The influence of SO2 and NO2 impurities on CO2 gas hydrate formation and stability

The sequestration of industrially emitted CO(2) in gas hydrate reservoirs has been recently discussed as an option to reduce atmospheric greenhouse gas. This CO(2) contains, despite much effort to clean it, traces of impurities such as SO(2) and NO(2) . Here, we present results of a pilot study on CO(2) hydrates contaminated with 1% SO(2) or 1% NO(2) and show the impact on hydrate formation and stability. Microscopic observations show similar hydrate formation rates, but an increase in hydrate stability in the presence of SO(2). Laser Raman spectroscopy indicates a strong enrichment of SO(2) in the liquid and hydrate phase and its incorporation in both large and small cages of the hydrate lattice. NO(2) is not verifiable by laser Raman spectroscopy, only the presence of nitrate ions could be confirmed. Differential scanning calorimetry analyses show that hydrate stability and dissociation enthalpy of mixed CO(2)-SO(2) hydrates increase, but that only negligible changes arise in the presence of NO(2) impurities. X-ray diffraction data reveal the formation of sI hydrate in all experiments. The conversion rates of ice+gas to hydrate increase in the presence of SO(2), but decrease in the presence of NO(2). After hydrate dissociation, SO(2) and NO(2) dissolved in water and form strong acids.     

Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity

In Fo?rster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 ? in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 ? is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 ?). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A detailed analysis of possible orientation effects (κ(2) problem) indicates that, for short linkers and unknown local environments, additional κ(2)-related uncertainties are clearly outweighed by better defined dye positions.     

Markov models of molecular kinetics: generation and validation

Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. This approach has many appealing characteristics compared to straightforward molecular dynamics simulation and analysis, including the potential to mitigate the sampling problem by extracting long-time kinetic information from short trajectories and the ability to straightforwardly calculate expectation values and statistical uncertainties of various stationary and dynamical molecular observables. In this paper, we summarize the current state of the art in generation and validation of MSMs and give some important new results. We describe an upper bound for the approximation error made by modeling molecular dynamics with a MSM and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast to previous practice, it becomes clear that the best MSM is not obtained by the most metastable discretization, but the MSM can be much improved if non-metastable states are introduced near the transition states. Moreover, we show that it is not necessary to resolve all slow processes by the state space partitioning, but individual dynamical processes of interest can be resolved separately. We also present an efficient estimator for reversible transition matrices and a robust test to validate that a MSM reproduces the kinetics of the molecular dynamics data.     

Extension of the benzyl alcohol route to metal sulfides: "nonhydrolytic" thio sol-gel synthesis of ZnS and SnS2

Crystalline ZnS and SnS(2) particles were synthesized by a modified benzyl alcohol route using benzyl mercaptan as solvent.     

Local-moment and itinerant antiferromagnetism in the heavy-fermion system Ce(Cu1−xNix)2Ge2

Elastic and inelastic neutron-scattering studies on the system Ce(Cu_1?xNi_x)₂Ge₂ are reported. These measurements are complemented by measurements of the magnetic susceptibility, high-field magnetization, heat capacity, thermal expansion, electrical resistivity and thermopower. The results reveal an interesting T-x phase diagram consisting of two different antiferromagnetic phases for x < 0.2 and 0.2 < x < 0.75, respectively, and a heavy-Fermi-liquid regime at higher Ni concentrations. The experimental results are interpreted in terms of an alloying-induced transition from local-moment to itinerant heavy-fermion magnetism. Fingerprints of this latter phase are a strongly reduced ordered moment and a short incommensurate ordering wave vector, in accord with theoretical predictions. A surprisingly good agreement between theory and experiment is found for x > 0.5. Further experimental evidence for different types of antiferromagnetic ordering derives from a line-shape analysis of the quasielastic neutron-scattering intensity, from magnetization and thermopower experiments.     

Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide

We report here an advanced approach for the characterization of the folding pattern of a de novo designed antiparallel coiled coil peptide by high-resolution methods. Incorporation of two fluorescence labels at the C- and N-terminus of the peptide chain as well as modification of two hydrophobic core positions by Phe/[15N,13C]Leu enable the study of the folding characteristics and of distinct amino acid side chain interactions by fluorescence resonance energy transfer (FRET) and NMR spectroscopy. Results of both experiments reveal the antiparallel alignment of the helices and thus prove the design concept. This finding is also supported by molecular dynamics simulations. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in combination with NMR experiments was used for verification of the oligomerization equilibria of the coiled coil peptide.     

Interaction between inner and outer layer in drag-reduced turbulent flows

Effects of wall-based skin-friction drag reduction strategies on the statistical properties of large-scale motions in moderate Reynolds number turbulent flows have been investigated by exploiting Direct Numerical Simulation of turbulent channels. To educe large scales, a new efficient parallel distributed memory algorithm has been implemented which delivers data-driven modes of increasing characteristic lengthscales: the Fast and Adaptive Bidimensional Empirical Mode Decomposition (FABEMD). The influence of wall-based skin friction reduction on large scales is studied by comparing single point statistics, such as r.m.s. fluctuations, and two-point statistics, as cross-correlation functions in controlled and uncontrolled channel flow fields at constant friction Reynolds number. The traditional way of observing large-scale footprinting at the wall, as cross-correlation of the streamwise velocity components at different wall distances, has been found to be unreliable when comparing drag-reduced flows, due to the arbitrary choice of a reference plane in the logarithmic layer. A more sound way of observing the footprinting via the correlation of the streamwise velocity with the friction velocity is addressed and shows an increase of the footprinting in drag-reduced flows. (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Thermodynamics of an interfacial fluid membrane

We discuss a closed system of field equations for a semipermeable membrane which has particle and heat exchange with its surroundings. In this case we consider a surface with an arbitrary shape for specific quantities and mechanical properties. A representation of the constitutive equations follows from the principle of material objectivity in space as well as on surfaces. The constitutive equations can be restricted by an entropy principle. We present both the Gibbs equation and the entropy flux. Furthermore, we obtain the surface stress and the chemical potential in terms of the specific free energy of the membrane. Both the heat flux and the particle flux normal to the membrane depend on the mean curvature and the friction between the particle across the membrane. The interaction tangential to the interface is dependent up on gradients of the surface stress as well as the chemical potential of the interface.