Dutch listeners' use of suprasegmental cues to English stress

Dutch listeners outperform native listeners in identifying syllable stress in English. This is because lexical stress is more useful in recognition of spoken words of Dutch than of English, so that Dutch listeners pay greater attention to stress in general. We examined Dutch listeners’ use of the acoustic correlates of English stress. Primary- and secondary-stressed syllables differ significantly on acoustic measures, and some differences, in F0 especially, correlate with data of earlier listening experiments. The correlations found in the Dutch responses were not paralleled in data from native listeners. Thus the acoustic cues which distinguish English primary versus secondary stress are better exploited by Dutch than by native listeners

Design principles for Bernal spirals and helices with tunable pitch

Using the framework of potential energy landscape theory, we describe two in silico designs for self-assembling helical colloidal superstructures based upon dipolar dumbbells and Janus-type building blocks, respectively. Helical superstructures with controllable pitch length are obtained using external magnetic field driven assembly of asymmetric dumbbells involving screened electrostatic as well as magnetic dipolar interactions. The pitch of the helix is tuned by modulating the Debye screening length over an experimentally accessible range. The second design is based on building blocks composed of rigidly linked spheres with short-range anisotropic interactions, which are predicted to self-assemble into Bernal spirals. These spirals are quite flexible, and longer helices undergo rearrangements via cooperative, hinge-like moves, in agreement with experiment

The Index Distribution of Gaussian Random Matrices

We compute analytically, for large N, the probability distribution of the number of positive eigenvalues (the index N_{+}) of a random NxN matrix belonging to Gaussian orthogonal (\beta=1), unitary (\beta=2) or symplectic (\beta=4) ensembles. The distribution of the fraction of positive eigenvalues c=N_{+}/N scales, for large N, as Prob(c,N)\simeq\exp[-\beta N^2 \Phi(c)] where the rate function \Phi(c), symmetric around c=1/2 and universal (independent of $\beta$), is calculated exactly. The distribution has non-Gaussian tails, but even near its peak at c=1/2 it is not strictly Gaussian due to an unusual logarithmic singularity in the rate function.Comment: 4 pages Revtex, 4 .eps figures include

Zero kinetic energy-pulsed field ionization and resonance enhanced multiphoton ionization photoelectron spectroscopy: Ionization dynamics of Rydberg states in HBr

The results of rotationally resolved resonance enhanced multiphoton ionization photoelectron spectroscopy and zero kinetic energy‐pulsed field ionization studies on HBr via various rotational levels of the F^ 1Δ_2 and f^ 3Δ_2 Rydberg states are reported. These studies lead to an accurate determination of the lowest ionization threshold as 94 098.9±1 cm^(−1). Observed rotational and spin–orbit branching ratios are compared to the results of ab initio calculations. The differences between theory and experiment highlight the dominant role of rotational and spin–orbit interactions for the dynamic properties of the high‐n Rydberg states involved in the pulsed field ionization process

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page

Identifying "communities" within energy landscapes

Potential energy landscapes can be represented as a network of minima linked by transition states. The community structure of such networks has been obtained for a series of small Lennard-Jones clusters. This community structure is compared to the concept of funnels in the potential energy landscape. Two existing algorithms have been used to find community structure, one involving removing edges with high betweenness, the other involving optimization of the modularity. The definition of the modularity has been refined, making it more appropriate for networks such as these where multiple edges and self-connections are not included. The optimization algorithm has also been improved, using Monte Carlo methods with simulated annealing and basin hopping, both often used successfully in other optimization problems. In addition to the small clusters, two examples with known heterogeneous landscapes, LJ_13 with one labelled atom and LJ_38, were studied with this approach. The network methods found communities that are comparable to those expected from landscape analyses. This is particularly interesting since the network model does not take any barrier heights or energies of minima into account. For comparison, the network associated with a two-dimensional hexagonal lattice is also studied and is found to have high modularity, thus raising some questions about the interpretation of the community structure associated with such partitions.Comment: 13 pages, 11 figure

A graph theoretical analysis of the energy landscape of model polymers

In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have non trivial effects on such networks and must be taken into account. We do this by means of a recently proposed renormalization procedure. This method is applied to analyze the topology of the network of metastable states for different polypeptidic sequences in a minimalistic polymer model. A smaller spectral dimension emerges as a hallmark of stability of the global energy minimum and highlights a non-obvious link between dynamic and thermodynamic properties.Comment: 15 pages, 15 figure

Energy Landscape and Global Optimization for a Frustrated Model Protein

The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure

Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling.

The study of "rare event" dynamics can be challenging despite continuing advances in computer hardware. A wide variety of methods based on the master equation approach have been developed to tackle such problems, where the focus is on Markovian dynamics between appropriately defined states. In this contribution, we employ the discrete path sampling approach to characterize pathways and rates for an adenine-adenine RNA conformational switch. The underlying free energy landscape supports competing structures separated by relatively high barriers, with the two principal funnels leading to the major and minor conformations identified by NMR experiments. The interconversion time scale is predicted to be a few hundred seconds, consistent with the experimental lower bound estimates. We find that conformational switching occurs via stacked intermediates, through a sliding mechanism, in agreement with a previous simulation study. By retaining full dimensionality and avoiding low-dimensional projections, the mechanism can be described at an atomistic level of detail.EPSRC, ERC

The Glassy Wormlike Chain

We introduce a new model for the dynamics of a wormlike chain in an environment that gives rise to a rough free energy landscape, which we baptise the glassy wormlike chain. It is obtained from the common wormlike chain by an exponential stretching of the relaxation spectrum of its long-wavelength eigenmodes, controlled by a single stretching parameter. Predictions for pertinent observables such as the dynamic structure factor and the microrheological susceptibility exhibit the characteristics of soft glassy rheology and compare favourably with experimental data for reconstituted cytoskeletal networks and live cells. We speculate about the possible microscopic origin of the stretching, implications for the nonlinear rheology, and the potential physiological significance of our results.Comment: 12 pages, 8 figures. Minor correction