Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.     

Direct Images,Fields of Hilbert Spaces,and Geometric Quantization

Geometric quantization often produces not one Hilbert space to represent the quantum states of a classical system but a whole family H _s of Hilbert spaces, and the question arises if the spaces H _s are canonically isomorphic. Axelrod et al. (J. Diff. Geo. 33:787–902, 1991) and Hitchin (Commun. Math. Phys. 131:347–380, 1990) suggest viewing H _s as fibers of a Hilbert bundle H, introduce a connection on H, and use parallel transport to identify different fibers. Here we explore to what extent this can be done. First we introduce the notion of smooth and analytic fields of Hilbert spaces, and prove that if an analytic field over a simply connected base is flat, then it corresponds to a Hermitian Hilbert bundle with a flat connection and path independent parallel transport. Second we address a general direct image problem in complex geometry: pushing forward a Hermitian holomorphic vector bundle ${E \to Y}$ along a non–proper map ${Y \to S}$ . We give criteria for the direct image to be a smooth field of Hilbert spaces. Third we consider quantizing an analytic Riemannian manifold M by endowing TM with the family of adapted Kähler structures from Lempert and Sz?ke (Bull. Lond. Math. Soc. 44:367–374, 2012). This leads to a direct image problem. When M is homogeneous, we prove the direct image is an analytic field of Hilbert spaces. For certain such M—but not all—the direct image is even flat; which means that in those cases quantization is unique.     

The Piracicaba River basin: isotope hydrology of a tropical river basin under anthropogenic stress

The stable isotope content of samples of precipitation and of the river water throughout the Piracicaba basin in Brazil was measured over a two-year period. The isotope values of precipitation follow a consistent pattern of relatively depleted values of both deuterium and oxygen 18 during the rainy summers and enriched ones during the dry winters, with all values aligned slightly above the Global Meteoric Water Line. The isotopic composition of the river water throughout the basin shows a remarkable spatial coherence and much smaller scatter of data than those of the precipitation. The isotope composition of river water is close to that of the precipitation in the rainy season, however, with a consistent lower d-excess value by 1/1000-2/1000. This is attributed to evaporative water loss in the basin, in part an expression of the recycling of water due to the anthropogenic activity in the region. The more divergent values are recorded during high-water stages in the rivers. In many cases, the floods during the beginning of the rainy season are characterized by an enrichment of the heavy isotopes and lower d-excess values when compared to the precipitation, with the opposite situation later in the rainy season. This is interpreted as resulting from the watershed/riverflow interaction pattern, and it thus suggests that the isotope composition can monitor the hydrologic situation in the basin and its changes.     

Review of fluorescence anisotropy decay analysis by frequency-domain fluorescence spectroscopy

This didactic paper summarizes the mathematical expressions needed for analysis of fluorescence anisotropy decays from polarized frequency-domain fluorescence data. The observed values are the phase angle difference between the polarized components of the emission and the modulated anisotropy, which is the ratio of the polarized and amplitude-modulated components of the emission. This procedure requires a separate measurement of the intensity decay of the total emission. The expressions are suitable for any number of exponential components in both the intensity decay and the anisotropy decay. The formalism is generalized for global analysis of anisotropy decays measured at different excitation wavelengths and for different intensity decay times as the result of quenching. Additionally, we describe the expressions required for associated anisotropy decays, that is, anisotropy decays where each correlation time is associated with a decay time present in the anisotropy decay. And finally, we present expressions appropriate for distributions of correlation times. This article should serve as a reference for researchers using frequency-domain fluorometry.     

Distance-dependent fluorescence quenching ofN-acetyl-l-tryptophanamide by acrylamide

We examined the time-dependent intensity decays ofN-acetyl-l-tryptophanamide (NATA) when collisionally quenched by acrylamide in propylene glycol over a range of temperatures. The intensity decays of NATA became increasingly heterogeneous in the presence of acrylamide. The NATA intensity decays were not consistent with the Collins-Kimball radiation boundary condition (RBC) model for quenching. The steady-state Stern-Volmer plots show significant upward curvature, and quenching of NATA by acrylamide was observed even in vitrified propylene glycol, where translational diffusion cannot occur during the lifetime of the excited state. These frequencydomain and steady-state data indicate a through-space quenching interaction between NATA and acrylamide, and the results are consistent with a rate constant for quenching that depends exponentially on the fluorophore-quencher separation distance. The exponential distance-dependent rate of quenching also explains the upward curvature of the Stern-Volmer plot, and the steady-state data aid in determining the interaction distance between NATA and acrylamide. These results suggest that the distance-dependent quenching rates need to be considered in the interpretation of acrylamide quenching of proteins.     

Ernst potentials for vacuum Bianchi models

We derive Ernst potentials for vacuum Bianchi I through VII models. A scheme to find inhomogeneous generalizations of such models by using generating techniques which incorporate electromagnetic fields or gravitational wave perturbations to a seed Bianchi solution is presented.On leave of absence from: Departamento de Fisica, CINVESTAV del IPN, Mexico     

Distance distributions and dynamics of a zinc finger peptide from fluorescence resonance energy transfer measurements

Time-resolved fluorescence resonance energy transfer (FRET) measurements were used to measure distance distributions and intramolecular dynamics (site-to-site diffusion) of a 28-residue single-domain zinc finger peptide in the absence and presence of zinc ion. Energy transfer was measured between TRP₁₄ and a N-terminal DNS group. As expected, the TRP-to-DNS distance distribution for zinc-bound peptide is shorter and narrower (R _av=11.2 Å,hw=2.8 Å) than the metal-free peptide (R _av=20.1 Å,hw=14.5 Å). The degree of mutual donor-to-acceptor diffusion (D) was also determined for these distributions. For zinc-bound peptide there is no detectible diffusion (D0.2 Ų/ns), whereas for metal-free peptide a considerable amount of motion is occurring between the donor and the acceptor (D=12 Ų/ns). These results indicate that the zinc-bound peptide folds into a unique, well-defined conformation, whereas the metal-free conformation is flexible and rapidly changing. The absence of detectible mutual site-to-site diffusion between the donor and the acceptor in the metal-bound zinc finger peptide indicates that intramolecular motion is essentially frozen out, on the FRET time scale, as a consequence of zinc coordination.Dedicated to the memory of Barbara D. Wells.