Search results for " Molecular modeling"

PET/PEN Blends of Industrial Interest as Barrier Materials. Part I. Many-Scale Molecular Modeling of PET/PEN Blends

2006

Mesoscale molecular simulations, based on parameters obtained through atomistic molecular dynamics and Monte Carlo calculations, have been used for modeling and predicting the behavior of PET/PEN blends. Different simulations have been performed in order to study and compare pure homopolymer blends with blends characterized by the presence of PET/PEN block copolymers acting as compatibilizer. A many-scale molecular modeling strategy was devised to evaluate PET/PEN blend characteristics, simulate phase segregation in pure PET/PEN blends, and demonstrate the improvement of miscibility due to the presence of the transesterification reaction products. The behavior of distribution densities and …

Critical phenomena without “hyper scaling”: How is the finite-size scaling analysis of Monte Carlo data affected?

2010

Abstract The finite size scaling analysis of Monte Carlo data is discussed for two models for which hyperscaling is violated: (i) the random field Ising model (using a model for a colloid-polymer mixture in a random matrix as a representative) (ii) The Ising bi-pyramid in computing surface fields.

Cross Correlations in Scaling Analyses of Phase Transitions

2008

Thermal or finite-size scaling analyses of importance sampling Monte Carlo time series in the vicinity of phase transition points often combine different estimates for the same quantity, such as a critical exponent, with the intent to reduce statistical fluctuations. We point out that the origin of such estimates in the same time series results in often pronounced cross-correlations which are usually ignored even in high-precision studies, generically leading to significant underestimation of statistical fluctuations. We suggest to use a simple extension of the conventional analysis taking correlation effects into account, which leads to improved estimators with often substantially reduced …

Monte Carlo Simulation of Crystal-Liquid Phase Coexistence

2016

When a crystal nucleus is surrounded by coexisting fluid in a finite volume in thermal equilibrium, the thermodynamic properties of the fluid (density, pressure, chemical potential) are uniquely related to the surface excess free energy of the nucleus. Using a model for weakly attractive soft colloidal particles, it is shown that this surface excess free energy can be determined accurately from Monte Carlo simulations over a wide range of nucleus volumes, and the resulting nucleation barriers are completely independent from the size of the total volume of the system. A necessary ingredient of the analysis, the pressure at phase coexistence in the thermodynamic limit, is obtained from the in…

Path-integral Monte Carlo study of crystalline Lennard-Jones systems.

1995

The capability of the path-integral Monte Carlo (PIMC) method to describe thermodynamic and structural properties of solids at low temperatures is studied in detail, considering the noble-gas crystals as examples. In order to reduce the systematic limitations due to finite Trotter number and finite particle number we propose a combined Trotter and finite-size scaling. As a special application of the PIMC method we investigate $^{40}\mathrm{Ar}$ at constant volume and in the harmonic approximation. Furthermore, isotope effects in the lattice constant of $^{20}\mathrm{Ne}$ and $^{22}\mathrm{Ne}$ are computed at zero pressure. The obtained results are compared with classical Monte Carlo result…

Statistical characterization of self-assembled charged nanoparticle structures

2013

We propose a novel approach for description of dynamics of nanostructure formation for a system consisting of oppositely charged particles. The combination of numerical solution of analytical Bogolyubov–Born–Green–Kirkwood–Yvon (BBGKY) type equation set with reverse Monte Carlo (RMC) method allows us to overcome difficulties of standard approaches, such as kinetic Monte Carlo or Molecular Dynamics, to describe effects of long-range Coulomb interactions. Moreover, this allows one to study the system dynamics on realistic time and length scales. We applied this method to a simple short-range Lenard–Jones (LJ)-like three- (3D) and two-dimensional (2D) system combining the long-range Coulomb an…

Theoretical Foundations of the Monte Carlo Method and Its Applications in Statistical Physics

2002

In this chapter we first introduce the basic concepts of Monte Carlo sampling, give some details on how Monte Carlo programs need to be organized, and then proceed to the interpretation and analysis of Monte Carlo results.

Monte Carlo simulations of the periodically forced autocatalyticA+B→2Breaction

2000

The one-parameter autocatalytic Lotka-like model, which exhibits self-organized oscillations, is considered on a two-dimensional lattice, using Monte Carlo computer simulations. Despite the simplicity of the model, periodic modulation of the only control parameter drives the system through a sequence of frequency locking, quasiperiodic, and resonance behavior.

Crossover scaling in semidilute polymer solutions: a Monte Carlo test

1991

DNA minor groove binders: an overview on molecular modeling and QSAR approaches

2007

Molecular recognition of DNA by small molecules and proteins is a fundamental problem in structural biology and drug design. Understanding of recognition in both sequence-selective and sequence neutral ways at the level of successful prediction of binding modes and site selectivity will be instrumental for improvements in the design and synthesis of new molecules as potent and selective gene-regulatory drugs. Minor groove is the target of a large number of non-covalent binding agents. DNA binding with specific sequences, mostly AT, takes place by means of a combination of directed hydrogen bonding to base pair edges, van der Waals interactions with the minor groove walls and generalized ele…