Alfred Hopkinson

A PhD student at InterCat studying the formation of organic molecules on carbonaceous grains.
A PhD student at InterCat studying the formation of organic molecules on carbonaceous grains.

Part a exam and a Danish masters

Hello, it has been a long time since the last blog post as Julia and I have been swamped and are working together on a new outreach method that we will unveil soon! This does mean we are going to leave the blog writing to the next new PhD students. However, in the meantime, I will write one final blog post to show what I have done recently and the progress that has been made.

Presenting my artistic drawing

Presenting my artistic drawing

As we have been getting further into the PhD the research being done by us has increased significantly. Both by doing our separate research but also joining each other for different projects and events throughout the past year. There have been plenty of very long days working, such as sitting in the basement under the physics department at Aarhus working with ultraviolet light. We still both enjoy our research, especially Julia when she can get her favorite popcorn ice cream!

Me and Julia having beamtime ice cream

Me and Julia having beamtime ice cream

I personally just finished my halfway progress report and defense. This is called my part a exam and involved writing a report and then defending it. I can happily report that I passed, the report was acceptable, the presentation was fairly smooth and the questions were hard. Afterward, we as a group could then all celebrate so it ended up being a good day.

Celebrating the Masters Degree

What this means for the future is that I have a Danish master’s degree and I can now continue my research into Interstellar space and forming amino acids within it! I am excited to be able to share more of what I find out in the near future and to be able to share it in a new way so be sure to look out for new announcements! Signing off then – Alfred

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Forskningens Døgn – Day of Research

Today, we here at InterCat have had an opportunity to show off what the center researches to the wider general public of Denmark and now to the wider scientific community via the blog. This is because today here at Aarhus University it is Forskningens Døgn, which translates roughly to day of research. We are aiming to tell visitors about what we do here at InterCat and how we investigate forming complex organic molecules on an interstellar dust grain.

Our outreach stall! Complete with banners and rollups.

For this day, my colleagues (Laura, Signe, Steffen) and I have set up a stall and have brought some activities and demonstrations for people to try. We have tried to get a range of different things that will appeal to a wide audience. The first, and in my opinion the most exciting (maybe because I helped make it), is a fake vacuum chamber. This is a small game that because its Denmark of course involves Lego! The aim is to reach into the box and feel what Lego structure is inside and then make this structure yourself and then see how alike your version is. This is to replicate a scanning tunneling microscope (STM) (video that demonstrates an STM here) and explain the concept in a simple to understand and hopefully fun way.

The replica vacuum chamber complete with Lego dust and Steffen giving it a try.

Our STM in the left and screen showing the atomic structure.


To compliment this we have also brought a real STM that has a video with it that shows how it allows us to see atomic structures. In this case, it is scanning on graphite and will show what we are able to do when investigating the formation of molecules on a surface.






We have also brought two rollups that demonstrate what the laboratory looks like and one with links to our Twitter and YouTube. Finally, we made a large banner, which graphically shows how molecules can form on a grain surface.

Bjørk and his game



Up to now, I have only talked about the contributions from the experimental group (as I am biased) but it would be remiss not to talk about our other collaborators. Firstly we have Bjørk, who as I am writing this is currently sat to my left busily setting up his contribution. He is showing how our theory group can use computer models to find different structures and chemical arrangements via a game he has made and I will try myself shortly!



To my right is the Stellar Astrophysics Centre who we have partnered up with for this event. They deal not with dust and organic chemistry, but with stars, as the name suggests. We obviously deal with different areas of space but they are very much linked. They have brought information on cube satellites such as Delphini and the currently running DISCO project that aims to launch these small satellites into orbit. They also have lots of information about stars and the sun and how these are modeled, observed and researched, but I will link to their page here if you want to know more, as I feel underqualified to talk at length about their research!

Stellar Astrophysics Centre

I hope anyone who comes to see us has a great time and enjoys the outreach events we will be running in the future but for now, I need to get back to talking to people about dust in space!

