Exact Sciences Master Guide2005/2006



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Part-time studying


In principle this Master's programme is full-time.
    1. Dual training


Under specific conditions, a tailored Master's programme can be composed, in which in-service training is included.
    1. Research tracks


Students who have chosen to follow the research-oriented variant (O-variant) first have to choose a specialist track. A choice can be made from the programmes in

  • Molecular Design, Synthesis and Catalysis

  • Laser Sciences / Molecular Photoscience

  • Analytical Sciences

  • Computational and Theoretical Sciences

  • Biochemistry / Biomolecular Sciences

 

Each track encompasses at least compulsory (theoretical) courses, a research project including Master's thesis (Major), literature thesis and colloquium, and optional courses or training (see scheme above). Generally spoken these students may aim at continuing their study with PhD education, in order to obtain an executive job as researcher, group leader etcetera at university, research institution, government or (industrial) company.


    1. Molecular Design, Synthesis and Catalysis

      1. Programme


Research training: MDSC Sciences (minimum 42 cp)

 

Master coordinators

VU: dr. M. Schakel, Room KA 3.41a, phone: +31 (0) 20 59 87462, m.schakel@few.vu.nl

UvA: prof. dr. C.J. Elsevier, Room B7.33, phone: +31 (0) 20 525 5653, else@science.uva.nl

 

Scientific research and education in the field of molecular chemistry are of utmost importance to society and industry. This broad discipline aspires to understand and influence chemical and physical properties at the molecular level.



The needs of society with respect to diagnostics, communication, energy, new materials and health care require the developments of molecules with dedicated well-controlled properties. A sustainable society needs efficient use of matter and energy and consequently demands selective new synthetic and catalytic methodologies for the preparation of advanced materials.

Organic, organometallic and coordination compounds are at the heart of this master's program. Novel structures with desirable properties (physical, chemical or biological) are devised by molecular design, often with the aid of computational methods. New synthetic methods are developed to obtain these compounds, which are then studied to enhance our knowledge of the relationship between structure and property. From a practical point of view, the research is directed at achieving efficient syntheses of enviable molecules, the development of novel catalysts to enable clean and selective transformations, and the design of novel bioactive molecules for application as drugs and agrochemicals.

 

The research training takes place in one of the 6 research groups that shape this master program. Students are urged to contact one of the Master coordinators of the MDSC program as soon as possible with their choice of research group. 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)

 

Molecular Inorganic Chemsitry (UvA)

prof. dr. C. J. Elsevier, dr. H. W. Frühauf, dr. G. Rothenberg

Contact: prof. dr. C.J. Elsevier, phone: +31 (0) 20 525 5653, elsevier@science.uva.nl

The research themes of this group are: (1) Synthesis and characterization of organometallic and coordination compounds which show special activity for forming or breaking chemical bonds. (2) Acquiring insight into the mechanism at catalytic reaction centres by manipulation of structural features with as objective to devise new and improved catalysts. (3) Study of (catalytic) reactions in media other than classic solvents, e.g. supercritical media and water. (4) Development of NMR methodologies for application in organometallic chemistry and homogeneous catalysis. (5) Development of new nano-cluster-based catalysts and materials. (6) High-throughput data analysis in homogeneous and heterogeneous catalysis.

 

Organic and Computational Chemistry (VU)

prof. dr.  K. Lammertsma, dr.  A. W. Ehlers, dr.  M. Schakel

Contact : prof. dr. K. Lammertsma phone: +31 (0) 20 59 87474, k.lammertsma@few.vu.nl

The organic chemistry of this group concentrates on developing and applying new classes of organophosphorus reagents for organic synthesis, metathesis processes, and for the design of new ligands suitable for homogeneous catalysts. The group concentrates on carbene-like reagents with transition metal groups and uses an integrated synthetic-computational approach that explores the close relationship between organophosphorus and hydrocarbon compounds.

The computational chemistry (ab initio, semi-empirical, and QM/MM) in this group is used to study reaction mechanisms, to design new reactive intermediates and catalysts, and to predict electronic properties of molecules. The focus is on organic reaction intermediates, transition metal complexes, and metallo­enzymes of which the role in catalytic processes and the dynamics of protein folding are important ingredients.

