| 1 | Advanced Protein Crystallography | WMBS008-05 |
This course will provide insights on the important fundamentals and practices of protein X-ray crystallography. The aims of the course are to learn how protein crystal structures are determined, and to acquire the knowledge and skills necessary for critically analysing a 3D crystal structure.
Subjects discussed during the course are:
• Protein crystallization and crystal geometry;
• Basic diffraction theory;
• X-ray instrumentation;
• Strategies for phase determination;
• Basics of model building and refinement;
• Structure validation: quality assessment of a protein crystal structure.
Lecture classes are combined with discussion/exercise sessions: students will obtain reading assignments, will have to answer exercises, and are requested to prepare questions and subjects for group discussions. The lecture/discussion/exercise course is complemented with a workshop on the use of the various protein crystallographic computer programs. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. A.M.W.H. Thunnissen | | Docent(en) | Prof. Dr. A. Guskovdr. A.M.W.H. Thunnissen | | Onderwijsvorm | Hoorcollege (LC), Practisch werk (PRC) | | Toetsvorm | Practisch werk (PR), Schriftelijk tentamen (WE) | | ECTS | 5 | | Entreevoorwaarden | The course unit assumes prior knowledge acquired from relevant courses in Bachelor’s programmes in Chemistry and/or in Biology, covering the following subjects: fundamentals of protein structure, mathematics (basic calculus and vectors), biophysical chemistry. Relevant courses in the BSc Chemistry and BSc Biology or LS&T programmes at the University of Groningen: Calculus I (WICAL1-12), Biochemistry (CHBC-10), Recombinant DNA and Biotechnology (CHRDNAB-11), Cell physiology: Energy and Structure (WLP10B18), Structural Biology (WLP10B22), Mathematics for Life Sciences (WLP10B22). | | Opmerkingen | Students from the degree programme Biomolecular Sciences have priority, to register please send an email to: academicadvisor.mscbio@rug.nl
Maximum capacity is 24 students. |
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| 2 | Advances in Chemical Biology | WMCH014-05 |
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| 3 | Astrochemistry (21/22) | WMAS018-05 |
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| 4 | Bio-based Products | WMCE001-05 |
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| 5 | Biocatalysis and Green Chemistry | WMCH027-05 |
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| 6 | Bioinspired Designer Materials | WMCH009-05 |
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| 7 | Biomaterials 2 | WMBE001-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. P. van Rijn | | Docent(en) | dr. P. van Rijn | | Onderwijsvorm | Bijeenkomst (S), Opdracht (ASM), Hoorcollege (LC) | | Toetsvorm | Opdracht (AST) | | ECTS | 5 |
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| 8 | Biophysical Imaging & Manipulation Techniques | WMPH047-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. W.H. Roos | | Docent(en) | prof. dr. W.H. Roos | | Onderwijsvorm | Hoorcollege (LC), Practisch werk (PRC), Werkcollege (T) | | Toetsvorm | Presentatie (P), Schriftelijk tentamen (WE), Verslag (R) | | ECTS | 5 |
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| 9 | Characterisation of Materials | WMPH021-05 |
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| 10 | Chemical Catalysis | WMCH015-05 |
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| 11 | Colloquium | WMCH001-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | C. Mayer, PhD. | | Docent(en) | C. Mayer, PhD. | | Onderwijsvorm | Werkcollege (T) | | Toetsvorm | Presentatie (P), Verslag (R) | | ECTS | 5 |
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| 12 | Computational Chemistry | WMCH022-05 |
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| 13 | Design of Industrial Catalysts | WMCE009-05 |
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| 14 | Final Exam | WMCH002-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. R.W.A. Havenith | | Docent(en) | | | Toetsvorm | Mondeling tentamen (OR) | | ECTS | 5 |
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| 15 | Functional Properties | WMPH015-05 |
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| 16 | Interfacial engineering | WMCE003-05 |
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| 17 | Master Research Project Chemistry | WMCH901-40 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | Prof. Dr. W.R. Browne | | Docent(en) | Individual Supervisor | | Onderwijsvorm | Bijeenkomst (S), Practisch werk (PRC) | | Toetsvorm | Practisch werk (PR), Presentatie (P), Verslag (R) | | ECTS | 40 |
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| 18 | Molecular Dynamics | WMBS003-05 |
Together with experiment and theory, computational modeling is one of the three pillars of modern science. In chemistry as well as in life sciences, modeling of the interactions between molecules is essential to understand the emerging behavior of complex systems. In particular the Molecular Dynamics (MD) simulation technique provides a detailed view of the behavior of molecules in space and time, at a resolution that cannot be attained by any single experimental technique.
