Molecular dynamics on curved surfaces
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. We show here that it is possible to take such interactions into account by combining standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface. This method is applicable to multiple curved/crowded systems in both biology and soft matter, e.g. ,the influence of crowding and shape on the lateral diffusion of proteins in curved membranes; and the self-assembly of a coarse-grained virus capsid protein model.
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This algorithm has been implemented a rattle constraint algorithm in the molecular dynamics package LAMMPS which allows it to be combined with an efficient parallelization and the usage of complex particle shapes. LAMPPS as well as our manifold constraint algorithm are available at: http://lammps.sandia.gov/
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References:
A method for molecular dynamics on curved surfaces; S. Paquay, R. Kusters; Biophysical Journal, vol. 1110, 1226-1233
Confinement without boundaries: anisotropic diffusion on the surface of a cylinder; R. Kusters, S. Paquay, C. Storm; Soft Matter, vol. 11, 1054-1057
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Crowding induced clustering
We study the collective behavior of driven particles embedded in a densely packed background consisting of passive particles. Depending on the driving force, their density and temperature we observe a dynamical phase separation of the driven particles, which cluster together in tight bands. We determine the critical conditions for such phase separation and provide a simple physical picture that explains the formation and subsequent growth of a jammed zone developing in front of the driven cluster. Our model correctly captures the observed scaling with time. We analyze the implications of this clustering transition for the driven transport in dense particulate flows, which due to a non-monotonic dependence on the applied driving force is not straightforwardly optimized. We provide proof-of-concept for a direct application of the clustering effect, and propose a 'colloidal chromatograph'; a setup that permits the separation of colloids by mass or size.
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References:
Crowding induced clustering under confinement; R. Kusters, C. Storm; Arxiv:1510.08816 (2015)
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