426 research outputs found
A minimal model for acoustic forces on Brownian particles
We present a generalization of the inertial coupling (IC) [Usabiaga et al. J.
Comp. Phys. 2013] which permits the resolution of radiation forces on small
particles with arbitrary acoustic contrast factor. The IC method is based on a
Eulerian-Lagrangian approach: particles move in continuum space while the fluid
equations are solved in a regular mesh (here we use the finite volume method).
Thermal fluctuations in the fluid stress, important below the micron scale, are
also taken into account following the Landau-Lifshitz fluid description. Each
particle is described by a minimal cost resolution which consists on a single
small kernel (bell-shaped function) concomitant to the particle. The main role
of the particle kernel is to interpolate fluid properties and spread particle
forces. Here, we extend the kernel functionality to allow for an arbitrary
particle compressibility. The particle-fluid force is obtained from an imposed
no-slip constraint which enforces similar particle and kernel fluid velocities.
This coupling is instantaneous and permits to capture the fast, non-linear
effects underlying the radiation forces on particles. Acoustic forces arise
either because an excess in particle compressibility (monopolar term) or in
mass (dipolar contribution) over the fluid values. Comparison with theoretical
expressions show that the present generalization of the IC method correctly
reproduces both contributions. Due to its low computational cost, the present
method allows for simulations with many particles using a standard Graphical
Processor Unit (GPU)
USHER: an algorithm for particle insertion in dense fluids
The insertion of solvent particles in molecular dynamics simulations of
complex fluids is required in many situations involving open systems, but this
challenging task has been scarcely explored in the literature. We propose a
simple and fast algorithm (USHER) that inserts the new solvent particles at
locations where the potential energy has the desired prespecified value. For
instance, this value may be set equal to the system's excess energy per
particle, in such way that the inserted particles are energetically
indistinguishable from the other particles present. During the search for the
insertion site, the USHER algorithm uses a steepest descent iterator with a
displacement whose magnitude is adapted to the local features of the energy
landscape. The only adjustable parameter in the algorithm is the maximum
displacement and we show that its optimal value can be extracted from an
analysis of the structure of the potential energy landscape. We present
insertion tests in periodic and non-periodic systems filled with a
Lennard-Jones fluid whose density ranges from moderate values to high values.Comment: 10 pages (Latex), 8 figures (postscript); J. Chem. Phys. (in press)
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Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent
We compare a newly developed hybrid simulation method which combines
classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a
simulation consisting only of molecular dynamics. The hybrid code is composed
of three regions: a classical MD region, a continuum domain where the dynamical
equations are solved by standard CFD methods, and an overlap domain where
transport information from the other two domains is exchanged. The exchange of
information in the overlap region ensures that momentum, energy and mass are
conserved. The validity of the hybrid code is demonstrated by studying a single
polymer tethered to a hard wall immersed in explicit solvent and undergoing
shear flow. In classical molecular dynamics simulation a great deal of
computational time is devoted to simulating solvent molecules, although the
solvent itself is of no direct interest. By contrast, the hybrid code simulates
the polymer and surrounding solvent explicitly, whereas the solvent farther
away from the polymer is modeled using a continuum description. In the hybrid
simulations the MD domain is an open system whose number of particles is
controlled to filter the perturbative density waves produced by the polymer
motion.We compare conformational properties of the polymer in both simulations
for various shear rates. In all cases polymer properties compare extremely well
between the two simulation scenarios, thereby demonstrating that this hybrid
method is a useful way to model a system with polymers and under nonzero flow
conditions. There is also good agreement between the MD and hybrid schemes and
experimental data on tethered DNA in flow. The computational cost of the hybrid
protocol can be reduced to less than 6% of the cost of updating the MD forces,
confirming the practical value of the method.Comment: 13 pages, 8 figure
Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water
We have conducted a triple-scale simulation of liquid water by concurrently
coupling atomistic, mesoscopic, and continuum models of the liquid. The
presented triple-scale hydrodynamic solver for molecular liquids enables the
insertion of large molecules into the atomistic domain through a mesoscopic
region. We show that the triple-scale scheme is robust against the details of
the mesoscopic model owing to the conservation of linear momentum by the
adaptive resolution forces. Our multiscale approach is designed for molecular
simulations of open domains with relatively large molecules, either in the
grand canonical ensemble or under non-equilibrium conditions.Comment: triple-scale simulation, molecular dynamics, continuum, wate
Multiscale modelling of liquids with molecular specificity
The separation between molecular and mesoscopic length and time scales poses
a severe limit to molecular simulations of mesoscale phenomena. We describe a
hybrid multiscale computational technique which address this problem by keeping
the full molecular nature of the system where it is of interest and
coarse-graining it elsewhere. This is made possible by coupling molecular
dynamics with a mesoscopic description of realistic liquids based on Landau's
fluctuating hydrodynamics. We show that our scheme correctly couples
hydrodynamics and that fluctuations, at both the molecular and continuum
levels, are thermodynamically consistent. Hybrid simulations of sound waves in
bulk water and reflected by a lipid monolayer are presented as illustrations of
the scheme
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