Studies on the conformational flexibility of α-L-rhamnose-containing oligosaccharides using 13C-site-specific labeling, NMR spectroscopy and molecular simulations: implications for the three-dimensional structure of bacterial rhamnan polysaccharides

Bacterial polysaccharides are comprised of a variety of monosaccharides, L-rhamnose (6-deoxy-L-mannose) being one of them. This sugar is often part of α-(1 → 2)- and/or α-(1 → 3)-linkages and we have therefore studied the disaccharide α-L-Rhap-(1 → 2)-α-L-Rhap-OMe to obtain information on conformational preferences at this glycosidic linkage. The target disaccharide was synthesized with (13)C site-specific labeling at C1' and at C2', i.e., in the terminal group. 2D (1)H,(13)C-HSQC-HECADE and (1)H,(13)C-J-HMBC NMR experiments, 1D (13)C and (1)H NMR spectra together with total line-shape analysis were used to extract conformationally dependent hetero- and homonuclear spin-spin coupling constants. This resulted in the determination of (2)J(C2',H1'), (3)J(C1',C1), (3)J(C1',C3), (3)J(C2',C2), (2)J(C1',C2), (1)J(C1',C2'), and (1)J(C1',H1'). These data together with previously determined J(CH) and (1)H,(1)H NOEs result in fourteen conformationally dependent NMR parameters that are available for analysis of glycosidic linkage flexibility and conformational preferences. A 100 ns molecular dynamics (MD) simulation of the disaccharide with explicit water molecules as solvent showed a major conformational state at φ(H)≈ 40° and ψ(H)≈-35°, consistent with experimental NMR data. In addition, MD simulations were carried out also for α-L-Rhap-(1 → 3)-α-L-Rhap-OMe and a rhamnan hexasaccharide. The gathered information on the oligosaccharides was used to address conformational preferences for a larger structure, a 2- and 3-linked nonasaccharide, with implications for the 3D structure of rhamnan polysaccharides, which should be regarded as flexible polymers.     

Evaluating glutamate and aspartate binding mechanisms to rutile (α-TiO2) via ATR-FTIR spectroscopy and quantum chemical calculations

Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy and quantum chemical calculations were used to elucidate the influence of solution chemistry (pH, amino acid concentration) on the binding mechanisms of glutamic and aspartic acid to rutile (α-TiO(2)). The amino acids, glutamate and aspartate, contain carboxyl and amine groups whose dissociation over a pH range results in changes of molecular charge and reactivity, including reactions with mineral surfaces. At pH 3, a decrease of IR bands corresponding to protonated carboxyl groups is observed upon reaction with TiO(2) and indicates involvement of distal carboxyl groups during sorption. In addition, decreased IR bands arising from carboxyl bonds at 1400 cm(-1), concomitant to shifts to higher wavenumbers for ν(as)(γ-COO(-)) and ν(as)(α-COO(-)) (particularly at low glutamate concentrations), are indicative of inner-sphere coordination of both carboxyl groups and therefore suggest a "lying down" surface species. IR spectra of aspartate reacted with rutile are similar to those of solution-phase samples, without peak shifts indicative of covalent bonding, and outer-sphere coordination is predicted. Quantum chemical calculations were carried out to assist in elucidating molecular mechanisms for glutamate binding to rutile and are in reasonable agreement with experimental data. The combined use of ATR-FTIR data and quantum calculations suggests three potential surface configurations, which include (1) bridging-bidentate where glutamate is "lying down" and binding occurs through inner-sphere coordination of both α- and γ-carboxyl groups; (2) chelating-monodentate in which glutamate binds through inner-sphere coordination with the γ-carboxyl group in a "standing up" configuration (with or without protonation of the α-carboxyl); and (3) another bridging-bidentate configuration where glutamate is binding to rutile via inner-sphere coordination of the α-carboxyl group and outer-sphere coordination with the γ-carboxyl ("lying down").     

Gln-Gly cleavage: Correlation between collision-induced dissociation and biological degradation

Tryptic digestion of the 150-residue human acidic salivary proline-rich protein 1 (PRP-1) generated eight peptides, two of which corresponded to the N-terminal 30-residue segment. In each of the other six tryptic peptides, a consensus repeat with the structure PQGPPQQGG was present. A facile Gln-Gly cleavage between the second and the third residues of the repeat was observed during collision-induced dissociation experiments. We postulate possible mechanisms to account for this reactivity, involving attack on the peptidyl carbonyl group by the Gln sidechain. Significantly, the Gln-Gly cleavage has been shown to be biologically important in the bacterial degradation of PRPs in saliva, generating bacteria-binding Pro-Gln C-termini. We suggest a link between the gas-phase chemistry and the biochemical degradation of these molecules.     

Large angle production of stable particles heavier than the proton and a search for quarks at the CERN intersecting storage rings

Measurements have been performed on production of particles with mass 1.5 GeV/c² and charge $\text{?}\text{2}\text{3}$ for θ_lab = 62.5° and $\text{s}\text{= 53}\text{GeV}$. At p_T = 0.7 GeV/c the relative rate of production of antideuterons to π^? is (5 ± 1) × 10^?5. The deuteron to antideuteron ratio is 3.7 ± 1.2. No new stable particle has been amongst 0.7 × 10⁸ charged particles entering our detector.     

