Exact Sciences Master Guide2005/2006



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Analytical Sciences

  1. Programme


Research training: Analytical Sciences (minimum 42 cp)

 

Master coordinators

VU: dr. H. Lingeman, room M3.30, phone: +31 (0) 20 59 8 7539

UvA: dr. W.Th. Kok, room B. 437, phone: +31 (0) 20 525 6539

 

The research training takes place in one of the 4 research groups. Students must contact the Master coordinator at least two months before they would like to start their research training. The research training (Major) starts with a literature study and ends with a Master thesis, an oral presentation and a poster presentation. The research training (Minor) also starts with a literature study and ends with a written report and an oral presentation.



 

The Master program Analytical Sciences is a unique combination of four strong

analytical groups from the Free University (VU) and the University of

Amsterdam (UvA). As these groups are complementary, a broad range of analytical topics is covered.

 

The program starts with an introductory course in which the basic concepts of



analytical chemistry and the different areas where it is used, with their own specific problems, are discussed. Then separation techniques, spectroscopy and statistics will be taught at the master level. After these compulsory topics the program leaves a lot of freedom to go in detail into some of the advanced topics.

 

Research group(s)

 

Applied spectroscopy (VU)

Lectures: dr. F. Ariese, prof. dr. C. Gooijer, dr. G. van der Zwan

The applied spectroscopy research focuses on the development of novel spectroscopic analytical approaches, including the coupling of laser-based methods to separation techniques such as liquid chromatography and capillary electrophoresis. The emphasis is on laser-based Raman spectroscopy and fluorescence/phosphorescence spectroscopy, including high-resolution cryogenic methods as fluorescence line-narrowing spectroscopy. In this context important developments are the use of spectroscopic techniques for biologically relevant systems. Time-resolved fluorescence and fluorescence resonance energy transfer are investigated for this study.

 

Bio-molecular Analysis (VU)

Lecturers: prof. dr. H. Irth, dr. H. Lingeman, prof. dr. W.M.A. Niessen, dr. J.J. Vreuls

The main goals are to improve selectivity and sensitivity / analyte detectability of total (bio)-analytical systems. With large sample series, as frequently encountered in real-life screening or monitoring studies, speed of analysis is another aspect of current interest. In this case the emphasis is on the development of on-line and, preferably, fully automated systems. This implies that much attention is devoted to the design and optimization of multidimensional methods. In this context important developments are in coupled systems, in combination with on-line bio-specific reaction units and mass spectrometric detection.

 

Polymer analysis (UvA)

Lecturers: dr. W.Th. Kok, prof. dr. ir. P.J. Schoenmakers

The objective the research group is to generate novel, or greatly improved techniques and methods for the analysis of natural and synthetic polymers. The main focus is on separations. Separations are essential to characterize the many distributions that are present in synthetic polymers, e.g. molecular mass, functionality, and chemical composition. Topics studied are 2D separations in the liquid phase, and the development of nanofluidic separation devices.

 

Biosystems Data Analysis (UVA)

 Lecturers: prof. dr. A.K. Smilde, dr. J. Westerhuis, dr. H. Hoefsloot

The aim of the research in this group is developing and validating methods for summarizing and visualizing complex biological and chemical data. Measurements on biological and chemical systems generate an abundance of data. This data has tob e transformed to information (summarize) and presented to the user (visualize). One way of doing both simultaneously is by using models. These models summarize the data and the model-parameters visualize the underlying biological or chemical processes. Different types of models will be developed: multiset models and grey models. These models and combinations thereof are generic tools for analyzing complex biologica lor chemica data.

 

Environmental analysis (VU)

Contact: dr. H. Lingeman

In addition to the above mentioned research groups, there is the possibility to study an environmentally-oriented (research) program. In addition to the compulsory courses, courses can be followed in environmental chemistry, environmental analysis, environmental toxicology, specialized courses in ecology, microbiology and hydrology. Research project, in most of these fields, will be performed in combination with external company training(s).

 

Literature thesis and colloquium

Contact: dr. F. Ariese, room O3.24, phone: +31 (0) 20 59 87524

 

Courses



Compulsory for the Analytical Sciences programme are the 4 compulsory courses, a research project (Major) with a minimum of 42 cp and at least 2 theoretical courses (Major). Students doing a Minor in the AS programme must choose at least 2 out of  4 compulsory courses (the course must be related to the research training). An overview of the available courses is given below. A description of the various courses can be found in the chapter Course Descriptions.
      1. Compulsory courses (Major)





Course code

Course name

Cr.

