Category Archives: PhD

Collaborations in a PhD student’s life

During a meeting, conference, workshop, or coffee break, a brilliant idea sometimes shines in the restless mind of a PhD student. Looking into it and trying to formulate a good plan to work on it, the student realizes that some aspects are way outside of her field of knowledge… and there is not enough time to become an expert in all scientific fields. This realization will undeniably lead the student to ask for help and hopefully, a collaboration will begin. As with any experiment, a collaboration can be fruitful and lead to high-value results which add to our understanding of the world. If things are not managed well however, an attempted collaboration can mean the end of a professional relationship, or even the abandonment of a project altogether. It’s all a matter of communication! Being clear about the expectations on everyone involved is a key ingredient of a successful collaboration. This has been an important lesson for me to learn at the beginning of my career, as I have had the opportunity to bring collaborators into my own projects and also had the chance to contribute to others’ work.

There are different degrees of involvement in a collaborative project. A seemingly simple or “small” contribution for me could be performing a short series of characterizations and the corresponding analyses. Such a seemingly small experiment, which might be quite easy for the person doing it, can generate data that are pivotal to a certain publication, yet contributions like this often go unrecognised. This leads to ethical issues such as people not being given credit for their work. It is a very fulfilling experience to have your intellectual work recognised as an actual contribution to a study, and the guidelines of the International Committee of Medical Journal Editors are very helpful in defining who should be listed as an author. I am happy and honoured to have recently been included in publications deriving from three interesting projects in which I performed lignin characterization by using nuclear magnetic resonance experiments and size exclusion chromatography. These are methods I am familiar with, but they take time and expertise to both perform and interpret.

In the first collaboration, published in the journal Cellulose (Ghaffari et al., Cellulose, 2023, 30, 3685–3698,, lignin diffusion through a cellulosic membrane was explored.  A diffusion cell was used as a model to study what happens during delignification of pulp. The success of this process depends on the effective diffusion of lignin through a cellulosic matrix, and this project aimed to understand the parameters that govern and can affect that process. The diffusion cell used in this study was equipped with a cellulosic membrane, and lignin solutions were provided on one side of the cell membrane. The impacts of lignin alkalinity and size were investigated by varying the pH of lignin solutions and the molecular weight of the lignin fraction used.

Molecular weight of lignin and pH of solution affect diffusion of lignin through a cellulosic membrane. Figure from Cellulose, 2023, 30, 3685–3698.

By performing a series of characterizations of the chemical properties of lignin in the donor and acceptor solutions, i.e. the solutions on each side of the cellulosic membrane, we could conclude that low molecular weight of lignin and high pH of the solution can increase diffusivity. This was attributed both to changes in the conformation of the polymeric structure of lignin and in the membrane itself. For example, high pH is known to reduce self-association of lignin, making it easier to diffuse through smaller pore size. We also found that alkalinity increases the porosity of the membrane, by swelling of cellulose. The results of this study can be used in the optimization of pulping to improve the yield and efficiency of the processes.

Next, two publications showcase the amazing properties of wood aerogels. The paper published in Advanced Functional Materials (Garemark et al. Advanced Functional Materials, 2023, 33 (4), 2208933, described the formation of a wood aerogel that can to be used as a power generator, by harvesting the hydrovoltaic energy produced during water evaporation. Wood samples were treated with sodium hydroxide at -6 °C, which led to the partial dissolution of the polymeric components of wood that diffuse to the empty lumen. Then, the dissolved polymers precipitated with the addition of water and formed a network of fibrils in the lumen. This re-distribution of the wood structure offers several advantages to this application. For example, the surface area of the material is increased, so there is an increased evaporation at the water-air interface. In a very cool demonstration of this technology, these wood power generators were connected in series and used to power a digital timer (, see Supplemental Video 1).

