String-like Clusters and Cooperative Motion in a Model Glass-Forming Liquid

A large-scale molecular dynamics simulation is performed on a glass-forming Lennard-Jones mixture to determine the nature of dynamical heterogeneities which arise in this model fragile liquid. We observe that the most mobile particles exhibit a cooperative motion in the form of string-like paths (``strings'') whose mean length and radius of gyration increase as the liquid is cooled. The length distribution of the strings is found to be similar to that expected for the equilibrium polymerization of linear polymer chains.Comment: 6 pages of RevTex, 6 postscript figures, uses epsf.st

Dynamical heterogeneities in a supercooled Lennard-Jones liquid

We present the results of a large scale molecular dynamics computer simulation study in which we investigate whether a supercooled Lennard-Jones liquid exhibits dynamical heterogeneities. We evaluate the non-Gaussian parameter for the self part of the van Hove correlation function and use it to identify ``mobile'' particles. We find that these particles form clusters whose size grows with decreasing temperature. We also find that the relaxation time of the mobile particles is significantly shorter than that of the bulk, and that this difference increases with decreasing temperature.Comment: 8 pages of RevTex, 4 ps figure

Segue Between Favorable and Unfavorable Solvation

Solvation of small and large clusters are studied by simulation, considering a range of solvent-solute attractive energy strengths. Over a wide range of conditions, both for solvation in the Lennard-Jones liquid and in the SPC model of water, it is shown that the mean solvent density varies linearly with changes in solvent-solute adhesion or attractive energy strength. This behavior is understood from the perspective of Weeks' theory of solvation [Ann. Rev. Phys. Chem. 2002, 53, 533] and supports theories based upon that perspective.Comment: 8 pages, 7 figure

Melting of Partially Fluorinated Graphene: From Detachment of Fluorine Atoms to Large Defects and Random Coils

The melting of fluorographene is very unusual and depends strongly on the degree of fluorination. For temperatures below 1000 K, fully fluorinated graphene (FFG) is thermo-mechanically more stable than graphene but at T$_m\approx$2800 K FFG transits to random coils which is almost twice lower than the melting temperature of graphene, i.e. 5300 K. For fluorinated graphene (PFG) up to 30 % ripples causes detachment of individual F-atoms around 2000 K while for 40-60 % fluorination, large defects are formed beyond 1500 K and beyond 60% of fluorination F-atoms remain bonded to graphene until melting. The results agree with recent experiments on the dependence of the reversibility of the fluorination process on the percentage of fluorination.Comment: 16 pages, 6 figure

Cones, pringles, and grain boundary landscapes in graphene topology

A polycrystalline graphene consists of perfect domains tilted at angle {\alpha} to each other and separated by the grain boundaries (GB). These nearly one-dimensional regions consist in turn of elementary topological defects, 5-pentagons and 7-heptagons, often paired up into 5-7 dislocations. Energy G({\alpha}) of GB computed for all range 0<={\alpha}<=Pi/3, shows a slightly asymmetric behavior, reaching ~5 eV/nm in the middle, where the 5's and 7's qualitatively reorganize in transition from nearly armchair to zigzag interfaces. Analysis shows that 2-dimensional nature permits the off-plane relaxation, unavailable in 3-dimensional materials, qualitatively reducing the energy of defects on one hand while forming stable 3D-landsapes on the other. Interestingly, while the GB display small off-plane elevation, the random distributions of 5's and 7's create roughness which scales inversely with defect concentration, h ~ n^(-1/2)Comment: 9 pages, 4 figure

