Exact Sciences Master Guide2005/2006

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Research groups VU

  1. Overview

In this section an overview of the research fields of the Department is given. Updated descriptions of Masters projects related to the research are given in http://www.nat.vu.nl/vakgroepen and further links. It is also possible to do the MSc project in the research group Clinical Physics & Informatics, which is part of the Faculty of Medicine, see end of this section.


Atomic and Laser Physics

Activities in the Atomic and Laser Physics group concentrate on four main research topics. Within each category several projects are executed. In all of these projects state-of-the-art laser systems play an essential role. This research forms part of the research activities within the Laser Centre of the university.


Physics with Cold Atoms The interaction between an atom and near-resonant laser radiation is used to decelerate and thereby effectively cool free atoms down to low temperatures. Using cold metastable helium-4 atoms (stable states with a high internal energy) efforts are under way to achieve Bose Einstein condensation, thus creating a new quantum state of matter. Possibilities to reach quantum degeneracy with fermionic helium-3 are explored as well.


Short-wavelength Laser Radiation: Spectroscopy of Atoms and Molecules

With powerful, pulsed laser systems the generation of narrowband and tunable coherent radiation at short wavelengths (in the extreme ultraviolet part of the electro- magnetic spectrum) via non-linear upconversion processes in dense gaseous media is investigated (generation of high harmonics). The energetic photons produced in such a way are used to investigate highly-excited states of light molecules of astrophysical interest such as H2 and N2.


Ultrafast Laser Physics and Frequency Metrology

A powerful phase-locked and ultrafast laser system is developed to study extreme non-linear optics, in particular X-ray generation near 3 nm ('the water window'). Advanced techniques are used to create pulses of infrared light with a reproducible and programmable electromagnetic wave. It is expected that with those pulses X-ray bursts as short as 200 attoseconds can be generated, which will allow studies of ultrafast dynamical processes at an atomic and molecular level. The phase-locked laser generates a comb of ultrastable optical frequencies that can be employed for precision metrology studies in atoms and molecules. The group is now starting a program in this direction with the aim of testing possible variations of fundamental constants over time.


Applied Laser Spectroscopy and Laser Development

In cooperation with industry prospects for laser separation of isotopes of the elements Yb and Ca are investigated. The goal is to establish efficient routes for the selective ionization of the required isotopes in a multi-step laser-excitation process as well as to address the question of related laser development. With cavity-ringdown spectroscopy absolute absorption cross sections of molecules relevant for the atmosphere are measured as input data for the interpretation of satellite observations of the earth. Recently a project was started to extend this CRD-technique in liquids and on surfaces of solids.



The research group investigates molecular processes and structures in living matter. The research is mainly aimed at the primary processes of photosynthesis; the conversion of light energy into a durable form, for instance by plants. To be more specific, the research is aimed at:


The absorption of light by chlorophyll-containing proteins and ultrafast transfer of excitation energy.

It is very important to determine how the chlorophyll molecules are organized and how the very efficient transfer of excitation energy occurs.


Charge separation in the photosynthetic reaction centre.

The reaction centre is a chlorophyll-containing protein that is capable, after excitation with light, of storing the captured energy in the form of a separated pair of charges. In this process several intermediate components are involved, in which the first step lasts less than a picosecond. Later steps are slower and the energy transfer is completed after about a microsecond. The efficiency of the total process is very high.


Nonlinear optical phenomena in biological/photosynthetic systems.

Because photosynthetic systems contain many coupled pigments, the optical properties of this material are strongly nonlinear when excited with high-intensity light. The study of these properties tells us much about all kinds of dynamic processes.


In addition, dynamics and structures of DNA-protein complexes are studied with spectroscopic techniques. The research group has many spectroscopic setups. The ultrafast phenomena from about 100 femtoseconds to 1 nanosecond are studied with two advanced laser systems that can produce these kind of short light pulses. The research group also has a number of versatile experimental setups that are used to study steady-state, polarized absorption and fluorescence spectroscopy with high resolution and, if necessary, at very low temperatures. There is also equipment available to study phenomena on a time scale slower than a nanosecond.


Condensed Matter Science (CMS)

Research in this group covers the following five areas:


The physics of metal-hydride switchable mirrors.

