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Through Monte Carlo simulations and the Associating Lattice Gas Model, the phases of a two-dimensional fluid under hydrophilic confinement are evaluated. The model, in its unconfined version, reproduces the anomalous behavior of water…
We report a very detailed relation about the study, by a constrained Monte Carlo dynamic, of a 4D EA spin glass model (J=+/- 1). In particular we concentrate our attention on the behaviour of the system under different bounds imposed in…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively…
We propose a hierarchy of multi-level kinetic Monte Carlo methods for sampling high-dimensional, stochastic lattice particle dynamics with complex interactions. The method is based on the efficient coupling of different spatial resolution…
The glass transition is considered within two toys models, a mean field spin glass and a directed polymer in a correlated random potential. In the spin glass model there occurs a dynamical transition, where the system condenses in a state…
Quasi-Monte Carlo algorithms are studied for designing discrete approximations of two-stage linear stochastic programs. Their integrands are piecewise linear, but neither smooth nor lie in the function spaces considered for QMC error…
The Shallow Recurrent Decoder networks are a novel paradigm recently introduced for state estimation, combining sparse observations with high-dimensional model data. This architecture features important advantages compared to standard…
In this paper, we consider a stochastic model of incompressible non-Newtonian fluids of second grade on a bounded domain of $\mathbb{R}^2$ with multiplicative noise. We first show that the solutions to the stochastic equations of second…
We investigate the quality of structural models generated by the Reverse Monte Carlo (RMC) method in a typical application to amorphous systems. To this end we calculate surrogate diffraction data from a Li2O-SiO2 molecular dynamics (MD)…
We analyze the transport properties of a low density ensemble of identical macroscopic particles immersed in an active fluid. The particles are modeled as inelastic hard spheres (granular gas). The non-homogeneous active fluid is modeled by…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HS). The idea behind the proposal is expanding volume instead of…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
Truly stable metastable states are an artifact of the mean-field approximation or the zero temperature limit. If such appealing concepts in glass theory as configurational entropy are to have a meaning beyond these approximations, one needs…
We apply optimization algorithms to the problem of finding ground states for crystalline surfaces and flux lines arrays in presence of disorder. The algorithms provide ground states in polynomial time, which provides for a more precise…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
This paper combines the particle-swap Monte Carlo algorithm with long GPU molecular dynamics simulations to analyze the dynamics of a ternary Lennard-Jones glass-forming liquid in the extremely viscous regime. The focus is on the inherent…
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…
A model for two-dimensional colloids confined laterally by "structured boundaries" (i.e., ones that impose a periodicity along the slit) is studied by Monte Carlo simulations. When the distance D between the confining walls is reduced at…