Inhoudsopgave 1 Faculty of Sciences 8



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subject

Protein Science

code

470145

lecturers

dr. D. Bald (co-ordinator); P. Voeller

credits

6

period

04.09.2006 - 29.09.2006

aim

Learn advanced protein science methods that you can apply to answer a wide range of biochemical, biomedical and biotechnical questions.

Students should be able to:



  • Apply advanced techniques for protein expression, purification, and investigation of protein-protein or protein-inhibitor interaction.

  • Set-up strategies for his/her own experiments

The student should know:

  • Principles of protein structure, function, dynamics, inhibition and engineering

  • Background of current protein science techniques

content

We start with a repetition/overview of protein structure, function, and inhibition. Then we go ahead with lab-practicals, supplemented by lectures, computer sessions and self-study. We will deal with several topics of Protein Science with an emphasis on principles/methods/techniques that you can apply to any protein. Examples are:

  • In vivo and in vitro expression of proteins

  • Advanced FPLC techniques for protein purification

  • Spectroscopic techniques to measure protein/protein and protein/inhibitor interaction (Biacore)

  • Protein Engineering Techniques, e.g. to modify the affinity of a protein for an antibiotic

Computer methods to predict and analyze protein structure and function

form of tuition

You carry out experiments in small groups (2-4 students) in the Structural Biology lab under supervision of a staff member (35 h), lectures and computer sessions(15h), supplemented by self-study. In groups you write a report and give an oral presentation about the experiments.

literature

No particular book required. For repetition please see any Biochemistry textbook. You will receive a CD with lectures and additional material.

mode of assessment

Written reports (1/3 oral presentation (1/3), active participation in the experiments (1/3)

entry requirements

The course is based on Bachelor-level Biochemistry courses

target audience

Master students Biomolecular Science, Biomedical Science, Biology, Pharmaceutical Sciences and Medical Natural Sciences

remarks

You need a white coat for the experimental part. Maximal number of students is 32.




subject

Protein Spectroscopy

code

435608

lecturer

dr. G. van der Zwan (contact)

credits

6

period

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

aim

Getting acquainted with the principles, techniques and methods, used to study the physico-chemical properties and to characterize proteins.

content

The topics discussed comprise the basic principles of fluorescence spectroscopy, time-resolved fluorescence and fluorescence resonance energy transfer are discussed, this to study the dynamics and kinetics of protein-folding mechanisms.

form of tuition

Lectures and tutorials.

literature

Recent summarizing articles provided by the lecturer.

mode of assessment

Written or oral examination.

entry requirements

Basic knowledge of spectroscopic techniques.

target audience

mCh




subject

Protocol Validation

code

400117

credits

6

period

5 and 6

lecturer

prof.dr. W.J. Fokkink

aim

Learning to use formal techniques for specification and validation of communication protocols.

content

This course is concerned with specification and validation of protocols, using formal methods. The course is based on a specification language based on process algebra combined with abstract data types, called mCRL. This language and its toolset can be used for specification of parallel, communicating processes with data. Model checking is a method for expressing properties of concurrent finite-state systems, which can be checked automatically. Interesting properties of a specification are: "something bad will never happen" (safety), and "something good will eventually happen" (liveness). In the lab we will teach the use of a tool for automated verification of the required properties of a specification.

form of tuition

Lectures with practical work. During the labs the mCRL-tool and a model checker will be used for validation of protocols discussed during lectures.

literature

Lecture notes: Groote, J.F., Fokkink, W., Reniers, M., Modelling Distributed Systems.

mode of assessment

Written exam, together with a homework assignment. The overall mark of the course is (H+3W)/4, where H is the mark for the homework assignment, and W is the mark for the written exam.

entry requirements

Inleiding Logica (400119), Datastructuren (400145).

target audience

3I, 3BI, 3AI, mCS, mPDCS

remarks

Once every other year, not in spring 2007.




naam

Psycholinguïstiek, 2

code

539152

docent

dr. H.D. van der Vliet

studiepunten

5

contacturen

28 (28 werkcollege)

periode

5

doel

Het verwerven van inzicht in taalproductie, en in psycholinguïstische vraagstellingen en inzichten

inhoud

Bij het luisteren naar taal en het spreken ervan spelen allerlei processen een rol. Het doel van deze cursus is deze processen te identificeren en bestuderen. Wij kijken daarvoor naar de belangrijkste studies binnen het vakgebied aan de hand van het tekstboek en een enkel wetenschappelijk artikel. Deze studies toetsen voornamelijk theorieën aan de hand van gegevens die verzameld zijn door observatie en experimentatie. Door het bestuderen van dit onderzoek zullen we dus ook inzicht krijgen in experimentele methodologie binnen het vakgebied. De resultaten van  het bestuderen onderzoek kunnen leiden tot verificatie, falsificatie of aanpassing van taalgebruikersmodellen die uitgebreid besproken zullen worden.

