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

Posted by Alfred Hopkinson in Alfie&Julia, 1 comment

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!

Posted by Alfred Hopkinson in Alfie&Julia, 1 comment

On non-thermal desorption and baked goods

In the beginning of the month I have had the opportunity to visit the oldest city in the Netherlands, Nijmegen. Besides trying the exquisite local delicacy called marikenbrood, the supplementary purpose of the trip was to take part in experiments utilizing the Free-Electron Lasers for Infrared eXperiments (FELIX) laboratory. This facility is part of Radboud University and, as the name implies, provides free-electron lasers that can be employed to all sorts of research. In our case, we wanted to utilize it to explore photodesorption processes potentially taking place in interstellar space.

Entrance to the building where FELIX is located. Photo credit:

My fellow foodies out in the world, I implore you: try a piece of the decadent marikenbrood if you have the chance to. Photo credit:

According to chemical models, interstellar molecules should be largely frozen out onto icy grains during the early stages of star and planet formation. In fact, species such as CO and CO2 should be completely depleted in the gas phase at such cold and dense environments. The detection of gaseous CO in dark clouds and the midplanes of protoplanetary disks thus implies that some sort of desorption must take place, efficiently transporting these molecules from the surface to the gas.


Given the low temperatures associated with these clouds (~10 K), thermal desorption should be negligible. There is simply not enough thermal energy available to desorb the chemical species from the sticky icy surfaces. Therefore, non-thermal processes are paramount to explain astronomical observations of many molecules. Many different pathways for these processes have been suggested so far. Some of them are:

  • Through photons impinging on the ice
  • Through the impact of cosmic rays, which can result in desorption either by direct heating of the ice or by exciting and ionizing species along its path that subsequently release chemical energy
  • As a result of exothermic reactions taking place in the ice


Scheme of UV-induced photodesorption. A CO molecule in the ice absorbs a UV photon and becomes excited. It transfers energy to the surface, resulting in the ejection of one N2 molecule from the ice. Figure credit:

Both theoretical and laboratory approaches have been extensively applied to study non-thermal desorption, which has been a constant topic of discussion due to its important implications on the chemistry of shielded interstellar regions.  However, there are still many questions to be answered regarding the specific mechanisms through which these processes take place. So it goes without saying that I am very excited to be able to perform experiments so different than what I routinely do, and to explore this particularly hot—or, should I say, non-hot—astrochemical topic!

Posted by Julia Santos in Alfie&Julia, 0 comments

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)

Posted by Alfred Hopkinson in Alfie&Julia, 0 comments

What I learned from the peer-review process (so far)

Positive referee reports are all alike; every negative report is negative in its own way.

Yesterday I submitted the first paper of my PhD.  As I mentioned in my last blog post, it is about my first project as a doctorate student, on the formation pathways of methanol in interstellar ices. This was also my first experience with writing an article on laboratory astrophysics, which gave a fun experimental spin to my writing modus operandi.

But this is not the first time I go through the peer review process. Shortly after I finished my bachelors and started my masters, I submitted my first first-author paper on a project I had been working on as a continuation of my undergraduate thesis. At the time, I was so exhilarated by the fact that something I did was—hopefully—going to be part of the scientific literature that what came next could not be described as anything less than a bucket of cold water.

Among the three referee reports received, one did not recommend the paper for publication. Not only that, but its content displayed the quintessential negative-and-borderline-hostile criticism we have all heard scary stories about. My giddy anticipation was instantly converted into disappointment, and the positive feedback of the other two referees was not nearly enough to assuage my hurt feelings.

Despite the unpleasantness of the situation, one must persevere. After three more reviewing rounds—at this point largely fueled by a spiteful belligerence worthy of George Constanza—the paper was finally accepted for publication. The fight was over: we won!

Weeks passed peacefully until the final version was published. In the meantime, I had not but once read the manuscript in question (for the proofreading, which we all know it’s a different kind of reading). Then, once it was out, I read it again. And as I went through it, it became increasingly clear to me how the comments of the infamous referee helped to improve the work. It is not that I hadn’t noticed this while working on the reviews, but it was partially obscured by my understandably negative feelings about the report. Although it would have been appreciated if they had chosen a different tone, their contribution indeed elevated the paper.

This experience taught me an important lesson about humility, maturity, and patience. Humility to recognize when someone notices something you did not, maturity to deal with scientific criticism without taking that personally, and patience to let go of hurtful and unhelpful comments.

Since then, none of the other peer-reviewed articles I published resulted in such an involving story, for which I am very thankful. Naturally, I hope things can go smoothly with this next one too. But, if it doesn’t, I can look back at this text and remember the Big Picture.

Posted by Julia Santos in Alfie&Julia, 0 comments

A quick look into my research

Regardless of wether in the broiling, effervescent December of Rio de Janeiro or the crisp and cosy dutch winter, I’m amazed to see how some universal end-of-the-year customs prevail. The nights illuminated by warm Christmas lights, the joyful anticipation for the year to come, and especially the mellow scents of roasted chestnuts, cinnamon and baked goods give a pleasant sense of belonging no matter the geographical location. That’s why in my mind December asks for pie, and especially apple pie. Thankfully, Sagan, the ingredients to make homemade apple pies can be easily acquired in any local market, and we do not need to first invent the universe. But—let me tell you this—that is something I would like to explore.

And with this sweet introduction I wanted so bad to put on paper I can segway into the actual topic of this post: my research work. Alfie’s last blog post inspired me to share a little bit more on the research I’ve been working recently and the main topic I want to tackle during my PhD. Or, at least, what my plans are for the near future, since three and a half years are simultaneously a heartbeat and an eternity when it comes to science.

