Cooperativity Mechanisms Analyzed by Cross-Bridge Model of Cardiac Contraction
Calcium sparks detection and analysis
Calcium fluxes in cardiomyocyte
Restricted ADP movement in cardiomyocytes
Morphology of trout cardiomyocytes
The location of energetic compartments affects energetic communication in cardiomyocytes
Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images
Unchanged mitochondrial organization and compartmentation of high-energy phosphates in creatine-deficient GAMT-/- mouse hearts
Analysis of molecular movement reveals latticelike obstructions to diffusion in heart muscle cells

The Laboratory of Systems Biology is a part of the Department of Cybernetics, School of Science, Tallinn University of Technology.


The main aim of the laboratory is to study regulation of intracellular processes and understand functional influences of intracellular interactions.
For this, a mixture of experimental and theoretical approaches are used.


  • Intracellular compartmentation and diffusion restrictions, influence on bioenergetics.
  • How the fine structure of mitochondrion is influencing the dynamics of oxidative phosphorylation?
  • Regulation of energy transfer in different types of cells.
  • Metabolic stability of heart muscle cells.
  • Interaction between mechanics and energetics of the heart.


We use interdisciplinary approaches to tackle questions in cardiac physiology. For that, we have formed a team of researchers with backgrounds in biophysics, biology, and applied mathematics/physics. As a result, we are able to approach scientific questions on different scales, from organ to molecular level, using combinations of different experimental and theoretical techniques. When needed, we find new ways to characterize the data, develop new mathematical models, build new hardware and program it to carry out novel experimental protocols. For example, we have developed mitochondrial positioning analysis in 2D and 3D, and built a confocal microscope to study diffusion in the cell. Among the experimental techniques routinely used in the laboratory are

  • kinetic measurements,
  • fluorescence correlation spectroscopy based techniques,
  • confocal and wide-field fluorescence imaging,
  • controlled single cell force measurements,
  • patch clamping.

We have developed models

  • to study energetics and mechanics of the left ventricle as well as intracellular diffusion using finite element method,
  • solved partial differential equations to analyze cross-bridge mechanoenergetics,
  • used molecular dynamics to analyze interaction between proteins and mitochondrial membrane,
  • designed multiple other models and computational techniques to analyze the experimental data.

The results of our work are distributed through publications and the open-source software that we develop.


The laboratory participates in the following research networks:

  • Mitochondrial mapping: Evolution – Age – Gender – Lifestyle – Environment, [CA COST Action CA15203, 2016-2020],
  • Realising the therapeutic potential of novel cardioprotective therapies, [CA COST Action CA16225, 2017-2021].


The research in laboratory is/was financed by


See list for proposed students topics under Positions.


Head: Marko Vendelin

Laboratory of Systems Biology
Department of Cybernetics
School of Science
Tallinn University of Technology
Akadeemia 21
12618 Tallinn

Fax:   +372 620 4151
Phone: +372 620 4169