 

Synthetic Organic Chemistry (UvA)

prof. dr.  H. Hiemstra, prof. dr.  H. E. Schoemaker, dr.  J. H. van Maarseveen

Contact: prof. dr. H. Hiemstra, phone: +31 (0) 20 525 5941, hiemstra@science.uva.nl

Two major themes can be distinguished in the research of this group. The first is the design and development of new and selective synthetic methods. A central issue is the synthetic application of carbocations stabilized by nitrogen and oxygen atoms and the corresponding radicals. Research is also directed at the use of organometallic compounds, the design of efficient catalytic procedures, reactions on the solid phase (combinatorial chemistry) and application of enzymes in organic synthesis with special attention for the production of enantiopure compounds. Recently, studies were started to enable difficult cyclization reactions by using so-called template molecules, in order to prepare medium-sized cyclic peptides and similar compounds, which are very interesting because of their biological activity. The second research theme is the target-oriented construction of challenging molecules, in particular biologically active natural products and their analogues. Nowadays, several alkaloids and amino acids are under investigation as well as the triterpene solanoeclepin A, which is excreted by the potato root and could play an important role to combat a serious potato disease.

 

Homogeneous Catalysis (UvA)

prof. dr. P. W. N. M. van Leeuwen, dr.  J. N. H. Reek, prof. dr. P. C. J. Kamer (guest)

Contact: prof. dr. P.W.N.M. van Leeuwen, phone +31 (0) 20 525 5419, pwnm@science.uva.nl.

The research in this group covers a broad area ranging from fundamental studies of homogeneous catalysis, involving the identification of reactive intermediates using spectroscopic methods, to more applied work in which practical aspects of catalysis are studied. The relationship between the structure of the catalyst and its performance in catalysis is investigated. Rational design of ligands that steer the catalytic reaction in an (enantio-)selective manner is a major aim of the group. New natural and hybrid transition metal enzyme catalysts for new reactions are being developed. Among the subjects studied are fundamental aspects of rhodium-catalysed hydroformylation, asymmetric hydroformylation of fine chemicals, homogeneous catalysis in water, catalysis with bidentate ligands with enforced less stable geometries, palladium-catalyzed reactions of CO with alkenes, asymmetric transfer hydrogenation, dendritic catalysts, sol gel catalysis, cross-coupling reactions, self-assembly of supramolecular catalyst systems and combinatorial ligand synthesis.

 

Bio-organic Chemistry (VU)

prof. dr. M.B. Groen, dr. ir.  R.V.A. Orru

Contact: dr. ir. R.V.A. Orru, phone: +31 (0) 20 59 87447, rva.orru@few.vu.nl

This group focuses on developing asymmetric synthetic methodologies for application in the synthesis of biologically relevant compounds. Biocatalytic steps are combined in enzyme-triggered cascade reactions for the synthesis of chiral building blocks, while multi-component reactions are exploited to improve the efficiency of natural product synthesis by mimicking enzymatic methodologies. The approach enables the rapid preparation of libraries of active compounds like the mureidomycin analogs. Other synthetic activities include the structural proof of recently discovered natural products by total synthesis and preparation of specifically labeled precursors of metabolites to investigate biosynthetic pathways in living organisms. 

 

Bio-organic Chemistry and Biocatalysis (UvA)

prof. dr R. Wever, prof. dr G.J. Koomen (guest)

Contact: prof. dr. R. Wever, phone: +31 (0) 20 525 5110, rwever@science.uva.nl

The group Wever focuses on the use and development of biocatalysts in synthetic organic chemistry as an alternative for existing chemical procedures. The group uses Directed Evolution as a tool to create enzymes with novel or other properties.  By this technique we have obtained a number of haloperoxidase  mutants that show a considerable shift in activity to more alkaline pH values.  Presently the kinetic and other properties of these mutants are studied. We have used acid phosphatases in the phosphorylation of a variety of substituted carbohydrates and alcohols. The enzymes are able to region selectively phosphorylate these compounds using pyrophosphate as a cheap phosphate donor. We conclude that these enzymes are useful alternatives to existing chemical methods in the phosphorylation of a number of substrates. The group Koomen concentrates on designing specific inhibitors that prevent the proliferation of micro organisms and as such have antibacterial activity.

