Related papers: Ideal Glasses and Protein Network Dynamics

The axiomatic theory of ideally glassy networks, which has proved effective in describing phase diagrams and properties of chalcogenide and oxide glasses and their foreign interfaces, is broadened here to include intermolecular interactions…

A simple spin system is studied as an analog for proteins. We investigate how the introduction of randomness and frustration into the system effects the designability and stability of ground state configurations. We observe that the spin…

Network glasses are the physical prototype for many self-organized systems, ranging from proteins to computer science. Conventional theories of gases, liquids, and crystals do not account for the strongly material-selective character of the…

Signatures of glassy dynamics have been identified experimentally for a rich variety of materials in which molecular networks provide rigidity. Here we present a theoretical framework to study the glassy behavior of both passive and active…

We introduce the ideal Gaussian glass-forming system as a model to describe the thermodynamics and dynamics of supercooled liquids on a local scale in terms of the properties of the potential energy landscape (PEL). The first ingredient is…

We use computer simulations to probe the thermodynamic and dynamic properties of a glass-former that undergoes an ideal glass-transition because of the presence of randomly pinned particles. We find that even deep in the equilibrium glass…

Proteins are aminoacid chains that diffusively fold or unfold depending on the thermal and chemical environmental conditions. While sophisticated models account for detailed aspects of real proteins, finding traits that unify protein…

Live cells have ambiguous mechanical properties. They were often described as either elastic solids or viscoelastic fluids and have recently been classified as soft glassy materials characterized by weak power-law rheology. Nonlinear…

Biological condensates are assemblies of proteins and nucleic acids that form membraneless compartments in cells and play essential roles in cellular functions. In many cases they exhibit the physical properties of liquid droplets that…

A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…

Hypotheses: Additives are commonly used to tune macromolecular conformational transitions. Among additives, trehalose is an excellent bioprotectant and among responsive polymers, PNIPAM is the most studied material. Nevertheless, their…

Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…

Dynamics is central to living systems. In the last two decades, experiments have revealed that the dynamics in diverse biological systems - from intracellular cytoplasm to cellular and organismal aggregates - are remarkably similar to that…

An analysis of the dynamics is performed, of exactly solvable models for fragile and strong glasses, exploiting the partitioning of the free energy landscape in inherent structures. The results are compared with the exact solution of the…

In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…

Many biological tissues are viscoelastic, behaving as elastic solids on short timescales and fluids on long timescales. This collective mechanical behavior enables and helps to guide pattern formation and tissue layering. Here we…

The mechanical properties of cells, which influence the properties of the tissue they belong to, are controlled by various mechanisms. Bi et al. theoretically demonstrated that density-independent rigidity transition occurs in…

Despite the diversity of materials designated as active matter, virtually all active systems undergo a form of dynamic arrest when crowding and activity compete, reminiscent of the dynamic arrest observed in colloidal and molecular fluids…

Glassy, nonexponential relaxations in globular proteins are typically attributed to conformational behaviors that are missing from intrinsically disordered proteins. Yet, we show that single molecules of a disordered-protein construct…

We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass…