iMOS Master: Infrared Spectroscopy of Highly Reactive Aggregates in…

Infrared Spectroscopy of Highly Reactive Aggregates in Helium Nanodroplets

Daniel Leicht

In my master thesis I investigated the infrared (i.e. the vibrational) spectrum of helium solvated allyl radicals. The radicals were produced by pyrolysis of 1,5-hexadiene and trapped in superfluid helium nanodroplets. The helium droplet beam was overlapped by the output of a tunable infrared laser to obtain the infrared spectrum. After obtaining the experimental infrared spectrum ab initio calculations were carried out as a basis of the spectral assignment. Different DFT methods were compared with respect to their viability since open-shell species often pose a problem in such computations.

Figure_DL

Spin density surface of the allyl radical.

Based on the quantum chemical calculations five CH-stretching bands were assigned to the observed spectral features. The rotational fine-structure of the recorded spectrum was investigated as well. Due to the very low droplet temperature of 0.37 K, also weakly bound complexes can be studied using this technique. As an outlook I proposed an investigation of the allyl:HCl complex, which has been carried out and published at a later time.

After finishing his iMOS Master’s thesis Daniel Leicht started his PhD research in the group of Prof. Havenith.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum

iMOS Master: Correlation of solvent fluctuations with dynamics of…

Correlation of solvent fluctuations with dynamics of simple ligand binding to biomolecular surfaces

Christopher Päslack

Image1_ChristopherWe   used   classical   atomistic   molecular   dynamics   (MD) simulations  to investigate how and to what extend collective protein-water motions affect the dynamics of ligand binding to a biomolecular surface. Therefore, the free energy surface (i.e. potential  of mean  force,  PMF)  along  the  reaction  coordinate was determined via Umbrella Sampling and based on that we obtained static one-body friction/diffusion profiles of the ligand along  the  reaction  coordinate.  The  reaction  coordinate  was defined  as  the distance  between  the  hydrophobic  patch  of ubiquitin and the ligand (LJ-spere).

We could show that dynamics of the ligand are affected both by the binding affinity in terms of the PMF as well as by internal motions  of  the  protein.  Furthermore,  the  ligand couples  to solvent  fluctuations  in  the  vicinity  of  the  hydrophobic  binding patch of ubiquitin.

Folie_Christ.1024_768After finishing his iMOS Master’s thesis Christopher Päslack started his PhD research in the group of Prof. Lars Schäfer.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum

iMOS Master: A high-dimensional neural network potential for…

A high-dimensional neural network potential for protonated water clusters, 2014

Suresh Natarajan

In the final semester of my iMOS studies, Dr. Jörg Behler from the theoretical chemistry department accepted to supervise my master thesis. Dr. Behler’s lab specializes in modelling reactive potential energy surfaces (PES) based on neural networks for describing molecular, bulk, and interfacial systems. Such a potential will provide maximum accuracy and efficiency in molecular dynamics (MD) simulations when fitted to the high level quantum chemical data. My project was to develop one such potential for protonated water clusters, which are important model systems in studying proton transfer mechanisms in general. I started with sampling the configurational space of the protoned water clusters from monomer (with one water molecule and a proton) to octamer (eight water molecule with a proton) using stochastic search. Energy and forces acting on these sampled molecular structures were computed with density functional theory (DFT) and it is to these data the neural networks are fitted.

Suresh Natarajan-image from thesis

Contour plot of protonated water dimer showing the evolution of a double minimum configuration.

MD simulations were carried out with the preliminary potential in order to sample additional conformations missed in the earlier stochastic sampling. These structures were added to the data set and the potential is refitted in order to improve reliability of the potential. Once a reliable potential was obtained that provided negligible error in the predicted energies and forces compared to the DFT values, it was ready for further analysis and MD simulations. The completed potential was then used to find the minimum energy structures, harmonic frequencies, proton transfer mechanisms and transition pathways between different minima of protonated water clusters as detailed in my thesis.

After finishing his iMOS Master’s Thesis Suresh Natarajan started his PhD research in the research group of Dr. Jörg Behler.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum

iMOS Master: On the Mechanism of ATP Hydrolysis in…

On the Mechanism of ATP Hydrolysis in ABC Transporter TAP, 2015

Hendrik Göddeke

Adenosine triphosphate (ATP) is the energy currency molecule in the cell, and its hydrolysis is one of the most fundamental chemical reactions in biological systems. One example of a protein family that requires ATP binding and hydrolysis for function are the ATP-binding cassette transporters (TAP). In order to study the ATP hydrolysis inside TAP, a hybrid quantum mechanics / molecular mechanics (QM/MM) approach was used to describe the hydrolysis reaction by means of density functional theory (DFT) and the rest of the system by means of a classical force field.

