Fluid transport in nanochannels induced by temperature gradients

We investigate the mechanisms of fluid transport driven by temperature gradients in nanochannels through molecular dynamics simulations. It is found that the fluid-wall interaction is critical in determining the flow direction. In channels of very low surface energy, where the fluid-wall binding energy ε(fw) is small, the fluid moves from high to low temperature and the flow is induced by a potential ratchet near the wall. In high surface energy channels, however, the fluid is pumped from low to high temperature and the pressure drop caused by the temperature gradient is the major driving force. In addition, as the fluid-wall interaction is strengthened, the flow flux assumes a maximum, where ε(fw) is close to the lower temperature T(L) of the channel and ε(fw)/kT(L) ≈ 1 is roughly satisfied.     

The structure of fluids confined in crystalline slitlike nanoscopic pores: bilayers

Grand canonical and canonical ensemble Monte Carlo simulation methods are used to study the structure and phase behavior of Lennard-Jones fluids confined between the parallel (100) planes of the face centered cubic crystal. Ultra thin slit pores of the width allowing for the formation of only two adsorbate layers are considered. It is demonstrated that the structure of adsorbed phases is very sensitive to the wall-wall separation and to the strength of the fluid-wall potential. It is also shown that the structure of low temperature (solid) phases strongly depends on the fluid density. In particular, when the surface field is sufficiently strong, then the high density phases may exhibit a domain wall structure, quite the same as found in monolayer films adsorbed at a single substrate wall. On the other hand, the weakening of the surface potential leads to the regime in which only the hexagonally ordered bilayer structure is stable. The phase diagrams for a series of systems are estimated. It is shown that, depending on the pore width and the temperature, the condensation leads to the formation of the commensurate or incommensurate phases. The incommensurate phases may have the domain-wall or the hexagonal structure depending on the pore width and the strength of the fluid-wall potential.     

Phase equilibria and interfacial tension of fluids confined in narrow pores

Correlation between phase behaviors of a Lennard-Jones fluid in and outside a pore is examined over wide thermodynamic conditions by grand canonical Monte Carlo simulations. A pressure tensor component of the confined fluid, a variable controllable in simulation but usually uncontrollable in experiment, is related with the pressure of a bulk homogeneous system in equilibrium with the confined system. Effects of the pore dimensionality, size, and attractive potential on the correlations between thermodynamic properties of the confined and bulk systems are clarified. A fluid-wall interfacial tension defined as an excess grand potential is evaluated as a function of the pore size. It is found that the tension decreases linearly with the inverse of the pore diameter or width.     

Brownian dynamics simulations of polyelectrolyte adsorption in shear flow with hydrodynamic interaction

The adsorption of single polyelectrolyte molecules in shear flow is studied using Brownian dynamics simulations with hydrodynamic interaction (HI). Simulations are performed with bead-rod and bead-spring chains, and electrostatic interactions are incorporated through a screened Coulombic potential with excluded volume accounted for by the repulsive part of a Lennard-Jones potential. A correction to the Rotne-Prager-Yamakawa tensor is derived that accounts for the presence of a planar wall. The simulations show that migration away from an uncharged wall, which is due to bead-wall HI, is enhanced by increases in the strength of flow and intrachain electrostatic repulsion, consistent with kinetic theory predictions. When the wall and polyelectrolyte are oppositely charged, chain behavior depends on the strength of electrostatic screening. For strong screening, chains get depleted from a region close to the wall and the thickness of this depletion layer scales as N(1/3)Wi(2/3) at high Wi, where N is the chain length and Wi is the Weissenberg number. At intermediate screening, bead-wall electrostatic attraction competes with bead-wall HI, and it is found that there is a critical Weissenberg number for desorption which scales as N(-1/2)kappa(-3)(l(B)|sigmaq|)(3/2), where kappa is the inverse screening length, l(B) is the Bjerrum length, sigma is the surface charge density, and q is the bead charge. When the screening is weak, adsorbed chains are observed to align in the vorticity direction at low shear rates due to the effects of repulsive intramolecular interactions. At higher shear rates, the chains align in the flow direction. The simulation method and results of this work are expected to be useful for a number of applications in biophysics and materials science in which polyelectrolyte adsorption plays a key role.     

