相关论文: Solvent-induced organization: A physical model of …
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…
We study the self-assembly of colloidal microgel particles at a quasi-two-dimensional air-water interface of a drying droplet. Using bright-field microscopy, we demonstrate that increasing particle elasticity drives interfacial organization…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
Fibrinogen is a protein found in blood that forms Fibrin polymer network to build a clot during wound healing process when there is a cut in the blood vessel. The fibrin fiber is highly stretchable and shows a complex mechanical properties.…
Collective cell motions underlie structure formation during embryonic development. Tissues exhibit emergent multicellular characteristics such as jamming, rigidity transitions, and glassy dynamics, but there remain questions about how those…
A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the…
Fibre-reinforced hydrogels are promising materials for biomedical applications due to their strength, toughness, and tunability. However, it remains unclear how to design fibre-reinforced hydrogels for use in specific applications due to…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
Conventional gas-liquid phase transitions feature a coexistence line that has a monotonic and positive slope in line with our intuition that cooling always leads to condensation. Here we study the inverse phenomenon, condensation of…
A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
The flow-induced flutter has a significant role in aircraft stability, renewable energy extraction, animal locomotion, among many other applications. While being a ubiquitous phenomenon, the control of the flutter response has been…
Inspired by dense contractile tissues, where cells are subject to periodic deformation, we formulate and study a generic hydrodynamic theory of pulsating active liquids. Combining mechanical and phenomenological arguments, we postulate that…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
When a multicomponent liquid composed of particles with random interactions is slowly cooled below the freezing temperature, the fluid reorganises in order to increase (decrease) the number of strong (weak) attractive interactions and…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
We describe a simple coarse-grained model which is suited to study lipid layers and their phase transitions. Lipids are modeled by short semiflexible chains of beads with a solvophilic head and a solvophobic tail component. They are forced…
Mechanical forces influence the development and behavior of biological tissues. In many situations these forces are exerted or resisted by elastic compliant structures such as the own-tissue cellular matrix or other surrounding tissues.…