Self-Assembly Pathways of Triblock Janus Particles into 3D Open Lattices.

The self-assembly of triblock Janus particles is simulated from a fluid to 3D open lattices: pyrochlore, perovskite, and diamond. The coarse-grained model explicitly takes into account the chemical details of the Janus particles (attractive patches at the poles and repulsion around the equator) and it contains explicit solvent particles. Hydrodynamic interactions are accounted for by dissipative particle dynamics. The relative stability of the crystals depends on the patch width. Narrow, intermediate, and wide patches stabilize the pyrochlore-, the perovskite-, and the diamond-lattice, respectively. The nucleation of all three lattices follows a two-step mechanism: the particles first agglomerate into a compact and disordered liquid cluster, which does not crystallize until it has grown to a threshold size. Second, the particles reorient inside this cluster to form crystalline nuclei. The free-energy barriers for the nucleation of pyrochlore and perovskite are ≈10 kBT, which are close to the nucleation barriers of previously studied 2D kagome lattices. The barrier height for the nucleation of diamond, however, is much larger (>20 kBT), as the symmetry of the triblock Janus particles is not perfect for a diamond structure. The large barrier is associated with the reorientation of particles, i.e., the second step of the nucleation mechanism.

Predicting the artificial dynamical acceleration of binary hydrocarbon mixtures upon coarse-graining with roughness volumes and simple averaging rules.

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.

Understanding Humidity-Enhanced Adhesion of Geckos: Deep Neural Network-Assisted Multi-Scale Molecular Modeling.

A higher relative humidity leads to an increased sticking power of gecko feet to surfaces. The molecular mechanism responsible for this increase, however, is not clear. Capillary forces, water mediating keratin-surface contacts and water-induced softening of the keratin are proposed as candidates. In previous work, strong evidence for water mediation is found but indirect effects via increased flexibility are not completely ruled out. This article studies the latter hypothesis by a bottom-up coarse-grained mesoscale model of an entire gecko spatula designed without explicit water particles, so that capillary action and water-mediation are excluded. The elasticity of this model is adjusted with a deep neural network to atomistic elastic constants, including water at different concentrations. Our results show clearly that on nanoscopic flat surfaces, the softening of keratin by water uptake cannot nearly account for the experimentally observed increase in gecko sticking power. Here, the dominant mechanism is the mediation of keratin-surface contacts by intervening water molecules. This mechanism remains important on nanostructured surfaces. Here, however, a water-induced increase of the keratin flexibility may enable the spatula to follow surface features smaller than itself and thereby increase the number of contacts with the surface. This leads to an appreciable but not dominant contribution to the humidity-increased adhesion. Recently, by atomistic grand-canonical molecular dynamics simulation, the room-temperature isotherm is obtained for the sorption of water into gecko keratin, to the authors' knowledge, the first such relation for any beta-keratin. In this work, it relates the equilibrium water content of the keratin to the ambient relative humidity.

Ion mobility in gas and liquid phases: How much orthogonality is obtained in capillary electrophoresis-ion mobility-mass spectrometry?

Ion mobility-mass spectrometry (IM-MS) is an ever-evolving tool to separate ions in the gas phase according to electrophoretic mobility with subsequent mass determination. CE is rarely coupled to IM-MS, possibly due to similar separation mechanisms based on electrophoretic mobility. Here, we investigate the orthogonality of CE and ion mobility (IM) by analyzing a complex peptide mixture (tryptic digest of HeLa proteins) with trapped ion mobility mass spectrometry (TIMS-MS). Using the nanoCEasy interface, excellent sensitivity was achieved by identifying thousands of peptides and achieving a peak capacity of 7500 (CE: 203-323 in a 150 cm long capillary, IM: 27-31). Plotting CE versus mass and CE versus (inverse) mobility, a clear grouping in curved striped patterns is observed according to the charge-to-size and mass-to-charge ratios. The peptide charge in the acidic background electrolyte can be estimated from the number of basic amino acids, with a few exceptions where neighboring effects reduce the positive charge. A surprisingly high orthogonality of CE and IM is observed, which is obviously caused by solvation effects leading to different charges and sizes in the liquid phase compared to the gas phase. A high orthogonality of CE and ion mobility is expected to be observed for other peptide samples as well as other substance classes, making CE-IM-MS a promising tool for various applications.

Gecko Adhesion on Flat and Rough Surfaces: Simulations with a Multi-Scale Molecular Model.