In a series of lectures, the underlying theory (statistical thermodynamics), the diversity of molecular models (atomistic, coarsegrained), and numerical techniques (integration of Newton's equations of motion) used in MD simulations will be discussed.
Applications of the technique will be shown, with a focus on simulation of biomolecular processes.
An important part of the course is hands-on experience using the GROMACS modeling software in a series of tutorials and practicals covering the basics of the techniques and selected applications, e.g. self-assembly of lipids in water or sampling the conformational space of proteins. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. S.J. Marrink | | Docent(en) | dr. A.H. de Vriesprof. dr. S.J. Marrink | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC) | | Toetsvorm | Practisch werk (PR), Presentatie (P), Schriftelijk tentamen (WE) | | ECTS | 5 | | Entreevoorwaarden | The course unit assumes prior knowledge acquired from Calculus, Classical Mechanics, Introduction to Thermodynamics, and Structural Biology, all at Bachelor Life Science and Technology level. This material is offered in various Life Science, Chemistry, and Physics courses. | | Opmerkingen | Students from the degree programme Biomolecular Sciences have priority, to register please send an email to: academicadvisor.mscbio@rug.nl
Max. 30 students |
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| 19 | Molecular Quantum Mechanics 1 | WMCH010-05 |
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| 20 | Molecular Quantum Mechanics 2 | WMCH016-05 |
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| 21 | Organic Synthesis: Methods and Strategy 1 | WMCH017-05 |
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| 22 | Organic Synthesis, Methods and Strategy 2 | WMCH024-05 |
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| 23 | Organometallic Chemistry | WMCH018-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. E. Otten | | Docent(en) | prof. dr. E. Otten | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Werkcollege (T) | | Toetsvorm | Opdracht (AST), Schriftelijk tentamen (WE) | | ECTS | 5 |
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| 24 | Photovoltaics Science and Energy | WMCH011-05 |
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| 25 | Physical Methods for Chemical Analysis | WMCH012-05 |
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| 26 | Polymer Physics | WMCH025-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | Prof. Dr. G. Portale | | Docent(en) | Prof. Dr. G. Portale | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Werkcollege (T) | | Toetsvorm | Presentatie (P), Schriftelijk tentamen (WE), Verslag (R) | | ECTS | 5 |
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| 27 | Polymer products | WMCE005-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | Dr. R.K. Bose | | Docent(en) | Dr. R.K. Bose Guest lecturer | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM) | | Toetsvorm | Opdracht (AST), Presentatie (P), Verslag (R) | | ECTS | 5 |
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| 28 | Practical Physical Chemistry of Polymers | WMCH030-05 |
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| 29 | Product Focused Process Design | WMCE011-05 |
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| 30 | Protein and Enzyme Engineering | WMBS004-05 |
This course aims to provide insight in the scientific basis and applications of protein engineering, especially of enzymes. Enzymes catalyze numerous biochemical reactions, and are highly important for bioprocessing, synthetic biology, biodegradation, as well as for diagnostics and therapeutics in medicine. They are attractive catalysts for the production of bioactive compounds because of their chemo-, regio- and stereoselectivity. Applications of enzymes often require protein engineering aimed at increasing catalytic activity, binding affinity or stability. For this, fundamental insight in structure-function relationships is of key importance. Furthermore, knowledge about methods in structure-based protein engineering and directed evolution contributes to solving many other problems in biomolecular sciences. The course trains students in the scientific background of protein engineering, including directed evolution, as well as the use of protein structures and computational methods. The course includes lectures, tutorials, computer practicals (computational protein design) and (for students lacking the experience) laboratory work to make students familiar with mutagenesis methods. Students are also trained in the ability to examine recent literature to critically present and discuss strategic options and experimental results.
