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Coarse-grained (CG) molecular models greatly reduce the computational cost of simulations allowing for longer and larger simulations, but come with an artificially increased acceleration of the dynamics when compared to the parent atomistic (AA) simulation. This impedes their use for the quantitative study of dynamical properties. During coarse-graining, grouping several atoms into one CG bead not only reduces the number of degrees of freedom but also reduces the roughness on the molecular surfaces, leading to the acceleration of dynamics. The RoughMob approach [M. K. Meinel and F. Müller-Plathe, J. Phys. Chem. B 126(20), 3737–3747 (2022)] quantifies this change in geometry and correlates it to the acceleration by making use of four so-called roughness volumes. This method was developed using simple one-bead CG models of a set of hydrocarbon liquids. Potentials for pure components are derived by the structure-based iterative Boltzmann inversion. In this paper, we find that, for binary mixtures of simple hydrocarbons, it is sufficient to use simple averaging rules to calculate the roughness volumes in mixtures from the roughness volumes of pure components and add a correction term quadratic in the concentration without the need to perform any calculation on AA or CG trajectories of the mixtures themselves. The acceleration factors of binary diffusion coefficients and both self-diffusion coefficients show a large dependence on the overall acceleration of the system and can be predicted a priori without the need for any AA simulations within a percentage error margin, which is comparable to routine measurement accuracies. Only if a qualitatively accurate description of the concentration dependence of the binary diffusion coefficient is desired, very few additional simulations of the pure components and the equimolar mixture are required. [ABSTRACT FROM AUTHOR]

The Cassie–Baxter state of wetting explains a large equilibrium contact angle and the slippery dynamics of a water droplet on a superhydrophobic rough surface. It also causes a contact angle hysteresis (CAH) that cannot be fully described by dynamic wetting theories including the molecular kinetic theory (MKT). We analyze the contact line dynamics on a superhydrophobic surface in the framework of the MKT. Multi-body dissipative particle dynamics simulations of a capillary bridge confined between two rough surfaces under steady shear are performed. We find that, in addition to the contact line friction force from the MKT, an additional friction force contribution is needed on rough surfaces. It can be obtained by subtracting from the total friction force the force solely caused by the actual liquid–solid contact area. We find that the additional force is almost constant at all contact line velocities. Thus, it is directly related to the CAH. The CAH originates not only from contact line pinning but also from the shear flow due to the strong friction in the central region of the liquid–solid interface away from the contact line. The analysis of the particle flow inside the capillary bridge shows that liquid particles trapped in the grooves of the surface texture actually move with the same velocity as the surface and exert strong additional friction to other liquid particles. This work extends the MKT to rough surfaces, as well as to elucidate the origin of the CAH of a capillary bridge. The finding would help to better understand other situations of dynamic wetting on superhydrophobic surfaces. [ABSTRACT FROM AUTHOR]

We propose a method to calculate the equilibrium contact angle of heterogeneous 3-phase solid/fluid/fluid systems using molecular dynamics simulations. The proposed method, which combines the phantom-wall method [F. Leroy and F. Müller-Plathe, J. Chem. Phys. 133, 044110 (2010)] and Bennett's acceptance ratio approach [C. H. Bennett, J. Comput. Phys. 22, 245 (1976)], is able to calculate the solid/fluid surface tension relative to the solid surface energy. The calculated relative surface tensions can then be used in Young's equation to estimate the equilibrium contact angle. A fluid droplet is not needed for the proposed method, in contrast to the situation for direct simulations of contact angles. In addition, while prior free-energy based methods for contact angles mainly focused on the wetting of fluids in coexistence with their vapor on solid surfaces, the proposed approach was designed to study the contact angles of fluid mixtures on solid surfaces above the fluid saturation pressures. Using the proposed approach, the contact angles of binary Lennard-Jones fluid mixtures on a non-polar solid substrate were calculated at various interaction parameters and the contact angle of water in equilibrium with CO2 on a hydrophilic polar silica surface was obtained. For both nonpolar and polar systems, the calculated contact angles from the proposed method were in agreement with those obtained from the geometry of a cylindrical droplet. The computational cost of the proposed method was found to be comparable to that of simulations that use fluid droplets, but the new method provides a way to calculate the contact angle directly from Young's equation without ambiguity. [ABSTRACT FROM AUTHOR]

Zusammenfassung Die rein klassisch‐thermodynamische Deutung der Entropie ist folgende: Die Änderung der Entropie eines Systems ist proportional zur relativen Änderung der thermischen Energie dieses Systems (Gleichung 3) durch reversiblen Transfer von Wärme; der Proportionalitätsfaktor ist nR. Diese Interpretation gilt in differentieller Form immer. In integraler Form gilt sie nur, wenn der Wärmetransfer isotherm verläuft (Gleichung 5).Diese klassische‐thermodynamische Interpretation der Entropie ist konsistent mit der rein statistischen Betrachtung der Entropie und kann aus den Entropie‐Definitionen von Boltzmann (Gleichung 6) oder Gibbs (Gleichung 9) abgeleitet werden.Bringt man die klassische und die statistische Definition der reduzierten Entropie zusammen, so erschließt sich unmittelbar, dass auch Änderungen in der Mikrozustandsverteilung von der relativen, nicht der absoluten Menge transferierter thermischer Energie bestimmt werden.Didaktik: Im Rahmen des Chemiestudiums lässt sich mit Punkt 1 die Entropie in der klassischen Thermodynamik ohne Vorgriff auf die statistischen Definitionen interpretieren. Die Äquivalenz von klassischem und statistischem Ergebnis bietet die Möglichkeit zur späteren Auffrischung des Sachverhalts innerhalb der statistischen Thermodynamik. [ABSTRACT FROM AUTHOR]