Wood aerogel formation for harvesting hydrovoltaic energy produced during water evaporation. Figure from Advanced Functional Materials, 2023, 33 (4), 2208933,

The second application we demonstrated, published in ACS Nano (Garemark et al. ACS Nano, 2023, 17, 5, 4775–4789,, was of a shape-memory wood aerogel. Polymeric shape-memory aerogels can be used in a variety of applications as insulators, actuators, or sensors. Currently they are mostly made of fossil-based materials and produced via complicated methodologies. As a result, this new wood-based application opens the way to sustainable development in this field. The wood aerogels are prepared by a one-pot treatment of wood samples with an ionic liquid and dimethylsulfoxide. There is a partial solubilization and redistribution of the wood components, as in the previous material. Upon the addition of water that leads to their precipitation, a fibrillar network is formed inside the lumen. Importantly, lignin is not severely modified during this process, and only a small degree of bond cleaving was observed, showing that ‘native’ or unmodified lignin has real technological applicability. The still-high lignin content in the aerogel, and the redistribution of the polymeric materials after solubilization and precipitation, is thought to be the cause of the excellent mechanical properties of the aerogel, which are in the same range as wood itself.

Participating in the above projects was an exciting experience as I was given the opportunity to discuss the relation of my own more “theoretical” lignin research in the context of specific material applications. My PhD thesis will discuss the importance of advanced knowledge of the native lignin structure, and how that can help design sustainable lignin-related processes and materials, and these works are important demonstrators of that concept. It is always nice to discuss with enthusiastic colleagues about cool projects and share your passion about your own research field. It is also a great accomplishment to use the skills that have been gained during your studies to contribute to others’ work, so I encourage all PhD students to talk to their supervisors about the potential for collaborative participation. I am looking forward to more collaborations like these.

PhD position available: Sustainable biotechnology to circularise forestry waste sludge

Note: the application process for this position closed in October 2022.

In brief: We have a PhD position available in our group, ideally to start in the spring of 2023. Email Lauren with questions. Full details below. You must apply at this link: apply here.

Scientific goals: Thousands of tonnes of sludge waste are produced each year at pulp and paper mills, and we aim to find new ways to recover components from this waste. The sludge contains valuable organic materials like starch, cellulose, and lignin, but it is heavily contaminated by metals and minerals that inhibit recycling. Most sludge is therefore sent to landfill. In this 4-year PhD project, we will use isolation techniques and DNA sequencing to identify the microbial species that thrive in this harsh industrial ecosystem, and use advanced “omics” methods to reveal the enzymes used in sludge breakdown. We will characterise these enzymes to create new precision tools for the forestry biorefinery, and to clean up the sludge by removing organic matter (leaving large amounts of recoverable metals, particularly aluminium). This project will advance fundamental knowledge and reduce industrial waste, helping to move the industry towards a more sustainable and circular model. You will be based at the KTH Division of Glycoscience, and your main supervisor will be Lauren McKee. You will collaborate closely with researchers at Chalmers University of Technology in the department of Industrial Biotechnology, as you will be co-supervised by Johan Larsbrink.

Where we work: KTH Royal Institute of Technology in Stockholm is one of Europe’s leading technical and engineering universities, as well as a key centre of intellectual talent and innovation. We are Sweden’s largest technical research and learning institution and home to students, researchers, and faculty from around the world. Our research and education covers a wide area including natural sciences and all branches of engineering, as well as architecture, industrial management, urban planning, history and philosophy. The Division of Glycoscience is a multi-disciplinary department focussed on solving environmental and industrial challenges relating to sustainable production and usage of renewable natural resources, as well as advancing fundamental knowledge of complex carbohydrates.

The broader context: This project is funded by the Wallenberg Wood Science Centre. The WWSC is a research centre striving for scientific excellence, with a focus on new materials from trees. The centre creates knowledge and builds competence for an innovative and sustainable future value creation from forest raw materials. WWSC is a multidisciplinary collaboration between KTH, Chalmers, and Linköping University. The funding base is a donation from Knut and Alice Wallenberg Foundation, and the Swedish forest industry is supporting the WWSC via the national platform Treesearch. As members of the WWSC, you and your supervisors will be expected to attend the workshops that take place in the Stockholm and Gothenburg areas twice per year, where you will present updates on your research and network with colleagues. You will be invited to regular Treesearch events, giving you further chances to present about your work and get access to the national Treesearch infrastructure platform.

