Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Efficient desalination of water continues to be a problem facing the society. Advances in nanotechnology have led to the development of a variety of nanoporous membranes for water purification. Here we show, by performing molecular dynamics simulations, that a nanopore in a single-layer molybdenum disulfide can effectively reject ions and allow transport of water at a high rate. More than 88% of ions are rejected by membranes having pore areas ranging from 20 to 60 A(2). Water flux is found to be two to five orders of magnitude greater than that of other known nanoporous membranes. Pore chemistry is shown to play a significant role in modulating the water flux. Pores with only molybdenum atoms on their edges lead to higher fluxes, which are ∼ 70% greater than that of graphene nanopores. These observations are explained by permeation coefficients, energy barriers, water density and velocity distributions in the pores.

/pdf/water-desalination-with-a-single-layer-mos2-nanopore-3bfq4da7ix.pdf

Water desalination with a single-layer MoS2 nanopore.

Because of the atomic thinness of graphene, its integration into a device will always involve its interaction with at least one supporting substrate, making the surface energy of graphene critical to its real-life applications. In the current paper, the contact angle of graphene synthesized by chemical vapor deposition (CVD) was monitored temporally after synthesis using water, diiodomethane, ethylene glycol, and glycerol. The surface energy was then calculated based on the contact angle data by the Fowkes, Owens–Wendt (extended Fowkes), and Neumann models. The surface energy of fresh CVD graphene grown on a copper substrate (G/Cu) immediately after synthesis was determined to be 62.2 ± 3.1 mJ/m2 (Fowkes), 53.0 ± 4.3 mJ/m2 (Owens–Wendt) and 63.8 ± 2.0 mJ/m2 (Neumann), which decreased to 45.6 ± 3.9, 37.5 ± 2.3, and 57.4 ± 2.1 mJ/m2, respectively, after 24 h of air exposure. The ellipsometry characterization indicates that the surface energy of G/Cu is affected by airborne hydrocarbon contamination. G/Cu ex...

http://pubs.acs.org/doi/pdf/10.1021/la5018328

Study on the surface energy of graphene by contact angle measurements.

Cell culturing, whether for tissue engineering or cell biology studies, always involves placing cells in a non-natural environment and no material currently exist that can mimic the entire complexity of natural tissues and variety of cell-matrix interactions that is found in vivo. Here, we review the vast range of hydrogels, composed of natural or synthetic polymers that provide a route to tailored microenvironments.

25th Anniversary Article: Designer Hydrogels for Cell Cultures: A Materials Selection Guide

The present study reports on molecular dynamics investigations of chemically cross-linked poly(ethylene glycol) hydrogels with the aim of exploring the diffusion properties of water, ions, and rhodamine within the polymer at the molecular level. The water structure and diffusion properties were studied at various cross-linking densities with molecular weights of the chains ranging from 572 to 3400. As the cross-linking density is increased, the water diffusion decreases and the slowdown in diffusion is more severe at the polymer-water interface. The water diffusion at various cross-linking densities is correlated with the water hydrogen bonding dynamics. The diffusion of ions and rhodamine also decreased as the cross-linking density is increased. The variation of diffusion coefficient with cross-linking density is related to the variation of water content at different cross-linking densities. Comparison of simulation results and obstruction scaling theory for hydrogels showed similar trends.

/pdf/effect-of-cross-linking-on-the-diffusion-of-water-ions-and-10uhfe185w.pdf

Effect of cross-linking on the diffusion of water, ions, and small molecules in hydrogels.

