Hybrid monte carlo method for simulation of two-component aerosol coagulation and phase segregation

The paper presents the development of a hybrid Monte Carlo (MC) method for the simulation of the simultaneous coagulation and phase segregation of an immiscible two-component binary aerosol. The model is intended to qualitatively model our prior studies of the synthesis of mixed metal oxides for which phase-segregated domains have been observed in molten nanodroplets. In our previous works (J. Aerosol Sci.32, 1479 (2001); Chem. Eng. Sci.56, 5763 (2001); submitted for publication) we developed sectional and monodisperse models where the internal state of the aerosol particles was described. These methods have certain limitations and it is difficult to include additional physical effects into the framework. Our new approach combines both constant volume and constant number Monte Carlo methods. Similar to our previous models, we assume that the phase segregation is kinetically controlled. The MC approach allows us to compute the mean number of enclosures (minor phase) per droplet, average enclosure volume, and the width of the enclosure size distribution. The results show that asymptotic behavior of enclosure distribution exists that is independent of initial conditions, which is very close to the continuum self-preserving distribution. Temperature is a key parameter because it allows for a significant change in the internal transport rate within each droplet. In particular, increasing the temperature significantly enhances the Brownian coagulation rate and lowers the number of enclosures per droplet. As a result, the MC results indicate that the growth of the minor phase can be moderated quite dramatically by small changes in system temperature. These results serve to illustrate the utility of this synthesis approach to the controlled growth of nanoparticles through the use of a majority matrix to slow down the encounter frequency of the minor phase and therefore its particle size.     

NMR and monte carlo simulation studies of water adsorption dynamics

Nuclear magnetic resonance water proton spin-spin relaxation time T(2) was measured in wood samples with moisture contents ranging from 0.50 to 26.4%. The experimental results are discussed in terms of Monte Carlo simulations, which determine the correlation times tau for reorientation of the water molecule proton-proton vectors. We demonstrate that 1/T(2) and tau qualitatively follow the same behavior with surface hydration. The common application of the multisite exchange model to hydrated systems is discussed in light of the new results.     

Statics and dynamics of dense polymer systems studied by monte carlo simulation

Monte Carlo simulations of coarse–grained models of macromolecules offer a unique tool to study the interplay between coil conformations, thermodynamic properties, and chain configurational relaxation and diffusion. Two examples are discussed where the chain conformation strongly differs from a gaussian coil: (i) collapsed chains in a bad solvent, where anomalous diffusion occurs in the Rouse limit and the relaxation time increases at least with the third power of chain length. (ii) Expulsion of a chain from a semidilute polymer brush. The initially stretched chain contracts to a gaussian coil and the center of mass moves outward with constant velocity until it reaches the region of the “last blob” where crossover to diffusive behavior occurs.     

用界面几何约束的多起点蒙特卡罗方法对蛋白质/ 短肽识别体系的对接计算

提出了一个界面几何约束的多起点蒙特卡罗构象搜索方法,并把这个方法用于三个丝氨酸蛋白酶/短肽抑制剂体系的刚性、部分柔性和全部柔性对接计算中。我们的方法成功地预测出了接近晶体结构的配体构象。与没有几何约束相比,我们的几何约束蒙特卡罗方法显示出了更好的收敛性质。     

Grand canonical monte carlo simulation study of water adsorption in silicalite at 300 K

This molecular simulation work focuses on the adsorption of water in a priori hydrophobic silicalite-1, a microporous ordered silica. The water-water interactions are described with the SPC model, while water-silica interactions are calculated in the framework of the PN-TrAZ model. The water adsorption isotherm at 300 K, the configurational energies, and the isosteric heat of adsorption are calculated by the grand canonical Monte Carlo (GCMC) simulation method. The thermodynamic integration scheme allows one to calculate the grand potential along the adsorption isotherm. The adsorption results are compared with experiments, showing only qualitative agreement. Indeed, the simulations do not reproduce the expected hydrophobicity of silicalite (Eroshenko, V.; Regis, R.-C.; Soulard, M.; Patarin, J. C. R. Phys. 2002, 3, 111). This indicates that common models used to describe confined polar molecules are far from being operative. In this work, it is shown, on the basis of periodic ab initio calculations, that confined water molecules in silicalite have a dipole value roughly 10% smaller than that in the bulk liquid phase, indicating that the environment felt by a confined water molecule in silicalite pores is not equivalent to that in the bulk liquid. This suggests that effective intermolecular potentials parametrized for bulk water are inefficient to describe ultraconfined water molecules. Reducing the SPC water dipole moment by 5% (i.e., decreasing water partial charges in magnitude) in GCMC calculations does allow reproducing the experimental water/silicalite isotherm at 300 K.     