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 naïve 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. [ABSTRACT FROM AUTHOR]

Different model Lennard-Jones solid-liquid interfaces have been considered. In the systems, either the interaction strength between solid and liquid was varied, or the topography of the solid surface was modified. In all situations, the solid-liquid interfacial free energy variations with respect to a reference solid-liquid interface were quantified by means of a thermodynamic integration method [F. Leroy et al., Macromol. Rapid Commun. 30, 864 (2009)], referred to as the phantom-wall method. Additionally, the liquid-vapor surface free energy was determined. This result was combined with Young’s equation for contact angle calculations of cylindrical liquid droplets. It allowed us to show that the change in contact angle of a droplet placed on smooth solid surfaces with respect to solid-liquid interaction strength could be obtained by neglecting the solid-vapor surface free energy contribution when the solid-liquid interaction was weak. We also showed that the implementation of roughness by means of parallel grooves whose the density was varied could yield either higher or lower solid-liquid surface free energy, depending on the solid-liquid surface free energy of the smooth interface. Roughness led to lower surface free energy when the smooth surface had favorable interaction with the liquid, while it led to a higher surface free energy when the smooth surface had loose interactions with the liquid, though the effect was found to be weak. The consistency of the whole set of results, as well as agreement with the existing results on similar systems, shows the ability of the thermodynamic integration method employed here to capture the variation of interfacial thermodynamic quantities when modifying either the chemical nature or the topography of a solid surface in contact with a given liquid phase. [ABSTRACT FROM AUTHOR]

In this work, our previous simulation method on the calculation of solubility of nonpolar solutes in nonpolar polymers [H. Eslami and F. Müller-Plathe, Macromolecules 40, 6413 (2007)] has been extended to the case of solubility calculation for water, as a polar penetrant, in poly(ethylene terephthalate), as a polar polymer. The chemical potentials of water in the polymer phase and in the gas phase have been calculated by employing our grand canonical ensemble molecular dynamics simulation method [H. Eslami and F. Müller-Plathe, J. Comput. Chem. 28, 1763 (2007)]. In this paper it is shown that performing just two independent simulations, one in the polymer phase and one in the vapor phase, in the grand canonical ensemble, is sufficient to calculate the phase coexistence point. The calculated solubilities, diffusion coefficients, and permeability coefficients are in good agreement with experimental data. Also the calculated glass transition temperature of the wet polymer is shown to be in a very good agreement with experiment. [ABSTRACT FROM AUTHOR]

The thermal conductivity of the crystalline δ phase of syndiotactic polystyrene has been investigated by reverse nonequilibrium molecular dynamics simulations. The results are in the expected range. An anisotropy is found for the thermal conductivity, with the component in chain direction being 2.5–3 larger than perpendicular to it. Any increase in the density causes an increase also in the thermal conductivity, particularly in the perpendicular directions. As side results, the simulations confirm an earlier finding on the force field dependence of the thermal conductivity: The thermal conductivity has a tendency to decrease when the number of active degrees of freedom in the system is reduced by the introduction of constraints. This dependence is, however, weaker and more erratic than previously found for molecular liquids and amorphous polymers. [ABSTRACT FROM AUTHOR]

A molecular dynamics model and its parametrization procedure are devised and used to study adsorption of isopropanol on platinum(111) (Pt(111)) surface in unsaturated and oversaturated coverages regimes. Static and dynamic properties of the interface between Pt(111) and liquid isopropanol are also investigated. The magnitude of the adsorption energy at unsaturated level increases at higher coverages. At the oversaturated coverage (multilayer adsorption) the adsorption energy reduces, which coincides with findings by Panja et al. in their temperature-programed desorption experiment [Surf. Sci. 395, 248 (1998)]. The density analysis showed a strong packing of molecules at the interface followed by a depletion layer and then by an oscillating density profile up to 3 nm. The distribution of individual atom types showed that the first adsorbed layer forms a hydrophobic methyl “brush.” This brush then determines the distributions further from the surface. In the second layer methyl and methine groups are closer to the surface and followed by the hydroxyl groups; the third layer has exactly the inverted distribution. The alternating pattern extends up to about 2 nm from the surface. The orientational structure of molecules as a function of distance of molecules is determined by the atom distribution and surprisingly does not depend on the electrostatic or chemical interactions of isopropanol with the metal surface. However, possible formation of hydrogen bonds in the first layer is notably influenced by these interactions. The surface-adsorbate interactions influence the mobility of isopropanol molecules only in the first layer. Mobility in the higher layers is independent of these interactions. [ABSTRACT FROM AUTHOR]

Thermal diffusion in dilute polymer solutions is studied by reverse nonequilibrium molecular dynamics. The polymers are represented by a generic bead-spring model. The influence of the solvent quality on the Soret coefficient is investigated. At constant temperature and monomer fraction, a better solvent quality causes a higher affinity for the polymer to the cold region. This may even go to thermal-diffusion-induced phase separation. The sign of the Soret coefficient changes in a symmetric nonideal binary Lennard-Jones solution when the solvent quality switches from good to poor. The known independence of the thermal diffusion coefficients of the molecular weight is reproduced for three groups of polymers with different chain stiffnesses. The thermal diffusion coefficients reach constant values at chain lengths of around two to three times the persistence length. Moreover, rigid polymers have higher Soret coefficients and thermal diffusion coefficients than more flexible polymers. [ABSTRACT FROM AUTHOR]

