Membrane Phase Transitions in Lipid-Wrapped Nanoparticles.

A Landau theory is constructed for the gel/fluid transition of a lipid bilayer wrapped around a spherical nanoparticle (lipid-wrapped nanoparticle, LNP). The bilayer is regarded as a regular solution of gel and fluid lipids with distinct inter- and intralayer interactions plus the interaction of the core with the inner layer. It is required that both the inner and the outer surfaces of the bilayer are perfectly covered with lipids, with the gel and fluid lipids having different areas/lipid.

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them.

Simulation of fluid/gel phase equilibrium in lipid vesicles.

Simulation of single component dipalmitoylphosphatidylcholine (DPPC) coarse-grained DRY-MARTINI lipid vesicles of diameter 10 nm (1350 lipids), 20 nm (5100 lipids) and 40 nm (17 600 lipids) is performed using statistical temperature molecular dynamics (STMD), to study finite size effects upon the order-disorder gel/fluid transition. STMD obtains enhanced sampling using a generalized ensemble, obtaining a flat energy distribution between upper and lower cutoffs, with little computational cost over canonical molecular dynamics. A single STMD trajectory of moderate length is sufficient to sample 20+ transition events, without trapping in the gel phase, and obtain well averaged properties.

Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways.

Gold nanoparticles (NPs) wrapped in a membrane can be utilized as artificial virus nanoparticles (AVNs) that combine the large nonblinking or bleaching optical cross-section of the NP core with the biological surface properties and functionalities provided by a self-assembled lipid membrane. We used these hybrid nanomaterials to test the roles of monosialodihexosylganglioside (GM3) and phosphatidylserine (PS) for a lipid-mediated targeting of virus-containing compartments (VCCs) in macrophages. GM3-presenting AVNs bind to CD169 (Siglec-1)-expressing macrophages, but inclusion of PS in the GM3-containing AVN membrane decreases binding.

Lipid Packing in Lipid-Wrapped Nanoparticles.

Equilibrium simulations of lipid-wrapped nanoparticles (LNP) were performed using a hybrid molecular dynamics/Monte Carlo (MD/MC) approach. The radius, R, of a spherical nanoparticle (NP) core was adjusted with MC moves while a surrounding lipid bilayer was treated with MD. A wide range of LNP sizes, with the largest R ∼ 40 nm, were studied to determine the average NP radius for a given total number of lipids, N, the number of lipids in each layer, and configurational information.

Membrane Fluidity Sensing on the Single Virus Particle Level with Plasmonic Nanoparticle Transducers.

Viral membranes are nanomaterials whose fluidity depends on their composition, in particular, the cholesterol (chol) content. As differences in the membrane composition of individual virus particles can lead to different intracellular fates, biophysical tools capable of sensing the membrane fluidity on the single-virus level are required. In this manuscript, we demonstrate that fluctuations in the polarization of light scattered off gold or silver nanoparticle (NP)-labeled virus-like-particles (VLPs) encode information about the membrane fluidity of individual VLPs.

Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers.

Freezing and melting of dipalmitoylphosphatidylcholine (DPPC) bilayers are simulated in both the explicit (Wet) and implicit solvent (Dry) coarse-grained MARTINI force fields with enhanced sampling, via the isobaric, molecular dynamics version of the generalized replica exchange method (gREM). Phase transitions are described with the entropic viewpoint, based upon the statistical temperature as a function of enthalpy, T(H) = 1/(dS(H)/dH), where S is the configurational entropy. Bilayer thickness, area per lipid, and the second-rank order parameter (P2) are calculated vs temperature in the transition range.

Hole wave functions and transport with deazaadenines replacing adenines in DNA.

Transport of a hole along the base stack of DNA is relatively facile for a series of adenines (As) paired with thymines (Ts) or for a series of guanines (Gs) paired with cytosines (Cs). However, the speed at which a hole was found to travel was much too small to make useful semiconductor-type devices. Quite recently it was found that replacing one of the electronegative nitrogens (N3 or N7) with a carbon and a hydrogen, thus turning A into deazaadenine, increased the hole speed in what was A/T by a factor 30.