Molecular dynamics study of the fragmentation of silicon doped fullerenes

Tight binding molecular dynamics simulations, with a non orthogonal basis set, are performed to study the fragmentation of carbon fullerenes doped with up to six silicon atoms. Both substitutional and adsorbed cases are considered. The fragmentation process is simulated starting from the equilibrium configuration in each case and imposing a high initial temperature to the atoms. Kinetic energy quickly converts into potential energy, so that the system oscillates for some picoseconds and eventually breaks up. The most probable first event for substituted fullerenes is the ejection of a C2 molecule, another very frequent event being that one Si atom goes to an adsorbed position. Adsorbed Si clusters tend to desorb as a whole when they have four or more atoms, while the smaller ones tend to dissociate and sometimes interchange positions with the C atoms. These results are compared with experimental information from mass abundance spectroscopy and the products of photofragmentation.Comment: Seven two-column pages, six postscript figures. To be published in Physical Review

Changes in Vegetation and Rainfall over West Africa during the Last Three Decades (1981-2010)

The decadal variability of rainfall and vegetation over West Africa have been studied over the last three decades, 1981-1990, 1991-2000 and 2001-2010 denoted as 1980s, 1990s and 2000s, respectively. Climate Research Unit (CRU) monthly precipitation and Normalized Difference Vegetation Index (NDVI) from the National Oceanic and Atmosphere Administration (NOAA), all covering the period 1981-2010 have been used. This study aimed to assess the changes in the land surface condition and the spatio-temporal distribution of rainfall over West Africa region. The relationship between rainfall and vegetation indices over this region was determined using Pearson’s correlation. Also, the decadal comparison between rainfall and NDVI over the region was based on the significant t-test and the Pearson’s correlation. Results showed that significant return to wet conditions is observed between decade 1980s and decade 1990s over West Africa, and also during decade 2000s with the exception of central Benin and the western Nigeria. Meanwhile, a regreening of the central Sahel and Sudano-Sahel regions is noted. From 1990s to 2000s, this regreening belt is located in the South and the coastal areas: the Guinea Coast, Sudano-Guinea and western Sahel regions. A northward displacement of this re-greening belt is also detected. Thus, a linear relationship occurs between rainfall and NDVI in the Sudanian savannah region, but it is not the case in the rest of West Africa. This may suggest that the re-growth of vegetation in the Sudanian savannah region may be linked to rainfall supplies. Therefore, re-greening over Sahel region in1990s is related to rainfall recovery. However, this re-greening was not sustained in the decade 2000s due to a slight decrease in rainfall

Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric aggregates

The presence of oligomeric aggregates, which is often observed during the process of amyloid formation, has recently attracted much attention since it has been associated with neurodegenerative conditions such as Alzheimer's and Parkinson's diseases. We provide a description of a sequence-indepedent mechanism by which polypeptide chains aggregate by forming metastable oligomeric intermediate states prior to converting into fibrillar structures. Our results illustrate how the formation of ordered arrays of hydrogen bonds drives the formation of beta-sheets within the disordered oligomeric aggregates that form early under the effect of hydrophobic forces. Initially individual beta-sheets form with random orientations, which subsequently tend to align into protofilaments as their lengths increases. Our results suggest that amyloid aggregation represents an example of the Ostwald step rule of first order phase transitions by showing that ordered cross-beta structures emerge preferentially from disordered compact dynamical intermediate assemblies.Comment: 14 pages, 4 figure

Supershells in Metal Clusters: Self-Consistent Calculations and their Semiclassical Interpretation

To understand the electronic shell- and supershell-structure in large metal clusters we have performed self-consistent calculations in the homogeneous, spherical jellium model for a variety of different materials. A scaling analysis of the results reveals a surprisingly simple dependence of the supershells on the jellium density. It is shown how this can be understood in the framework of a periodic-orbit-expansion by analytically extending the well-known semiclassical treatment of a spherical cavity to more realistic potentials.Comment: 4 pages, revtex, 3 eps figures included, for additional information see http://radix2.mpi-stuttgart.mpg.de/koch/Diss

Structure and Magnetism of well-defined cobalt nanoparticles embedded in a niobium matrix

Our recent studies on Co-clusters embedded in various matrices reveal that the co-deposition technique (simultaneous deposition of two beams : one for the pre-formed clusters and one for the matrix atoms) is a powerful tool to prepare magnetic nanostructures with any couple of materials even though they are miscible. We study, both sharply related, structure and magnetism of the Co/Nb system. Because such a heterogeneous system needs to be described at different scales, we used microscopic and macroscopic techniques but also local selective absorption ones. We conclude that our clusters are 3 nm diameter f.c.c truncated octahedrons with a pure cobalt core and a solid solution between Co and Nb located at the interface which could be responsible for the magnetically inactive monolayers we found. The use of a very diluted Co/Nb film, further lithographed, would allow us to achieve a pattern of microsquid devices in view to study the magnetic dynamics of a single-Co cluster.Comment: 7 TeX pages, 9 Postscript figures, detailed heading adde