Education and skills development: You will perform your PhD within the scope of the WWSC Academy. As a WWSC PhD student, you will attend two week-long graduate schools per year. This programme gives you a broad and deep insight into diverse forest-related topics, and helps you build a community of students aiming towards similar goals on the same timeline as you. You will also get to visit industrial sites and areas of natural beauty around Sweden, helping you get to know the country and its landscape as well. To complement your academy training, you will take doctoral courses at KTH, including online learning, lectures, and short lab projects. In addition, you will receive formal training in scientific writing and data visualisation. As part of your research, we will help you to write funding proposals to access additional financial support for travel and experimentation, giving you an even broader range of experience in science communication. I will also encourage you to write semi-regular pieces for this blog and to use other online channels to communicate with the public about your research.

Responsibilities as a PhD student: Your primary responsibility will of course be to advance the research project and to complete sufficient doctoral-level courses to earn the 60 credits you need to graduate. Your supervisors will help you to make sure you achieve these goals on time. In addition, you will spend up to 10 % of your time on Division/Departmental duties such as being responsible for a piece of equipment in the lab. Finally, you will take part in teaching younger students. The details of teaching are decided once the PhD has begun and the amount of teaching you do will be balanced against your other roles, but typically you will do some combination of lab teaching in a course for 1 or 2 years, supervising 1 or 2 MSc thesis students, and supervising 1 or 2 groups of BSc thesis students.

Eligibility for the position: To be eligible for this position, you should have a Master of Science or Engineering degree or equivalent qualification in a relevant subject area such as biotechnology. You should have completed a practical research-based (wet lab) thesis project. Documented proof of experience in areas such as molecular biology, biochemistry, and enzyme characterisation is appreciated but not necessarily required. Please email Lauren (find my email address at my KTH profile page) if you have queries about your eligibility for the role.

How to apply: You can find further specific details about this positon on the official advert, available at this link: apply here. Please note: applications can only be considered if they are made through the KTH application portal, linked at the bottom of the advert. Informal applications made by email cannot be considered. However, you are welcome to email Lauren if you have questions or are curious about this position.

My first big conference in real life – a travel blog

A few weeks ago, I travelled to France to present our research at an international conference. This whole sentence seems surreal now that I see it written! Due to the Covid-19 pandemic, most meetings, workshops, courses, and conferences have been online for almost two years, basically since the start of my PhD. Going to a real-life event after a long time of working from home as much as possible felt awkwardly real. I want to write about my experience as a record of my first international meeting as a PhD student. I will start from the beginning of the trip since conveniently enough for the timeline of this post, my presentation was one of the very last of the whole conference!

The 7th International Congress of the European Polysaccharide Network of Excellence (EPNOE) took place in Nantes, France. Apart from the interesting sessions and the networking opportunities, a trip to France was a golden opportunity for me to practice my long-forgotten French…and reminded me that it is indeed long-forgotten. The trip started on a Sunday morning with a ride to the airport in Stockholm, and we arrived to our final destination late on Sunday evening. I was excited to spend a week with warm and sunny weather to contrast the often cold and gloomy autumn in Stockholm. Due to the pandemic, we had to have our vaccination certificates scanned before we were allowed to enter shops and restaurants, and of course the same applied to the conference venue, reminding us that we are not exactly “back to normal”, not just yet.

The regulations regarding face masks requirements indoors changed the week before the conference and it was no longer mandatory to wear a face mask in the conference venue, which made it a lot easier to meet and discuss with people. This was a great relief, since I already find it difficult enough trying to remember new faces and match them with names! I hope “practice makes perfect” applies here too.