 

Courses

Compulsory for students doing a Major in the MDSC-Master programme are 4 out of 7 compulsory courses. Students doing a Minor in the MDSC programme must choose at least 1 out of 7 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

435664

Coordination and Organometallic Chemistry

6

1

435663

Physical-Organic Chemistry

6

1

435665

Synthetic Organic Chemistry

6

2

435666

Molecular Computational Chemistry

6

2

435667

Nuclear Magnetic Resonance

6

3

435668

Homogeneous Calatysis

6

4

435669

Bio-Organic Chemistry

6

4



      1. Optional courses (Major)





Course code

Course name

Cr.

Period

435653

Supramolecular Chemistry and Nanomaterials

6

6



    1. Laser Science / Molecular Photoscience

      1. Programme


Research training (Major) consists of laboratory research, theoretical courses, a literature study and colloquium and a master thesis with oral presentation. Research training (Minor) ends with a written report. Students are urged to contact the Master coordinator Chemistry VU (dr. M.H.M. Janssen) as soon as possible with their choice of research group (see description below). 

 

Master coordinators

VU Chemistry: dr. M.H.M. Janssen, room O1.36, phone: +31 (0) 20 59 87632 (Physical Chemistry)

UvA: prof. dr. W.J. Buma

 

The Vrije Universiteit and the Universiteit van Amsterdam hold a strong position in research in several areas of laser physics, photochemistry, photophysics and photobiology. By bringing together the scientific expertise of a number of research groups a training programme for M.Sc. students in Laser Sciences / Molecular Photosciences of a high international standard and unique in The Netherlands has been developed. The common denominator in the scientific interests is the interaction of light and matter. Since the detailed subjects of study vary from atoms via small organic and inorganic molecules to biological photoreceptor proteins the programme covers large areas of chemistry, physics and biology. Applications can be found in the fields of nanoscience, quantum computing, atmospheric science, analytical chemistry and materials science.



 

Research group(s) Chemistry-VU

 

All research projects at the VU are carried out at the Laser Centre Vrije Universiteit (http://www.chem.vu.nl/~laser), a European large scale research facility for multi-disciplinary and interdisciplinary laser based research in chemistry, physics and life sciences. The LCVU is part of LaserLab-Europe (http://www.laserlab-europe.net), an integrated consortium of 17 leading national laser laboratories in Europe. The LCVU has a very international setting with many foreign guests and visitors.



 

Physical Chemistry (Division Chemistry)

Staff researchers: dr. J. Bulthuis, dr. H.V.J. Linnartz, dr. M.H.M. Janssen, prof. dr. S. Stolte

Contact: dr. M.H.M. Jansen, phone: +31 (0) 20 59 87632, mhm.janssen@few.vu.nl

The research of the division Physical Chemistry focuses on the dynamics of reactivity, photodissociation and high resolution spectroscopy of small molecules, radicals and ions. We combine state-of-the-art laser spectroscopic and molecular beam techniques with a focus on systems of elementary chemical and atmospheric or interstellar importance. We run benchmark experiments that establish a firm base in understanding chemical processes and that provide input information for ab initio based calculations as well as atmospheric and astronomical studies. We study both collisional and (ultrafast) photochemical dynamics to measure interactive forces and to understand the processes responsible for the breaking and forming of chemical bonds. In addition, we determine the structural and dynamical properties of highly unstable species - typically reactive intermediates - in ultra sensitive spectroscopic detection experiments, covering the spectral region from the ultra-violet to the far infrared.

For more information see: http://www.chem.vu.nl/fc

 

Analytical Chemistry and Applied Spectroscopy (Division Chemistry)

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

Contact: prof. dr. C. Gooijer, phone: +31 (0) 20 59 87544, c.gooijer@few.vu.nl

The central research theme of the department focuses on the development and application of novel analytical technologies to study and measure the interaction of (small) molecules and (bio)macromolecular systems. Both bio-analytical chemistry and physical chemistry are performed within this context, characterized by a strong mutual overlap. The analytical chemistry research program is multidisciplinary emphasizing the integration of analytical separation techniques and advanced spectroscopic detection/identification methods with the focus on molecular laser techniques and mass spectrometry.

