Modeling of covalent modifications of histones to estimate the binding affinity.

Covalent histone modifications such as methylation, acetylation, phosphorylation, and other epigenetic modifications of the chromatin play an essential role in regulating eukaryotic cells of which most of these reactions are catalyzed by the enzymes. The binding energy of enzymes is often determined by experimental data via mathematical and statistical models due to specific modifications. Many theoretical models have been introduced to study histone modifications and reprogramming experiments in mammalian cells, in which all efforts in determining the affinity binding are essential part of the work. Here, we introduce a one-dimensional statistical Potts model to accurately determine the enzyme's binding free energy using the experimental data for various types of cells. We study the methylation of lysine 4 and 27 on histone H3 and suppose that each histone has one modification site with one of the seven states: H3K27me3, H3K27me2, H3K27me1, unmodified, H3K4me1, H3K4me2, and H3K4me3. Based on this model, the histone covalent modification is described. Moreover, by using simulation data, the histone's binding free energy and the energy of chromatin states are determined, when they are subject to changes from unmodified to active or repressive states, by finding the probability of the transition.

The effects of temperature on the dynamics of the biological neural network.

The nerve cells are responsible for transmitting messages through the action potential, which generates electrical stimulation. One of the methods and tools of electrical stimulation is infrared neural stimulation (INS). Since the mechanism of INS is based on electromagnetic radiation, it explains how a neuron is stimulated by the heat distribution which is generated by the laser. The present study is focused on modeling and simulating the conditions in which deformed temperature related to the Hodgkin and Huxley model can be effectively and safely used to activate the neurons, the fires of which depend on temperature. The results explain ionic channels in the single and network neurons, which behave differently when thermal stimulation is applied to the cell. It causes the variation of the pattern of the action potential in the Hodgkin-Huxley (HH) model. The stability of the phase-plane at high temperatures has lower fluctuations than at low temperatures, so the channel gates open and close faster. The behavior of these channels under various membrane temperatures shows that the firing rate increases with temperature. Also, the domain of the spikes reduces and the spikes occur faster with increasing temperature.