On the use of the gaussian chain as a monte carlo simulation model for the equilibrium properties of polymer solutions

We have explored the performance of a simulation model for Gaussian chains at different concentrations in a good solvent. The Gaussian statistics for the distances between contiguous beads in the model is directly implemented in the individual moves of a Monte Carlo algorithm. When the results of conformational properties for the Gaussian model are compared with those provided by a freely jointed model in the same conditions, significant differences arise at finite concentrations. The modeled Gaussian chain yields incorrect results for the quadratic average dimensions 〈R²〉 and 〈S²〉 at high concentrations, but correctly reproduces the results for the scaled end-to-end distance distribution function at any concentration, showing the effects of the screening of excluded volume when concentration increases. The reason for the wrong behavior of the simulated Gaussian model comes from a strong distortion of the “bond distance” distribution as a result of the concentration increase. We conclude that this model can only be safely applied to infinitely dilute solutions.     

Grand canonical monte carlo simulation study of methane adsorption at an open graphite surface and in slit-like carbon pores at 273 K

Grand canonical Monte Carlo (GCMC) simulation was used for the systematic investigation of the supercritical methane adsorption at 273 K on an open graphite surface and in slit-like micropores of different sizes. For both considered adsorption systems the calculated excess adsorption isotherms exhibit a maximum. The effect of the pore size on the maximum surface excess and isosteric enthalpy of adsorption for methane storage at 273 K is discussed. The microscopic detailed picture of methane densification near the homogeneous graphite wall and in slit-like pores at 273 K is presented with selected local density profiles and snapshots. Finally, the reliable pore size distributions, obtained in the range of the microporosity, for two pitch-based microporous activated carbon fibers are calculated from the local excess adsorption isotherms obtained via the GCMC simulation. The current systematic study of supercritical methane adsorption both on an open graphite surface and in slit-like micropores performed by the GCMC summarizes recent investigations performed at slightly different temperatures and usually a lower pressure range by advanced methods based on the statistical thermodynamics.     

Absorption and engulfing transitions in nanoparticle infiltration into a polymer brush: A monte carlo simulation

We study the structure of an infiltrating hard spherical nanoparticle into a polymer brush using extensive off‐lattice Monte Carlo simulations of a basic theoretical model. We show that as long as the spherical particle is coated with a surface layer that interacts attractively with brush monomers, it can penetrate deeply into a dense polymer brush near the grafting surface. The infiltration process contains two stages: diffusing nanoparticle absorbing onto the surface of the polymer brush and engulfing of the nanoparticle by polymer chains. After the nanoparticle fully immerses in the dense polymer brush region, the buoyant forces levels off because of symmetric repulsions that endows increasing nanoparticle mobility and encourages the second transition. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Effects of chain flexibility on polymer conformation in dilute solution studied by lattice monte carlo simulation

Effects of chain flexibility on the conformation of homopolymers in good solvents have been investigated by Monte Carlo simulation. Bond angle constraint coupled with persistence length of polymer chains has been introduced in the modified eight-site bond fluctuation simulation model. The study about the effects of chain flexibility on polymer sizes reveals that the orientation of polymer chains under confinement is driven by the loss of conformation entropy.The conformation of polymer chains undergoing a gradual change from spherical iso-diametric ellipsoid to rodlike iso-diametric ellipsoid with the decrease of polymer chain flexibility in a wide region has been clearly illustrated from several aspects. Furthermore, a comparison of the freely jointed chain (FJC) model and the wormlike chain (WLC) model has also been made to describe the polymer sizes in terms of chain flexibility and quasi-quantitative boundary toward the suitability of the models.     

Competition between liquid-crystalline ordering and glassy freezing in melts of semiflexible polymers: A monte carlo simulation

We present results of a Monte Carlo simulation of dense melts of semi-flexible polymers using the bond-fluctuation model. The chosen Hamiltonian increases the chain stiffness upon cooling which in turn leads to glass-transition like freezing of the polymer mobility. Employing an efficient simulation algorithm, which is able to equilibrate the simulated systems to lower temperature than the Rouse-type algorithm showing the glassy freezing, we are able to observe an isotropic-nematic phase transition. This transition lies above the glass transition temperature one would extrapolate from the observed freezing behavior.     

Surface excitations involving headgroup conformations and molecular protrusions. a monte carlo study of surface forces.

