475 research outputs found
Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces
We develop an efficient parallel multiscale method that bridges the atomistic
and mesoscale regimes, from nanometer to micron and beyond, via concurrent
coupling of atomistic simulation and mesoscopic dynamics. In particular, we
combine an all-atom molecular dynamics (MD) description for specific atomistic
details in the vicinity of the functional surface, with a dissipative particle
dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain
away from the functional surface. In order to achieve a seamless transition in
dynamic properties we endow the MD simulation with a DPD thermostat, which is
validated against experimental results by modeling water at different
temperatures. We then validate the MD-DPD coupling method for transient Couette
and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can
resolve accurately the continuum-based analytical solutions. Subsequently, we
simulate shear flows over polydimethylsiloxane (PDMS)-grafted surfaces (polymer
brushes) for various grafting densities, and investigate the slip flow as a
function of the shear stress. We verify that a "universal" power law exists for
the sliplength, in agreement with published results. Having validated the
MD-DPD coupling method, we simulate time-dependent flows past an endothelial
glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate
the dynamics of EGL changing from an equilibrium state to a compressed state
under shear by aligning the molecular structures along the shear direction.
MD-DPD simulation results agree well with results of a single MD simulation,
but with the former more than two orders of magnitude faster than the latter
for system sizes above one micron.Comment: 11 pages, 12 figure
How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers
[Image: see text] In recent years, computational methods have become an essential element of studies focusing on the self-assembly process. Although they provide unique insights, they face challenges, from which two are the most often mentioned in the literature: the temporal and spatial scale of the self-assembly. A less often mentioned issue, but not less important, is the choice of the force-field. The repetitive nature of the supramolecular structure results in many similar interactions. Consequently, even a small deviation in these interactions can lead to significant energy differences in the whole structure. However, studies comparing different force-fields for self-assembling systems are scarce. In this article, we compare molecular dynamics simulations for trifold hydrogen-bonded fibers performed with different force-fields, namely GROMOS, CHARMM General Force Field (CGenFF), CHARMM Drude, General Amber Force-Field (GAFF), Martini, and polarized Martini. Briefly, we tested the force-fields by simulating: (i) spontaneous self-assembly (none form a fiber within 500 ns), (ii) stability of the fiber (observed for CHARMM Drude, GAFF, MartiniP), (iii) dimerization (observed for GROMOS, GAFF, and MartiniP), and (iv) oligomerization (observed for CHARMM Drude and MartiniP). This system shows that knowledge of the force-field behavior regarding interactions in oligomer and larger self-assembled structures is crucial for designing efficient simulation protocols for self-assembling systems
- …