literatuur

Wordt op eerste college bekend gemaakt

toetsing

Opdrachten en tentamen

doelgroep

2e jaars studenten Taalwetenschap en minorstudenten (m.n. studenten Talen, studenten Psycologie of Artificiële Intelligentie)

opmerkingen

Inschrijven verplicht via TIS

voorkennisvak

500011 : Inleiding algemene taalwetenschap, 1 (of 1e jaar Taalwetenschap)




subject

Putting Electrons to Work: the Science behind Modern Devices

code

420060

lecturers

dr. T. Gregorkiewicz (UvA); dr. E.H. Brück (UvA, phone: +31 (0) 20 525 5640, e-mail: bruck@science.uva.nl)

credits

6

period

4 and/or 5

aim

Discussion of the subtle physics behind modern electronic and magnetic devices.

content

  • Electrons in semiconductors & metals: Doping: effective mass approximation, Spin scattering & Magneto-resistance.

  • Low dimensional structures: Quantum dots and wires, 2-D structures, Magnetic multilayers, Spin-valves.

  • Optical properties: Optical doping, Dynamical aspects, Magneto-optics.

  • Experimental techniques: Photoluminescence, Absorption, Raman spectroscopy, Magneto-optics and magnetic resonance, Magnetization, Magneto-transport.

  • Devices: Diodes and transistors, LED's, Semiconductor lasers, Magnetic disks, MO storage, MRAM, GMR sensors, Spin-polarized FET.

form of tuition

Interactive course.

literature

S. Elliott: The Physics and Chemistry of Solids; F.G. Smith and T.A. King: Optics and Photonics: an Introduction Physics Today, Special Issue Magneto Electronics, April 1995 48(4), 1995

mode of assessment

Excercises, examination and presentation.

target audience

mPhys, mCh

remarks

Registration via http://studieweb.student.uva.nl three weeks prior to the start of the course. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: +31 (0) 20 525 7100, e-mail: ondwns@science.uva.nl. For the course schedules consult the separate schedule guide or see http://www.student.uva.nl/ or contact the dr. Brück.




naam

Qualitative and Quantitative Research Methods

code

470582

co-ordinator

dr. M.B.M. Zweekhorst

lecturers

dr. M.B.M. Zweekhorst; dr. C.M. Koolstra; prof.dr. J.J. Beishuizen; dr. J.F. Hoorn; guest lecturers

studiepunten

6

aim

  • Understanding the difference between beta- and gamma research

  • Hypothesis development on how to bring scientific knowledge to the public (understand science so to help society) and how to bring insights of the public back to science (understand society to help direct scientific questions)

  • To acquire further insights into various quantitative and qualitative research methods of data collection and analysis, such as interviews (structured, semi-structured and open), visualization and diagramming techniques, focus groups, surveys (postal/internet), structured questionnaires, participative research and experimental design

  • Know how to interpret quantitative and qualitative findings

  • Familiarity with univariate and multivariate analysis techniques as well as data mining and neural net analysis

  • To make an adequate research design for the investigation of a specific societal or communication problem with regard to science and a specific science problem with regard to communication and society

content

The course has an integrative character in that students are supposed to formulate hypotheses from a natural science and a social science viewpoint. The natural science hypotheses should be prompted by a societal of communication problem. The gamma hypotheses should be instigated by a science problem. Research topics could be communication of and dealing with the avian flu, obesity, nuclear and wind energy, HIV-AIDS, automation of health care. Typical for these questions is that natural, social, and communication science should be integrated with knowledge of the public.

During this course you will deepen your knowledge on quantitative and qualitative research methods, including interviews (open semi-structured, in-depth as well as several interactive and participatory methods such as focus group discussions, citizen panels, diagramming, and other visualisation techniques). In addition, you deepen your knowledge on surveys (postal/ internet), structured questionnaire design, and experimental design. You will also gain insight in possible set-ups of a study to collect, analyse, and integrate information of a variety of actors that are involved in a societal dilemma.