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential

A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.     

Effect of fluid-solid interactions on symmetry breaking in closed nanoslits

The possibility of symmetry breaking of the fluid (argon) density distribution across a long closed slit with identical walls composed of solid carbon dioxide was noted in previous papers by the authors. The main conclusion was that there is a range of average densities in which symmetry breaking occurs and that outside that range the fluid density profile is symmetrical. A critical temperature T(sb) was also identified below which symmetry breaking can occur. In this paper, symmetry breaking is examined for walls made of other materials and it is shown that it occurs only when the energy parameter epsilon(fw) of the fluid-wall interaction in the Lennard-Jones potential satisfies the inequalities epsilon(fw1) < or = epsilon(fw) < or = epsilon(fw2), where epsilon(fw1) and epsilon(fw2) are temperature-dependent critical values of epsilon(fw). The value of epsilon(fw1) increases and that of epsilon(fw2) decreases with increasing temperature. The comparison of the theory with Monte Carlo simulations confirms the existence of symmetry breaking across the slit. The possibility of symmetry breaking along the slit is also noted.     

Study on Non-Newtonian Behaviors of Lennard-Jones Fluids via Molecular Dynamics Simulations

Using nonequilibrium molecular dynamics simulations, we study the non-Newtonian rheological behaviors of a monoatomic fluid governed by the Lennard-Jones potential. Both steady Couette and oscillatory shear flows are investigated. Shear thinning and normal stress effects are observed in the steady Couette flow simulations. The radial distribution function is calculated at different shear rates to exhibit the change of the microscopic structure of molecules due to shear. We observe that for a larger shear rate the repulsion between molecules is more powerful while the attraction is weaker, and the above phenomena can also be confirmed by the analyses of the potential energy. By applying an oscillatory shear to the system, several findings are worth mentioning here:First, the phase difference between the shear stress and shear rate increases with the frequency. Second, the real part of complex viscosity first increases and then decreases while the imaginary part tends to increase monotonically, which results in the increase of the proportion of the imaginary part to the real part with the increasing frequency. Third, the ratio of the elastic modulus to the viscous modulus also increases with the frequency. These phenomena all indicate the appearance of viscoelasticity and the domination of elasticity over viscosity at high oscillation frequency for Lennard-Jones fluids.     

Tests of an approximate scaling principle for dynamics of classical fluids

We used molecular dynamics computer simulations to test an approximate scaling principle that conjectures that two equilibrium atomic liquids have very similar dynamical properties if they have the same density and similar static pair correlation functions when the length scales of the two liquids are adjusted appropriately, even if they have different interatomic potentials and different temperatures. The simulations were performed on two types of model atomic liquids at various temperatures at the same density. In the first type, the interatomic potential is the Lennard-Jones potential (LJ). In the second type, the interatomic potential is the repulsive part of the Lennard-Jones potential (RLJ). We identified pairs of systems that have very similar pair correlation functions despite the fact that they had different potentials. Each pair consisted of an LJ liquid at a specific temperature and a corresponding RLJ liquid at a lower temperature. We compared various time correlation functions and transport coefficients of the two systems in each pair. Many dynamical properties are very similar in each pair, in accordance with the approximate scaling principle, whereas others are significantly different. The results indicate that certain dynamical properties are very insensitive to large changes in the interatomic potential that leave the pair correlation function largely unchanged, whereas other dynamical properties are much more sensitive to such changes in the potential. The transport coefficients for diffusion and viscosity are among the dynamical properties that are insensitive to such changes in the potential, and this may be part of the reason transport properties of many fluids have been calculated or rationalized in terms of a simple hard sphere model of liquids.     

