Back

Quantifying the Influence of the Actin Cytoskeleton on Ion Transport in Dendritic Spines by Homogenization of the Poisson-Nernst-Planck Equations

Eberhardt, F.

2023-08-05 biophysics
10.1101/2023.08.03.551796 bioRxiv
Show abstract

Dendritic spines are filled with a very dense actin cytoskeleton. However, due to their small size, the impact of this mesh on biophysical parameters has not been studied so far, and it remains unclear to what extent it might affect ion flow in dendritic spines. Only recently has the three-dimensional internal structure of dendritic spines been quantified in great detail in electron microscopic tomography data. Based on these results, we estimate the effect of the spine actin cytoskeleton on diffusion and permittivity. We apply a method called homogenization to estimate effective diffusion tensors and permittivity tensors in Poisson-Nernst-Planck (PNP) equations. We find that the volume taken up by the intracellular structure alone cannot explain the changes in these biophysical parameters. The characteristic architecture of the intracellular space in dendritic spines will reduce the diffusion of ions by 33% to 46% and the permittivity by 30% to 42%, compared to values found for the cytosol free of intracellular structures. These results can be used to improve computational studies using PNP equations and help to better interpret experimental results of electrical and chemical compartmentalization.

Matching journals

The top 7 journals account for 50% of the predicted probability mass.

1
Physical Review E
● 112 papers in training set
Top 0.1%
11.9%
Similar papers in this journal
2
PLOS ONE
● 5266 papers in training set
Top 18%
9.7%
Similar papers in this journal
3
Biophysical Journal
○ 631 papers in training set
Top 0.8%
8.9%
Similar papers in this journal
4
PLOS Computational Biology
● 1863 papers in training set
Top 5%
6.7%
Similar papers in this journal
5
Scientific Reports
○ 3612 papers in training set
Top 10%
6.7%
Similar papers in this journal
6
The European Physical Journal Plus
○ 13 papers in training set
Top 0.1%
5.5%
7
International Journal for Numerical Methods in Biomedical Engineering
○ 14 papers in training set
Top 0.1%
4.9%
50% of probability mass above
8
Journal of Biomechanical Engineering
● 20 papers in training set
Top 0.2%
3.2%
9
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
● 15 papers in training set
Top 0.1%
2.8%
10
Bulletin of Mathematical Biology
○ 92 papers in training set
Top 0.6%
2.6%
11
Physical Review Letters
● 47 papers in training set
Top 0.2%
2.4%
12
Soft Matter
● 60 papers in training set
Top 0.4%
2.1%
13
Journal of Mathematical Biology
○ 40 papers in training set
Top 0.2%
2.1%
14
Physical Review Research
● 49 papers in training set
Top 0.4%
2.1%
15
Frontiers in Physics
○ 21 papers in training set
Top 0.1%
1.3%
16
Journal of The Royal Society Interface
● 235 papers in training set
Top 3%
1.3%
17
The European Physical Journal E
○ 14 papers in training set
Top 0.1%
1.1%
18
Fluids and Barriers of the CNS
○ 28 papers in training set
Top 0.3%
1.1%
19
New Journal of Physics
○ 10 papers in training set
Top 0.1%
1.1%
20
The Journal of Chemical Physics
● 56 papers in training set
Top 0.5%
0.8%
21
eLife
● 5828 papers in training set
Top 66%
0.8%
22
Physical Biology
○ 46 papers in training set
Top 0.9%
0.8%
23
Biomechanics and Modeling in Mechanobiology
○ 29 papers in training set
Top 0.4%
0.8%
24
Interface Focus
● 14 papers in training set
Top 0.2%
0.6%
25
Computers in Biology and Medicine
○ 128 papers in training set
Top 5%
0.6%
26
Physica A: Statistical Mechanics and its Applications
○ 13 papers in training set
Top 0.3%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.