In the fourth week of this course, together with other students, you will apply the theoretical knowledge gained in the previous three weeks by designing and presenting your own study, which should include a selection of research methods.

form of tuition

Lectures, training workshops, self study

literature

Reader or Book (Details will be announced on blackboard)

mode of assessment

Written exam, presentation of your study design

target audience

Compulsory course within the C-differentiations for FEW and FALW students and compulsory course in the Masterprogramme Management, Policy Analysis and entrepreneurship for the health and life sciences (MPA). Optional course for students in one of the Health, Life and Natural Sciences Masters programmes.

period

08.01.2007-02.02.2007

remarks

Attendance of training workshops is compulsory. For information and application: ciska.heuvelman@falw.vu.nl




subject

Qualitative Research Methods for the Information Sciences

code

400290

credits

3

period

3

lecturer

prof.dr. J.M. Akkermans (with prof. dr. J.F. Schreinemakers and dr. ing. J. Gordijn)

aim

This course helps prepare students who want to embark on their (Master) research.

content

The course provides an overview and assessment of different scientific research methods, needed in a multi-disciplinary approach to Information Systems and how they function in an organizational context. Topics are:

  • developing the research questions you want to answer;

  • make a research design and planning your research;

  • research methods relevant for IS (e.g. interview, case study, action research, ethnography, survey, modelling, simulation, prototyping);

  • aspects of theory formation and validation; triangulation

  • how do you (and others) know that your research results are valid?;

  • research report writing.

form of tuition

Workshop-like. In two consecutive (full) days we will not just discuss textbook material, but do several hands-on exercises and assignments in class. Furthermore, a critical review of existing IS Master theses has to be written.

literature

  • Reader with recent articles

  • Pervez Ghauri and Kjell Gronhaug, Research Methods in Business Studies 3rd ed. Prentice Hall, Essex, UK, 2005.

mode of assessment

Written review essay, active workshop participation, and written examination.

entry requirements

Bachelor-level IK, I or AI

target audience

mIS, mCS, mAI

remarks

A useful reference point is the protocol that specifies the procedures and criteria for Master research in IS (see study guide).




subject

Quantum Field Theory

code

420081

 

This course can be extended with 2 credit points in period 3.

tutor

prof.dr. P.J.G. Mulders

credits

6

period

1 and 2

aim

Quantum field theory is indispensable to theoretical physics. Applications of quantum field theory can be found in statistical physics, solid state physics and subatomic physics. Also in the analysis of experiments, in particular in particle physics, insight in field-theoretical methods is of great importance.

content

The course aims to treat several of the basic aspects of quantum fields using examples that relate as closely as possible to contemporary interests in the various application areas. Among them:

  • Poincare-group and relativistic equations of motion.

  • Classical field theory, lagrange formalism, symmetries, currents and conservation laws.

  • Path integral formalism, quantization, Feynman diagrams.

  • Gauge theories with applications in quantum electrodynamics.

  • Reaction cross sections and decay processes.

  • Introduction to nonabelian gauge theories and the standard model.

form of tuition

Lectures and tutorials.

literature

Lecture notes will be made available. Useful books are

  • L.H. Ryder, Quantum Field Theory, Cambridge University Press

  • M. E. Peshkin and D.V. Schroeder, Quantum Field Theory, Addison Wesley

The latter will also be useful for the course 'Particles and Fields'.

mode of assessment

Active participation in lectures and exercise sessions, handing in exercises and final (oral) examination.

target audience

mPhys




subject

Quantum Field Theory Extension

code

420077

credits

2

period

3




subject

Quantum Groups and Knot Theory

code

400343

lecturers

prof.dr. E.M. Opdam (Phone: +31 (0) 20 525 5205, e-mail: opdam@science.uva.nl); dr. J.V. Stokman

credits

6

period

Semester 2.

aim

Acquaintance with tensor categories and their applications in topology and mathematical physics.

content

Introduction to the categorial construction of topological invariants of knots and links. Topics covered are: knots and tangles, the Jones-Conway polynomial, the Yang-Baxter equation, Hopf algebras, tensor and ribbon categories.

form of tuition

Lectures.

literature

Christian Kassel, Quantum Groups, Graduate Texts in Mathematics 155. Springer Verlag.
Additional literature: W.B. Raymond Lickorish, An Introduction to Knot Theory, Graduate Texts in Mathematics 175. Springer Verlag.

mode of assessment

Take home examination.

target audience

mMath

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: WI406046. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult http://www.student.uva.nl or contact the coordinator.



