The use of the isotropic orientation factor in fluorescence resonance energy transfer (FRET) studies of the actin filament

A Dale-Eisinger style analysis (R. E. Daleet al., Biophys. J. 26, 161, 1979) is used to produce three-dimensional plots that display the limits on the average orientation factor k ² that is required to calculate molecular distances in F-actin from fluorescence resonance energy transfer measurements. Maxima and minima plots are generated for the transfer of energy from a donor to a single acceptor and for transfer to multiple acceptors that are related by F-actin helical symmetry. The analysis is performed in terms of dipole cone half-angles rather than depolarization factors, in order to facilitate the modeling of the multiple acceptor problem. Calculations are carried out under the restrictive condition of a single electric dipole moment per fluorophore. In addition, both surface and volume averaging of the donor and acceptor dipoles are considered. Comparisons between the plots show that for the multiple acceptor cases with F-actin symmetry, there is a great reduction in the range for maxima and minima limits on k ². The calculations also suggest guidelines for the choice of fluorescence label that will result in an average orientation factor occurring within acceptable limits, i.e., inside the limits for which k ²=2/3 may be employed. Thus, without having detailed knowledge of the mean donor or acceptor dipole relative orientations, the use of k ²=2/3 in radial coordinate studies of F-actin is more than reasonable and is fairly assured of being correct.     

Ethanol-induced conformational fluctuations of NMDA receptors

Alcohol addiction ranks among the leading global causes of preventable death and disabilities in human population. Understanding the sites of ethanol action that mediate its acute and chronic neural and behavioural effects is critical to develop appropriate treatment options for this disorder. The N-methyl-d-asparate (NMDA) receptors are ligand-gated heterotetrameric ion channels, which are known to directly interact with alcohol in a concentration-dependent manner. Yet, the exact molecular mechanisms and conformational dynamics of this interaction are not well understood. Here, we conducted a series of molecular dynamics simulations of the interaction of moderate ethanol concentrations with rat's wild-type GluN1–GluN2B NMDA Receptor under physiological conditions. The simulations suggest that glutamate or glycine alone induce an intermediate conformational state and point towards the transmembrane domain (TMD) as the site of action of ethanol molecules. Ethanol interacts by double hydrogen bonds with Trp635 and Phe638 at the transmembrane M3 helix of GluN2B. Alcohol not only reduces the pore radius of the ion channel within the TMD but also decreases accessibility of glutamate and glycine to the ligand-binding sites by altering the structure of the ligand-binding domain and significantly widening the receptor in that area.     

Evolution on a smooth landscape

We study in detail a recently proposed simple discrete model for evolution on smooth landscapes. An asymptotic solution of this model for long times is constructed. We find that the dynamics of the population is governed by correlation functions that although being formally down by powers ofN (the population size), nonetheless control the evolution process after a very short transient. The long-time behavior can be found analytically since only one of these higher order correlators (the two-point function) is relevant. We compare and contrast the exact findings derived herein with a previously proposed phenomenological treatment employing mean-field theory supplemented with a cutoff at small population density. Finally, we relate our results to the recently studied case of mutation on a totally flat landscape.     

Homo- and heteronuclear 2D NMR approaches to analyse a mixture of deuterated unlike/like stereoisomers using weakly ordering chiral liquid crystals

We describe several homo- and heteronuclear 2D NMR strategies dedicated to the analysis of anisotropic (2)H spectra of a mixture of dideuterated unlike/like stereoisomers with two remote stereogenic centers, using weakly orienting chiral liquid crystals. To this end, we propose various 2D correlation experiments, denoted "D(H)(n)D" or "D(H)(n)C" (with n=1, 2), that involve two heteronuclear polarization transfers of INEPT-type with one or two proton relays. The analytical expressions of correlation signals for four pulse sequences reported here were calculated using the product-operators formalism for spin I=1 and S=1/2. The features and advantages of each scheme are presented and discussed. The efficiency of these 2D sequences is illustrated using various deuterated model molecules, dissolved in organic solutions of polypeptides made of poly-gamma-benzyl-L-glutamate (PBLG) or poly-epsilon-carbobenzyloxy-L-lysine (PCBLL) and NMR numerical simulations.     

