Bird’s-eye View

Most of us work on the “dark” side of Chemicum. Meeri is from the “rusted” Physicus (on the back plan), where they have a nice sauna.

From left to right: A, B, C and D wings of Chemicum (chem.ut.ee/en). A is for lobby and cateen, B is for lecture halls, C and D are for offices and laboratory. On the back plan there is Physicum (fi.ut.ee/en).
We are in the upper left corner of the middle-part of Chemicum.

A valuable message

My friend Olga Jasnovidova has recently finished her PhD studies in Brno in Czech republic. In her acknowledgement speech she concluded the 7 years-long work and gave a message for young ones. Here it is.

“””
“Science is one of the most creative fields to work in”

Through my PhD studies I have learned that science has two dimensions: one scientific, and one human… and that, of the two, the human dimension is the more difficult to grasp.

I understood that, in order to achieve your goals, you must not only care about your work or yourself. You have got to care about the people around you: senior and junior students, technicians, facility managers, senior colleagues, your supervisors. As you step into PhD studies, you should not expect them to support and motivate you, but rather you yourself should start by supporting and motivating them.

I have also learned that one of the most effective ways to grow and develop is to ask for feedback, then learn to accept it and moreover learn to give constructive feedback yourself. This process can be painful for our egos, but it is the only way to grow.

Most importantly, I have learned that there are always several ways to achieve the same goal. There is no one correct way to reach one’s target. Therefore, you should always stay open to new ways to achieve your goals.

Based on my experience, I would like to say to younger students that they should not fear anything new or unfamiliar. Please don’t create any mental barriers for yourselves. Academic research seems like a very conventional and strict field after Bachelor’s or Master’s studies or peer review, but it is not so. Science is one of the most creative fields to work in, providing endless opportunities to grow and discover. Just learn the rules and then use them to create. You can do something truly unique for the first time in human history, something that will lay a path for many to follow. Believe in your own abilities. Every single day you have an opportunity to do something amazing — don’t waste it.
“””

P.S. Olga, congratulations!

P.P.S. Meanwhile Samual Coles defended his PhD thesis in Oxford. Grande Sam! Sam, congratulations!

The second visit of Iuliia

By Iuliia:

“””

I have been collaborating with the Electrical Double Layer group from the University of Tartu since the beginning of 2016. I had been to Tartu once, in March’2016, and this August I have visited the group again. During this visit, I was accompanied by Dr. Marco Preto, Researcher in Novelmar Project from Interdisciplinary Centre of Marine and Environmental Research of the University of Porto.
The host institution received us very warmly. There was no need to settle any bureaucracy procedures – Estonian efficiency does not cease to amaze me. Everything was taken care of in advance, and we immediately got out a working spaces, keys or anything we could need for work. I think such attitude is very important for these short visits.
In Estonia we spent two wonderful weeks with work and leisure interconnected. Most of the time in Tartu we worked closely with Dr. Vladislav Ivaništšev and his team, where very productive work was carried out, with social activity interludes that recharged us with a relaxed exchange of ideas. During this visit, the work on developing of an approach to an analysis of electrical double layer in ionic liquids systems was conducted, and an article on our previously done work was prepared for submission.
Among all the Master and PhD students, that are being trained at the group, Meeri Lembinen must be acknowledged especially. Meeri, besides being a brilliant student, is a perfect manager. I suspect, due to her care and attention we have not got a single problem at the university and during the whole stay were accompanied by her and felt like at home.
I hope, our fruitful collaboration is to be continued!

“””

Iuliia (left), Meeri (right)

Omnipotent compose key

Two keyboard layouts are all you need. I have a Cyrillic and a Latin one. So I can type in Russian and many-many other languages including Estonian. For the later one, I use the omnipotent compose key. The compose key is a key to trigger the insertion of a precomposed character. Shortly, it allows me to type “äöüõ”. Moreover, it simplifies typing “š” in my family name (Ivaništšev). Believe me, this is more difficult with the Estonian layout. Also, I can type “€” sign.

On Linux (Gnome) you can activate it as: System > Preferences > Keyboard > Layouts > Layout Options > Compose key. Choose the preferred button that will turn on the composition mode. I prefer Caps Lock. On Windows one requires special software. For example, wincompose.

The life seems so beautiful when everything is set, and the UK layout is set to default.

