Anisotropic heat transport in nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation

While polymers are known as thermal insulators, recent studies show that stretched single chains of polymers have a very high thermal conductivity. In this work, our new simulation scheme for simulation of heat flow in nanoconfined fluids [H. Eslami, L. Mohammadzadeh, and N. Mehdipour, J. Chem. Phys. 135, 064703 (2011)] is employed to study the effect of chain ordering (stretching) on the rate of heat transfer in polyamide-6,6 nanoconfined between graphene surfaces. Our results for the heat flow in the parallel direction (the plane of surfaces) show that the coefficient of thermal conductivity depends on the intersurface distance and is much higher than that of the bulk polymer. A comparison of results in this work with our former findings on the heat flow in the perpendicular direction, with the coefficient of heat conductivity less than the bulk sample, reveal that well-organized polymer layers between the confining surfaces show an anisotropic heat conduction; the heat conduction in the direction parallel to the surfaces is much higher than that in the perpendicular direction. The origin of such anisotropy in nanometric heat flow is shown to be the dramatic anisotropy in chain conformations (chain stretching) beside the confining surfaces. The results indicate that the coefficients of heat conductivity in both directions, normal and parallel to the surfaces, depend on the degree of polymer layering between the surfaces and the pore width.     

Coarse Grained Molecular Dynamics Simulation of Nanoconfined Water

A coarse‐grained (CG) model for the simulation of nanoconfined water between graphene surfaces is developed. For this purpose, mixed‐grained simulations are done, in which the two‐site water model of Riniker and van Gunsteren [S. Riniker, W. F. van Gunsteren, J. Chem. Phys. 2011 , 134, 084110] is simulated between atomistically resolved graphene surfaces. In the developed pure CG model, the two interaction sites of water and a combination of eight carbon atoms in the graphene surface are grouped together to construct water and surface CG beads. The pure CG potentials are constructed by iteratively matching the radial distribution functions and the density profiles of water beads in the pore with the corresponding mixed‐grained distributions. The constructed potentials are shown to be pore‐size transferable, capable of predicting structural properties of confined water over the whole range of pore sizes, ranging from extremely narrow pores to bulk water. The model is used to simulate a number of nanoconfined systems of a variety of pore sizes at constant temperature, constant parallel component of pressure, and constant surface area of the confining surfaces. The model is shown to predict the layering of water in contact with the surfaces, and the solvation force is in complete agreement with the mixed‐grained model. It is shown that water molecules in the pore have smaller parallel diffusion coefficients compared to bulk water. Well‐organized layers beside the surfaces are shown to have lower diffusion coefficients than diffuse layers. More information on the dynamics of water in the pore is obtained by calculating the rate of water exchange between slabs parallel to the surfaces. The time scale to achieve equilibrium for this process, depending on the pore width and on the degree of layering of water beside the surfaces, is a few nanoseconds in nanometric pores.     

Solvated calcium ions in charged silica nanopores

Hydroxyl surface density in porous silica drops down to nearly zero when the pH of the confined aqueous solution is greater than 10.5. To study such extreme conditions, we developed a model of slit silica nanopores where all the hydrogen atoms of the hydroxylated surface are removed and the negative charge of the resulting oxygen dangling bonds is compensated by Ca(2+) counterions. We employed grand canonical Monte Carlo and molecular dynamics simulations to address how the Ca(2+) counterions affect the thermodynamics, structure, and dynamics of confined water. While most of the Ca(2+) counterions arrange themselves according to the so-called "Stern layer," no diffuse layer is observed. The presence of Ca(2+) counterions affects the pore filling for strong confinement where the surface effects are large. At full loading, no significant changes are observed in the layering of the first two adsorbed water layers compared to nanopores with fully hydroxylated surfaces. However, the water structure and water orientational ordering with respect to the surface is much more disturbed. Due to the super hydrophilicity of the Ca(2+)-silica nanopores, water dynamics is slowed down and vicinal water molecules stick to the pore surface over longer times than in the case of hydroxylated silica surfaces. These findings, which suggest the breakdown of the linear Poisson-Boltzmann theory, provide important information about the properties of nanoconfined electrolytes upon extreme conditions where the surface charge and ion concentration are large.     

