At the division, we investigate a range of different aspects of chemical physics with a combination of experimental and theoretical techniques. You can read more about the on-going activities under the "Research groups" page and follow the links to the different research projects.

Investigating the role of water in the protein dynamic transition - Master project

Representation of hydrated proteins
A representation of hydrated proteins

Maddalena Bin joined the chemical physics division as an exchange Erasmus student for doing her master thesis project. She studied the structure and dynamics of protein aqueous solutions, with particular focus on the interaction of proteins with their surrounding thin layer of water, termed hydration water. She built a humidity chamber to prepare hydrated protein samples and measured them employing techniques such as infrared spectroscopy and X-ray diffraction from ambient to supercooled temperatures. After finishing her master thesis, Maddalena continued with PhD studies at the chemical physics division of Stockholm University at the group of structural dynamics of aqueous solutions.

Maddalena Bin’s master thesis

Investigating the influence of water in lysozyme structure and dynamics using FT-IR and XRD - Bachelor project

A model of aqueous lysozyme showing a secondary structure of the protein and an atomic solvent model
A model of aqueous lysozyme

Rafat Yousif joined the chemical physics department for his bachelor thesis due his interested in the role of water in biophysical processes. He did experiments with different state of the art techniques, such as Fourier Transform Infrared Spectroscopy (FT-IR) and X-Ray Diffraction (XRD) and performed high-level data analysis using Python packages. The main focus of his investigations was to study the spectrum and structure of lysozyme in aqueous solution from ambient conditions to supercooled regime, as well as the influence of crystallization on the protein activity. After his bachelor thesis, he continued working in the group as a research assistant and his results were the starting point of several further investigations in the group using x-ray synchrotrons and free-electron lasers.

Bachelor's thesis of Rafat Yousif

Hydration models for thione-, thiol- and deprotonised 2-Mercaptopyridine, from molecular dynamics simulations - Bachelor project (2016)

Structures of solvated mercaptopyridines

As a student in the Bachelor's programme at Fysikum, Anton Ljungdahl performed molecular dynamics simulations as his thesis project. He simulated three variations of the small organic molecule 2-Mercaptopyridine in aqueous solution, with the aim to study the first solvation shell near sulphur and nitrogen sites. The results will to be used by the research group as a basis for quantum chemical calculations of excited state proton dynamics. After finishing the Bachelor's programme Anton continued to study at the master's programme in theoretical physics at Stockholm University.

Bachelor's thesis of Anton Ljungdahl (3538 Kb)


Adsorption of carboxyl groups and phosphate groups on the surface of titanium dioxide - Bachelor project (2016)

Adsorption structure of CH3PO3H2- on anatase(101)

Mathias Poline, while studying at the Bachelor's program at Fysikum, made his thesis project on the adsorption on anatase(TiO2) of anchoring groups using in solar cell applications. The project will be further developed by the research group for the interpretation of ultra-high vacuum experiments on well-prepared single crystal surfaces and in-situ experiments on solar cell materials. After finishing the Bachelor's programme Mathias continued to study at the master's programme in physics, at Stockholm University.
Bachelor Thesis of Mathias Poline (1590 Kb)

Time-dependent study on direct dissociative excitation - Master project (2013)

Direct dissociative excitation

Direct dissociative excitation is a reaction where an inelastic collision between a molecular ion and an electron leads to dissociation of the molecular ion. The process is usually studied time-independently. Emelie Ertan did a master in computational physics and as Master project, she developed a time-dependent method to study this process, where the nuclear dissociation is described using propagation of wave packets. Emelie continued with PhD studies at the chemical physics division at Fysikum, SU.

Master Project of Emelie Ertan (855 Kb)

Reorientation Dynamics of nitrate in water - Master project (2011)

Solvation of NO3-(aq)

Being a well trained programmer, Thomas Ogden was attracted to Stockholm University by the Master programme in computational chemistry at Fysikum. In his Master project, he studied the solvation dynamics of nitrate ions in aqueous solution. The work was subsequently forming the theoretical basis for a study of ultra-fast hydrogen bond dynamics in relation to 2D-infrared spectroscopy. Thomas continued to Durham University for his Ph.D. studies.

Master thesis by Thomas Ogden (6306 Kb)

Molecular dynamics in the vicinity of a conical intersection - Master project (2011)

Anomalous effects near conical intersections

A common approximation in molecular physics is to separate the motions of electrons and nuclei. This approximation is not valid when electronic states are close in energy. In 2011, Elham Nour Ghassemi performed theoretical studies of Li3. This is a system where the lowest two states are not only close in energy, but degenerate - a conical intersection. This will cause anomalous effect in the molecular dynamics in the vicinity of the intersection. Elham obtained a Master in Physics, and she is continued to work as a PhD student at Leiden University in the Netherlands.

Master thesis by Elham Nour Ghassemi (2108 Kb)

Simulations of a Ruthenium Complex and the Iodide/Triiodide Redox Couple in Aqueous Solution: Solvation and Electronic Structure - Magister project (2010)

Modeling processes in solar cells

After starting her university studies with the intention to become a teacher, Ida Josefsson was fascinated by the physics subject and she switched instead to the physics programme. Ida performed a Magister project in Stockholm, while affiliated with Uppsala University, about theoretical simulations of processes in dye-sensitized solar cells. After the Magister project, Ida continued as a Ph.D. student at the Division of chemical physics at Stockholm University working with quantum chemistry and molecular dynamics simulations.

Magister project by Ida Josefsson


Ultrafast Dynamics in Condensed Matter related projects:

[T] indicates a more theoretical project, [E] an experimental one. Those are tentative project titles, you are always welcome to discuss possible changes or to suggest new ideas.

Master Thesis

  1. Implementation of Data Acquisition software for pump probe measurements [T/E]
  2. Simulation of ultrafast lattice dynamics combined with experiments using visible light or femtoslicing at synchrotron x-ray sources [T/E]
  3. Implementation of a ferromagnetic resonance spectrometer based on femtosecond pump-probe measurements [T/E]
  4. Implementation of a frequency-resolved optical gating (FROG) setup for characterization of femtosecond optical pulses [E]

Bachelor Thesis

  1. Simulations of ultrafast lattice dynamics in Matlab using the package udkm1Dsim [T]
  2. Build up of a magneto-optical Kerr effect (MOKE) magnetometer based on continuous wave laser source and analog detection [E]
  3. Implementation of digital detection for a magneto-optical Kerr effect (MOKE) magnetometer based on continuous wave laser source [T/E]
  4. Simulation of x-ray diffraction traces from thin film multilayers using the package xrayutilities, combined with measurements from an x-ray diffractometer [T/E]

For Ultrafast Dynamics in Condensed Matter projects, contact Stefano Bonetti.