Potential thesis projects at IceLab

Senior researchers at IceLab supervise a number of masters projects each year, in addition to PhD projects. At this page, we have collected a few ideas for potential thesis projects. You are always welcome to contact us if you are interested in any of the suggestions presented below, or if you have own ideas that you would like to discuss.

In short the list of suggested projects includes:

Determine invasion fitness in models of increasing complexityDNA dynamics in nano-channelsEvolvability of functional complexesEvolution of reproductive isolationModelling gene regulation and gene activity under crowded conditionsModelling the large-scale organisation of DNA as a space-filling curveOrigin of asymmetric distribution of protein aggregates in bacteriaSimulerad LiDAR-data

Determine invasion fitness in models of increasing complexity

Long-term evolutionary change can be studied using a set of tools known as adaptive dynamics. At the heart of any such study lies the determination of invasion fitness, defined as the long-term growth rate of a small gropu of mutants in a resident population. The aim of this thesis project is to demonstrate how invasion fitness is determined in models of increasing complexity: unstructured models, stage-structured models, physiologically structured models, site-based models, spatially-structured models, and demographic models on networks. Please contact Åke Brännström for more information about this project.

DNA dynamics in nano-channels

Recent years have witnessed a tremendous development in bionanotechnology which has given means to study and track motion of individual molecules. We have an ongoing experimental collaboration with a research group at Lund University which study stretched DNA polymers in nano-fluidic channels. In this project there is opportunity to setup a numerical simulation of a confined polymer in a narrow channel which would complement ongoing experiments.  Please contact Ludvig Lizana for more information about this project.

Evolvability of functional complexes

Organisms are not loose collections of individual traits. Instead, they are complexes of functionally related traits, many of which are adapted not only to the environment, but also or even mainly to each other. This project aims to investigate the adaptive potential of traits that are parts of such a functionally integrated complex. Please contact Folmer Bokma for more information about this project.

Evolution of reproductive isolation

Under the so-called “biological species concept”, species are groups of organisms that can reproduce with members of their own group, but not with members of other groups. Nature is full of exceptions to this rule, but the development of reproductive isolation between species is not very well understood. It is often assumed that reproductive isolation developes as a consequence of different mutations emerging in isolated populations, which turn out incompatible in secondary contact. An interesting but largely neglected alternative idea is that reproductive isolation develops quickly as the result of “genetic revolutions”: major alterations of the genetic regulatory network, potentially triggered by very few genes. This project would study the evolution of reproductive isolation on molecular phylogenies of species to distinguish between these alternatives. Please contact Folmer Bokma for more information about this project.

Modelling gene regulation and gene activity under crowded conditions

Proteins are essential for a biological cell to live and be functional. Whenever a specific protein is needed, the cell initiates a series o f steps which involve reading the DNA and putting together the array of amino acids that builds up the final protein. The first step in this process, and perhaps the most essential one, is to activate the gene which holds t he "recipe" for the particular protein. The activation is carried out by a transcription factor (a special type of biomolecule). When the transcription factor binds to a specific location on the DNA the required gene(s) is turned on and the relevant genetic code is accessible by other biomolecules eventually leading to protein synthesis. The question is, out of all genes (the human genome contains bout 20 000 genes) how does the transcription factor find its proper target? Also, how long does it take and how is the search time affected by the three dimensional organisation of the DNA as whole? What is the role of molecular crowding (that is, the fact that the transcription factor is surrounded by a huge number of other macromolecules)? These are open and urgent problems at the forefront of biophysics research today which we want to explore. One example project could be to implement a simple numerical model that captures the effect of crowding in a situation where one macromolecule is searching (by diffusion) for a target along a one dimensional DNA on which there are obstacles in the way. Please contact Ludvig Lizana for more information about this project.

Modelling the large-scale organisation of DNA as a space-filling curve

DNA is a huge polymer and i t is truly amazing that that it fits inside a living cell. If a human cell was the size of the allowed hand luggage on airline travel, the the full length of the DNA would reach from Ystad to Tromsö (2000 km). But not only is it carefully packaged, it must be folded in such a way that the genetic code can be accessed (typically by various biomolecules such as transcription factors and the RNA polymerase). This means that the DNA in addition to being extremely compact also needs to be manageable which implies a tremendous amount of organisational structure on various levels. There is one class of well studied mathematical objects which has several organisational features of DNA, namely so called space filling curves. We wish to investigate how the structure of such a DNA affect important biological functions such as gene regulation and gene activity. Please contact Ludvig Lizana for more information about this project.

Origin of asymmetric distribution of protein aggregates in bacteria

Protein aggregates occurs in all living cells and may disrupt cellular function. For example, protein aggregation in human nerve cells underlies neurological disorders such as Parkinson's and Alzheimer's disease. All kingdoms of life have developed strategies for dealing with unwanted protein aggregation. For example, in humans, aggregates are being removed by de gradation whereas in bacteria, aggregates are transported to one side of the cell (interestingly only the old side!) such that after cell division only one of the daughter cells holds the "garbage". In this project we will s et up a simple model for aggregate diffusion and simulate the process numerically. There is also the chance to d o analytical work. Please contact Ludvig Lizana for more information about this project.

Simulerad LiDAR-data

LiDAR (Light Detection and Ranging) is a technique for remote sensing which can be used for forest inventory. A laser is used to measure the location of sampled points and a typical data set consists of triplets (x,y,z) corresponding to the spatial coordinates of the point at which the laser reflected. The aim of this project is to (a) develop a simulator for LiDAR data, (b) implement one or several methods for positioning of trees, and (c) explore how robust the method(s) are to sampling frequency and uncertainties in the position of points. The project could favorably be carried out in collaboration with SLU's remote sensing group. Please contact Åke Brännström for more information about this project.


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