Recently we discovered that palladium protected metal-hydride films of yttrium, lanthanum and Rare-Earth metals (RE) can be simply, reversibly and rapidly switched between a shiny metal and a transparent large gap semiconductor. In Mg- RE-hydride and Mg-Ni-hydride even transitions to a highly absorbing state can be induced. We study the physical mechanisms responsible for the metal-insulator transition, the optical and electrical properties and the diffusion of hydrogen waves in switchable mirrors.


Light-weight metal-hydride storage materials.

Metal-hydrides absorb hydrogen to a higher density than liquid hydrogen. Metal-hydrides, however are considered too heavy for implementation in cars. Complex metal-hydrides could be "the" solution. Within FOM and the NWO National Sustainable Hydrogen Programme, our search for new complex metal-hydride storage materials uses thin film sputter deposition in a highly efficient combinatorial approach. The catalytic hydrogen uptake is investigated by Scanning Tunneling Spectroscopy/Microscopy. In addition, structural/chemical modeling is developed to facilitate the prediction of new hydrogen storage compounds.


Smart coatings based on metal-hydrides.

The switchable metal-hydrides may have applications as large area displays, smart windows in buildings,variable reflectance coatings and active layer in fiber optic hydrogen sensors. Therefore, we study the fundamental issues involved in making such devices. This involves the deposition (by sputtering and pulsed laser deposition) and characterisation (High-resolution XRD, RBS, AFM/STM) of relevant thin films. In collaboration with ECN we  develop a demonstrator variable reflectance device that is to be used within a hybrid photovoltaic/solar collector device.


Non-linear dynamics and pattern formation in superconductors.

Patterns of currents and magnetic flux in superconductors are investigated by means of high-resolution magneto-optics. Superconductors are an attractive model-system to study pattern formation because the experimental time scales can be made relatively short. We study frustration phenomena and front instabilities in type-I superconductors and roughening of interfaces in type-II superconductors. We also study the patterns induced by the non-linear current-voltage characteristics in inclined-field configurations and in nano-patterned thin films.


Experimental investigation of self-organized criticality.

Self-organized criticality (SOC) occurs in many systems in nature ranging from earthquakes to the extinction of species in biology. We study SOC in superconductors by means of high-resolution magneto-optics and in a rice-pile of one square meter floor area using a unique camera system to accurately measure the shape of the pile. Questions of main interest are whether the many exponent scaling relations that were found to hold analytically or in numerical simulations, can also be observed for a real physical system and whether it is possible to keep a system away from SOC behaviour such that e.g. devastating avalanches can be prevented. For our rice pile, both questions seem to have a positive answer.


Physics Applied Computer Science

The continuous interaction between experimenting, modeling, and simulation is an essential feature of physics research. Preferably this interaction is done in real time, which requires clever algorithms as well as computational power. In the past decade the automation and development of dedicated software for activities in fields like data acquisition / process control, data analysis and large scale computing have dominated the research of the Physics Applied Computer Science Group (PACS). In recent years these research themes have been augmented with virtual reality techniques and user guidance.


The long term research goal is the integration of components in three major fields:

- High Performance Computing (HPC),

- Visualization & Virtual Reality (VR),and

- Modeling

into so-called Problem Solving Environments (PSEs) for physics applications. These PSEs combine state of the art computer science methodologies and technologies with domain specific knowledge on the abstraction level of the physicist user. The field of HPC encompasses parallel computing and distributed computing. Visualization extends from image processing to virtual reality techniques and focuses on the measurements in VR. Modeling is a prerequisite for parameter estimation and simulation.


Our research focuses on the applicability of these PSEs and their structural requirements from a physics point of view. Essential for this research is that it is application driven and takes place in close collaboration with application areas of other departments and groups. The PACS contributes the expertise in the areas of automated data processing and the other departments supply the domain specific knowledge. The research covers four distinct sub projects:

NI 1: CAVE Study: A Computational Steering Environment for Virtual Reality

NI 2: Measurements in Virtual Reality

NI 3: Distributed Autonomous Measurement Systems

NI 4: Modeling and Parameter Estimation


Physics of Complex Systems

The research programme focuses on experimental studies of soft condensed matter systems, with a special emphasis on biological and biologically inspired systems. The general theme relating the projects is the study of dynamic physical properties of complex biological macromolecules, using a combination of microscopies and single molecule manipulation techniques, combined with physical modeling. The following is an outline of the main research projects in the group:


Mechanisms of Motor Proteins

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, and present a case where the non-equilibrium dynamics of these biological macromolecules, usually embedded in a complex regulatory and functional environment, are the essence of their function.


