Virtual Bead Research Articles

Molecular Dynamics Simulations of Curved Lipid Membranes.

Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.

Virtual bead representation and surface roughness evaluation challenges for additive manufacturing material extrusion processes

Additive manufacturing (AM) processes, such as material extrusion, are part of a popular growing technology field; with limited human assistance required and advanced rapid prototyping capabilities, this technology is advertised to have limitless possibilities. The common challenge faced by users is a lack of design control of the surface roughness, which is highlighted by a characteristic “stair case” layering effect at the boundary. Focusing on material extrusion processes, the goal of this research is to model representative bead shapes, and highlight the surface roughness challenges for assessing boundary-fill regions. Various bead shapes are explored and compared through virtual simulation. Unique material extrusion AM-related issues arise, and it is shown that machining solutions may not provide the desired surface smoothness. This research illustrates that specific physical and virtual assessment tools and standards need to be further developed to convey surface roughness attributes for material extrusion additive manufactured components.

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules. To improve the stability and accuracy of coarse-grained molecular dynamics simulations, we propose two approaches. The first makes use of improved forms for the angle potentials: the restricted bending (ReB) potential prevents torsion angles from visiting unstable or unphysical configurations and the combined bending-torsion (CBT) potential smoothly flattens the interactions when such configurations are sampled. In the second approach, dummy-assisted dihedral (DAD), the torsion potential is applied differently: instead of acting directly on the beads, it acts on virtual beads, bound to the real ones. For simple geometrical reasons, the unstable region is excluded from the accessible conformational space. The benefits of the new approaches are demonstrated in simulations of polyethylene glycol (PEG), polystyrene (PS), and polypeptide molecules described by the MARTINI coarse-grained force field. The new potentials are implemented in an in-house version of the Gromacs package, publicly available.

Collective navigation of cargo-carrying swarms

Much effort has been devoted to the study of swarming and collective navigation of micro-organisms, insects, fish, birds and other organisms, as well as multi-agent simulations and to the study of real robots. It is well known that insect swarms can carry cargo. The studies here are motivated by a less well-known phenomenon: cargo transport by bacteria swarms. We begin with a concise review of how bacteria swarms carry natural, micrometre-scale objects larger than the bacteria (e.g. fungal spores) as well as man-made beads and capsules (for drug delivery). A comparison of the trajectories of virtual beads in simulations (using different putative coupling between the virtual beads and the bacteria) with the observed trajectories of transported fungal spores implies the existence of adaptable coupling. Motivated by these observations, we devised new, multi-agent-based studies of cargo transport by agent swarms. As a first step, we extended previous modelling of collective navigation of simple bacteria-inspired agents in complex terrain, using three putative models of agent-cargo coupling. We found that cargo-carrying swarms can navigate efficiently in a complex landscape. We further investigated how the stability, elasticity and other features of agent-cargo bonds influence the collective motion and the transport of the cargo, and found sharp phase shifts and dual successful strategies for cargo delivery. Further understanding of such mechanisms may provide valuable clues to understand cargo-transport by smart swarms of other organisms as well as by man-made swarming robots.

Brownian dynamics simulations of charged semiflexible polymers confined to curved surfaces

As an extension of the generalized bead–rod model developed earlier by the authors, this paper proposes a method for Brownian dynamics simulations of charged semiflexible polymers confined to various curved surfaces such as spherical, cylindrical, ellipsoidal and toroidal. We model charged semiflexible polymers as discrete wormlike chains consisting of virtual beads connected by inextensible rods with length varying according to the characteristic radius of curvature of the confining surface. The long-range electrostatic interactions are incorporated via the Debye–Hueckel potential. The geometrical constraints associated with the inextensible rods are realized by the so-called linear constraint solver. For a semiflexible polymer chain confined to a spherical surface, an analytical expression for the winding number is obtained by using an existing exact closed-form solution of the mean-square end-to-end distance. The proposed simulation method is then validated against theoretical predictions for both charged and uncharged polymer chains under surface confinements.