Reverse nonequilibrium molecular dynamics is the method applied here for the investigation of thermal diffusion in realistic molecular fluids. The Soret coefficients of benzene/cyclohexane mixtures are calculated using an all-atom model. The autocorrelation functions indicate that the mole fraction gradient converges much slower than the temperature gradient. Compared to experimental data, the results show the same tendency of the Soret coefficient variation versus the mole fraction. Although a systematic error exists for the magnitude of the Soret coefficient, a meanwhile systematic error for both the mutual diffusion and thermal diffusion coefficients provides some explanation of it; and the calculation with different force field parameters indicates a possibility to annihilate the systematic error. The influences of algorithm variables such as cutoff lengths and perturbation intensities are tested. Furthermore the temperature dependence of the Soret effect is observed, yielding the same trend as previous studies. [ABSTRACT FROM AUTHOR]

Systems of lithium iodide dissolved in poly(ethylene oxide), which are prototypes of polymer electrolytes used, for example, in batteries were studied by means of molecular dynamics simulations. Investigations were aimed at the molecular driving force behind the salt uptake, the mechanism of ion transport, participation of the polymer in ion transport, ion clustering, change of polymer properties by the presence of ions, and ionic conductivity. Particular attention has been given to the differences in behavior between (previously studied) neutral and ionic species dissolved in polymers. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We have studied the behavior of carbon dioxide and methane in crystalline poly(4-methyl-1-pentene) (PMP) by means of molecular simulation. Gas diffusion coefficients in the direction of the crystal axes have been determined by equilibrium and nonequilibrium molecular dynamics techniques. We find that both gases diffuse along the channels of free volume between the PMP helices as well as perpendicular to these channels. The diffusion of CH4 is more isotropic than that of CO2: It diffuses perpendicular to the helices with almost the same rate as parallel. This is attributed to the fact that CH4 dissolves better in the outer perimeters of the PMP helices which are not dissimilar to fluid alkanes. A map of the local relative free energy of sorption within the unit cell is calculated both by test-particle insertion and from the residence periods of gas molecules at certain positions. It also shows that the barriers to perpendicular diffusion are lower for CH4 than for CO2. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Solvent effects on the conformational equilibria of dimethoxyethane (DME, CH3–O–CH2–CH2–O–CH3) have been studied using molecular dynamics simulation with a combined molecular mechanical and semiempirical quantum mechanical potential energy function. The potential of mean force around the central O–C–C–O dihedral angle of DME in water was determined using umbrella sampling, with the DME molecule treated by the modified intermediate neglect of diatomic differential overlap (MNDO) method and water molecules described using the extended simple point charge model. This potential of mean force shows the same bias as the gas phase potential energy surface calculated by MNDO: the heights of the barriers are underestimated and the stability of the gauche conformation with respect to the trans conformation is overestimated. However, the calculated stabilization of the gauche state by solvation is in good agreement with experimental results, suggesting a quite reasonable description of this system by the combined potential energy function. The solute–water atom pair distributions and the averaged percentage of solute–water hydrogen bonding does not change much when the central dihedral angle changes, but in the gauche conformation one water hydrogen can be hydrogen bonded with the two solute oxygen atoms simultaneously. The interactions between DME and its explicit water environment favor the gauche over the trans conformation much more than predicted by the reaction field model, although the overall relative stabilities predicted by the latter model are not so biased due to compensation of errors. The trans conformation of the outer C–O–C–C dihedral angles is most favored during the simulations, which is qualitatively different from the reaction field prediction that the trans–gauche+–gauche- would be the most stable conformer in solution. © 1995 American... [ABSTRACT FROM AUTHOR]

Molecular dynamics calculations are reported on the sorption and diffusion of small gas molecules (He, H2, and O2) in amorphous polyisobutylene. An all-atom force field (with explicit hydrogen atoms) was used. In addition to the standard method of obtaining the diffusion coefficient from an equilibrium calculation via the mean-square displacement we used a nonequilibrium technique that applies a fictitious external field selectively to the gas molecules. To our knowledge, nonequilibrium MD is, for the first time, applied to the problem of gas diffusion in polymers. Results of both techniques are compared. Energy profiles of the jump events underlying gas diffusion through polymers are studied. We also discuss the possible presence of anomalous (non-Einstein) behavior of gas molecules diffusing through an amorphous polymer. Gas solubilities in polyisobutylene are calculated by particle-insertion techniques. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are performed on polypropylene-penetrant systems with the penetrant being molecular hydrogen, molecular oxygen, and methane. Well equilibrated initial configurations of the amorphous polypropylene are generated by the method of Theodorou and Suter. At the qualitative level, a hopping motion is found to be the underlying mechanism for penetrant diffusion. Coefficients for the diffusion of the penetrant molecules in polypropylene are obtained from their mean-square displacements. The agreement with experimental results, where available, is satisfactory. A relation between the penetrant’s diffusion coefficient and its size frequently observed in experiments is confirmed by the present results. [ABSTRACT FROM AUTHOR]

Molecular dynamics calculations are performed that simulate the diffusion of penetrant molecules through an amorphous polymer. For the polymer and the penetrant molecules, model potentials are chosen that approximate polyethylene and methane, respectively. The simulations extend over several hundred picoseconds. The results indicate that permeation proceeds by a hopping mechanism: The penetrants dwell in voids in the polymer matrix for a considerable time and perform fast jumps between neighboring voids. A potential scaling technique based on the fact that individual jump events are activated processes is presented by which the calculation of penetrant self-diffusion coefficients is speeded up. [ABSTRACT FROM AUTHOR]

Fully numerical Hartree–Fock calculations have been performed for the BeH(X2Σ+), BeH(A2Πr), CH(X2Πr), NH(X3Σ-), OH(X2 Πi), MgH(X2Σ+), and SiH(X2Πr) molecules. Total and orbital energies and multipole moments are reported for these molecules at the experimental bond distances. The dependence of the basis-set truncation error on the internuclear separation has been studied. [ABSTRACT FROM AUTHOR]