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What else should a PhD student do?

Through making the blog, I have detailed the process I have been through. The past year has seen me being stuck in the UK, moving to Denmark and being able to start my own research. I have talked more in depth about this and have explained some of what it is like moving abroad to study. However, I have now been doing my PhD for a year and have lived in Denmark for eight months and wanted to update you on what else I have been doing now I have settled into the city of Aarhus.

Moving abroad to live for an extended period of time has been a strange process. You move your entire life to a new unknown place and leave what you know behind. It has been an exciting process and as part of InterCat I have done a lot of new things as I have talked about in this blog. From my experience, you should do three things once you have settled into your new city. The first is to see more of the country you have moved too, the second is to try to do or try something new every so often and the third is to keep up contact with the people you have met up to this point. I would recommend anyone who moves to a different country to work or study, to do these things. I realized that in 8 months I had not seen much of Denmark as it is easy to forget there is more to your new home than what is in your immediate surroundings (as nice as they are). Therefore, to remedy this I have been on road trips to the very north of the country, to a place called Skagen.

The map of Denmark with Skagen labeled

I did this with a few of my friends I made when I lived in my student dorm and it was good to catch up with them again. We stopped several places along the way to Skagen and it was a good experience to see more of the rural parts of Denmark. In a few weeks, I will be also visiting the capital city, Copenhagen. I figured it was about time I see Denmark’s biggest city and see what it is like on the Danish islands (despite being assured its worse than the mainland by the Jutlanders). Despite going for only a weekend, I have been assured we have a full plan of things to do and so I am really looking forward to it.

Covid restrictions have been lifted here too, which is great as it means we are now able to enjoy things again. It has meant that the new courses I am taking and teach can once again be in person, which is a much more enjoyable experience.

It is good to remember when you are a PhD student to experience as much as you can as you have a great opportunity to do so and it helps you have some variation so you are not in the laboratory all the time!

We saw the point where the Baltic meets the North sea (it was very cold)

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What is my research?

Throughout the blog, I have often talked about the fact I do scientific research as part of my PhD. However, I wanted to take this blog post as an opportunity to actually explain what my area of research is and how I do it. I got this idea when talking to people at my accommodation who I have probably bored with work stories (sorry about that). I realized they have no context to what I am saying and have not had the chance to see the equipment I get to use!

I will start by explaining that my research uses ultra-high vacuum (UHV) chambers and inside these is a surface that allows us to mimic an interstellar gain. You can see more about UHV chambers in this video so I will not explain them any further in this blog post.

When I first arrived, I spent my time working with Frederik and Rijutha helping them with their research while learning how to use a UHV chamber and the different methods we can use to investigate reactions in interstellar space. At the beginning of this month, I stopped helping Frederik and have been able to start my own experiments. I aim to investigate putting glycine onto a surface and then exposing it to hydrogen to see what reactions occur. Believe me this sounds much easier than it actually is and I will explain why I am doing this, what glycine is and how I have been/plan to do this. I have been using the Big Chamber, which you can read more about here or just look at this photo of it.

The Big Chamber

Glycine is an amino acid, which are known as building blocks of life. They are called this as they are the simplest component that joins together to form proteins that organisms need for life to function. Discovering if these molecules can form and then survive in the conditions found in interstellar space is necessary to answer the question of how life first originated. Hydrogen is found in these conditions and so seeing how it reacts with amino acids is a crucial component. I chose glycine as it is the simplest of the amino acids and so it is the easiest to form. You can see below what the structure of a single glycine molecule looks like.

Glycine Molecule

I have put the glycine into a molecular doser which heats the glycine and causes it to be deposited onto the surface (step 1 in the figure below). It builds up on the surface to form a multilayer, which means it assembles into several layers. I then heat the surface causing all the layers apart from the first to be removed. This layer remains due to its stronger interactions with the surface. This single layer of glycine is called a monolayer and is the step I am currently at.