Structural and dynamical properties for confined polymers undergoing planar Poiseuille flow

The authors present the results from nonequilibrium molecular dynamics simulations for the structural and dynamical properties of highly confined linear polymer fluids undergoing planar Poiseuille flow. They study systems confined within pores of several atomic diameters in width and investigate the dependence of the density profiles, the mean squared radius of gyration, the mean squared end-to-end distance, streaming velocity, strain rate, shear stress, and streaming angular velocity as functions of average fluid density and chain length. Their simulation results show that, sufficiently far from the walls, the radius of gyration for molecules under shear in the middle of the pore follows the power law Rg=ANbnu, where Nb is the number of bonds and the exponent has a value of 0.5 which resembles the value for a homogeneous equilibrium fluid. Under the conditions simulated, the authors find the onset of flat velocity profiles but with very little wall slippage. These flat profiles are most likely due to the restricted layering of the fluid into just one or two molecular layers for narrow pore widths compared to chain length, rather than typical plug-flow conditions. The angular velocity is shown to be proportional to half the strain rate in the pore interior when the chain length is sufficiently small compared to the pore width, consistent with the behavior for homogeneous fluids in the linear regime.     

Molecular dynamics simulation of the diffusion of nanoconfined fluids

A new molecular dynamics simulation technique for simulating fluids in confinement [H. Eslami, F. Mozaffari, J. Moghadasi, F. Müller-Plathe, J. Chem. Phys. 129 (2008) 194702] is employed to simulate the diffusion coefficient of nanoconfined Lennard-Jones fluid. The diffusing fluid is liquid Ar and the confining surfaces are solid Ar fcc (100) surfaces, which are kept frozen during the simulation. In this simulation just the fluid in confinement is simulated at a constant temperature and a constant parallel component of pressure, which is assumed to be equal to the bulk pressure. It is shown that the calculated parallel (to the surfaces) component of the diffusion coefficients depends on the distance between the surfaces (pore size) and shows oscillatory behavior with respect to the intersurface separations. Our results show that on formation of well-organized layers between the surfaces, the parallel diffusion coefficients decrease considerably with respect to the bulk fluid. The effect of pressure on the parallel diffusion coefficients has also been studied. Better organized layers, and hence, lower diffusion coefficients are observed with increasing the pressure.     

Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study

Grand canonical ensemble Monte Carlo simulation (GCMC) combined with the histogram reweighting technique was used to study the thermodynamic equilibrium of a homopolymer solution between a bulk and a slit pore. GCMC gives the partition coefficients that agree with those from canonical ensemble Monte Carlo simulations in a twin box, and it also gives results that are not accessible through the regular canonical ensemble simulation such as the osmotic pressure of the solution. In a bulk polymer solution, the calculated osmotic pressure agrees very well with the scaling theory predictions both for the athermal polymer solution and the theta solution. However, one cannot obtain the osmotic pressure of the confined solution in the same way since the osmotic pressure of the confined solution is anisotropic. The chemical potentials in GCMC simulations were found to differ by a translational term from the chemical potentials obtained from canonical ensemble Monte Carlo simulations with the chain insertion method. This confirms the equilibrium condition of a polymer solution partition between the bulk and a slit pore: the chemical potentials of the polymer chain including the translational term are equal at equilibrium. The histogram reweighting method enables us to obtain the partition coefficients in the whole range of concentrations based on a limited set of simulations. Those predicted bulk-pore partition coefficient data enable us to perform further theoretical analysis. Scaling predictions of the partition coefficient at different regimes were given and were confirmed by the simulation data.     