By employing reverse non-equilibrium molecular dynamics simulations in a united-atom resolution, the influence of grafted polyamide-6,6 (PA) chains on the heat transfer between two parallel carbon nanotubes (CNTs) in a PA matrix is analyzed by calculating the thermal resistance. We show that grafted chains can reduce the thermal resistance between the CNTs significantly. Specifically, the thermal resistance between the CNTs decreases continuously with the grafting density and grafting length. In addition, the thermal resistance between the CNTs gradually increases with the increase of the distance between the CNTs. When the CNTs are directly linked by PA chains, the thermal resistance is even more reduced. The number of linking PA chains is the main factor that controls the thermal resistance, rather than their length. The relationship between the thermal resistance and the different parameters (grafting density, grafting length, number of linking chains, the intertube distance) can be described by an empirical equation. The heat transfer process from one CNT to another can be approximately described by a thermal circuit model between the CNTs. For the grafted CNTs, the model underestimates the simulated thermal resistance, whereas for the PA-linked CNTs, it overestimates it. However, for the grafted CNTs with very high grafting density and very short grafting length, the model significantly underestimates the simulated thermal resistance because of the appearance of a new interface between grafted PA and free PA. [ABSTRACT FROM AUTHOR]

We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81 W m-1 K-1. It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system. [ABSTRACT FROM AUTHOR]

Standard molecular dynamics (MD) and Monte Carlo (MC) simulations deal with spherical particles. Extending the standard simulation methodologies to the nonspherical objects is non‐trivial. To circumvent this problem, nonspherical bodies are often treated as a collection of constituent spherical objects. As the number of these constituent objects becomes large, the computational burden to simulate the system also increases. Here, an alternative way is proposed to simulate nonspherical rigid bodies having pairwise repulsive interactions. This approach is based on a machine learning (ML)‐based model, which predicts the overlap between two nonspherical bodies. The ML model is easy to train and the computation cost of its implementation remains independent of the number of constituent spheres used to represent a nonspherical rigid body. When used in MC simulation, this method is faster than the standard implementation, where overlap determination is based on calculating the distance between constituent spheres. This proposed ML‐based MC method produces similar structural features (in comparison to the standard implementation) in both two and three dimensions, and can qualitatively capture the isotropic to nematic transition of rigid rods in three dimensions. It is believed that this work is a step toward a time‐efficient simulation of non‐spherical rigid bodies. [ABSTRACT FROM AUTHOR]

Confinement effects on the accessible volume and the cavity size distribution in polystyrene - silica nanocomposites are studied by atomistic molecular dynamics simulations. Atomistically derived properties of pure polystyrene are compared against coarse-grained data. Microstructures for various nanoparticle diameters and grafting densities are analyzed using a geometrical procedure to determine the accessible volume and cavities which provide sufficient space for a hard-sphere probe particle with a radius between 0 and 0.25 nm. The spatial distribution of the accessible volume depends weakly on the size and grafting density of the nanoparticle. Contrary to intuitive expectations, variations of the accessible volume are not directly related to changes of the specific volume. The separation from the nanoparticle to achieve bulk behavior of the accessible volume depends also weakly on the size of the probe particle. For a zero-radius probe particle, the spatial variation of the unoccupied volume is shorter than the one of the specific volume. Average cavity sizes in the vicinity of a nanoparticle are smaller than in the bulk. They are of ellipsoidal shape and inclined from the nanoparticle surface by approximately 30°. Both the size of the nanoparticle and its grafting density induce minor effects on the cavity properties. Peculiarities in the spatial distribution of the cavity sizes persist for larger separations from the nanoparticle than modifications in the specific volume. The validity of approximating the accessible volume and the cavity size distribution with the help of quantities derived by a Voronoi tessellation is tested. It is shown that the volume of a Voronoi cell does not provide such a description. Nevertheless, it is possible to correlate the rather abstract Voronoi related properties to structural details of the polymer matrix. We demonstrate that the volume of an atomic Voronoi cell is reduced with an increasing number of bonded neighbors. Its shape becomes elongated when the number of bonds per atom is raised. [ABSTRACT FROM AUTHOR]

By employing reverse nonequilibrium molecular dynamics simulations in a full atomistic resolution, the effect of surface-grafted chains on the thermal conductivity of graphene-polyamide-6.6 (PA) nanocomposites has been investigated. The interfacial thermal conductivity perpendicular to the graphene plane is proportional to the grafting density, while it first increases and then saturates with the grafting length. Meanwhile, the intrinsic in-plane thermal conductivity of graphene drops sharply as the grafting density increases. The maximum overall thermal conductivity of nanocomposites appears at an intermediate grafting density because of these two competing effects. The thermal conductivity of the composite parallel to the graphene plane increases with the grafting density and grafting length which is attributed to better interfacial coupling between graphene and PA. There exists an optimal balance between grafting density and grafting length to obtain the highest interfacial and parallel thermal conductivity. Two empirical formulas are suggested, which quantitatively account for the effects of grafting length and density on the interfacial and parallel thermal conductivity. Combined with effective medium approximation, for ungrafted graphene in random orientation, the model overestimates the thermal conductivity at low graphene volume fraction (f < 10%) compared with experiments, while it underestimates it at high graphene volume fraction (f > 10%). For unoriented grafted graphene, the model matches the experimental results well. In short, this work provides some valuable guides to obtain the nanocomposites with high thermal conductivity by grafting chain on the surface of graphene. [ABSTRACT FROM AUTHOR]

We introduce a new tool for the performance of Hueckel molecular orbital calculations on a smartphone using a simple graphical input. It produces all routine output expected from a Hueckel calculation. Advanced users may also study things like Moebius rings, hetero systems, or Pauli-antisymmetry constraints in monocycles. In short, in addition to its main use in teaching, the app can also be employed for fast estimate in research, be it only to assess whether the application of state-of-the-art quantum chemical calculations may be warranted. [ABSTRACT FROM AUTHOR]