Monte Carlo versus molecular dynamics simulations in heterogeneous systems: an application to the n-pentane liquid-vapor interface

The Monte Carlo (MC) and molecular dynamics (MD) methodologies are now well established for computing equilibrium properties in homogeneous fluids. This is not yet the case for the direct simulation of two-phase systems, which exhibit nonuniformity of the density distribution across the interface. We have performed direct MC and MD simulations of the liquid-gas interface of n-pentane using a standard force-field model. We obtained density and pressure components profiles along the direction normal to the interface that can be very different, depending on the truncation and long range correction strategies. We discuss the influence on predicted properties of different potential truncation schemes implemented in both MC and MD simulations. We show that the MD and MC profiles can be made in agreement by using a Lennard-Jones potential truncated via a polynomial function that makes the first and second derivatives of the potential continuous at the cutoff distance. In this case however, the predicted thermodynamic properties (phase envelope, surface tension) deviate from experiments, because of the changes made in the potential. A further readjustment of the potential parameters is needed if one wants to use this method. We conclude that a straightforward use of bulk phase force fields in MD simulations may lead to some physical inconsistencies when computing interfacial properties.     

Low density mesostructures of confined dipolar particles in an external field

Mesostructures formed by dipolar particles confined between two parallel walls and subjected to an external field are studied by Monte Carlo simulations. The main focus of the work is the structural behavior of the Stockmayer fluid in the low density regime. The dependence of cluster thickness and ordering is estimated as a function of density and wall separation, the two most influential parameters, for large dipole moments and high field strengths. The great sensitivity of the structure to details of the short-range part of the interactions is pointed out. In particular, the attractive part of the Lennard-Jones potential is shown to play a major role in driving chain aggregation. The effect of confinement, evaluated by comparison with results for a bulk system, is most pronounced for a short range hard sphere potential. No evidence is found for a novel "gel-like" phase recently uncovered in low density dipolar colloidal suspensions [A. K. Agarwal and A. Yethiraj, Phys. Rev. Lett. 102, 198301 (2009)].     

Boundary slip and wetting properties of interfaces: correlation of the contact angle with the slip length

Correlations between contact angle, a measure of the wetting of surfaces, and slip length are developed using nonequilibrium molecular dynamics for a Lennard-Jones fluid in Couette flow between graphitelike hexagonal-lattice walls. The fluid-wall interaction is varied by modulating the interfacial energy parameter epsilonr=epsilonsfepsilonff and the size parameter sigmar=sigmasfsigmaff, (s=solid, f=fluid) to achieve hydrophobicity (solvophobicity) or hydrophilicity (solvophilicity). The effects of surface chemistry, as well as the effects of temperature and shear rate on the slip length are determined. The contact angle increases from 25 degrees to 147 degrees on highly hydrophobic surfaces (as epsilonr decreases from 0.5 to 0.1), as expected. The slip length is functionally dependent on the affinity strength parameters epsilonr and sigmar: increasing logarithmically with decreasing surface energy epsilonr (i.e., more hydrophobic), while decreasing with power law with decreasing size sigmar. The mechanism for the latter is different from the energetic case. While weak wall forces (small epsilonr) produce hydrophobicity, larger sigmar smoothes out the surface roughness. Both tend to increase the slip. The slip length grows rapidly with a high shear rate, as wall velocity increases three decades from 100 to 10(5) ms. We demonstrate that fluid-solid interfaces with low epsilonr and high sigmar should be chosen to increase slip and are prime candidates for drag reduction.     