Location: UvA.




subject

Quantum Liquids

code

420177

credits

6

period

Not in 2006/2007

target audience

mPhys




subject

Quantum Optics

code

420118

lecturer

dr. T.D. Visser

credits

6

period

4 and 5

aim

To become familiar with various formalisms and methods in
the description of the electromagnetic field, its quantization and its
interaction with matter. To acquire essential knowledge, overview and expertise in quantum optics in order for the students to be able to find their way further into the literature.

content

  • Planck's law, the Einstein coefficients

  • Lineshape broadening and susceptibility

  • The Bloch equations

  • Beam splitters and optical coherence

  • Quantization of the electromagnetic field

  • Single-mode quantum optics

form of tuition

Lectures.

literature

The Quantum Theory of Light, third ed., by R. Loudon (Oxford University Press, Oxford, 2000)

mode of assessment

Oral examination.

target audience

3N, mPhys, mCh




subject

Queueing Theory

code

400397

credits

6

period

4 and 5

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




subject

Random Networks for Communications

code

400425

lecturer

prof.dr. R. Meester

credits

6

period

1 and 2

aim

Introduction in spatial probability.

content

We study random networks, where the nodes are typically formed by a Poisson process in a bounded domain. We are interested in questions concerning connectivity, the existence of isolated nodes, phase-transitions, etcetera. The networks find their motivation from real problems in communication engineering, like questions concerning mobile phone networks. It turns out that with a relatively small number of theoretical ideas, already very interesting probability theory is possible. There are many connections with percolation theory - the study of infinite random networks. We will introduce these as well, when the need arises.

form of tuition

Lectures with time for exercises.

literature

The lecturer provides a reader.

mode of assessment

Oral or written exam, depending on the number of participants.

entry requirements

Kansrekening I en Kansrekening II.

target audience

mMath




subject

Receptor Structure and Function

code

435680

coördinator

dr. M.J. Smit

lecturers

dr. M.J. Smit; dr. H.F. Vischer; prof.dr. R. Leurs

credits

6

period

5 and 6

aim

To obtain extensive knowledge of the molecular aspects of drug targets and their interaction with ligands.

content

This course comprises a more elaborate study of fundamental principles and aspects of receptor structure and function within the field of Molecular Pharmacology. In depth insight in molecular mechanisms by which most important groups of drugs act will be provided, focusing on ligand-receptor interactions and intracellular signalling pathways activated by these receptors. Modern pharmacological concepts such as e.g. constitutive receptor activity, receptor regulation and dimerization will be addressed.

form of tuition

Lectures, tutorials and self-study.

literature

J.C.Foreman and T. Johansen (ed.), Receptor Pharmacology, second edition (ISBN 0- 8493-1029-6).
Selected primary (original research papers) and secondary (review papers) literature.

mode of assessment

Written examination assignments.

entry requirements

Course on Molecular Pharmacology and toxicology of drugs.

target audience

mPhar, mMNS/molecular medicine.

remarks

Please contact the coordinator four weeks prior to the start of the course (e-mail: mj.smit@few.vu.nl).




naam

Rechtzoeken (B2/BN2)

code

200201

studiepunten

2,9

coördinator

drs. A.J. Wolthuis (kamer 7A-37, tel. (020) 59 86326)

periode

Rechtzoeken wordt tweemaal per jaar gegeven: direct na de zomervakantie en direct na de kerstvakantie. Let goed op de collegeroosters voor de precieze datum van het hoorcollege.

doel

Rechtzoeken is een vaardighedenvak. U schrijft een werkstuk en houdt een toespraak aan de hand van een door de docent op het hoorcollege uit te reiken opdracht. U werkt samen met één andere student. Door een werkstuk te maken en een toespraak te houden, oefent u in het vinden en raadplegen van juridische bronnen, het begrijpen van juridische teksten, het stellen en beantwoorden van een juridische vraag en het schrijven en presenteren van een juridisch betoog. Tenslotte oefent u de vaardigheid samen met een ander binnen een bepaalde termijn een opdracht uit te voeren.

