Mechanical resistance in unstructured proteins

Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force resistance, we perform pulling simulations of the amyloid {\beta}-peptide (A{\beta}) and {\alpha}-synuclein ({\alpha}S), starting from simulated conformational ensembles for the free monomers. For both proteins, the simulations yield a set of rupture events that agree well with the experimental data. By analyzing the conformations right before rupture in each event, we find that the mechanically resistant structures share a common architecture, with similarities to the folds adopted by A{\beta} and {\alpha}S in amyloid fibrils. The disease-linked Arctic mutation of A{\beta} is found to increase the occurrence of highly force-resistant structures. Our study suggests that the high rupture forces observed in A{\beta} and {\alpha}S pulling experiments are caused by structures that might have a key role in amyloid formation.Comment: v3: Added correct journal reference plus minor correction

Molecular Dynamics Simulations of a Pressure-induced Glass Transition

We simulate the compression of a two-component Lennard-Jones liquid at a variety of constant temperatures using a molecular dynamics algorithm in an isobaric-isothermal ensemble. The viscosity of the liquid increases with pressure, undergoing a broadened transition into a structurally arrested, amorphous state. This transition, like the more familiar one induced by cooling, is correlated with a significant increase in icosahedral ordering. In fact, the structure of the final state, as measured by an analysis of the bonding, is essentially the same in the glassy, frozen state whether produced by squeezing or by cooling under pressure. We have computed an effective hard-sphere packing fraction at the transition, defining the transition pressure or temperature by a cutoff in the diffusion constant, analogous to the traditional laboratory definition of the glass transition by an arbitrary, low cutoff in viscosity. The packing fraction at this transition point is not constant, but is consistently higher for runs compressed at higher temperature. We show that this is because the transition point defined by a constant cutoff in the diffusion constant is not the same as the point of structural arrest, at which further changes in pressure induce no further structural changes, but that the two alternate descriptions may be reconciled by using a thermally activated cutoff for the diffusion constant. This enables estimation of the characteristic activation energy for diffusion at the point of structural arrest.Comment: Latex using Revtex macro

Self-learning Kinetic Monte-Carlo method: application to Cu(111)

We present a novel way of performing kinetic Monte Carlo simulations which does not require an {\it a priori} list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation, energetics for all possible (single or multi-atom) processes, within a specific interaction range, are either computed accurately using a saddle point search procedure, or retrieved from a database in which previously encountered processes are stored. This self-learning procedure enhances the speed of the simulations along with a substantial gain in reliability because of the inclusion of many-particle processes. Accompanying results from the application of the method to the case of two-dimensional Cu adatom-cluster diffusion and coalescence on Cu(111) with detailed statistics of involved atomistic processes and contributing diffusion coefficients attest to the suitability of the method for the purpose.Comment: 18 pages, 9 figure

The effect of confinement and defects on the thermal stability of skyrmions

The stability of magnetic skyrmions against thermal fluctuations and external perturbations is investigated within the framework of harmonic transition state theory for magnetic degrees of freedom. The influence of confined geometry and atomic scale non-magnetic defects on the skyrmion lifetime is estimated. It is shown that a skyrmion on a track has lower activation energy for annihilation and higher energy for nucleation if the size of the skyrmion is comparable with the width of the track. Two mechanisms of skyrmion annihilation are considered: inside the track and escape through the boundary. For both mechanisms, the dependence of activation energy on the track width is calculated. Non-magnetic defects are found to localize skyrmions in their neighborhood and strongly decrease the activation energy for creation and annihilation. This is in agreement with experimental measurements that have found nucleation of skyrmions in presence of spin-polarized current preferably occurring near structural defects

Equilibrium shape and dislocation nucleation in strained epitaxial nanoislands

We study numerically the equilibrium shapes, shape transitions and dislocation nucleation of small strained epitaxial islands with a two-dimensional atomistic model, using simple interatomic pair potentials. We first map out the phase diagram for the equilibrium island shapes as a function of island size (up to N = 105 atoms) and lattice misfit with the substrate and show that nanoscopic islands have four generic equilibrium shapes, in contrast with predictions from the continuum theory of elasticity. For increasing substrate-adsorbate attraction, we find islands that form on top of a finite wetting layer as observed in Stranski-Krastanow growth. We also investigate energy barriers and transition paths for transitions between different shapes of the islands and for dislocation nucleation in initially coherent islands. In particular, we find that dislocations nucleate spontaneously at the edges of the adsorbate-substrate interface above a critical size or lattice misfit.Comment: 4 pages, 3 figures, uses wrapfig.sty and epsfig.st

