Thermal noise and dephasing due to electron interactions in non-trivial geometries

We study Johnson-Nyquist noise in macroscopically inhomogeneous disordered metals and give a microscopic derivation of the correlation function of the scalar electric potentials in real space. Starting from the interacting Hamiltonian for electrons in a metal and the random phase approximation, we find a relation between the correlation function of the electric potentials and the density fluctuations which is valid for arbitrary geometry and dimensionality. We show that the potential fluctuations are proportional to the solution of the diffusion equation, taken at zero frequency. As an example, we consider networks of quasi-1D disordered wires and give an explicit expression for the correlation function in a ring attached via arms to absorbing leads. We use this result in order to develop a theory of dephasing by electronic noise in multiply-connected systems.Comment: 9 pages, 6 figures (version submitted to PRB

Quantum dynamics of the avian compass

The ability of migratory birds to orient relative to the Earth's magnetic field is believed to involve a coherent superposition of two spin states of a radical electron pair. However, the mechanism by which this coherence can be maintained in the face of strong interactions with the cellular environment has remained unclear. This Letter addresses the problem of decoherence between two electron spins due to hyperfine interaction with a bath of spin 1/2 nuclei. Dynamics of the radical pair density matrix are derived and shown to yield a simple mechanism for sensing magnetic field orientation. Rates of dephasing and decoherence are calculated ab initio and found to yield millisecond coherence times, consistent with behavioral experiments

Mechanical unfolding of RNA hairpins

Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA hairpins to explore forced-unfolding over a broad range of temperatures. A number of predictions that are amenable to experimental tests are made. At the critical force the hairpin jumps between folded and unfolded conformations without populating any discernible intermediates. The phase diagram in the force-temperature (f,T) plane shows that the hairpin unfolds by an all-or-none process. The cooperativity of the unfolding transition increases dramatically at low temperatures. Free energy of stability, obtained from time averages of mechanical unfolding trajectories, coincide with ensemble averages which establishes ergodicity. The hopping time between the the native basin of attraction (NBA) and the unfolded basin increases dramatically along the phase boundary. Thermal unfolding is stochastic whereas mechanical unfolding occurs in "quantized steps" with great variations in the step lengths. Refolding times, upon force quench, from stretched states to the NBA is "at least an order of magnitude" greater than folding times by temperature quench. Upon force quench from stretched states the NBA is reached in at least three stages. In the initial stages the mean end-to-end distance decreases nearly continuously and only in the last stage there is a sudden transition to the NBA. Because of the generality of the results we propose that similar behavior should be observed in force quench refolding of proteins.Comment: 23 pages, 6 Figures. in press (Proc. Natl. Acad. Sci.

Exploring the influence of micro-structure on the mechanical properties and crack bridging mechanisms of fibrous tufts

AbstractA constitutive model for tufts bridging a mode I delamination is presented. The tuft is modelled as a rod, laterally supported by an elastic medium and clamped at both ends. A fracture mechanics approach is introduced to describe the progressive debonding of the tuft from the embedding laminate. The debonding model requires the identification of stiffness, strength and toughness properties, which depend both on the laminate/tuft architecture and the constituent materials. Such identification is carried out via experimental data obtained from tensile tests on single tufts inserted in a pre-delaminated non-crimp fabric composite. The experimental results are complemented by micro-scale finite element analysis. The mode I bridging law obtained from the constitutive model is implemented into a meso-scale cohesive zone formulation. This formulation is applied to predict the response to delamination of tufted Double Cantilever Beam (DCB) coupons. The cohesive zone approach is validated by means of experimental data from DCB tests. It is shown that the proposed micro- to meso-scale modelling approach yields results in good agreement with the experiments

DNA Methylation Mediates the Discriminatory Power of Associative Long-Term Memory in Honeybees

Memory is created by several interlinked processes in the brain, some of which require long-term gene regulation. Epigenetic mechanisms are likely candidates for regulating memory-related genes. Among these, DNA methylation is known to be a long lasting genomic mark and may be involved in the establishment of long-term memory. Here we demonstrate that DNA methyltransferases, which induce and maintain DNA methylation, are involved in a particular aspect of associative long-term memory formation in honeybees, but are not required for short-term memory formation. While long-term memory strength itself was not affected by blocking DNA methyltransferases, odor specificity of the memory (memory discriminatory power) was. Conversely, perceptual discriminatory power was normal. These results suggest that different genetic pathways are involved in mediating the strength and discriminatory power of associative odor memories and provide, to our knowledge, the first indication that DNA methyltransferases are involved in stimulus-specific associative long-term memory formation