Abstract: Coarse-grained molecular dynamics simulations of a nanostructure-forming ionic liquid are performed. The reverse non-equilibrium molecular dynamics (RNEMD) technique is used to investigate the stability of the nanostructure under shear conditions. The calculations indicate that even extreme shear cannot break up these structures or alter them significantly. Thus, they are unlikely to be an impediment to shear and a cause for high viscosities. [Copyright &y& Elsevier]

Coarse-grained molecular dynamics is utilized to quantify the behavior of a supercooled water drop on smooth and rough surfaces. Crystallization on rough surface is characterized based on wetting states. Freezing temperature and work of adhesion of water droplet are linearly associated with roughness parameters corresponding to the Cassie-Baxter and Wenzel states. The behavior is insensitive to different surface-fluid affinity. We show in general, for Wenzel states, work of adhesion is higher than that of Cassie-Baxter state for surfaces that have identical freezing temperatures. [ABSTRACT FROM AUTHOR]

We analyze the range of validityof the empirical excess entropyscalings proposed independently by Rosenfeld and Dzugutov for theviscosity and the diffusion coefficient of monodisperse Lennard-Joneschains. They are long enough to be considered as entangled. Thus,the influence of entanglements on entropy scalings can be quantified.We make use of thermodynamic integration to determine the exact excessentropy. Different ways of approximating the excess entropy eitherbased on conformational information or by employing the self-associatingfluid theory (SAFT) are explored. The correlations between the variousexcess entropy estimates are investigated in detail. The conformationalroute appears to be the most suitable way for the studied Lennard-Jonessystems. Its prediction is in qualitative agreement with those obtainedby thermodynamic integration, which is computationally more demanding.The SAFT results are not always consistent with the simulation data.The main qualitative feature of both the Rosenfeld and Dzugutov scalingis the coexistence of two linear regimes in the correlation of differententropy expressions. The sharpness of the transition regime dependson the way the excess entropy is approximated. The Dzugutov scalingfor the viscosity seems to have certain advantages in comparison tothe Rosenfeld one. The influence of the chain length on the parametersappearing in the excess entropy scaling relationships is examined.Despite the pronounced chain length dependence of the scaling parameters,a master curve relating the diffusion coefficient to the excess entropyis derived when performing a suitable renormalization. The relationbetween the scaling parameters of the viscosity and the diffusioncoefficient arewith one exceptionin line with thepredictions of the Stokes–Einstein law. [ABSTRACT FROM AUTHOR]

This review paper discusses known methods and their prediction accuracy for the thermal conductivity calculation as well as their application to molecular liquids, polymers, and carbon nanotubes. Particular attention has been paid to the influence of simulation parameters, size-effects, and force field on the thermal conductivity calculated. The simulation parameters, such as the use of thermostat, exchange period in the algorithm, and atomic vs. molecular exchange, have the lowest impact on the calculated value. Variation of simulation parameters in reasonable ranges results in the mutual deviations of thermal conductivities within the respective error bars only. Size effects can be avoided, but should be considered for each particular system. For molecular liquids as well as for polymers, a simulation box of several nanometers length seems to be reasonable, whereas, for carbon nanotubes even several hundred nanometers are not enough due to the divergence of the thermal conductivity with the tube length. The choice of the force field appears to be most decisive for the calculated thermal conductivity. Correctly tuned united-atom models together with bond constraints lead to significant improvements in the prediction accuracy. [ABSTRACT FROM PUBLISHER]

Our recently developed molecular dynamics simulation method forsimulating fluids confined in nanometric pores [Eslami et al. J. Chem. Phys.2008, 129,194702] is employed to simulate nanoconfined polyamide-6,6+water incontact with graphene monolayers. In this work, a number of dry andwet polymer samples, containing 3 and 6 wt % water at 350 K, confinedin pores of different sizes as well as the bulk polymer samples aresimulated. It is shown that both water and polymer molecules formorganized layers beside the surfaces. The effect of nanoconfinementon the hydrogen bonding in the polymer+water system is studied indetail. It is shown that addition of water to the polymer replacesa fraction of looser amide–amide hydrogen bonds with amide–waterones. The distribution of hydrogen bond lengths shows that both thepolymer and water form shorter length hydrogen bonds in the confinedregion compared to the bulk system. The number of hydrogen bonds betweenpolymer and water molecules is shown to depend on the pore size andon the water content. In small pores, water molecules are forced bythe surfaces into the polymer layers and form strong hydrogen bondswith the amide groups, a process that increases the water solubilityof the polymer in small pores. Increasing the water content in largerpores increases the number of hydrogen bonds between water moleculesand causes the formation of big clusters in the central region ofthe pore. In simulations of to 50 ns, it is shown that such big clustersgrow with of time, and hence, phase separate out from the mixture. [ABSTRACT FROM AUTHOR]

To investigate heat transport across a biological membrane, we performed a series of reverse nonequilibrium molecular dynamics (RNEMD) simulations on a model dipalmitoylphosphatidylcholine (DPPC) bilayer system at the atomistic level. In a detailed analysis of the initially irritating results, we show how and to which extent the RNEMD method (in the special case of an ordered, heterogeneous system, like a bilayer in water) is influenced by simulation conditions. We prove that the interplay between the description of the long range forces and the nonequilibrium algorithm can lead to significant changes in the apparent local thermal conductivity profile across the membrane. As this is the first case reported where the otherwise robust RNEMD results are not directly interpretable, we discuss not only the reasons but also several concepts to handle this effect. Note that this is not a flaw of the RNEMD method but of the simulation framework it is performed in. Therefore, the considerations apply to other equilibrium and nonequilibrium molecular dynamics simulations of the thermal conductivities, too, and care must be taken when heterogeneous systems or interfaces appear in simulations. The complete understanding of the directly obtained results finally allows us to describe the heat flow across the membrane qualitatively. On this basis, we show that the tail-tail interface of the bilayer is the most hindering region for the heat flow, and thus, dominates the overall thermal conductivity of the membrane. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

