Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an α-Helix

A simulation study of the coupled dynamics of amide I and amide II vibrations in an α-helix dissolved in water shows that two-dimensional (2D) infrared spectroscopy may be used to disentangle the energy transport along the helix through each of these modes from the energy relaxation between them. Time scales for both types of processes are obtained. Using polarization-dependent 2D spectroscopy is an important ingredient in the method we propose. The method may also be applied to other two-band systems, both in the infrared (collective vibrations) and the visible (excitons) parts of the spectrum.

Surficial Redistribution of Fallout 131iodine in a Small Temperate Catchment

Isotopes of iodine play significant environmental roles, including a limiting micronutrient (127I), an acute radiotoxin (131I), and a geochemical tracer (129I). But the cycling of iodine through terrestrial ecosystems is poorly understood, due to its complex environmental chemistry and low natural abundance. To better understand iodine transport and fate in a terrestrial ecosystem, we traced fallout 131iodine throughout a small temperate catchment following contamination by the 11 March 2011 failure of the Fukushima Daiichi nuclear power facility. We find that radioiodine fallout is actively and efficiently scavenged by the soil system, where it is continuously focused to surface soils over a period of weeks following deposition. Mobilization of historic (pre-Fukushima) 137cesium observed concurrently in these soils suggests that the focusing of iodine to surface soils may be biologically mediated. Atmospherically deposited iodine is subsequently redistributed from the soil system via fluvial processes in a manner analogous to that of the particle-reactive tracer 7beryllium, a consequence of the radionuclides’ shared sorption affinity for fine, particulate organic matter. These processes of surficial redistribution create iodine hotspots in the terrestrial environment where fine, particulate organic matter accumulates, and in this manner regulate the delivery of iodine nutrients and toxins alike from small catchments to larger river systems, lakes and estuaries

Resonance structure in the Li^- photodetachment cross section

We report on the first observation of resonance structure in the total cross section for the photodetachment of Li^-. The structure arises from the autodetaching decay of doubly excited ^1P states of Li^- that are bound with respect to the 3p state of the Li atom. Calculations have been performed for both Li^- and H^- to assist in the identification of these resonances. The lowest lying resonance is a symmetrically excited intrashell resonance. Higher lying asymmetrically excited intershell states are observed which converge on the Li(3p) limit.Comment: 4 pages, 2 figure, 19 references, RevTeX, figures in ep

All-optical retrieval of the global phase for two-dimensional Fourier-transform spectroscopy

A combination of spatial interference patterns and spectral interferometry are used to find the global phase for non-collinear two-dimensional Fourier-transform (2DFT) spectra. Results are compared with those using the spectrally resolved transient absorption (STRA) method to find the global phase when excitation is with co-linear polarization. Additionally cross-linear polarized 2DFT spectra are correctly phased using the all-optical technique, where the SRTA is not applicable.Comment: 6 pages, 7 figures, journal publicatio

Two-Dimensional Infrared Spectroscopy of Antiparallel β-Sheet Secondary Structure

We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel β-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-L-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-L-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel β-sheet. In the proteins with antiparallel β-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic “Z”-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.

Cohomology of bundles on homological Hopf manifold

We discuss the properties of complex manifolds having rational homology of $S^1 \times S^{2n-1}$ including those constructed by Hopf, Kodaira and Brieskorn-van de Ven. We extend certain previously known vanishing properties of cohomology of bundles on such manifolds.As an application we consider degeneration of Hodge-deRham spectral sequence in this non Kahler setting.Comment: To appear in Proceedings of 2007 conference on Several complex variables and Complex Geometry. Xiamen. Chin

Vibrational Spectra of a Mechanosensitive Channel

We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening process. Linear dichroism cannot distinguish an intermediate structure from the closed structure, but sum-frequency generation can. In addition, we find that two-dimensional infrared spectroscopy can be used to distinguish all three investigated gating states of the mechanosensitive membrane channel.

Revisiting geochemical controls on patterns of carbonate deposition through the lens of multiple pathways to mineralization

