Mol. Cell. Proteomics

Chemical cross-linking in combination with mass spectrometric analysis offers the potential to obtain low-resolution structural information from proteins and protein complexes. Identification of peptides connected by a cross-link provides direct evidence for the physical interaction of amino acid side chains, information that can be used for computational modeling purposes. Despite impressive advances that were made in recent years, the number of experimentally observed cross-links still falls below the number of possible contacts of cross-linkable side chains within the span of the cross-linker. Here, we propose two complementary experimental strategies to expand cross-linking data sets. First, enrichment of cross-linked peptides by size exclusion chromatography selects cross-linked peptides based on their higher molecular mass, thereby depleting the majority of unmodified peptides present in proteolytic digests of cross-linked samples. Second, we demonstrate that the use of proteases in addition to trypsin, such as Asp-N, can additionally boost the number of observable cross-linking sites. The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe

Reconstruction of eye movements during blinks

In eye movement research in reading, the amount of data plays a crucial role for the validation of results. A methodological problem for the analysis of the eye movement in reading are blinks, when readers close their eyes. Blinking rate increases with increasing reading time, resulting in high data losses, especially for older adults or reading impaired subjects. We present a method, based on the symbolic sequence dynamics of the eye movements, that reconstructs the horizontal position of the eyes while the reader blinks. The method makes use of an observed fact that the movements of the eyes before closing or after opening contain information about the eyes movements during blinks. Test results indicate that our reconstruction method is superior to methods that use simpler interpolation approaches. In addition, analyses of the reconstructed data show no significant deviation from the usual behavior observed in readers

Tuning p-wave interactions in an ultracold Fermi gas of atoms

We have measured a p-wave Feshbach resonance in a single-component, ultracold Fermi gas of potassium atoms. We have used this resonance to enhance the normally suppressed p-wave collision cross-section to values larger than the background s-wave cross-section between potassium atoms in different spin-states. In addition to the modification of two-body elastic processes, the resonance dramatically enhances three-body inelastic collisional loss.Comment: 4 pages, 5 figure

Chaotic Orbits in Thermal-Equilibrium Beams: Existence and Dynamical Implications

Phase mixing of chaotic orbits exponentially distributes these orbits through their accessible phase space. This phenomenon, commonly called ``chaotic mixing'', stands in marked contrast to phase mixing of regular orbits which proceeds as a power law in time. It is operationally irreversible; hence, its associated e-folding time scale sets a condition on any process envisioned for emittance compensation. A key question is whether beams can support chaotic orbits, and if so, under what conditions? We numerically investigate the parameter space of three-dimensional thermal-equilibrium beams with space charge, confined by linear external focusing forces, to determine whether the associated potentials support chaotic orbits. We find that a large subset of the parameter space does support chaos and, in turn, chaotic mixing. Details and implications are enumerated.Comment: 39 pages, including 14 figure

A Dielectric Superfluid of Polar Molecules

We show that, under achievable experimental conditions, a Bose-Einstein condensate (BEC) of polar molecules can exhibit dielectric character. In particular, we derive a set of self-consistent mean-field equations that couple the condensate density to its electric dipole field, leading to the emergence of polarization modes that are coupled to the rich quasiparticle spectrum of the condensate. While the usual roton instability is suppressed in this system, the coupling can give rise to a phonon-like instability that is characteristic of a dielectric material with a negative static dielectric function.Comment: Version published in New Journal of Physics, 11+ pages, 4 figure

How Does a Dipolar Bose-Einstein Condensate Collapse?

We emphasize that the macroscopic collapse of a dipolar Bose-Einstein condensate in a pancake-shaped trap occurs through local density fluctuations, rather than through a global collapse to the trap center. This hypothesis is supported by a recent experiment in a chromium condensate.Comment: Proceedings of 17th International Laser Physics Worksho

The role of plant functional trade-offs for biodiversity changes and biome shifts under scenarios of global climatic change

