes for high-performance zinc-ion batteries. Unlike lithium, zinc is abundant, non-toxic, and operates in aqueous environments, making it safer and more affordable. However, challenges such as zinc dendrite formation, limited electrolyte stability, and slow ion mobility need to be addressed for ZIBs to compete with LIBs in commercial applications.

Primary Objectives:

1. Design and optimize both aqueous and non-aqueous electrolyte systems, incorporating novel additives, ionic liquids, and solid-state options to enhance performance. This will involve addressing key challenges such as zinc dendrite formation, side reactions, and limited electrochemical stability.
2. Investigate strategies to prevent zinc dendrite formation and improve the cycling stability of zinc anodes. By optimizing the electrolyte composition, we aim to extend the battery's lifespan and enhance safety.
3. Investigate the interaction between electrolytes and various cathode materials to ensure compatibility and maximize energy density, charging speed, and cycle life. This will help identify the best electrolyte-cathode combinations for specific applications.
4. Utilize advanced electrochemical characterization techniques and computational modeling to understand the mechanisms governing electrolyte performance, ion transport, and electrode stability. These insights will inform the rational design of next-generation electrolytes.

The project will explore the balance between aqueous and non-aqueous systems, considering factors such as ion mobility, corrosion resistance, and electrochemical window. By enhancing zinc ion transport and overall battery efficiency, this research aims to push the boundaries of green energy technology.

The outcome will be a new generation of high-performance, scalable, and sustainable ZIBs, providing a viable solution for grid energy storage, electric vehicles, and renewable energy applications.

Please direct informal enquiries and requests for further information to Dr. Peisan E (Sharel) (Email Address: Sharel.E@ed.ac.uk), and provide a CV.

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity: https://www.ed.ac.uk/equality-diversity

Essential Experience:

• BSc and/or Masters Degree in Chemical Engineering, Chemistry, Physics, Engineering, Mathematics, Computer Science, Data Science, Machine Learning or Artificial Intelligence
• A minimum 2:1 undergraduate degree (or equivalent)
• Excellent spoken and written English and good communication skills. Further information on English language requirements for EU/Overseas applicants.
• Experience using modelling and simulation techniques
• Literature surveys, documentation and reporting

Applications are welcomed from self-funded students, or students who are applying for scholarships from the University of Edinburgh or elsewhere, as explained below.

PhD studentships managed by the School of Engineering at the University of Edinburgh are available every year through a competitive process.

Applicants interested in applying for a University-administered award should e-mail the supervisors (sharel.e@ed.ac.uk) as soon as possible to begin discussions, explaining how your experience meets the Applicant Requirements given above. Application deadlines vary from mid-January to late March.

Further information and other funding options.

Do you want to design and construct synthetic life-like cells? A major goal of synthetic biology is to create life-like artificial cells from non-living components, i.e. the bottom-up approach. This exciting project will focus on designing, constructing, and testing synthetic cells with multiple sub-compartments. Just like their living counterparts (i.e. eukaryotic cells), synthetic cells with different inner compartments allow multiple and advanced functionalities.

The building blocks will be lipid vesicles, both large unilamellar vesicles (LUVs) and giant unilamellar vesicles (GUVs), as well as membrane embedded and encapsulated proteins. To do so, the student will develop methodologies for lipid vesicle formation, including bulk techniques such as water-in-oil emulsions, and microfluidic systems (e.g. micro-droplets). Bottom-up synthetic cells can shed light on natural biological cell functions but can also be used for future industrial applications like biofuel production or in biomedical applications such as drug delivery.

Possible outcomes and goals:

• Studying the interaction of collections of synthetic cells (i.e. proto-tissues) for tissue engineering and regenerative medicine applications.
• Setting-up enzymatic reactions between sub-compartments to model and understand eukaryotic cellular metabolism.
• Developing new microfluidic tools to construct multi-compartment synthetic cells for drug delivery applications.

Methods:

• Lipid vesicle preparation
• Microfluidics
• Confocal microscopy
• Membrane protein reconstitution
• Cell-free protein expression

Location and skills:

The project will be carried out at the Institute for Bioengineering (IBioE) at the University of Edinburgh. The student will attain skills in microfluidics, lipid chemistry, membrane protein reconstitution, optical microscopy, as well as data and image analysis. The student will also learn various experimental techniques including microfabrication, protein preparation, lipid handling, and confocal microscopy. These skills will be essential for a student perusing an industrial career in the biotechnology sector; in addition they will be important for an academic career in Chemical or (Bio)engineering.

Career development:

• Institutional and Peer Support: you will benefit from an excellent supportive environment at the School of Engineering within the Institute for Bioengineering at The University of Edinburgh.
• International Collaboration: the successful student will also have to opportunity visit and interact with our network of international collaborators.
• Impactful publications and dissemination: the student will also benefit from strong support towards publications in world class journals (including the ACS Nano and Lab on a Chip) and participation in major conferences (including the Biophysical Meeting and the European Biophysical Congress).
• Teaching and Research Development: the potential student will have the opportunity (once trained and familiar with relevant materials) to become a teaching assistant for courses offered at the School of Engineering.

Please note this position will remain open until filled. Please contact tom.robinson@ed.ac.uk before applying.

https://www.eng.ed.ac.uk/about/people/dr-tom-robinson

Relevant publications:

Shetty, S. C. et al. (2021) ‘Directed Signaling Cascades in Monodisperse Artificial Eukaryotic Cells’, ACS Nano. American Chemical Society, 15(10), pp. 15656–15666. doi: 10.1021/acsnano.1c04219.