A multiscale modeling approach is used to develop a particle-based mesoscale gecko spatula model that is able to link atomistic simulations and mesoscale (0.44 µm) simulations. It is used to study the detachment of spatulae from flat as well as nanostructured surfaces. The spatula model is based on microscopical information about spatulae structure and on atomistic molecular simulation results. Target properties for the coarse-graining result from a united-atom model of gecko keratin in periodic boundary conditions (PBC), previously developed by the authors. Pull-off forces necessary to detach gecko keratin under 2D PBC parallel to the surface are previously overestimated when only a small region of a spatula is examined. It is shown here that this is due to the restricted geometry (i.e., missing peel-off mode) and not model parameters. The spatula model peels off when pulled away from a surface, both in the molecular picture of the pull-off process and in the force-extension curve of non-equilibrium simulations mimicking single-spatula detachment studied with atomic force microscopy equipment. The force field and spatula model can reproduce experimental pull-off forces. Inspired by experimental results, the underlying mechanism that causes pull-off forces to be at a minimum on surfaces of varying roughnesses is also investigated. A clear sigmoidal increase in the pull-off force of spatulae with surface roughness shows that adhesion is determined by the ratio between spatula pad area and the area between surface peaks. Experiments showed a correlation with root-mean-square roughness of the surface, but the results of this work indicate that this is not a causality but depends on the area accessible.

Gecko adhesion: a molecular-simulation perspective on the effect of humidity.

Gecko adhesion is investigated by molecular dynamics simulations. It is known, that the gecko adhesion system shows increased pull-off forces in humid environments. A coarse-grained model of gecko beta keratin, previously developed in our group, is extended and used to elucidate the molecular mechanisms involved in this humidity effect on adhesion. We show that neither the change of the elastic properties of gecko keratin, nor capillary forces, can solely explain the increased pull-off forces of wet gecko keratin. Instead, we establish a molecular picture of gecko adhesion where the interplay between capillary bridges and a mediator effect of water, enhances pull-off forces, consistent with observations in AFM experiments at high humidities. We find that water density is raised locally, in molecular scale asperities of the gecko keratin and that this increase in local water density smoothes the surface-spatula interface. Water, which is absorbed into the keratin, acts as a mediator, and leads during pull-off to the dominant contribution in the van der Waals energy, because the dispersion interactions between water and surface are primarily opposing the pull-off.

Computing the Work of Solid-Liquid Adhesion in Systems with Damped Coulomb Interactions via Molecular Dynamics: Approaches and Insights.

Recently, the dry-surface method [ Langmuir 2016, 31, 8335-8345] has been developed to compute the work of adhesion of solid-liquid and other interfaces using molecular dynamics via thermodynamic integration. Unfortunately, when long-range Coulombic interactions are present in the interface, a special treatment is required, such as solving additional Poisson equations, which is usually not implemented in generic molecular dynamics software, or as fixing some groups of atoms in place, which is undesirable most of the time. In this work, we replace the long-range Coulombic interactions with damped Coulomb interactions, and explore several thermal integration paths. We demonstrate that regardless of the integration path, the same work of adhesion values are obtained as long as the path is reversible, but the numerical efficiency differs vastly. Simple scaling of the interactions is most efficient, requiring as little as 8 sampling points, followed by changing the Coulomb damping parameter, while modifying the Coulomb interaction cutoff length performs worst. We also demonstrate that switching long-range Coulombic interactions to damped ones results in a higher work of adhesion by about 10 mJ/m2 because of slightly different liquid molecule orientation at the solid-liquid interface, and this value is mostly unchanged for surfaces with substantially different Coulombic interactions at the solid-liquid interface. Finally, even though it is possible to split the work of adhesion into van der Waals and Coulomb components, it is known that the specific per-component values are highly dependent on the integration path. We obtain an extreme case, which demonstrates that caution should be taken even when restricting to qualitative comparison.

Contact line friction and dynamic contact angles of a capillary bridge between superhydrophobic nanostructured surfaces.

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.

Atomistic hybrid particle-field molecular dynamics combined with slip-springs: Restoring entangled dynamics to simulations of polymer melts.

In hybrid particle-field (hPF) simulations (J. Chem. Phys., 2009 130, 214106), the entangled dynamics of polymer melts is lost due to chain crossability. Chains cross, because the field-treatment of the nonbonded interactions makes them effectively soft-core. We introduce a multi-chain slip-spring model (J. Chem. Phys., 2013 138, 104907) into the hPF scheme to mimic the topological constraints of entanglements. The structure of the polymer chains is consistent with that of regular molecular dynamics simulations and is not affected by the introduction of slip-springs. Although slight deviations are seen at short times, dynamical properties such as mean-square displacements and reorientational relaxation times are in good agreement with traditional molecular dynamics simulations and theoretical predictions at long times.