Dynamics of DNA Enzymes

The dynamics of selected DNA enzymes will be investigated in single molecule experiments. Many DNA enzymes perform highly complex mechanical tasks in replication, transcription, or packing of DNA, the detailed dynamics of which are not yet understood.


Cytoskeleton / Semiflexible Polymers

Networks of semiflexible protein networks are investigated, in vitro and also in living cells, with the goal of understanding the functional principles of the cytoskeleton, which plays crucial roles in processes such as cell division, cell locomotion, or cell growth. Semiflexible polymers are a so far not well understood new class of polymers also with potential use as technical materials.


Instrumentation and Technology Development

New experimental techniques will be developed and further developed, focusing on high resolution microscopy methods and single molecule manipulation techniques (optical tweezers, atomic force microscopy) and single molecule fluorescence/spectroscopy techniques.


Subatomic Physics

The Subatomic Physics group is active in a scientific programme that spans strong-interaction physics to the study of CP-violation and other rare phenomena in the decays of B-mesons. New initiatives have been developed, most importantly the participation in the Babar-experiment at SLAC (Stanford).


A study of the spin structure of the nucleon has high priority since the inclusive experiments at CERN, SLAC and DESY have shown that the quarks (corresponding to the quark fields in the QCD Lagrangian) carry little of the axial charge of the nucleon. On the other hand the magnetic moments of hadrons are well explained by the quark model (essentially a quasi-particle description). With HERMES we continue our investigation of the nucleon spin structure with deep-inelastic scattering, with emphasis on semi-inclusive reactions (e.g. flavour decompositions). New equipment for particle identification (Lambda wheel) was added to the experiment.


The Subatomic Physics group increases its involvement in the physics of B-mesons. Prof. dr. J.F.J. van den Brand is program leader of the FOM-project: Study of charge-parity violation with the LHCb experiment at CERN. Since December 2002 active participation in the Babar-collaboration at SLAC (Stanford) puts the group at the frontier of research in this field. The central theme is the study of symmetries, most importantly that of CP-violation. With the preparation for LHCb emphasis is placed on precise vertex reconstruction and particle identification, since various decay channels of B-mesons need to be measured with great precision. For the handling of the large amounts of data at Babvar and later at the LMC we participate in GRID computing challenges and operate a modest computerfarm on campus.


In the research group at the VU, applied nuclear physics is also carried out in-house with a 1.7 MV Pelletron accelerator in combination with a microbeam set-up. With this equipment concentrations of trace elements (for instance in meteorites and biological samples) can be investigated on a micron scale. This facility will be integrated in a world wide virtual laboratory for advanced material analysis.


There are ample research possibilities for students. Depending on their interests, they can participate in the development and testing of equipment, the preparation and execution of experiments, and the analysis and theoretical interpretation of the results.


Theoretical Physics

Complex Systems

The Complex Systems group focuses on the physics of soft condensed matter and biomaterials. These complex materials exhibit rich dynamics as well as material properties intermediate between conventional solids and liquids. They pose fundamental challenges, for instance as model systems to study such basic questions as non-equilibrium physics.


Granular materials such as sand consist of macroscopic grains which collectively can exhibit properties superficially similar to solids, liquids and gases. The principal interest in these systems is their dissipative or non-equilibrium nature which results in complex dynamics.


Nature expresses chirality (the lack of mirror symmetry) at all levels, from molecules to individual seashells. Quantitative prediction, however, of the spontaneous assembly of small molecules to form larger chiral structures remains a challenging theoretical problem of interest.


Biological cells exhibit a range of materials with properties quite different from conventional synthetic materials. Specific interests of this group range from the dynamics of individual biopolymers to the dynamic and structural properties of the networks they form.


