Complex Dynamics

Centre of Excellence in Computational Complex Systems Research

 

Current projects

Polymer dynamics
Research area The group’s research is motivated by analysis of experiments on structurally and dynamically complex systems in biology. Also non-physical complex structures, where unrestricted connectivity induces complex behaviour, are studied. Many biologically relevant structures and processes are characterised by their elasticity and rheology, whose interplay results in highly complex dynamics. In addition, the investigated structures, like the cytoskeleton, are heterogeneous, which paradoxically places a requirement of complete understanding of the object's mechanics in order to be able to interpret measurements correctly. Hence, the only way to find the correct structure and mechanics of the object is to construct a computational model that gives the experimentally observed behaviour.

Our aim is to develop the computational models to encompass increasingly complex structures. At a later stage these models will be used to analyse experiments on e.g. lipid bilayer structures and viral capsids. High-quality experimental data on lipid bilayer structures will be available via collaboration with Helsinki Biophysics and Biomembrane group. Experimental data on translocation of RNA across pores on viral capsids will be available from the Molecular and Cellular Biology group in University of California Davis.
Researchers Riku Linna, Ph.D., Senior Researcher
Kaski Kimmo, Professor
Ville Lehtola, M.Sc., Researcher
References 2009
V.V. Lehtola; R.P. Linna; K. Kaski
Dynamics of forced biopolymer translocation
accepted in Europhys. Lett.

2008
Linna, Riku; Lehtola, Ville; Kaski, Kimmo
Coarse-grained simulations of Biological Polymers and Related Processes.
In: Landau, David; Binder, Kurt, Computer Simulation Studies in Condensed Matter Physics XXI. Berlin 2008, Springer Vaerlag,

Lehtola, Ville; Linna, Riku; Kaski, Kimmo
Critical evaluation of the computational methods used in the forced polymer translocation.
Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 2008. Vol. 78, 61803-61010.

Linna, Riku; Kaski, Kimmo
Analysis of DNA elasticity.
Physical Review Letters, 2008. Vol. 100, nro 16, pp. 168104-168107.
http://dx.doi.org/10.1103/PhysRevLett.100.168104

Percolation and fragmentation of complex networks
Research area Methods for analysing complex networks are studied. These generic methods have much in common with those needed for understanding complex structures in biology. Contrary to random structures having a finite dimension, the studied complex networks have no topological restrictions to the connectivity, i.e. any site can have an unlimited number of connections (links) to other sites.

Presently, we are studying how the concepts of percolation and fragmentation can be used in analysing networks. We have adopted different parametrisations for studying data from a mobile phone network of 3.9 million nodes. We have investigated further the percolation-like transition of this network and refined quite substantially the picture of the percolation-like transition related to the weight distribution of this network.
Researchers Riku Linna, Ph.D., Senior Researcher
Kaski Kimmo, Professor
Klaus Kyttä, M.Sc., Researcher
References


Department of Biomedical Engineering and Computational Science
Helsinki University of Technology
P.O.Box 9203, FIN-02015 TKK, Finland