The carbonate sedimentary record contains diverse compositions and textures that reflect the evolution of oceans and atmospheres through geological time. Efforts to reconstruct paleoenvironmental conditions from these deposits continue to be hindered by the need for process-based models that can explain observed shifts in carbonate chemistry and form. Traditional interpretations assume minerals precipitate and grow by classical ion-by-ion addition processes but are unable to reconcile a number of unusual features contained in Proterozoic carbonates. The realization that diverse organisms produce high Mg carbonate skeletal structures by non-classical pathways involving amorphous intermediates raises the question of whether similar processes are also active in sedimentary environments. This study examines the hypothesis that non-classical pathways to mineralization are the physical basis for some of the carbonate morphologies and compositions observed in natural and laboratory settings. We designed experiments with a series of different solution Mg : Ca ratios and saturation environments to investigate the effects on carbonate phase, Mg content, and morphology. Our observations of diverse carbonate mineral compositions and textures suggest geochemical conditions bias the mineralization pathway by a systematic relationship to Mg : Ca ratio and the abundance of carbonate ions. Environments with low Mg levels produce calcite crystallites with 0–12 mol% MgCO_3. In contrast, the combination of high initial Mg : Ca and rapidly increasing saturation opens a non-classical pathway that begins with extensive precipitation of an amorphous calcium carbonate (ACC). This phase slowly transforms to aggregates of very high Mg calcite nanoparticles whose structures and compositions are similar to natural disordered dolomites. The non-classical pathways are favored when the local environment contains sufficient Mg to inhibit calcite growth through increased solubility—a thermodynamic factor, and achieves saturation with respect to ACC on a timescale that is shorter than the rate of aragonite nucleation—a kinetic factor. Aragonite is produced when Mg levels are high but saturation is insufficient for ACC precipitation. The findings provide a physical basis for anecdotal claims that the interplay of kinetic and thermodynamic factors underlies patterns of carbonate precipitation and suggest the need to expand traditional interpretations of geological carbonate formation to include non-classical pathways to mineralization

Self-consistent solution for the polarized vacuum in a no-photon QED model

We study the Bogoliubov-Dirac-Fock model introduced by Chaix and Iracane ({\it J. Phys. B.}, 22, 3791--3814, 1989) which is a mean-field theory deduced from no-photon QED. The associated functional is bounded from below. In the presence of an external field, a minimizer, if it exists, is interpreted as the polarized vacuum and it solves a self-consistent equation. In a recent paper math-ph/0403005, we proved the convergence of the iterative fixed-point scheme naturally associated with this equation to a global minimizer of the BDF functional, under some restrictive conditions on the external potential, the ultraviolet cut-off $\Lambda$ and the bare fine structure constant $\alpha$. In the present work, we improve this result by showing the existence of the minimizer by a variational method, for any cut-off $\Lambda$ and without any constraint on the external field. We also study the behaviour of the minimizer as $\Lambda$ goes to infinity and show that the theory is "nullified" in that limit, as predicted first by Landau: the vacuum totally kills the external potential. Therefore the limit case of an infinite cut-off makes no sense both from a physical and mathematical point of view. Finally, we perform a charge and density renormalization scheme applying simultaneously to all orders of the fine structure constant $\alpha$, on a simplified model where the exchange term is neglected.Comment: Final version, to appear in J. Phys. A: Math. Ge

Bivalirudin started during emergency transport for primary PCI.

BACKGROUND: Bivalirudin, as compared with heparin and glycoprotein IIb/IIIa inhibitors, has been shown to reduce rates of bleeding and death in patients undergoing primary percutaneous coronary intervention (PCI). Whether these benefits persist in contemporary practice characterized by prehospital initiation of treatment, optional use of glycoprotein IIb/IIIa inhibitors and novel P2Y12 inhibitors, and radial-artery PCI access use is unknown. METHODS: We randomly assigned 2218 patients with ST-segment elevation myocardial infarction (STEMI) who were being transported for primary PCI to receive either bivalirudin or unfractionated or low-molecular-weight heparin with optional glycoprotein IIb/IIIa inhibitors (control group). The primary outcome at 30 days was a composite of death or major bleeding not associated with coronary-artery bypass grafting (CABG), and the principal secondary outcome was a composite of death, reinfarction, or non-CABG major bleeding. RESULTS: Bivalirudin, as compared with the control intervention, reduced the risk of the primary outcome (5.1% vs. 8.5%; relative risk, 0.60; 95% confidence interval [CI], 0.43 to 0.82; P=0.001) and the principal secondary outcome (6.6% vs. 9.2%; relative risk, 0.72; 95% CI, 0.54 to 0.96; P=0.02). Bivalirudin also reduced the risk of major bleeding (2.6% vs. 6.0%; relative risk, 0.43; 95% CI, 0.28 to 0.66; P<0.001). The risk of acute stent thrombosis was higher with bivalirudin (1.1% vs. 0.2%; relative risk, 6.11; 95% CI, 1.37 to 27.24; P=0.007). There was no significant difference in rates of death (2.9% vs. 3.1%) or reinfarction (1.7% vs. 0.9%). Results were consistent across subgroups of patients. CONCLUSIONS: Bivalirudin, started during transport for primary PCI, improved 30-day clinical outcomes with a reduction in major bleeding but with an increase in acute stent thrombosis. (Funded by the Medicines Company; EUROMAX ClinicalTrials.gov number, NCT01087723.)