| Language of instruction : English |
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Sequentiality
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Advising sequentiality bound on the level of programme components
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Advice
The student has preferably taken one of the following trajectory courses (2nd Ma Materiomics, Semester 1)
- or: 4992 Molecular modelling - from principle to application in materials science
- or: 4893 Density functional theory: the workhorse of first principles modelling of solids and molecules
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| Degree programme | | Study hours | Credits | P2 SBU | P2 SP | 2nd Chance Exam1 | Tolerance2 | Final grade3 | |
 | 2nd year Master of Materiomics specialisatie opleidingsonderdelen | Optional | 81 | 3,0 | 81 | 3,0 | Yes | Yes | Numerical |  |
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| | | Learning outcomes |
- EC
| EC 2. The graduate of the Master of Materiomics programme can combine chemical and physical principles enabling the discovery of new material concepts based on an interdisciplinary approach. | | | - DC
| DC2.4 The student has knowledge of chemical concepts and methods. [learning pathway interdisciplinarity - identification: the students knows which phenomena are studied in the various disciplines and which methods and theories are used] | | | - DC
| DC2.5 The student has knowledge of physical concepts and methods. [learning pathway interdisciplinarity - identification: the student knows which phenomena are studied in the various disciplines and which methods and theories are used] | - EC
| EC 3. The graduate of the Master of Materiomics programme has insight in how modelling or synthesis methods predict and affect functional properties and is able to design sustainable materials based on in-operando functionality making optimal use of the synergy between computational and experimental methods. | | | - DC
| DC3.4 The student is able to select, justify and optimize the appropriate characterization/modeling technique and method to investigate structure, synthesis, properties of materials and devices. | | | - DC
| DC3.8 The student has knowledge of computational concepts and methods. [learning pathway interdisciplinarity - identification: the student knows which phenomena are studied in the various disciplines and which methods and theories are used] | - EC
| EC 4. The graduate of the Master of Materiomics programme is able to autonomously consult, summarise and critically interpret international scientific literature, reference it correctly and use it to explore and identify new domains relevant to the field. | | | - DC
| DC4.3 The student is able to critically interpret, evaluate, compare, and/or summarize relevant scientific literature related to materials-related problems or research questions. | - EC
| EC 6. The graduate of the Master of Materiomics programme is able to communicate in both written and spoken form and to take a well-argued position in a scientific discussion, going from a general to a specialist level, adapted to the target audience. | | | - DC
| DC6.3 The student is able to take and defend a logically constructed position, based on relevant and scientifically supported arguments. | - EC
| EC 8. The graduate of the Master of Materiomics programme is able to act with integrity and independently judge ethical and societal implications of scientific developments in one’s domain with particular attention to sustainability. | | | - DC
| DC8.4 The student is able to explain the applicable code of conduct regarding research integrity, reflect on it and act accordingly. | - EC
| EC 10. The graduate of the Master of Materiomics programme is able to autonomously acquire new knowledge and monitor, evaluate and adjust one’s learning process. | | | - DC
| DC10.3 The student is able to autonomously acquire, process, and critically interpret new information. |
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| | EC = learning outcomes DC = partial outcomes BC = evaluation criteria |
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The student should have prior knowledge of the following general topics in physics/chemistry:
- basic concepts from quantum mechanics/chemistry
- basic concepts from Newtonian mechanics
- the concepts of chemical bonding and crystal structure
- basic knowledge of the electronic structure of molecules and solids
- basic concepts of statistics
- basic concepts from computational modelling
The student has preferably taken one of the following trajectory courses (2nd Ma Materiomics, Semester 1)
- or: 4992 Molecular modelling - from principle to application in materials science
- or: 4893 Density functional theory: the workhorse of first principles modelling of solids and molecules
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Within the specialization course "Computational modelling in health and medicine" the student is introduced to the various modelling methods that find their application within the context of health care and pharmaceuticals. Here, attention is paid both to the design of new functional drugs and the modelling of their action and interaction with the (biological) environment. The various topics are divided into three modules:
Module 1: Rational design of drugs and small molecules.
In this module the focus is on developing new drugs that meet one or more specific conditions. The starting point is both the screening of existing databases and sampling from the entire chemical space. The following topics are covered:
- the screening funnel
- multi-objective design & pareto surfaces
- the chemical space
- QSAR
- the role of artificial intelligence
Module 2: Reactions and kinetics
In this module the focus is on chemical reactions and kinetics.
We look at pharmacokinetics (ADME) and (bio)degradation of small (drug) molecules. Mechanisms are sought which enhance the functionality of the drug within the context of its administration (Administration), diffusion through the body (Distribution), processing by the body (Metabolism) and final removal from the body (Excretion). This includes looking at the breakdown of these molecules in the body and the environment (Biodegradation).
We also take the reverse reaction step: modelling the necessary synthesis reactions that allow molecular modules to couple into a working drug/small molecule. Besides synthesis, the role of polymorphism is also addressed, studying the impact of different conformers, isomers and crystal structures on functionality. A third and final aspect covered here is solubility, both of the drug in a medium and of water (and other molecules) in the crystal lattice of a drug.
