2-D islanding of dodecane on an Au(111) surface: an investigation using he beam reflectivity and Monte Carlo modeling

Dodecane is deposited at submonolayer coverages onto an Au(111) surface forming two-dimensional (2-D) islands. The islands sublimate to a 2-D gas at higher substrate temperatures. We observe island formation and subsequent 2-D sublimation between substrate temperatures of 40 and 350 K, using low-energy helium reflectivity. A computer model of the submonolayer islanding process using Monte Carlo simulations shows significant agreement with experimental data and yields an intermolecular potential of 0.10+/-0.03 eV (about half that of the bulk substance) and a significantly higher corrugation potential of 0.3+/-0.1 eV.     

Interaction between two star polymers in a good solvent

An off-lattice bead model with a hard-spheres potential is used to characterize the two-body properties of star polymers of functionalities f=4–18 in good solvent conditions through Monte Carlo simulations. The second virial results complement a previous study performed with a Lennard-Jones potential. Some intrinsic viscosity numerical data are also obtained. The second virial coefficient and viscosity data are combined in terms of a single parameter, with apparently anomalous features in terms of the star functionalities which are also observed from existing experimental data. The effective intermolecular potential is compared with a global potential recently proposed.     

Simulations of self-assembling systems

The previous focus on the thermodynamics of self-assembly of surfactants in solution through simulations is now being expanded to include phenomena in the fluid dynamic regime. This expansion implies that a formal edifice must be built to link molecular dynamics smoothly to mesoscopic and macroscopic length and time scales. We summarize and comment on recent trends in this area along with new results based on classical approaches. The latter include molecular dynamics as well as off-lattice Monte Carlo simulations and lattice-based Guggenheim-type models.     

Monte carlo simulation of polymers in steady potential flows

This work presents a study of the configurational properties of bead-spring chains in steady-state potential flows. These properties are obtained from off-lattice Monte Carlo simulations. The results of our simulations compare favourably with theoretical results for phantom chains. We investigate the effects of excluded volume and hydrodynamic interaction on the configurations of the chains, and compare our results to the predictions of scaling arguments. The scaling law observed here for the latter case deviates from theoretical predictions but is in agreement with findings reported from molecular dynamics simulations.     

Capillary Condensation in Pores with Energetically Heterogeneous Walls: Density Functional versus Monte Carlo Calculations

We investigate adsorption of a Lennard-Jones fluid in slit-like pores with energetically heterogeneous walls by using Grand Canonical Monte Carlo simulations and a density functional approach. The model of a fluid-wall potential is qualitatively similar to that invoked by R?cken et al. (J. Chem. Phys. 108, 8089, (1999); i.e., it consists of a homogeneous part that varies in the direction perpendicular to the wall and a periodic part, varying also in one direction parallel to the wall, but in contrast to the above mentioned work, both parts of the fluid-wall potential are modeled by Lennard-Jones (9, 3) type functions. The structure of the adsorbed film is characterized by local densities. We evaluate the phase diagrams for several systems characterized by different corrugation of the adsorbing potential and discuss the discrepancies between theoretical predictions and computer simulations. Copyright 2001 Academic Press.     

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.     

Structure formation in bis(terpyridine) derivative adlayers: molecule-substrate versus molecule-molecule interactions

The influence of the substrate and the deposition conditions-vapor deposition versus deposition from solution-on the structures formed upon self-assembly of deposited bis(terpyridine) derivative (2,4'-BTP) monolayers on different hexagonal substrates, including highly oriented pyrolytic graphite (HOPG), Au(111), and (111)-oriented Ag thin films, was investigated by high-resolution scanning tunneling microscopy and by model calculations of the intermolecular energies and the lateral corrugation of the substrate-adsorbate interaction. Similar quasi-quadratic network structures with almost the same lattice constants obtained on all substrates are essentially identical to the optimum configuration expected from an optimization of the adlayer structure with C-H...N-type bridging bonds as a structure-determining factor, which underlines a key role of the intermolecular interactions in adlayer order. Slight distortions from the optimum values to form commensurate adlayer structures on the metal substrates and the preferential orientation of the adlayer with respect to the substrate are attributed to the substrate-adsorbate interactions, specifically, the lateral corrugation in the substrate-adsorbate interaction upon lateral displacement and rotation of the adsorbed BTP molecules. The fact that similar adlayer structures are obtained on HOPG under ultrahigh vacuum conditions (solid|gas interface) and on HOPG in trichlorobenzene (solid|liquid interface) indicates that the intermolecular interactions are not severely affected by the solvent.     