The first day of the conference started after lunch, with a plenary lecture by Prof. Ingo Burgert from ETH Zürich, who talked about using wood as a renewable resource for sustainable materials. The lecture underlined the necessity of replacing mineral-based construction materials as society moves towards greater sustainability. According to the United Nations Environment Programme, energy consumption in building/construction represents about 36% of the global demand, and the related emissions reach approximately 40%. Wood is a common building material in Sweden, as it has compelling properties that make it useful for many types of construction. Of course, wood has always been used as a construction material, but more advanced techniques are now available to enhance certain properties of wood. For example, partial delignification allows larger deformation of wood which in turn can enhance its inherent piezoelectric properties for applications in smart building technologies.

The Urbach Tower in Germany is a great example of how interdisciplinary collaborations in basic research can shape a sustainable future. Mechanical methods for wood deformation for architectural and building purposes have been known for many years. With these methods, wood is mechanically forced to take a desired shape. This is usually done while carefully controlling the relative humidity of the environment during the process, since changes in the moisture content of timber cause natural deformations and shrinking. However, by understanding the science behind this effect, it is possible to model and predict these deformations and allow a “self-shaping” process to take place. Another extraordinary example of what can be achieved with wood is the production of Janus membranes. Their ability to transport water in only one direction, while blocking movement in the other direction, is fascinating to me, and could have an incredible impact if used in smart building technologies, such as for collecting water from fog.

The closing talk for the first day was especially interesting to me, as I begin to look ahead to life post-PhD. Three professors shared their experiences of moving from the academy to industry and back, and urged us to explore every diverse opportunity we come across, since we can never know what the future holds for us. This was a fascinating session, although it would have been inspiring to also hear about some similar experiences from women who have moved from the academy into entrepeneurship.

The welcome reception was the perfect ending to this first busy day. A variety of French cheese, cold cuts, and oysters were served in the foyer where most of the posters were already placed, inviting interesting conversations to begin.

Over the next few days, I had the opportunity to attend talks and lectures that made me reflect on sustainability even more. It is a well-known fact that food and agricultural waste is a big problem and fast action is required to minimize waste production as we move to a “greener” future. However, since national-scale overhaul of entire industrial sectors is a rather slow process, we might as well find ways to utilize waste as an intermediate step. Several talks focused on the extraction of hemicelluloses from different starting materials, using combinations of enzymes, optimized chemical extractions, and mechanical pre-treatments. Just to summarize the societal impact of this research with an example, mushroom “waste” biomass accounts for approximately 200 kg per capita per year of food waste. At the same time, fungal biomass is an important raw material that can be used for the extraction of polysaccharides via green methods. The extracts can then be utilized in the food industry as food additives or as raw materials for other high-value applications. The EU-funded FungusChain project is just one research initiative focussed on this hot topic.

Analytical methods for polysaccharide characterization was another important topic of the conference: if you want to design technologies for extracting polysaccharides from biomass, or for using them in high-value applications, you first need information on what they look like, since this impacts the properties they will have! Since my research does not focus solely on polysaccharides but on wood biomass as a whole, I found this section especially helpful. I was happy to hear that Nuclear Magnetic Resonance (NMR) spectroscopy is considered a powerful technique, although it is not as popular in carbohydrate chemistry compared to in lignin analysis, due to difficulties posed by the nature of the raw materials. Inspiring talks by Dr Alistair King (University of Helsinki) and Dr Marion Gaborieau (Western Sydney University) showcased the spectrum of NMR applications in the polysaccharide field.

One of the last sections of the conference explored end-of-life assessment of bio-based materials. Do we really know the difference between bio-based and biodegradable materials, or do we put them both under the same umbrella? If it says “bio-“, it must be good for the environment, right? Well, not exactly. Bio-based materials are built from renewable biological resources, but by design they have the exact same properties as their fossil-based homologues. This is not by accident: bio-plastic must have all the same properties as conventional plastic, or it will not be an effective substitute. The difference between PET and bio-based PET lies solely in the raw material used for production; the production method used does not change the fact that we need to come up with solutions for the recycling and reduced use of plastics.