Magnetic Anisotropy of a Single Cobalt Nanoparticle

Using a new microSQUID set-up, we investigate magnetic anisotropy in a single 1000-atoms cobalt cluster. This system opens new fields in the characterization and the understanding of the origin of magnetic anisotropy in such nanoparticles. For this purpose, we report three-dimensional switching field measurements performed on a 3 nm cobalt cluster embedded in a niobium matrix. We are able to separate the different magnetic anisotropy contributions and evidence the dominating role of the cluster surface.Comment: 4 pages, 8 figure

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation

Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse the self- assembly of peptides into fibrillar structures. The simulation of a system of hundreds of peptides over the millisecond timescale enables us to show that the mechanism of aggregation involves a first phase in which small structurally disordered oligomers assemble onto the nanoparticle and a second phase in which they evolve into highly ordered beta-sheets as their size increases

Work functions, ionization potentials, and in-between: Scaling relations based on the image charge model

We revisit a model in which the ionization energy of a metal particle is associated with the work done by the image charge force in moving the electron from infinity to a small cut-off distance just outside the surface. We show that this model can be compactly, and productively, employed to study the size dependence of electron removal energies over the range encompassing bulk surfaces, finite clusters, and individual atoms. It accounts in a straightforward manner for the empirically known correlation between the atomic ionization potential (IP) and the metal work function (WF), IP/WF$\sim$2. We formulate simple expressions for the model parameters, requiring only a single property (the atomic polarizability or the nearest neighbor distance) as input. Without any additional adjustable parameters, the model yields both the IP and the WF within $\sim$10% for all metallic elements, as well as matches the size evolution of the ionization potentials of finite metal clusters for a large fraction of the experimental data. The parametrization takes advantage of a remarkably constant numerical correlation between the nearest-neighbor distance in a crystal, the cube root of the atomic polarizability, and the image force cutoff length. The paper also includes an analytical derivation of the relation of the outer radius of a cluster of close-packed spheres to its geometric structure.Comment: Original submission: 8 pages with 7 figures incorporated in the text. Revised submission (added one more paragraph about alloy work functions): 18 double spaced pages + 8 separate figures. Accepted for publication in PR

Periodic orbit theory for realistic cluster potentials: The leptodermous expansion

The formation of supershells observed in large metal clusters can be qualitatively understood from a periodic-orbit-expansion for a spherical cavity. To describe the changes in the supershell structure for different materials, one has, however, to go beyond that simple model. We show how periodic-orbit-expansions for realistic cluster potentials can be derived by expanding only the classical radial action around the limiting case of a spherical potential well. We give analytical results for the leptodermous expansion of Woods-Saxon potentials and show that it describes the shift of the supershells as the surface of a cluster potential gets softer. As a byproduct of our work, we find that the electronic shell and supershell structure is not affected by a lattice contraction, which might be present in small clusters.Comment: 15 pages RevTex, 11 eps figures, additional information at http://www.mpi-stuttgart.mpg.de/docs/ANDERSEN/users/koch/Diss

Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5

Citation: Obayashi, E., Luna, R. E., Nagata, T., Martin-Marcos, P., Hiraishi, H., Singh, C. R., . . . Asano, K. (2017). Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5. Cell Reports, 18(11), 2651-2663. doi:10.1016/j.celrep.2017.02.052During eukaryotic translation initiation, eIF3 binds the solvent-accessible side of the 40S ribosome and recruits the gate-keeper protein eIF1 and eIF5 to the decoding center. This is largely mediated by the N-terminal domain (NTD) of eIF3c, which can be divided into three parts: 3c0, 3c1, and 3c2. The N-terminal part, 3c0, binds eIF5 strongly but only weakly to the ribosome-binding surface of eIF1, whereas 3c1 and 3c2 form a stoichiometric complex with eIF1. 3c1 contacts eIF1 through Arg-53 and Leu-96, while 3c2 faces 40S protein uS15/S13, to anchor eIF1 to the scanning pre-initiation complex (PIC). We propose that the 3c0:eIF1 interaction diminishes eIF1 binding to the 40S, whereas 3c0:eIF5 interaction stabilizes the scanning PIC by precluding this inhibitory interaction. Upon start codon recognition, interactions involving eIF5, and ultimately 3c0:eIF1 association, facilitate eIF1 release. Our results reveal intricate molecular interactions within the PIC, programmed for rapid scanning-arrest at the start codon