Besides, one can enable compose for Greek alphabet by adding to ~/.XCompose file:

# GREEK CAPITAL LETTERS
<Multi_key> <G> <A> : "Α" U0391 # GREEK CAPITAL LETTER ALPHA
<Multi_key> <G> <B> : "Β" U0392 # GREEK CAPITAL LETTER BETA
<Multi_key> <G> <G> : "Γ" U0393 # GREEK CAPITAL LETTER GAMMA
<Multi_key> <G> <D> : "Δ" U0394 # GREEK CAPITAL LETTER DELTA
<Multi_key> <G> <E> : "Ε" U0395 # GREEK CAPITAL LETTER EPSILON
<Multi_key> <G> <Z> : "Ζ" U0396 # GREEK CAPITAL LETTER ZETA
<Multi_key> <G> <H> : "Η" U0397 # GREEK CAPITAL LETTER ETA
<Multi_key> <G> <I> : "Ι" U0399 # GREEK CAPITAL LETTER IOTA
<Multi_key> <G> <K> : "Κ" U039A # GREEK CAPITAL LETTER KAPPA
<Multi_key> <G> <L> : "Λ" U039B # GREEK CAPITAL LETTER LAMDA
<Multi_key> <G> <M> : "Μ" U039C # GREEK CAPITAL LETTER MU
<Multi_key> <G> <N> : "Ν" U039D # GREEK CAPITAL LETTER NU
<Multi_key> <G> <P> : "Π" U03A0 # GREEK CAPITAL LETTER PI
<Multi_key> <G> <R> : "Ρ" U03A1 # GREEK CAPITAL LETTER RHO
<Multi_key> <G> <S> : "Σ" U03A3 # GREEK CAPITAL LETTER SIGMA
<Multi_key> <G> <T> : "Τ" U03A4 # GREEK CAPITAL LETTER TAU
<Multi_key> <G> <U> : "Υ" U03A5 # GREEK CAPITAL LETTER UPSILON
<Multi_key> <G> <F> : "Φ" U03A6 # GREEK CAPITAL LETTER PHI
<Multi_key> <G> <X> : "Χ" U03A7 # GREEK CAPITAL LETTER CHI
<Multi_key> <G> <W> : "Ω" U03A9 # GREEK CAPITAL LETTER OMEGA
<Multi_key> <G> <O> : "Θ" U0398 # GREEK CAPITAL LETTER THETA
<Multi_key> <G> <Y> : "Ψ" U03A8 # GREEK CAPITAL LETTER PSI
<Multi_key> <G> <C> : "Ξ" U039E # GREEK CAPITAL LETTER XI

# greek small letters
<Multi_key> <g> <a> : "α" U03B1 # GREEK SMALL LETTER ALPHA
<Multi_key> <g> <b> : "β" U03B2 # GREEK SMALL LETTER BETA
<Multi_key> <g> <g> : "γ" U03B3 # GREEK SMALL LETTER GAMMA
<Multi_key> <g> <d> : "δ" U03B4 # GREEK SMALL LETTER DELTA
<Multi_key> <g> <e> : "ε" U03B5 # GREEK SMALL LETTER EPSILON
<Multi_key> <g> <z> : "ζ" U03B6 # GREEK SMALL LETTER ZETA
<Multi_key> <g> <h> : "η" U03B7 # GREEK SMALL LETTER ETA
<Multi_key> <g> <i> : "ι" U03B9 # GREEK SMALL LETTER IOTA
<Multi_key> <g> <k> : "κ" U03BA # GREEK SMALL LETTER KAPPA
<Multi_key> <g> <l> : "λ" U03BB # GREEK SMALL LETTER LAMDA
<Multi_key> <g> <m> : "μ" U03BC # GREEK SMALL LETTER MU
<Multi_key> <g> <n> : "ν" U03BD # GREEK SMALL LETTER NU
<Multi_key> <g> <p> : "π" U03C0 # GREEK SMALL LETTER PI
<Multi_key> <g> <r> : "ρ" U03C1 # GREEK SMALL LETTER RHO
<Multi_key> <g> <s> : "σ" U03C3 # GREEK SMALL LETTER SIGMA
<Multi_key> <g> <t> : "τ" U03C4 # GREEK SMALL LETTER TAU
<Multi_key> <g> <u> : "υ" U03C5 # GREEK SMALL LETTER UPSILON
<Multi_key> <g> <f> : "φ" U03C6 # GREEK SMALL LETTER PHI
<Multi_key> <g> <x> : "χ" U03C7 # GREEK SMALL LETTER CHI
<Multi_key> <g> <w> : "ω" U03C9 # GREEK SMALL LETTER OMEGA
<Multi_key> <g> <t> : "o" U03B8 # GREEK SMALL LETTER THETA
<Multi_key> <g> <y> : "ψ" U03C8 # GREEK SMALL LETTER PSI
<Multi_key> <g> <c> : "ξ" U03BE # GREEK SMALL LETTER XI