A large-deviations analysis of the GI/GI/1 SRPT queue

We consider a GI/GI/1 queue with the shortest remaining processing time discipline (SRPT) and light-tailed service times. Our interest is focused on the tail behavior of the sojourn-time distribution. We obtain a general expression for its large-deviations decay rate. The value of this decay rate critically depends on whether there is mass in the endpoint of the service-time distribution or not. An auxiliary priority queue, for which we obtain some new results, plays an important role in our analysis. We apply our SRPT results to compare SRPT with FIFO from a large-deviations point of view. 2000 Mathematics Subject Classification: Primary—60K25; Secondary—60F10; 90B22     

Valuations and multiplier ideals

We present a new approach to the study of multiplier ideals in a local, two-dimensional setting. Our method allows us to deal with ideals, graded systems of ideals and plurisubharmonic functions in a unified way. Among the applications are a formula for the complex integrability exponent of a plurisubharmonic function in terms of Kiselman numbers, and a proof of the openness conjecture by Demailly and Kollár. Our technique also yields new proofs of two recent results: one on the structure of the set of complex singularity exponents for holomorphic functions; the other by Lipman and Watanabe on the realization of ideals as multiplier ideals.

     

Causality and Dispersion Relations and the Role of the S-Matrix in the Ongoing Research

The adaptation of the Kramers-Kronig dispersion relations to the causal localization structure of QFT led to an important project in particle physics, the only one with a successful closure. The same cannot be said about the subsequent attempts to formulate particle physics as a pure S-matrix project. The feasibility of a pure S-matrix approach are critically analyzed and their serious shortcomings are highlighted. Whereas the conceptual/mathematical demands of renormalized perturbation theory are modest and misunderstandings could easily be corrected, the correct understanding about the origin of the crossing property requires the use of the mathematical theory of modular localization and its relation to the thermal KMS condition. These new concepts, which combine localization, vacuum polarization and thermal properties under the roof of modular theory, will be explained and their potential use in a new constructive (nonperturbative) approach to QFT will be indicated. The S-matrix still plays a predominant role but, different from Heisenberg’s and Mandelstam’s proposals, the new project is not a pure S-matrix approach. The S-matrix plays a new role as a “relative modular invariant”.     

Carbon Deposit Analysis in Catalyst Deactivation,Regeneration, and Rejuvenation

Hydrocarbon conversion catalysts suffer from deactivation by deposition or formation of carbon deposits. Carbon deposit formation is thermodynamically favored above 350 °C, even in some hydrogen-rich environments. We discuss four basic mechanisms: a carbenium-ion based mechanism taking place on acid sites of zeolites or bifunctional catalysts, a metal-induced formation of soft coke (i.e., oligomers of small olefins) on bifunctional catalysts, a radical-mediated mechanism in higher-temperature processes, and fast-growing carbon filament formation. Catalysts deactivate because carbon deposits block pores at different length scales, or directly block active sites. Some deactivated catalysts can be re-used, others can be regenerated or have to be discarded. Catalyst and process design can mitigate the effects of deactivation. New analytical tools allow for the direct observation (in some cases even under in situ or operando conditions) of the 3D-distribution of coke-type species as a function of catalyst structure and lifetime.     

The rôle of chain ends in the thermal degradation of anionic polystyrene

Direct evidence is given of the initiating rôle played in the thermal degradation of anionic polystyrene by chain ends, either present originally or formed during the degradation. In the early stages of degradation, the most likely bond scission in polystyrenes with benzylic type units (CH₂(C₆H₅)) at both chain ends involves the formation of toluene and an unsaturated terminal unit (CH₂C(C₆H₅)CH₂). The depolymerisation of polystyrene to a mixture of monomer and dimeric, trimeric, etc., fragments is then initiated by further scission at such unsaturated chain ends, giving α-methyl styrene and a depolymerising macroradical.After the early stage of degradation, a further overwhelming contribution to the formation of unsaturated chain ends is derived from chain transfer which occurs during depolymerisation. The concentration of unsaturated chain ends increases throughout the degradation process, thus accelerating the formation of the volatile products of depolymerisation. According to this mechanism of initiation, a constant ratio is found between rates of weight loss and of α-methyl styrene evolution throughout the degradation, independently of the original molecular weight of the polymer.     

Voter models and external influence

ABSTRACT

In this paper, we extend the voter model (VM) and the threshold voter model (TVM) to include external influences modeled as a jump process. We study the newly-formulated models both analytically and computationally, employing diffusion approximations and mean field approximations. We derive results pertaining to the probability of reaching consensus on a particular opinion and also the expected consensus time. We find that although including an external influence leads to a faster consensus in general, this effect is more pronounced in the VM as compared to the TVM. Our findings suggest the potential importance of external influences in addition to local interactions.