On the same note, the bio-degradability of any material depends on the precise way in which we dispose of a product, and is not an inherent property of any material. If we are using a compostable plastic, but it ends up in the ocean because of bad disposal, we really defeat the purpose of using it in the first place, as composting cannot occur in an aquatic environment. Industry has been collaborating with research on biodegradability assessments of materials, on finding new, more efficient methods of degrading plastic. But these efforts could be undermined if we, as consumers, are not well informed about how exactly we should dispose of our waste.

My contribution to this conference was about the effect of the presence of hemicelluloses on the structure of extracellular lignin and as a result the final structure of the cell wall in Spruce cell cultures. This was my first conference presentation in real life and although I was excited, I was also becoming increasingly nervous throughout the whole week, until Friday afternoon. Right up until I saw my title slide set up on the big screen, I could feel my heart beating so loudly that I thought the people around me must be able to hear it as well. Until the moment I stood up and faced the audience. In those seconds before I started talking, I realized that these people are actually interested in my research, they are here to learn about what we are doing, and I am here to present our data. My stress disappeared! Excitement kicked in and I felt confident as I was going through my slides: seeing people in the audience nodding in understanding was definitely motivating, and is so welcome after a long period of Zoom seminars. This amazing opportunity to share knowledge with scientists from around the world was so much better IRL than just talking at my laptop screen. I cannot find the words to describe the energy in the room during my almost 20-minute presentation. Saying that the experience was “amazing”, “rewarding”, and “exciting” are truly understatements.

To conclude my trip and this travel blog, I want to acknowlegde that this experience will stay with me for a long time. Being immersed in conference life for a whole week, I had the time to reflect on sustainability and my role as a scientist and as a consumer. I got to admire again the tremendous potential of wood and other plant biomass as a raw material, I networked with interesting scientists from all over the world, and I had a lot of fun! It was a week full of new experiences and I cannot wait to see what comes up next! I hope that every PhD student has such a positive experience with their first big conference.

My Top Five List For Your First Conference

1. Be prepared. Book all the tickets you will need before you start your journey and plan your trip in as much detail as possible. This is especially useful if the conference takes place in another country and will let you focus your mind on the conference itself.

2. Socialize. One of the main reasons you attend a conference is to meet new people and network! Take the chance and talk to as many people as possible.

3. Explore the city. Yes, the main event is the conference and yes, it takes up most of the day (if not all of it). However, if you are in a new city, take the opportunity to explore it with your colleagues!

4. Know your stuff! If you are there to present your own research, remember that you are the expert, and you are more than capable to discuss it with other researchers. But it never hurts to do some extra reading to clear up any “foggy” aspects before you arrive.

5. Have fun! You are in a venue full of people ready to engage in scientific discussions, socialize, and create an inspiring network. Enjoy the experience!!

Half-time review seminar – thoughts on native lignin and personal development

In the beginning of a PhD student employment, an introductory meeting takes place where the student is introduced to the director of studies, the PhD administrator, and the HR team. During this meeting, I felt overwhelmed by all the information I was receiving but also excited about my new start. The concept of the “half-time review seminar” was explained to me back then and it seemed to be so far in the future. Two quick years later, the moment to have my seminar has come and it feels that my introductory meeting was only a few days ago.

The half-time review seminar is a requirement for doctoral students employed at KTH. The student presents an overview of the research so far, participation at conferences, courses completed, workshops attended, and so on. An important part of the seminar is the plan for future work. The evaluators and director of studies need to see that the student not only has been making progress in the first years but also that the progress will continue in the following years of the doctoral studies. Furthermore, the seminar is a great opportunity to evaluate if the workload of the student is bearable and if adaptations to the plan are required.