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Lecture ✔
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Practical ✔
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Quiz ✔
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Response lecture ✔
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Video lecture ✔
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Case study ✔
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Homework ✔
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Presentation ✔
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Workshop ✔
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Period 2 Credits 3,00
| Evaluation method | |
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| Written evaluaton during teaching periode | 20 % |
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| Transfer of partial marks within the academic year | ✔ |
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| Conditions transfer of partial marks within the academic year | The student achieves a minimum of 10/20. |
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| Oral evaluation during teaching period | 10 % |
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| Transfer of partial marks within the academic year | ✔ |
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| Conditions transfer of partial marks within the academic year | The student achieves a minimum of 10/20. |
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| Written exam | 70 % |
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| Transfer of partial marks within the academic year | ✔ |
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| Conditions transfer of partial marks within the academic year | The student achieves a minimum of 10/20. |
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| Additional information | For students with an exam contract the scheduled evaluations during the teaching period are replaced with an alternative, individual assignment during the exam period. |
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Second examination period
| Evaluation second examination opportunity different from first examination opprt | |
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| Compulsory textbooks (bookshop) |
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Molecular Modeling: principles and applications,A.R. Leach,2nd,Pearson,9780582382107 |
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| Compulsory course material |
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Course notes, powerpoint slides, selected (review) articles: Blackboard
Obligatory software on personal hardware (laptop): Python and KNIME (free to install) |
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| Remarks |
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The textbook is also used in '4992 Molecular modelling - from principle to application in materials science'. |
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| Exchange Programme materiomics | Optional | 81 | 3,0 | 81 | 3,0 | Yes | Yes | Numerical | |
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|
|
The student should have prior knowledge of the following general topics in physics/chemistry:
- basic concepts from quantum mechanics/chemistry
- basic concepts from Newtonian mechanics
- the concepts of chemical bonding and crystal structure
- basic knowledge of the electronic structure of molecules and solids
- basic concepts of statistics
- basic concepts from computational modelling
The student has preferably taken one of the following trajectory courses (2nd Ma Materiomics, Semester 1)
- or: 4992 Molecular modelling - from principle to application in materials science
- or: 4893 Density functional theory: the workhorse of first principles modelling of solids and molecules
|
|
|
|
Within the specialization course "Computational modelling in health and medicine" the student is introduced to the various modelling methods that find their application within the context of health care and pharmaceuticals. Here, attention is paid both to the design of new functional drugs and the modelling of their action and interaction with the (biological) environment. The various topics are divided into three modules:
Module 1: Rational design of drugs and small molecules.
In this module the focus is on developing new drugs that meet one or more specific conditions. The starting point is both the screening of existing databases and sampling from the entire chemical space. The following topics are covered:
- the screening funnel
- multi-objective design & pareto surfaces
- the chemical space
- QSAR
- the role of artificial intelligence
Module 2: Reactions and kinetics
In this module the focus is on chemical reactions and kinetics.
We look at pharmacokinetics (ADME) and (bio)degradation of small (drug) molecules. Mechanisms are sought which enhance the functionality of the drug within the context of its administration (Administration), diffusion through the body (Distribution), processing by the body (Metabolism) and final removal from the body (Excretion). This includes looking at the breakdown of these molecules in the body and the environment (Biodegradation).
We also take the reverse reaction step: modelling the necessary synthesis reactions that allow molecular modules to couple into a working drug/small molecule. Besides synthesis, the role of polymorphism is also addressed, studying the impact of different conformers, isomers and crystal structures on functionality. A third and final aspect covered here is solubility, both of the drug in a medium and of water (and other molecules) in the crystal lattice of a drug.
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|
|
|
|
|
|
|
|
Lecture ✔
|
|
|
|
Practical ✔
|
|
|
|
Quiz ✔
|
|
|
|
Response lecture ✔
|
|
|
|
Video lecture ✔
|
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|
|
|
|
|
|
Case study ✔
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Homework ✔
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|
Presentation ✔
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|
|
Workshop ✔
|
|
|
|
Period 2 Credits 3,00
| Evaluation method | |
|
| Written evaluaton during teaching periode | 20 % |
|
| Transfer of partial marks within the academic year | ✔ |
|
| Conditions transfer of partial marks within the academic year | The student achieves a minimum of 10/20. |
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|
|
|
|
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|
| Oral evaluation during teaching period | 10 % |
|
| Transfer of partial marks within the academic year | ✔ |
|
| Conditions transfer of partial marks within the academic year | The student achieves a minimum of 10/20. |
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|
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| Written exam | 70 % |
|
| Transfer of partial marks within the academic year | ✔ |
|
| Conditions transfer of partial marks within the academic year | The student achieves a minimum of 10/20. |
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|
|
|
|
|
|
|
| Additional information | For students with an exam contract the scheduled evaluations during the teaching period are replaced with an alternative, individual assignment during the exam period. |
|
Second examination period
| Evaluation second examination opportunity different from first examination opprt | |
|
|
|
| Compulsory textbooks (bookshop) |
| |
Molecular Modeling: principles and applications,A.R. Leach,2nd,Pearson,9780582382107 |
|
|
| Compulsory course material |
| |
Course notes, powerpoint slides, selected (review) articles: Blackboard
Obligatory software on personal hardware (laptop): Python and KNIME (free to install) |
|
|
| Remarks |
| |
The textbook is also used in '4992 Molecular modelling - from principle to application in materials science'. |
|
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1 Education, Examination and Legal Position Regulations art.12.2, section 2. |
| 2 Education, Examination and Legal Position Regulations art.16.9, section 2. |
3 Education, Examination and Legal Position Regulations art.15.1, section 3.
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| Legend |
| SBU : course load | SP : ECTS | N : Dutch | E : English |
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