Related papers: Method for the Monte Carlo based Simulation of Lip…
The multiscale Monte-Carlo algorithm outlined in Bai and Brandt[1] is applied to a simple model of the polypeptide backbone. Effective coarse level Hamiltonians are derived by a fast Newtonian iterative scheme. The coarse Hamiltonian…
Multiphase field models have emerged as an important computational tool for understanding biological tissue while resolving single-cell properties. While they have successfully reproduced many experimentally observed behaviors of living…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
We put forward a simple procedure for extracting dynamical information from Monte Carlo simulations, by appropriate matching of the short-time diffusion tensor with its infinite-dilution limit counterpart, which is supposed to be known.…
Motivated by the experimental study of Tayebi et al. [Nature Mater. 11, 1074 (2012)] on phase separation of stacked multi-component lipid bilayers, we propose a model composed of stacked two-dimensional Ising spins. We study both its static…
We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the…
A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo J. Chem.…
An attempt is made to simulate the homoepitaxial growth of a Si(111) surface by the kinetic Monte Carlo method in which the standard Solid-on-Solid model and the planar model of the (7x7) surface reconstruction are used in combination. By…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those…
Monte Carlo simulation provides a powerful tool for understanding and exploring thermodynamic phase equilibria in many-particle interacting systems. Among the most physically intuitive simulation methods is Gibbs ensemble Monte Carlo…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
Monte Carlo simulations are performed to study the properties of type-II superconducting films in a magnetic field in which the vortices move in the two-dimensional geometry represented by the surface of a sphere. No numerical evidence is…
An efficient method for the simulation of strained heteroepitaxial growth with intermixing using kinetic Monte Carlo is presented. The model used is based on a solid-on-solid bond counting formulation in which elastic effects are…
Fibers of bent-core liquid crystals present an internal structure of a rolled smectic layer and can be used as optical waveguides. We used a field-theoretical Monte Carlo simulation to analyze the internal configuration of such fibers as a…
A simple solid-on-solid model, proposed earlier to describe overlayer-induced faceting of bcc(111) surface, is applied to faceting of spherical surfaces covered by adsorbate monolayer. Monte Carlo simulation results show that morphology of…
A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their…
In any valid Monte Carlo sampling that realizes microcanonical property we can collect statistics for a transition matrix in energy. This matrix is used to determine the density of states, from which most of the thermodynamical averages can…