An Efficient Cell List Implementation for Monte Carlo Simulation on GPUs

Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance improvements often require algorithmic redesigns to more closely exploit the target architecture. In this paper, we focus on efficient molecular simulations for the GPU and propose a novel cell list algorithm that better utilizes its parallel resources. Our goal is an efficient GPU implementation of large-scale Monte Carlo simulations for the grand canonical ensemble. This is a particularly challenging application because there is inherently less computation and parallelism than in similar applications with molecular dynamics. Consistent with the results of prior researchers, our simulation results show traditional cell list implementations for Monte Carlo simulations of molecular systems offer effectively no performance improvement for small systems [5, 14], even when porting to the GPU. However for larger systems, the cell list implementation offers significant gains in performance. Furthermore, our novel cell list approach results in better performance for all problem sizes when compared with other GPU implementations with or without cell lists.Comment: 30 page

Monte Carlo Simulations in Multibaric-Multithermal Ensemble

We propose a new generalized-ensemble algorithm, which we refer to as the multibaric-multithermal Monte Carlo method. The multibaric-multithermal Monte Carlo simulations perform random walks widely both in volume space and in potential energy space. From only one simulation run, one can calculate isobaric-isothermal-ensemble averages at any pressure and any temperature. We test the effectiveness of this algorithm by applying it to the Lennard-Jones 12-6 potential system with 500 particles. It is found that a single simulation of the new method indeed gives accurate average quantities in isobaric-isothermal ensemble for a wide range of pressure and temperature.Comment: 8 pages, (RevTeX), 5 figure

Surface critical behavior of fluids: Lennard-Jones fluid near weakly attractive substrate

The phase behavior of fluids near weakly attractive substrates is studied by computer simulations of the coexistence curve of a Lennard-Jones (LJ) fluid confined in a slitlike pore. The temperature dependence of the density profiles of the LJ fluid is found to be very similar to the behavior of water near hydrophobic surfaces (Brovchenko et al. J.Phys.: Cond.Matt. v.16, 2004). A universal critical behavior of the local order parameter, defined as the difference between the local densities of the coexisting liquid and vapor phases at some distance z from the pore walls, Deltarho(z) = (rho_l(z) - rho_v(z))/2, is observed in a wide temperature range and found to be consistent with the surface critical behavior of the Ising model. Near the surface the dependence of the order parameter on the reduced temperature tau = (T_c - T)/T_c obeys a scaling law ~ tau^(beta_1) with a critical exponent beta_1 of about 0.8, corresponding to the ordinary surface transition. A crossover from bulk-like to surface-like critical behavior with increasing temperature occurs, when the correlation length is about half the distance to the surface. Relations between the ordinary and normal transitions in Ising systems and the surface critical behavior of fluids are discussed.Comment: 14 pages, 19 figures, submitted to PR

Simple model of adsorption on external surface of carbon nanotubes: a new analytical approach basing on molecular simulation data

Nitrogen adsorption on carbon nanotubes is wide- ly studied because nitrogen adsorption isotherm measurement is a standard method applied for porosity characterization. A further reason is that carbon nanotubes are potential adsorbents for separation of nitrogen from oxygen in air. The study presented here describes the results of GCMC simulations of nitrogen (three site model) adsorption on single and multi walled closed nanotubes. The results obtained are described by a new adsorption isotherm model proposed in this study. The model can be treated as the tube analogue of the GAB isotherm taking into account the lateral adsorbate-adsorbate interactions. We show that the model describes the simulated data satisfactorily. Next this new approach is applied for a description of experimental data measured on different commercially available (and characterized using HRTEM) carbon nanotubes. We show that generally a quite good fit is observed and therefore it is suggested that the observed mechanism of adsorption in the studied materials is mainly determined by adsorption on tubes separated at large distances, so the tubes behave almost independently

Molecular simulation of carbon dioxide adsorption in chemically and structurally heterogeneous porous carbons

