Neuronal Biophysics

We search for simple biophysical and mathematical laws that define the behavior of cells, and specifically of neurons. Our primary biophysical goal in our neurophysiological studies is to understand and measure the relation between neuronal activity and mechanical events.

The process of nerve excitation is commonly regarded an electro-chemical mechanism. However, it was shown that electrical activity is associated with a variety of structural changes in the excited nerve fibers, such as swelling and beading, which are not included in the HH model. 

The swelling has been shown in different nerve fibers, including the squid giant axon, where an outward displacement with an amplitude of 1-3nm of the axon surface occurs during the depolarizing phase. The action potential starts at the onset of swelling of the nerve fiber and the peak of the action potential coincides with the maximum of swelling. Tasaki suggested a phenomenological approach to describe the behavior of the nerve membrane during these changes. His theory refers to the ectoplasm which is located at the cortex of the nerve cell, sometimes related as a gel layer, containing compact networks of macromolecules closely associated with the axolemma. Tasaki emphasizes the important role played by Ca2+ and water molecules in the process of nerve excitation. The water content in the superficial gel layer of the axon is governed by the balance between two opposing forces, namely, between the attractive force exerted by Ca2+ upon the negatively charged sites of the strands (which tends to make the gel shrink) and the osmotic pressure exerted by the unbound cations in the gel (which tends to expand the gel). Tasaki suggests that during an action potential, these Ca2+ ions could be replaced with Na+ ions from the cytoplasm, causing the layer to undergo a discontinuous transition from a compact state to a swollen state, as seen to happen in polymer gels.

Another mechanical phenomenon documented in neurons is pearling, or beading. Unlike swelling, beading is related to stress and excessive neuronal activity (high firing rate, for a few minutes) and will be discussed in Beading in neurons. 

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B

A - Fluorescent staining of neurons
B - Alga plant - a model for study action potential and mechanical events.

Cell Studio – Agent Based Modelling platform

Cell Studio is a unique platform for modelling complex biological systems. It provides an advanced environment specifically designed for non-coding researchers, including a visual interface, modelling of biological, biophysical, and chemical data. Its goal is to realistically describe a multi-scale, hierarchical system that operates at molecular, cellular, tissue and organ levels (e.g. the immune system). The computational core of the platform utilizes Agent-Based-Modeling, a powerful tool assisting life scientists in better understanding complex biological systems. In this framework the behavior of each CELL is modeled and simulated as a native agent whose interactions with proteins, molecules, medium and other cells, define the main dynmical features of a biological scenario. Using parallel and high-performance computing, the platform can simulate hundreds of thousands of agents/cells for extended biological time intervals, of the order of weeks. 

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