werkwijze

U dient zich samen met een collega-student voor het vak in te schrijven op een lijst die op de balie van het studie-informatiepunt (kamer 5A-13) ligt. Het is verstandig u al vóór de vakantie in te schrijven voor de cursus, die direct na de vakantie van start gaat. U schrijft zich automatisch in voor een presentatiedatum. Schrijf uw naam onder een presentatiedatum die u schikt. Noteer uw inschrijfnummer en de presentatiedatum.
Rechtzoeken kent per gelegenheid één hoorcollege waar uitgelegd wordt wat van u wordt verwacht. Op dat hoorcollege worden bovendien de opdrachten uitgedeeld. Als het hoorcollege is verstreken, worden geen opdrachten meer uitgereikt.
Het werkstuk moet twee weken na het uitdelen worden ingeleverd bij het studie-informatiepunt. Wanneer u een onvoldoende voor het werkstuk hebt behaald, komt u niet in aanmerking voor het houden van een presentatie. De docent zendt u in dat geval enkele dagen vóór de presentatiedatum een e-mail met daarin uw cijfer en commentaar op uw werkstuk. Wanneer u het werkstuk voldoende hebt gemaakt, krijgt u pas na uw presentatiedatum een e-mailbericht met daarin uw cijfer en het commentaar.

literatuur

Syllabus Rechtzoeken 2006 (te zijner tijd verkrijgbaar via Blackboard).

toetsing

Werkstuk en presentatie

voorkennis

Als 6 (zes) van de 10 (tien) vakken van het eerste bachelorjaar Rechtsgeleerdheid en Project zijn behaald.

voorkennisvak

200109 : Project (B1)




subject

Research Methods

code

470577

lecturers

prof.dr. J.F.G. Bunders-Aelen (co-ordinator); dr. M.B.M. Zweekhorst; dr. J.E.W. Broerse; guest lecturers

credits

6

period

04.09.2006-29.09.2006

aim

  • To acquire further insights into various quantitative and qualitative research methods (data collection and analysis)

  • To know how to interpret quantitative and qualitative findings

  • To acquire insight into how to involve community members to include their views and jointly decide on the needs and priorities. This includes interactive and participatory methods for transdisciplinary research, such as focus groups, citizen panels, diagramming, mapping and other visualisation techniques.

  • To be able to make an adequate research design for the investigation of a specific health problem.

content

It is necessary to act on more than one level and with a variety of actors when addressing illnesses and their causes in the fight to reduce the burden of the disease. Therefore, various research methods and a transdisciplinary approach are needed. During this course you will further deepen your knowledge on quantitative and qualitative research methods; including interviews (questionnaire, semi-structured, in-depth), as well as several interactive and participatory methods such as focus group discussions, citizen panels, diagramming, mapping and other visualisation techniques. You will also gain insight in possible set-ups of a study to address certain needs.

In the fourth week of this course, together with other students, you will apply the theoretical knowledge that you have gained in the previous three weeks by designing and presenting your own study. The set-up of this study should aim to investigate needs concerning public health in a particular setting through a transdisciplinary approach. It should include a selection of research methods.



form of tuition

Lectures, training workshops, self study

literature

Reader; Book

mode of assessment

Written exam, presentation of your study design

target audience

Compulsory course for second year students of the Master Management, Policy Analysis and Entrepreneurship for the health and life sciences (MPA)

remarks

Attendance of training workshops is compulsory.

For information and application: ciska.heuvelman@falw.vu.nl






subject

Research Proposal Writing

code

400364

lecturer

prof.dr. A.S. Tanenbaum

credits

9

period

1, 2 and 3

content

This course has the single main aim to teach students the first steps of writing a research proposal. Students are asked to evaluate a number of existing proposals that were submitted by staff members in recent years. In addition, each student will also have to write his or her own proposal, which is then evaluated by fellow students following a procedure very similar to what happens in real life.

target audience

mPDCS




subject

Riemann Surfaces

code

400325

credits

8

period

4 and 5

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl




subject

Scheduling

code

400396

credits

6

period

4 and 5

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




subject

Science and Technology of Hydrogen in Metal

code

420065

lecturer

prof.dr. R.P. Griessen

credits

6

period

Not in 2006/2007

aim

Understanding the remarkable physical properties of metal-hydrides and their applications within a future hydrogen energy scenario.

content

This course provides a playground for applications of essentially all concepts in Condensed Matter Physics: electronic band structure, zero-point-motion, anharmonicity, correlation and screening effects in negative H-ion, optical phonons, electron scattering by optical phonons, diffusion (also driven by external fields), phase diagrams, spinodal decomposition, macroscopic density modes, metal-insulator transition, and optical properties (bulk and nanostructured in naturally disproportionated hydrides). Hydrogen storage materials, batteries, and hydrogen operated devices are discussed within the context of a sustainable hydrogen energy scenario.

form of tuition

Selfstudy and a number of contact hours.

literature

The course is based on the new lecture notes "Science and Technology of Hydrogen in Metals" and a number of review papers.