There are 2 schemes to follow this course:
A) compact (full time), with all parts in three weeks (lectures, tutorials, computer practicals, lab practicals, assignments presentation, assignment report). Best for students full time Biomolecular Sciences or those who have exemption form the lab practicals. This may be too crowded for students who do not have an exemption for the laboratory practical and for students (chemistry, CB) who follow another course in parallel.
B) stretched (for chemistry), with most parts (lectures, tutorials, computer practicals, lab practicals) in the first three weeks, but with the assignment presentation and reports scheduled in week 40. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | Prof. Dr. G. Maglia, PhD. | | Docent(en) | C.N. Pinto Teixeira, PHD.prof. dr. J.G. Roelfesdr. A.M.W.H. Thunnissendr. H.J. Wijma | | Onderwijsvorm | Practisch werk (PRC), Werkcollege (T), Hoorcollege (LC), Opdracht (ASM) | | Toetsvorm | Opdracht (AST), Practisch werk (PR), Presentatie (P) | | ECTS | 5 | | Entreevoorwaarden | For students admitted to Biomolecular Sciences and Chemistry track: Chemical Biology
The course requires prior knowledge about biochemistry, molecular biology, organic chemistry, and catalysis, all studied in the first or second years of the BSc program Chemistry (tracks Life or Sustainability, both are fine) or Biology (Molecular Life Sciences). Basic experience with molecular biology is required. Note: students with hands-on skills in oligonucleotide-assisted mutagenesis (e.g. QuikChange, Gibson cloning) may request exemption from the laboratory practicals. Such a request should be carefully motivated and can be made to the coordinator. | | Opmerkingen | Register for this course by sending an email to: academicadvisor.mscbio@rug.nl
Obligatory:
Filling out and handing in answers to any questions handed out during lectures, tutorials and computer practicals is mandatory (>80% correct).
Mid-term review of the assignment and participation in the final presentation plus discussion are mandatory.
Attending and active participation in laboratory practicals is obligatory (unless exemption).
Participation in the GBB symposium is mandatory. |
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| 31 | Reaction Mechanisms | WMCH006-05 |
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| 32 | Scientific Integrity | WMCH007-00 |
Note: Scientific integrity will be offered in Ia and IIa. You only have to participate this meeting once during your master degree.
This course unit consists of one mandatory lecture. Attendance at this lecture is required to pass the course.
The student will be exposed to various topics on the research misconduct in plagiarism, proper way of allocating credit, whistleblowing. The course will also include case studies for typical examples of research misconduct. The case study will be also extended to two famous real cases in research history. |
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| 33 | Second Research Project | WMCH903-20 |
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| 34 | Skills in Science Communication | WMEC006-05 |
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| 35 | Stereochemistry | WMCH013-05 |
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| 36 | Structure at Macro, Meso and Nano Scale | WMPH020-05 |
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| 37 | Structure determination with spectroscopic methods | WMCH008-05 |
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| 38 | Supramolecular chemistry | WMCH020-05 |
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| 39 | Sustainability for Engineers | WMIE020-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. ir. G.H. Jonker | | Docent(en) | dr. ir. G.H. Jonker | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Werkcollege (T) | | Toetsvorm | Opdracht (AST) | | ECTS | 5 |
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| 40 | Sustainable Electric Energy Storage | WMCH029-05 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. M. Tromp | | Docent(en) | | | ECTS | 5 |
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| 41 | Synthetic Biology and Systems Chemistry | WMCH021-05 |
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| 42 | Topics in chemistry with Python | WMCH028-05 |
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