After I successfully do this I will expose the surface to the hydrogen for varying periods of time (step 2 in the figure below). Now I need a way of finding out what I have formed. To do this I am using a temperature programmed desorption which I have talked about before but is simply heating the surface such that the molecules desorb (are released from) the surface where I can then detect them using a mass spectrometer (step 3 in the figure below). I hope to see that the hydrogen has bonded to the glycine to form a radical and its mass is increased by one hydrogen mass.

The process of a Temperature Programmed Desorption (TPD) measurement.

I will be doing more than just this for the next four years and I will use different techniques but it is a good feeling to have started on my own research! I now just need to do what I have said I will do in this blog post but I can assure you after being stuck in the UK for months being unable to do the experimental research I wanted it is very enjoyable to feel like I am progressing onto the real science work.

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Importance of scientific outreach

When Julia and I started the blog in March 2021 we aimed to document and share our experience of starting a PhD during the outbreak of the coronavirus pandemic. We firstly talked about how we were still trying to be productive while being stuck in our separate countries (such as in this post) and it has developed over time as our journeys have progressed. As such, it has become more focused on our research, which we both agreed is a good direction for the blog.

We think this due to the fact that scientific outreach is an underappreciated yet extremely important part of research. It can show what happens in the field of science and may encourage more people to enter the world of physics and astrochemistry. InterCat has been making an effort to communicate the research we do to the public and has been doing this in several ways. We have obviously started a blog that you are reading now and you may have seen my previous blog post about the videos I made while stuck in the UK. 

When the group at Leiden and here in Aarhus met for our retreat we all decided to make some outreach videos covering a variety of different topics. I thought this blog would be a good opportunity to show you some of these videos and that it would be the best way to give you a much broader insight into the different types of research we do. I hope you enjoy them and there will be more coming over time!

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My experience of a conference

In the last post, which you can find here, Julia talked about being able to go to in person conferences. In two weeks we both went to Sandbjerg Gods for the InterCat retreat and then to Capri for the 2020 European Conference on Laboratory Astrophysics. She talked about how best to navigate a conference and some of the challenges faced getting used to meeting in person again. That means it is my opportunity to tell you about some of the science that we did on these trips.

I will start by talking about the retreat where there was a focus on the members of the different groups in InterCat meeting for the first time. This was the first time Julia and I met in person and was a brilliant chance to talk with people that I have never seen in 3D before. The other focus for this retreat was for us as a center to present our ideas so everyone could familiarize themselves with what the other members of the group aimed to research and how our projects fit in with the centers research aims as a whole.  We achieved this by listening to talks by some of the professors and postdocs about their previous research, which I found very interesting. As part of my research, I have read research papers the groups at Leiden have published and have spoken before with other members of the research group here at Aarhus. However, what I found particularly interesting was to listen to some of the things Bjørk Hammer’s theory group have been doing. I admit it is my fault I had not looked into their research as much as I could have, despite speaking to them every week! Their talks and presentations have given me a new way to look at my own research and how we would be able to work together in the future.

A part of the retreat was to do a poster presentation. Each PhD student had made and printed out a poster (actually Karin Vittrup our center administrator did all the work with the poster organization so thank you) about their research aims. Here are mine and Julia’s as an example!

Alfred Poster

Alfred’s Poster

Julia’s Poster

As you can see, we followed a template so each poster can be easily discussed and compared with one another. It was really good to be able to see what my colleagues plan to do and how we can work together. They are now placed on our corridor and in the lab so now the pressure is to live up to the aims we set ourselves! There will be another retreat next year where we will all be able to revisit our previous ideas and see how the research projects have evolved over this next year.