mode of assessment

Oral examination

entry requirements

Condensed matter physics, statistical physics and quantum mechanics (Ba-physics level).

target audience

mPhys, mChem

remarks

Registration for this course via https://tisvu.vu.nl/tis/menu, two weeks prior to the start. This is an optional course for master students condensed matter science.




subject

Scientific Writing and Presenting

code

815101

credits

6

lecturer

dr. J.B. Deijen (coordinator)

period

1 (not in 06/07)

aim

Training skills for oral presentations and writing a paper.

content

This intensive course reviews methods to support the critical, analytical reading of research articles (critical thinking), provides an introduction into how to develop and write an empirical research article according to APA norms, and how to present one's research in form of a poster or a powerpoint presentation.

form of tuition

6 two-hours lectures and workshops.

literature

Reader Scientific English

mode of assessment

Grades are based on oral demo presentations and a term paper




naam

Semantiek, 3

code

539176

docent

dr. H.D. van der Vliet

studiepunten

5

contacturen

14 (14 college)

periode

2

doel

Verdieping van de kennis van de lexicale semantiek en de zinssemantiek

inhoud

Op de colleges worden enkele onderwerpen uit de zinssemantiek en de lexicale semantiek behandeld. Mogelijke onderwerpen zijn: de relatie tussen taal, denken en werkelijkheid; thematische rollen; cognitieve semantiek. Studenten kunnen ook zelf met suggesties komen.

werkwijze

Gezamenlijk literatuuronderzoek, studenten verzorgen presentaties, docent levert achtergrondkennis. Studenten participeren zodoende in het verzamelen van materiaal en het beantwoorden van de probleemstellingen

literatuur

Tijdens de colleges vast te stellen

toetsing

Werkstuk en opdrachten

entreevoorwaarden

1e jaars vak Semantiek (Taalwetenschap) of vergelijkbaar vak elders gevolgd

doelgroep

3e jaars studenten Taalwetenschap: ATW

opmerkingen

  • Dit vak staat nadrukkelijk open voor niet-TW'ers met enige kennis van de semantiek

  • Inschrijven verplicht via TIS




subject

Seminar Attention (Seminar Attention)

code

815100

credits

6

period

6

lecturer

prof.dr. J.L. Theeuwes

aim

To learn how to interpret and analyze theories and findings on attention and eye-movements. Learn how to set up experiments.

content

The format of the seminar will be a discussion of one or two target articles, and student presentations, each week. Target articles for each week will be "classic" articles representing early and/or important studies on a specific topic or recent new papers in attention and eye movements. For the presentations, each student has to present the main findings of the target article for that week and is required to find a recent paper on the topic covered by the target article. Students have to prepare a 20 minute oral presentation in Microsoft Powerpoint. The rest of the class will be spent discussing the target articles and their relationship to the presented papers. Each student will give two presentations. The presentation will determine 50% of the course grade for each student. The target papers will be available on the course website and accessible via blackboard.
One week after the last class, each student will submit a final paper (up to 20 pages, 12 pt. font, double spaced) on one of the topics covered in class. The paper will consist of a brief review of (at least) 6 research papers (including those already covered on that topic in class) and a proposal for a new experiment. The paper will be worth 50%.

form of tuition

Lectures and practical assignments

literature

Articles

mode of assessment

Student presentation and writing a paper. Students are required to be present during all meetings. Penalty for being absent is 5% each time a student is absent.

remarks

The course Attention (Dr. M. Donk; BA3) is required to enroll.




subject

Seminar Cognitive Neuroscience

code

815098

credits

6

period

4

lecturer

dr. D. Talsma

aim

Extending the particpants' knowledge in the field of Cognitive Neuroscience.

content

Over the last two decennia, scientific research in the field of Cognitive Neuroscience has led to fundamental new insights in the relation between brain function and behavior. This is an ongoing process, and in many cases, the newest insights have not yet traversed their ways down into the regular textbooks. This seminar offers the students the possibility to discuss state of the art research, and will include themes such as Selective Attention, Multisensory Perception, Working Memory, Motor Control, and higher cognitive functioning.

form of tuition

During each workgroup, students will discuss recent research papers. On occasion, guest speakers will be invited.

literature

Research papers. The exact papers will be announced and distributed via blackboard.

mode of assessment

Paper




subject

Seminar Mathematical Physics

code

400467

coördinator

prof.dr. E.M. Opdam

credits

6

period

Semester 2.

content

To be announced.

form of tuition

Seminar; lectures by the participants.

mode of assessment

Through the lectures of the students, preparation of a paper.