Thermodynamics of Go-type models for protein folding

Go-type potentials, based on the inter-residue contacts present in the native structure of a protein, are frequently used to predict dynamic and structural features of the folding pathways through computer simulations. However, the mathematical form used to define the model interactions includes several arbitrary choices, whose consequences are not usually analyzed. In this work, we use a simple off-lattice protein model and a parallel tempering Monte Carlo simulation technique to carry out such analysis, centered in the thermodynamic characteristics of the folding transition. We show how the definition of a native contact has a deep impact on the presence of simple or complex transitions, with or without thermodynamic intermediates. In addition, we have checked that the width of the attractive wells has a profound effect on the free-energy barrier between the folded and unfolded states, mainly through its influence on the entropy of the denatured state.     

Simulation study of semi-crystalline polymer interphases

The study of structure and properties of semi-crystalline polymer inter-phases is important to explain and extend polymer applications. In this region, polymer chains exist in three distinct populations: tie chains that bridge the two crystals, chain folds and chain ends. The distribution of these populations influences the properties of the interphase. We have developed off-lattice Monte Carlo simulations of constrained interphases of semi-crystalline polymers which utilize robust off-lattice moves. A united atom model with polyethylene-like interactions and with freely rotating bonds is used to mimic the prototypical flexible chain structure. These simulations capture the limiting distributions of tight and loose chain folds and of tie chains within the metastable phase. The dissipation in order and density between the crystal and amorphous regions has been studied, and results for freely rotating chains indicate that the characteristic decay of anisotropy occurs in a length scale of ca. 10 Å. Simulation results for the effect of system size and molecular weight for freely rotating chains have also been investigated.     

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.     

Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations

Many structural models for the stationary phase in reversed-phase liquid chromatography (RPLC) systems have been suggested from thermodynamic and spectroscopic measurements and theoretical considerations. To provide a molecular picture of chain conformation and solvent partitioning in a typical RPLC system, a particle-based Monte Carlo simulation study is undertaken for a dimethyl octadecyl (C(18)) bonded stationary phase on a model siliceous substrate in contact with mobile phases having different methanol/water concentrations. Following upon previous simulations for gas-liquid chromatography and liquid-liquid phase equilibria, the simulations are conducted using the configurational-bias Monte Carlo method in the Gibbs ensemble and the transferable potentials for phase equilibria force field. The simulations are performed for a chain surface density of 2.9 micromol/m(2), which is a typical bonded-phase coverage for mono-functional alkyl silanes. The solvent concentrations used here are pure water, approximately 33 and 67% mole fraction of methanol and pure methanol. The simulations show that the chain conformation depends only weakly on the solvent composition. Most chains are conformationally disordered and tilt away from the substrate normal. The interfacial width increases with increasing methanol content and, for mixtures, the solvent shows an enhancement of the methanol concentration in a 10 Angstrom region outside the Gibbs dividing surface. Residual surface silanol groups are found to provide hydrogen bonding sites that lead to the formation of substrate bound water and methanol clusters, including bridging clusters that penetrate from the solvent/chain interfacial region all the way to the silica surface.     

An off-lattice, self-learning kinetic Monte Carlo method using local environments

We present a method called local environment kinetic Monte Carlo (LE-KMC) method for efficiently performing off-lattice, self-learning kinetic Monte Carlo (KMC) simulations of activated processes in material systems. Like other off-lattice KMC schemes, new atomic processes can be found on-the-fly in LE-KMC. However, a unique feature of LE-KMC is that as long as the assumption that all processes and rates depend only on the local environment is satisfied, LE-KMC provides a general algorithm for (i) unambiguously describing a process in terms of its local atomic environments, (ii) storing new processes and environments in a catalog for later use with standard KMC, and (iii) updating the system based on the local information once a process has been selected for a KMC move. Search, classification, storage and retrieval steps needed while employing local environments and processes in the LE-KMC method are discussed. The advantages and computational cost of LE-KMC are discussed. We assess the performance of the LE-KMC algorithm by considering test systems involving diffusion in a submonolayer Ag and Ag-Cu alloy films on Ag(001) surface.     

