相关论文: Ideal Glasses and Protein Network Dynamics
Elastic models of the glass transition relate the relaxation dynamics and the elastic properties of structural glasses. They are based on the assumption that the relaxation dynamics occurs through activated events in the energy landscape…
In spin glass models one can remove minimization of free energy by some order parameter. One can consider hierarchy of order parameters. It is possible to divide energy among these parts. We can consider relaxation process in glass system…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
We report Molecular Dynamics simulations for a new model of tetrahedral network glass-former, based on short-range, spherical potentials. Despite the simplicity of the forcefield employed, our model reproduces some essential physical…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
We develop a minimal model to describe growing dense active matter such as biological tissues, bacterial colonies and biofilms, that are driven by a competition between particle division and steric repulsion. We provide a detailed numerical…
We present a simple mathematical model of glassy dynamics seen as a random walk in a directed, weighted network of minima taken as a representation of the energy landscape. Our approach gives a broader perspective to previous studies…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ \AA )…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
Atomistic deformation simulations in the nominally elastic regime are performed for a model binary glass with strain rates as low as $10^{4}$/sec (corresponding to 0.01 shear strain per 1$\mu$sec). A robust elasticity is revealed that…
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…
The axiomatic theory of ideally glassy networks, which has proved effective in describing phase diagrams and many properties of chalcogenide, oxide, and even molecular glasses, is here broadened to describe both geometrical properties, such…
Active glasses refer to a class of driven non-equilibrium systems that share remarkably similar dynamical behavior as conventional glass-formers in equilibrium. Glass-like dynamical characteristics have been observed in various biological…
Simulations are used to examine the microscopic origins of strain hardening in polymer glasses. While traditional entropic network models can be fit to the total stress, their underlying assumptions are inconsistent with simulation results.…
We conduct a numerical study of the dynamical behavior of a system of three-dimensional crosses, particles that consist of three mutually perpendicular line segments rigidly joined at their midpoints. In an earlier study [W. van Ketel et…
In this work we study spin-glass (SG) like behavior in the dynamics of multiple agents in a social or economic context using interactions which are similar to the physical case. The different preferences shown by individual agents are…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
A model is derived for the viscoelastic response of glasses at isothermal uniaxial deformation with small strains. A glass is treated as an ensemble of relaxing units with various activation energies for rearrangement. With reference to the…
We attribute similarities in the rheology of many soft materials (foams, emulsions, slurries, etc.) to the shared features of structural disorder and metastability. A generic model for the mesoscopic dynamics of ``soft glassy matter'' is…