scholarly journals Elucidating Invisible Barriers and Obstacles to Molecular Diffusion in Live Cells by the Spatial Pair-Correlation Function: A Connectivity View of the Cell

2018 ◽  
Vol 114 (3) ◽  
pp. 166a
Author(s):  
Leonel S. Malacrida ◽  
Per Niklas Hedde ◽  
Suman Ranjit ◽  
Francesco Cardarelli ◽  
Enrico Gratton
2020 ◽  
Vol 1 (2) ◽  
Author(s):  
Leonel Malacrida ◽  
Per Niklas Hedde ◽  
Belen Torrado ◽  
Enrico Gratton

ABSTRACT Transient barriers are fundamental to cell supramolecular organization and assembly. Discontinuities between spaces can be generated by a physical barrier but also by thermodynamic barriers achieved by phase separation of molecules. However, because of the transient nature and the lack of a visible barrier, the existence of phase separation is difficult to demonstrate experimentally. We describe an approach based on the 2-dimensional pair correlation function (2D-pCF) analysis of the spatial connectivity in a cell. The educational aim of the article is to present both a model suitable for explaining diffusion barrier measurements to a broad range of courses and examples of biological situations. If there are no barriers to diffusion, particles could diffuse equally in all directions. In this situation the pair correlation function introduced in this article is independent of the direction and is uniform in all directions. However, in the presence of obstacles, the shape of the 2D-pCF is distorted to reflect how the obstacle position and orientation change the flow of molecules. In the example shown in this article, measurements of diffusion of enhanced green fluorescent protein moving in live cells show the lack of connectivity at the nucleolus surface for shorter distances. We also observe a gradual increase in the connectivity for longer distances or times, presumably because of molecular trajectories around the nucleolus.


Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4876
Author(s):  
Shenshen Li ◽  
Jijun Xiao

In order to better understand the role of binder content, molecular dynamics (MD) simulations were performed to study the interfacial interactions, sensitivity and mechanical properties of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT) based polymer-bonded explosives (PBXs) with fluorine rubber F2311. The binding energy between CL-20/TNT co-crystal (1 0 0) surface and F2311, pair correlation function, the maximum bond length of the N–NO2 trigger bond, and the mechanical properties of the PBXs were reported. From the calculated binding energy, it was found that binding energy increases with increasing F2311 content. Additionally, according to the results of pair correlation function, it turns out that H–O hydrogen bonds and H–F hydrogen bonds exist between F2311 molecules and the molecules in CL-20/TNT. The length of trigger bond in CL-20/TNT were adopted as theoretical criterion of sensitivity. The maximum bond length of the N–NO2 trigger bond decreased very significantly when the F2311 content increased from 0 to 9.2%. This indicated increasing F2311 content can reduce sensitivity and improve thermal stability. However, the maximum bond length of the N–NO2 trigger bond remained essentially unchanged when the F2311 content was further increased. Additionally, the calculated mechanical data indicated that with the increase in F2311 content, the rigidity of CL-20/TNT based PBXs was decrease, the toughness was improved.


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