Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment

A pathogenetic feature of Alzhemier disease is the aggregation of monomeric beta-amyloid proteins (Abeta) to form oligomers. Usually these oligomers of long peptides aggregate on time scales of microseconds or longer, making computational studies using atomistic molecular dynamics models prohibitively expensive and making it essential to develop computational models that are cheaper and at the same time faithful to physical features of the process. We benchmark the ability of our implicit solvent model to describe equilibrium and dynamic properties of monomeric Abeta(10-35) using all-atom Langevin dynamics (LD) simulations, since Alphabeta(10-35) is the only fragment whose monomeric properties have been measured. The accuracy of the implicit solvent model is tested by comparing its predictions with experiment and with those from a new explicit water MD simulation, (performed using CHARMM and the TIP3P water model) which is approximately 200 times slower than the implicit water simulations. The dependence on force field is investigated by running multiple trajectories for Alphabeta(10-35) using the CHARMM, OPLS-aal, and GS-AMBER94 force fields, whereas the convergence to equilibrium is tested for each force field by beginning separate trajectories from the native NMR structure, a completely stretched structure, and from unfolded initial structures. The NMR order parameter, S2, is computed for each trajectory and is compared with experimental data to assess the best choice for treating aggregates of Alphabeta. The computed order parameters vary significantly with force field. Explicit and implicit solvent simulations using the CHARMM force fields display excellent agreement with each other and once again support the accuracy of the implicit solvent model. Alphabeta(10-35) exhibits great flexibility, consistent with experiment data for the monomer in solution, while maintaining a general strand-loop-strand motif with a solvent-exposed hydrophobic patch that is believed to be important for aggregation. Finally, equilibration of the peptide structure requires an implicit solvent LD simulation as long as 30 ns.     

Isostructural or not? Adducts of some aryl­tin halides with (E)‐1,2‐bis(4‐pyridyl)­ethene

The title complexes [μ‐(E)‐4,4′‐(ethene‐1,2‐diyl)­di­pyridine‐κ²N:N′]­bis­[halotris(4‐methyl­phenyl)­tin(IV)], [Sn₂(C₇H₇)₆X₂(C₁₂H₁₀N₂)], where halo is chloro (X = Cl) and bromo (X = Br) are isostructural. In both crystals, the mol­ecules lie on inversion centers, and there are voids of ca 80 ų that could, but apparently do not, accommodate water mol­ecules. The corresponding iodo structure (X = I) is almost, but not quite, isostructural with the other two compounds; when Br is changed to I, the length of the c axis decreases by more than 1 Å and the voids are no longer large enough to accomodate any solvent mol­ecule. The related complex [μ‐(E)‐4,4′‐(ethene‐1,2‐diyl)­di­pyridine‐κ²N:N′]­bis­[chloro­tri­phenyl­tin(IV)], [Sn₂(C₆H₅)₆Cl₂(C₁₂H₁₀N₂)], crystallizes in a related structure, but the mol­ecules lie on general rather than on special positions. The molecular structures of the four complexes are similar, but the conformation of the phenyl derivative is approximately eclipsed rather than staggered.     

Direct measurements of (p, \gamma) cross-sections at astrophysical energies using radioactive beams and the Daresbury Recoil Separator

There are a number of astrophysical environments in which the path of nucleosynthesis proceeds through proton-rich nuclei. These nuclei have traditionally not been available as beams, and thus proton-capture reactions on these nuclei could only be studied indirectly. At the Holifield Radioactive Ion Beam Facility (HRIBF), some of the first direct measurements of (p, $ \gamma$ ) cross-sections on radioactive beams have been made. The Daresbury Recoil Separator (DRS) has been used to separate the recoils of interest from the unreacted primary beam and identify them in an isobutane-filled ionization counter. First data from ¹⁷F (p, $ \gamma$ ¹⁸Ne and ⁷Be (p, $ \gamma$ ⁸B measurements are presented.     

