Coarse-grained Simulations of Chemical Oscillation in Lattice Brusselator System

The oscillation behavior of a two-dimension lattice-gas Brusselator model was investigated. We have adopted a coarse-grained kinetic Monte Carlo (CG-KMC) procedure, where m￡m microscopic lattice sites are grouped together to form a CG cell, upon which CG processes take place with well-defined CG rates. Such a CG approach almost fails if the CG rates are obtained by a simple local mean field (s-LMF) approximation, due to the ignorance of correlation among adjcent cells resulting from the trimolecular reaction in this nonlinear system. By proper incorporating such boundary effects, thus introduce the so-called b-LMF CG approach. Extensive numerical simulations demonstrate that the b-LMF method can reproduce the oscillation behavior of the system quite well, given that the diffusion constant is not too small. In addition, the deviation from the KMC results reaches a nearly zero minimum level at an intermediate cell size, which lies in between the effective diffusion length and the minimal size required to sustain a well-defined temporal oscillation.     

Phase behavior of the lattice restricted primitive model with nearest neighbor exclusion

The global phase behavior of the lattice restricted primitive model with nearest neighbor exclusion has been studied by grand canonical Monte Carlo simulations. The phase diagram is dominated by a fluid (or charge-disordered solid) to charge-ordered solid transition that terminates at the maximum density rho*(max)= sqrt 2 and reduced temperature T* approximately equal to 0.29. At that point, there is a first-order phase transition between two phases of the same density, one charge-ordered, and the other charge-disordered. The liquid-vapor transition for the model is metastable, lying entirely within the fluid-solid phase envelope.     

Phase behavior and structure formation in linear multiblock copolymer solutions by Monte Carlo simulation

The solution phase behavior of short, strictly alternating multiblock copolymers of type (A(n)B(n))(m) was studied using lattice Monte Carlo simulations. The polymer molecules were modeled as flexible chains in a monomeric solvent selective for block type A. The degree of block polymerization n and the number of diblock units per chain m were treated as variables. We show that within the regime of parameters accessible to our study, the thermodynamic phase transition type is dependent on the ratio of m / n. The simulations show microscopic phase separation into roughly spherical aggregates for m / n ratios less than a critical value and first-order macroscopic precipitation otherwise. In general, increasing m at fixed n, or n at fixed m, promotes the tendency toward macroscopic phase precipitation. The enthalpic driving force of phase change is found to universally scale with chain length for all multiblock systems considered and is independent of the existence of a true phase transition. For aggregate forming systems at low amphiphile concentrations, multiblock chains are shown to self-assemble into intramolecular, multichain clusters. Predictions for microstructural dimensions, including critical micelle concentration, equilibrium size, shape, aggregation parameters, and density distributions, are provided. At increasing amphiphile density, interaggregate bridging is shown to result in the formation of networked structures, leading to an eventual solution-gel transition. The gel is swollen and consists of highly interconnected aggregates of approximately spherical morphology. Qualitative agreement is found between experimentally observed physical property changes and phase transitions predicted by simulations. Thus, a potential application of the simulations is the design of multiblock copolymer systems which can be optimized with regard to solution phase behavior and ultimately physical and mechanical properties.     

Reactive Monte Carlo and grand-canonical Monte Carlo simulations of the propene metathesis reaction system

The influence of silicalite-1 pores on the reaction equilibria and the selectivity of the propene metathesis reaction system in the temperature range between 300 and 600 K and the pressure range from 0.5 to 7 bars has been investigated with molecular simulations. The reactive Monte Carlo (RxMC) technique was applied for bulk-phase simulations in the isobaric-isothermal ensemble and for two phase systems in the Gibbs ensemble. Additionally, Monte Carlo simulations in the grand-canonical ensemble (GCMC) have been carried out with and without using the RxMC technique. The various simulation procedures were combined with the configurational-bias Monte Carlo approach. It was found that the GCMC simulations are superior to the Gibbs ensemble simulations for reactions where the bulk-phase equilibrium can be calculated in advance and does not have to be simulated simultaneously with the molecules inside the pore. The confined environment can increase the conversion significantly. A large change in selectivity between the bulk phase and the pore phase is observed. Pressure and temperature have strong influences on both conversion and selectivity. At low pressure and temperature both conversion and selectivity have the highest values. The effect of confinement decreases as the temperature increases.     

