Related papers: Elastic Network Models: Theoretical and Empirical …
We study the elastic properties of thermal networks of Hookean springs. In the purely mechanical limit, such systems are known to have vanishing rigidity when their connectivity falls below a critical, isostatic value. In this work we show…
Active adaptive matter has attracted considerable interest due to its rich, largely unexplained dynamics and its relevance to a wide range of synthetic and biological materials. An important subclass of such systems consists of active…
Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
Particle based methods such as the Discrete Element Method and the Lattice Spring Method may be used for describing the behaviour of isotropic linear elastic materials. However, the common bond models employed to describe the interaction…
Elastic microphase separation refers to equilibrium patterns that form by phase separation in elastic gels. Recent experiments revealed a continuous phase transition from the homogeneous phase to a regularly patterned phase, whose period…
We propose a link prediction algorithm that is based on spring-electrical models. The idea to study these models came from the fact that spring-electrical models have been successfully used for networks visualization. A good network…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
Networks of elastic beams can deform either by stretching or bending of their members. The primary mode of deformation (bending or stretching) crucially depends on the specific details of the network architecture. In order to shed light on…
This paper first reviews the shoving model for the non-Arrhenius viscosity of viscous liquids. According to this model the main contribution to the activation energy of a flow event is the energy needed for molecules to shove aside the…
How do networks of relationships evolve over time? We analyse a dataset tracking the social interactions of 900 individuals over four years. Despite continuous shifts in individual relationships, the macroscopic structural properties of the…
We study the dynamics of a single semiflexible filament coupled to a Hookean spring at its boundary. The spring produces a fluctuating tensile force on the filament, whose value depends on the filament's instantaneous end-to-end length. The…
The H\"uckel Hamiltonian is an incredibly simple tight-binding model famed for its ability to capture qualitative physics phenomena arising from electron interactions in molecules and materials. Part of its simplicity arises from using only…
We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Temporal networks of face-to-face interactions between individuals are useful proxies of the dynamics of social systems on fast time scales. Several empirical statistical properties of these networks have been shown to be robust across a…
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…