# special characters
<Multi_key> <minus> <minus> <minus>     : "−" U2212 # MINUS
<Multi_key> <minus> <minus> <greater>   : "→" U2191 # RIGHTWARDS ARROW
<Multi_key> <minus> <minus> <less>      : "←" U2193 # LEFTWARDS ARROW
<Multi_key> <minus> <greater> <greater> : "↑" U2191 # UPWARDS ARROW
<Multi_key> <minus> <less> <less>       : "↓" U2193 # DOWNWARDS ARROW
<Multi_key> <minus> <less> <greater>    : "⇌" U21cc # EQUILIBRIUM ARROW
<Multi_key> <minus> <greater> <less>    : "⇄" U21c4 # BACKFORWARD ARROW

P.S. a useful link https://tuttle.github.io/python-useful/compose-key-cheat-sheet.html
P.P.S. the missing signs can be inserted as Ctrl+Shift+U+XXXX+Enter, 2212 for −, 21cc for ⇌, 21c4 for ⇄, 2191 for ↑, 2193 for ↓.

Feedback from a Sci & Tech student

It was a pleasure to work with Ahmed Helmi. That is what he wrote after finishing a project with me and Jaanus:
“Thanks a lot for you and for Jaanus, now I know a lot about linux commands and technical details about graphs and how to make a good report. Have a nice day.”
Usually Ahmed ends his emails with a citation:
“Most of the important things in the world have been accomplished by people who have kept on trying when there seemed to be no hope at all”
Indeed, for Ahmed there were a lot new things to learn. He managed very well, as he is a quick learner and a great person.

Nasty PBC

In most cases the output gro files cut particles at the PBC borders. This does not look too nice to me, when visualized in VMD. Fortunately, it can be fairly easily fixed by:

gmx trjconv -f NVT.xtc -s NVT.tpr -n index.ndx -o NVT_mol.xtc -pbc mol

or, simpler, in the VMD terminal:

pbc unwrap

pdftk allmighty

For the Estonian chemistry competition I had to work a lot with pdf-s. pdftk utilite turned to be extremely useful.
To split pdf-s into peaces:
pdftk in.pdf cat N output cut.pdf
To rotate pdf-s:
pdftk in.pdf cat 1east 2east output rotated.pdf
To merge pdf-s:
pdftk in*.pdf cat output merged.pdf

Predictions of Physicochemical Properties of Ionic Liquids with DFT

We have published an article in Computation, where we discuss predicting both static and dynamic physicochemical properties of ionic liquids with density functional theory. We prepared a workflow using NaRIBaS and conducted the calculations with 48 common ionic pairs. Thence, we estimated relevant properties for practical electrochemical applications, such as electrochemical stability and viscosity.

This work is an example how a simplistic computational model can be used in combination with informatics techniques to obtain relevant information about the ionic liquids. It can be found at the MDPI Journal website (Computation 2016, 4(3), 25; doi:10.3390/computation4030025).


Figure 6 from the article.
Figure 6 from the article. The relation between the electrochemical stability window (EW) and the estimated activation energy of viscosity (Eaest).

Cool Science & Technology Bachelor’s programmes in English

Do you want to become a next generation creative scientist or engineer? The University of Tartu provides an excellent opportunity! See here http://st.ut.ee The application deadline is 15th of April.

Margaret Fomenko visited us to learn more about the programme. Here is what she thinks: “I fell in love with Tartu since first second I saw it. Small city with it’s history and close-knit community attracts to consider studying. Moreover, I liked the program Tartu university offers, science and technology. It covers various fields of science, like programming, biology and chemistry and allows to make research on interesting topics in modern laboratories.”