MarkoLAB: A simulator to study ionic channel's stochastic behavior

Robson Rodrigues da Silva, Daniel Gustavo Goroso, Donald M Bers, José Luis Puglisi

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Summary Mathematical models of the cardiac cell have started to include markovian representations of the ionic channels instead of the traditional Hodgkin & Huxley formulations. There are many reasons for this: Markov models are not restricted to the idea of independent gates defining the channel, they allow more complex description with specific transitions between open, closed or inactivated states, and more importantly those states can be closely related to the underlying channel structure and conformational changes. Methods We used the LabVIEW® and MATLAB® programs to implement the simulator MarkoLAB that allow a dynamical 3D representation of the markovian model of the channel. The Monte Carlo simulation was used to implement the stochastic transitions among states. The user can specify the voltage protocol by setting the holding potential, the step-to voltage and the duration of the stimuli. Results The most studied feature of a channel is the current flowing through it. This happens when the channel stays in the open state, but most of the time, as revealed by the low open probability values, the channel remains on the inactive or closed states. By focusing only when the channel enters or leaves the open state we are missing most of its activity. MarkoLAB proved to be quite useful to visualize the whole behavior of the channel and not only when the channel produces a current. Such dynamic representation provides more complete information about channel kinetics and will be a powerful tool to demonstrate the effect of gene mutations or drugs on the channel function. Conclusions MarkoLAB provides an original way of visualizing the stochastic behavior of a channel. It clarifies concepts, such as recovery from inactivation, calcium- versus voltage-dependent inactivation, and tail currents. It is not restricted to ionic channels only but it can be extended to other transporters, such as exchangers and pumps. This program is intended as a didactical tool to illustrate the dynamical behavior of a channel. It has been implemented in two platforms MATLAB® and LabVIEW® to enhance the target users of this new didactical tool. The computational cost of implementing a stochastic simulation is within the range of a personal computer performance; making MarkoLAB suitable to be run during a lecture or presentation.

Original languageEnglish (US)
Pages (from-to)258-270
Number of pages13
JournalComputers in Biology and Medicine
Volume87
DOIs
StatePublished - Aug 1 2017

Fingerprint

Ion Channels
Simulators
MATLAB
Microcomputers
Electric potential
Hodgkin Disease
Theoretical Models
Calcium
Costs and Cost Analysis
Personal computers
Mutation
Genes
Pumps
Pharmaceutical Preparations
Mathematical models
Network protocols
Recovery
Kinetics
Costs

Keywords

  • Experiments in silico
  • Ionic channels
  • Markov models
  • Simulator
  • Teaching

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

MarkoLAB : A simulator to study ionic channel's stochastic behavior. / da Silva, Robson Rodrigues; Goroso, Daniel Gustavo; Bers, Donald M; Puglisi, José Luis.

In: Computers in Biology and Medicine, Vol. 87, 01.08.2017, p. 258-270.

Research output: Contribution to journalArticle

da Silva, Robson Rodrigues ; Goroso, Daniel Gustavo ; Bers, Donald M ; Puglisi, José Luis. / MarkoLAB : A simulator to study ionic channel's stochastic behavior. In: Computers in Biology and Medicine. 2017 ; Vol. 87. pp. 258-270.
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