Extending the simple weighted density approximation for a hard-sphere fluid to a Lennard-Jones fluid II. Application

A simple weighted density approximation (SWDA) was extended to nonuniform Lennard-Jones fluids by following the spirit of a partitioned density function theory [S. Zhou, Phys. Rev. E 68 (2003) 061201] and mapping the hard-core part onto an effective hard-sphere fluid whose higher order terms beyond the second order of the functional perturbation expansion are treated by the SWDA. The resultant DFT formalism performs well for Lennard-Jones fluids under the influence of diverse external fields. With the present DFT formalism, we investigate in detail the structure and adsorption properties of a low-density LJ gas in a spherical cavity with a wall consisting of hard-sphere or LJ particles. It was found that when the cavity wall exerts an attractive external potential on the LJ particles in the cavity, the excess adsorption decreases as the temperature increases, while when the cavity wall exerts a hard repulsive external potential on the LJ particles in the cavity, the excess adsorption increases as the temperature increases.     

Molecular dynamics simulations of capillary rise experiments in nanotubes coated with polymer brushes

The capillary filling of a nanotube coated with a polymer brush is studied by molecular dynamics simulations of a coarse-grained model, assuming various conditions for the fluid-wall and fluid-brush interactions. Whereas the fluid is modeled by simple point particles interacting with Lennard-Jones forces, the (end-grafted, fully flexible) polymers that form the brush coating are described by a standard bead-spring model. Our experiments reveal that capillary filling is observed even for walls that would not be wetted by the fluid, provided the polymer brush coating itself wets. Generally, it is found that the capillary rise always proceeds through a t1/2 law with time t while the underlying molecular mechanism differs for wettable and nonwettable walls. For wettable walls, fluid imbibition is compatible with the Lucas-Washburn mechanism whereby the total influx of matter drops steadily with growing chain length N and the meniscus speed goes through a minimum at intermediate chain lengths. Moreover, because of flow, the polymer brush reorganizes its structure by forming a dense plug of chain segments under the meniscus that follows the meniscus in its motion. When the tube wall does not wet, one observes no meniscus formation for short chains although the fluid seeps through the wet brush. For a brush coating with longer chains, axial segregation between the brush segments and the fluid occurs by a kind of diffusive spreading, reminiscent of invasion percolation transport in a random medium, leading to the formation of a moving meniscus. For even longer chains that reach the tube axis, the rise of a meniscus with vanishing curvature-like imbibition in a porous medium is observed to take place.     

Wall-liquid and wall-crystal interfacial free energies via thermodynamic integration: A molecular dynamics simulation study

A method is proposed to compute the interfacial free energy of a Lennard-Jones system in contact with a structured wall by molecular dynamics simulation. Both the bulk liquid and bulk face-centered-cubic crystal phase along the (111) orientation are considered. Our approach is based on a thermodynamic integration scheme where first the bulk Lennard-Jones system is reversibly transformed to a state where it interacts with a structureless flat wall. In a second step, the flat structureless wall is reversibly transformed into an atomistic wall with crystalline structure. The dependence of the interfacial free energy on various parameters such as the wall potential, the density and orientation of the wall is investigated. The conditions are indicated under which a Lennard-Jones crystal partially wets a flat wall.     

Interatomic potential-based semiclassical theory for Lennard-Jones fluids

An interatomic potential based semiclassical theory is proposed to predict the concentration and potential profiles of a Lennard-Jones (LJ) fluid confined in a channel. The inputs to the semiclassical formulation are the LJ parameters of the fluid and the wall, the density of channel wall atoms, and the average concentration of the fluid inside the channel. Using the semiclassical formulation, fluid confinement in channel with widths ranging from 2sigma ff to 100sigma ff, where sigma ff is the fluid-fluid LJ distance parameter, is investigated. The concentration and potential predicted by the semiclassical formulation are found to be in good agreement with those from equilibrium molecular dynamics simulations. While atomistic simulations in large channels are computationally expensive, the proposed semiclassical formulation can rapidly and accurately predict the concentration and potential profiles. The proposed semiclassical theory is thus a robust and fast method to predict the interfacial and "bulk" fluid phenomena in channels with widths ranging from the macroscale down to the scale of a few atomic diameters.     

