Non-bonded Particles Research Articles

Hierarchical Machine Learning of Low-Resolution Coarse-Grained Free Energy Potentials.

A force-matching-based method for supervised machine learning (ML) of coarse-grained (CG) free energy (FE) potentials─known as multiscale coarse-graining via force-matching (MSCG/FM)─is an efficient method to develop microscopically informed CG models that are thermodynamically and statistically equivalent to the reference microscopic models. For low-resolution models, when the coarse-graining is at supramolecular scales, objective-oriented clustering of nonbonded particles is required and the reduced description becomes a function of the clustering algorithm. In the present work, we explore the dependence of the ML of the CG Helmholtz FE potential on the clustering algorithm. We consider coarse-graining based on partitional (k-means, leading to Voronoi diagram) and hierarchical agglomerative (bottom-up) clustering algorithms common in unsupervised ML and develop theory connecting the MSCG/FM learned CG Helmholtz potential and the clustering statistics. By combining the agglomerative clustering and the MSCG/FM learning in a recursive manner, we propose an efficient ML methodology to develop the fine-to-low resolution hierarchies of the CG models. The methodology does not suffer from degrading accuracy or increased computational cost to construct larger hierarchies and as such does not impose an upper size limitation of the CG particles resulting from the extended hierarchies. The utility of the methodology is demonstrated by obtaining the bottom-up agglomerative hierarchy for liquid nitromethane from all-atom molecular dynamics (MD) simulations. For agglomerative hierarchies, we prove the existence of renormalization group transformations that indicate self-similarity and allow for learning the low-resolution MSCG/FM potentials at low computational cost by rescaling and renormalizing the certain finer-resolution members of the hierarchy. The hierarchies of the CG models can be used to carry out simulations under constant-pressure conditions.

Cloaking Transition of Droplets on Lubricated Brushes.

We study the equilibrium properties and the wetting behavior of a simple liquid on a polymer brush, with and without the presence of lubricant by multibody Dissipative Particle Dynamics simulations. The lubricant is modeled as a polymeric liquid consisting of short chains that are chemically identical with the brush polymers. We investigate the behavior of the brush in terms of the grafting density and the amount of lubricant present. Regarding the wetting behavior, we study a sessile droplet on top of the brush. The droplet consists of nonbonded particles that form a dense phase. Our model and choice of parameters result in the formation of a wetting ridge and in the cloaking of the droplet by the lubricant; i.e., the lubricant chains creep up onto the droplet and eventually cover its surface completely. Cloaking is a phenomenon that is observed experimentally and is of integral importance to the dynamics of sliding droplets. We quantify the cloaking in terms of its thickness, which increases with the amount of lubricant present. The analysis reveals a well-defined transition point where the cloaking sets in. We propose a thermodynamic theory to explain this behavior. In addition, we investigate the dependence of the contact angles on the size of the droplet and the possible effect of line tension. We quantify the variation of the contact angle with the curvature of the contact line on a lubricant free brush and find a negative value for the line tension. Finally we investigate the effect of cloaking/lubrication on the contact angles and the wetting ridge. We find that lubrication and cloaking reduce the contact angles by a couple of degrees. The effect on the wetting ridge is a reduction in the extension of the brush chains near the three phase contact line, an effect that was also observed in experiments of droplets on cross-linked gels.

From canyons to valleys: Numerically continuing sticky-hard-sphere clusters to the landscapes of smoother potentials.

We study the energy landscapes of particles with short-range attractive interactions as the range of the interactions increases. Starting with the set of local minima for 6≤N≤12 hard spheres that are "sticky," i.e., they interact only when their surfaces are exactly in contact, we use numerical continuation to evolve the local minima (clusters) as the range of the potential increases, using both the Lennard-Jones and Morse families of interaction potentials. As the range increases, clusters merge, until at long ranges only one or two clusters are left. We compare clusters obtained by continuation with different potentials and find that for short and medium ranges, up to about 30% of particle diameter, the continued clusters are nearly identical, both within and across families of potentials. For longer ranges, the clusters vary significantly, with more variation between families of potentials than within a family. We analyze the mechanisms behind the merge events and find that most rearrangements occur when a pair of nonbonded particles comes within the range of the potential. An exception occurs for nonharmonic clusters, i.e., those that have a zero eigenvalue in their Hessian, which undergo a more global rearrangement.

On the theoretical description of the liquid-vapor coexistence of water-like models with square-well attraction and site-site chemical association

A liquid-vapor coexistence envelope for water-like models with square-well attraction between particles and with four attractive associating sites per particle has been investigated. The mean-field theory and the first-order mean spherical approximation for attractive interactions together with the first-order thermodynamic perturbation theory of Wertheim for association have been applied to construct the temperature - density and the temperature - chemical potential projections of the equation of state. In addition, the dependence of the fraction of non-bonded particles on the parameters of the models has been evaluated and analyzed. We explored a set of models with different square-well width and energy of associative interaction. In some cases a comparison with computer simulation data has been performed. For two specific parameter sets previously proposed to mimic water properties a comparison with experimental data for the vapor-liquid coexistence envelope and for vapor pressure has been performed. It is shown that the applied theoretical procedures are successful and can be used with confidence. On the other hand, they provide solid basis to apply in the theory of inhomogeneous associating fluids.

