1,998 research outputs found
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
), 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
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