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We study the dynamic structure factor of fluctuating elastic thin sheets subject to conservative (athermal) random forcing. In Steinbock, Katzav & Boudaoud, Phys. Rev. Research 4, 033096 (2022), the static structure factor of such a sheet…
Using Langevin dynamics simulations, we study elastic response of single semiflexible polyelectrolytes to an external force pulling on the chain ends, to mimic the stretching of DNA molecules by optical tweezers. The linear chains are…
The vibrational dynamics of protein folding is analyzed in the framework of Tsallis thermostatistics. The generalized partition functions, internal energies, free energies and temperature factor (or Debye-Waller factor) are calculated. It…
We examine the effects of thermal fluctuations on thin elastic filaments with non-circular cross-section and arbitrary spontaneous curvature and torsion. Analytical expressions for orientational correlation functions and for the persistence…
Glass formers exhibit a viscoelastic behavior: at the laboratory timescale, they behave like (glassy) solids at low temperatures, and like liquids at high temperatures. Based on this observation, elastic models relate the long time…
We carried out dynamic force manipulations $in$ $silico$ on a variety of superhelical protein fragments from myosin, chemotaxis receptor, vimentin, fibrin, and phenylalanine zippers that vary in size and topology of their $\alpha$-helical…
The discrete modeling of a large class of mechanical structures can be based on a stick-and-spring concept. We here present a stick-and-spring theory with potential application to the statics and the dynamics of such nanostructures as…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
Mechanical unfolding of several domains of calmodulin and titin is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. It is shown that this simple model captures the experimentally observed…
We measure the transport properties of mechanically strained single crystals of BaFe$_{2}$(As$_{1-x}$P$_{x}$)$_{2}$ over a wide range of $x$. The N\'eel transition is extremely sensitive to stress and this sensitivity increases as optimal…
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.…
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…
We study by mean-field analysis and stochastic simulations chemical models for genetic toggle switches formed from pairs of genes that mutually repress each other. In order to determine the stability of the genetic switches, we make a…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
We present a comprehensive first-principles study of the structural and elastic properties of 2H-MX$_2$ transition metal dichalcogenides (TMDs) (M = W, Mo, Ta, Nb; X = S, Se). Using density functional theory with various van der Waals…
The mechanical behavior of two-dimensional (2D) materials across 2D phase changes is unknown, and the finite temperature ($T$) elasticity of paradigmatic SnSe monolayers -- ferroelectric 2D materials turning paraelectric as their unit cell…
We study an elasticity model for compressed protein monolayers or particle rafts at a liquid interface. Based on the microscopic view of hard-core particles with soft shells, a bead-spring model is formulated and analyzed in terms of…