Related papers: Method for the Monte Carlo based Simulation of Lip…
Mono- and poly-disperse melts of oligomers (average length 10 monomers) of trans-1,4-polyisoprene are simulated in full atomistic detail. The force-field is developed by means of a mixture of ab initio quantum-chemistry and an automatic…
For a wide class of applications of the Monte Carlo method, we describe a general sampling methodology that is guaranteed to converge to a specified equilibrium distribution function. The method is distinct from that of Metropolis in that…
Using the Monte Carlo method, we have studied the pulsed laser deposition process at the sub-monolayer regime. In our simulations, dissociation of an atom from a cluster is incorporated. Our results indicate that the pulsed laser deposition…
Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…
The task of accurately locating fluid phase boundaries by means of computer simulation is hampered by problems associated with sampling both coexisting phases in a single simulation run. We explain the physical background to these problems…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
We describe a complete methodology to bridge the scales between nanoscale Molecular Dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species…
A grand canonical Monte Carlo method for the simulation of a simple colloid-polymer mixture called the AO model will be described. The phase separation known to occur in this model is driven by entropy. The phase diagram of the unmixing…
We consider the formation of finite-size domains in lipid bilayers consisting of saturated and hybrid lipids. First, we describe a monolayer model that includes a coupling between a compositional scalar field and a two-dimensional vectorial…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
The jump-walking Monte-Carlo algorithm is revisited and updated to study the equilibrium properties of systems exhibiting quasi-ergodicity. It is designed for a single processing thread as opposed to currently predominant algorithms for…
We propose a model describing liquid-solid phase coexistence in mixed lipid membranes by including explicitly the occurrence of a rippled phase. For a single component membrane, we employ a previous model in which the membrane thickness is…
We investigate solid-solid and solid-liquid transitions of elastic flexible off-lattice polymers with Lennard-Jones monomer-monomer interaction and anharmonic springs by means of sophisticated variants of multicanonical Monte Carlo methods.…
A continuous-time projection quantum Monte Carlo algorithm is employed to simulate the ground state of a short-range quantum spin-glass model, namely, the two-dimensional Edwards-Anderson Hamiltonian with transverse field, featuring…
The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are…
This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…
We report a kinetic Monte Carlo modeling study of nanocrystal layer sintering. Features that are of interest for the dynamics of the layer as a whole, especially the morphology of the evolving structure, are considered. It is found that the…
A classical Monte Carlo algorithm based on the quasi-classical approximation is applied to the pseudospin Hamiltonian of the model cuprate. The model takes into account both local and non-local correlations, Heisenberg spin-exchange…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
A new Monte Carlo algorithm is introduced for the simulation of supercooled liquids and glass formers, and tested in two model glasses. The algorithm is shown to thermalize well below the Mode Coupling temperature and to outperform other…