As we said, we also went to Capri for a conference where we spent a week engaging in scientific discussions, listening to scientists present their work and having less formal networking events. I found it to be a great opportunity to engage in the wider field of research for the first time and after listening to other people went away with new experimental ideas and ways I want to research. Of course it being on the beautiful island of Capri made the experience helped as you can see from these pictures.

The view from my hotel

Georgios taking a photo of the beautiful Capri

This has been a few weeks of intense scientific work but we have also been attempting to do some public outreach. This is a very important yet often overlooked part of being a scientist. To do this we have been making videos, which we will release when they are finished and upload here!

Despite now meeting Julia on two separate occasions, we have not managed/remembered to get a photo together! We managed to remedy that last week and so finally have proof, we know each other and are real people. Sadly we do not have Capri as a background but the InterCat coffee room will have to do for now!

Me and Julia in the coffee room

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Settling in

The first two months of being in Denmark have been very busy with administrative things such as getting new IDs and fishing licenses. Its also involved a lot of working in my new office and within the lab as I detailed in my last blog post. But like Julia I have started to settle into my new life in Denmark.

I have gone to grab a drink after work with colleagues at something called a Fredagsbar (Friday bar). This is an extremely Danish idea where after work in the same building you should be able to go and grab a cheap beer with your friends. It is very much like a pub at work and I have to admit I think is a tradition that should be adopted in other countries. Although I will say that in Denmark they often seem to not use cash or cards and utilize mobile pay which requires a Danish bank card so, if you are thinking of coming be sure you have a few friends to buy you a beer (sorry guys I will pay you back eventually). Other than socializing, I have gone to try my hand fishing a few times as Aarhus is a perfect place to easily get to the sea and cast out a line. I still have a lot to learn as I regularly catch less than the Danes fishing around me, but I have started getting better. To answer your question Julia, its very common in Denmark to ride a bike and they are plentiful around the university and the city as a whole. I have not yet joined this group as I am still getting to grips with the traffic moving on the other side of the road and realized I should learn to walk before I run (cycle). I will keep you updated on my cycling progress if you do with yours?

With regard to my research and work, I have been trying my best to learn as much as I can before the semester starts. I have been finishing courses I had started when in the UK, such as my visualize your science course that I mentioned in this previous post. I had to make an example poster you can see here!

The poster I made for my visualize your science course

Julia mentioned we have an InterCat retreat coming up in the middle of September, which will enable us all to meet in person for the first time (hopefully). It will be a great chance for me to learn some more about what the Leiden group does and finally meet Julia in person. We have to create a poster for this event and I wondered how making it was going for you Julia? We will be sure to make a post detailing how the retreat went and the types of things we did while there shortly after it happens!

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Getting to grips with my ‘new normal’

I don’t know about you Julia, but Denmark is a very different world to the one I have left in the UK. Here they have done much better in their fight against Covid and there are a lot more things you can safely do. I have even been able to get a negative test and go into the university to see the members of InterCat who are yet to go on vacation! This isn’t the only difference, the weather has been sunny and hot (which I am told isn’t typical of Denmark, but I am enjoying it regardless) and I am getting to experience Danish food.

During the first week and a half I have been allowed out of my room, I have been trying to settle in and get used to my new surroundings. I am currently in student accommodation, which is vastly different to British halls of residence. These dormitories have pleasant living room kitchens where people play games, party or make a big group meal. It is a good way to meet people and build a community spirit and I as an incomer have really appreciated it. I will say I was surprised at the quality of the food, the things people make are much nicer than many of the meals I have seen in British student accommodation…

July was an odd time to arrive as many people have just gone on vacation and so my accommodation was quite quiet but I have still met a few housemates who have been very welcoming. Although I will freely admit to being jealous of them being able to enjoy the nice weather by going to the beach or taking a boat trip while I was at the university. They have helped me with a variety of different issues and have been teaching me some more Danish. I can now say jeg spiser æbler og drikker øl eller vand. (It isn’t that versatile but has its uses)

Julia asked me if I had seen any interesting facilities in her last post and the answer is yes. I have really made an effort to go into the university and spend time in the laboratory for astrochemistry and reactions on surfaces. This is where we have some of the ultra-high vacuum chambers (UHV) and has provided me with many opportunities to look at some interesting physics. I have been helping Frederik with his work before he goes on vacation which has required me to learn how to do a temperature programmed desorption (you can see what this is here) on a  UHV chamber (specifically the big chamber).