Long story short, I am fascinated by the chemical lavishness associated with star- and planet-forming regions, and how their chemical inventory evolves in complexity, ultimately leading to the building-blocks of life. In my PhD, I want to explore this connection by studying in the laboratory the chemical reactions that happen in interstellar ices, and how those can lead to the formation of complex organics and prebiotic molecules.

The different types of surface chemistry that happen in interstellar ices and lead to the formation of complex organics. Image credit: Jenny Leibundgut of Leibundgut Designs, Center for Space and Habitability (CSH).

Right now, we are finishing-up a project on the formation of methanol (CH3OH) in space. This molecule plays an important role in the chemical network of the interstellar medium, and that’s why it’s important to understand its chemistry in as much detail as possible. Accordingly, we have performed experiments in the ultra-high-vacuum setup SURFRESIDE3 in Leiden to create analogues of the interstellar ices rich in CO and to see how it interacts with hydrogen atoms to form methanol. In the end, we were able to employ a quantum-mechanics phenomenon called the kinetic isotope effect to assess the contribution from different chemical routes to forming CH3OH. 

Me and my daily companion, SURFRESIDE.

I couldn’t agree more with Alfie when he says how enjoyable it is to see our own scientific progress. It would be hard for the early-2021 Julia stuck at home unable to travel to Europe to believe all we’ve accomplished in the last couple of months. One can’t help but wonder which scientific adventures the next year will bring, and I’m looking forward to them.

Posted by Julia Santos in Alfie&Julia, 0 comments

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.

Posted by Alfred Hopkinson in Alfie&Julia, 0 comments

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!

Posted by Alfred Hopkinson in Alfie&Julia, 0 comments

Dez perguntas para uma astroquímica na Holanda

Recentemente, eu superei minha implicância (bem justificada, diga-se de passagem) com tudo relacionado à indústria da moda e resolvi assistir um dos famosos vídeos de 73 perguntas da Vogue. Escolhi a entrevista com a primorosa Olivia Colman, o que obviamente minimizou consideravelmente a probabilidade de ter sido uma experiência negativa. Gostei tanto, inclusive, que me veio a vontade de participar de algo semelhante. Como a minha nomeação ao Oscar, porém, ainda está sendo deliberada pela Academia, penso que quase uma centena de respostas beira o limite da empáfia.

Numa alternativa mais comedida, minha amiga e breve membro do InterCat, Luise Butzke, produziu um vídeo com apenas quinze perguntas sobre sua pesquisa e a vida na Dinamarca. Para dar continuidade à iniciativa da Luise, e para poder me ufanar inofensivamente do meu tópico de estudo — eu sou, no fim das contas, uma acadêmica — resolvi responder nesse post dez perguntas para uma astroquímica na Holanda:

1. Qual sua cidade natal?
Eu nasci e cresci no Rio de Janeiro, Brasil. Tenho “r” e “s” puxados e muita saudade de Matte Leão. Em tempo: é bixcoito.

2. O que você está fazendo em Leiden?
Estou aqui para fazer meu doutorado. Cheguei há mais ou menos quatro meses, então ainda tenho mais três anos e oito meses pela frente!

3. Sobre o que é o seu doutorado?
É sobre a formação de moléculas orgânicas complexas em gelos interestelares. Basicamente, eu simulo ambientes espaciais no laboratório e estudo as reações químicas que acontecem na fase sólida nesses ambientes super gelados.

Essa é a máquina que eu uso nos meus experimentos para simular a química do espaço

4. Que tipos de experimentos você anda conduzindo ultimamente?
Recentemente eu finalizei o meu primeiro projeto do doutorado. Fiz uma série de experimentos para investigar as rotas de formação de metanol no espaço! Quando o artigo for aceito eu conto mais detalhes. 😉

5. Como tem sido essa experiência do doutorado?
Tem sido super estimulante. Eu sou completamente apaixonada por ciência e pelo meu tópico de estudo, então todo dia é como uma aventura para mim. Desde criança eu sempre quis ser cientista. É muito louco poder dizer que estou vivendo meu sonho de infância.

6. O que você mais gosta sobre sua área de pesquisa?
Eu gosto de pensar sobre como um ambiente tão vazio e hostil como o meio interestelar/circumstellar pode dar origem a essencialmente todo o inventário molecular que temos na Terra. E eu gosto de poder explorar essa química exótica em laboratório, colocando a mão da massa mesmo.

7. E o que você gosta sobre Leiden?
Eu gosto da atmosfera da cidade. É muito diferente do Rio e de São Paulo, onde eu morei antes. Aqui é bem mais tranquilo e com bem menos gente. Ainda assim, tem muita coisa pra fazer de lazer.

8. Algo inesperado sobre a vida na Holanda?
Uma coisa que já tinham me contado antes, mas que mesmo assim me surpreendeu foi que todo mundo aqui fala inglês. Realmente todo mundo! Eu comecei a aprender Holandês porque estudar línguas é um hobbie meu, mas é tranquilamente possível viver aqui só falando inglês.

9. O que mais você gosta de fazer em Leiden além da pesquisa?
Eu gosto bastante de visitar os museus que têm aqui por perto e de ir ao cinema. Semana passada estava tendo um festival de cinema na cidade e eu e meu namorado assistimos uns dez filmes! Temos até cartões fidelidade dos museus e cinemas.

O museu de antiguidades de Leiden é um dos meus favoritos

10. E quais são os planos para o futuro?
No futuro próximo eu espero aproveitar o inverno batávico com muitas combinações de stroopwaffels e bebidas quentes. Mais pra frente, espero poder continuar fazendo ciência nessa área que eu tanto gosto e continuar compartilhando mais do meu trabalho por aqui!

Posted by Julia Santos in Alfie&Julia, 0 comments

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

Posted by Alfred Hopkinson in Alfie&Julia, 0 comments