1,004 research outputs found
Evaporation of Lennard-Jones Fluids
Evaporation and condensation at a liquid/vapor interface are ubiquitous
interphase mass and energy transfer phenomena that are still not well
understood. We have carried out large scale molecular dynamics simulations of
Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to
investigate these processes with molecular detail. For LJ monomers in contact
with a vacuum, the evaporation rate is found to be very high with significant
evaporative cooling and an accompanying density gradient in the liquid domain
near the liquid/vapor interface. Increasing the chain length to just dimers
significantly reduces the evaporation rate. We confirm that mechanical
equilibrium plays a key role in determining the evaporation rate and the
density and temperature profiles across the liquid/vapor interface. The
velocity distributions of evaporated molecules and the evaporation and
condensation coefficients are measured and compared to the predictions of an
existing model based on kinetic theory of gases. Our results indicate that for
both monatomic and polyatomic molecules, the evaporation and condensation
coefficients are equal when systems are not far from equilibrium and smaller
than one, and decrease with increasing temperature. For the same reduced
temperature , where is the critical temperature, these two
coefficients are higher for LJ dimers and trimers than for monomers, in
contrast to the traditional viewpoint that they are close to unity for
monatomic molecules and decrease for polyatomic molecules. Furthermore, data
for the two coefficients collapse onto a master curve when plotted against a
translational length ratio between the liquid and vapor phase.Comment: revised version, 15 pages, 15 figures, to appear in J. Chem. Phy
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
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
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
T2800 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
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
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
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
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Parallel algorithm for transient solid dynamics simulations using finite elements and smoothed particle hydrodynamics
An efficient, scalable, parallel algorithm for treating contacts in solid mechanics has been applied to interactions between particles in smooth particle hydrodynamics (SPH). The algorithm uses three different decompositions within a single timestep: (1) a static FE-decomposition of mesh elements; (2) a dynamic SPH-decomposition of SPH particles; (3) and a dynamic contact-decomposition of contact nodes and SPH particles. The overhead cost of such a scheme is the cost of moving mesh and particle data between the decompositions. This cost turns out to be small in practice, leading to a highly load-balanced decomposition in which to perform each of the three major computational states within a timestep
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
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