Diffusion of hydrocarbons in confined media: translational and rotational motion

Diffusion of monatomic guest species within confined media has been understood to a good degree due to investigations carried out during the past decade and a half. Most guest species that are of industrial relevance are actually polyatomics such as, for example, hydrocarbons in zeolites. We attempt to investigate the influence of non-spherical nature of guest species on diffusion. Recent molecular dynamics (MD) simulations of motion of methane in NaCaA and NaY, benzene in NaY and one-dimensional channels AlPO4−5, VPI-5 and carbon nanotube indicate interesting insights into the influence of the host on rotational degrees of freedom and orientational properties. It is shown that benzene in one-dimensional channels where the levitation parameter is near unity exhibits translational motion opposite to what is expected on the basis of molecular anisotropy. Rotational motion of benzene also possesses rotational diffusivities aroundC6 and C2axes opposite to what is expected on the basis of molecular geometry. Methane shows orientational preference for 2+2 or 1+3 depending on the magnitude of the levitation parameter

Diffusive and Superdiffusive Motion of sorbates in Carbon nanotubes

Molecular dynamics simulations of sorbates of different sizes confined to the interior of carbon nanotubes are reported. The mean squared displacement shows gradual change from diffusive for small sorbates to superdiffusive for intermediate sized-sorbates to ballistic for sizes comparable to the channel diameter. We show that this crossover behaviour can be understood on the basis of a gradual decrease of the x-y component of the force with the levitation parameter. The analysis can also help to rationalize some recently published results.Comment: 3 pages, 3 figure

Methane and carbon dioxide adsorption on edge-functionalized graphene: A comparative DFT study

With a view towards optimizing gas storage and separation in crystalline and disordered nanoporous carbon-based materials, we use ab initio density functional theory calculations to explore the effect of chemical functionalization on gas binding to exposed edges within model carbon nanostructures. We test the geometry, energetics, and charge distribution of in-plane and out-of-plane binding of CO2 and CH4 to model zigzag graphene nanoribbons edge-functionalized with COOH, OH, NH2, H2PO3, NO2, and CH3. Although different choices for the exchange-correlation functional lead to a spread of values for the binding energy, trends across the functional groups are largely preserved for each choice, as are the final orientations of the adsorbed gas molecules. We find binding of CO2 to exceed that of CH4 by roughly a factor of two. However, the two gases follow very similar trends with changes in the attached functional group, despite different molecular symmetries. Our results indicate that the presence of NH2, H2PO3, NO2, and COOH functional groups can significantly enhance gas binding with respect to a hydrogen-passivated edge, making the edges potentially viable binding sites in materials with high concentrations of edge carbons. To first order, in-plane binding strength correlates with the larger permanent and induced dipole moments on these groups. Implications for tailoring carbon structures for increased gas uptake and improved CO2/CH4 selectivity are discussed.Comment: 12 pages, 7 figure

Next Generation Sequencing Assay for Detection of Circulating HPV DNA (cHPV-DNA) in Patients Undergoing Radical (Chemo)Radiotherapy in Anal Squamous Cell Carcinoma (ASCC).

Background: Following chemo-radiotherapy (CRT) for human papilloma virus positive (HPV+) anal squamous cell carcinoma (ASCC), detection of residual/recurrent disease is challenging. Patients frequently undergo unnecessary repeated biopsies for abnormal MRI/clinical findings. In a pilot study we assessed the role of circulating HPV-DNA in identifying "true" residual disease. Methods: We prospectively collected plasma samples at baseline (n = 21) and 12 weeks post-CRT (n = 17). Circulating HPV-DNA (cHPV DNA) was measured using a novel next generation sequencing (NGS) assay, panHPV-detect, comprising of two primer pools covering distinct regions of eight high-risk HPV genomes (16, 18, 31, 33, 35, 45, 52, and 58) to detect circulating HPV-DNA (cHPV DNA). cHPV-DNA levels post-CRT were correlated to disease response. Results: In pre-CRT samples, panHPV-detect demonstrated 100% sensitivity and specificity for HPV associated ASCC. PanHPV-detect was able to demonstrate cHPV-DNA in 100% (9/9) patients with T1/T2N0 cancers. cHPV-DNA was detectable 12 weeks post CRT in just 2/17 patients, both of whom relapsed. 1/16 patients who had a clinical complete response (CR) at 3 months post-CRT but relapsed at 9 months and 1/1 patient with a partial response (PR). PanHPV-detect demonstrated 100% sensitivity and specificity in predicting response to CRT. Conclusion: We demonstrate that panHPV-detect, an NSG assay is a highly sensitive and specific test for the identification of cHPV-DNA in plasma at diagnosis. cHPV-DNA post-treatment may predict clinical response to CRT

Evidence for a Low-Spin to Intermediate-Spin State Transition in LaCoO3

We present measurements of the magnetic susceptibility and of the thermal expansion of a LaCoO$_3$ single crystal. Both quantities show a strongly anomalous temperature dependence. Our data are consistently described in terms of a spin-state transition of the Co$^{3+}$ ions with increasing temperature from a low-spin ground state to an intermediate-spin state without (100K - 500K) and with (>500K) orbital degeneracy. We attribute the lack of orbital degeneracy up to 500K to (probably local) Jahn-Teller distortions of the CoO$_6$ octahedra. A strong reduction or disappearance of the Jahn-Teller distortions seems to arise from the insulator-to-metal transition around 500 K.Comment: an error in the scaling factor of Eq.(4) and consequently 2 values of table I have been corrected. The conclusions of the paper remain unchanged. See also: C. Zobel et al. Phys. Rev. B 71, 019902 (2005) and J. Baier et al. Phys. Rev. B 71, 014443 (2005