Yandrapalli, N. et al. (2021) ‘Surfactant-free production of biomimetic giant unilamellar vesicles using PDMS-based microfluidics’, Communications Chemistry. Nature Publishing Group, 4(1), p. 100. doi: 10.1038/s42004-021-00530-1.

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity. Please see details here: https://www.ed.ac.uk/equality-diversity

Honours degree at 2:1 or above (or international equivalent) in any of these areas Chemistry, Biochemistry, Biotechnology, Chemical Engineering, Mechanical Engineering, Bioengineering or related discipline, possibly supported by an MSc Degree.

Experimental experience in one or several of the following areas would be advantageous:

• Microfluidics
• Fluorescence microscopy
• Image analysis / analysis of reaction kinetics data

Previous experience with biological samples, such as protein reconstitution, lipid vesicles (e.g. GUVs or LUVs), or cell-free expression.

Further information on English language requirements for EU/Overseas applicants.

Full funding (tuition fees + stipend) is available for Home and Overseas applicants.

Further information and other funding options.

Electrosynbionics [1] involves the use of biological parts to create devices that generate electricity, such as biological photovoltaics and biobatteries. Electrosynbionic systems can be sustainable power sources for electronics, supporting the Green Transition.

Biosensing involves detection of biological targets, often for diagnosing or monitoring disease. Cheap and effective biosensors can save lives.

Biomimetic membranes can be vital components of electrosynbionic or biosensing devices. For maximizing performance, we need to use sophisticated nature-inspired membranes that are folded or crinkled. The PhD student will investigate different biomimetic materials and explore how to build membranes with complicated morphologies that will deliver optimal performance in devices.

The project will begin with a literature review. This will be coupled to a technoeconomic analysis of biomimetic membranes, the aim of which will be to assess suitability of different materials for applications involving mass production. For training purposes, the student will reproduce selected literature results before moving on to systems of their own design. They will design, build and characterise complex membrane structures, demonstrating the ability to engineer the membrane shape. They will test the effect of using their structures in selected devices.

The student will be trained in wet lab techniques and advanced characterisation methods. Subject to student eligibility and availability of opportunities, they will be able to teach, engage in public outreach or explore other opportunities complementary to their research. They will be encouraged to engage with appropriate training via the University’s Institute for Academic Development, Edinburgh Innovations or otherwise, as well as to participate in the intellectual community provided by the School of Engineering’s Institute for Bioengineering, in which they will be based.

As this project will complement other research with commercial applications and/or industrial partners, the student will be required to assign intellectual property arising from their PhD to the university, as a condition of accepting the offer. The PhD is fully-funded for Home Students, with a budget for research consumables.

[1] Dunn, K.E. The emerging science of electrosynbionics Bioinspiration & biomimetics (2020) DOI: 10.1088/1748-3190/ab654f

Katherine Dunn research group website: https://www.katherinedunnresearch.eng.ed.ac.uk/

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity. Please see details here: https://www.ed.ac.uk/equality-diversity

Minimum entry qualification - an Honours degree at 2:1 or above (or International equivalent) in a relevant science or engineering discipline, possibly supported by an MSc Degree. Further information on English language requirements for EU/Overseas applicants.

Tuition fees  + stipend are available for Home students.

Further information and other funding options.

The antimicrobial coating industry is experiencing rapid growth as the need to prevent the serious challenges posed by bacterial adhesion and the subsequent formation of biofilms on device surfaces becomes increasingly critical. Biofilm formation can lead to chronic infections, device failures, and significant healthcare complications, making the development of effective antimicrobial coatings more vital than ever. At the Institute for Bioengineering at the University of Edinburgh, we are launching a cutting-edge project that combines advanced anti-adhesive strategies to prevent bacterial attachment with bactericidal methods to create highly effective antimicrobial coatings.

This innovative research aims to tackle the global issue of infection control by developing coatings that not only resist bacterial adhesion but also actively kill bacteria, offering a dual approach to ensuring safer, longer-lasting medical and industrial devices. By integrating state-of-the-art materials and technologies, our goal is to enhance the performance of antimicrobial surfaces and contribute to a healthier, more sustainable future.

We are seeking a highly motivated and skilled candidate with hands-on experience in materials science, nanotechnology, chemistry, or biology to join this exciting project. The ideal candidate will be passionate about advancing science and technology in the field of antimicrobial solutions and eager to make a tangible impact on public health. Join us at the forefront of this dynamic industry and contribute to groundbreaking research that could revolutionize infection prevention and device safety.

Chemical Engineering for Biology & Medicine website: https://xianfengchen.wixsite.com/biomaterials

The University of Edinburgh is committed to equality of opportunity for all its staff and students, and promotes a culture of inclusivity. Please see details here: https://www.ed.ac.uk/equality-diversity

Minimum entry qualification – an Honours degree at 2:1 or above (or international equivalent) in chemical engineering, chemistry, materials science, biomedical engineering, or cell biology.

English language requirements need to be satisfied by EU/Overseas applicants.  Further information on English language requirements for EU/Overseas applicants.

Applications are welcomed from self-funded students, or students who are applying for scholarships from the University of Edinburgh or elsewhere.

Further information and other funding options.