Phase diagram of self-assembled rigid rods on two-dimensional lattices: theory and Monte Carlo simulations

Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a two-dimensional system of particles with two bonding sites that, by decreasing temperature or increasing density, polymerize reversibly into chains with discrete orientational degrees of freedom and, at the same time, undergo a continuous isotropic-nematic (IN) transition. A complete phase diagram was obtained as a function of temperature and density. The numerical results were compared with mean field (MF) and real space renormalization group (RSRG) analytical predictions about the IN transformation. While the RSRG approach supports the continuous nature of the transition, the MF solution predicts a first-order transition line and a tricritical point, at variance with the simulation results.     

Coarse-grained model for phospholipid/cholesterol bilayer

We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system. We find that the coarse-grained model for the DPPC/cholesterol bilayer is substantially more efficient than atomistic models, providing a speedup of approximately eight orders of magnitude. The results are in favor of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the experimental phase diagram of the system. We also explore the limits of the coarse-grained model, and discuss the general validity and applicability of the present approach.     

Coarse-grained lattice kinetic Monte Carlo simulation of systems of strongly interacting particles

A general approach is presented for spatially coarse-graining lattice kinetic Monte Carlo (LKMC) simulations of systems containing strongly interacting particles. While previous work has relied on approximations that are valid in the limit of weak interactions, here we show that it is possible to compute coarse-grained transition rates for strongly interacting systems without a large computational burden. A two-dimensional square lattice is employed on which a collection of (supersaturated) strongly interacting particles is allowed to reversibly evolve into clusters. A detailed analysis is presented of the various approximations applied in LKMC coarse graining, and a number of numerical closure rules are contrasted and compared. In each case, the overall cluster size distribution and individual cluster structures are used to assess the accuracy of the coarse-graining approach. The resulting closure approach is shown to provide an excellent coarse-grained representation of the systems considered in this study.     

Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system

The computational costs associated with performing molecular dynamics (MD) simulations are still somewhat prohibitive and therefore limit the time and length scales that can be currently achieved. One approach to overcoming the limited size and duration of a simulation is to reduce the amount of detail when representing a system of interest, generally termed "coarse-graining". An alternative approach is via more efficient sampling methods that offer an enhanced search of a complex multidimensional energy landscape. One could also combine enhanced sampling methods with a coarse-grained (CG) force field. Here, we apply generalized shadow hybrid Monte Carlo (GSHMC), a recently proposed simulation protocol, to a biomolecular system of moderate size and show that GSHMC offers improved sampling compared to standard MD simulation. Our test system is a CG representation of a small peptide toxin interacting with a phospholipid bilayer. Specifically, we show that GSHMC allows for a quicker localization of the toxin to its equilibrium location of interaction at the headgroup/water interface of the bilayer. GSHMC therefore potentially allows for future exploration of larger and more complex systems over longer periods, which would otherwise be impractical to perform using conventional simulation methodology.     

A lattice-gas model for halide adsorption on single-crystal electrodes

A lattice-gas model is described for the adsorption of halides on single-crystal electrodes. The lateral interactions between the adsorbed halides include a short-range nearest-neighbor interaction and a long-range electrostatic interaction. By Monte Carlo simulations the model is used to fit the experimental isotherm of bromide adsorption on Ag(100), giving information about the relative importance of the long-range and short-range interactions. The model reproduces the order–disorder transition observed experimentally, and the way in which the long-ranged interactions influence the properties of this phase transition is discussed. The Monte Carlo simulations are also compared to analytical mean-field and quasi-chemical approximations to the isotherm. Finally, the kinetics of the disorder–order transition are studied by dynamic Monte Carlo simulations, and some results on isotherms and ordered phases on (110) and (111) surfaces are described.     

