Mol D-Struct – Molecular Dynamics & Structure

We are a group within the Division of X-ray Photon Science 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.

We are part of the Biophysics Initiative at the Department of Physics and Astronomy, and the Biophysics Network at the Faculty of Science and Technology.

People

The group currently consists of the following people:

Carl Caleman
PhD in Molecular Biophysics 2007. Docent in Physics 2018.

Nicusor Timneanu
PhD in Theoretical Particle Physics 2002, Docent in Molecular Biophysics 2009.

Isaak Unger (post doc)

Kajwal Patra (post doc)

Emiliano de Santis (post doc)

Sebastian Cardoch (PhD student)

Ibrahim Dawod (PhD student)

Pamela Svenson (PhD student)

Thomas Mandl (PhD student)

Previous members

Christofer Östlin – PhD 2019
Clara Saak – PhD 2019
Olof Jönsson – PhD 2017
Davide Ragazzon – postdoc

Research

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.

Publications

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.

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• Ingress: Senaste publikationer
• Antal publ: 5
• Person id: chros789 OR cajca839 OR davra358 OR olojo993 OR nti19847
• Publikationstyp: article
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Senaste publikationer

• Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions.Cardoch, S., Trost, F., Scott, H., Chapman, H., Caleman, C. et al. (2023). Physical review. E, . vol. 107DOI
• Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC.Kierspel, T., Kadek, A., Barran, P., Bellina, B., Bijedic, A. et al. (2023). Analytical and Bioanalytical Chemistry .DOI
• Speckle contrast of interfering fluorescence X-rays.Trost, F., Ayyer, K., Oberthuer, D., Yefanov, O., Bajt, S. et al. (2023). Journal of Synchrotron Radiation, . vol. 30, ss. 11-23DOI
• Imaging via Correlation of X-Ray Fluorescence Photons.Trost, F., Ayyer, K., Prasciolu, M., Fleckenstein, H., Barthelmess, M. et al. (2023). Physical Review Letters, . vol. 130DOI
• Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins.Brodmerkel, M., De Santis, E., Uetrecht, C., Caleman, C., Marklund, E. (2022). Current Research in Structural Biology, . vol. 4, ss. 338-348DOI