Sea Changes Ashore : The Ocean and Iceland's Herring Captial

The story of Siglufjörður (Siglufjordur), a north Iceland village that became the "Herring Capital of the World," provides a case study of complex interactions between physical, biological, and social systems. Siglufjörður's natural capital - a good harbor and proximity to prime herring grounds - contributed to its development as a major fishing center during the first half of the 20th century. This herring fishery was initiated by Norwegians, but subsequently expanded by Icelanders to such an extent that the fishery, and Siglufjörður in particular, became engines helping to pull the whole Icelandic economy. During the golden years of this "herring adventure," Siglufjörður opened unprecedented economic and social opportunities. Unfortunately, the fishing boom reflected unsustainably high catch rates. In the years following World War II, overfishing by an international fleet eroded the once-huge herring stock. Then, in the mid-1960s, large-scale physical changes took place in the seas north of Iceland. These physical changes had ecological consequences that led to the loss of the herring's main food supply. Severe environmental stress, combined with heavy fishing pressure, drove the herring stocks toward collapse. Siglufjörður found itself first marginalized, then shut out as the herring progressively vanished. During the decades following the 1968 collapse, this former boomtown has sought alternatives for sustainable development.L'histoire de Siglufjörður (Siglufjordur), un village du nord de l'Islande qui acquit le statut de «Capitale mondiale du hareng», offre une étude de cas des interactions complexes qui ont lieu entre des systèmes physiques, biologiques et sociaux. Le capital naturel de Siglufjörður - un bon port et la proximité de bancs de harengs exceptionnels - a contribué à sa mise en valeur comme grand centre de pêche durant la première moitié du XXe siècle. La pêche au hareng, pratiquée tout d'abord par les Norvégiens, prit un tel essor avec les Islandais qu'elle devint, avec Siglufjörður en particulier, le moteur qui contribua à faire marcher toute l'économie de l'Islande. Durant les années fastes de cette «ère du hareng», il y eut à Siglufjörður des ouvertures économiques et sociales sans précédent. Malheureusement, le boom de la pêche représentait des taux de prises trop élevés pour être durables. Au cours des années qui suivirent la Deuxième Guerre mondiale, la surpêche pratiquée par une flottille internationale fit baisser le stock de harengs jadis abondant. Puis au milieu des années 1960, il se produisit, dans les eaux situées au nord de l'Islande, des changements à grande échelle sur le plan physique. Ces derniers eurent des conséquences écologiques qui aboutirent à la disparition de la source principale de nourriture du hareng. Un stress environnemental très fort, joint à des pressions pour augmenter encore plus les prises, mena les stocks de harengs à l'effondrement. Siglufjörður se trouva tout d'abord marginalisé, puis, à mesure que le hareng disparaissait, carrément exclu. Durant les décennies suivant l'effondrement de 1968, cette ancienne ville champignon a tenté de trouver des solutions de rechange pour se développer de façon durable

Bayesian imaging of the 2000 Western Tottori (Japan) earthquake through fitting of strong motion and GPS data

We image the rupture process of the 2000 Western Tottori earthquake (Mw = 6.6) through fitting of strong motion and GPS data. We consider an observational network consisting of 18 strong motion and 16 GPS stations, located within three fault lengths from the epicentre. We assume a planar fault and compute Green's functions for a 1-D velocity model. The earthquake rupture is described as a shear dislocation parameterized in terms of peak slip velocity, rake angle, rupture time and rise time, defined on a regular grid of nodes on the fault surface and derived at inner points through bilinear interpolation. Our inversion procedure is based on a Bayesian approach. The solution of the inverse problem is stated in terms of a posterior probability density function (pdf), representing the conjunction of prior information with information contained in the data and in the physical law relating model parameters with data. Inferences on model parameters are thus expressed in terms of posterior marginal pdfs. Due to the non-linearity of the problem, we use a Markov Chain Monte Carlo (MCMC) method, based on the Metropolis algorithm, to compute posterior marginals. Except for a few cases posterior marginals do not show a Gaussian-like distribution. This prevents us from providing a mean model and from characterizing uncertainties in terms of standard deviations only. Resolution on each single parameter is analysed by looking at the difference between prior and posterior marginal pdfs. Posterior marginals indicate that the best resolved feature is a major slip patch (peak value of 311 ± 140 cm), located between the hypocentre and the top edge of the fault, centered at a depth of 4.5 km. This shallow slip patch is triggered about 3 s after the earthquake nucleated and required about 4 s to reach its final slip value. The presence of this shallow slip patch is common to all previous studies. In contrast to some previous studies, we do not identify any significant slip (>1 m) at the bottom of the fault. We also compare inferences from both strong motion and GPS data with inferences derived from strong motion data only. In both cases the shallow slip patch is identified. At other locations, the main effect of the GPS data is in reducing the probability associated with high values of slip. GPS data reduce the presence of spurious fault slip and therefore strongly influence the resulting final seismic momen

New insights into the volume isotope effect of ice Ih from polarizable many-body potentials

NWO723.014.009Theoretical Chemistr

Stress release mechanisms for Cu on Pd(111) in the submonolayer and monolayer regimes

We study the strain relaxation mechanisms of Cu on Pd(111) up to the monolayer regime using two different computational methodologies, basin-hopping global optimization and energy minimization with a repulsive bias potential. Our numerical results are consistent with experimentally observed layer-by-layer growth mode. However, we find that the structure of the Cu layer is not fully pseudomorphic even at low coverages. Instead, the Cu adsorbates forms fcc and hcp stacking domains, separated by partial misfit dislocations. We also estimate the minimum energy path and energy barriers for transitions from the ideal epitaxial state to the fcc-hcp domain pattern.Comment: 4 pages, 4 figure