Microscopic approaches to liquid nitromethane detonation properties

In this paper, thermodynamic and chemical properties of nitromethane are investigated using microscopic simulations. The Hugoniot curve of the inert explosive is computed using Monte Carlo simulations with a modified version of the adaptative Erpenbeck equation of state and a recently developed intermolecular potential. Molecular dynamic simulations of nitromethane decomposition have been performed using a reactive potential, allowing the calculation of kinetic rate constants and activation energies. Finally, the Crussard curve of detonation products as well as thermodynamic properties at the Chapman-Jouguet (CJ) point are computed using reactive ensemble Monte Carlo simulations. Results are in good agreement with both thermochemical calculations and experimental measurements.     

Mode excitation Monte Carlo simulations of mesoscopically large membranes

Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is limited by the slow relaxation time of the longest bending mode. Here, we present a Monte Carlo algorithm with update moves in which all the lipids are simultaneously displaced. These collective moves result in fast excitation and relaxation of the long wavelength thermal fluctuations. We apply the method to simulations of a bilayer membrane with linear size of approximately 50 nm and show reduction in the relaxation time by two orders of magnitudes when compared to conventional Monte Carlo.     

Phase behavior of linear heterogeneous trimers on a square lattice

Monte Carlo simulations in the grand canonical ensemble, the multiple-histogram analysis and finite-size scaling techniques have been used to study a phase behavior of trimer BAB on a square lattice. The systems with the same energies u(AA) = u(BB) and different strengths of interactions between unlike segments are considered. The AB-contacts are energetically unprofitable. There are two phase transitions: the first-order vapor-liquid transition and the second-order structural transition in the supercritical fluid. The phase diagram topology depends on the energy u(AB). The crossover between the tricritical point phase diagram topology and the critical end phase diagram topology is found. It is demonstrated that the transition to the ordered strip-like phase is non-universal.     

Isotropic-nematic phase transition in the Lebwohl-Lasher model from density of states simulations

Density of states Monte Carlo simulations have been performed to study the isotropic-nematic (IN) transition of the Lebwohl-Lasher model for liquid crystals. The IN transition temperature was calculated as a function of system size using expanded ensemble density of states simulations with histogram reweighting. The IN temperature for infinite system size was obtained by extrapolation of three independent measures. A subsequent analysis of the kinetics in the model showed that the transition occurs via spinodal decomposition through aggregation of clusters of liquid crystal molecules.     

Density-functional theory and Monte Carlo simulation study on the electric double layer around DNA in mixed-size counterion systems

A density-functional approach and canonical Monte Carlo simulations are presented for describing the ionic microscopic structure around the DNA molecule immersed in mixed-size counterion solutions. In the density-functional approach, the hard-sphere contribution to the Helmholtz energy functional is obtained from the modified fundamental measure theory [Y.-X. Yu and J. Z. Wu, J. Chem. Phys. 117, 10156 (2002)], and the electrostatic contribution is evaluated through a quadratic functional Taylor expansion. The new theory is suitable to the systems containing ions of arbitrary sizes and valences. In the established canonical Monte Carlo simulation, an iterative self-consistent method is used to evaluate the long-range energy, and another iterative algorithm is adopted to obtain desired bulk ionic concentrations. The ion distributions from the density-functional theory (DFT) are in good agreement with those from the corresponding Monte Carlo (MC) simulations. It is found that the ratio of the bulk concentrations of two species of counterions (cations) makes significant contribution to the ion distributions in the vicinity of DNA. Comparisons with the electrostatic potential profiles from the MC simulations show that the accuracy of the DFT becomes low when a small divalent cation exists. Both the DFT and MC simulation results illustrate that the electrostatic potential at the surface of DNA increases as the anion diameter or the total cation concentration is increased and decreases as the diameter of one cation species is increased. The calculation of electrostatic potential using real ion diameters shows that the accuracy of DFT predictions for divalent ions is also acceptable.     

