Biopolymers tend to form fibrils that self-assemble into open network structures. While permanently crosslinked flexible polymers are relatively well understood, structure-property relationships of open networks and pseudo-gels formed by bundles of biopolymers are still controversial. Here we employ a generic coarse-grained bead-spring chain model incorporating semiflexibility and cohesive nonbonded interactions, that forms physical instead of chemical crosslinks. For flexible chains, the cohesive forces lead to the formation of a droplet phase while, at the same concentration, stiffer chains form bundles that self-assemble into percolated networks. From comprehensive molecular dynamics simulations we find that the reversible crosslinks allow for permanent relaxation processes. However, the associated reorganization of the filamentous network is severely hindered, leading to aging of its topology. Based on morphometric analyses, the ultra-slow coarsening in these systems is proven to be self-similar, which implies a number of scaling relations between structural quantities as the networks age. The percolated structures are characterized by different dynamic regimes of slow, anomalous diffusion with highly non-Gaussian displacements. Relaxation dynamics is found to become extremely slow already on moderate length scales and further slowing down as coarsening proceeds. Using a minimal model supported by observations on filament rupture and rearrangement, our study helps to shed light on various interrelated structural and dynamical aspects of coarsening nonergodic systems relevant for fibrous networks, pseudo-gels, and physical fibrillar gels.
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Soft Matter
March 2025
School of Mathematical, Physical, and Computational Sciences, University of Reading, Reading, RG6 6AX, UK.
Biopolymers tend to form fibrils that self-assemble into open network structures. While permanently crosslinked flexible polymers are relatively well understood, structure-property relationships of open networks and pseudo-gels formed by bundles of biopolymers are still controversial. Here we employ a generic coarse-grained bead-spring chain model incorporating semiflexibility and cohesive nonbonded interactions, that forms physical instead of chemical crosslinks.
View Article and Find Full Text PDFJ Chem Inf Model
March 2025
Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, People's Republic of China.
Chronic traumatic encephalopathy (CTE) is a unique tauopathy mostly diagnosed in contact sports athletes, such as those active in American football, boxing, soccer, etc. The hyperphosphorylated fibrillar aggregates composed of self-assembled tau protein are the pathological hallmark of CTE, and inhibiting the aggregation or disassociating the fibrillar aggregates has been considered a promising avenue to prevent or treat CTE. Caffeine (CA) is a well-known psychostimulant and can be found in coffee, tea, and soft drinks.
View Article and Find Full Text PDFJ Phys Chem Lett
February 2025
Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India.
Self-assembly of small molecules has always been an attractive topic of research in the field of physical chemistry. Fluorescence lifetime imaging microscopy (FLIM) expands our understanding by offering a molecular-level perspective to gain deeper knowledge about the microenvironments. In this work, we have unveiled the self-aggregation mechanism of two naturally occurring polyphenolic molecules named gallic acid (GA) and its derivative methyl gallate (MG), resulting in ineffectiveness as a drug molecule.
View Article and Find Full Text PDFInt J Mol Sci
February 2025
School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an RNA-binding protein containing low-complexity domains (LCDs), which are known to regulate protein behavior under stress conditions. This study demonstrates the ability to control hnRNPK's transitions into four distinct material states-monomer, soluble aggregate, liquid droplet, and fibrillar hydrogel-by modulating environmental factors such as temperature and protein concentration. Importantly, the phase-separated and hydrogel states are newly identified for eGFP-hnRNPK, marking a significant advancement in understanding its material properties.
View Article and Find Full Text PDFSci Rep
February 2025
Laser Research Centre, Faculty of Physics, Vilnius University, Vilnius, Lithuania.
Second harmonic generation (SHG) microscopy is a powerful tool for imaging collagen and other noncentrosymmetric fibrillar structures in biological tissue. Polarimetric SHG measurements provide ultrastructural information about the fibrillar organization in a focal volume (voxel). We present a reduced nonlinear polarimetry method named double Stokes polarimetry (DSP) for quick characterization of chiral symmetry fibers without data fitting that simplifies and speeds up the polarimetric analysis.
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