An experimental study of the atmospheric boundary layer modified by a change in surface roughness and surface temperature

Turbulent flow, resembling an on-shore flow from the ocean crossing the beach at an oblique angle, is investigated. Measurements of this flow have been taken at high sample rates and include measurements at various heights, high enough to describe the portion of the mean wind and temperature profiles and fluxes that are of interest for the solution of practical engineering problems. These problems could include air pollution (fumigation and plume trapping), operation of low flying aircraft, crop-spraying and crop-dusting operations

The molecular basis of electroporation

BACKGROUND: Electroporation is a common method to introduce foreign molecules into cells, but its molecular basis is poorly understood. Here I investigate the mechanism of pore formation by direct molecular dynamics simulations of phospholipid bilayers of a size of 256 and of more than 2000 lipids as well as simulations of simpler interface systems with applied electric fields of different strengths. RESULTS: In a bilayer of 26 × 29 nm multiple pores form independently with sizes of up to 10 nm on a time scale of nanoseconds with an applied field of 0.5 V/nm. Pore formation is accompanied by curving of the bilayer. In smaller bilayers of ca. 6 × 6 nm, a single pore forms on a nanosecond time scale in lipid bilayers with applied fields of at least 0.4 V/nm, corresponding to transmembrane voltages of ca. 3 V. The presence of 1 M salt does not seem to change the mechanism. In an even simpler system, consisting of a 3 nm thick octane layer, pores also form, despite the fact that there are no charged headgroups and no salt in this system. In all cases pore formation begins with the formation of single-file like water defects penetrating into the bilayer or octane. CONCLUSIONS: The simulations suggest that pore formation is driven by local electric field gradients at the water/lipid interface. Water molecules move in these field gradients, which increases the probability of water defects penetrating into the bilayer interior. Such water defects cause a further increase in the local electric field, accelerating the process of pore formation. The likelihood of pore formation appears to be increased by local membrane defects involving lipid headgroups. Simulations with and without salt show little difference in the observed pore formation process. The resulting pores are hydrophilic, lined by phospholipid headgroups

Effect of Lipid Bilayers on Prion Peptide Aggregation: Insights from Coarse-Grained Molecular Simulations

No. 4841 - No. 484

Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces

BACKGROUND: Peptide-membrane interactions play a key role in the binding, partitioning and folding of membrane proteins, the activity of antimicrobial and fusion peptides, and a number of other processes. To gain a better understanding of the thermodynamics of such interactions, White and Wimley created an interfacial hydrophobicity scale based of the transfer free energy from water to octanol or lipid bilayers of a series of synthetic peptapeptides (Ace-WLXLL, with X being any of the twenty natural amino acids) (White and Wimley (1996) Nat. Struct. Biol. 3, 842–848). In this study, we performed molecular dynamics simulations of a representative set of ten of these peptides (X = D, K, R, N, A, T, S, I, F and W) in two membrane mimetic interfaces: water-cyclohexane (10 ns) and a fully solvated dioleoylphosphatidylcholine (DOPC) bilayer (50 ns) using both constant pressure and constant area ensembles. We focus on partitioning of the ten peptides at the cyclohexane/water and lipid/water interfaces. RESULTS: The peptides rapidly equilibrate (< 2 ns) and partition at the cyclohexane/water interface. The X3 guest residue assumes average orientations that depend on the nature of the side chain. At the DOPC/water interface, dynamics is much slower and convergence is difficult to achieve on a 50 ns timescale. Nonetheless, all peptides partition to the lipid/water interface with distributions with widths of 1–2 nm. The peptides assume a broad range of side chain and backbone orientations and have only a small effect on the area of the unit cell. On average, hydrophobic guest residues partition deeper into the hydrophobic core than hydrophilic residues. In some cases the peptides penetrate sufficiently deep to somewhat affect the distribution of the C=C double bond in DOPC. The relative distribution of the X3 guest residue compared to W1 and L5 is similar in the water/cyclohexane and water/lipid simulations. Snapshots show mostly extended backbone conformations in both environments. There is little difference between simulations at a constant area of 0.66 nm(2 )and simulations at constant pressure that approximately yield the same average area of 0.66 nm(2). CONCLUSION: These peptides were designed to assume extended conformations, which is confirmed by the simulations. The distribution of the X3 side chain depends on its nature, and can be determined from molecular dynamics simulations. The time scale of peptide motion at a phospholipids-water interface is too long to directly calculate the experimentally measured hydrophobicity scale to test and improve the simulation parameters. This should be possible at the water/cyclohexane interface and likely will become feasible in the future for the phospholipids/water case

Kinetic models of ion transport through a nanopore

Kinetic equations for the stationary state distribution function of ions moving through narrow pores are solved for a number of one-dimensional models of single ion transport. Ions move through pores of length $L$, under the action of a constant external field and of a concentration gradient. The interaction of single ions with the confining pore surface and with water molecules inside the pore are modelled by a Fokker-Planck term in the kinetic equation, or by uncorrelated collisions with thermalizing centres distributed along the pore. The temporary binding of ions to polar residues lining the pore is modelled by stopping traps or energy barriers. Analytic expressions for the stationary ion current through the pore are derived for several versions of the model, as functions of key physical parameters. In all cases, saturation of the current at high fields is predicted. Such simple models, for which results are analytic, may prove useful in the study of the current/voltage relations of ion channels through membranes

Water permeation through gramicidin A: Desformylation and the double helix: A molecular dynamics study

Multinanosecond molecular dynamics simulations of gramicidin A embedded in a dimyristoylphosphatidylcholine bilayer show a remarkable structural stability for both experimentally determined conformations: the head-to-head helical dimer and the double helix. Water permeability was found to be much higher in the double helical conformation, which is explained by lower hydrogen bond-mediated enthalpic barriers at the channel entrance and its larger pore size. Free-energy perturbation calculations show that the double helical structure is stabilized by the positive charges at the N termini introduced by the desformylation, whereas the helical dimer is destabilized. Together with the recent experimental observation that desformyl gramicidin conducts water hundredfold better than gramicidin, this suggests that desformyl gramicidin A predominantly occurs in the double helical conformation