Abstract: In the present molecular dynamics simulations we study the chemical warfare agent sulfur mustard (bis(2-chloroethyl) sulfide) and the alkane heptane inserted into a dipalmitoylphosphatidylcholine (DPPC) bilayer, a generic model for a biological membrane. We investigate the diffusion, the orientation, the preferred positioning, and the end-to-end distance of the solutes within the membrane as well as the corresponding coupling times. We compare results of equilibrium simulations and simulation at different external forces, which drag the solutes through the membrane. These properties lead to a general comparison of the rotational and translational behaviors of the two solutes during the penetration of the membrane. We show that sulfur mustard, due to its atomic charge polarization, its bigger flexibility and its smaller molecular volume, is the faster moving molecule within the membrane. In last consequence, we show that this leads to different limits for the transport mechanism as observed in these simulations. For heptane the hindrance to penetrate into the membrane is significantly higher than for sulfur mustard. In contrast to heptane molecules, which spend the most of the time penetrating the tail groups, sulfur mustard needs more time to escape the tail group–head group interface of the membrane. [Copyright &y& Elsevier]

An extended system Hamiltonian is proposed to perform molecular dynamics (MD) simulation in the grand canonical ensemble. The Hamiltonian is similar to the one proposed by Lynch and Pettitt (Lynch and Pettitt, J Chem Phys 1997, 107, 8594), which consists of the kinetic and potential energies for real and fractional particles as well as the kinetic and potential energy terms for material and heat reservoirs interacting with the system. We perform a nonlinear scaling of the potential energy parameters of the fractional particle, as well as its mass to vary the number of particles dynamically. On the basis of the equations of motion derived from this Hamiltonian, an algorithm has been proposed for MD simulation at constant chemical potential. The algorithm has been tested for the ideal gas, for the Lennard–Jones fluid over a wide range of temperatures and densities, and for water. The results for the low-density Lennard–Jones fluid are compared with the predictions from a truncated virial equation of state. In the case of the dense Lennard–Jones fluid and water our predicted results are compared with the results reported using other available methods for the calculation of the chemical potential. The method is also applied to the case of vapor-liquid coexistence point predictions. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are used to study the structure and dynamics of the platinum(111)/poly(vinyl alcohol) (PVA) oligomers (10 monomers long) interface at 400 K. The mass density and number density distribution of separate atoms along the surface normal resemble, in general, the distributions obtained for the platinum(111)/liquid isopropanol interface 28. The small discrepancies are dictated by the chemical bonds between monomers within PVA chains. The differences between PVA and isopropanol in the orientational structure of O-H and O-C bond vectors are large immediately at the platinum surface. The connectivity of monomers within PVA chains is also the main driving force of these changes. At longer distances, the structure of the PVA melt resembles approximately that of liquid isopropnaol. The PVA chains, which are directly adsorbed on the surface, extend into the bulk up to 2.25 nm. There exists a region where adsorbed chains mix with nonadsorbed ones and, therefore, form very likely hydrogen bonds between each other. Thus, it is expected that PVA melt, unlike liquid isopropanol, attaches relatively strongly onto the metal surface. [ABSTRACT FROM AUTHOR]

This synopsis discusses the effects of surface structures of nanometer dimensions on the hydrophobicity of a material. They are investigated by atomistic molecular dynamics simulations of water and salt solutions near appropriately structured model surfaces designed to represent hydrocarbon and fluorocarbon materials. It is found that surface structuring does increase the hydrophobicity of these already inherently hydrophobic materials, and that, among the structures investigated, circular holes and protrusions of about 2.5 nm diameter and 0.5 nm depth or height, respectively, are most effective. The mechanism of the hydrophobicity increase is molecular and different from the macroscopic lotus effect: Water assumes a much reduced, but still liquid‐like density around the surface structures. It does not avoid them altogether. The hydrophobicity increase due to surface nanostructuring is material‐independent and is also present at higher temperatures and for aqueous alkali halide solutions. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of liquid tetrahydrofuran have been performed with different force fields to illustrate that there is no unique way to model a given system of molecules. Parameters for the force fields have been taken from existing force fields and have been used as starting guesses for a simplex optimization. In spite of the very different final parameter values, all optimized force fields reproduce properly the physical properties for which they have been optimized, but not necessarily other ones. [ABSTRACT FROM AUTHOR]

Polymer simulations can be performed at many different length scales by using techniques ranging from quantum chemistry to finite element via a hierarchy of coarser and coarser particle or field-based methods. Recent years have seen many efforts to connect simulations at different levels to 1) indirectly predict large-scale properties starting from fundamental models and 2) to accelerate the equilibration at more fundamental levels via the detour of coarse-grained levels. It is the purpose of the present synopsis to review some of the recent methodological advances concerning the systematic and, where available, automatic bridging between different levels of polymer simulation. [ABSTRACT FROM AUTHOR]