For more information see: http://www.chem.vu.nl/acas

 
Bio Physics (Division Physics)

Staff researchers: dr. J.P. Dekker. dr. M.-L. Groot, prof.dr. R. van Grondelle

Contact: prof. dr. R. van Grondelle, phone: +31 (0) 20 59 87930, r.van.grondelle@few.vu.nl. The research is aimed at obtaining fundamental knowledge on the relation between the structure, function and dynamics of proteins and other biological molecules. Molecular processes at the basis of the action of proteins usually involve the transfer of electrons, protons, hydrogen or hydride atoms, which are often coupled to the motion of (charged) molecular groups. Fundamental research in this field requires highly purified, sometimes genetically engineered, biological material with well-defined physical, chemical and biological properties. Thus, a multi-disciplinary approach involving several disciplines (physics, chemistry, biology, mathematics, genetics) is absolutely essential for competitive research in this branch of science.

For more information see: http://www.nat.vu.nl/bio

 

Atomic Physics (Division Physics)

Staff researchers: dr. W. Vassen, dr. K.S.E. Eikema, prof. dr. W. Ubachs

Contact: dr. W. Vassen, phone: +31 (0) 20  59 87949, U2.24, w.vassen@few.vu.nl

Activities in the Atomic and Laser Physics group concentrate on four main research topics, cold atoms, XUV Laser physics and dynamics, ultrafast physics and applied spectroscopy. Within each category several projects are executed. In all of these projects state-of-the-art laser systems play an essential role.

For more information see: http://www.nat.vu.nl/atom

 

Theoretical Physics: Quantum Electronics and Optics (Division Physics)

Staff researchers: dr. T. Visser, prof. dr. D. Lenstra

Contact: prof. dr. D. Lenstra, phone: +31 (0) 20  59 87855, U2.24, d.lenstra@few.vu.nl

Non-linear dynamics of semiconductor lasers Ultrafast photonics. Theory of near-field optics, optical coherence, diffraction and scattering.

For more information see: http://www.nat.vu.nl/theo

 

Research group(s) Chemistry-UvA

 

Molecular Photonics (Division Chemistry)

Staff researchers: prof. dr. W.J. Buma, dr. A.M. Brouwer, dr. R.M. Williams, dr. H. Zhang

Contact: prof. dr. W.J. Buma, phone +31 (0) 20 525 6973, wybren@science,uva.nl; dr. A.M. Brouwer, phone +31 (0) 20 525 5491, fred@science.uva.nl;  dr. R.M. Williams, phone +31 (0) 20 525 5477, williams@science.uva.nl ; dr. H. Zhang, phone +31 (0) 20  525 6976, hong@science.uva.nl

The Molecular Photonics research theme of HIMS aims to develop novel, intelligent photoresponsive materials by understanding and manipulating the interaction between light and materials at the molecular level. The research covers all aspects from design and synthesis of new (supra)molecular systems to testing of devices based on these systems. One line of research is concerned with 'high-resolution' spectroscopic studies on molecular systems. In the frequency domain, high-resolution studies are performed in the gas phase on isolated molecules that range from simple chromophores to large supramolecular systems in order to investigate their electronic and geometric structure, how these are affected by energy absorption, and - ultimately -  how these are related to their (photoactive) function. In the time-domain, high-resolution studies are mainly performed under non-isolated conditions with various femtosecond laser spectroscopic techniques in order to answer the question as to what the molecule does with the energy that is absorbed in the form of photons, i.e., we  "watch the energy flow". A second line of research is specifically concentrated on the dynamics of (organic) molecules in solution and/or solid state. Photoinduced electron transfer is an important theme in this research. It is an elementary chemical reaction that leads to important follow-up processes from the charge-separated states prepared, such as multistep electron transport, redox reactions, charge transfer emission, photocatalysis and large-amplitude molecular motions. A continuous effort is made to apply the know-how gained to the development of photonic molecular systems and materials with potential practical use. These comprise luminescent optical probes, materials with nonlinear optical properties, electroluminescent devices, and molecular switches. Microphotochemistry and microspectroscopy, including single-molecule detection, have proven to be exciting new experimental approaches to advance the research in these directions.