Hendrik-Diagram from m.thesis_1340x768

Potential of Mean Force (PMF) along the associative reaction coordinate.

All examined mechanisms (associative, dissociative, concerted, glutamate-catalyzed and histidine-catalyzed) failed to capture the exothermicity of ATP hydrolysis, in line with previous QM/MM studies. Due to computational costs, only one water molecule was included in the QM subsystem for the nucleophilic attack, excluding a possible mechanism involving proton wires with several waters. Therefore, including more water molecules in the QM subsystem could provide a more realistic picture and hence, could help in understanding the power stroke of ABC transporters.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum


About the Author

Henfrik GoddekeHendrik Göddeke was born in Meschede and holds a BSc in Molecular Biology with a focus on Bioinformatics from Westphalian University Gelsenkirchen. He then moved to Bochum for iMOS. The international course was carried out in the Tobias lab at UC Irvine. He finished iMOS in September 2015 and is now doing his PhD in the Schäfer group.

My iMOS Internship at the University of California

From September until December 2014 I did my iMOS internship at the University of California, Irvine. I joined the Tobias group which focuses on molecular dynamics simulation of biomolecular structure. My job was to simulate Hv1(a proton channel in a variety of organisms) under a depolarizing potential in order to investigate the opening mechanism of the channel. Fortunately for that purpose we got 75.000h computational time on Anton which is one of the fastest supercomputers for MD simulations. These simulations provided some interesting information about the opening mechanism and the work will be published soon.

University of California, Irvin - Kopie (2)

University of California, Irvine

I lived off-campus and shared a small house with five guys. Even though I just had approximately 20sq m the rent was about $950 per month. Finding a place to live in Irvine for such a short period is very difficult and expensive and if you are thinking about doing your internship in Irvine as well, search and apply for housing as soon as possible. The city itself is one of the safest places in the USA. It is very modern and beautiful as well. The university is around 5 miles away from the beach and the beaches in California are just awesome. When I arrived the temperature was about 32 degrees Celsius and during my time it did not go below 20 degrees. That is one reason for living in California. The other reason is UCI. It is one of the best public universities in the USA and the campus is modern, clean and well organized. The faculties are located around the Aldrich Park which is a botanical garden and the heart of UCI. There is no canteen or something comparable as known from Germany but there are several restaurants such as Subway, Panda Express or Blaze Pizza.

Irvine

San Francisco

During my time I met lots of nice people, visited a few beaches of California and did a short trip to San Francisco with another iMOS student from Santa Barbara. Overall I enjoyed my time really much and can highly recommend UCI and especially the Tobias group for doing an internship. Last but not least I would like to thank Prof Marx who not only arranged the internship but rather gave me the opportunity being a part of such a great group.

Link to University of California

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum


About the Author

Henfrik GoddekeHendrik Göddeke was born in Meschede and holds a BSc in Molecular Biology with a focus on Bioinformatics from Westphalian University Gelsenkirchen. He then moved to Bochum for iMOS. The international course was carried out in the Tobias lab at UC Irvine. He finished iMOS in September 2015 and is now doing his PhD in the Schäfer group.

iMOS Course at First Glance

Arriving at a country where you have never been before, knowing that you will continue your life there for a certain period of time, gives you a fresh dash. Instead of the accustomed environment, the unfamiliar things will make you explore them. In my 22 years I have had about seven moves, went to four different primary schools, so regularly changing the surroundings are part of my being. After London, Bochum in Germany is the second foreign city where I have lived for longer term. New place, new level of education. That’s what it means for me coming to the Ruhr-University for the Master course in Molecular Sciences and Simulation (iMOS).

I met the opportunity of studying here in early August, when I was in London, carrying out a 6-months internship in a laboratory of physical and theoretical chemistry with Erasmus scholarship. A German student from Ruhr-University visited the lab for two weeks, he was in his final year of the iMOS program. Based on his description of the course, and after reading the information on its website, I decided to apply, however, I had already been accepted for two other master’s in London. The application process went smoothly, after reading through my application profile the course director invited me for a skype-interview, and within about two weeks I received the acceptance letter. Except the secured student accommodation, I didn’t have a detailed view of how I would finance myself -as it was too late for applying to a scholarship-, but thank to the helpfulness of the science manager of the course, everything has worked out.

I arrived on 7th October, two weeks before the start of the lectures. The first days were about administration at the university and registration at ‘Rathaus’ of Bochum. Besides, I explored the city centre, the shops and the beautiful area of Kemnader-See with some of my housemates. In the first week of the semester we were given an introduction to each course, and also our science manager toured us around the huge campus. The major destination in every building was of course the ‘Cafeteria’!

