In Febuary and March last year I visited Tartu to work with the double layer group on a short term scientific mission funded by COST action MP1306. The aim of my visit was to develop a molecular dynamics setup for performing simulations of boundary film shear. During this mission I worked closely with Dr Vladislav Ivaništšev on developing simulation setups and developing a scripting framework. This works is a three way collaboration between the group in Tartu, The group of my supervisor Prof. Susan Perkin and Prof. Maxim Federov at the University of Strathclyde.
During the STSM I also got to explore both Tartu and Estonia more widly. The beauty and historical interest of the area was a welcome distraction from work, during an otherwise highly productive STSM.
Dr. Iuliia Voroshylova from the University of Porto came to visit us in March for a short term scientific mission. Thank you for the cooperation and work done here.
Abstract
In this STSM visit molecular dynamic simulations of mixtures of two ionic liquids (ILs) – [EMIM][NTf2] and [EMIM][FEP] – were performed in a wide concentration range near neutral and charged Au(111) and Hg(111) surfaces. The focus of this study was on the electrochemical properties of an ionic liquid mixture at an electrified interface that results from the restructuring of the electrical double layer induced by the applied potential and by the variation of the ionic liquid composition. For this study, the new method of representing of electrodes was developed. This method involves a positioning of an additional layer, composed of tiny charged spheres, in front of the electrode. This allows an effective account of surface charge. The steric effects and the inter-ion interactions in the electrical double layer next to the charged and neutral gold and mercury interfaces were accessed. The main mechanisms of ionic interaction in these mixtures related to the layered structure of the IL at the electrolyte–electrode interface that imposes potential energy barriers for the ions moving the direction normal to the electrode surface was studied.
While submitting the other, we encountered some problems when compiling the source tex-file. It turned out that one should add \pdfoutput=1 to get everything work. As a result, the second article was successfully archived at the arXiv:
My Estonia experience has come to an end a few days ago when I returned to my habitual residence in Portugal after having spent one important month in the amazing Tartu, where I had such great time and made so many truly amazing friends with whom I shared so many fantastic moments!
I spend last March in The University of Tartu, with a Short Term Scientific Mission funded by COST action CM1206. The visit was meant to be a start of a new collaboration between our two research groups: the host group lead by Prof. Enn Lust (University of Tartu, Estonia) and the home group lead by Prof. Carlos M. Pereira and Prof. M. Natália D. S. Cordeiro (University of Porto, Portugal), and it definitely was a promising start! In the Analytical and Electroanalytical Chemistry Group (where my superviser in prof. Carlos M. Pereira) we study electrical double layer in solutions of ionic liquids experimentally, and in the Theoretical Chemistry Group (under the guidance of prof. M. Natália D. S. Cordeiro) we simulate bulk properties of ionic liquids and ionic liquids behavior on uncharged surfaces. The idea of this collaboration was to learn approaches to access electrical double layer phenomenon, observed experimentally, in computer simulation. The host group has an experience in simulation of charged electrode surfaces and in automating the computation work flow, as the leading developer of the NaRIBaS scripting framework, Dr. Vladislav Ivaništšev, works there. Thus, it was a perfect match! I could not find another group where I could learn all the “tricks” about simulation the charged interfaces and automate my calculations at the same time. During this mission I worked closely with Dr. Vladislav Ivaništšev on developing simulation setups and methods of charging the electrode’s surface. During my visit, besides workshops on working in Atomic Simulation Environment, I attended a very useful workshop on Scientific Writing, given by Djuddah A. J. Leijen in AVOK – Centre for Academic Writing and Communication. The ideas I learned there I implemented in my every day work, which made me more productive.
