Rate constant and reaction coordinate of Trp-cage folding in explicit water

We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the protein maintains its compact configuration, while a (de)increase of secondary structure is observed. The calculated folding rate agrees reasonably with experiment, while the unfolding rate is 10 times higher. We discuss possible origins for this mismatch. We recomputed the rates with the forward flux sampling method, and found a discrepancy of four orders of magnitude, probably caused by the method's higher sensitivity to the choice of order parameter with respect to transition interface sampling. Finally, we used the previously computed transition path-sampling ensemble to screen combinations of many order parameters for the best model of the reaction coordinate by employing likelihood maximization. We found that a combination of the root mean-square deviation of the helix and of the entire protein was, of the set of tried order parameters, the one that best describes the reaction coordination

Influence of the electronic polymorphism of Ni on the classification and design of high entropy alloys

According to a recent Hume-Rothery approach, the electron concentration, e/a, and the average radius can be used to identify the domain of stability of HEAs and to estimate the phases that may occur in the alloy. The present study investigates the influence of the electronic polymorphism of nickel on the efficiency of the classification and on the design of HEAs for magnetic applications. Many different compositions were used, based on 4 to 7 elements out of a total 13 different elements (Co, Cr, Fe, Ni, Al, Cu, Pd, Ti, Mn, V, Nb, Sn, Ru). Phases have been determined by X-ray and neutron diffraction as well as in some cases high energy X-ray diffraction. The e/a for the constituent elements is calculated according to Massalski. The two polymorphic electronic structure of nickel, namely (e/a)Ni = 1 or (e/a)Ni = 2 are considered. The average e/a for the alloy is calculated assuming a solid solution case. The electronic structure [Ar] 3d9 4s1 seems to be more appropriate for the classification of HEAs. Based on a Self-organising Map predictions are made for the average magnetic moment at saturation for this electronic structure of Ni. Non-saturated values and data from the literature are compared with the predictions. The consequences of such results when modelling the structure and properties of Ni containing HEAs are presented, in particular the consideration of the shape and transformation of the Brillouin zone

3D atom probe tomography of swift heavy ion irradiated multilayers

International audienceNanometer scale layered systems are well suited to investigate atomic transport processes induced by high-energy electronic excitations in materials, through the characterization of the interface transformation. In this study, we used the atom probe technique to determine the distribution of the different elements in an (amorphous-Fe$_2$Tb 5 nm/hcp-Co 3 nm)$_{20}$ multilayer before and after irradiation with Pb ions in the electronic stopping power regime. Atom probe tomography is based on reconstruction of a small volume of a sharp tip evaporated by field effect. It has unique capabilities to characterize internal interfaces and layer chemistry with sub-nanometer scale resolution in three dimensions. Depth composition profiles and 3D element mapping have been determined, evidencing for asymetric interfaces in the as-deposited sample, and very efficient Fe-Co intermixing after irradiation at the fluence $7\times10^{12}$ ion cm$^{-2}$. Estimation of effective atomic diffusion coefficients after irradiation suggests that mixing results from interdiffusion in a molten track across the interface in agreement with the thermal spike model

Forward Flux Sampling for rare event simulations

Rare events are ubiquitous in many different fields, yet they are notoriously difficult to simulate because few, if any, events are observed in a conventiona l simulation run. Over the past several decades, specialised simulation methods have been developed to overcome this problem. We review one recently-developed class of such methods, known as Forward Flux Sampling. Forward Flux Sampling uses a series of interfaces between the initial and final states to calculate rate constants and generate transition paths, for rare events in equilibrium or nonequilibrium systems with stochastic dynamics. This review draws together a number of recent advances, summarizes several applications of the method and highlights challenges that remain to be overcome.Comment: minor typos in the manuscript. J.Phys.:Condensed Matter (accepted for publication

Early aberrant angiogenesis due to elastic fiber fragmentation in aortic valve disease

Elastic fiber fragmentation (EFF) is a hallmark of aortic valve disease (AVD), and neovascularization has been identified as a late finding related to inflammation. We sought to characterize the relationship between early EFF and aberrant angiogenesis. To examine disease progression, regional anatomy and pathology of aortic valve tissue were assessed using histochemistry, immunohistochemistry, and electron microscopy from early-onset (\u3c40 yo) and late-onset (≥40 yo) non-syndromic AVD specimens. To assess the effects of EFF on early AVD processes, valve tissue from Williams and Marfan syndrome patients was also analyzed. Bicuspid aortic valve was more common in early-onset AVD, and cardiovascular comorbidities were more common in late-onset AVD. Early-onset AVD specimens demonstrated angiogenesis without inflammation or atherosclerosis. A distinct pattern of elastic fiber components surrounded early-onset AVD neovessels, including increased emilin-1 and decreased fibulin-5. Different types of EFF were present in Williams syndrome (WS) and Marfan syndrome (MFS) aortic valves; WS but not MFS aortic valves demonstrated angiogenesis. Aberrant angiogenesis occurs in early-onset AVD in the absence of inflammation, implicating EFF. Elucidation of underlying mechanisms may inform the development of new pharmacologic treatments

Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables.

Numerically predicting rate constants of protein folding and other relevant biological events is still a significant challenge. We show that the combination of partial path transition interface sampling with the optimal interfaces and free-energy profiles provided by path collective variables makes the rate calculation for practical biological applications feasible and efficient. This methodology can reproduce the experimental rate constant of Trp-cage miniprotein folding with the same level of accuracy as transition path sampling at a fraction of the cost

New HI-detected Galaxies in the Zone of Avoidance

We present the first results of a blind HI survey for galaxies in the southern Zone of Avoidance with a multibeam receiver on the Parkes telescope. This survey is eventually expected to catalog several thousand galaxies within Galactic latitude |b|<5 degrees, mostly unrecognised before due to Galactic extinction and confusion. We present here results of the first three detections to have been imaged with the Australia Telescope Compact Array (ATCA). The galaxies all lie near Galactic longitude 325 degrees and were selected because of their large angular sizes, up to 1.3 degrees. Linear sizes range from 53 to 108 kpc. The first galaxy is a massive 5.7x10^11 solar mass disk galaxy with a faint optical counterpart, SGC 1511.1--5249. The second is probably an interacting group of galaxies straddling the Galactic equator. No optical identification is possible. The third object appears to be an interacting pair of low column density galaxies, possibly belonging to an extended Circinus or Centaurus A galaxy group. No optical counterpart has been seen despite the predicted extinction (A(B) = 2.7 - 4.4 mag) not being excessive. We discuss the implications of the results, in particular the low HI column densities (~10^19 atoms/sq.cm) found for two of the three galaxies.Comment: 17 pages, 8 figures (Fig.1 in three parts, Fig.5 in two parts). To appear in Astronomical Journal (Dec 1998). See http://www.atnf.csiro.au/research/multibea