We performed coarse-grained computer simulations using MARTINI force field to study the difference in the self-assembly and possible pore creation in DPPC phospholipid membranes by two different antimicrobial peptides: magainin-2 and melittin. Simulations showed that magainin-2 peptides create large sized disordered toroidal pores that allow easy water permeation across them. Melittin assemblies contain peptides in U-shaped conformations that, although creating holes in membranes, block effectively the passage of water. These observed structures are consistent with the dye efflux experiments performed on vesicles exposed to solutions containing antimicrobial peptides.

We used MARTINI coarse-grained force field to study poration of a lipid bilayer by a shock wave induced nanobubble collapse. Different systems containing different sized nanobubbles that were exposed to shock waves propagating with different velocities were simulated. We observed creation of pores and damage to bilayers and also subsequent pore closing and the bilayer recovery after shock wave passed the bilayer. In all our systems where bilayers were damaged, they recovered; nevertheless we observed that a large amount of water crossed the pore that was temporarily created. We also observed that not every lipid molecule remained in the bilayer after recovery, some lipids moved out into water and created micelles.

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To study the interaction between melittin peptides and lipid bilayer, we performed coarse-grained simulations on systems containing melittin interacting with a bilayer containing zwitterionic dipalmitoylphosphatidylcholine (DPPC) and anionic palmitoyloleoylphosphatidylglycerol (POPG) phospholipids in a 7:3 ratio. Eight different systems were considered: four at low and four at high peptide to lipid (P/L) ratios. In case of low P/L ratio we did not observe any pore creation in the bilayer. In two out of four of the simulations with the high P/L ratio, appearance of transient pores in the bilayer was observed. These pores were created due to an assembly of 3-5 melittin peptides. Not all of the peptides in the pores were in a transmembrane conformation; many of them had their termini residues anchored to the same leaflet, and these peptides assumed bent, U-shaped, conformations. We propose that when an assembly of melittin peptides creates pores, such an assembly acts as a "wedge" that splits the bilayer. To get a more detailed description of melittin on the bilayer surface and in transient pores, we performed coarse-grained to united-atom scale transformations and after that performed 50 ns molecular dynamics simulations using the united atom description of the systems. While these simulations did not show much of the change in the pore structure during the 50 ns time interval, they clearly showed the presence of water in the transient pores. The appearance of transient pores together with the translocation of peptides across the membranes is consistent with the mechanism proposed to explain graded dye leakage from large vesicles in the presence of melittin.

We used molecular dynamics simulations to study creation of pores in lipid bilayer membranes by inducing shock waves in systems containing arrays of nanobubbles next to these membranes. Shock waves impinged on the bubbles imploding them and produced nanojets that subsequently hit the bilayers making pores in them. Our simulations were performed using the MARTINI coarse-grained force field. The emphasis in our study was on the interaction of shock waves with two-bubble arrays when the bubbles were placed in different alignments. We observed that the largest damage to the bilayer was produced when two bubbles were positioned in a serial alignment and the bubbles touched each other. When two touching each other bubbles were located parallel to the membrane surface and at the same distance from the surface, the membrane damage was reduced, compared to the damage done by explosion of two independent nanobubbles. When two nanobubbles were placed in slanted configurations, the damage was intermediate between damages produced by two bubbles in parallel or serial alignment. Damage to the membrane produced by arrays containing more than two bubbles can be understood as a combination of damage produced by all three alignments of two bubbles.

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When a salt is added to a polymer solution, metal cations may coordinate with polymer ligands forming interchain and intrachain links. Metal coordination leads to drastic changes of polymer morphology, formation of clusters, and, ultimately, a sol−gel transition that affect the solution rheology. Although metal coordination is ubiquitous in polymeric systems, the physical mechanisms of coordination-induced morphological and rheological changes are still poorly understood due to the multiscale nature of this phenomenon. Here, we propose a coarse-grained dissipative particle dynamics (DPD) model to study morphological and rheological properties of concentrated solutions of polymers in the presence of multivalent cations that can coordinate the polymer ligands. The coordinating metal is introduced as a 3D complex of planar, tetrahedral, or octahedral geometry with the central DPD bead representing the metal cation surrounded at the vertices by either four or six dummy beads representing coordination sites, some of which are occupied by counterions to provide electroneutrality of the complex. Coordination is modeled as the dynamic formation and dissociation of a reversible link between the vacant coordination site and a ligand described by the Morse potential. The proposed model is applied to study the specifics of the equilibrium morphology and shearing flow in polyvinylpyrrolidone−dimethylformamide solutions in the presence of metal chlorides. Coordination leads to interchain and intrachain cross-links as well as to metal cations grafted onto polymer chains by a single link. The interchain cross-links induce a sol−gel transition to a weak gel phase as the metal concentration increases. Because of the reversible nature of interchain cross-links, the weak gel phase behaves as a viscoelastic fluid, the viscosity of which gradually increases with the metal concentration and decreases as the shear rate increases. The change of viscosity due to interchain coordination cross-links scales with the interchain cross-link density and the metal concentration according to the power law with the exponent ν ≈ 1.15. The influence of the grafted metal atoms on the viscosity is found to be much weaker, while the effect of the intrachain cross-links is found to be negligible. The simulation results are in qualitative agreement with available literature data. The proposed DPD model provides a physical insight into the morphological features of polymer solutions in the presence of multivalent slats and can be extended to other coordinating systems such as metal-substituted polyelectrolytes.

This work explores interactions of functionalized nanoparticles (NP) with polymer brushes (PB) in a binary mixture of good and poor solvents. NP-PB systems are used in multiple applications, and we are particularly interested in the problem of chromatographic separation of NPs on polymer-grafted porous columns. This process involves NP flow through the pore channels with walls covered by PBs. NP-PB adhesion is governed by adsorption of polymer chains to NP surface and entropic repulsion caused by the polymer chain confinement between NP and the channel wall. Both factors depend on the solvent composition, variation of which causes contraction or expansion of PB. Using dissipative particle dynamics simulations in conjunction with the ghost tweezers free energy calculation technique, we examine the free energy landscapes of functionalized NPs within PB-grafted channels depending on the solvent composition at different PB grafting densities and polymer-solvent affinities. The free energy landscape determines the probability of NP location at a given distance to the surface, positions of equilibrium adhesion states, and the Henry constant that characterizes adsorption equilibrium and NP partitioning between the stationary phase of PB and mobile phase of flowing solvent. We analyze NP transport through a polymer-grafted channel and calculate the mean velocity and retention time of NP depending on the NP size and solvent composition. We find that, with the increase of the bad (poor) solvent fraction and respective PB contraction, NP separation exhibits a transition from the hydrodynamic size exclusion regime with larger NPs having shorter retention time to the adsorption regime with smaller NPs having shorter retention time. The observed reversal of the sequence of elution is reminiscent of the critical condition in polymer chromatography at which the retention time is molecular weight independent. This finding suggests the possibility of the existence of an analogous special regime in nanoparticle chromatography at which NPs with like surface properties elute together regardless of their size. The latter has important practical implications: NPs can be separated by surface chemistry rather than by their size employing the gradient mode of elution with controlled variation of solvent composition.