Monte Carlo simulation of structure and nanoscale interactions in polymer nanocomposites

Off-lattice Monte Carlo simulations in the canonical ensemble are used to study polymer-particle interactions in nanocomposite materials. Specifically, nanoscale interactions between long polymer chains (N=550) and strongly adsorbing colloidal particles of comparable size to the polymer coils are quantified and their influence on nanocomposite structure and dynamics investigated. In this work, polymer-particle interactions are computed from the integrated force-distance curve on a pair of particles approaching each other in an isotropic polymer medium. Two distinct contributions to the polymer-particle interaction potential are identified: a damped oscillatory component that is due to chain density fluctuations and a steric repulsive component that arises from polymer confinement between the surfaces of approaching particles. Significantly, in systems where particles are in a dense polymer melt, the latter effect is found to be much stronger than the attractive polymer bridging effect. The polymer-particle interaction potential and the van der Waals potential between particles determine the equilibrium particle structure. Under thermodynamic equilibrium, particle aggregation is observed and there exists a fully developed polymer-particle network at a particle volume fraction of 11.3%. Near-surface polymer chain configurations deduced from our simulations are in good agreement with results from previous simulation studies.     

Effect of surface functionalities on gas adsorption in microporous carbons: a grand canonical Monte Carlo study

In an attempt to offer a more realistic picture of adsorption in highly heterogeneous porous systems, such as oxygen functionalized porous carbons, we consider a series of carbon surfaces baring different amounts of oxygen functionalities (hydroxyl and epoxy). These surfaces are used to construct “oxidized” slit pores of varying width and functionality. With the aid of such inhomogeneous structures we study the interaction of Ar (87 K) inside “functionalized” pores and report grand canonical Monte Carlo adsorption simulations results. Based on our simulation data, we discuss the role of chemical heterogeneity on adsorbed/gas phase equilibrium properties such as density, heat of adsorption, and molecular packing within the pores. Comparisons are made with the case of the oxygen–free (completely homogeneous) slit pore models and conclusions on the suitability of Ar based pore size distributions for functionalized porous carbons are drawn.     

Coarse‐grained molecular dynamics simulations of polymerization with forward and backward reactions

We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non‐bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse‐grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain‐specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc.     

Fluids in nanospaces: molecular simulation studies to find out key mechanisms for engineering

We have analyzed various phenomena that occur in nanopores, focusing on elucidating their key mechanisms, to advance the effective engineering use of nanoporous materials. As ideal experimental systems, molecular simulations can effectively provide information at the molecular level that leads to mechanistic insight. In this short review, several of our recent results are presented. The first topic is the critical point depression of Lennard-Jones fluid in silica slit pores due to finite size effects, studied by our original Monte Carlo (MC) technique. We demonstrate that the first layers of adsorbed molecules in contact with the pore walls act as a “fluid wall” and impose extra finite size effects on the fluid confined in the central portion of the pore. We next present a new kernel for pore size distribution (PSD) analysis, based entirely on molecular simulation, which consists of local isotherms for nitrogen adsorption in carbon slit pores at 77 K. The kernel is obtained by combining grand canonical Monte Carlo (GCMC) method and open pore cell MC method that was developed in the previous study. We show that overall trends of the PSDs of activated carbons calculated with our new kernel and with conventional kernel from non-local density functional theory are nearly the same; however, apparent difference can be seen between them. As the third topic, we apply a free energy analysis method with the aid of GCMC simulations to investigate the gating behavior observed in a porous coordination polymer, and propose a mechanism for the adsorption-induced structural transition based on both the theory of equilibrium and kinetics. Finally, we construct an atomistic silica pore model that mimics MCM-41, which has atomic-level surface roughness, and perform molecular simulations to understand the mechanism of capillary condensation with hysteresis. We calculate the work required for the gas–liquid transition from the simulation data, and show that the adsorption branch with hysteresis for MCM-41 arise from spontaneous capillary condensation from a metastable state.     

