The research in the Neural Microenvironment laboratory comprises three types of work: 1) Experimental animal work and mathematical modeling related to the microenvironment of the mammalian retina, 2) Experimental work on the microenvironment of the brain, and 3) Computational models of neurons. This site is devoted to the computational models and makes software available for use.
(Please do not be concerned by the warning prompt when downloading. The files are safe)
Ions-Voltage-Volume
Screenshot of Cell GUI 3.09 (click to enlarge)
Cell GUI is a Java (click here for Java) program written by Andrey V. Dmitriev (general concept) and Alexander A. Dmitriev (program development) that calculates how cellular ionic concentrations, membrane potentials, cell volume, and energy expenditure vary with time for a cell in which initial concentrations, conductances, and rates of membrane pumps can be set by the user. The program itself and the basic tutorial about how it runs are in the files below. Further descriptions of the modeling process and some results from the model are in this paper (Dmitriev, A.V., Dmitriev, A.A, and Linsenmeier, R.A. The logic of ionic homeostasis: cations are for voltage, but not for volume).
Resting potential by GHK and CC
Screenshot of Em Calculator
The Em Calculator is a Java (click here for Java) program written by Alexander A. Dmitriev (the code) and Andrey V. Dmitriev (the concept) to calculate resting potential for three main voltage-generating ions (Na+, K+, and Cl–) knowing their extra- and intracellular concentrations and relative conductances. Two different equations – the Goldman-Hodgkin-Katz equation (GHK) and the Chord conductance equation (CC) – are used for calculations. Somewhat uncomfortably, GHK and CC equations predict different resting potentials with the same set of concentrations and relative conductances. The majority of researchers prefer GHK, but when the resting potential was calculated by an independent “charge-difference” method (Dmitriev, A.V., Dmitriev, A.A, and Linsenmeier, R.A. The logic of ionic homeostasis: cations are for voltage, but not for volume, 2019) results were in agreement with CC. The calculator itself, basic explanations of it, and our arguments in favor of CC equation as a better way to determine Em are in the files below.
Hemichannels and Electrical Feedback
Screenshot of ParShunt.exe
The paper below is a computational evaluation of the hypothetical electrical mechanism presumably underlying the negative feedback from the horizontal cells to the cone photoreceptors. The electrical model of the horizontal cell designed for this purpose (so called “parallel shunt” model) was calculated with an original custom made C++ program (A. Dmitriev), which is also available for download. This is an old style DOS-like dialog program and it should be easy to use after reading the paper.
Dmitriev A.V., Mangel S. C. Electrical feedback in the cone pedicle: A computational analysis. 2006
SAC, DS and nonequilibrium Cl-
Screenshot of SACdenFin.exe
The paper below presents a quantitative explanation of two experimental facts: 1) the participation of starburst amacrine cells (SACs) in retinal direction selectivity (DS), and 2) the dependence of DS on a nonequilibrium distribution of Cl– due to activity of cation-Cl– cotransporters. The custom made C++ program that calculates the local voltage in the model of SAC dendrites during stimulation with moving light stimuli is available for download. Before using of this old style DOS-like dialog program it is advised to contact A. V. Dmitriev for some tips.