Two non-equilibrium methods (called bubble method and splitting method, respectively) have been developed and tested to study the steady state evaporation of a droplet surrounded by its vapor, where the evaporation continuously occurs at the vapor-liquid interface while the droplet size remains constant. In the bubble method, gas molecules are continuously reinserted into a free volume (represented by a bubble) located at the centre of mass of the droplet to keep the droplet size constant. In the splitting method, a molecule close to the centre of mass of the droplet is split into two: In this way, the droplet size is also maintained during the evaporation. By additional local thermostats confined to the area of insertion, the effect of frequent insertions on properties such as density and temperature can be limited to the immediate insertion area. Perturbations are not observed in other parts of the droplet. In the end, both the bubble method and the splitting method achieve steady-state droplet evaporation. Although these methods have been developed using an isolated droplet, we anticipate that they will find a wide range of applications in the study of the evaporation of isolated films and droplets or thin films on heated substrates or under confinement. They can in principle also be used to study the steady-state of other physical processes, such as the diffusion or permeation of gas molecules or ions in a pressure gradient or a concentration gradient. [ABSTRACT FROM AUTHOR]

The article presents the author's comment on the article "A nonequilibrium molecular-dynamics method for thermal conductivities based on thermal noise" published in 2005 issue of the "Journal of Chemical Physics." Now referred to as I, the author have presented a way of setting up a nonequilibrium situation in a molecular dynamics simulation by using the thermal noise from the pair-potential truncation as a uniform heat source and the thermostat as the heat sink. In I, the Berendsen thermostat was employed. In order to localize its action, only the atoms in the control volume were used to calculate the actual temperature and only their velocities were rescaled in response to the deviation of the actual temperature from the target value. In I, rescaling was applied to only a subset of the atoms, whose collective momentum P was initially not zero. Hence, the collective momentum was also rescaled P'=λP.

Ice and water droplets on graphite have been studied by quantum path integral and classical molecular dynamics simulations. The point-charge q-TIP4P/F potential was used to model the interaction between flexible water molecules, while the water-graphite interaction was described by a Lennard-Jones potential previously used to reproduce the macroscopic contact angle of water droplets on graphite. Several energetic and structural properties of water droplets with sizes between 10² and 10³ molecules were analyzed in a temperature interval of 50-350 K. The vibrational density of states of crystalline and amorphous ice drops was correlated to the one of ice Ih to assess the influence of the droplet interface and molecular disorder on the vibrational properties. The average distance of covalent OH bonds is found 0.01 Å larger in the quantum limit than in the classical one. The OO distances are elongated by 0.03 Å in the quantum simulations at 50 K. Bond distance fluctuations are large as a consequence of the zero-point vibrations. The analysis of the H-bond network shows that the liquid droplet is more structured in the classical limit than in the quantum case. The average kinetic and potential energy of the ice and water droplets on graphite has been compared with the values of ice Ih and liquid water as a function of temperature. The droplet kinetic energy shows a temperature dependence similar to the one of liquid water, without apparent discontinuity at temperatures where the droplet is solid. However, the droplet potential energy becomes significantly larger than the one of ice or water at the same temperature. In the quantum limit, the ice droplet is more expanded than in a classical description. Liquid droplets display identical density profiles and liquid-vapor interfaces in the quantum and classical limits. The value of the contact angle is not influenced by quantum effects. Contact angles of droplets decrease as the size of the water droplet increases which implies a positive sign of the line tension of the droplet. [ABSTRACT FROM AUTHOR]

Based on a mesoscale model developed recently for polyamide-66, here we present a simple algorithm for reinserting the atomistic details neglected in the coarse-grained (CG) description. The resulting CG and detailed models are tested successfully against several structural properties including the number of hydrogen bonds (HBs). From a quantitative analysis of the HB dynamics and thermodynamics it turns out that the CG model is characterized by a weaker HB network than the corresponding atomic model. We show that the relaxation of the HB network and the diffusion of the polymer chains are coupled. Moreover, we find that the temperature-dependent scaling factor accounting for the fast dynamics of the CG model is strongly linked to the relaxation time of the HB at each temperature. [ABSTRACT FROM AUTHOR]

Thermal diffusion forced Rayleigh scattering measurements on binary mixtures of carbon tetrabromide (CBr4), tetraethylsilane, and di-tert-butylsilane in carbon tetrachloride (CCl4) are reported at different temperatures and concentrations. The Soret coefficient of CBr4 in CCl4 is positive and ST of both silanes in CCl4 is negative, which implies that the heavier component always moves to the cold side. This is the expected behavior for unpolar simple molecules. Both silanes have the same mass so the influence of the difference in shape and moment of inertia could be studied. For all three systems, ST decreases with decreasing CCl4 concentration. The results are discussed in the framework of thermodynamic theories and the Hildebrand parameter concept. Additionally, the Soret coefficients for both silane/CCl4 systems were determined by nonequilibrium molecular-dynamics calculations. The simulations predict the correct direction of the thermophoretic motion and reflect the stronger drive toward the warm side for di-tert-butylsilane compared to the more symmetric tetraethylsilane. The values deviate systematically between 9% and 18% from the experimental values. [ABSTRACT FROM AUTHOR]

Ethanol is highly effective against various enveloped viruses and can disable the virus by disintegrating the protective envelope surrounding it. The interactions between the coronavirus envelope (E) protein and its membrane environment play key roles in the stability and function of the viral envelope. By using molecular dynamics simulation, we explore the underlying mechanism of ethanol-induced disruption of a model coronavirus membrane and, in detail, interactions of the E-protein and lipids. We model the membrane bilayer as N-palmitoyl-sphingomyelin and 1-palmitoyl-2-oleoylphosphatidylcholine lipids and the coronavirus E-protein. The study reveals that ethanol causes an increase in the lateral area of the bilayer along with thinning of the bilayer membrane and orientational disordering of lipid tails. Ethanol resides at the head–tail region of the membrane and enhances bilayer permeability. We found an envelope-protein-mediated increase in the ordering of lipid tails. Our simulations also provide important insights into the orientation of the envelope protein in a model membrane environment. At ∼25 mol. % of ethanol in the surrounding ethanol–water phase, we observe disintegration of the lipid bilayer and dislocation of the E-protein from the membrane environment. [ABSTRACT FROM AUTHOR]