A lattice Monte Carlo simulation of the FePt alloy using a first-principles renormalized four-body interaction

Although a lattice Monte Carlo method provides an effective, simple, and fast way to study thermodynamic properties of substitutional alloys, it cannot treat by itself the off-lattice effects, such as thermal vibrations and local distortions. Therefore, even if the interaction among atoms at lattice points is calculated accurately by means of first-principles calculations, the lattice Monte Carlo simulation overestimates the order-disorder phase transition temperature. In this paper, we treat this problem in the investigation of the FePt alloy, which has recently attracted considerable interest in its magnetic properties. We apply a simple version of the potential renormalization theory to determine the interaction among atoms, including partly the off-lattice effects by means of first-principles calculations. Then, we use the interaction to perform a lattice Monte Carlo simulation of the FePt alloy on a fcc lattice. From the results, we find that the transition temperature obtained after the present renormalization procedure becomes closer to the experimental value.     

Computer simulation of linkage of two ring chains

We performed off-lattice Monte Carlo simulations of links of two model ring chains with chain length N up to 32,768 in the theta solution or amorphous bulk state by using a random walk model (Model I), and molecular dynamics simulations of two model ring chains in solution with excluded volume interaction (Model II) to investigate topological effects on the geometry of link and ring conformation. In the case of Model I, the mean squared linking number, its distribution, and the size of two chains with fixed linking number are investigated. Our simulation results confirm the previous theoretical prediction that the mean squared linking number decays as pe(-qs(2)) with the distance of centers of chain mass s, where p and q are found to be chain length dependent and q asymptotically approaches to 0.75 as chain length increases. The linking number distribution of two chains has a universal form for long chains, but our simulation results clearly show that the distribution function deviates from the Gaussian distribution, a fact not predicted by any previous theoretical work. A scaling prediction is proposed to predict the link size, and is checked for our simulations for the Model II. The simulation results confirmed the scaling prediction of the blob picture that the link with linking number m occupies a compact volume of m blobs, and the size of the link is asymptotic to R(L) ≈ bN(ν)m(1/3-ν), where N is the chain length, and v is the Flory exponent of polymer in solutions.     

Driven polymer transport through a nanopore controlled by a rotating electric field: off-lattice computer simulations

The driven translocation kinetics of a single strand polynucleotide chain through a nanopore is studied using off-lattice Monte Carlo simulations, by which the authors demonstrate a novel method in controlling the driven polymer transport through a nanopore by a rotating electric field. The recorded time series of blockade current from the driven polynucleotide transport are used to determine the sequence of polynucleotides by implementing a modified Monte Carlo algorithm, in which the energy landscape paving technique is incorporated to avoid trapping at deep local minima. It is found that only six-time series of block current are required to completely determine the polynucleotide sequence if the average missing rate (AMR) of current signals in these time series is smaller than 20%. For those time series with AMR greater than 20%, the error rate in sequencing an unknown polynucleotide decreases rapidly by increasing the number of time series. To find the most appropriate experimental conditions, the authors have investigated the dependence of AMR of current signals and qualified rate of measured time series of blockade current on various controllable experimental variables.     

Monte Carlo modeling of chiral adsorption on nanostructured chiral surfaces and slit pores

Adsorptive separation of chiral molecules is a powerful technique that has long been used in the chemical and pharmaceutical industries. An important challenge in this field is to design and optimize new adsorbents to provide selective discrimination of enantiomers. In this article, we introduce an off-lattice model of chiral adsorption on nanostructured surfaces and slit pores with the aim of predicting their enantioslective properties. The concept presented here involves finding the optimal chiral pattern of active sites on the pore walls that maximizes the difference between the binding energies of the enantiomers. Our initial effort focuses on chiral molecules that do not have specific interactions with the pore surface. One candidate meeting this requirement is 1,2-dimethylcyclopropane (DMCP), a chiral hydrocarbon whose interaction with a model pore surface was described using the Lennard-Jones potential. To model the adsorption of DMCP, we used the Monte Carlo simulation method. It was demonstrated that the separation of the enantiomers of DMCP is hardly obtainable because of the smoothness of the potential energy surface for molecules physisorbed in the pore. However, the simulated results allowed the identification of key factors that influence the binding of the enantiomers of DMCP to the pore walls with a special distribution of active sites. This information will be useful in future considerations of the adsorption of more complex chiral molecules.     