Quantum Electronics and Quantum Optics

The research deals with the interaction of light and matter. A prominent object of our studies is the semiconductor laser. Because of its many applications (the CD player, optical communications) this device is becoming more and more important. Under certain circumstances the intensity of the light that the laser emits fluctuates wildly: its behavior has become chaotic. The physics of this process is analyzed with nonlinear dynamics and bifurcation theory.


Another topic is the influence of the dielectric environment on the spontaneous and stimulated emission of light by an optically active element. For instance that of the layered structure like in a vertical cavity surface emitting laser (VCSEL) or in cases of other interesting geometries. An effective fully quantumelectrodynamical framework is used.


A third line of research is near-field optics. With this new technique individual atoms can be imaged. We study how light is scattered by objects that are much smaller than the wavelength, the key role played by optical vortices and how this light can best be detected.


The complete list of research topics in Quantum Electronics and Quantum Optics is: Optical Amplifiers, Nonlinear Dynamics in Diode Lasers, Ultra Short Pulse propagation in non-linear media, Quantum Optics of Small Structures, and Near-Field Optics.


Subatomics Physics

The main focus is on elementary particles and their fundamental interactions. One of these interactions, the strong force, is described within a gauge field theory, quantum chromodynamics (QCD). The strong force binds colored quarks and gluons through the exchange of gluons into color-neutral objects, the hadrons, such as nucleons and pions. The nucleons, proton and neutron, are the building blocks of the atomic nuclei, where the exchange of pions manifests itself as the long-range remnant of the strong force. Bound states in QCD are studied in light-cone quantization.


Leptons, such as electrons or muons, do not feel the strong force, but only the electroweak forces mediated by photons or W- and Z-bosons. This makes them suitable particles to probe the quark and gluon structure of hadrons, in particular at high energies which implies high spatial resolution. From a theoretical point of view it is possible to describe the short-distance behavior of field theories in a very precise way and compare its surprisingly rich structure with the results of high-energy scattering processes.


The study of the fundamental interactions of matter, including gravity, also has cosmological impact because these forces have governed the dynamics of the universe during the first seconds after the big bang. In the earliest phases of the expanding universe, quantum gravity effects must have been important, but such effects are not well-understood. Classical and quantum properties of gravity are studied, emphasizing the concept of supersymmetry. In a slightly later époque of the universe all kinds of phase transitions may have preceded the formation of the protons and neutrons, such as color-superconductivity. The possible existence of such phases is studied.


Clinical Physics & Informatics (VU medical centre)

The research of the department of Clinical Physics & Informatics is aimed mainly at the following organs and organ systems: the heart and circulation, the eye, the brain, and the skeleton and gait system.


The heart and circulation

Mechanics of the cardiac muscle. In this research project the patterns of motion of the cardiac muscle of patients and healthy volunteers is being recorded by the latest MRI-techniques and subsequently analysed. Much attention is focussed on modelling of the relationship between contraction and local blood circulation. Enhancement and analysis of images play an important role.


Determination of parameters of heart function using an electrical bio-impedance technique. In this research project these parameters are assessed fully noninvasively using a very small alternating electrical current, which is harmless and not perceptible to the patient. From the resulting heart synchronous voltages, recorded at the skin, heart function is assessed using various models.


The eye

The research in the field of the eye focuses on three projects: topography of the cornea, perfusion of the retina and ageing of the lens. The aim of the first project is to develop a method to measure the shape of the cornea as precisely as possible. The second project attempts to measure the perfusion and oxygen saturation of the retina by means of reflection of light.


The brain

Using two highly sophisticated techniques, Magneto-Encephalography (MEG) and Positron Emission Tomography (PET), the reaction in different areas of the brain to external stimuli is measured, both in patients and healthy volunteers, in order to study brain function and to map this function to different anatomical structures.


The skeleton and gait system

This project studies physical processes determining growth and degeneration of bone tissue. Both experimenting and modelling are crucial in this project.


Because the department of clinical physics & informatics has close relationships with numerous clinical departments, there are frequently various projects in other fields for undergraduate students. The research of the department frequently leads to new techniques and methods in health care.


General information: prof. dr. R.M. Heethaar, PhD, VUmc, -1.Nbi.129, phone: +31 (0)20  444 0175.

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