Robustness and time-scale hierarchy in biological systems
This project addresses the issue of the emergence of robustness as a consequence of time-scale hierarchy, applying thermodynamic and dynamic assumptions. In [1] the theoretical considerations of how the time-scale hierarchy can decouple physiological regulatory mechanisms were discussed. One of the examples was a model for a CO₂-concentrating mechanism in Chlamydo-monas reinhardtii, basen on the action of lumenal carboanhydrase. The model (Fig.1), explicitly shows how the time-scale hierarchy provides for accumulating CO₂ in stroma for further scavenging by Rubisco. Further details may be found in [1].

 

A model for segregation of photo-systems in thylakoids of green plants
We address the issue of segregation of photo-systems I and II in thylakoid membranes by molecular dynamics method. In [2] we assume a 2-dimensional (in-plane) problem with PSI and PSII being represented by particles with different values of negative charge. The pair interactions between particles include a screened Coulomb repulsion, and exponentially decaying attraction. The system is found to have a complicated phase diagram, including a quasi-crystalline phase at low screening, a disordered phase and, at high screening, a ĒclottingĒ phase, where the photo-systems tend to clot together.

 

Time rescaling and generalized entropy in relation to the internal measurement concept
A phenomenon of rescaling of the internal time in systems with a finite number of states is discussed in the context of the internal measurement concept in theoretical biology. In [3] a connection between time rescaling and generalized statistics is established. Numerical examples show a correspondence between the entropy values and the time rescaling parameter.

 

Pathway representation for metabolic processes
In [4] we discuss a problem of achieving a mapping of formalisms in statistical physics and theoretical biology to information theory. We present a way to introduce a pathway representation to describe metabolic processes. In [5] we work out a simple diagrammatic approach for time evolution of metabolite concentrationsÍ fluctuations around steady state.

 

Genetic Databases in Virtual Reality
We develop a new representation of a genetic sequences database as a collection of objects on a virtual landscape. The geometric properties of the objects (shape, color, transparency, etc) represent different properties of the sequences depicted by these objects [Fig. 2]. Browsing of a database becomes then a journey in the virtual landscape. A working demo, implementing such concept is discussed in [6].

Selected publications:

 

1. Rojdestvenski, I., Cottam, M., Park, Y.-I. and ÷quist, G. () Robustness and time-scale hierarchy in biological systems, BioSystems, 5

 

2. Rojdestvenski, I., Ivanov, A.G., Cottam, M. and ÷quist, G. () A two-dimensional many body system with competing interactions as a model for segregation of photosystems in thylakoids of green plants, Eur.Biophys. Journ, in progress.

 

3. Rojdestvenski, I. () Time rescaling and generalized entropy in relation to the internal measurement concept, Physica A, in press.

 

4. Rojdestvenski, I. and Cottam, M. () Mapping of statistical physics to information theory with application to biological systems, J. Theor. Biol, 202

 

5. Rojdestvenski, I. and Cottam, M. () Diagrammatic approach to calculation of the fluctuation correlation matrix in a metabolic system. BioSystems, in progress.

 

6. Rojdestvenski, I., Modjeska, D., Pettersson, F., Rojdestvenskaia, M., Gustafsson, P.() Sequence World: A Genetic Database in Virtual Reality, in preparation.