Capillary condensation in pores with rough walls: a density functional approach

The effect of surface roughness of slit-like pore walls on the capillary condensation of a spherical particles and short chains is studied. The gas molecules interact with the substrate by a Lennard-Jones (9,3) potential. The rough layer at each pore wall has a variable thickness and density and consists of a disordered quenched matrix of spherical particles. The system is described in the framework of a density functional approach and using computer simulations. The contribution due to attractive van der Waals interactions between adsorbate molecules is described by using first-order mean spherical approximation and mean-field approximation.     

Rydberg-London potential for diatomic molecules and unbonded atom pairs

We propose and test a pair potential that is accurate at all relevant distances and simple enough for use in large-scale computer simulations. A combination of the Rydberg potential from spectroscopy and the London inverse-sixth-power energy, the proposed form fits spectroscopically determined potentials better than the Morse, Varnshi, and Hulburt-Hirschfelder potentials and much better than the Lennard-Jones and harmonic potentials. At long distances, it goes smoothly to the London force appropriate for gases and preserves van der Waals's "continuity of the gas and liquid states," which is routinely violated by coefficients assigned to the Lennard-Jones 6-12 form.     

Cluster pair correlation function of simple fluids: energetic connectivity criteria

We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integral equation for the pair connectedness function, proposed by two of the authors [Phys. Rev. E 61, R6067 (2000)], is solved for this criterion and the results are compared with those obtained from molecular dynamics simulations and from a connectedness Percus-Yevick-type integral equation for a velocity-averaged version of Hill's energetic criterion.     

Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent

The partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations samples a wide range of an important part of the potential energy. Although it is a strong technique for structure prediction of biomolecules, the choice of the partial potential energy has not been optimized. In order to find the best choice, partial multicanonical molecular dynamics simulations of an alanine dipeptide in explicit water solvent were performed with 15 trial choices for the partial potential energy. The best choice was found to be the sum of the electrostatic, Lennard-Jones, and torsion-angle potential energies between solute atoms. In this case, the partial multicanonical simulation sampled all of the local-minimum free-energy states of the P(II), C(5), α(R), α(P), α(L), and C states and visited these states most frequently. Furthermore, backbone dihedral angles ? and ψ rotated very well. It is also found that the most important term among these three terms is the electrostatic potential energy and that the Lennard-Jones term also helps the simulation to overcome the steric restrictions. On the other hand, multicanonical simulation sampled all of the six states, but visited these states fewer times. Conventional canonical simulation sampled only four of the six states: The P(II), C(5), α(R), and α(P) states.     

NVU dynamics. II. Comparing to four other dynamics

In the companion paper [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schr?der, and J. C. Dyre, "NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface," J. Chem. Phys. (in press)] an algorithm was developed for tracing out a geodesic curve on the constant-potential-energy hypersurface. Here, simulations of NVU dynamics are compared to results for four other dynamics, both deterministic and stochastic. First, NVU dynamics is compared to the standard energy-conserving Newtonian NVE dynamics by simulations of the Kob-Andersen binary Lennard-Jones liquid, its WCA version (i.e., with cut-off's at the pair potential minima), and the Lennard-Jones Gaussian liquid. We find identical results for all quantities probed: radial distribution functions, incoherent intermediate scattering functions, and mean-square displacement as function of time. Arguments are presented for the equivalence of NVU and NVE dynamics in the thermodynamic limit; in particular, to leading order in 1∕N these two dynamics give identical time-autocorrelation functions. In the final part of the paper, NVU dynamics is compared to Monte Carlo dynamics, to a diffusive dynamics of small-step random walks on the constant-potential-energy hypersurface, and to Nose?-Hoover NVT dynamics. If time is scaled for the two stochastic dynamics to make single-particle diffusion constants identical to that of NVE dynamics, the simulations show that all five dynamics are equivalent at low temperatures except at short times.