Mol D-Struct – Molecular Dynamics & Structure
We are a group within the Division of Molecular and Condensed Matter Physics that focuses on research of structure and dynamics of molecular systems. We mainly use X-rays from synchrotrons as well as X-ray Free-Electron Lasers to investigate matter at an atomic level.
The group consists of researchers of varying backgrounds involved in a number of different projects. To gain further insight into our research you may read through some of our published articles. We also offer various student projects in our group.
The group currently consists of the following people:
PhD in Molecular Biophysics from Uppsala University 2007.
PhD in Theoretical Particle Physics 2002, Docent in Molecular Biophysics 2009.
Davide Ragazzon (post doc)
PhD in Physics from Uppsala University 2014.
Olof Jönsson (PhD student)
MSc in Molecular Biotechnology Engineering from Uppsala University 2010, Licentiate in Biophysics from Uppsala University 2016.
Clara Saak (PhD student)
MSc ETH in Chemistry 2014.
Christofer Östlin (PhD student)
MSc in Molecular Biotechnology Engineering and BSc in Mathematics from Uppsala University 2014.
A main part of our research revolves around X-ray free-electron lasers, which are novel light sources that provide extremely intense (1012 photons/pulse) and ultrashort (10-100 fs) X-ray pulses. These unique properties open new possibilities to determine structural information of biomolecules with atomic resolution, using a technique called diffraction before destruction. We are studying radiation damage and non-thermal heating induced by X-ray free electron lasers in biological samples.
We use Molecular Dynamics simulations and Quantum Chemistry to study ultrafast electron dynamics in biomolecules. We are also interested in the atomic dynamics, and study the orientation of molecules using laser fields, or orientation in-silico of biomolecules after being exposed to an X-ray pulse. Furthermore, we are working on force field development in molecular dynamics.
In close collaboration with experiments, we investigate liquid surfaces using synchrotron radiation as well as Molecular Dynamics simulations. We study the solvation properties of inorganic salts close to the water/vapor interface.
Bachelor and master projects
We offer students at both bachelor and master levels the possibility to carry out their thesis work with us. This is an excellent opportunity to establish academic contacts while also gaining insight into the world of research. Below is a list of current project proposals. Also have a look at our published master theses.
¤ Molecular dynamics simulations of protein molecules in laser fields
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.
¤ Validating water models for molecular modeling
In molecular modeling water is often present in one way or another. There are over 50 different water models used by scientists when modeling different phenomena. This project is about comparing the physical and chemical properties of a subset of all the available models to decide which models that are good at what. The project will involve learning how to use the molecular dynamics program GROMACS and learning how to evaluate simulations.
¤ Molecular dynamics of organic molecules on water surfaces
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 that come from studies at synchrotron sources such as MAXlab.
¤ Shockwaves in materials induced by an X-ray laser
X-ray lasers are new types of lasers, which produce extremely intense and short X-ray pulses. In this project you will use computer simulations to study how shockwaves can be created in a material (e.g. metal) when it is hit by a focused laser beam and turns into a plasma. This will help us understand how the structure of the material changes and how to control such an extreme process.
¤ Experimental Study and Simulation of Liquid Interfaces
The properties of liquid surfaces and interfaces differ fundamentally from the bulk. It is therefore crucial to understand the behaviour of solutions in proximity to such an interface. Two powerful tools to study these systems are photoelectron spectroscopy and molecular dynamics (MD) simulations. In this project you would study aqueous solutions containing various solutes (e.g. small molecules and ions) using our in-house experiment as well as synchrotron light source setups. Our setup combines a liquid jet with a hemispherical photoelectron analyzer, which allows us to selectively observe the interface of the liquid and can also be modified to study aerosols. The experimental results would then be supported by MD simulations which are crucial if one wants to understand the mechanisms behind the observed experimental effect.
The findings of this group has been published in a variety of different journals throughout the years, oftentimes in collaboration with other research teams around the world. You may browse our publications by following the links below.
- Scientific Reports, . vol. 9 DOI
- Proceedings of the National Academy of Sciences of the United States of America, vol. 115, ss. 5652-5657 DOI
Strong Enrichment of Atmospherically Relevant Organic Ions at the Aqueous Interface: The Role of Ion Pairing and Cooperative Effects.(2018). Physical Chemistry, Chemical Physics - PCCP, vol. 20, ss. 27185-27191 DOI
- Journal of Physical Chemistry B, vol. 122, ss. 688-694 DOI
Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields.(2018). Journal of Chemical Theory and Computation, vol. 14, ss. 5553-5566 DOI