Master programs
Coordinator: Dr. ir. G.J.L. Wuite (gwuite@nat.vu.nl)
Our group offers three masters programs. Please select one of the links
below for more information
about these programs.
Masters projects
Within the Master programs you have to do a Masters project. This project
usually takes one year and is the most important feature of the
programs. The following is a list of possible masters projects in our
group, but according to the personal interest of a candidate we can always
discuss further
possibilities. For up-to-date information please contact the group.
Description
of current projects
1) Mechanisms
of Motor Proteins
Lecturers: Prof. Dr. C.F. Schmidt, Dr. ir. E.J. Peterman, T068a,
tel. (44)47576, erwinp@nat.vu.nl
Biological motor proteins are studied in single-molecule experiments
with the goal of understanding
the physical principles of biological force generation in a multitude
of active transport processes.
Motor proteins are the ubiquitous nanometer scale mechanical engines
at the basis of many
crucial processes of life. Examples are intracellular transport processes,
cell division, cell locomotion, and in complex large scale assemblies
also macroscopic motion, such as muscle contraction,
or flagella motion. The nonequilibrium dynamics of these specialized
enzymes, usually embedded in
a complex regulatory and functional environment, are the essence of their
function.
2) Dynamics of DNA
Enzymes
Lecturers: Dr. ir. G.J.L. Wuite, T061, tel.(44) 47987, gwuite@nat.vu.nl,
Dr. ir. E.J. Peterman
The research in this project focuses on experimentally exploring the
dynamic function of DNA enzymes. For example, many DNA enzymes perform
highly complex mechanical tasks in replication, transcription or packing
of DNA, of which the detailed dynamics are not yet understood. Single
molecule experiments using optical tweezers technology and scanning force
microscopy will be used for the exploration of
the highly complex mechanical tasks of these enzymes. Knowing the dynamic
physical processes
of the interaction of these bio-molecules is a very important part of
the understanding of this machinery. The increasingly microscopic and
quantitative analysis, possible with single molecule methods, will
push the limits towards progressively more exact and physical/mathematical
understanding of molecular functions. This goal is spanning boundaries
between biology, biochemistry, physics and mathematics.
3) Cytoskeleton / Semiflexible
Polymers
Lecturer: Prof. dr. C.F. Schmidt, T067, tel. (44) 47972, cfs@nat.vu.nl
The mechanical framework or cytoskeleton of eukaryotic cells consists
of a complex assembly
of filamentous proteins, interacting with a multitude of accessory proteins,
effecting for example cross-linking, length control, bundling, polymerization
control. This composite polymer structure governs
the internal organization of most plant and animal cells, serves as a
transport network for active intracellular transport, and drives cellular
motility, for example in cell division, cell growth or cell locomotion.
It is also responsible for the mechanical rigidity of cells and the response
of cells to
external mechanical stresses. The network of actin network is a highly
dynamic structure, being
locally assembled and disassembled, which plays a crucial role in cellular
response to stresses.
This project focuses on the investigation of these networks of semi-flexible
protein, in vitro and also i
n living cells, with the goal of understanding the functional principles
of the cytoskeleton.
Semi-flexible polymers are a so far not well-understood new class of
polymers also with potential use
as technical materials.
4) Viral structural biology
Lecturers: Dr. ir. G.J.L. Wuite, T061, tel. (44) 47987, gwuite@nat.vu.nl,
Prof. dr. C.F. Schmidt
Many complex biological structures and materials, for example bones,
spider silk or snail
shells, have extraordinary physical properties far superior in certain
aspects to man made
materials. Understanding the construction principles of these materials
is a challenge to physics, and
holds the promise of delivering a future generation of bio-mimicking
technical materials. Viruses are the
simplest, smallest and often most rugged forms of life. Nature had to
solve some extraordinary design
challenges to construct these nanometer-sized machines. In this project
we focus on the
investigation of the micro-mechanical properties of viral shells using
Scanning Force Microscopy
(SFM). The experiments will be performed in collaboration with theoretical
modeling as well as
finite element numerical modeling.
5) Development of Optical Tweezers and Related Technologies
Lecturers: Dr. ir. E.J. Peterman, T068a, tel. (44)47576, erwinp@nat.vu.nl,
Prof. dr. C.F. Schmidt,
Dr. ir. G.J.L. Wuite
Most of the experimental techniques
we use are rather new and in a state of development. Therefore
we spend considerable effort on understanding and improving the methods.
Current topics of interest
are various interferometric detection methods to monitor motion in optical
traps with Angstrom-resolution, noise limitations on the experiments,
focusing of high numerical aperture laser beams and
optical aberrations, interesting side effects of optical trapping such
as 'optical binding forces',
dissipative effects etc. |
