PhD in Computational Prediction of Nanoplastic Impact on Protein Function
2 maanden geleden
Do you enjoy working on interdisciplinary research at the crossroads of physics, chemistry, biology and computational science? Are you interested in using simulations and artificial intelligence to understand key molecular processes for human and planetary health? The Van ‘t Hoff Institute for Molecular Sciences (HIMS) and the Informatics Institute (IvI) are looking for an ambitious PhD student to develop and apply an automated computational framework for the prediction of nanoplastic impact on protein function. This research will be part of the Computational Soft Matter Lab.
At the molecular level, complex physicochemical processes can be understood in terms of free-energy landscapes, which map metastable states and pathways onto key system descriptors. These surfaces can be explored via advanced simulations; exploiting machine learning and data mining to find optimal descriptors and boost the sampling of functional dynamics. Most importantly, in silico we can predict changes in the shape of these landscapes, identifying valleys and channels sculpted by internal or external factors. You will work on predicting nanoplastic-induced changes to a protein’s free-energy landscape—i.e., structure and function—and collaborate with various computational and experimental groups to confirm your predictions.
What are you going to do?
This project focuses on developing and applying a forefront computational framework for predicting nanoplastic impact on protein function. You will:
Automate descriptor discovery for chemical and conformational transitions of proteins interacting with nanoplastics; Perform machine learning-augmented free-energy calculations; Build predictive models to effectively screen for relevant nanoplastic-induced changes in a protein’s free-energy landscape; Apply the framework to various nanoplastics and proteins to deliver actionable predictions for medical centers, policy makers and plastic manufacturers.Tasks and responsibilities:
Conduct independent research in the Computational Soft Matter Lab; Collaborate with the Computational Chemistry group at HIMS, the Computational Science Lab at IvI, and experimental groups at HIMS, the Institute of Physics (IoP) and the Amsterdam University Medical Center (UMC); Publish and present your work within the project and on international scientific platforms, such as peer-reviewed international journals, books and conferences; Contribute to the supervision of BSc/MSc student projects; Contribute to the teaching activities of the department.Your experience and profile
An MSc degree in science, preferably in physics, engineering physics, chemistry, chemical engineering, materials science, or computational science with a specialization in natural science; A strong background in physics, chemistry, and/or computational science; Experience with molecular simulation is preferred; Experience with machine learning is preferred; Good programming skills; Good communication skills in oral and written English; Strong initiative and good time management skills; Interest in collaborating with students, PhDs and postdoctoral researchers in related projects and research groups within and outside the Netherlands.Our offer
A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is November 2024 to February 2025. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.
The gross monthly salary, based on 38 hours per week and dependent on relevant experience, ranges between €2.872 - €3.670. UvA additionally offers an extensive package of secondary benefits, including 8% holiday allowance and a year-end bonus of 8.3%. The UFO profile name profile and level is applicable.
The Collective Labour Agreement of Universities of the Netherlands is applicable.
Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:
232 holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January; Multiple courses to follow from our Teaching and Learning Centre; A complete educational program for PhD students; Multiple courses on topics such as leadership for academic staff; Multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses; 7 weeks birth leave (partner leave) with 100% salary; Partly paid parental leave; The possibility to set up a workplace at home; A pension at ABP for which UvA pays two third part of the contribution; The possibility to follow courses to learn Dutch.-
Amsterdam, Noord-Holland, Nederland Universiteit van Amsterdam VoltijdJob DescriptionWe are seeking a highly motivated and skilled PhD candidate to join our team at the Universiteit van Amsterdam. The successful candidate will be part of a forefront research project focused on developing and applying a computational framework for predicting nanoplastic impact on protein function.Key ResponsibilitiesAutomate descriptor...
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Amsterdam, Noord-Holland, Nederland Universiteit van Amsterdam VoltijdJob DescriptionWe are seeking a highly motivated and skilled PhD researcher to join our team at the Universiteit van Amsterdam. The successful candidate will be part of the Computational Soft Matter Lab and will work on developing and applying a forefront computational framework for predicting nanoplastic impact on protein function.Key...
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Amsterdam, Noord-Holland, Nederland Universiteit van Amsterdam VoltijdJob DescriptionWe are seeking a highly motivated and skilled PhD candidate to join our team at the Universiteit van Amsterdam. The successful candidate will be part of a forefront research project focused on developing and applying a computational framework for predicting nanoplastic impact on protein function.Key ResponsibilitiesAutomate descriptor...
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Amsterdam, Noord-Holland, Nederland Universiteit van Amsterdam VoltijdJob DescriptionWe are seeking a highly motivated and skilled PhD researcher to join our team at the Universiteit van Amsterdam. The successful candidate will be part of the Computational Soft Matter Lab and will work on developing and applying a forefront computational framework for predicting nanoplastic impact on protein function.Key...
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Amsterdam, Nederland Universiteit van Amsterdam VoltijdWhat are you going to do ? This project focuses on developing and applying a forefront computational framework for predicting nanoplastic impact on protein function. You will: • Automate descriptor discovery for chemical and conformational transitions of proteins interacting with nanoplastics; • Perform machine learning-augmented free-energy...
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Amsterdam, Noord-Holland, Nederland Universiteit van Amsterdam VoltijdJob SummaryThis is a research position in the Computational Soft Matter Lab at the Universiteit van Amsterdam. The successful candidate will work on developing and applying a computational framework for predicting nanoplastic impact on protein function.Key ResponsibilitiesAutomate descriptor discovery for chemical and conformational transitions of proteins...
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Amsterdam, Noord-Holland, Nederland Universiteit van Amsterdam VoltijdJob DescriptionWe are seeking a highly motivated and skilled PhD researcher to join our team at the Universiteit van Amsterdam. The successful candidate will be part of the Computational Soft Matter Lab and will work on developing and applying a forefront computational framework for predicting nanoplastic impact on protein function.Key...
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