Atomistic Simulations of Rare Gas Transport through Breathable Single-wall Nanotubes with Constrictions and Knees

We present the results of molecular dynamics (MD) computer simulations of rare gas diffusion through breathable nanotubes with pentagon–heptagon pair defects resulting in constrictions and knees. Diffusion involves interrupted high speed “choppy” motion with intermittent reversal in velocity direction. Single atoms exhibit a spiral-like path, in contrast to atoms traveling in groups. Considerable resistance to flow appears to reside in the upstream section of the nanotube where density gradients are small, prior to the constriction. Subsequently, considerable density gradients are present and speeds increase, becoming greatest at the tube exit. For the nanotubes examined, Kr and Xe diffusion was too hindered to provide reliable results. Diffusion of He through the nanotubes with knees occurs in a single-file fashion nearly along the center of the tube and the knee has no detectable effect on the diffusion kinetics. Transport diffusion coefficients are in the order of 10^-4–10^-2?cm²/s.     

Molecular dynamics simulation of diffusion of hydrogen in binary hydrogen–tetrahydrofuran hydrate

The binary structure II hydrogen–tetrahydrofuran (THF) hydrate was studied with molecular dynamics simulation. The simulations were carried out at 300, 310 K and 10.1 MPa, and with various contents of hydrogen and THF. The migrations of hydrogen molecules from cage to cage were observed. The migration process of hydrogen was also analysed, and the diffusion coefficients of hydrogen in the hydrate were calculated. The calculated diffusion coefficients qualitatively agreed with the experimental data. Double and quintet occupancies of hydrogen molecules were observed in the small and large cages, respectively, without changing the hydrate structure.     

Gas adsorption and diffusion in a highly CO2 selective metal–organic framework: molecular simulations

Grand canonical Monte Carlo and equilibrium molecular dynamics simulations were used to assess the performance of an rht-type metal–organic framework (MOF), Cu-TDPAT, in adsorption-based and membrane-based separation of CH₄/H₂, CO₂/CH₄ and CO₂/H₂ mixtures. Adsorption isotherms and self-diffusivities of pure gases and binary gas mixtures in Cu-TDPAT were computed using detailed molecular simulations. Several properties of Cu-TDPAT such as adsorption selectivity, working capacity, diffusion selectivity, gas permeability and permeation selectivity were computed and compared with well-known zeolites and MOFs. Results showed that Cu-TDPAT is a very promising adsorbent and membrane material especially for separation of CO₂ and it can outperform traditional zeolites and MOFs such as DDR, MFI, CuBTC, IRMOF-1 in adsorption-based CO₂/CH₄ and CO₂/H₂ separations.     

New software for finding transition states by probing accessible,or ergodic,regions

An automated, iterative approach to finding the lowest energy, ionic diffusion paths through a periodic structure has been developed within our new code (written in FORTRAN 77 and named Bubble). The approach is quite general in that it can be applied to find, at a chosen temperature, the accessible (ergodic) regions of a hyper-surface, which is defined across a uniform grid [1 Schön, J.C., Putz, H. and Jansen, M. 1996. Studying the energy hypersurface of continuous system—The threshold algorithm. J. Phys.-Conden. Matt., 8: 143[Crossref] , [Google Scholar]]. We describe both our implementation within the Bubble code and its application to locating the approximate transition states for Mg interstitial diffusion in forsterite, which can then be refined using standard transition state searching [2 Banerjee, A., Adams, N., Simons, J. and Shepard, R. 1985. Search for stationary points on surfaces. J. Phys. Chem., 89: 52[Crossref], [Web of Science ®] , [Google Scholar]].     

In vitro evaluation of archaeosome vehicles for transdermal vaccine delivery

Abstract

Archaeosomes composed of archaeal total polar lipids (TPL) or semi-synthetic analog vesicles have been used as vaccine adjuvants and delivery systems in animal models for many years. Typically administered by intramuscular or subcutaneous injections, archaeosomes can induce robust, long-lasting humoral and cell-mediated immune responses against entrapped antigens and provide protection in murine models of infectious disease and cancer. Herein, we evaluated various archaeosomes for transdermal delivery, since this route may help eliminate needle-stick injuries and needle re-use, and therefore increase patient compliance. Archaeosomes composed of TPL from different archaea (Halobacterium salinarum, Methanobrevibacter smithii, Haloferax volcanii) and various semi-synthetic glycolipid combinations were evaluated for their ability to diffuse across the skin barrier using an ex vivo pig skin model and the results were compared to conventional synthetic ester liposomes. Physicochemical characteristics were determined for selected formulations including vesicle size, size distribution, zeta potential, fluidity, antigen (ovalbumin) incorporation efficiency and release. Archaeosomes, in particular those composed of M. smithii TPL or the synthetic glycolipid sulfated S-lactosylarchaeol (SLA) mixed with uncharged glycolipid lactosyl archaeol (LA), appeared to be effective carriers for ovalbumin, achieving much better antigen distribution and vesicle accumulation in the skin epidermis than conventional liposomes. The enhanced skin permeation of archaeosomes may be attributed to their chemical structure and physicochemical properties such as particle size, surface charge, stability, and fluidity of their lipid bilayer.     

Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles

Cell milking is a 100% renewable green energy for CO₂ by extraction of biofuels inside the cytosol of photosynthetic micro-organisms as microalgae and bacteria. The cells are exposed to a hydrophobic solvent forming holes and cracks through their membranes from which the biofuels can leak out. In protein folding, the goal would be to find pathways to the unique functional protein conformer. However, in the lipid-bilayer interaction with the solvent for milking, the objective is to block the pathways for damaged membrane conformations of low free energy with undesired nanostructures, using the solvent properties, as shown with an ab initio structural bioinformatic model. Statistical thermodynamics is used to compute the free energy (including entropy) from the molecular dynamics trajectory of the biomolecular system with many conformational changes. This model can be extended to the general problem of biomolecules folding as for proteins and nucleic acids. Using an adaptation of the Einstein diffusion law, the conformational change dynamics of the lipid bilayer depends on the two diffusion coefficients of the solvent: D₁ before the irreversible folding transition time and the much smaller D₂ thereafter. In contrast to the n-hexane and n-heptane hydrocarbons of smaller size, the residual D₂?=?4.7?×?10^?7?cm²/s of the n-decane solvent, with the highest partition coefficient among the three extractors, is the only to present a D₂ value that is significantly below the critical threshold of 10^?6?cm²/s. Therefore, the membrane would resist to long hydrocarbons and the exposed cells would remain viable for milking.     

Anatomical location of the medial lemniscus and spinothalamic tract at the pons in the human brain: A diffusion tensor tractography study

Abstract

Using diffusion tensor tractography, we investigated the anatomical location of medial lemniscus (ML) and spinothalamic tract (STT) at pons. We recruited 47 healthy volunteers. Evaluation of the anatomical location of ML and STT was performed using the highest probabilistic location at the upper, middle, and lower pons. According to findings, MLs were located around the middle to medial one-third, between midline and lateral boundary of pons in the pontine tegmentum and STTs were located posterolaterally to ML.     

Joint distribution of first exit times of a two dimensional Wiener process with jumps with application to a pair of coupled neurons

Motivated by a neuronal modeling problem, a bivariate Wiener process with two independent components is considered. Each component evolves independently until one of them reaches a threshold value. If the first component crosses the threshold value, it is reset while the dynamics of the other component remains unchanged. But, if this happens to the second component, the first one has a jump of constant amplitude; the second component is then reset to its starting value and its evolution restarts. Both processes evolve once again until one of them reaches again its boundary. In this work, the coupling of the first exit times of the two connected processes is studied.     

Reduction of molecular gas diffusion through gaskets in leaf gas exchange cuvettes by leaf‐mediated pores

There is an ongoing debate on how to correct leaf gas exchange measurements for the unavoidable diffusion leakage that occurs when measurements are done in non‐ambient CO₂ concentrations. In this study, we present a theory on how the CO₂ diffusion gradient over the gasket is affected by leaf‐mediated pores (LMP) and how LMP reduce diffusive exchange across the gaskets. Recent discussions have so far neglected the processes in the quasi‐laminar boundary layer around the gasket. Counter intuitively, LMP reduce the leakage through gaskets, which can be explained by assuming that the boundary layer at the exterior of the cuvette is enriched with air from the inside of the cuvette. The effect can thus be reduced by reducing the boundary layer thickness. The theory clarifies conflicting results from earlier studies. We developed leaf adaptor frames that eliminate LMP during measurements on delicate plant material such as grass leaves with circular cross section, and the effectiveness is shown with respiration measurements on a harp of Deschampsia flexuosa leaves. We conclude that the best solution for measurements with portable photosynthesis systems is to avoid LMP rather than trying to correct for the effects.     

Serum albumin acts as a shuttle to enhance cholesterol efflux from cells

An important mechanism contributing to cell cholesterol efflux is aqueous transfer in which cholesterol diffuses from cells into the aqueous phase and becomes incorporated into an acceptor particle. Some compounds can enhance diffusion by acting as shuttles transferring cholesterol to cholesterol acceptors, which act as cholesterol sinks. We have examined whether particles in serum can enhance cholesterol efflux by acting as shuttles. This task was accomplished by incubating radiolabeled J774 cells with increasing concentrations of lipoprotein-depleted sera (LPDS) or components present in serum as shuttles and a constant amount of LDL, small unilamellar vesicles, or red blood cells (RBC) as sinks. Synergistic efflux was measured as the difference in fractional efflux in excess of that predicted by the addition of the individual efflux values of sink and shuttle alone. Synergistic efflux was obtained when LPDS was incubated with cells and LDL. When different components of LPDS were used as shuttles, albumin produced synergistic efflux, while apoA-I did not. A synergistic effect was also obtained when RBC was used as the sink and albumin as shuttle. The previously observed negative association of albumin with coronary artery disease might be linked to reduced cholesterol shuttling that would occur when serum albumin levels are low.