Student projects in biophysics
We are always looking for students interested in research projects. Contact the researchers below to discuss possible topics and current opportunities.
Imaging of biological structures
Work with lensless X-ray imaging, X-ray free-electron lasers and cryo-electron microscopy to study biological structures. Projects can involve diffraction, image reconstruction, simulations and sample delivery methods for extracting structural information from X-ray imaging data. Current work also includes cryo-EM for time resolved studies.
Tools and methods: Single-particle imaging (SPI), coherent diffractive imaging, cryo-EM, Condor, Hawk, and X-ray ptychography.
Contact: Filipe Maia · filipe.maia@icm.uu.se
Biomaterials and molecular dynamics
Study biomaterials such as cellulose, lignin and wood using atomistic models and molecular dynamics simulations. Projects can investigate molecular structure, interactions, moisture and material properties across different length scales.
Tools and methods: GROMACS, atomistic molecular dynamics, finite-element modelling, X-ray computed tomography and multiscale modelling.
Contact: Malin Wohlert · malin.wohlert@angstrom.uu.se
Nanobiotechnology and atomistic computational materials science
Use atomistic computational materials science to study nano-bio systems for the purpose of sensing individual molecules. Topics can include nanopores for sequencing of DNA and proteins.
Tools and methods: Density functional theory (DFT) using SIESTA, electronic-transport calculations using the non-equilibrium Green's function (NEGF) method, and molecular dynamics simulations using NAMD or GROMACS.
Contact: Ralph Scheicher · ralph.scheicher@physics.uu.se
Molecular dynamics and X-ray matter interaction
Use molecular dynamics simulations to study proteins, ions and organic molecules, including their response to electric fields, laser fields and water surfaces. Projects can also investigate ionisation, radiation damage and the interaction of intense X-ray pulses with biological matter.
Tools and methods: GROMACS, MolDStruct, molecular dynamics, and density functional theory (DFT), MS SPIDOC [https://www.ms-spidoc.eu/] and XFEL/synchrotron experiments.
Contact: Carl Caleman · carl.caleman@physics.uu.se
Protein dynamics and interactions
Study the dynamics and interactions of proteins and protein complexes using simulations together with mass-spectrometric experiments. Projects can investigate protein structure and motion in solution and in the gas phase.
Tools and methods: GROMACS, molecular dynamics, native mass spectrometry, ion-mobility mass spectrometry (IM-MS) and collision-cross-section calculations.
Contact: Erik Marklund · erik.marklund@kemi.uu.se
Ultrafast X-ray interaction with matter
Study what happens when biological samples and other materials are exposed to intense ultrafast X-ray pulses. Projects can involve ionisation, electron and atomic dynamics, plasma formation, radiation damage and extreme states of matter.
Tools and methods: GROMACS, MolDStruct, non-LTE plasma modelling, X-ray spectroscopy and XFEL/synchrotron experiments.
Contact: Nicusor Timneanu · nicusor.timneanu@physics.uu.se