This is my diary about my period abroad to develop my master’s thesis work on Vascular Biomechanics at the KTH Solid Mechanics department. I will tell the whole period in several articles, let’s continue with October.
It is Monday, Sep 26th, and a new week it is started.
Now it is time to start considering more complex simulations. Let’s consider some multiphysics coupling that Comsol allows us to simulate. We can try to relate thermal dilatation to the mechanical descriptions by considering both mechanical and thermal phenomena inside a material. So we can combine the mechanical strain with the one introduced by the thermal effect directly multiplicative decomposing the deformation gradient.
It leads to a coupled simulation that could be solved both with a fully coupled or staggered approach in Comsol. This coupled approach allows us to study the temperature effect on material but also makes available one extra degree of freedom in every element that we can use to describe this volumetric (thermal) strain.
But there are not only FEM analyses and today I’m going to see a football match, Sweden vs Slovenia, in the National League. The match is played at the Friends Arena in Solna.
It is Friday, Sep 30th, and today I have to move and change apartments. I’m moving to another area of Stockholm, called Lidingo. It is an island on the east side and it is really different from Kista. I’m in Larsberg, in Lidingo, and it is full of green areas with a lot of trees. I’m actually on the 6th floor and I can see both the green area and the center of Stockholm in the background. With less than 10 minutes I can reach the water with a spectacular trail.
Near to the apartment building, there is an ICA, the biggest groceries shop in Stockholm, and a tram stop. The tram can take me to Ropsten in less than 10 minutes and passes every 8 minutes. From Ropsten I can go everywhere by metro or the bus and I can reach my office at KTH in 15 minutes. Very well connected.
Obviously, everything deserves some surprise and what about not finding the apartment keys with the automatic check-in? Luckily, after some messages with the landlord, it turns out the cleaning company had the keys. It requires at least 30 minutes of chatting and testing different keys from the check-in box situated on the ground floor and the apartment on the 6th, with all the luggage.
New studio apartment
Yes, the apartment has some problems. First of all the door is not so well isolated and a lot of air can enter from the bottom part. This is probably related to the differences in pressure generate by the ventilation system. Every apartment has their inlet and outlet for ventilation and heating. Furthermore, the shower hasn’t a curtain and also a plate rack is missing. It would have been easy to go and buy all this but I preferred to make do, at least for the insulation of the door. Instead of buying an expensive new gasket, I preferred to make some shim with the engineer’s favorite tool. Yes, I’m talking about the duct tape. By using it and some cable ties I can solve every problem in the apartment.
Luckily there is a vacuum cleaner that results to be very helpful for cleaning. Furthermore, the bathroom sink seems a little small and I’m wondering what I should actually wash in it, considering they don’t even have a bidet here.
But these problems are insignificant considering the nice view from the large bright window.
And for the first time in my life, I have seen a man-size drier to both dry and iron clothes. It is located in the laundry room, shared between several apartments. Everyone, with a magnetic tag, can book a three hours turn from the four groups of washing+drier present in the two laundry rooms. The booking system is electronic and fully automatized also for the room door opening. These machines are fantastic. Large washing machine and a maxi drier that can dry more than 8-10 kg of clothes in less than 30 minutes. You don’t even need to iron most of your clothes.
Furthermore, there is also a gym near the flat building and I’m thinking of sing up. I want to try to go to the gym in the morning, between 6 and 8, every working day. And spoiler I did it for every day in October, also by adding a walk or run on the weekend. It gave me a lot of motivation and energy to work focused on my thesis during the rest of the day.
It is Monday 3rd of October, and I have just received all the complete files for the patient’s CTA. Now I can start creating the mesh and running the mechanical analysis. The first step is to compare simulations with homogenous and inhomogenous tissue properties. This should not be so difficult but will require a lot of time to find the optimal value for every parameter.
Today, Oct 7th, I’m going to watch for the first time an ice hockey match. The local team, Djurgården, will play against Södertälje Sportklubb. It is my first time watching an ice hockey match, but I have studied some rules and it is very entertaining.
This week I have also tried the ferry boat. I can take it in Dalenum, 5 minutes from the apartment, and reach the center of Stockholm in Nybroplan. It requires more or less 40 minutes with 5 or 6 stops but there is also an express line that goes directly to the center without extra stops. Here ferries are an effective part of public transport and work very well, a nice boat with heating systems and both indoor and outdoor seats. I have taken the boat named Maria on line 80.
It is Oct 12th and today my girlfriend is coming back to Stockholm. At midnight it will be her birthday.
This time we visited more natural places. A great walk around Lidingo’s largest lake and the coast of the island. But we also visited some places in the center and did some shopping. It starts to be cold but during daylight, the sun still warms. We also discovered Max, a Swedish fast food corporation better and tastier than Mc Donalds, and Keane Brewing, a local brewery in front of my apartments. It looks really interesting.
Come back to work. New week but the simulations remain the same together with the problems. However, now I have the powerful computer that my girlfriend brought me from Italy.
Alert! The following paragraphs contain nerdy talk!
Reduction in computational time means more time to design it and to think about the formulation. But it is not only about to be faster, I need to overcome the problem of being out of core in Comsol. During the solution of the simulation, the solver needs to store the data (effectively the algebraic system matrix) in the ram. However, if the RAM is not sufficient it starts to save data on the storage. First of all, every storage is slower than RAM but an SSD NVME could help in order to speed up the process.
I’m using models with 3-4 hundred thousand elements that led to more or less 1.5 million degrees of freedom. However, with coupled simulation and extra variables, it is easy to arrive, for the same number of elements, at 30-40 million degrees of freedom. Comsol documentation suggests providing 1 GB of RAM per million degrees of freedom and it means that I should have like 64 GB. Yes, theoretically I need less but there can’t be anything between 32 and 64 GB in computer RAM. However, I would like to find a way to make up for the 32GB of my laptop.
So, I continue every day with simulations and literature research. In the meantime, I’ve also become a pro at cooking, ironing, and washing the house. I have foreseen one or more cleaning days per week dedicated to fixing the apartments. I cook every day after work, both for dinner and for lunch of the following day. I like to eat healthy food and respect some good general rules for food intake like macros distribution and a not-so-precise calorie count.
It is Friday, October 21st and I’m going to see the Ph.D. defense of Andrew J. Buckler. He is the president of Elucid and coauthor of one of the starting papers for my thesis work. He is now working as Ph.D. for the Karolinska Institute in the department of vascular surgery. His thesis is a very interesting work that goes in the direction of improving vascular disease therapy selection and follow-up.
This work starts from the premise that it is possible to provide analysis of plaque biology from non-invasive imaging and results in the ability to stratify risk and determine statistically the contribution of several druggable pathways. I’m not really interested in transcriptomics but biomechanical assessments are very encouraging.
I’m now going deep into Comsol’s features. I’m studying and testing many advanced options by replacing constant parameters with ad hoc functions. It seems that every day begins with a breakfast of biscuits and Comsol documentation.
Now it is the weekend, October 30th. Joey and I go for a walk to a place I never expected to see in Stockholm. It consists of several streets with abandoned buildings covered with graffiti and street art. it is located in the south part of Stockholm, in Rågsved, and it can be reached easily by subway.
In these weeks, I started to familiarize myself with their food. I am especially in love with mashed potatoes and find it very good to cook them. It is practical, fast, and tastes great but not all dinners always go as planned.
Another month is passed and we will talk about the following weeks in the next articles.