Period

435600

Principles of Analytical Sciences

6

1

435609

Separation Sciences

6

2

435624

Statistics and Chemometrics

6

3

435607

Molecular Spectroscopy

6

4



      1. Theoretical courses (Major)





Course code

Course name

Cr.

Period

435603

Bio-Analytical Chemistry I

6

1

435604

Mass Spectrometry

6

2

435601

Industrial Analysis

6

4

435602

Computational Data Analysis

6

5



      1. Optional courses (Major)





Course code

Course name

Cr.

Period

435623

Bio-Analytical Chemistry II

6

3

435610

Emission Spectroscopy

6

5

435608

Protein Spectroscopy

6

Not scheduled, can be taken by self-study under the supervision of the lecturer.

435605

Capillary Electrophoresis

6

by appointment



    1. Computational and Theoretical Sciences

      1. Programme


Research training: Computational and Theoretical Sciences (minimum 42 cp)

 

Master coordinator

VU: dr. F.M. Bickelhaupt, room R1.40, phone: +31 (0) 20 59 87617

UvA: dr. E.J. Meijer, room B633, phone: +31 (0) 20 525 6448

 

The research training takes place in one of the two research groups. Research training (Major) includes a Master thesis and an oral presentation.The compulsory literature study and colloquium (12 cp) is taken at the end of the course and is directed towards broadening the scope of the research training.



 

Research group(s)

 

Theoretical Chemistry (VU)

Lecturers: prof. dr. E. J. Baerends, dr. F. M. Bickelhaupt, dr. L. Visscher

The Theoretical Chemistry department develops molecular electronic structure theory and devises quantum chemical methods for the calculation of the electronic structure and the properties following from it. Research focusses on physical models, numerical methods and computer implementations. Density functional theory and methods are a central theme, as well as ab initio and DFT methods for the simultaneous treatment of relativistic effects and electron correlation. Actual electronic structure investigations ("applications") are carried out to understand and predict phenomena in a variety of chemical subdisciplines. Important themes are:



  • Metal-ligand and metal-metal bonding in organometallic chemistry (including photochemistry and homogeneous catalysis)

  • Electronic absorption spectra and nonlinear optical properties of large molecules

  • Relativistic effects in heavy element chemistry and spectroscopy

  • Reactivity at and scattering from crystal surfaces (heterogeneous catalysis)

  • Structure, reactivity and catalysis

  • Hydrogen bonding in DNA and molecular recognition in general.

 

Computational Physics and Chemistry & Macromolecular Simulation (UvA)

Lecturers: prof. B. Smit, prof. D. Frenkel, prof. R. Krishna, prof. A. Fasolino, dr. P.G. Bolhuis, dr. C.P. Lowe, dr. E.J. Meijer.

The groups Computational Physics and Chemistry (prof. Smit) and Macromolecular Simulation (prof. Frenkel) of the University of Amsterdam focus on the development and application of Monte Carlo, molecular dynamics, and ab initio (Car-Parrinello) simulation techniques to study, on a microscopic level, the properties and behavior of condensed-phase systems. Topics are selected on basis of their scientific and/or technological interest. Themes of current interest include:


  • Adsorption and catalysis in confined geometries (zeolites and clays)

  • Modelling of structure and (hydro)dynamics of mesoscopic materials (colloids, micro-porous structures, membranes, and polymeric liquids)

  • Predicting the rate of activated processes (crystal nucleation, protein folding)

  • Condensed-phase chemistry (aqueous proton transport and homogeneous catalysis in solution).

  • Carbon-Based materials

 

Literature thesis and colloquium:

Contact: dr. F.M. Bickelhaupt, room R1.40, phone: +31 (0) 20 59 87617

 

Courses

Compulsory for the CTS programme are two courses (max. four) out of the courses listed below, depending on the research training. A description of the various courses can be found in the chapter Course Descriptions.



      1. Courses (Major)





Course code

Course name

Cr.

Period

435628

Principles of Condensed Matter Science

6

1

435629

Programming, Datastructures, and Algorithms

6

1

435631

Basic Group Theory

6

2

435630

Principles of Theoretical Chemistry

6

2

435633

Molecular Simulation

6

3

435632

Intermolecular and Surface Forces

6

4

435612

Applied Theoretical Chemistry

6

4

435635

Ab Initio Molecular Dynamics

6

5



    1. Biochemistry / Biomolecular Sciences

      1. Programme


Research training: Biochemistry / Biomolecular Sciences (minimum 42 cp);

See also: Master programme in Biomolecular Complexity (Medical Natural Sciences).

