Probing the glycosidic linkage: UV and IR ion-dip spectroscopy of a lactoside

The beta(1-->4) glycosidic linkage found in lactose is a prevalent structural motif in many carbohydrates and glycoconjugates. Using UV and IR ion-dip spectroscopies to probe benzyl lactoside isolated in the gas phase, we find that the disaccharide unit adopts only a single, rigid structure. Its fully resolved infrared ion-dip spectrum is in excellent agreement with that of the global minimum structure computed ab initio. This has glycosidic torsion angles of phi(H) (H1-C1-O-C4') approximately 180 degrees and psi(H) (C1-O-C4'-H4') approximately 0 degrees which correspond to a rotation of approximately 150 degrees about the glycosidic bond compared to the accepted solution-phase conformation. We discuss the biological implications of this discovery and the generality of the strategies employed in making it.     

Adding water to sugar: a spectroscopic and computational study of alpha- and beta-phenylxyloside in the gas phase

The gas phase structures of phenyl alpha- and beta-d-xylopyranoside (alpha- and beta-pXyl) and their mono-hydrates have been investigated using a combination of resonant two-photon ionization (R2PI), ultra-violet hole-burning and resonant infrared ion dip spectroscopy, coupled with density functional theory (DFT) and ab initio computation. The hole-burning experiments indicate the population of a single conformer only, in each of the two anomers. Their experimental and calculated infrared spectra are both consistent with a conformational assignment corresponding to the computed global minimum configuration. All three OH groups are oriented towards the oxygen atom (O1) on the anomeric carbon atom to form an all trans(ttt) counter-clockwise chain of hydrogen bonds. The mono-hydrates, alpha- and beta-pXyl(H(2)O) each populate two distinct structures in the molecular beam environment, with the water molecule inserted between OH4 and OH3 or between OH3 and OH2 in alpha-pXyl(H2O), and between OH2 and O1 in either of two alternative orientations, in beta-pXyl(H2O). In all of the mono-hydrated xyloside complexes, the water molecule inserts into the weakest link of the sugar molecules' hydrogen-bonded chain of hydroxy groups, creating a single extended chain, strengthened by co-operativity. The all-trans configuration of the xylose moiety is retained and the mono-hydrate structures correspond to those calculated to lie at the lowest relative energies.     

Spin singlet mott states and evidence for spin singlet quantum condensates of spin-one bosons in lattices

We have investigated spin singlet Mott states of spin-one bosons with antiferromagnetic interactions. These spin singlet states do not break rotational symmetry and exhibit remarkably different macroscopic properties compared with nematic Mott states of spin-one bosons. We demonstrate that the dynamics of spin singlet Mott states is fully characterized by even- or odd-class quantum dimer models. The difference between spin singlet Mott states for even and odd numbers of atoms per site can be attributed to a selection rule in the low energy sectors of on-site Hilbert spaces; alternatively, it can also be attributed to an effect of Berry’s phases on bosonic Mott states. We also discuss evidence for spin singlet quantum condensate of spin-one atoms. Our main finding is that in a projected spin singlet Hilbert space, the low energy physics of spin-one bosons is equivalent to that of a Bose-Hubbard model for spinless bosons interacting via Ising gauge fields. The other major finding is spin-charge separation in some one-dimensional Mott states. We propose charge-e spin singlet superfluid for an odd number of atoms per lattice site and charge-2e spin singlet superfluid for an even number of atoms per lattice site in one-dimensional lattices. All discussions in this article are limited to integer numbers of bosons per site.     

Identification of a set of genes showing regionally enriched expression in the mouse brain

Background

We have recorded responses from single neurons in murine visual cortex to determine the effectiveness of the input from the two murine cone photoreceptor mechanisms and whether there is any unique selectivity for cone inputs at this higher region of the visual system that would support the possibility of colour vision in mice. Each eye was stimulated by diffuse light, either 370 (strong stimulus for the ultra-violet (UV) cone opsin) or 505 nm (exclusively stimulating the middle wavelength sensitive (M) cone opsin), obtained from light emitting diodes (LEDs) in the presence of a strong adapting light that suppressed the responses of rods.

Results

Single cells responded to these diffuse stimuli in all areas of striate cortex. Two types of responsive cells were encountered. One type (135/323 – 42%) had little to no spontaneous activity and responded at either the on and/or the off phase of the light stimulus with a few impulses often of relatively large amplitude. A second type (166/323 – 51%) had spontaneous activity and responded tonically to light stimuli with impulses often of small amplitude. Most of the cells responded similarly to both spectral stimuli. A few (18/323 – 6%) responded strongly or exclusively to one or the other spectral stimulus and rarely in a spectrally opponent manner.

Conclusion

Most cells in murine striate cortex receive excitatory inputs from both UV- and M-cones. A small fraction shows either strong selectivity for one or the other cone mechanism and occasionally cone opponent responses. Cells that could underlie chromatic contrast detection are present but extremely rare in murine striate cortex.     

Supersolid bose-fermi mixtures in optical lattices

We study a mixture of strongly interacting bosons and spinless fermions with on-site repulsion in a three-dimensional optical lattice. For this purpose we develop and apply a generalized dynamical mean-field theory, which is exact in infinite dimensions and reliably describes the full range from weak to strong coupling. We restrict ourselves to half filling. For weak Bose-Fermi repulsion a supersolid forms, in which bosonic superfluidity coexists with charge-density wave order. For stronger interspecies repulsion the bosons become localized while the charge-density wave order persists. The system is unstable against phase separation for weak repulsion among the bosons.     

Vibrational Spectroscopy and Conformational Structure of Protonated Polyalanine Peptides Isolated in the Gas Phase

The conformational structures of protonated polyalanine peptides, Ala(n)H(+), have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala(3)H(+), adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala(7)H(+), adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.     

Conformations of 2-phenylethanol and its singly hydrated complexes: UV–UV and IR–UV ion-dip spectroscopy

The structures of 2-phenylethanol and its 1:1 water complexes have been investigated by UV–UV holeburning and IR–UV ion-dip spectroscopy, coupled with ab initio computation. The most populated molecular conformer is stabilized by an intramolecular π-type H-bond and its rotational band contours suggest the incidence of vibronic coupling involving motion of the side chain. Its 1:1 water complexes are associated with two distinct structures – water binds either as a proton donor or an acceptor. In the latter, the intramolecular H-bond is disrupted and the water molecule inserts between the OH and the aromatic ring. A second, extended anti conformer can also be detected.     

Sampling the Variational Posterior with Local Refinement

Variational inference is an optimization-based method for approximating the posterior distribution of the parameters in Bayesian probabilistic models. A key challenge of variational inference is to approximate the posterior with a distribution that is computationally tractable yet sufficiently expressive. We propose a novel method for generating samples from a highly flexible variational approximation. The method starts with a coarse initial approximation and generates samples by refining it in selected, local regions. This allows the samples to capture dependencies and multi-modality in the posterior, even when these are absent from the initial approximation. We demonstrate theoretically that our method always improves the quality of the approximation (as measured by the evidence lower bound). In experiments, our method consistently outperforms recent variational inference methods in terms of log-likelihood and ELBO across three example tasks: the Eight-Schools example (an inference task in a hierarchical model), training a ResNet-20 (Bayesian inference in a large neural network), and the Mushroom task (posterior sampling in a contextual bandit problem).