Suppressing the rebound of impacting droplets from solvophobic surfaces by polymer additives: polymer adsorption and molecular mechanisms.

A liquid droplet impacting on a solvophobic surface normally rebounds. The rebound is suppressed by a small amount of dissolved polymer. In this work, using multi-body dissipative particle dynamics simulations, two anti-rebound mechanisms, the slow-retraction and the slow-hopping mechanisms, are identified. Which of them dominates depends on the polymer-surface attraction strength. However, these two mechanisms do not exclude each other but may coexist. During the droplet rebound, the surface-adsorbed polymer acts in two ways: the adsorbed beads mediate the solvent-surface interactions, and the highly stretching unadsorbed polymer segment exerts a retraction force on the liquid. Both actions increase the friction against retraction and the resistance against hopping. We also investigate the effects of the molecular weight and the concentration of the polymer additive, the droplet size, and the impact velocity on the rebound tendency. As the first work to provide a microscopic explanation of the anti-rebound mechanism by polymer additives, this study allows better understanding of wetting behavior by polymer-solution droplets.

The role of the envelope protein in the stability of a coronavirus model membrane against an ethanolic disinfectant.

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.

Coarse-grained molecular dynamics simulation of activated penetrant transport in glassy polymers.

Membrane separations of gas mixtures strive to maximize the permeability of a desired species while keeping out undesired ones. Permeability vs. selectivity data from many polymer membranes for a given gas pair with diameters dA and dB are typically collected in a "Robeson plot"', and are bound from above by a line with a slope λ = (dB/dA)2 - 1. A microscopic understanding of this relationship, especially λ, is still missing. We perform molecular dynamics simulations of penetrant diffusion using three different coarse-grained polymer models over a wide range of penetrant sizes, temperatures, and monomer densities. The empirically relevant λ = (dB/dA)2 - 1 is only found for polymers that are either supercooled liquids with caged segmental dynamics or glasses and when the penetrant size is approximately half the Kuhn length of the chains, for which the penetrant diffusion is an activated process.

Local bond order parameters for accurate determination of crystal structures in two and three dimensions.

Local order parameters for the characterization of liquid and different two- and three-dimensional crystalline structures are presented. The order parameters are expressed in terms of the angular correlations between a vector (defined in terms of the spherical harmonics, identifying the local environment around a central particle) and its neighboring vectors. For the three-dimensional systems, we have undertaken simulation of the Lennard-Jones (12-6) particles and metallic systems at the melting temperature. The proposed order parameters are shown to accurately discriminate between liquid, fcc, hcp, and bcc phases. The simulated two-dimensional systems consist of liquid, Kagome, square, honeycomb, and hexagonal phases formed from a solution of triblock Janus colloidal particles, sedimented on the top of a supporting surface. The presented order parameters resolve all phases. A comparison was made between the predictive ability of the present order parameters and the popular three-dimensional [Lechner and Dellago, J. Chem. Phys., 2008, 129, 114707] and two-dimensional [Mermin, Phys. Rev., 1968, 176, 250] order parameters in the literature in the identification of crystal structures. In both cases, advancements in the present scheme, over the existing methods in the literature, are seen.

Molecular dynamics analysis of the influence of Coulomb and van der Waals interactions on the work of adhesion at the solid-liquid interface.

We investigated the solid-liquid work of adhesion of water on a model silica surface by molecular dynamics simulations, where a methodology previously developed to determine the work of adhesion through thermodynamic integration was extended to a system with long-range electrostatic interactions between solid and liquid. In agreement with previous studies, the work of adhesion increased when the magnitude of the surface polarity was increased. On the other hand, we found that when comparing two systems with and without solid-liquid electrostatic interactions, which were set to have approximately the same total solid-liquid interfacial energy, former had a significantly smaller work of adhesion and a broader distribution in the interfacial energies, which has not been previously reported in detail. This was explained by the entropy contribution to the adhesion free energy; i.e., the former with a broader energy distribution had a larger interfacial entropy than the latter. While the entropy contribution to the work of adhesion has already been known, as a work of adhesion itself is free energy, these results indicate that, contrary to common belief, wetting behavior such as the contact angle is not only governed by the interfacial energy but also significantly affected by the interfacial entropy. Finally, a new interpretation of interfacial entropy in the context of solid-liquid energy variance was offered, from which a fast way to qualitatively estimate the work of adhesion was also presented.

Adaptive-numerical-bias metadynamics.

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.

Solid-Liquid Interface Thermal Resistance Affects the Evaporation Rate of Droplets from a Surface: A Study of Perfluorohexane on Chromium Using Molecular Dynamics and Continuum Theory.