A rare event sampling method for diffusion Monte Carlo using smart darting

We identify a set of multidimensional potential energy surfaces sufficiently complex to cause both the classical parallel tempering and the guided or unguided diffusion Monte Carlo methods to converge too inefficiently for practical applications. The mathematical model is constructed as a linear combination of decoupled Double Wells [(DDW)(n)]. We show that the set (DDW)(n) provides a serious test for new methods aimed at addressing rare event sampling in stochastic simulations. Unlike the typical numerical tests used in these cases, the thermodynamics and the quantum dynamics for (DDW)(n) can be solved deterministically. We use the potential energy set (DDW)(n) to explore and identify methods that can enhance the diffusion Monte Carlo algorithm. We demonstrate that the smart darting method succeeds at reducing quasiergodicity for n ? 100 using just 1 × 10(6) moves in classical simulations (DDW)(n). Finally, we prove that smart darting, when incorporated into the regular or the guided diffusion Monte Carlo algorithm, drastically improves its convergence. The new method promises to significantly extend the range of systems computationally tractable by the diffusion Monte Carlo algorithm.     

Adlayer morphologies and free energy landscapes of clusters of bis-fullerenes on model gold surfaces

There have been a few experimental reports of self-assembled adlayers of bis-fullerene molecules on solid substrates. Most of these studies suggest the adsorbate molecules are lying down on the surface, with the fullerene moieties almost close packed. However, very little theoretical work has been carried out on such systems, and little is known about the roles played by different parts of the potential energy in driving the self-assembly. We carry out a Temperature Replica Exchange Monte Carlo study here of two representative bis-fullerene molecules on a metal substrate. We use a coarse-grained model potential energy function, in which certain parameters can be varied within the range of their experimental uncertainty. The molecules investigated consist of two fullerene moieties bonded by a rigid bridging group. In particular, the effect of the strength of the fullerene interaction E(FG) with the substrate (nominally Au(111)) has been investigated in detail. To ensure efficient sampling of the rugged potential energy surfaces encountered in the simulations, we utilize replica exchange techniques. These enable us to construct free energy landscapes for the system. We find that for relatively low values of E(FG) the molecules form standing-up adlayers. By contrast, for higher values of E(FG), lying-down adlayers dominate. For one molecule, two different crystalline adlayer morphologies have been identified. The detailed structure of the lying-down layer is a function of the temperature and of the group used to bridge the fullerene moieties.     

Influence of quantum effects on the mechanism of adsorption and phase diagram of rare gases in carbon nanotubes

We present results of grand canonical Monte Carlo simulations of rare gases (He, Ne, Ar, Kr and Xe) adsorption in carbon nanotubes. The interaction model includes both quantum effects (via effective Feymann-Hibbs potential) and the atomic roughness of the tube. We show that the quantum contribution to interactions does not suppress the energetic corrugation of carbon nanotube but decreases only its average strength. In the case of Ne, the phase diagram and, in particular, the melting temperature for layers adsorbed on and within an individual tube does not depend on tube chirality. However, the structure of layers adsorbed on outer surface of the tube is strongly related to the atomic structure of the underlying tube.     

Stability of thin polymer films: influence of solvents

The interface and surface properties and the wetting behavior of polymer-solvent mixtures are investigated using Monte Carlo simulations and self-consistent field calculations. We carry out Monte Carlo simulations in the framework of a coarse-grained bead-spring model using short chains (oligomers) of N(P)=5 beads and a monomeric solvent, N(S)=1. The self-consistent field calculations are based on a simple phenomenological equation of state for compressible binary mixtures and we employ Gaussian chain model. The bulk behavior of the polymer-solvent mixture belongs to type III in the classification of van Konynenburg and Scott [Phil. Trans. R. Soc. London, Ser. A 298, 495 (1980)]. It is characterized by a triple line on which the polymer-liquid coexists with solvent-vapor and a solvent-rich liquid. The solvent is not homogeneously distributed across the dense polymer film but tends to accumulate at the surface and the polymer-vapor interface. This solvent enrichment at the interface and surface becomes more pronounced upon increasing the vapor pressure and alters the surface and interface tensions. This effect gives rise to a nonmonotonic dependence of the contact angle on the vapor pressure and one might observe reentrant wetting. The results of the Monte Carlo simulations and the self-consistent field calculations qualitatively agree. The profiles of drops are investigated by Monte Carlo simulations and a pronounced solvent enrichment is observed at the wedge formed by the substrate and the liquid-vapor interface at the three-phase contact line.