A method for automatic adjustment of force field parameters to known liquid properties is described. The method works by coupling the time derivative of the force field parameter to the deviation of the actual value of the observable from prescribed reference value. The method is generally applicable, if (i) a strong relationship between a parameter and an observable exists, and (ii) if this relationship is monotonic within the convergence interval of the parameter. The method is applied to the Lennard-Jones potential energy function. It is shown computationally that it is feasible to couple the Lennard-Jones ε parameter to the heat of vaporization or to the chemical potential, and the Lennard-Jones σ parameter to the pressure or the diffusion coefficient of a liquid. It is also shown that it is possible to couple simultaneously two parameters to two observables. With the range of applicability established, the technique is then tested on liquid mercury. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper double differential cross sections are calculated for the interaction of electrons with a water molecule, a cluster of water molecules, and thereby in a certain approximation for liquid water. It is intended to use the data generated, in a Monte Carlo track structure code, so that the data needs to be comprehensive and accurate especially where the cross sections are largest. The method employed uses only the electron density which is calculated by means of LCAO methods using extended basis sets of atomic wave functions to approximate the total wave function. The response of the system is then calculated via an integral formulation of the density functional theory based on a path integral representation of the one particle Green’s function. This leads in the first approximation to the local density approximation in a modified form which can now be derived rigorously. The DDCS’s can be expressed in terms of the linear response of the molecular system to a moving charge. [ABSTRACT FROM AUTHOR]

The absorption properties of a dye molecule depend on its orientation relative to the light source. Thus the ability to predict how well a particular dye aligns with a liquid crystal host will improve the design of smart materials. One measurement of this alignment is the order parameter, which can be calculated from molecular dynamics simulations. The results for three dyes are presented here. The orientation of the long molecular axis of the dye relative to the liquid crystal director can range from perpendicular to parallel, with the dyes studied having an average order para- meter of the dye similar to the average order parameter of the host. [ABSTRACT FROM AUTHOR]

We demonstrate that polymer number distribution (PND) for polymer grafted nanoparticles (NPs) fabricated via the grafting-to technique can be described, without any fitting parameters, as a function of the conversion of polymer chains. This distribution function is convenient to be applied since the variables in PND are directly linked to experimental measurements and easy to be obtained. As an independent validation, the molecular dynamics simulation in this study is important since the experimental approach may be prone to artifacts that result from the complex parameters. This distribution is further generalized to describe the PNDs for polymer grafted NPs fabricated via the grafting-from technique. Our study implies that the grafting process, no matter grafting-to or grafting-from, does not alter the heterogeneity. Our results also provide evidence that the Poisson model, often invoked to describe the PND in previous experiments, is not accurate. We also show that the binomial form function of PND will not break down even in the cases of relatively large polymer chain length, high binding site density, and high polymer concentration. This function is quite effective since it naturally involves most influencing factors through polymer chain conversion. This study helps to better understand the ligand chain number distribution for polymer-grafted NPs fabricated via both grafting-to and grafting-from techniques. [ABSTRACT FROM AUTHOR]

The mechanical properties of gecko setae and spatulae are investigated with a coarse-grained model having two bead types. The two-bead model is based on both experimental information of the internal structure of setae and the chemical amino acid composition. Because the seta is composed of a stiff fibril region and a soft matrix region, we model each of the regions separately. Our model is parameterized in a bottom-up way, and it successfully predicts essential mechanical properties without optimization against the macroscopic properties of keratin. Young's modulus of the fibril area (13.2 ± 0.02 GPa) is 6 times stiffer than that of the pure matrix (2.13 ± 0.059 GPa). Because the volume fraction of the matrix decreases toward the top of a seta, its distal area should be stiffer than its proximal area. The anisotropy of the fibrils is clearly confirmed by the comparison between Young's modulus and the shear modulus of the fibril region. Our model also lends some support to the notion that water uptake selectively weakens the axial cohesion of the fibrils, which leads to the experimentally observed plateau in the stress-strain curves beyond 2% strain for setae under high relative humidity. [ABSTRACT FROM AUTHOR]

A metadynamics scheme is presented in which the free energy surface is filled with progressively adding adaptive biasing potentials, obtained from the accumulated probability distribution of the collective variables. Instead of adding Gaussians with assigned height and width in conventional metadynamics method, here we add a more realistic adaptive biasing potential to the Hamiltonian of the system. The shape of the adaptive biasing potential is adjusted on the fly by sampling over the visited states. As the top of the barrier is approached, the biasing potentials become wider. This decreases the problem of trapping the system in the niches, introduced by the addition of Gaussians of fixed height in metadynamics. Our results for the free energy profiles of three test systems show that this method is more accurate and converges more quickly than the conventional metadynamics, and is quite comparable (in accuracy and convergence rate) with the well-tempered metadynamics method. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

In a recent publication, a reverse nonequilibrium molecular dynamics method was introduced to calculate the mutual diffusion (binary diffusion, interdiffusion) coefficient of binary Lennard-Jones mixture directly. In this work, modification is made to this method for calculation the mutual diffusion coefficient of complicated binary mixture of molecules containing the same number of particle in calculation. As test, this method is applied to calculate the mutual diffusion coefficient of water/deuterium oxide (H2O/D2O) and benzene/cyclohexane (C6H6/C6H12) systems. Steady mass flows are induced by suitably exchanging molecule positions and velocities in different regions. The analysis of the resulting steady state concentration profiles allows the calculation of mutual diffusion coefficient. The obtained results are qualitative agreement with the references. The excess energy introduced by swapping molecules becomes strong when the studied mixture contains large and/or complicated molecules. For the systems studied, however, a standard thermostat is still able to remove the excess energy efficiently. [ABSTRACT FROM AUTHOR]