Capture of carbon dioxide from fossil fuel power plants via adsorption and sequestration of carbon dioxide in unmineable coal seams are achievable near-term methods of reducing atmospheric emissions of this greenhouse gas. To investigate the influence of surface heterogeneity upon predicted adsorption behavior in activated carbons and coal, isotherms were generated via grand canonical Monte Carlo simulation for CO 2 adsorption in slit-shaped pores with underlying graphitic structure and several variations of chemical heterogeneity (oxygen and hydrogen content), pore width, and surface functional group orientation. Adsorption generally increased with increasing surface oxygen content, although exceptions to this trend were observed on structurally heterogeneous surfaces with holes or furrows that yield strongly adsorbing preferred binding sites. Among the heterogeneous pore structures investigated, those with coal-like surfaces adsorbed carbon dioxide more strongly than planar, homogeneous graphitic slit pores of comparable width. Electrostatic adsorbate–adsorbent interactions significantly influenced adsorption onto model surfaces. © 2006 American Institute of Chemical Engineers Environ Prog, 25: 343–354, 2006Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55883/1/10168_ftp.pd

Homogeneous Bubble Nucleation driven by local hot spots: a Molecular Dynamics Study

We report a Molecular Dynamics study of homogenous bubble nucleation in a Lennard-Jones fluid. The rate of bubble nucleation is estimated using forward-flux sampling (FFS). We find that cavitation starts with compact bubbles rather than with ramified structures as had been suggested by Shen and Debenedetti (J. Chem. Phys. 111:3581, 1999). Our estimate of the bubble-nucleation rate is higher than predicted on the basis of Classical Nucleation Theory (CNT). Our simulations show that local temperature fluctuations correlate strongly with subsequent bubble formation - this mechanism is not taken into account in CNT

Monte Carlo Methods for Estimating Interfacial Free Energies and Line Tensions

Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal growth, etc.). This article reviews two methods to estimate both interfacial free energies and line tensions by Monte Carlo simulations of simple models, (e.g. the Ising model, a symmetrical binary Lennard-Jones fluid exhibiting a miscibility gap, and a simple Lennard-Jones fluid). One method is based on thermodynamic integration. This method is useful to study flat and inclined interfaces for Ising lattices, allowing also the estimation of line tensions of three-phase contact lines, when the interfaces meet walls (where "surface fields" may act). A generalization to off-lattice systems is described as well. The second method is based on the sampling of the order parameter distribution of the system throughout the two-phase coexistence region of the model. Both the interface free energies of flat interfaces and of (spherical or cylindrical) droplets (or bubbles) can be estimated, including also systems with walls, where sphere-cap shaped wall-attached droplets occur. The curvature-dependence of the interfacial free energy is discussed, and estimates for the line tensions are compared to results from the thermodynamic integration method. Basic limitations of all these methods are critically discussed, and an outlook on other approaches is given

A New Method for the Generation of Realistic Atomistic Models of Siliceous MCM-41

A new method is outlined for constructing realistic models of the mesoporous amorphous silica adsorbent, MCM-41. The procedure uses the melt-quench molecular dynamics technique. Previous methods are either computationally expensive or overly simplified, missing key details necessary for agreement with experimental data. Our approach enables a whole family of models spanning a range of pore widths and wall thicknesses to be efficiently developed and yet sophisticated enough to allow functionalisation of the surface – necessary for modelling systems such as self-assembled monolayers on mesoporous supports (SAMMS), used in nuclear effluent clean-up. The models were validated in two ways. The first method involved the construction of adsorption isotherms from grand canonical Monte Carlo simulations, which were in line with experimental data. The second method involved computing isosteric heats at zero coverage and Henry law coefficients for small adsorbate molecules. The values obtained for carbon dioxide gave good agreement with experimental values. We use the new method to explore the effect of increasing the preparation quench rate, pore diameter and wall thickness on low pressure adsorption. Our results show that tailoring a material to have a narrow pore diameter can enhance the physisorption of gas species to MCM-41 at low pressure

Porosity of closed carbon nanotubes compressed using hydraulic pressure

Experimental data of nitrogen adsorption (T = 77.3 K) from gaseous phase measured on commercial closed carbon nanotubes are presented. Additionally, we show the results of N2 adsorption on compressed (using hydraulic press) CNTs. In order to explain the experimental observations the results of GCMC simulations of N2 adsorption on isolated or bundled multi-walled closed nanotubes (four models of bundles) are discussed. We show that the changes of the experimental adsorption isotherms are related to the compression of the investigated adsorbents. They are qualitatively similar to the theoretical observations. Taking into account all results it is concluded that in the "architecture" of nanotubes very important role has been played by isolated nanotubes