Vi utbildar för framtiden och skapar samhällsnytta genom vår forskning som levandegörs i nära samarbete med näringslivet. Vi bedriver forskning inom computer science, datateknik, software engineering och interaktionsdesign - från grundforskning till direkta tillämpningar. Institutionen har en stark internationell prägel och är delad mellan Chalmers och Göteborgs universitet.
We are engaged in research and education across the full spectrum of computer science, computer engineering, software engineering, and interaction design, from foundations to applications. We educate for the future, conduct research with high international visibility, and create societal benefits through close cooperation with businesses and industry. The department is joint between Chalmers and the University of Gothenburg.
(2014) Ludvigsson, Maximilian; Kalldal, Oscar; Ngu, Johnny; Nilsson, Per Andreas; Öhman, Gustav; Börjesson, Linus; Chalmers tekniska högskola / Institutionen för data- och informationsteknik (Chalmers); Chalmers University of Technology / Department of Computer Science and Engineering (Chalmers)
How an arbitrary coil of amino acids folds into its functional structure is known as the protein folding problem. Since the underlying mechanisms that guide protein folding in nature are widely unknown, simpli ed models are studied. Many of these models have energy levels as the focal point in order to nd the native state and may ignore other relevant constraints. While these simpli ed models may seem too trivial to have any resemblance to the physical reality, they can be used to explore concepts and ideas that may lead to further insights on how proteins fold. This thesis studies the use of simulated annealing optimization techniques to find low energy states in simple lattice and off-lattice models. A certain emphasis is placed upon looking for patterns in the results emerging. One simple off-lattice model and two lattice models are considered, a cubic lattice and a face-centered cubic lattice. Compared to the optimal energy, low energy conformations of 48- residue chains are found in reasonable time. It is concluded that while the method can not be said to exhibit the behavior of nding one consistent native state each time it is run, patterns do emerge in the results.
(2016) Erngren, Josefin; Karlsson, Kerstin; Qvick, Jan; Stigsson, Anders; Tobin, Johan; Chalmers tekniska högskola / Institutionen för data- och informationsteknik (Chalmers); Chalmers University of Technology / Department of Computer Science and Engineering (Chalmers)
Amyloid fibrils are misfolded proteins related to several different diseases, such as Alzheimer’s and Parkinson’s disease. The aims of the report are to computationally analyze significant patterns and distributions of certain amino acids in the structure of amyloid fibrils. The direction relative to the fibril core is investigated for the charged amino acids and those present in bends. Amino acids in the amyloid fibrils tend to stack upon each other, these stacks are identified for the amino acids containing aromatic rings and the tilt of the aromatic rings are calculated relative to the axis of the fibril. The result from the analysis of the bends does not show significant patterns exclusive to amyloid fibrils, while the analysis of the charged amino acids indicates that they tend to face outwards relative to the fibril core. The tilt of the aromatic rings tends to be distributed around 55°. The results are consistent with previous findings and provide some information which could be of use when predicting the structure of amyloid fibrils.