 

Master coordinator



VU: via the Director of Education, prof. dr. W.H. Mager, room O1.43, odchem@few.vu.nl, phone: +31 (0) 20 59 87445

 

The research training takes place in one of the  research groups. Research training (Major) starts with a literature study and colloquium (12 cp) and ends with a master thesis, an oral presentation and a poster presentation. Research training (Minor) ends with a written report.



 

Research group(s)

 

Protein folding and the biology of molecular chaperones

Lecturers: prof. dr. S.M. van der Vies, dr. H. van Heerikhuizen, dr. M.H. Siderius

Molecular chaperones function inside the living cell where they prevent incorrect inter- and intra-molecular interactions of polypeptide chains. They are essential in a variety of cellular processes such as polypeptide folding, degradation and translocation across membranes, vesicle trafficking, and the activation of a number of crucial regulatory proteins. Molecular chaperone activity is needed in particular under stress conditions, to prevent and limit damage to proteins and to assist the activation of signaling molecules essential for an adequate stress response. The research is aimed at deciphering the molecular details of the interactions of chaperones and their substrate proteins and the regulation of the folding activity by co-chaperones under physiological as well as stress-induced conditions.

 

Stress-responsive signal transduction in Saccharomyces cerevisiae

Lecturers: prof. dr. S.M. van der Vies, dr. M.H. Siderius

Signal transduction pathways in a cell are organised in such a way that a certain stimulus evokes a specific output in terms of the activation and inactivation of particular (sets of) genes. The research concerns the osmo-responsive HOG/MAP-kinase pathway that is one of at least five MAP-kinase pathways in yeast. The functioning of the pathway in concert with the other MAP-kinase routes, as well as the pathways involved in e.g. cell cycle control and metabolic control is being studied. The aim is to identify regulatory proteins for the osmoadaptive signaling pathway(s), and elucidate the mechanisms by which they function inside the cell. Furthermore, the dynamic protein complexes of signaling molecules which mediate specificity and integrated output is being investigated.

 

Ribosome biogenesis in Saccharomyces cerevisiae

Lecturer: dr. J.C. Vos

This research is aimed at identification of trans-acting proteins and RNA molecules, that are instrumental in the dynamic interplay between the pre-ribosomal RNA precursor and the ribosomal proteins in the assembly of a large, functional macromolecular structure. The rRNA processing pathway is studied in detail with respect to the function of trans-acting factors as well as the role of antibiotics. Genetic screens are designed to identify further components of the molecular machinery required to build the ribosomal subunits.

 

Dynamics of biomolecules and macromolecular complexes (CCM programme)

Lecturers: prof. dr. S.M. van de Vies, dr. H. van Heerikhuizen, dr M.H. Siderius

The research programme aims to gain novel insights into the mechanisms by which proteins attain their biologically active structure and perform their biological function. Molecular chaperone-assisted protein folding and cytochrome P450-catalysed bio-transformation are the targets of this programme. The dynamics and structural properties of these systems will be analysed on different time scales using a multitude of methods. The CCM-initiative incorporates Chemistry, Biology and Physics.

 

Additional research projects

Additional research projects, offered by the faculty of Earth and Life Sciences (FALW) or the University of Amsterdam, will be available on request.

 

Methodology



The power of genetics in combination with knowledge of the genomes of the model organisms Escherichia coli and Saccharomyces cerevisiae is used to delete, modify or amplify genes of interest. Biochemical approaches are used to purify and characterize macromolecular complexes that are formed during the biogenesis of ribosomes, signal transduction or the folding of nascent polypeptide chains. Advanced spectroscopic techniques and computational chemistry are employed to study the structure and dynamic properties of biomolecules.

 

Literature thesis and colloquium



Contact: via the Director of Education, prof. dr. W.H. Mager, room O.143, odchem@few.vu.nl, phone: +31 (0) 20 59 87445

 

Courses



Compulsory for the BC programme are the courses Metabolism & Energy Production and Genetic Information as well as 2 of the 6 optional courses. An overview of the available courses is given below. A description of the various courses can be found in the chapter Course Descriptions.
      1. Compulsory Courses (Major)





Course code

Course name

Cr.

Period

435621

Biochemistry A: Metabolism and Energy Production

6

by appointment

435622

Biochemistry B: Genetic Information

6

by appointment



      1. Optional Courses (Major)





Course code

Course name

Cr.

Period

430054

Advanced Structural Biology

6

2





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