The force between two parallel zwitterionic surfaces has been calculated using Monte Carlo computer simulations. The zwitterions are modelled as two oppositely charged hard spheres joined by a string of length L with parameters chosen to mimic a phospholipid system. All centers interact by a homogeneous Coulomb interaction and by a hard sphere exclusion. The anchoring of the negative centers to the surfaces has been treated within two different models. They were either anchored by a parabolic potential or by a protrusion potential, i.e., a potential proportional to the distance between the center and the surface. The latter model gives a more realistic picture of the interaction between amphiphilic surfaces in aqueous solution but here only repulsive forces could be calculated. The first model also allowed the calculation of attractive forces.For distances D between the surfaces, as defined by the location of the negative centers, that are larger than 2L there is an attractive force of the classical van der Waals type. When, on the other hand, D < 2L a strong repulsive force appears, which in the limit D ⪡ 2L is analogous to a double layer force.Recently it was suggested (Israelachvili and Wennerström, Langmuir, 6 (1990) 873 ) that the repulsive so called hydration force observed for biological lipid systems has its origin in confinements of surface excitations induced by a second surface. Here we demonstrate how this mechanism works in a particular microscopic model of the surface and we show that it gives an important contribution to the total force. Although still simplistic several qualitative features of the force in the phospholipid systems are reproduced in the calculations. For example, a reduction of the size of the charged centers leads to a decrease in the repulsive force. This mimics the observed difference between phosphatidyl choline and phosphatidyl ethanolamine.     

Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy, S, and free energy, F, from a trajectory generated by any simulation technique. HSMC was applied initially to fluids (argon and water) and later to peptides and self-avoiding walks on a lattice. In this paper we make a step further and apply it to a model of decaglycine (at T = 300 K) in vacuum with constant bond lengths where external stretching forces are exerted at the end points; the changes in S and F are calculated as the forces are increased. The molecule is placed initially in a helical structure, which is changed to an extended structure after a short simulation time due to the exerted forces. This study has relevance to problems in polymers (e.g., rubber elasticity) and to the analysis of experiments where individual molecules are stretched by atomic force microscopy (AFM), for example. The results for S and F are accurate and are significantly better than those obtained by the quasi-harmonic approximation and the local states method. However, the molecule is quite stiff due to the strong bond angle potentials and the extensions are small even for relatively large forces. Correspondingly, as the force is increased the decrease in the entropy is relatively small while the potential energy is enhanced significantly. Still, differences, TDeltaS, for different forces are obtained with very good accuracy of approximately 0.2 kcal/mol.     

Scaled equations for the coexistence curve,the capillary constant and the surface tension of n-alkanes

A review of experimental data of several fluids shows that their coexistence curve follows a power law in reduced temperature at the approach of the critical point, with an universal exponent equal to 0.325, their capillary constant a power law with an universal exponent equal to 0.925 and their surface tension a power law with an universal exponent equal to 1.26. In the critical region, the concept of two-scale-factor universality was used to predict the density difference amplitude, the capillary constant amplitude, and the surface tension amplitude between near critical vapor and liquid phases. A comparison with amplitudes determined from experimental data is given. In order to extend this universality all along the liquid–gas coexistence curve from the triple point to the critical point for n-alkanes, a mean field approximation was used far away from T_C. We show that the density difference, the capillary constant and the surface tension can be calculated with a reasonable accuracy by generalized scaled equations adding only two empirical constants. A comparison between calculated and experimental data is presented.     

Vapor-liquid phase coexistence and transport properties of two-dimensional oligomers

Grand-canonical transition-matrix Monte Carlo and histogram reweighting techniques are used herein to study the vapor-liquid coexistence properties of two-dimensional (2D) flexible oligomers with varying chain lengths (m = 1-8). The phase diagrams of the various 2D oligomers follow the correspondence state (CS) principle, akin to the behavior observed for bulk oligomers. The 2D critical density is not influenced by the oligomer chain length, which contrasts with the observation for the bulk oligomers. Line tension, calculated using Binder's formalism, in the reduced plot is found to be independent of chain length in contrast to the 3D behavior. The dynamical properties of 2D fluids are evaluated using molecular dynamics simulations, and the velocity and pressure autocorrelation functions are investigated using Green-Kubo (GK) relations to yield the diffusion and viscosity. The viscosity determined from 2D non-equilibrium molecular dynamics simulation is compared with the viscosity estimated from the GK relations. The GK relations prove to be reliable and efficient for the calculation of 2D transport properties. Normal diffusive regions are identified in dense oligomeric fluid systems. The influence of molecular size on the diffusivity and viscosity is found to be diminished at specific CS points for the 2D oligomers considered herein. In contrast, the viscosity and diffusion of the 3D bulk fluid, at a reduced temperature and density, are strongly dependent on the molecular size at the same CS points. Furthermore, the viscosity increases and the diffusion decreases multifold in the 2D system relative to those in the 3D system, at the CS points.     