Interpreting the Wide Scattering of Synchronized Traffic Data by Time Gap Statistics

Based on the statistical evaluation of experimental single-vehicle data, we propose a quantitative interpretation of the erratic scattering of flow-density data in synchronized traffic flows. A correlation analysis suggests that the dynamical flow-density data are well compatible with the so-called jam line characterizing fully developed traffic jams, if one takes into account the variation of their propagation speed due to the large variation of the netto time gaps (the inhomogeneity of traffic flow). The form of the time gap distribution depends not only on the density, but also on the measurement cross section: The most probable netto time gap in congested traffic flow upstream of a bottleneck is significantly increased compared to uncongested freeway sections. Moreover, we identify different power-law scaling laws for the relative variance of netto time gaps as a function of the sampling size. While the exponent is -1 in free traffic corresponding to statistically independent time gaps, the exponent is about -2/3 in congested traffic flow because of correlations between queued vehicles.Comment: For related publications see http://www.helbing.or

Estimating Acceleration and Lane-Changing Dynamics Based on NGSIM Trajectory Data

The NGSIM trajectory data sets provide longitudinal and lateral positional information for all vehicles in certain spatiotemporal regions. Velocity and acceleration information cannot be extracted directly since the noise in the NGSIM positional information is greatly increased by the necessary numerical differentiations. We propose a smoothing algorithm for positions, velocities and accelerations that can also be applied near the boundaries. The smoothing time interval is estimated based on velocity time series and the variance of the processed acceleration time series. The velocity information obtained in this way is then applied to calculate the density function of the two-dimensional distribution of velocity and inverse distance, and the density of the distribution corresponding to the ``microscopic'' fundamental diagram. Furthermore, it is used to calculate the distributions of time gaps and times-to-collision, conditioned to several ranges of velocities and velocity differences. By simulating virtual stationary detectors we show that the probability for critical values of the times-to-collision is greatly underestimated when estimated from single-vehicle data of stationary detectors. Finally, we investigate the lane-changing process and formulate a quantitative criterion for the duration of lane changes that is based on the trajectory density in normalized coordinates. Remarkably, there is a very noisy but significant velocity advantage in favor of the targeted lane that decreases immediately before the change due to anticipatory accelerations

Regulated dicing of pre-mir-144 via reshaping of its terminal loop.

Although the route to generate microRNAs (miRNAs) is often depicted as a linear series of sequential and constitutive cleavages, we now appreciate multiple alternative pathways as well as diverse strategies to modulate their processing and function. Here, we identify an unusually profound regulatory role of conserved loop sequences in vertebrate pre-mir-144, which are essential for its cleavage by the Dicer RNase III enzyme in human and zebrafish models. Our data indicate that pre-mir-144 dicing is positively regulated via its terminal loop, and involves the ILF3 complex (NF90 and its partner NF45/ILF2). We provide further evidence that this regulatory switch involves reshaping of the pre-mir-144 apical loop into a structure that is appropriate for Dicer cleavage. In light of our recent findings that mir-144 promotes the nuclear biogenesis of its neighbor mir-451, these data extend the complex hierarchy of nuclear and cytoplasmic regulatory events that can control the maturation of clustered miRNAs

Towards a Macroscopic Modelling of the Complexity in Traffic Flow

We present a macroscopic traffic flow model that extends existing fluid-like models by an additional term containing the second derivative of the safe velocity. Two qualitatively different shapes of the safe velocity are explored: a conventional Fermi-type function and a function exhibiting a plateau at intermediate densities. The suggested model shows an extremely rich dynamical behaviour and shows many features found in real-world traffic data.Comment: submitted to Phys. Rev.

Direct observation of twist mode in electroconvection in I52

I report on the direct observation of a uniform twist mode of the director field in electroconvection in I52. Recent theoretical work suggests that such a uniform twist mode of the director field is responsible for a number of secondary bifurcations in both electroconvection and thermal convection in nematics. I show here evidence that the proposed mechanisms are consistent with being the source of the previously reported SO2 state of electroconvection in I52. The same mechanisms also contribute to a tertiary Hopf bifurcation that I observe in electroconvection in I52. There are quantitative differences between the experiment and calculations that only include the twist mode. These differences suggest that a complete description must include effects described by the weak-electrolyte model of electroconvection