Related papers: A one-dimensional model for theoretical analysis o…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and…
Although the stretching of polymers and biomolecules is important in numerous settings, their response when confined to two-dimensions is relatively poorly-studied. In this paper, we derive closed-form analytical expressions for the…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve…
We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these…
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…
The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions are investigated by molecular dynamics simulations. Three different scenarios are considered: The force-extension relation of…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
In this paper we study the unfolding transition observed in polymer stretching experiments. We use a known model and extend it with a mean-field-like interaction. Expressions for all necessary thermodynamic variables as a function of the…
The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Force versus extension curves measure entropic elasticity of single polymer chain in force spectroscopy experiments. A Worm-like Chain model is used to describe force extension experiments with an intrinsic chain parameter called…
Recent advances in single macromolecule experiments have sparked interest in the ensemble dependence of force-extension relations. The thermodynamic limit may not be attainable for such systems, that leads to inequivalence of the…
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…
In this work, we compare the structural and dynamic behavior of active filaments in two dimensions using tangential and push-pull models, including a variant with passive end monomers. These models serve as valuable frameworks for…
We show how to construct non-equilibrium thermodynamics for systems too small to be considered thermodynamically in a traditional sense. Through the use of a non-equilibrium ensemble of many replicas of the system which can be viewed as a…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…