Weak links between fast mobility and local structure in molecular and atomic liquids.

We investigate by molecular-dynamics simulations, the fast mobility-the rattling amplitude of the particles temporarily trapped by the cage of the neighbors-in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

Effect of gas diffusion electrode pre-treatment by ultrasonic bath cleaning technique on proton exchange membrane fuel cell performance

Ultrasonic bath cleaning technique was successfully applied for the pre-treatment of the gas diffusion electrode (GDE) before membrane-electrode assembly (MEA). The results show that ultrasonic bath pre-treatment significantly improves MEA performance in all current density regions, especially at the high current density region. This technique also reduces the time of the MEA conditioning, at least 30%. Electrochemical impedance spectroscopy (EIS) results demonstrate that pre-treatment of GDEs by ultrasonic bath technique leads to a decrease in the cell impedance especially in the ohmic resistance, which is very well due to the GDE cleaning process.The investigation of the GDE performance under different relative humidity (RH) of gases indicates that ultrasonic bath pre-treatment of the GDE is caused a delay in GDE flooding specially at high RH. This result demonstrates that removing non-bonded particles or creating new transfer passage by ultrasonic bath improves transfer of species within the GDE.GDE pre-treatment carried out in two ultrasonic bath solvents; water and an aqueous solution of isopropyl alcohol 10% (v/v). Results indicate that the aqueous solution of isopropyl alcohol 10% (v/v) can improve mass transfer of species within the electrode as well as water compared to the untreated GDE.

Two‐dimensional distinct element modeling of the structure and growth of normal faults in multilayer sequences: 1. Model calibration, boundary conditions, and selected results

The distinct element method is used for modeling the growth of normal faults in layered sequences. The models consist of circular particles that can be bonded together with breakable cement. Size effects of the model mechanical properties were studied for a constant average particle size and various sample widths. The study revealed that the bulk strength of the model material decreases with increasing sample size. Consequently, numerical lab tests and the associated construction of failure envelopes were performed for the specific layer width to particle diameter ratios used in the multilayer models. The normal faulting models are composed of strong layers (bonded particles) and weak layers (nonbonded particles) that are deformed in response to movement on a predefined fault at the base of the sequence. The modeling reproduces many of the geometries observed in natural faults, including (1) changes in fault dip due to different modes of failure in the strong and weak layers, (2) fault bifurcation (splaying), (3) the flexure of strong layers and the rotation of associated blocks to form normal drag, and (4) the progressive linkage of fault segments. The model fault zone geometries and their growth are compared to natural faults from Kilve foreshore (Somerset, United Kingdom). Both the model and natural faults provide support for the well‐known general trend that fault zone width increases with increasing displacement.

Two‐dimensional distinct element modeling of the structure and growth of normal faults in multilayer sequences: 2. Impact of confining pressure and strength contrast on fault zone geometry and growth

The growth of normal faults in periodically layered sequences with varying strength contrast and at varying confining pressure is modeled using the distinct element method. The normal faulting models are composed of strong layers (bonded particles) and weak layers (nonbonded particles) that are deformed using a predefined fault at the base of the sequence. The model results suggest that faults in sequences with high strength contrast at low confining pressure are highly segmented because of different types of failure (extension versus shear failure) in the different layers. The degree of segmentation decreases as the strength contrast decreases and confining pressure increases. Faults at low confining pressure localize as extension (mode I) fractures within the strong layers and are later linked via shallow dipping faults in the weak ones. This leads to initial staircase geometries that, with increasing displacement, cause space problems that are later resolved by splaying and segmentation. As confining pressure increases, the modeled faults show a transition from extension to hybrid to shear fracture and an associated decrease in fault refraction, with a consequent decrease in fault surface irregularities. Therefore the mode of fracture which is active in the strong layers of a mechanical multilayer at a particular confining pressure exerts an important control on the final fault geometry.

Coarse Graining of Nonbonded Degrees of Freedom

We investigate the physical meaning of coarse-grained beads generated by coarse graining of nonbonded particles such as solvent molecules in a solution. Starting from the partition function, we analytically coarse grain an N-particle fluid to a system containing N-2 of the original particles plus a bead representing the two remaining particles. As a direct consequence of the lack of bonding interactions, the resulting effective potential becomes independent of the bead coordinates, i.e., ideal-gas-like, in the thermodynamic limit. Thus, there are no conservative forces between coarse-grained beads representing assemblies of nonbonded molecules nor between these beads and any other species in the system.

Molecular Dynamic Simulation of Side‐Chain Liquid Crystalline Elastomer

AbstractSummary: Molecular dynamic simulation of side chain liquid crystalline elastomer has been carried out. As an initial state a flexible polymer network in a low molecular liquid‐crystal (LC) solvent was used. The LC solvent comprises of anisotropic rod‐like semiflexible linear molecules (mesogens) composed of particles bonded into the chain by FENE potential. Rigidity of LC molecules was induced by a bending potential. All interactions between nonbonded particles are described by a repulsive Lennard‐Jones potential. For the systems with different values of density and order parameter obtained after sufficiently long trajectory the attachment of ends of mesogens to the polymer network was simulated. The kinetic of the process of mesogens attachment to network was studied as well as morphology of attachment. The structural and dynamical behaviour of side chain LC elastomer was studied and compared with systems of polymer network in low molecular LC solvent.