The Influence of Molecular Adsorption on Elongating Gold Nanowires

Using molecular dynamics simulations, we study the impact of physisorbing adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs) undergoing elongation. We used various adsorbate models in our simulations, with each model giving rise to a different surface coverage and mobility of the adsorbed phase. We find that the local structure and mobility of the adsorbed phase remains relatively uniform across all segments of an elongating AuNW, except for the thinning region of the wire where the high mobility of Au atoms disrupts the monolayer structure, giving rise to higher solvent mobility. We analyzed the AuNW trajectories by measuring the ductile elongation of the wires and detecting the presence of characteristic structural motifs that appeared during elongation. Our findings indicate that adsorbates facilitate the formation of high-energy structural motifs and lead to significantly higher ductile elongations. In particular, our simulations result in a large number of monatomic chains and helical structures possessing mechanical stability in excess of what we observe in vacuum. Conversely, we find that a molecular species that interacts weakly (i.e., does not adsorb) with AuNWs worsens the mechanical stability of monatomic chains.Comment: To appear in Journal of Physical Chemistry

Spreading Dynamics of Polymer Nanodroplets

The spreading of polymer droplets is studied using molecular dynamics simulations. To study the dynamics of both the precursor foot and the bulk droplet, large drops of ~200,000 monomers are simulated using a bead-spring model for polymers of chain length 10, 20, and 40 monomers per chain. We compare spreading on flat and atomistic surfaces, chain length effects, and different applications of the Langevin and dissipative particle dynamics thermostats. We find diffusive behavior for the precursor foot and good agreement with the molecular kinetic model of droplet spreading using both flat and atomistic surfaces. Despite the large system size and long simulation time relative to previous simulations, we find no evidence of hydrodynamic behavior in the spreading droplet.Comment: Physical Review E 11 pages 10 figure

Fluctuations of water near extended hydrophobic and hydrophilic surfaces

We use molecular dynamics simulations of the SPC-E model of liquid water to derive probability distributions for water density fluctuations in probe volumes of different shapes and sizes, both in the bulk as well as near hydrophobic and hydrophilic surfaces. To obtain our results, we introduce a biased sampling of coarse-grained densities, which in turn biases the actual solvent density. The technique is easily combined with molecular dynamics integration algorithms. Our principal result is that the probability for density fluctuations of water near a hydrophobic surface, with or without surface-water attractions, is akin to density fluctuations at the water-vapor interface. Specifically, the probability of density depletion near the surface is significantly larger than that in bulk. In contrast, we find that the statistics of water density fluctuations near a model hydrophilic surface are similar to that in the bulk

Structure and dynamics of ring polymers: entanglement effects because of solution density and ring topology

The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typically profiled as a function of ring contour length at fixed solution density. Here, we use a different approach to investigate numerically the equilibrium and kinetic properties of solutions of model ring polymers. Specifically, the ring contour length is maintained fixed, while the interplay of inter- and intra-chain entanglement is modulated by varying both solution density (from infinite dilution up to \approx 40 % volume occupancy) and ring topology (by considering unknotted and trefoil-knotted chains). The equilibrium metric properties of rings with either topology are found to be only weakly affected by the increase of solution density. Even at the highest density, the average ring size, shape anisotropy and length of the knotted region differ at most by 40% from those of isolated rings. Conversely, kinetics are strongly affected by the degree of inter-chain entanglement: for both unknots and trefoils the characteristic times of ring size relaxation, reorientation and diffusion change by one order of magnitude across the considered range of concentrations. Yet, significant topology-dependent differences in kinetics are observed only for very dilute solutions (much below the ring overlap threshold). For knotted rings, the slowest kinetic process is found to correspond to the diffusion of the knotted region along the ring backbone.Comment: 17 pages, 11 figure

Large-Scale Atomistic Simulations of Environmental Effects on the Formation and Properties of Molecular Junctions

Using an updated simulation tool, we examine molecular junctions comprised of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and inter-electrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multi-molecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high density. We demonstrate that tip geometry and monolayer interactions, two factors that are often neglected in simulation, affect the bonding geometry and tilt angle of bridged molecules. We further show that the structures of bridged molecules at 298 and 77 K are similar.Comment: To appear in ACS Nano, 30 pages, 5 figure