For more information see: http://www.science.uva.nl/hims

 

Molecular Microbial Physiology (Division MicroBiology)

Staff researchers: prof. dr. K.J. Hellingwerf, dr. W. Crielaard

Contact: prof. dr. K.J. Hellingwerf, phone: +31 (0) 20 525 7055, khelling@science.uva.nl

In this group a number of photoactive proteins (e.g. green fluorescent protein, phytochrome, xanthopsin, etc.) are studied with respect to their role in biological signal transduction and their application as bio-photonic materials. The conformational transitions that are relevant for signal generation and transduction in PhotoactiveYellow Protein are studied through several collaborative projects, making use of advanced forms of (optical) spectroscopy, Raman-, FTIR- and NMR-spectroscopy and recently also using time resolved X-ray crystallography. By applying our current understanding on protein folding and protein molecular- and essential-dynamics on PYP, we have been able to generate an insight into the basic mechanisms underlying biological signal generation and transduction. By using the bacteriophytochrome Cph1 these studies are extended to achieve understanding of the coupling of input of free energy (e.g. ATP) to signal transduction in the intact cell.

For more information see: http://www.science.uva.nl/sils

 

Vibrational Dynamics (Division Chemistry)

Staff researchers: prof. dr. H.J. Bakker

Contact: prof. dr. H.J. Bakker, phone: +31 (0) 20 608 1257, h.bakker@amolf.nl

In this group the dynamics and microscopic structure of water and other hydrogen-bonded liquids, water at surfaces and the mechanisms of proton and electron transport in hydrogen-bonded systems is investigated using nonlinear optical techniques like pump-probe, photon-echo spectroscopy and surface sum-frequency generation.

For more information see:http://www.amolf.nl/

 

Quantum Gases Atom Optics (Division Physics)

Staff researchers: prof. dr. J. Walraven, prof. dr. B. van Linden van den Heuvell, dr. R. Spreeuw, dr. K.-J. van Druten

Contact: dr. R. Spreeuw, phone: +31 (0) 20 525 5663, spreeuw@science.uva.nl

Our research concentrates around the following projects: Evanescent-wave atom mirror; Thin-film magnetic atom chips, Tonks gas on a chip, Quantum information and entanglement.

For more information see: http://www.science.uva.nl/research/aplp

 

Literature thesis and colloquium

dr. M.H.M. Janssen, room O1.36, phone +31 (0) 20 59 87632

 

Courses

The master programme Laser Sciences is a broad programme provided by groups and staff working in the Laser Centre VU and at the UvA. All students joining this programme start choosing 2 out of the 3 compulsory courses and 2 out of the 7 theoretical courses (Major), where depending on the research project (Major) at least 1 of the courses is compulsory. Subsequently, a research project (Major) with a mimimum of 42 cp and at least 2 theoretical courses (Major). Students doing a Minor in the LS programme must choose at least 1 out of the 3 compulsory courses and 1 out of 5 theoretical courses (Major) (the course must be related to the research training). Depending of the research training 1 or more of the optional courses may be compulsory.

An overview of the available courses is given below. A description of the various courses can be found at the back op this guide and on the following webpage http://www.nat.vu.nl/~laser/master_program.html


      1. Compulsory courses (Major, choose 2)





Course code

Course name

Cr.

Period

420036

Molecular Photochemistry and Photophysics

6

1

420033

Introduction to Lasers and Techniques

6

1

420006

Atoms, Molecules and Light

6

1



      1. Theoretical courses (Major, choose 2)





Course code

Course name

Cr.

Period

420085

Molecular Reaction Dynamics

6

2

420113

Elementary Methods in Experimental Physics

6

2

420144

Advanced Biophysics

6

2

435665

Synthetic Organic Chemistry

6

2

435666

Molecular Computational Chemistry

6

2

420003

Advanced Quantum Mechanics

6

4

420118

Advanced Electrodynamics and Quantum Optics

6

4 and 5



      1. Optional courses (Major)





Course code

Course name

Cr.

Period

435607

Molecular Spectroscopy

6

4

420089

Elementary Events in Photobiology

6

4

435649

Advanced Femtosecond Lasers and Techniques

6

4

420090

Spectroscopy, Astrophysics and the Earth's Atmosphere

6

5

420091

Cold Atoms

6

5

435653

Supramolecular Chemistry and Nanomaterials

6

6

435652

Reaction Dynamics in Condensed Phase and Bio-Systems

6

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

420080

Nonlinear Dynamics and Chaos

6

This course will not be given in 2005/2006.





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