3 Nov 2023
Uppsala University, Department of Physics and Astronomy
- Research Field
- Researcher Profile
First Stage Researcher (R1)
- Application Deadline
27 Nov 2023 - 22:59 (UTC)
- Type of Contract
- Job Status
- Is the job funded through the EU Research Framework Programme?
H2020 / Marie Skłodowska-Curie Actions
- Is the Job related to staff position within a Research Infrastructure?
PhD student in Physics with specialization on photon matter interaction
“SPIDoc’s – The next generation MS SPIDoc’s” is funded within the Marie Skłodowska-Curie Actions, composed by 7 beneficiaries and 8 associated partners, including academic and non-academic sectors located in 8 countries. SPIDoc’s projects will apply cutting-edge technologies, like native mass spectrometry (MS), X-rays for single particle imaging (SPI) and molecular dynamics simulation to understand the dynamics of viral particle. Each SPIDoc’s PhD project will include multiple secondments at beneficiaries’ or associated partners’ location, allowing an international and interdisciplinary exchange for the progresses of the project and for the development of the doctoral candidate. The doctoral candidates will receive scientific training spanning from theory, instrument development and application by winter and summer schools including practical sessions and online lectures. Additionally, they will be trained on data management and will have the unique opportunity to contribute to the establishment of standards for native MS metadata. The scientific training programme will be complemented by soft skills training providing support for career and personal development of the doctoral candidates. Read more: https://www.ms-spidoc.eu/spidocs/
The research conducted at the Department of Physics and Astronomy encompasses a wide range of physics topics, distributed over nine divisions. The department is located in the Ångström laboratory and employs nearly 400 people, 100 of whom are doctoral students. It offers a broad physics curriculum to undergraduate and graduate students, participation in nationally and internationally leading projects for researchers, and opportunities for partnership with industry and various outreach activities. Read more on www.physics.uu.se
The division of X-ray Photon Science is world-leading in the use of advanced spectroscopy methods. This puts us in the forefront in atomic-level studies of atoms, molecules and condensed matter. This division includes the research programme Chemical and Bio-Molecular Physics, which as host of the project has a special focus on the fundamental properties and ultrafast processes in atoms, molecules, chemical systems, and proteins. With X-ray scattering and spectroscopy, we reveal how electrons and nuclei move and interact to explain how properties and function emerge.
Single particle imaging using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallised samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Simulations have predicted that the orientation of the protein at the instant when it is exposed to the X-ray pulse, can be determined by mapping the distribution of the ejected ions as the sample undergoes a Coulomb explosion following the intense ionisation. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. This idea has potential to develop into a crucial tool for orientation retrievement in SPI experiments, but for it to reach its full potential we need to do further studies, both experimentally and using simulations. This project focuses on the simulations, with the goal to answer questions such as: “What is the dependence between the reproducibility of the ion distribution maps and the structure of the protein?”, “Can we determine the structure of the original molecule based on the information in the explosion?” You will study the X-ray-induced explosion dynamics of biomolecules using classical molecular dynamics and quantum mechanics simulations. The ion distribution maps will in the next step be analyzed to recover information of the structure of the original molecule. This will be done using machine learning algorithms, and combined with other types data, such as the aminoacid sequence, diffraction image and ion-spectra.
The Ph.D. student shall primarily focus on postgraduate studies, but other duties related to teaching and administrative work may be involved, up to a maximum of 20% of the time. Information about doctoral education, eligibility requirements and admission rules can be found at the faculty website, http://www.teknat.uu.se/utbildning/utbildning-pa-forskarniva/
This project includes additional secondments within the SPIDocs consortium at DESY in Hamburg. Additional short visits will be arranged in agreement with the supervisor of the research project. Moreover, you will attend international conferences, participate in periodical project meetings and training schools as well as in specialized courses at different universities to complement your knowledge. A certain amount of travelling is foreseen in relation to these activities.
To comply with the mobility rule of the MSCA programme, you are eligible if you have not resided or carried out their main activity like work or studies, in Sweden for more than 12 months in the 36 months immediately before the date of recruitment.
To meet the entry requirements for doctoral studies, you must
- hold a Master’s (second-cycle) degree in Physics, or
- have completed at least 240 credits in a relevant field, such as Physics, Chemistry or Materials science, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
- have acquired substantially equivalent knowledge in some other way.
Additionally to the mobility rule, you are eligible for the SPIDoc’s programme, if you are not be already in possession of a doctoral degree at the date of the recruitment. If you have successfully defended your doctoral thesis but who have not yet formally been awarded the doctoral degree, you will not be considered eligible.
Fluency in both spoken and written English is a prerequisite.
Your application should be written in English and include:
- A personal letter where you describe yourself, your research interest, your experiences and why you are interested in the position (max. 2 pages).
- A CV containing your education and other qualifications; certificate of language proficiency test, if obtained; certificates of exams, degrees and grades, diplomas; a copy of the Master thesis or equivalent, published articles if relevant.
- Candidates are encouraged to provide letters of recommendation or contact information to two reference persons.
Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.
About the employment
The employment is atemporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Ideally, the starting date is between 1 March - 1 April 2024. Please, contact us in case the ideal starting date cannot be met and only a later date is possible. Placement: Uppsala
For further information about the position please contact: Carl Caleman, email [email protected]
Please submit your application by 27 November 2023, UFV-PA 2023/3826.
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- Research Field
- Education Level
- Master Degree or equivalent
- Research Field
- Years of Research Experience
- Number of offers available
- Uppsala universitet
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