Related papers: Lattice stretching bistability and dynamic heterog…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
We study a model describing some aspects of the dynamics of biopolymers. The models involve either one or two finite chains with a number N of sites that represent the "units" of a biophysical system. The mechanical degrees of freedom of…
We develop an analytical theory for lattice relaxation in twisted moir\'e heterobilayers, accounting for lattice mismatch, twist, external biaxial heterostrain, and different elastic constants. Starting from continuum elasticity, we derive…
We investigate the dynamics of a lattice soliton on a monatomic chain in the presence of damping and external forces. We consider Stokes and hydrodynamical damping. In the quasi-continuum limit the discrete system leads to a damped and…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
A two-dimensional bistable lattice is a periodic triangular network of non-linear bi-stable rods. The energy of each rod is piecewise quadratic and has two minima. Consequently, a rod undergoes a reversible phase transition when its…
We construct a three-dimensional lattice model for biological gels in which straight lines of bonds correspond to filamentous semi-flexible polymers and lattice sites, which are exactly four-fold coordinated, to crosslinks. With only…
We investigate the ground state of a one-dimensional lattice system that hosts two different kinds of excitations (species) which interact with a power-law potential. Interactions are only present between excitations of the same kind and…
With the advent of quantum simulators, exploring exotic collective phenomena in lattice models with local symmetries and unconventional geometries is at reach of near-term experiments. Motivated by recent progress in this direction, we…
We study simple lattice systems to demonstrate the influence of interpenetrating bond networks on phase behavior. We promote interpenetration by using a Hamiltonian with a weakly repulsive interaction with nearest neighbors and an…
Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…
We characterize equilibrium properties and relaxation dynamics of a two-dimensional lattice containing, at each site, two particles connected by a double-well potential (dumbbell). Dumbbells are oriented in the orthogonal direction with…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
Using molecular dynamic simulation, we study the stretching of an adsorbed homopolymer in a poor solvent with one end held at a distance $z_e$ from the substrate. We measure the vertical force $f$ on the end of the chain as a function of…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…