Student projects in biophysics

Temperature and concentration dependence of ions at water surface (MW/CC)

The project is about investigating temperature and concentration dependence of ions at water surfaces with Molecular Dynamics simulations.

Lignin tetramers at cellulose surfaces (MW)

Lignin is, next to cellulose, the most abundant natural polymer on earth. It consists of aromatic rings that are linked in complex structures. In native wood, lignin acts as a matrix polymer between the stiff and strong cellulose fibers. This project aims to investigate lignin at a cellulose surface with the aid of atomistic models and Molecular Dynamics simulations. Different types of lignin will be investigated in terms of their structure and interaction with cellulose.

Molecular dynamics simulations of protein molecules in laser fields (CC)

Simulation study of how the native atomic structure of a protein is affected as it is exposed to a laserfield. Lasers are used as optical tweezers and this study aims to understand how the electric field, the laser field, actually affects the protein structure. The project will involve learning how to use the molecular dynamics program GROMACS.

Molecular dynamics of organic molecules on water surfaces (CC)

The behavior of small organic molecules on water surfaces is important for atmospheric chemistry. Molecules that show surface preference have a larger possibility to interact with the surrounding atmosphere. We have studied how small organic molecules such as carboxylic acids and alcohols behave in a water/gas interphase both experimentally and using molecular dynamics.

This project is focused on doing a simulation study of how the structure of different organic molecules affect the molecules surface preference. Simulations will be done using the molecular dynamics package GROMACS and will be strongly connected to experimental results from studies at synchrotron sources such as MAXlab.

High-resolution imaging of single particles using X-ray Free Electron Lasers by reducing the background scattering of gases (TVY)

Structure solution from single particles such as proteins is the holy grail of structural biology. This was one of the goals in mind during the development of X-ray free electron lasers (XFELs). XFELs with their intense brilliance and pulse length on femtosecond scale mean a paradigm shift for structural biology.

So far high-resolution single particle imaging (SPI) has not been achieved. Compared to other methods, SPI suffers from low signal intensity, which is determined by the sample properties and the XFEL parameters. In order to improve the signal to noise ratio the sample environment must be improved. With our current setup, an electrospray aerosolizer used for sample delivery in combination with the ‘Uppsala injector’, we are able to deliver particles of 70-2000 nm diameter into the XFEL-beam.

The project aims at reducing the background noise created by various gases used for aerosol injection, by using specially a designed capillary head to reduce the mass flow of sheath gases required to maintain a Taylor cone. And to track particles down to 20 nm using Rayleigh-scattering microscopy as they exit the injector.

Interested students ideally have a background in engineering, physics or a related field and have some knowledge of coding in python not compulsory. Also, should be open to acquire knowledge from other scientific areas since our projects reach across the borders of traditional scientific subjects.