The global geographic distribution of biodiversity and biomes is determined by species-specific physiological tolerances to climatic constraints. Current vegetation models employ empirical bioclimatic relationships to predict present-day vegetation patterns and to forecast biodiversity changes and biome shifts under climatic change. In this paper, we consider trade-offs in plant functioning and their responses under climatic changes to forecast and explain changes in plant functional richness and shifts in biome geographic distributions. <br><br> The Jena Diversity model (JeDi) simulates plant survival according to essential plant functional trade-offs, including ecophysiological processes such as water uptake, photosynthesis, allocation, reproduction and phenology. We use JeDi to quantify changes in plant functional richness and biome shifts between present-day and a range of possible future climates from two SRES emission scenarios (A2 and B1) and seven global climate models using metrics of plant functional richness and functional identity. <br><br> Our results show (i) a significant loss of plant functional richness in the tropics, (ii) an increase in plant functional richness at mid and high latitudes, and (iii) a pole-ward shift of biomes. While these results are consistent with the findings of empirical approaches, we are able to explain them in terms of the plant functional trade-offs involved in the allocation, metabolic and reproduction strategies of plants. We conclude that general aspects of plant physiological tolerances can be derived from functional trade-offs, which may provide a useful process- and trait-based alternative to bioclimatic relationships. Such a mechanistic approach may be particularly relevant when addressing vegetation responses to climatic changes that encounter novel combinations of climate parameters that do not exist under contemporary climate

FIIs and Indian Stock Market: A Causality Investigation

While the volatility associated with portfolio capital flows is well known, there is also a concern that foreign institutional investors might introduce distortions in the host country markets due to the pressure on them to secure capital gains. In this context, present chapter attempts to find out the direction of causality between foreign institutional investors (FIIs) and performance of Indian stock market. To facilitate a better understanding of the causal linkage between FII flows and contemporaneous stock market returns (BSE National Index), a period of nineteen consecutive financial years ranging from January 1992 to December 2010 is selected. Granger Causality Test has been applied to test the direction of causality.Aczkolwiek brak stabilności związany z przepływami kapitału portfelowego jest dobrze znany, to istnieje również obawa, że zagraniczni inwestorzy instytucjonalni mogą wprowadzać zakłócenia na rynkach krajów przyjmujących z uwagi na wywieraną na nich presję, aby zapewniać zyski kapitałowe. W tym kontekście niniejszy rozdział próbuje poznać kierunek przyczynowości pomiędzy zagranicznymi inwestorami instytucjonalnymi (FIIs) i działaniem indyjskiej giełdy. Aby ułatwić lepsze zrozumienie związku przyczynowego między przepływami FII i mającymi miejsce w tym samym czasie wynikami giełdy papierów wartościowych (BSE National Index), wybrany został okres dziewiętnastu kolejnych lat począwszy od stycznia 1992 do grudnia 2010. Do zbadania kierunku przyczynowości zastosowano test przyczynowości Grangera

Ultracold collisions of oxygen molecules

Collision cross sections and rate constants between two ground- state oxygen molecules are investigated theoretically at translational energies below $\sim 1$K and in zero magnetic field. We present calculations for elastic and spin- changing inelastic collision rates for different isotopic combinations of oxygen atoms as a prelude to understanding their collisional stability in ultracold magnetic traps. A numerical analysis has been made in the framework of a rigid- rotor model that accounts fully for the singlet, triplet, and quintet potential energy surfaces in this system. The results offer insights into the effectiveness of evaporative cooling and the properties of molecular Bose- Einstein condensates, as well as estimates of collisional lifetimes in magnetic traps. Specifically, $^{17}O_{2}$ looks like a good candidate for ultracold studies, while $^{16}O_{2}$ is unlikely to survive evaporative cooling. Since $^{17}O_{2}$ is representative of a wide class of molecules that are paramagnetic in their ground state we conclude that many molecules can be successfully magnetically trapped at ultralow temperatures.Comment: 15 pages, 9 figure

Rotational Feshbach Resonances in Ultracold Molecular Collisions

In collisions at ultralow temperatures, molecules will possess Feshbach resonances, foreign to ultracold atoms, whose virtual excited states consist of rotations of the molecules. We estimate the mean spacing and mean widths of these resonant states, exploiting the fact the molecular collisions at low energy display chaotic motion. As examples, we consider the experimentally relevant molecules O_2, OH, and PbO. The density of s-wave resonant states for these species is quite high, implying that a large number of narrow resonant states will exist.Comment: 4 pages, 2 figure