Working on the big chamber with Frederik and Georgios

I have now almost learnt how to do this and over the next week have the opportunity to do it on my own and put my newfound knowledge to the test! For the rest of the summer I will aim to do a wide mix of different activities such as making a poster for the InterCat retreat and discussing with John about how to incorporate a Fourier Transform Infrared spectrometer (FTIR) into my research. The plan is to try to learn as much as I can during these summer months so in September I can hit the ground running and make up for lost time! Do you have any aims for the summer Julia other than getting ready for the cold winters of Europe?

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Arriving in Denmark

Moving to another country is a big task and Julia talked about how much she had to prepare and how Covid made this even harder. I read what Julia did and so did much the same. Following her advice, I have now safely made it to Denmark and I am in my new accommodation!

It was exciting getting on the airplane, explaining why I should be allowed into the country while showing my admission forms and negative Covid test. I then took a bus journey to Aarhus, where Gabi helped me take my things to my accommodation and provided me with some food to last me a few days. I now have to isolate and wait for another negative Covid test, which will let me leave my room and explore my new home, Aarhus. Isolating is hard enough at the best of times but is especially difficult in a new country when you know very few people. Therefore, I thought I would give some tips and advice on how to get through it based on my experience.


The most important factor in keeping sane while stuck in one room is to try to develop a routine. This does not have to be a rigorous routine that you stick to with rigid discipline and instead should be a loose routine with lots of flexibility. It should keep you in a rhythm that gives you a sense of time and purpose. It sounds corny and something a life coach would say but it really does help in staying optimistic and productive. For example, I have organized my day around my working routine I had at my home before I moved. This consists of making sure I am up and have eaten breakfast in a reasonable time and then checking my emails, which leads me into the day. Then once I have finished working I will have some food before watching a programme or speaking to a friend and finally standing outside on my balcony to get some fresh air. This keeps me sane and focused as otherwise I would lie in bed and barely notice the difference between night and day!


Keeping focused on the reason I have moved is a good distraction from being trapped inside four walls. I am in the lucky position of enjoying my work and so have found it calming to do a bit of research, make a presentation for a course or even write a blog post. I am trying to make the most of this isolation period to catch up on some of the work and progress I have missed while I was doing the research from my home in the UK.

Learning Danish

Anyone who knows me knows that I am dyslexic and have been known to on occasion struggle with the English luggage language. The thought of learning a foreign language has always daunted me and before now, I have ashamedly refused to try to learn anything and just rely on other people’s grasp of English. I do not want this to be the case and I am learning some Danish so I can have a basic grasp of it in the hope that once I finish my PhD I may be able to speak with a Dane in their native tongue and surprise my Danish aunt with a fully Danish conversation. However, the learning is hard and I am using a mixture of the Duolingo app and a pocket English to Danish book, which are useful tools to learn a little Danish before I am able to explore Aarhus.

I hope this will be helpful for people who also have to isolate or are interested in what my experience moving to a different country during a global pandemic has been like. As for me, I can’t wait to be allowed out of my room to meet my colleagues in person and dip my toes into the Danish way of life. Wish me luck!

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Starting a PhD in a pandemic

I have been turning my hand to video editing and voice overs recently, as you can see in my last blog post. I have now made another video talking about what it has been like starting my PhD at a distance during a pandemic. It features me and other people in InterCat and shows off some of the equipment we have at Aarhus that I can’t yet use!

I hope you liked the video. Normal written posts will resume next week!


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