chemistry

Dec

2021

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.

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.

Dec

2021

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.

Nov

2021

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!

Oct

2021

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’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

Jul

2021

First weeks as a doctoral candidate

Since my last blog post, I’ve been dedicating my time to learn all the ins and outs of SURFRESIDE3. As I jokingly said to my daily supervisor at the end of the first week in the lab, “I feel like my brain is now twice the size it was five days ago”—and I mean that in the most positive, Seuss-esque possible way. I have also been seizing opportunities to explore the different facilities at the University, which are filled with historical value.

The laboratory astrochemistry field is dedicated to studying the chemistry of space by recreating its conditions in the lab. This usually involves achieving very low pressures (around 10^-9mbar or 10¹² times below atmospheric pressure), and temperatures. Interstellar dark clouds are typically at around 10 K, or approximately -260 °C, so low that we need cryogenic techniques to reach them. At SURFRESIDE3, we achieve that with a closed-cycle Helium cryocooler, which only rarely requires refilling with He gas. However, some experiments involve additional apparatus that also need to be routinely cooled down.

Coincidently this week, we ran out of liquid N₂in the lab, which resulted in the coolest (pun absolutely intended) visit to the Cryogenics Department at Leiden to refill our tank. On the way there, we made a stop at the display of the first system that succeeded in liquefying He, developed by Dr. Heike Onnes in his lab at Leiden University in the beginning of the 20^thcentury. I wonder if Alfie has visited some interesting facilities too!

Replica of the apparatus Onnes used to liquify Helium for the first time. It yielded a sardonic final amount of about one tea cup of liquid He.

It feels good to be back in a lab, conducting experiments and exploring the idiosyncratic ways chemistry works at such extreme conditions as one finds in interstellar clouds.

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