Modeling the Self-Assembly of Lipids and Nanotubes in Solution: Forming Vesicles and Bicelles with Transmembrane Nanotube Channels

Abstract

Via dissipative particle dynamics (DPD), we simulate the self-assembly of end-functionalized, amphiphilic nanotubes and lipids in a hydrophilic solvent. Each nanotube encompasses a hydrophobic stalk and two hydrophilic ends, which are functionalized with end-tethered chains. With a relatively low number of the nanotubes in solution, the components self-assemble into stable lipid-nanotube vesicles. As the number of nanotubes is increased, the system exhibits a vesicle-to-bicelle transition, resulting in stable hybrid bicelle. Moreover, our results reveal that the nanotubes cluster into distinct tripod-like structures within the vesicles and aggregate into a ring-like assembly within the bicelles. For both the vesicles and bicelles, the nanotubes assume trans-membrane orientations, with the tethered hairs extending into the surrounding solution or the encapsulated fluid. Thus, the hairs provide a means of regulating the transport of species through the self-assembled structures. Our findings provide guidelines for creating nanotube clusters with distinctive morphologies that might be difficult to achieve through more conventional means. The results also yield design rules for creating synthetic cell-like objects or microreactors that can exhibit biomimetic functionality.

The design of shape-tunable hairy vesicles

“…DPD is a mesoscopic simulation technique that uses soft-sphere coarse-grained models to capture both the molecular details of the nanoscopic building blocks and their supramolecular organization while simultaneously resolving the hydrodynamics of the system over extended time scales [19,23,31]. In order to capture the dynamics of the soft spheres, the DPD technique integrates Newton's equation of motion via the use of similar numerical integrators used in other deterministic particle-based simulation methods [23,32].…”

“…Two consecutive beads in a chain are connected via a bond that is described by the harmonic spring potential E bond = K bond ((r − b)/r c ) 2 , where K bond is the bond constant and b is the equilibrium bond length. The constants, K bond and b are assigned values of 64ε and 0.5r c , respectively [19,20]. The three-body stiffness potential along the lipid tails has the form E angle = K angle (1 + cos Â) where  is the angle formed by three adjacent beads.…”

“…We have adopted a molecular dynamics (MD)-based mesoscopic simulation technique entitled dissipative particle dynamics (DPD) [19][20][21][22][23] which simultaneously resolves both the molecular and continuum scales, for the investigations presented in this paper. The DPD method has been used to investigate the dynamics and morphology of self-assembly, phase separation and phase transition in lipid systems [24,25], block co-polymers [26], dense colloidal suspensions [27], polymers in dilute solution or in a melt [28], and chains in microfluidic channels [29,30].…”

Topology and Shape Control for Assemblies of Block Copolymer Blends in Solution

“…DPD is widely used in the modeling soft matter. 43,[46][47][48][49][50] We refer the reader to the Supporting Information (SI), for a detailed discussion of the model and simulation method.…”

Simulation‐Experimental Approach to Investigate the Role of Interfaces in Self‐Replenishing Composite Coatings

“…First, a simulation set up was generated for the composite coating using a Dissipative Particle Dynamics (DPD) method which allows studying phenomena for relatively long time and length scales. This method has been previously reported for several soft matter systems, such as polymers [ 14 ] and colloids [ 15,16 ] as well as complex systems and processes such as vesicle formation [ 17,18 ] and polyelectrolytes. [ 19,20 ] In parallel, composite coatings were prepared experimentally, containing the selfreplenishing polymer layer and single-size inorganic nanoparticles (SiO 2 with ≈700 nm average diameter).…”