Discontinuous molecular dynamics for rigid bodies: applications

Event-driven molecular dynamics simulations are carried out on two rigid-body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous potentials are compared with simulations in which the molecules interact through standard continuous Lennard-Jones potentials. It is shown that under similar conditions of temperature and pressure, the rigid discontinuous molecular dynamics method reproduces the essential dynamical and structural features found in continuous-potential simulations at both gas and liquid densities. Moreover, the discontinuous molecular dynamics approach is demonstrated to be between 3 and 100 times more efficient than the standard molecular dynamics method depending on the specific conditions of the simulation. The rigid discontinuous molecular dynamics method is also applied to a discontinuous-potential model of a liquid composed of rigid benzene molecules, and equilibrium and dynamical properties are shown to be in qualitative agreement with more detailed continuous-potential models of benzene. The few qualitative differences in the angular dynamics of the two models are related to the relatively crude treatment of variations in the discontinuous repulsive interactions as one benzene molecule rotates by another.     

Simulating rare events in equilibrium or nonequilibrium stochastic systems

We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase-space density and are suitable for equilibrium or nonequilibrium systems in stationary state. All the methods use a series of interfaces in phase space, between the initial and final states, to generate transition paths as chains of connected partial paths, in a ratchetlike manner. No assumptions are made about the distribution of paths at the interfaces. The three methods differ in the way that the transition path ensemble is generated. We apply the algorithms to kinetic Monte Carlo simulations of a genetic switch and to Langevin dynamics simulations of intermittently driven polymer translocation through a pore. We find that the three methods are all of comparable efficiency, and that all the methods are much more efficient than brute-force simulation.     

Thermal conductivity of carbon nanotube-polyamide-6,6 nanocomposites: reverse non-equilibrium molecular dynamics simulations

The thermal conductivity of composites of carbon nanotubes and polyamide-6,6 has been investigated using reverse non-equilibrium molecular dynamics simulations in a full atomistic resolution. It is found, in line with experiments, that the composites have thermal conductivities, which are only moderately larger than that of pure polyamide. The composite conductivities are orders of magnitude less than what would be expected from nai?ve additivity arguments. This means that the intrinsic thermal conductivities of isolated nanotubes, which exceed the best-conducting metals, cannot be harnessed for heat transport, when the nanotubes are embedded in a polymer matrix. The main reason is the high interfacial thermal resistance between the nanotubes and the polymer, which was calculated in addition to the total composite thermal conductivity as well as that of the subsystem. It hinders heat to be transferred from the slow-conducting polymer into the fast-conducting nanotubes and back into the polymer. This interpretation is in line with the majority of recent simulation works. An alternative explanation, namely, the damping of the long-wavelength phonons in nanotubes by the polymer matrix is not supported by the present calculations. These modes provide most of the polymers heat conduction. An additional minor effect is caused by the anisotropic structure of the polymer phase induced by the nearby nanotube surfaces. The thermal conductivity of the polymer matrix increases slightly in the direction parallel to the nanotubes, whereas it decreases perpendicular to it.     

Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling

We present multiple dynamic transition pathways on the two-dimensional dihedral plane between conformational states of the alanine dipeptide. The method used in this study is dynamic importance sampling (DIMS). To perform DIMS, unbiased molecular dynamic simulations are used to generate equilibrium ensembles for the alanine dipeptide within different states. Free energy surfaces on the dihedral plane are calculated from the equilibrium simulations, and four energy minima defined from the surface are used as the starting and ending points for DIMS dynamics. The DIMS method represents an important step towards finding multiple transition pathways within complex biomolecular systems.     

On the manifestation of hydrophobicity at the nanoscale

The manifestation of hydrophobicity at the nanoscale has been shown to depend on the topology of the solute. Using various nanoscopic hydrophobic plates, molecular dynamics simulation has been employed to explore the hydration and dewetting at the nanoscale. The topology of the solute regulates the behavior of nanoconfined water, resulting in any of the wet, dry, and intermittent wet-dry intersolute states. The present result reconciles apparently contrasting literature reports on how water behaves at extended hydrophobic surfaces and sheds light on the mechanism of dewetting.     