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: WI406036. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.



Location: UvA.




naam

Semiotiek van woord en beeld, 1

code

513703

docent

prof.dr. L.H. Hoek

studiepunten

5

contacturen

28 (28 college)

periode

4

doel

Eerste kennismaking met de elementaire begrippen van de semiotiek; inleiding in de semiotische methodologie en semiotische analyse van de interactie tussen de mens en zijn omgeving aan het eind van de twintigste eeuw.

inhoud

De volgende onderwerpen komen aan de orde: wat is semiotiek, tekenstructuur, tekens en betekenis, constructie van de werkelijkheid, codes en codificatie, semiosis, mythologie en ideologie, semiotiek van de massamedia.

werkwijze

Combinatie van hoor- en werkcollege; presentatie en discussie van onderwerpen aan de hand van een handboek

literatuur

K.L. Kim, Caged in our own signs: A book about Semiotics, 1996, Norwood (N), Ablex Publishing Corporation

toetsing

Schriftelijk tentamen

doelgroep

1e jaars studenten major ACW

opmerkingen

Inschrijven verplicht via TIS




subject

Separation Sciences

code

435609

coördinator

dr. H. Lingeman

lecturers

dr. W.T. Kok; dr. H. Lingeman; prof.dr.ir. P.J. Schoenmakers; dr. J.J. Vreuls

credits

6

period

2

aim

Getting acquainted with the theory and practice of the main techniques in modern analytical separation science.

content

The topics discussed comprise the fundamentals, theory and practice of gas and liquid chromatography, electrophoresis.

form of tuition

Lectures and tutorials. Students have to summarize and present an (assigned) recent article on separation science.

literature

Hand-outs.

mode of assessment

Written examination and a mark for the article presentation.

entry requirements

Basic knowledge of biochemistry, chromatography, electrophoresis and mass spectrometry.

target audience

mCh, mPhar




subject

Sequence Analysis

code

430045

coördinator

prof.dr. J. Heringa

lecturer

prof.dr. J. Heringa (and other lecturers)

credits

6

period

2

aim

A theoretical and practical bioinformatics course about biological sequence analysis. The course provides an introduction to the algorithmic and biological principles of sequence analysis, as well as practical implications.

Goals:

  • At the end of the course, the student will be aware of the major issues, methodology and available algorithms in sequence analysis.

  • At the end of the course, the student will have hands-on experience in tackling biological problems in sequence analysis.

content

Theory:

  • Dynamic programming, Sequence homology searching, pairwise and multiple alignment, probabilistic methods, pattern matching, evolutionary models, and phylogeny.

Practical:

  • Assignment programming own alignment software based on dynamic programming

  • Assignment homology searching and pattern recognition using biological and disease examples

  • Assignment multiple alignment of biological sequences

form of tuition

13 Lectures (2 two-hour lectures per week), Assignment introductions, Computer practicals, Hands-on support

literature

  • E-course material: http://ibivu.cs.vu.nl

  • Richard Durbin, Sean R Eddy, Anders Krogh, Graeme Mitchison, Biological Sequence Analysis, Cambridge University Press, 350 pp., ISBN 0521629713, 1998.

mode of assessment

Assignment results and oral or written exam (depending on number of course students)

entry requirements

Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences. Some experience in programming is required.

target audience

Students with Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, or Medical Natural Sciences, with a strong interest in Bioinformatics

remarks

Active participation is required.
The course is taught in English.




subject

Signal Analysis and Parameter Estimation in Brain Imaging

code

430030

lecturers

dr.ir. Th.J.C. Faes; dr. J.C. de Munck

credits

6

period

4 and 5

aim

Part 1: Inverse problems
After the course, the student should be able:

  • To understand the basic principles of (model based) parameter estimation

  • To read and understand the current literature on MEG and fMRI data analysis

  • To adopt a critical attitude towards model based parameter estimation.

Part 2: Filtering and viusalisation
After a succefull completion of the course, the student is able:

  • To use dedicated software to visualise, render, manipulate and fuse medical brain imagies

  • To understand/apply the basic principles of filtering of 1D-signals and 2D and 3d images

  • To improve the quality of brain signals and images.

content

Part 1: Inverse problems

ML estimation, OLS-GLS estimation, linear, non-linear parameters, nuiscence parameters, statitical tests (T- and F-), multiple comparisons, confidence intervals, BIC and AIC criteria.



