Mean first passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding

We have analyzed dynamics on the complex free energy landscape of protein folding in the FOLD-X model, by calculating for each state of the system the mean first passage time to the folded state. The resulting kinetic map of the folding process shows that it proceeds in jumps between well-defined, local free energy minima. Closer analysis of the different local minima allows us to reveal secondary, parallel pathways as well as dead ends.Comment: 7 page

In search of phylogenetic congruence between molecular and morphological data in bryozoans with extreme adult skeletal heteromorphy

peerreview_statement: The publishing and review policy for this title is described in its Aims & Scope. aims_and_scope_url: http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=tsab20© Crown Copyright 2015. This document is the author's final accepted/submitted version of the journal article. You are advised to consult the publisher's version if you wish to cite from it

Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment

Background: Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans. Results: We first examined whether mice and humans experience similar patterns of change in the methylome with age. We found moderate conservation of CpG sites for which methylation is altered with age, with both species showing an increase in methylome disorder during aging. Based on this analysis, we formulated an epigenetic-aging model in mice using the liver methylomes of 107 mice from 0.2 to 26.0 months old. To examine whether epigenetic aging signatures are slowed by longevity-promoting interventions, we analyzed 28 additional methylomes from mice subjected to lifespan-extending conditions, including Prop1df/df dwarfism, calorie restriction or dietary rapamycin. We found that mice treated with these lifespan-extending interventions were significantly younger in epigenetic age than their untreated, wild-type age-matched controls. Conclusions: This study shows that lifespan-extending conditions can slow molecular changes associated with an epigenetic clock in mice livers

Strategies for Waste Recycling: The Mechanical Performance of Concrete Based on Limestone and Plastic Waste

Recycling is among the best management strategies to avoid dispersion of several types of wastes in the environment. Research in recycling strategies is gaining increased importance in view of Circular Economy principles. The exploitation of waste, or byproducts, as alternative aggregate in concrete, results in a reduction in the exploitation of scarce natural resources. On the other hand, a productive use of waste leads to a reduction in the landfilling of waste material through the transformation of waste into a resource. In this frame of reference, the paper discusses how to use concrete as a container of waste focusing on the waste produced in limestone quarries and taking the challenge of introducing plastic waste into ordinary concrete mixes. To prove the possibility of reaching this objective with acceptable loss of performance, the mechanical characteristics of concrete mixed with additional alternative aggregates classified as waste are investigated and dis-cussed in this paper through the presentation of two experimental campaigns. The first experimental investigation refers to concrete made with fine limestone waste used as a replacement for fine aggregate (sand), while the second experimental program refers to the inclusion of three types of plastic wastes in the concrete. Different mixes with different percentages of wastes are investigated to identify possible fields of application. The experimental results indicate that use of limestone quarry waste and use of plastic waste are possible within significant percentage ranges, having recognized a limited reduction of concrete strength that makes concrete itself appropriate for different practical applications

Analysis of strain and stacking faults in single nanowires using Bragg coherent diffraction imaging

Coherent diffraction imaging (CDI) on Bragg reflections is a promising technique for the study of three-dimensional (3D) composition and strain fields in nanostructures, which can be recovered directly from the coherent diffraction data recorded on single objects. In this article we report results obtained for single homogeneous and heterogeneous nanowires with a diameter smaller than 100 nm, for which we used CDI to retrieve information about deformation and faults existing in these wires. The article also discusses the influence of stacking faults, which can create artefacts during the reconstruction of the nanowire shape and deformation.Comment: 18 pages, 6 figures Submitted to New Journal of Physic

Interrelation of structural and electronic properties of InGaN/GaN quantum dots using an eight-band k.p model

We present an eight-band k.p model for the calculation of the electronic structure of wurtzite semiconductor quantum dots (QDs) and its application to indium gallium nitride (InGaN) QDs formed by composition fluctuations in InGaN layers. The eight-band k.p model accounts for strain effects, piezoelectric and pyroelectricity, spin-orbit and crystal field splitting. Exciton binding energies are calculated using the self-consistent Hartree method. Using this model, we studied the electronic properties of InGaN QDs and their dependence on structural properties, i.e., their chemical composition, height, and lateral diameter. We found a dominant influence of the built-in piezoelectric and pyroelectric fields, causing a spatial separation of the bound electron and hole states and a redshift of the exciton transition energies. The single-particle energies as well as the exciton energies depend heavily on the composition and geometry of the QDs

Retinal metric: a stimulus distance measure derived from population neural responses

The ability of the organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this "neural metric" tells us how distinguishable a pair of stimulus clips is to the retina, given the noise in the neural population response. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the SVM-like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.Comment: 5 pages, 4 figures, to appear in Phys Rev Let

Measuring the proton spectrum in neutron decay - latest results with aSPECT

The retardation spectrometer aSPECT was built to measure the shape of the proton spectrum in free neutron decay with high precision. This allows us to determine the antineutrino electron angular correlation coefficient a. We aim for a precision more than one order of magnitude better than the present best value, which is Delta_a /a = 5%. In a recent beam time performed at the Institut Laue-Langevin during April / May 2008 we reached a statistical accuracy of about 2% per 24 hours measurement time. Several systematic effects were investigated experimentally. We expect the total relative uncertainty to be well below 5%.Comment: Accepted for publication in the Conference Proceedings of the International Workshop on Particle Physics with Slow Neutrons 2008 held at the ILL, France. To be published in Nuclear Instruments and Methods in Physics Research, Section

SEM-EDS analyses of small craters in stardust aluminium foils: implications for the Wild-2 dust distribution

Implications for the Wild-2 dust distribution of the statistical results obtained by SEM-EDS from nearly 300 impact craters on aluminium foils of the Stardust sample tray assembly

On the incompatibility of strains and its application to mesoscopic studies of plasticity

Structural transitions are invariably affected by lattice distortions. If the body is to remain crack-free, the strain field cannot be arbitrary but has to satisfy the Saint-Venant compatibility constraint. Equivalently, an incompatibility constraint consistent with the actual dislocation network has to be satisfied in media with dislocations. This constraint can be incorporated into strain-based free energy functionals to study the influence of dislocations on phase stability. We provide a systematic analysis of this constraint in three dimensions and show how three incompatibility equations accommodate an arbitrary dislocation density. This approach allows the internal stress field to be calculated for an anisotropic material with spatially inhomogeneous microstructure and distribution of dislocations by minimizing the free energy. This is illustrated by calculating the stress field of an edge dislocation and comparing it with that of an edge dislocation in an infinite isotropic medium. We outline how this procedure can be utilized to study the interaction of plasticity with polarization and magnetization.Comment: 6 pages, 2 figures; will appear in Phys. Rev.