Related papers: Elastic Network Models: Theoretical and Empirical …
The elastic response of mechanical, chemical, and biological systems is often modeled using a discrete arrangement of Hookean springs, either representing finite material elements or even the molecular bonds of a system. However, to date,…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Many organisms have an elastic skeleton that consists of a closed shell of epithelial cells that is filled with fluid, and can actively regulate both elastic forces in the shell and hydrostatic pressure inside it. In this work we introduce…
Disordered soft materials, such as fibrous networks in biological contexts exhibit a nonlinear elastic response. We study such nonlinear behavior with a minimal model for networks on lattice geometries with simple Hookian elements with…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
The thermodynamics and dynamics of supercooled liquids correlate with their elasticity. In particular for covalent networks, the jump of specific heat is small and the liquid is {\it strong} near the threshold valence where the network…
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…
We investigate a model for colloidal network formation using Brownian Dynamics computer simulations. Hysteretic springs establish transient bonds between particles with repulsive core. If a bonded pair is separated by a cutoff distance, the…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Elastic netwok models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the…
We contrast the distinct frameworks of materials design and physical learning in creating elastic networks with desired stable states. In design, the desired states are specified in advance and material parameters can be optimized on a…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
Models of complex networks often incorporate node-intrinsic properties abstracted as hidden variables. The probability of connections in the network is then a function of these variables. Real-world networks evolve over time, and many…
Complex molecules and mesoscopic structures are naturally described by general networks of elementary building blocks and tight-binding is one of the simplest quantum model suitable for studying the physical properties arising from the…
Solids built out of active components can exhibit non-reciprocal elastic coefficients that give rise to non-Hermitian wave phenomena. Here, we investigate non-Hermitian effects present at the boundary of two-dimensional active elastic media…
Liquid drops when subjected to external periodic perturbations can execute polygonal oscillations. In this work, a simple model is presented that demonstrates these oscillations and their characteristic properties. The model consists of a…
Disordered spring networks are a useful paradigm to examine macroscopic mechanical properties of amorphous materials. Here, we study the elastic behavior of under-constrained spring networks, i.e.\ networks with more degrees of freedom than…
Floppy microscale spring networks are widely studied in theory and simulations, but no well-controlled experimental system currently exists. Here, we show that square lattices consisting of colloid-supported lipid bilayers functionalized…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…