Acoustic features of objects matched by an echolocating bottlenose dolphin

The focus of this study was to investigate how dolphins use acoustic features in returning echolocation signals to discriminate among objects. An echolocating dolphin performed a match-to-sample task with objects that varied in size, shape, material, and texture. After the task was completed, the features of the object echoes were measured (e.g., target strength, peak frequency). The dolphin's error patterns were examined in conjunction with the between-object variation in acoustic features to identify the acoustic features that the dolphin used to discriminate among the objects. The present study explored two hypotheses regarding the way dolphins use acoustic information in echoes: (1) use of a single feature, or (2) use of a linear combination of multiple features. The results suggested that dolphins do not use a single feature across all object sets or a linear combination of six echo features. Five features appeared to be important to the dolphin on four or more sets: the echo spectrum shape, the pattern of changes in target strength and number of highlights as a function of object orientation, and peak and center frequency. These data suggest that dolphins use multiple features and integrate information across echoes from a range of object orientations.     

Generalized eikonal treatment of the Gouy phase shift

We use a generalized refractive index that includes diffraction effects to show that the Gouy phase shift can be seen as an intensity averaged optical path difference between the generalized eikonal and the geometrical eikonal. This approach generalizes previous treatments to include the effects of phase distortion and confirms the role of transverse spatial confinement in the Gouy shift.     

Multifractal moving average analysis and test of multifractal model with tuned correlations

We address two common major problems in the study of time series characterizing fluctuations in complex systems: multifractal analysis and multifractal modeling. Specifically, we introduce a multi-fractal centered moving average (MF-CMA) analysis, which is computationally easier but equivalently performing compared with the well-established multi-fractal detrended fluctuation analysis (MF-DFA) with linear detrending. In addition, we study in detail a generalized binomial multi-fractal model (GB-MFM) to conveniently and reliably generate multifractal surrogate data with arbitrary singularity strengths and arbitrary long-term persistence. We use the data generated by this model as well as realistic, by construction monofractal data series with crossovers and trends to test and compare the multifractal analysis methods and discuss finite-size effects as well as limitations due to spurious multifractality.     

On spurious and corrupted multifractality: The effects of additive noise, short-term memory and periodic trends

We study the performance of multifractal detrended fluctuation analysis (MF-DFA) applied to long-term correlated and multifractal data records in the presence of additive white noise, short-term memory and periodicities. Such additions and disturbances that can be typically found in the observational records of various complex systems ranging from climate dynamics to physiology, network traffic, and finance. In monofractal records, we find that (i) additive white noise hardly results in spurious multifractality, but causes underestimated generalized Hurst exponents h(q) for all q values; (ii) short-range correlations lead to pronounced crossovers in the generalized fluctuation functions F_q(s) at positions that decrease with increasing moment q, thus causing significantly overestimated h(q) for small q and spurious multifractality; (iii) periodicities like seasonal trends (with standard deviations comparable with the one of the studied process) result in spurious “reversed” multifractality where h(q) increases with increasing q (except for very short time windows). We also show that in multifractal cascades moderate additions of noise, short-range memory, or periodic trends cause flawed results for h(q) with q<2, while h(q) with q>2 remains nearly unchanged.     

Dark matter results from 100 live days of XENON100 data

We present results from the direct search for dark matter with the XENON100 detector, installed underground at the Laboratori Nazionali del Gran Sasso of INFN, Italy. XENON100 is a two-phase time-projection chamber with a 62 kg liquid xenon target. Interaction vertex reconstruction in three dimensions with millimeter precision allows the selection of only the innermost 48 kg as the ultralow background fiducial target. In 100.9 live days of data, acquired between January and June 2010, no evidence for dark matter is found. Three candidate events were observed in the signal region with an expected background of (1.8 ± 0.6) events. This leads to the most stringent limit on dark matter interactions today, excluding spin-independent elastic weakly interacting massive particle (WIMP) nucleon scattering cross sections above 7.0 × 10(-45) cm(2) for a WIMP mass of 50 GeV/c(2) at 90% confidence level.