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Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
Protein-protein interactions are central mediators in many biological processes. Accurately predicting the effects of mutations on interactions is crucial for guiding the modulation of these interactions, thereby playing a significant role…
How do topological defects affect the degree of order in active matter? To answer this question we investigate an agent-based model of self-propelled particles, which accounts for polar alignment and short-ranged repulsive interactions. For…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
We demonstrate that internal pivot-like defects, arising from rigor mutant motor proteins that bind without stepping, fundamentally reshape the dynamics of semiflexible filaments in two-dimensional motility assays. Using large-scale…
Living cells inherently reorganize their intracellular structures in response to mechanical cues from their environment. Among these responses, the formation of actin-based stress fibers exhibits a series of structural transitions depending…
Phase transitions in disordered systems can be smeared if rare spatial regions develop true static order while the bulk system is in the disordered phase. Here, we study the effects of spatial disorder correlations on such smeared phase…
In this study, we employed a Raman spectroscopic analysis of the amide I band of polymerized samples of tubulin exposed to pulsed low-intensity NIR radiation (810 nm, 10 Hz, 22.5 J/cm$^{2}$ dose). Peaks in the Raman fingerprint region…
Computational models of neurodegeneration aim to emulate the evolving pattern of pathology in the brain during neurodegenerative disease, such as Alzheimer's disease. Previous studies have made specific choices on the mechanisms of…
For multi-stage, displacive structural transitions we present a general framework that accounts for various intermediate modulated phases, elastic constant, phonon and related thermodynamic anomalies. Based on the presence or absence of…
Stabilizing thermodynamically unstable phases in many-body systems, such as suppressing pathological neuronal synchronization in Parkinson's disease or maintaining magnetic order across broad temperature ranges, remains a persistent…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…
Mammalian cell polarization and motility are important processes involved in many physiological and pathological phenomena, such as embryonic development, wound healing, and cancer metastasis. The traditional view of mammalian cell motility…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Spherical confinement can act either stabilizing or destabilizing on the collapsed state of a semi-flexible polymer. General free-energy arguments suggest that the order of the unconstrained collapse transition is the distinguishing factor:…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…