Borrelia valaisiana resist complement-mediated killing independently of the recruitment of immune regulators and inactivation of complement components

Spirochetes belonging to the Borrelia (B.) burgdorferi sensu lato complex differ in their resistance to complement-mediated killing, particularly in regard to human serum. In the present study, we elucidate the serum and complement susceptibility of B. valaisiana, a genospecies with the potential to cause Lyme disease in Europe as well as in Asia. Among the investigated isolates, growth of ZWU3 Ny3 was not affected while growth of VS116 and Bv9 was strongly inhibited in the presence of 50% human serum. Analyzing complement activation, complement components C3, C4 and C6 were deposited on the surface of isolates VS116 and Bv9, and similarly the membrane attack complex was formed on their surface. In contrast, no surface-deposited components and no aberrations in cell morphology were detected for serum-resistant ZWU3 Ny3. While further investigating the protective role of bound complement regulators in mediating complement resistance, we discovered that none of the B. valaisiana isolates analyzed bound complement regulators Factor H, Factor H-like protein 1, C4b binding protein or C1 esterase inhibitor. In addition, B. valaisiana also lacked intrinsic proteolytic activity to degrade complement components C3, C3b, C4, C4b, and C5. Taken together, these findings suggest that certain B. valaisiana isolates differ in their capability to resist complement-mediating killing by human serum. The molecular mechanism utilized by B. valaisiana to inhibit bacteriolysis appears not to involve binding of the key host complement regulators of the alternative, classical, and lectin pathways as already known for serum-resistant Lyme disease or relapsing fever borreliae

Carbon Nanotubes by a CVD Method. Part I: Synthesis and Characterization of the (Mg, Fe)O Catalysts

The controlled synthesis of carbon nanotubes by chemical vapor deposition requires tailored and wellcharacterized catalyst materials. We attempted to synthesize Mg1-xFexO oxide solid solutions by the combustion route, with the aim of performing a detailed investigation of the influence of the synthesis conditions (nitrate/urea ratio and the iron content) on the valency and distribution of the iron ions and phases. Notably, characterization of the catalyst materials is performed using 57Fe Mo¨ssbauer spectroscopy, X-ray diffraction, and electron microscopy. Several iron species are detected including Fe2+ ions substituting for Mg2+ in the MgO lattice, Fe3+ ions dispersed in the octahedral sites of MgO, different clusters of Fe3+ ions, and MgFe2O4-like nanoparticles. The dispersion of these species and the microstructure of the oxides are discussed. Powders markedly different from one another that may serve as model systems for further study are identified. The formation of carbon nanotubes upon reduction in a H2/CH4 gas atmosphere of the selected powders is reported in a companion paper

Influences of Excluded Volume of Molecules on Signaling Processes on Biomembrane

We investigate the influences of the excluded volume of molecules on biochemical reaction processes on 2-dimensional surfaces using a model of signal transduction processes on biomembranes. We perform simulations of the 2-dimensional cell-based model, which describes the reactions and diffusion of the receptors, signaling proteins, target proteins, and crowders on the cell membrane. The signaling proteins are activated by receptors, and these activated signaling proteins activate target proteins that bind autonomously from the cytoplasm to the membrane, and unbind from the membrane if activated. If the target proteins bind frequently, the volume fraction of molecules on the membrane becomes so large that the excluded volume of the molecules for the reaction and diffusion dynamics cannot be negligible. We find that such excluded volume effects of the molecules induce non-trivial variations of the signal flow, defined as the activation frequency of target proteins, as follows. With an increase in the binding rate of target proteins, the signal flow varies by i) monotonically increasing; ii) increasing then decreasing in a bell-shaped curve; or iii) increasing, decreasing, then increasing in an S-shaped curve. We further demonstrate that the excluded volume of molecules influences the hierarchical molecular distributions throughout the reaction processes. In particular, when the system exhibits a large signal flow, the signaling proteins tend to surround the receptors to form receptor-signaling protein clusters, and the target proteins tend to become distributed around such clusters. To explain these phenomena, we analyze the stochastic model of the local motions of molecules around the receptor.Comment: 31 pages, 10 figure

Fe/Co Alloys for the Catalytic Chemical Vapor Deposition Synthesis of Single- and Double-Walled Carbon Nanotubes (CNTs). 1. The CNT−Fe/Co−MgO System

Mg0.90FexCoyO (x + y ) 0.1) solid solutions were synthesized by the ureic combustion route. Upon reduction at 1000 °C in H2-CH4 of these powders, Fe/Co alloy nanoparticles are formed, which are involved in the formation of carbon nanotubes, which are mostly single and double walled, with an average diameter close to 2.5 nm. Characterizations of the materials are performed using 57Fe Mo¨ssbauer spectroscopy and electron microscopy, and a well-established macroscopic method, based on specific-surface-area measurements, was applied to quantify the carbon quality and the nanotubes quantity. A detailed investigation of the Fe/Co alloys’ formation and composition is reported. An increasing fraction of Co2+ ions hinders the dissolution of iron in the MgO lattice and favors the formation of MgFe2O4-like particles in the oxide powders. Upon reduction, these particles form R-Fe/Co particles with a size and composition (close to Fe0.50Co0.50) adequate for the increased production of carbon nanotubes. However, larger particles are also produced resulting in the formation of undesirable carbon species. The highest CNT quantity and carbon quality are eventually obtained upon reduction of the iron-free Mg0.90Co0.10O solid solution, in the absence of clusters of metal ions in the starting material. Introduction Catalyti