Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

<p>Abstract</p> <p>Background</p> <p>Automatic protein modelling pipelines are becoming ever more accurate; this has come hand in hand with an increasingly complicated interplay between all components involved. Nevertheless, there are still potential improvements to be made in template selection, refinement and protein model selection.</p> <p>Results</p> <p>In the context of an automatic modelling pipeline, we analysed each step separately, revealing several non-intuitive trends and explored a new strategy for protein conformation sampling using Genetic Algorithms (GA). We apply the concept of alternating evolutionary pressure (AEP), i.e. intermediate rounds within the GA runs where unrestrained, linear growth of the model populations is allowed.</p> <p>Conclusion</p> <p>This approach improves the overall performance of the GA by allowing models to overcome local energy barriers. AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA.</p

Corticobulbar tract changes as predictors of dysarthria in childhood brain injury.

To identify corticobulbar tract changes that may predict chronic dysarthria in young people who have sustained a traumatic brain injury (TBI) in childhood using diffusion MRI tractography

Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation

Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation

Electronic Instability in a Zero-Gap Semiconductor: The Charge-DensityWave in (TaSe4)(2)I

We report a comprehensive study of the paradigmatic quasi-1D compound (TaSe4)(2)I performed by means of angle-resolved photoemission spectroscopy (ARPES) and first-principles electronic structure calculations. We find it to be a zero-gap semiconductor in the nondistorted structure, with non-negligible interchain coupling. Theory and experiment support a Peierls-like scenario for the charge-density wave formation below T-CDW = 263 K, where the incommensurability is a direct consequence of the finite interchain coupling. The formation of small polarons, strongly suggested by the ARPES data, explains the puzzling semiconductor-to-semiconductor transition observed in transport at T-CDW.open114sciescopu

Glass transition in biomolecules and the liquid-liquid critical point of water

Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a ``protein glass transition'', occurs at the temperature of dynamic crossover in the diffusivity of hydration water, and also coincides with the maxima of the isobaric specific heat $C_P$ and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.Comment: 10 Pages, 12 figure

Giant alkali-metal-induced lattice relaxation as the driving force of the insulating phase of alkali-metal/Si(111):B

Ab initio density-functional theory calculations, photoemission spectroscopy (PES), scanning tunneling microscopy, and spectroscopy (STM, STS) have been used to solve the 2√3 x 2√3R30 surface reconstruction observed previously by LEED on 0.5 ML K/Si:B. A large K-induced vertical lattice relaxation occurring only for 3/4 of Si adatoms is shown to quantitatively explain both the chemical shift of 1.14 eV and the ratio 1/3 measured on the two distinct B 1s core levels. A gap is observed between valence and conduction surface bands by ARPES and STS which is shown to have mainly a Si-B character. Finally, the calculated STM images agree with our experimental results. This work solves the controversy about the origin of the insulating ground state of alkali-metal/Si(111):B semiconducting interfaces which were believed previously to be related to many-body effectsThis work has received the financial support of the French ANR SURMOTT program (ANR-09-BLAN- 0210-01) and the Spanish MICIIN under Project No. FIS2010-1604

Giant ambipolar Rashba effect in a semiconductor: BiTeI

We observe a giant spin-orbit splitting in bulk and surface states of the non-centrosymmetric semiconductor BiTeI. We show that the Fermi level can be placed in the valence or in the conduction band by controlling the surface termination. In both cases it intersects spin-polarized bands, in the corresponding surface depletion and accumulation layers. The momentum splitting of these bands is not affected by adsorbate-induced changes in the surface potential. These findings demonstrate that two properties crucial for enabling semiconductor-based spin electronics -- a large, robust spin splitting and ambipolar conduction -- are present in this material.Comment: 4 pages, 3 figure

The momentum and photon energy dependence of the circular dichroic photoemission in the bulk Rashba semiconductors BiTeX (X = I, Br, Cl)

Bulk Rashba systems BiTeX (X = I, Br, Cl) are emerging as important candidates for developing spintronics devices, because of the coexistence of spin-split bulk and surface states, along with the ambipolar character of the surface charge carriers. The need of studying the spin texture of strongly spin-orbit coupled materials has recently promoted circular dichroic Angular Resolved Photoelectron Spectroscopy (cd-ARPES) as an indirect tool to measure the spin and the angular degrees of freedom. Here we report a detailed photon energy dependent study of the cd-ARPES spectra in BiTeX (X = I, Br and Cl). Our work reveals a large variation of the magnitude and sign of the dichroism. Interestingly, we find that the dichroic signal modulates differently for the three compounds and for the different spin-split states. These findings show a momentum and photon energy dependence for the cd-ARPES signals in the bulk Rashba semiconductor BiTeX (X = I, Br, Cl). Finally, the outcome of our experiment indicates the important relation between the modulation of the dichroism and the phase differences between the wave-functions involved in the photoemission process. This phase difference can be due to initial or final state effects. In the former case the phase difference results in possible interference effects among the photo-electrons emitted from different atomic layers and characterized by entangled spin-orbital polarized bands. In the latter case the phase difference results from the relative phases of the expansion of the final state in different outgoing partial waves.Comment: 6 pages, 4 figure

Intercomparison of stratospheric gravity wave observations with AIRS and IASI

Gravity waves are an important driver for the atmospheric circulation and have substantial impact on weather and climate. Satellite instruments offer excellent opportunities to study gravity waves on a global scale. This study focuses on observations from the Atmospheric Infrared Sounder (AIRS) onboard the National Aeronautics and Space Administration's Aqua satellite and the Infrared Atmospheric Sounding Interferometer (IASI) onboard the European MetOp satellites. The main aim of this study is an intercomparison of stratospheric gravity wave observations of both instruments. In particular, we analyzed AIRS and IASI 4.3 μm brightness temperature measurements, which directly relate to stratospheric temperature. Three case studies showed that AIRS and IASI provide a clear and consistent picture of the temporal development of individual gravity wave events. Statistical comparisons based on a five-year period of measurements (2008-2012) showed similar spatial and temporal patterns of gravity wave activity. However, the statistical comparisons also revealed systematic differences of variances between AIRS and IASI (about 45%) that we attribute to the different spatial measurement characteristics of both instruments. We also found differences between day- and nighttime data (about 30%) that are partly due to the local time variations of the gravity wave sources. While AIRS has been used successfully in many previous gravity wave studies, IASI data are applied here for the first time for that purpose. Our study shows that gravity wave observations from different hyperspectral infrared sounders such as AIRS and IASI can be directly related to each other, if instrument-specific characteristics such as different noise levels and spatial resolution and sampling are carefully considered. The ability to combine observations from different satellites provides an opportunity to create a long-term record, which is an exciting prospect for future climatological studies of stratospheric gravity wave activity

Electronic Instability in a Zero-Gap Semiconductor: The Charge-DensityWave in (TaSe4)(2)I

International audienceWe report a comprehensive study of the paradigmatic quasi-1D compound (TaSe4)(2)I performed by means of angle-resolved photoemission spectroscopy (ARPES) and first-principles electronic structure calculations. We find it to be a zero-gap semiconductor in the nondistorted structure, with non-negligible interchain coupling. Theory and experiment support a Peierls-like scenario for the charge-density wave formation below T-CDW = 263 K, where the incommensurability is a direct consequence of the finite interchain coupling. The formation of small polarons, strongly suggested by the ARPES data, explains the puzzling semiconductor-to-semiconductor transition observed in transport at T-CDW