Modeling high-pressure adsorption of gas mixtures on activated carbon and coal using a simplified local-density model

The simplified local-density (SLD) theory was investigated regarding its ability to provide accurate representations and predictions of high-pressure supercritical adsorption isotherms encountered in coalbed methane (CBM) recovery and CO2 sequestration. Attention was focused on the ability of the SLD theory to predict mixed-gas adsorption solely on the basis of information from pure gas isotherms using a modified Peng-Robinson (PR) equation of state (EOS). An extensive set of high-pressure adsorption measurements was used in this evaluation. These measurements included pure and binary mixture adsorption measurements for several gas compositions up to 14 MPa for Calgon F-400 activated carbon and three water-moistened coals. Also included were ternary measurements for the activated carbon and one coal. For the adsorption of methane, nitrogen, and CO2 on dry activated carbon, the SLD-PR can predict the component mixture adsorption within about 2.2 times the experimental uncertainty on average solely on the basis of pure-component adsorption isotherms. For the adsorption of methane, nitrogen, and CO2 on two of the three wet coals, the SLD-PR model can predict the component adsorption within the experimental uncertainties on average for all feed fractions (nominally molar compositions of 20/80, 40/60, 60/40, and 80/20) of the three binary gas mixture combinations, although predictions for some specific feed fractions are outside of their experimental uncertainties.     

Propagation of S-polarized surface polaritons circumferentially around a locally cylindrical surface

The dispersion relation is derived and solved for s-polarized surface polaritons propagating circumferentially around a portion of a cylindrical interface between vacuum and an isotropic dielectric. In the case that the dielectric is convex toward the vacuum these modes are found to be radiative, and consequently are attenuated as they propagate on the cylindrical surface. When the dielectric is concave toward the vacuum the resulting surface polaritons are nonradiative and propagate unattenuated on the cylinder. Such modes do not exist in the case of a planar interface between a homogeneous isotropic dielectric and vacuum.     

Niobium-93 MQMAS NMR spectroscopic study of alkali and lead niobates.

93Nb (I = 9/2) multiple-quantum magic-angle spinning (MQMAS) NMR spectra of a series of inorganic niobates have been measured. 93Nb MQMAS spectroscopy yields spectra with typically an order of magnitude higher resolution than that obtainable with 93Nb MAS spectroscopy and 93Nb dynamic-angle spinning (DAS) spectroscopy. For example, the full-width at half-maximums of the 93Nb resonances of LiNbO3 were 9 (MAS), 5.8 (DAS), and 0.7 kHz (MQMAS). Broadening of the 93Nb MAS and DAS spectra is due to the second-order quadrupolar and homonuclear dipolar interactions, respectively. The quadrupolar products (P(O)) and isotropic chemical shifts (delta(iso)) of the 93Nb resonances of LiNbO3, NaNbO3, PbNb2O6, Pb2Nb2O7, Pb3Nb2O8, Pb3Nb4O15, Pb3Nb4O13, and Pb1.83Nb1.71Mg0.29O6.39 were determined from MQMAS spectra and range from 13.6 to 26.8 MHz and from -951 to -1113 ppm, respectively. Resonances with relatively large quadrupolar coupling constants (> 30 MHz) were not observed using MQMAS spectroscopy, but were detected using nutation spectroscopy. The applicability and limitations of MQMAS spectroscopy in studying inorganic niobates containing multiple 93Nb resonances are addressed and compared with those of MAS, nutation, and DAS spectroscopies.     

Magnetic resonance imaging: application in musculoskeletal infection

Forty-two patients with clinically suspected osteomyelitis were examined using magnetic resonance imaging (MRI). Twenty-seven patients (64%) had previous surgery or fracture, and 15 (36%) were referred for differentiation of acute osteomyelitis from bone tumors or other pathologic conditions. MRI was compared with computed tomography in 12 cases and with 111In-labeled leukocytes scans in 22. With MRI, 92% of proved infections were detected, and bone and soft-tissue changes were more evident than with routine radiographs, tomography, or computed tomography. In patients with negative cultures and no previous surgery or fracture, it was difficult for MRI to differentiate operative changes from infection. In these patients, 111In-labeled leukocyte images were more specific than MRI.     

Represented value sets for integral binary quadratic forms and lattices

A characterization is given for the integral binary quadratic forms for which the set of represented values is closed under products. It is also proved that for an integral binary quadratic lattice over a Dedekind domain, the product of three values represented by the form is again a value represented by the form. This generalizes the trigroup property observed by V. Arnold in the case of integral binary quadratic forms.