Thin-thick surface phase coexistence and boundary tension of the square-well fluid on a weak attractive surface

Prewetting transition is studied for the square-well fluid of attractive-well diameter lambda(ff)sigma(ff)=1.5 in the presence of a homogeneous surface modeled by the square-well potential of attractive well from 0.8sigma(ff) to 1.8sigma(ff). We investigate surface phase coexistence of thin-thick film transition using grand-canonical transition matrix Monte Carlo (GC-TMMC) and histogram reweighting techniques. Molecular dynamics (MD) and GC-TMMC are utilized to predict the properties of the fluid for various surface fluid affinities. Occurrences of prewetting transition with the variation of surface affinity are observed for a domain of reduced temperature from T(*)=0.62 to 0.75. We have used MD and GC-TMMC+finite size scaling (FSS) simulations to calculate the boundary tension as a function of temperature as well as surface affinity. Boundary tensions via MD and GC-TMMC+FSS methods are in good agreement. The boundary tension increases with the decrease of wall-fluid affinity. Prewetting critical properties are calculated using rectilinear diameter approach and scaling analysis. We found that critical temperature and density increase with the decrease of wall-fluid affinity.     

A hybrid all-atom/coarse grain model for multiscale simulations of DNA

Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulations. Our method allows us to forthrightly link a state-of-the-art force field for AA simulations of DNA with a CG representation developed by our group. We show that no modification is needed for any of the existing residues (neither AA nor CG). Only the bonding parameters at the hybrid interface are enough to produce a smooth transition of electrostatic, mechanic and dynamic features in different AA/CG systems, which are studied by molecular dynamics simulations using an implicit solvent. The simplicity of the approach potentially permits us to study the effect of mutations/modifications as well as DNA binding molecules at the atomistic level within a significantly larger DNA scaffold considered at the CG level. Since all the interactions are computed within the same classical Hamiltonian, the extension to a quantum/classical/coarse-grain multilayer approach using QM/MM modules implemented in widely used simulation packages is straightforward.     

Liquid-liquid phase transitions in supercooled water studied by computer simulations of various water models

Liquid-liquid and liquid-vapor coexistence regions of various water models were determined by Monte Carlo (MC) simulations of isotherms of density fluctuation-restricted systems and by Gibbs ensemble MC simulations. All studied water models show multiple liquid-liquid phase transitions in the supercooled region: we observe two transitions of the TIP4P, TIP5P, and SPCE models and three transitions of the ST2 model. The location of these phase transitions with respect to the liquid-vapor coexistence curve and the glass temperature is highly sensitive to the water model and its implementation. We suggest that the apparent thermodynamic singularity of real liquid water in the supercooled region at about 228 K is caused by an approach to the spinodal of the first (lowest density) liquid-liquid phase transition. The well-known density maximum of liquid water at 277 K is related to the second liquid-liquid phase transition, which is located at positive pressures with a critical point close to the maximum. A possible order parameter and the universality class of liquid-liquid phase transitions in one-component fluids are discussed.     

Configurational temperature and local properties of the anisotropic Gay-Berne liquid crystal model: applications to the isotropic liquid/vapor interface and isotropic/nematic transition

Molecular simulations in the isothermal statistical ensembles require that the macroscopic thermal and mechanical equilibriums are respected and that the local values of these properties are constant at every point in the system. The thermal equilibrium in Monte Carlo simulations can be checked through the calculation of the configurational temperature, k(B)T(conf)=<|?(r)U(r(N))|(2)>/, where ?(r) is the nabla operator of position vector r. As far as we know, T(conf) was never calculated with the anisotropic Gay-Berne potential, whereas the calculation of T(conf) is much more widespread with more common potentials (Lennard Jones, electrostatic, ...). We establish here an operational expression of the macroscopic and local configurational temperatures, and we investigate locally the isotropic liquid phase, the liquid?/?vapor interface, and the isotropic-nematic transition by Monte Carlo simulations.