Projects

The biophysics group have a number of projects suited for Bachelor and Master projects. Please contact us for further details.

 

At the moment the following bachelor projects are particularly relevant:

Molecular dynamics simulation of small de novo synthesized proteins

 

De novo protein design is a powerful tool in understanding protein folding and also shows tremendous prospect in making artificial proteins with functional properties similar to real proteins. The project involves performing atomistic molecular dynamics simulations in explicit solvent of small artificial proteins. The simulation results will be compared with structural data already obtained with small-angle x-ray scattering.

As a student you will:

• get an understanding of the fundamentals of molecular dynamics simulation (MD)
• perform atomistic MD independently using Gromacs (or similar package)
• do molecular sculpting of small molecules and prepare these for simulation
• learn about polymer physics/chemistry and de novo protein synthesis
• learn about small-angle scattering techniques and advanced data treatment of these

CONTACT: Jacob Kirkensgaard (), Rasmus Høiberg-Nielsen (rhn@life.ku.dk) or Knud J. Jensen (kjj@life.ku.dk), all at KU-Life

 

Nano-scale food science

 

 

Fødevarer på nanoskala: Sammenhæng mellem makro-, mikro- og nanostruktur af mayonnaise.

 

Mayonnaise har struktur på mange længdeskalaer og det er samspillet mellem mikro- og nanostrukturen af mayonnaisen, der giver den karakteristiske makroskopiske struktur og konsistens. I det foreslåede bachelor-projekt skal de studerende undersøge og sammenligne makro-, mikro- og nanostrukturen af hhv. hjemmelavet og industrielt fremstillet mayonnaise ved hjælp af rheologi, lysmikroskopi og Røntgenstråling. Projektet foregår i samarbejde med Jens Risbo fra Institut for Fødevareforskning på KU-Life.

 

 

Vejledere: Robert Feidenhans’l (KU-Nat) og Lise Arleth (KU-Life): lia@life.ku.dk

 

Coarse grained molecular dynamics simulation of branched polymer self-assembly

 

The project involves modifying an existing simulation package (Espresso/mbtools) to allow the simulation of branced polymers using bead models, i.e. a coarse grained approach. The simulations will be directly compared with structural data already obtained with small-angle neutron scattering with the purpose of explaining these measurements.

As a student you will:

• get an understanding of the fundamentals of molecular dynamics simulation (MD)
• perform coarse grained MD independently
• do a little Tcl programming to modify the setup
• learn something about polymer physics/chemistry
• learn about small angle scattering techniques, especially using neutrons

CONTACT: Jacob Kirkensgaard (kirkensgaard@life.ku.dk) or Kell Mortensen (kell@life.ku.dk), both at KU-Life