Kemnader-See-720x540-b

Kemnader-See

The iMOS group is very diverse in terms of the countries represented, my six course-mates are from Germany, China, Thailand, Turkey and Afghanistan, and I am Hungarian. Three males, four females. Most of us came here with a bachelor in chemistry, except Özlem, who studied chemical engineering, and Yichen has a degree in physics. Our study plan is busy on Mondays and Tuesdays, having lectures from 8/9am till 4/6pm, but the weekdays afterwards are easier, with 1 or 2 seminars. The work continues at home with reviewing and learning the thought topics, and preparing exercises, homeworks. This Molecular Sciences and Simulation master’s is a very unique course, it is based on 21st century’s most emerging scientific area, that is quantum mechanics.


Science Zone

Quantum mechanics is the universal language of describing the properties and behaviour of matter, determined at the atomic scale. We should never believe that scientific knowledge is absolute, since we can only depict systems after introducing artificial constraints, instead of grasping the entire phenomena at once. Quantum mechanics is, however, the most precise approximation to the reality today, taking into account many variables to qualitatively predict or explain phenomena. The very core of life itself is researched from the aspect of quantum mechanics. It seems that the former, classical descriptions of existence’s different fields (such as mathematics, physics, biology and chemistry) unite to form a universal picture.


How can we understand quantum mechanics? My conception for that is:
Anything can be learned, if the order and magnitude of steps in the study process is consequently structured. Since scientific knowledge is being built by humans, we don’t necessarily need to understand everything, in many cases we just need to accept and work with the definitions and concepts previously led down by the relevant scientists (or find our own interpretation!). This applies to quantum mechanics as well. First we need to ‘speak’ a good level of mathematics to be able to understand the procedure of how quantum mechanics has been developed. After that we can get an insight into the areas and methodology of its application for a broad spectra of research topics. After acquiring the appropriate amount of theoretical knowledge and experience, we can then use the concepts and experimental tools (eg. softwares such as Gromacs, Gaussian 09 etc.) to study our own scientific questions we are interested in.

The iMOS course is an excellent program, guiding us through the above mentioned  stages, starting with the basics of quantum mechanics. Lecturers give every support to us during their presentations and we can also contact them in their office hours to ask for their help in understanding the subject. Sometimes the explanation for a specific abstract phenomena will be given with a very humorous picture.

I am convinced that the next two years of my stay here in Bochum will provide many excellent opportunities for me to progress in both my professional and personal life, and so I am very glad I could start this course.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum


About the Author

Debora Beeri is one of the new iMOS-students in this Wintersemester 2015/16 at Ruhr-Universität Bochum. She obtained her Chemistry BSc degree in Hungary, after which she went to London for a six-months internship in a Theoretical Chemistry lab, where she gained research experience.

From the Perspective of a New iMOS Student

When I thought about doing a Master’s degree, the image in my mind was to follow my dreams. I always had the ambition to learn more in detail about the physical world around me. It was the world of atoms and molecules which was quickening my pulse and whispering me: “Apply for a Master’s program on molecular simulations and spectroscopy”. That’s how I found out about the iMOS program. Then started the journey of applications.

The application to the iMOS program is very easy. One of the things that you may like is that in Germany, most of the universities do not require an English language test such as IELTS or TOEFL if your language of study was English in your Bachelor’s degree. The rest of the documents are mostly to be sure that you are applying for the program that you really want to study. You can find the whole set of required documents from the iMOS web page.

Now, I want to talk about my visa application process, because it can be very daunting for the applicants from non-EU countries. I am from Turkey and this was the first time for me to go abroad. So the whole process was very unfamiliar to me. There is a list of required documents which you can check from the embassy’s website for a national visa for educational purposes. For me the most time consuming part of the story was to get the proof of my financial resources. There are a number of ways to do it. You can present a scholarship award notification which makes everything easier. You can also get a guarantee, if someone with permanent residence in Germany is willing to take responsibility. This guarantee, called “Verpflichtungserklärung” in German, can be get by your guarantor. If you can get hold of one of these this would be a good option.

