scholarly journals Multiscale Network Modeling of Fibrin Fibers and Fibrin Clots with Protofibril Binding Mechanics

Polymers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1223
Author(s):  
Sumith Yesudasan ◽  
Rodney D. Averett

The multiscale mechanical behavior of individual fibrin fibers and fibrin clots was modeled by coupling atomistic simulation data and microscopic experimental data. We propose a new protofibril element composed of a nonlinear spring network, and constructed this based on molecular simulations and atomic force microscopy results to simulate the force extension behavior of fibrin fibers. This new network model also accounts for the complex interaction of protofibrils with one another, the effects of the presence of a solvent, Coulombic attraction, and other binding forces. The network model was formulated to simulate the force–extension mechanical behavior of single fibrin fibers from atomic force microscopy experiments, and shows good agreement. The validated fibrin fiber network model was then combined with a modified version of the Arruda–Boyce eight-chain model to estimate the force extension behavior of the fibrin clot at the continuum level, which shows very good correlation. The results show that our network model is able to predict the behavior of fibrin fibers as well as fibrin clots at small strains, large strains, and close to the break strain. We used the network model to explain why the mechanical response of fibrin clots and fibrin fibers deviates from worm-like chain behavior, and instead behaves like a nonlinear spring.

1995 ◽  
Vol 68 (4) ◽  
pp. 652-659 ◽  
Author(s):  
S. Maas ◽  
W. Gronski

Abstract The changes of the filler morphology of SBR vulcanizates loaded with 10 phr carbon black (N234 and N990) subjected to large strains were studied by Atomic Force Microscopy and image analysis. It was found that the filler particles tend to align in the force field. The average distance of the filler particles at the surface in the direction parallel and perpendicular to the strain direction is much smaller then according to affine deformation. The measurements give evidence of the inhomogeneous deformation of the rubber matrix and demonstrate the onset of failure at large deformation.


Langmuir ◽  
2005 ◽  
Vol 21 (15) ◽  
pp. 6934-6943 ◽  
Author(s):  
Pascal Martin ◽  
Sophie Marsaudon ◽  
Laurent Thomas ◽  
Bernard Desbat ◽  
Jean-Pierre Aimé ◽  
...  

2010 ◽  
Vol 5 (4) ◽  
pp. 670-677 ◽  
Author(s):  
Jürgen J Heinisch ◽  
Vincent Dupres ◽  
David Alsteens ◽  
Yves F Dufrêne

2005 ◽  
Vol 187 (6) ◽  
pp. 2127-2137 ◽  
Author(s):  
Brian H. Lower ◽  
Ruchirej Yongsunthon ◽  
F. Paul Vellano ◽  
Steven K. Lower

ABSTRACT All microbial biofilms are initiated through direct physical contact between a bacterium and a solid surface, a step that is controlled by inter- and intramolecular forces. Atomic force microscopy and confocal laser scanning microscopy were used simultaneously to observe the formation of a bond between a fluorescent chimeric protein on the surface of a living Escherichia coli bacterium and a solid substrate in situ. The chimera was composed of a portion of outer membrane protein A (OmpA) fused to the cyan-fluorescent protein AmCyan. Sucrose gradient centrifugation and fluorescent confocal slices through bacteria demonstrated that the chimeric protein was targeted and anchored to the external cell surface. The wormlike chain theory predicted that this protein should exhibit a nonlinear force-extension “signature” consistent with the sequential unraveling of the AmCyan and OmpA domains. Experimentally measured force-extension curves revealed a unique pair of “sawtooth” features that were present when a bond formed between a silicon nitride surface (atomic force microscopy tip) and E. coli cells expressing the OmpA-AmCyan protein. The observed sawtooth pair closely matched the wormlike chain model prediction for the mechanical unfolding of the AmCyan and OmpA substructures in series. These sawteeth disappeared from the measured force-extension curves when cells were treated with proteinase K. Furthermore, these unique sawteeth were absent for a mutant stain of E. coli incapable of expressing the AmCyan protein on its outer surface. Together, these data show that specific proteins exhibit unique force signatures characteristic of the bond that is formed between a living bacterium and another surface.


2011 ◽  
Vol 44 (2) ◽  
pp. 368-374 ◽  
Author(s):  
Davide Tranchida ◽  
Elena Sperotto ◽  
Antoine Chateauminois ◽  
Holger Schönherr

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3089-3089
Author(s):  
Andre E.X. Brown ◽  
Rustem I. Litvinov ◽  
Prashant Purohit ◽  
Dennis E. Discher ◽  
John Weisel

Abstract Although we know a great deal about the structure, properties and many functions of fibrin(ogen), we still know very little about the microscopic and molecular origins of the clot’s mechanical properties, even though they are necessary for its functions, since hemostasis is essentially a mechanical process. In addition, it has been shown that individuals who have myocardial infarction at an early age tend to form very stiff clots. We have carried out studies at different levels of structure and integrated the results through a model that demonstrates that fibrin clot mechanical properties are manifestations of the observed mechanical characteristics of fibrin(ogen) molecules. By stretching whole fibrin clots with an extensional rheometer, we observed fibrin’s remarkable extensibility with a mechanical response that was initially linear with an increase in stiffness at larger elongation, above two-fold. These results are consistent with the large extensibility that has been observed in single fibrin fibers and may also play a role in the mechanics of blood clots at high strain, as in arterial blood flow. Furthermore, we found that protein structural transitions are required even at lower elongations. Some of the corresponding structural changes in the clots with stretching up to about four-fold were observed by electron microscopy. Scanning electron microscopy of the clots revealed extensive reorientation of the fibers making up the clots in the direction of applied stress. The orientational order was quantified from the scanning electron microscope images using a custom, automated image analysis algorithm that calculates a network order parameter, revealing a high degree of alignment for stretched, initially unoriented fibrin gels. Crosssections of stretched clots were examined by transmission electron microscopy. The most striking change observed was a huge (up to 10-fold) decrease in volume with stretching, with aggregation or bundling of fibers. Basic features of the mechanics of single fibrin fibers are known. These measurements have recently been extended to the level of single molecules using atomic force microscopy. When factor XIIIa-ligated fibrinogen oligomers were stretched by atomic force microscopy, the coiled-coils were found to unfold first under force. Until now, these observations at the molecular and fiber levels have not been correlated with the behavior of whole fibrin clots. These levels of structure were bridged through small angle X-ray fiber diffraction patterns obtained from fibrin clots, since the primary peaks in the X-ray diffraction pattern correspond to the characteristic 22.5 nm repeat distance in fibrin fibers arising from the molecular packing. In contrast to some earlier reported results, there was no change in periodicity with stretching. Instead, these peaks broadened as the sample was stretched, consistent with structural disruptions like protein unfolding while the position of the 22.5 nm peak corresponding to the fibrin repeat remained constant. Since all of these measurements are quantitative, we developed a constitutive model, including all of the features observed, that suggests that the whole clot and fiber mechanical properties are a consequence of coiled-coil unfolding. All together, this study has allowed us to develop a truly multiscale understanding of fibrin mechanics that reveals how clots or thrombi, even though they are made up of relatively stiff fibers, can still have large extensibility that allows them to withstand large strains and open and permeable structures such that they are readily lysed. Understanding how the network, fiber, and molecular properties give rise to fibrin mechanics could contribute to designs of tougher or more extensible clots or lead to new strategies for breaking up clots or making them less occlusive.


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