In this study, we develop graphitic carbon-water nonbonded interaction parameters entirely from ab initio calculation data of interaction energies between graphene and a single water molecule. First, we employ the Moller-Plesset perturbation theory of the second order (MP2) method to compute the polycyclic aromatic hydrocarbon (PAH)-water interaction energies, with proper size of basis sets and energy component analysis to extrapolate to infinite-sized graphene limit. Then, we develop graphitic carbon-water interaction parameters based on the MP2 data from this work and the ab initio data available in the literature from other methods such as random-phase approximation (RPA), density functional theory-symmetry-adapted perturbation theory (DFT-SAPT), and coupled cluster treatment with single and double excitations and perturbative triples (CCSD(T)). The accuracy of the interaction parameters is evaluated by predicting water contact angle on graphite and carbon nanotube (CNT) radial breathing mode (RBM) frequency shift and comparing them with experimental data. The interaction parameters obtained from MP2 data predict the CNT RBM frequency shift that is in good agreement with experiments. The interaction parameters obtained from RPA and DFT-SAPT data predict the contact angles and the CNT RBM frequency shift that agree well with experiments. The interaction parameters obtained from CCSD(T) data underestimate the contact angles and overestimate the CNT RBM frequency shift probably due to the use of small basis sets in CCSD(T) calculations.

Graphitic carbon-water nonbonded interaction parameters

We report that substrate doping-induced charge carrier density modulation leads to the tunable wettability and adhesion of graphene. Graphene’s water contact angle changes by as much as 13° as a result of a 300 meV change in doping level. Upon either n- or p-type doping with subsurface polyelectrolytes, graphene exhibits increased hydrophilicity. Adhesion force measurements using a hydrophobic self-assembled monolayer-coated atomic force microscopy probe reveal enhanced attraction toward undoped graphene, consistent with wettability modulation. This doping-induced wettability modulation is also achieved via a lateral metal–graphene heterojunction or subsurface metal doping. Combined first-principles and atomistic calculations show that doping modulates the binding energy between water and graphene and thus increases its hydrophilicity. Our study suggests for the first time that the doping-induced modulation of the charge carrier density in graphene influences its wettability and adhesion. This opens up un...

Doping-Induced Tunable Wettability and Adhesion of Graphene

The study of hexagonal boron nitride (hBN) in microfluidic and nanofluidic applications at the atomic level requires accurate force field parameters to describe the water-hBN interaction. In this work, we begin with benchmark quality first principles quantum Monte Carlo calculations on the interaction energy between water and hBN, which are used to validate random phase approximation (RPA) calculations. We then proceed with RPA to derive force field parameters, which are used to simulate water contact angle on bulk hBN, attaining a value within the experimental uncertainties. This paper demonstrates that end-to-end multiscale modeling, starting at detailed many-body quantum mechanics and ending with macroscopic properties, with the approximations controlled along the way, is feasible for these systems.

Hexagonal boron nitride and water interaction parameters

We report the intrinsic water contact angle (WCA) of multilayer graphene, explore different methods of cleaning multilayer graphene, and evaluate the efficiency of those methods on the basis of spectroscopic analysis. Highly ordered pyrolytic graphite (HOPG) was used as a model material system to study the wettability of the multilayer graphene surface by WCA measurements. A WCA value of 45° ± 3° was measured for a clean HOPG surface, which can serve as the intrinsic WCA for multilayer graphene. A 1 min plasma treatment (100 W) decreased the WCA to 6°, owing to the creation of surface defects and functionalization by oxygen-containing groups. Molecular dynamics simulations of water droplets on the HOPG surface with or without the oxygen-containing defect sites confirmed the experimental results. Heat treatment at near atmospheric pressure and wet chemical cleaning methods using hydrofluoric acid and chloroform did not change the WCA significantly. Low-pressure, high-temperature annealing under argon and h...

Yanbin Wu

Papers

Effect of cross-linking on the diffusion of water, ions, and small molecules in hydrogels.

Graphitic carbon-water nonbonded interaction parameters

Doping-Induced Tunable Wettability and Adhesion of Graphene

Hexagonal boron nitride and water interaction parameters

Spectroscopic investigation of the wettability of multilayer graphene using highly ordered pyrolytic graphite as a model material.