Related papers: Temperature- and Force-Induced beta-Sheet Unfoldin…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…
When $d\ge 3$, the directed polymer a in random environment on $\mathbb Z^d$ is known to display a phase transition from a diffusive phase, known as \textit{weak disorder} to a localized phase, referred to as \textit{strong disorder}. This…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
The size and shape of a large variety of polymeric particles, including biological cells, star polymers, dendrimes, and microgels, depend on the applied stresses as the particles are extremely soft. In high-density suspensions these…
Kinetic-scale current sheets observed in the solar wind are frequently approximately force-free despite the fact that their plasma $\beta$ is of the order of one. In-situ measurements have recently shown that plasma density and temperature…
Numerical simulations of thin sheets undergoing large deformations are computationally challenging. Depending on the scenario, they may spontaneously buckle, wrinkle, fold, or crumple. Nature's thin tissues often experience significant…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N=55 using exact enumeration…
We present Molecular Dynamics simulations of the thermal glass transition in a dense model polymer liquid. We performed a comparative study of both constant volume and constant pressure cooling of the polymer melt. Great emphasis was laid…
We study the statistics of thermodynamic quantities in two related systems with quenched disorder: A (1+1)-dimensional planar lattice of elastic lines in a random potential and the 2-dimensional random bond dimer model. The first system is…
Sequence heterogeneity broadens the binding transition of a polymer onto a linear or planar substrate. This effect is analyzed in a real-space renormalization group scheme designed to capture the statistics of rare events. In the strongly…
Within the resistive magnetohydrodynamic model, high-Lundquist number reconnection layers are unstable to the plasmoid instability, leading to a turbulent evolution where the reconnection rate can be independent of the underlying…
The thermodynamic nature of two-dimensional vortex matter is studied theoretically through a duality analysis of the XY model over the square lattice with low uniform frustration. A phase-coherent vortex lattice state is found at low…
Discovering novel emergent behavior in quantum many-body systems is a main objective of contemporary research. In this paper, we explore the effects on phases and phase transitions of the proximity to a Ruelle-Fisher instability, marking…
We study the out-of-equilibrium dynamics of bosonic atoms in a 1D optical lattice, after the ground-state is excited by a single spontaneous emission event, i.e. after an absorption and re-emission of a lattice photon. This is an important…