During my stay in Tartu University I had a chance to work in several university buildings. First two weeks, I worked on the Institute of Phisics, so called “Physicum”, and the last two weeks I staying in the Institute of Chemistry, the “Chemicum” building. Both building are modern, spacious and luninous, and I found it to be very inspiring to work there. But … that was only during the working day! The evenings and weekends were intense and highly saturated with cultural events. Time I spent in Tartu University was not only a great period of learning and collaboration, but also a great traveling experience. As it was my first time not only in Tartu, but in Estonia as well, each evening and weekend me and my new estonian friends and colleagues were exploring Estonia. Most of ours attention was dedicated the city of Tartu, of course. I have been to University of Tartu Natural History Museum, to AHHAA Science Center, I visited Orchid exhibition in Tartu University Botanical Garden, Historical building of Tartu University. Almost every day I was visiting Tartu Old City with its parks and gardens, ruins of Tartu Cathedral, the Kissing Students monument and lovely little cafes. I was invited to attend a Movie Night in the C!FP Sorority, where learned the history of this remarkable organization and of Estonia itself. Also I visited the capital of Estonia, Tallinn, and now I can say that it is known as “Pearl of the Baltic Sea” because of a good reason. The capital if very beautiful, and it looks like a town from a fairy tale. A small and lovely town of Viljandi, which is considered to be cultural capital of Estonia, partly due to the Viljandi Culture Academy being located there, impressed me with its landscapes and ruins of an ancient castle. In all my adventures I was accompanied by a PhD student of the host group, Meeri Lembinen who is a remarkably friendly and helpful person.
From left to right: Vladislav Ivanistsev, Iuliia Voroshilova, Isabel Lage, Meeri Lembinen, Samuel Coles
Summarizing, I would like to say, that my visit to Tartu University was a beautiful, intense and influential time, full of impression and emotions, replete with studying, friendship, collaboration, and travels. I learned a lot not only about simulation (which was huge!), but also about Estonian culture and history. I met good people, which become my friends. I would like to thank for all the help and hospitatily to Meeri Lembinen and Vladislav Ivaništšev, who made my visit truly productive in all senses. It was my first visit to Estonia, but it will not be the last, definitely!
Our Open Access “Electrochemical Characterization of Iodide Ions Adsorption Kinetics at Bi(111) Electrode from Three-Component Ionic Liquids Mixtures” is among the most-read articles during February 2016.
Thesis writing and, in general, academic writing is a skill. Not everyone has that skill, but certainly most can get it. To develop an understanding of the behaviours associated with successful writing, we organized a workshop with the help of AVOK – Centre for Academic Writing and Communication. Under the supervision of Djuddah A. J. Leijen, we started this four-hour workshop with Q&A followed by sessions about time management, in particular how to avoid procrastination, and, of course, grammar.
First, when advanced spell checking is needed, the LaTeX could be converted to plain-text using: detex filename > filename.txt (note the omission of .tex extension).
Most LaTeX distributions come with detex program which simply strips LaTeX commands.
Second, when working with vector figures it might be a good idea to convert all texts to paths. Remember that eps-format does not support transparency.
Third, in order to count words in the final pdf-file use pdftotext filename.pdf - | tr -d '.' | wc -w. This will return the number of words in our file.
Finally, to generate a pdf-file that is acceptable by manuscriptcentral add \pdfminorversion 4 to your LaTeX-source.
Otherwise, if you use pdflatex to produce your pdf-file, manuscriptcentral will give a notice “failed to convert to the appropriate pdf”. Read this blog-post for details.
Our work group member Dr. Vladislav Ivaništšev went to University of Santiago de Compostela, Spain for a short term scientific mission. Thank you for the brilliant work there.
Abstract
In this STSM visit were performed molecular dynamic simulations of mixtures of ionic liquids (ILs) with water, mono- and divalent salts of electrochemical interest both in the bulk and near neutral and charged graphene walls. The focus was on the general trends that determine ionic solvation and solute–electrode interactions in ILs and we show the main mechanisms of ionic solvation in these dense ionic media related to the layered structure of the IL at the electrolyte–electrode interface that imposes potential energy barriers for the ions moving the direction normal to the electrode surface. Specifically, we studied the solvation of mono- and divalent ions in ILs and we also obtained results for structure and single-particle dynamics of mixtures of divalent salts with a 1-butyl-3-methylimidazolium tetrafluoroborate. The effect of salt concentration and of the size and valence of the salt cations on the ionic solvation and on the barriers’ parameters was analyzed. For example, we found that the stronger solvation of Li+ in the ionic liquid leads to a formation of significantly higher interfacial free energy barriers for Li+ to come to the electrode than for K+. Moreover, some preliminary insights were obtained for the interfacial behavior of mixtures of ILs with water, studying the effect of the latter on the structure of the interface under normal and nano-confined conditions.
Self-interaction error appears to be important for certain type of DFT and for some ionic liquids 10.1039/C5CP05922D
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My work was supported by the Estonian Research Council under grants PUT1107, PRG259 and STP52. My research was supported by the from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101031656. All related posts are tagged with MSCA.