We study the role of solid-liquid interface thermal resistance (Kapitza resistance) on the evaporation rate of droplets on a heated surface by using a multiscale combination of molecular dynamics (MD) simulations and analytical continuum theory. We parametrize the nonbonded interaction potential between perfluorohexane (C6F14) and a face-centered-cubic solid surface to reproduce the experimental wetting behavior of C6F14 on black chromium through the solid-liquid work of adhesion (quantity directly related to the wetting angle). The thermal conductances between C6F14 and (100) and (111) solid substrates are evaluated by a nonequilibrium molecular dynamics approach for a liquid pressure lower than 2 MPa. Finally, we examine the influence of the Kapitza resistance on evaporation of droplets in the vicinity of a three-phase contact line with continuum theory, where the thermal resistance of liquid layer is comparable with the Kapitza resistance. We determine the thermodynamic conditions under which the Kapitza resistance plays an important role in correctly predicting the evaporation heat flux.

Contact angles from Young's equation in molecular dynamics simulations.

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 non-polar 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.

Formation of coffee-stain patterns at the nanoscale: The role of nanoparticle solubility and solvent evaporation rate.

When droplets of nanoparticle suspension evaporate from surfaces, they leave behind a deposit of nanoparticles. The mechanism of evaporation-induced pattern formation in the deposit is studied by molecular dynamics simulations for sessile nanodroplets. The influence of the interaction between nanoparticles and liquid molecules and the influence of the evaporation rate on the final deposition pattern are addressed. When the nanoparticle-liquid interaction is weaker than the liquid-liquid interaction, an interaction-driven or evaporation-induced layer of nanoparticles appears at the liquid-vapor interface and eventually collapses onto the solid surface to form a uniform deposit independently of the evaporation rate. When the nanoparticle-liquid and liquid-liquid interactions are comparable, the nanoparticles are dispersed inside the droplet and evaporation takes place with the contact line pinned at a surface defect. In such a case, a pattern with an approximate ring-like shape is found with fast evaporation, while a more uniform distribution is observed with slower evaporation. When the liquid-nanoparticle interaction is stronger than the liquid-liquid interaction, evaporation always occurs with receding contact line. The final deposition pattern changes from volcano-like to pancake-like with decreasing evaporation rate. These findings might help to design nanoscale structures like nanopatterns or nanowires on surface through controlled solvent evaporation.

A kinetic chain growth algorithm in coarse-grained simulations.

We propose a kinetic chain growth algorithm for coarse-grained (CG) simulations in this work. By defining the reaction probability, it delivers a description of consecutive polymerization process. This algorithm is validated by modeling the process of individual styrene monomers polymerizing into polystyrene chains, which is proved to correctly reproduce the properties of polymers in experiments. By bridging the relationship between the generic chain growth process in CG simulations and the chemical details, the impediment to reaction can be reflected. Regarding to the kinetics, it models a polymerization process with an Arrhenius-type reaction rate coefficient. Moreover, this algorithm can model both the gradual and jump processes of the bond formation, thus it readily encompasses several kinds of previous CG models of chain growth. With conducting smooth simulations, this algorithm can be potentially applied to describe the variable macroscopic features of polymers with the process of polymerization. The algorithm details and techniques are introduced in this article. © 2016 Wiley Periodicals, Inc.

Adsorption and separation of binary and ternary mixtures of SO2, CO2 and N2 by ordered carbon nanotube arrays: grand-canonical Monte Carlo simulations.

The adsorption and separation behavior of SO2-CO2, SO2-N2 and CO2-N2 binary mixtures in bundles of aligned double-walled carbon nanotubes is investigated using the grand-canonical Monte Carlo (GCMC) method and ideal adsorbed solution theory. Simulations were performed at 303 K with nanotubes of 3 nm inner diameter and various intertube distances. The results showed that the packing with an intertube distance d = 0 has the highest selectivity for SO2-N2 and CO2-N2 binary mixtures. For the SO2-CO2 case, the optimum intertube distance for having the maximum selectivity depends on the applied pressure, so that at p < 0.8 bar d = 0 shows the highest selectivity and at 0.8 bar < p < 2.5 bar, the highest selectivity belongs to d = 0.5 nm. Ideal adsorbed solution theory cannot predict the adsorption of the binary systems containing SO2, especially when d = 0. As the intertube distance is increased, the ideal adsorbed solution theory based predictions become closer to those of GCMC simulations. Only in the case of CO2-N2, ideal adsorbed solution theory is everywhere in good agreement with simulations. In a ternary mixture of all three gases, the behavior of SO2 and CO2 remains similar to that in a SO2-CO2 binary mixture because of the weak interaction between N2 molecules and CNTs.