Rational surface design for molecular dynamics simulations of porous polymer adsorbent media

The construction and use of nonflat agarose surfaces in a simulation box, together with the employment of criteria for the immobilization of a set of dextran polymer chains on the nonflat agarose surfaces whose mathematical physics is compatible with that of the criteria used for the immobilization of the same set of dextran polymer chains on flat agarose surfaces, are shown to generate, through the use of molecular dynamics simulations whose simulation box has linear dimensions along the lateral directions that are the same when flat and nonflat agarose surfaces are used, dextran porous polymer structures whose pore sizes at the outermost surface and in the vicinity of the outermost surface of the porous medium can be controlled by an indirect manner through the variation of the parameters that characterize the nonflat surface. The use of a nonflat surface for the generation of desired large pores requires only a small or modest increase in the number of solvent molecules in the simulation box, while the use of a flat surface for the construction of the same desired large pores requires significant increases in the size of the linear dimensions of the flat surface. This increases so substantially the number of solvent molecules that the computational loads become intractable. The results in this work show that through the use of nonflat surfaces porous dextran polymer layers having pores of desired sizes can be effectively constructed, and this approach could be used for the design and construction of polymer-based porous adsorbent media that could effectively facilitate the transport and adsorption of an adsorbate biomolecule of interest that must be separated from a mixture of components. A useful definition about the properties that a porous polymer structure must have in order to become, for an adsorbate biomolecule of interest of known molecular size, a useful adsorbent medium, is presented and is used to (1) evaluate the porous polymer structures generated through the employment of different nonflat surface models and (2) determine and select the nonflat surface model from a set of nonflat surface models that is effective in producing promising porous structures. Then a procedure is presented by which a set of porous polymer media is generated through the use of the selected nonflat surface model, and the desired porous structure from this set is determined and could be considered to be used for the transport and immobilization of the selected affinity groups/ligands and the subsequent transport and adsorption of the desired to be separated adsorbate.     

Molecular Mechanisms Causing Anomalously High Thermal Expansion of Nanoconfined Water

Anomalously high thermal expansion is measured in water confined in nanoscale pores in amorphous silica and the molecular mechanisms are identified by molecular dynamics (MD) simulations using an accurate dissociative water potential. The experimentally measured coefficient of thermal expansion (CTE) of nanoconfined water increases as pore dimension decreases. The simulations match this behavior for water confined in 30 Å and 70 Å pores in silica. The cause of the high expansion is associated with the structure and increased CTE of a region of water ～6 Å thick adjacent to the silica. The structure of water in the first 3 Å of this interface is templated by the atomically rough silica surface, while the water in the second 3 Å just beyond the atomically rough silica surface sits in an asymmetric potential well and displays a high density, with a structure comparable to bulk water at higher pressure.     

Binary fluids in planar nanopores: Adsorptive selectivity, heat capacity and self-diffusivity

Monte Carlo and molecular dynamics simulations are performed to study fluid adsorption of a two component fluid in slit pores of nanoscopic dimensions. The slit pores are immersed in a binary fluid bath, which is comprised of spherical molecules having a size ratio of 1.43, at constant temperature and composition. Pore width is varied to determine how the heat capacity and self-diffusion coefficient are linked to the composition and structure of the adsorbed fluid. In pores where the fluid structure is most pronounced, we observe: perfect (or near perfect) exclusion of one component by the other component, a heat capacity that rapidly oscillates and is of greater magnitude than in the fluid bath, and self-diffusion coefficients on the order of 10^–8 cm²/s. The behavior of the heat capacity and diffusion coefficients appears to arise from a near solid-like layering of OMCTS that occurs at certain favorable pore widths.