Mathematica (Wolfram Research), MATLAB (MathWorks), Huygens (Scientific Volume Imaging), pClamp (Axon Instruments), Origin (OriginLab), Chimera (UCSF), SITUS (Biomachina.org), LAS X (Leica), Modeller (salilab.org), original software in C++
Methods of analysis
analysis of measurements and simulations of isolated channels, and of recordings of ion currents
analysis of cellular calcium signals
analysis of passive electrical properties of cells
localization of protein structures into electron density maps
3D reconstruction of confocal and wide-field image series
deconvolution of confocal and wide-field image series
quantitative morphometry by the method of vertical sections
Computer methods and simulation are used for:
Development of gating models of the ryanodine receptor (RYR) that link the binding of ligands (Ca2+, Mg2+, ATP …) to individual RYR monomers to the ability of RYR tetramers to open
Development of stochastic models that link the activity of individual channel molecules to activity of channel ensembles (cluster forming the dyad) in the cardiac myocyte
Simulation of activity of single channels and channel ensembles
Simulation of calcium spark formation and of propagation of calcium waves
Construction of geometrical models of muscle cells
Modelling of protein structure
The objective of these studies is to understand the relationships between the structure and the function of channels, and the relationship between the activity of channels in isolation and in the cell.
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