And just like that I realized that I am now half-way through my doctoral studies. That realization shocked me, as it means that two years from now I will give up the title “student”. This title followed me for about 22 years and soon I will no longer be associated with it. No more ECTS will be required of me, and my continuous learning will be driven solely by my own curiosity. Until now I always had a plan and knew what lay ahead. At least I had a pretty good idea. However, this next chapter of my life comes closer every day, as the defence of my PhD will signify the end of my current path of being a student. In front of me there is a sea of endless possibilities. Should I continue with a career in the academy? This work environment is very demanding but somehow also familiar. A researcher’s position in industry sounds intriguing too. Or should I start something of my own? After all I live in Sweden, an ideal country to found a start-up. The fact that I have so many options is proof of the great teachers and mentors I had all these years and especially during the past six months since I joined the CAZyme group. The support and bonding in this group is the perfect ground to grow, be creative, and dare to develop as a researcher.

A couple of weeks ago I faced my first public evaluation, during my half-time review seminar. I started my presentation nervously, with an introduction to the subject of my doctoral studies: native (i.e. natural, unmodified) lignin. Native lignin is an intriguing material, absolutely ideal to fuel my curiosity as a soon-to-be independent researcher. I initially decided to apply for this particular PhD project mainly because I was fascinated by the fact that gaps in fundamental knowledge still exist for the second most abundant biopolymer on Earth! Lignin is a major component of plants and yet so far, we have failed to quite grasp its native structure and many aspects of its biosynthesis. There are several factors that affect the structure of lignin, summarised in the image below. The plant species, cell type, and plant age are only a few. From my point of view, the complexity of the biomolecule’s nature is linked to one of its biological roles as a response to stress. By definition, trying to perform reproducible research on a molecule that can be provoked as the defence mechanism of a living organism cannot be an easy task! Sometimes I like to think of native lignin like a property in quantum mechanics; when we take a measurement the wavefunction collapses at the resulting value. The measurement method we choose to use has a specific influence on what is observed, and the two are inextricably linked. Similarly, as an example, an extraction protocol that is optimized to obtain high amounts of a specific bond within the lignin polymer might fail to give high overall lignin yields, meaning that only a fraction of total lignin is studied. This irony is inherent in classical methods of lignin analysis. We cannot avoid affecting the structure and chemical properties of a molecule that forms via radical polymerization, especially one that can rearrange its bond structure to defend the plant. The different extraction methods one can use have different yields and show variations in relative amounts of the lignin interunit linkages. The classical methods that are typically used to produce standard lignins are simply no longer good enough to answer the remaining fundamental biological questions about lignin. This is what motivates me in my doctoral work.

Lots of different factors can affect the structure and properties of lignin, including all of the natural phenomena mentioned here as well as the method we use to extract it for analysis. This last factor is the focus of much of my current research – I want to understand how we change lignin when we decide to study it! Figure made by Ioanna Sapouna using stock image photos.

After my presentation at the half-time meeting, the evaluators asked questions about my studies in general and about my research in specifics. My two evaluators were not from the same field, which gave me the opportunity to discuss lignin from different perspectives. The first one was an expert in extraction and valorisation of technical lignins. The discussion with her was focused on the experimental part of our previous work on extracting lignin, details like the yields and standards used for comparing our results to previous work. I was relieved to be able to easily answer these questions, and felt secure and confident because I performed the experimental work myself. The second evaluator was an expert in biotechnology. Being a chemist myself, I was nervous about being challenged on the biotech implications of lignin. However, during the discussion with him I had the opportunity and pleasure to express my thoughts about the versatility of lignin in the cell wall and the effect that has on its extractability. I couldn’t help but notice my personal development during these past two years. Before I started my studies I only had some basic knowledge about this molecule and here I am, two years later, developing my own ideas and hypotheses on its native aspects.

To be able to defend these thoughts and ideas is really a privilege gained by working with Lauren. It takes a Teacher to build a student’s confidence and help her move towards being an independent researcher, and Lauren surely is. Unfortunately, women in academia are still underrepresented and the importance of having strong female role models is greater than ever. I consider myself lucky to work in such an environment and to be inspired by strong women who thrive in science. After my half-time seminar I feel a stronger connection to my work and its significance to society. I aspire to complete my studies and be of service to the scientific community as a researcher and as a person.