Another option is to open a blocked account which is what I used for my visa application. You need to make a security payment with an amount of one year of living expenses. This was a minimum of € 8,040 during my application for visa. But there is also € 50 fee billed for the registration of blocking account, so you need to transfer at least € 8,090 to the account. The procedure is different for each bank. In my case, I opened the account from Deutsche Bank. For the case of Deutsche Bank, you need to sign the application form in the presence of an embassy official. For this approval I got an appointment online and went to the embassy with my passport and admission letter. This approval cost €20. Afterwards, I posted the application form to the Hamburg branch of Deutsche Bank together with my admission letter from the university and a copy of my passport with express post. Unfortunately, it took more than a month for the post to reach because Deutsche Post was on a strike. In the following week I got an e-mail regarding the opening of my bank account. Then I delivered the required amount via a SWIFT.This also takes a few days. After the money transferred, I got a second e-mail proving the blocked amount.

And voilà! This is the document that you need to print out and give to the embassy for your visa application. If you survived until now nothing can stop you. In my case it took even longer than getting my visa. Including the time I spent to get the required documents, in total it took around two months to get the visa. So I recommend you to do everything as early as possible so that you can cheerfully buy the cheapest ticket without carrying the worry of not getting the visa until then.

The first place I came to was not Bochum. I went to Munich to visit a friend from university. Meanwhile I had the chance to have a smooth adaptation period to the German culture. It might sound funny but the first moment I saw a squirrel was very fascinating for me. It was the first time in my life that I was seeing a living squirrel. But it is a usual thing in here. Because in Germany they have a lot of oak trees. Oak tree is called “Eiche” in German, and a squirrel is called “Eichhörnchen”. I think, it is also a cuddly word to pronounce.

View from the top of Hoher Fricken facing Kloster Ettal

While in Munich I also went hiking in the Alps. We climbed the Hoher Fricken, a mountain in the Bavarian Prealps. There was a little fog in the morning but it faded and a sunny day encouraged us. We came across with a lot of nature lovers during our walk. There was even a woman who was hiking with her dog. I strongly recommend you to see the Alpine region. If you go to Munich, also keep in mind that on Sundays the entry fee to most of the museums is only € 1. During my time in Munich I also had chance to listen some seminars in the Max Planck Institute of Biochemistry in Martinsried. The Max Planck Society is one the biggest societies in Germany in research. As a person interested in natural sciences, life sciences, social sciences, and/or the humanities you will be fascinated with this society and they are everywhere in Germany!

The orientation week was to start at the third week of October. Therefore, I bought my ticket to Bochum for the beginning of October so that I had enough time to settle. The cost of a room is generally € 260 per month. My room was without furniture but I found almost everything for free. If you are also considering renting a flat without furniture, it is not that hard to find cheap or free furniture, though it will take some time and effort. I enrolled to the university and applied for the residence permit in the first week of October. However, you can also do these in the orientation week, because there are volunteers helping you. But if you want to extent your residence permit yourself, I can explain briefly. You should first register at the city with your contract for your flat. Now with your approved address, you can apply for the activation of your Deutsche Bank account and discharge required amount for the visa extension fee, if you don’t have it in cash already. For the visa extension you need to get an appointment from the Foreign Citizens’ Office and go there with the required documents. When I was finished with those I was very eager to start the lectures.

19th of October, I met with the other iMOS students. It was Lisa who suggested this small meeting just before we were going to our first lecture. Now I am in my third week and it is fascinating to get more into spectroscopic techniques and molecular interactions. As a part of Dynamics and Simulation course we also make simulations using GROMACS package. For example, this week we calculated diffusivity of Argon in Argon for solid, liquid and gas phases looking at the change of mean squared displacement within time. Maybe it does not sound very fancy but when you know the basics, you can put on it! We also have courses on quantum mechanics, thermodynamics and statistical mechanics which are very supportive to understand the other courses in depth.

Now after my first month in Bochum, I can say that there is a lot to live here. I already feel like at home. Here the nature touches your soul. I regularly join the running group of the “Hochschulsport” of the Ruhr-Universität Bochum and enjoy the beauty of Kemnader Lake and the forest. If you are interested there is also a Music and Arts Center in the university. Here, I am practicing piano. To take a little break I sometimes go the studios and work there with wood, paints, etching in brief almost anything you would like work with. You can work on your own or you can take courses. To be allowed to use these studios, you need to pay € 35 per semester but it includes the materials as well.

I am wondering what the future will bring, but now I feel like I am following my dreams.


About the Author

oezlem-yoenderÖzlem Yönder was born 1991 in Ankara and holds a BSc in Chemical Engineering from Middle East Technical University, Ankara. After her degree, she started a Master’s program there; however, after deciding she wants to learn in depth molecular simulation and characterization techniques she didn’t complete her MSc degree in engineering. Instead, she currently studies in Molecular Sciences with a Focus on Spectroscopy and Simulation (iMOS) program at Ruhr-Universität Bochum.