Neutron scattering and monte carlo determination of the variation of the critical nucleus size with quench depth

We have used a combination of neutron scattering experiments and Monte Carlo simulations to study the initial stages of first-order phase transitions. We focus on quenches wherein the nascent phase is formed by homogeneous nucleation, and we approach the spinodal, i.e., the quench depth at which the original phase becomes unstable. In this regime, we show how critical nuclei sizes are determined from neutron scattering structure factors. Prevailing thought is that the size of the critical nucleus should increase with increasing quench depth and diverge at the spinodal. To the contrary, our experiments and simulations indicate that the critical nucleus size decreases monotonically as quench depth is increased and is finite at the spinodal.     

Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics

Self‐assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self‐organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self‐organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN Explorer (MesoBioNano Explorer) aiming to provide a universal approach to study self‐assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN Explorer that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three‐dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. © 2014 Wiley Periodicals, Inc.     

The evaluation of probabilistic classification methods : Part 1. A monte carlo study with ALLOC

Probabilistic classification (i.e., classification of individuals into one of several groups by assigning probabilities of classification to each individual) is desirable when the main interest is in individuals rather than the whole group. The evaluation of probabilistic assignments is described in detail, including statistical features such as measures for the sharpness of the classification, the predictive ability and the reliability of the probability values. In a simulation study, the influence of the objects—variable ratio and the interclass distance on the results was examined for the training data themselves (resubstitution method), an independent test set, and a pseudo-independent test set created from the training set (leave-one-out method). The results indicate that the leave-one-method can often be used instead of an independent test set. In many cases, the assignments cited as probabilities are not probabilities at all, because the classification system is too over-confident.     

Quantum monte carlo study of heats of formation and bond dissociation energies of small hydrocarbons

A quantum Monte Carlo (QMC) benchmark study of heats of formation at 298 K and bond dissociation energies (BDEs) of 22 small hydrocarbons is reported. Diffusion Monte Carlo (DMC) results, obtained using a simple product trial wavefunctions consisting of a single determinant and correlation function, are compared to experiment and to other theory including a version of complete basis set theory (CBS‐Q) and density functional theory (DFT) with the B3LYP functional. For heats of formation, the findings are a mean absolute deviation from experiment of 1.2 kcal/mol for CBS‐Q, 2.0 kcal/mol for B3LYP, and 2.2 kcal/mol for DMC. The mean absolute deviation of 31 BDEs is 2.0 kcal/mol for CBS‐Q, 4.2 kcal/mol for B3LYP, and 2.5 kcal/mol for DMC. These findings are for 17 BDEs of closed‐shell molecules that have mean absolute deviations from experiment of 1.7 kcal/mol (CBS‐Q), 4.0 kcal/mol (B3LYP), and 2.2 kcal/mol (DMC). The corresponding results for the 14 BDEs of open‐shell molecules studied are 2.4 kcal/mol (CBS‐Q), 4.3 kcal/mol (B3LYP), and 2.9 kcal/mol (DMC). The DMC results provide a baseline from which improvement using multideterminant trial functions can be measured. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 583–592, 2005     

Adhesion and tack of polymers: Influence of mechanical properties and surface tensions

The adhesion of various polymers used as model adhesives, polyisobutylene, polyacrylates etc. has been investigated by means of an apparatus measuring the adhesive failure energyw in dependence on contact time, contact pressure, rate of separation, and temperature. The adhesive failure energy of adhesive joints formed with low contact pressure during a short contact time is called tack. After a sufficiently long contact time and with a high bonding pressure an adhesive joint exhibits its maximum energy of separationw _m .The viscoelastic properties of the model adhesives were characterized by creep experiments in dependence on time and temperature. The surface tension of the polymer adhesives and adherents could be determined by contact angle measurements. Adhesion measurements of polyisobutylene on a number of adherents were carried out in air and in various liquids in order to obtain information about the influence of surface tension on tack and maximum adhesive failure energy. w _m can be written as the product of two terms: the thermodynamic work of adhesionW _A which is related to the surface and interfacial tensions of adhesive and adherent and a dimensionless function dependent on temperature and rate of separation which describes the viscoeleastic properties of the adhesive and which obeys the rate-temperature superposition principle known from linear viscoelasticity. The tack is related to incomplete bond formation and cannot be described in the same manner. It is, however, strongly dependent on the viscoelastic properties of the adhesive showing a maximum at about 50 to 70 °C above the glass transition temperature. It is, moreover, influenced by the compliance in the plateau range above the glass transition which is determined by the entanglement network of the polymer. Wetting of the adherent by the adhesive is a further important condition for high tack values which is fulfilled if the adherent has a higher surface tension than the adhesive.