Related papers: RNA Secondary Structures: Complex Statics and Glas…
We use molecular dynamics simulation to study the relationship between structure and dynamics in supercooled binary Lennard--Jones nanoparticles over a range of particle sizes. The glass transition temperature of the nanoparticles is found…
Using a {\it collective} Monte Carlo algorithm we study the low-temperature and long-distance properties of two systems of two-dimensional classical tops. Both systems have the same spin-wave dynamics (low-temperature behavior) as a large…
A simple, non-disordered spin model has been studied in an effort to understand the origin of the precipitous slowing down of dynamics observed in supercooled liquids approaching the glass transition. A combination of Monte Carlo…
An open question is whether the liquid and glassy phases of water are thermodynamically distinct or continuous. Here we address this question using molecular dynamics simulations in comparison with neutron scattering experiments to study…
We study secondary structures of random RNA molecules by means of a renormalized field theory based on an expansion in the sequence disorder. We show that there is a continuous phase transition from a molten phase at higher temperatures to…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
We study numerically a monodisperse model of interacting classical particles predicted to exhibit a static liquid-glass transition. Using a dynamical Monte Carlo method we show that the model does not freeze into a glassy phase at low…
In order to understand the mechanisms for glassy dynamics in biological tissues and shed light on those in non-biological materials, we study the low-temperature disordered phase of 2D vertex-like models. Recently it has been noted that…
We present a quantum Monte Carlo method capable of sampling the full density matrix of a many-particle system at finite temperature. This allows arbitrary reduced density matrix elements and expectation values of complicated non-local…
A theoretical analysis [Angelani et al., Phys. Rev. Lett. 96, 065702 (2006)] predicts glassy behaviour of light in a nonlinear random medium. This implies slow dynamics related to the presence of many metastable states. We consider very…
We analyse metastable states in the East model, using a recently-proposed patch-repetition analysis based on time-averaged density profiles. The results reveal a hierarchy of states of varying lifetimes, consistent with previous studies in…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also…
Metropolis Monte Carlo simulations of the eutectic NaK alloy are performed using the Second Moment Approximation (SMA) model potential across a wide range of temperatures at constant pressure. The alloy structure and thermodynamics are…
We discuss two methods of an exact stochastic representation of the non-Markovian quantum dynamics of open systems. The first method employs a pair of stochastic product vectors in the total system's state space, while the second method…
The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…
A continuous time Monte Carlo lattice gas dynamics is developed to model driven steady states of vortices in two dimensional superconducting networks. Dramatic differences are found when compared to a simpler Metropolis dynamics. Subtle…
We study the thermodynamic and dynamic phase transitions in two-dimensional polydisperse hard disks using Monte Carlo methods. A conventional local Monte Carlo algorithm allows us to observe a dynamic liquid-glass transition at a density,…