Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.     

Stimuli-responsive electrospun fibers and their applications

Stimuli-responsive electrospun nanofibers are gaining considerable attention as highly versatile tools which offer great potential in the biomedical field. In this critical review, an overview is given on recent advances made in the development and application of stimuli-responsive fibers. The specific features of these electrospun fibers are highlighted and discussed in view of the properties required for the diverse applications. Furthermore, several novel biomedical applications are discussed and the respective advantages and shortcomings inherent to stimuli-responsive electrospun fibers are addressed (136 references).     

Growth mechanisms involved in the synthesis of smooth and microtextured films by acetylene magnetron discharges

The growth of hydrogenated amorphous carbons (a-C:H) produced by continuous or pulsed discharges of acetylene (C(2)H(2)) in an unbalanced magnetron setup was investigated. At 5 × 10(-3) Torr, only smooth films are obtained, whereas at 5 × 10(-1) Torr using a pulsed discharge some microtextured films are formed if the duty cycle is low. The morphology of these microtextured films consists of nanoparticles, filamentary particles, and particular agglomerates ("microflowers"). This paper presents a study of acetylene gas phase polymerization by mass spectrometry, and a detailed analysis of bulk structure of films by combining three techniques which include IR spectroscopy, Raman spectroscopy, and laser desorption/ionization Fourier transform mass spectrometry (LDI-FTMS). Finally, based on the study of gas phase and film structure, we propose a model for the growth of both smooth and microtextured films.     

Influence of surface roughness on cetyltrimethylammonium bromide adsorption from aqueous solution

The influence of surface roughness on surfactant adsorption was studied using a quartz crystal microbalance with dissipation (QCM-D). The sensors employed had root-mean-square (R) roughness values of 2.3, 3.1, and 5.8 nm, corresponding to fractal-calculated surface area ratios (actual/nominal) of 1.13, 1.73, and 2.53, respectively. Adsorption isotherms measured at 25 °C showed that adsorbed mass of cetyltrimethylammonium bromide per unit of actual surface area below 0.8 cmc, or above 1.2 cmc, decreases as the surface roughness increases. At the cmc, both the measured adsorbed amount and the measured dissipation increased dramatically on the rougher surfaces. These results are consistent with the presence of impurities, suggesting that roughness exacerbates well-known phenomena reported in the literature of peak impurity-related adsorption at the cmc. The magnitude of the increase, especially in dissipation, suggests that changes in adsorbed amount may not be the only reason for the observed results, as aggregates at the cmc on rougher surfaces are more flexible and likely contain larger amounts of solvent. Differences in adsorption kinetics were also found as a function of surface roughness, with data showing a second, slower adsorption rate after rapid initial adsorption. A two-rate Langmuir model was used to further examine this effect. Although adsorption completes faster on the smoother surfaces, initial adsorption at zero surface coverage is faster on the rougher surfaces, suggesting the presence of more high-energy sites on the rougher surfaces.     

Regioselectivity of the Claisen rearrangement in meta-allyloxy aryl ketones: an experimental and computational study, and application in the synthesis of (R)-(-)-pestalotheol D

A study of the regioselectivity of the Claisen rearrangement of meta-allyloxy aryl ketones showed that the electron-withdrawing carbonyl group has a major influence and strongly directs rearrangement to the more hindered ortho position. However, when the ketone is part of a ring structure, its electronic effect can be negated by conversion into its triisopropylsilyl enol ether, which dramatically reverses the regiochemistry of the Claisen rearrangement. DFT calculations suggest that the effect is electronic although there is also a steric effect of the bulky silyl group. This strategy for influencing the regiochemical outcome of the Claisen rearrangement was then employed in a short synthesis of the furo[2,3-g]chromene, (-)-pestalotheol D, that confirms the absolute stereochemistry of the natural product.     

Differentiation of Regioisomeric Aromatic Ketocarboxylic Acids by Positive Mode Atmospheric Pressure Chemical Ionization Collision-Activated Dissociation Tandem Mass Spectrometry in a Linear Quadrupole Ion Trap Mass Spectrometer

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS ⁿ ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at different collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.     

Stereochemical dependence of 3JCH coupling constants in 2-substituted 4-t-butyl-cyclohexanone and their alcohol derivatives

Theoretical and experimental studies on (3)J(C2H6eq) NMR spin-spin coupling constants in both the 2-X-4-t-butyl-cyclohexanone (X = H, CH(3), F, Cl, and Br) and in their alcohol derivatives series are reported. Results thus found are rationalized in terms of the transmission of the Fermi contact contribution to such couplings. To this end, dependencies of (3)J(C2H6eq) couplings versus the C(2)-C(1)-C(6) angle are compared in both series for equatorial and axial X orientations. The main trend is described in terms of the rear lobes interaction. Besides, for X = halogen atom in equatorial orientation a rather strong interaction between oxygen and halogen lone pairs is observed, and its influence on (3)J(C2H6eq) couplings is discussed and rationalized in terms of different Fermi contact transmission pathways.     

Polynomial approximation of nonlinear differential systems with prefixed accuracy

This paper presents a method for constructing polynomial approximations of the solutions of nonlinear initial value systems of differential equations. Given an a priori chosen accuracy, the degree of the vector polynomial can be adapted so that the approximate solution has the required precision. The method is based on the AI-method of Dzyadyk developed for the scalar case, and the computational cost is shown to be competitive with other methods.