Part 2: Filtering and visualisation

1. 1D filtering: time invariant filters, fourier transforms, discretized signals, aliasing, relation to parameter estimation (part 1).


2. 2D/3D filtering: (Gaussian) smoothing, feature detection
3. Image fusion, (Delaunay) triangulation, volume and surface rendering.  

form of tuition

Working group.

literature

Reader (introductory text of 30 pp + several scientific papers on MEG/fMRI analysis).

mode of assessment

Written examination.

entry requirements

Part 1: Inverse problems

Knowledge of calculus (partial differentiation, multidimensional Taylor series, matrix vector calculus) and statistics (contineous probability desity distributions, statistical testing).



Part 2: Filtering and visualisation

Knowledge of MRI, CT, PET. Toegepaste informatica (dr. I. van stokkum) Basic calculus.



target audience

mMNS, mPhys, Neuroscience.

remarks

Part 1: Inverse problems

The underlying philosophy of the course is that parameter estimation and detection problems are abound in science and in medical physics in particular. The general theory is highly abstract and difficult to follow. Therefore, in this course the theory is explained by mainly two topics in which parameter estimation problems play a major role: dipole estimation based on MEG/EEG data and detection of activated brain regions using fMRI. It appears that almost all general aspects of parameter estimation play a role in these two subjects. Therefore, we expect that the student will master parameter estimation theory by studying these specific examples, and that the student in his/her future scientific work will be able to adopt the appropriate parameter estimation technique and interpretation of his data, by drawing analogies with the two examples treated in the course.



Part 2: Filtering and visualisation

Modern hospitals have many modalities to make images of patient organs, of which MRI, CT, SPECT and PET are the most well-known. To extract clinically useful information from these images, algorithms are needed to combine informtaion from multiple image sources, to detect abnormalities or to visualize the available information in a meaningful way. The main topic of this course is to discuss these algorithms in terms of performance, accuracy and (clinical) significance.



The whole subject amounts to 6 ECTS. Each part is allocated 3 ECTS.




subject

Simulation

code

400447

credits

6

period

1 and 2

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




subject

Simulation Methods in Statistics

code

400258

credits

6

lecturer

dr. A.J. van Es (Phone: +31 (0) 20 525 5365, e-mail: vanes@science.uva.nl)

period

Semester 1

aim

Making students familiar with two recent methods in statistics that involve simulation, i.e. the bootstrap method and the Monte Carlo Markov chain method.

content

Nowadays simulation methods based on random number generation on powerful computers play an important role in statistics. We highlight two methodologies, the bootstrap and Monte Carlo Markov chain simulation. The bootstrap method has been introduced in 1977 by Efron. This is a useful, generally applicable, but computationally intensive, method to construct, for instance, confidence intervals. The basic idea of the method is resampling from the original data. The naive bootstrap, paramatric bootstrap and smooth bootstrap shall be discussed. By running a computer simulated Markov chain for a suitably long time we can generate observations from a distribution close to the stationary distribution of the Markov chain. By choosing suitable transition probabilities practically any distribution can be simulated in this way. We will discuss the Gibbs and Metropolis algorithms, the basic algorithms for this kind of simulation, as well some of their refinements, bearing in mind the relevance for statistics.

form of tuition

Lectures and exercises.

literature

Lecture notes.

mode of assessment

Exercises and oral examination.

entry requirements

Knowledge of basic statistics, measure theoretic probability.

target audience

mMath, mSFM

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: ST402046. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.



Location: UvA.




subject

Soft Condensed Matter and Biological Physics

code

420167

lecturers

dr.ir. G.J.L. Wuite; dr. E. Eiser; dr.ir. E.J.G. Peterman

credits

6

period

2

aim

To provide insight into the phisics of biological systems and soft condensed matter and into some recent examples of the scientific literature in this field.

content

  • The building blocks of cells.

  • Statistical physics applied to soft-condensed matter.

  • Random Walks, Friction and Diffusion.

  • Life at low Reynolds number.

  • Entropic forces at work.

  • Chemical forces & self-assembly.

  • The cytoskeleton, a semiflexible, crosslinked polymer network.

  • Enzymes and molecular machines.

  • Molecular motor proteins, the lorrries in our cells.

form of tuition

Lectures, and self-study.

literature

Philip Nelson: Biological Physics, Energy, Information, Life W.H. Freeman and Company, New York, 2004.
ISBN 0-7167-4372-8

mode of assessment

Homework and (literature) presentations.

target audience

mMNS, mPhys, mCh, mPhar (and 3N optional course).


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