Consensus for the Fip35 folding mechanism?

Recent advances in computational power and simulation programs finally delivered the first examples of reversible folding for small proteins with an all-atom description. But having at hand the atomistic details of the process did not lead to a straightforward interpretation of the mechanism. For the case of the Fip35 WW-domain where multiple long trajectories of 100 {\mu}s are available from D. E. Shaw Research, different interpretations emerged. Some of those are in clear contradiction with each other while others are in qualitative agreement. Here, we present a network-based analysis of the same data by looking at the local fluctuations of conventional order parameters for folding. We found that folding occurs through two major pathways, one almost four times more populated than the other. Each pathway involves the formation of an intermediate with one of the two hairpins in a native configuration. The quantitative agreement of our results with a state-of-the-art reaction coordinate optimization procedure as well as qualitative agreement with other Markov-state-models and different simulation schemes provides strong evidence for a multiple folding pathways scenario with the presence of intermediates.Comment: 7 pages, 7 figure

The quest for self-consistency in hydrogen-bond definitions

In the last decades several hydrogen-bond definitions were proposed by classical computer simulations. Aiming at validating their self-consistency on a wide range of conditions, here we present a comparative study of six among the most common hydrogen-bond definitions for temperatures ranging from 220K to 400K and six classical water models. Our results show that, in the interval of temperatures investigated, a generally weak agreement among definitions is present. Moreover, cutoff choice for geometrically based definitions depends on both temperature and water model. As such, analysis of the same water model at different temperatures as well as different water models at the same temperature would require the development of specific cutoff values. Interestingly, large discrepancies were found between two hydrogen-bond definitions which were recently introduced to improve on more conventional methods. Our results anticipate that a more universal way to characterize hydrogen-bonds in classical molecular systems is needed.Comment: 7 pages, 7 figure

Accounting for the kinetics in order parameter analysis: lessons from theoretical models and a disordered peptide

Molecular simulations as well as single molecule experiments have been widely analyzed in terms order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive, mounting evidence showed that such description is not accurate, leading to ambiguous definitions of states and wrong kinetics. To overcome these limitations a framework making use of order parameter fluctuations in conjunction with complex network analysis is investigated. Derived from recent advances in the analysis of single molecule time traces, this approach takes into account of the fluctuations around each time point to distinguish between states that have similar values of the order parameter but different dynamics. Snapshots with similar fluctuations are used as nodes of a transition network, the clusterization of which into states provides accurate Markov-State-Models of the system under study. Application of the methodology to theoretical models with a noisy order parameter as well as the dynamics of a disordered peptide illustrates the possibility to build accurate descriptions of molecular processes on the sole basis of order parameter time series without using any supplementary information.Comment: 7 pages, 4 figure

Crossed Andreev reflection-induced magnetoresistance

We show that very large negative magnetoresistance can be obtained in magnetic trilayers in a current-in-plane geometry owing to the existence of crossed Andreev reflection. This spin-valve consists of a thin superconducting film sandwiched between two ferromagnetic layers whose magnetization is allowed to be either parallelly or antiparallelly aligned. For a suitable choice of structure parameters and nearly fully spin-polarized ferromagnets the magnetoresistance can exceed -80%. Our results are relevant for the design and implementation of spintronic devices exploiting ferromagnet-superconductor structures.Comment: 5 pages, 4 figures, final published versio

The clustering of galaxies at z~0.5 in the SDSS-III Data Release 9 BOSS-CMASS sample: a test for the LCDM cosmology

We present results on the clustering of 282,068 galaxies in the Baryon Oscillation Spectroscopic Survey (BOSS) sample of massive galaxies with redshifts 0.4<z<0.7 which is part of the Sloan Digital Sky Survey III project. Our results cover a large range of scales from ~0.5 to ~90 Mpc/h. We compare these estimates with the expectations of the flat LCDM cosmological model with parameters compatible with WMAP7 data. We use the MultiDark cosmological simulation together with a simple halo abundance matching technique, to estimate galaxy correlation functions, power spectra, abundance of subhaloes and galaxy biases. We find that the LCDM model gives a reasonable description to the observed correlation functions at z~0.5, which is a remarkably good agreement considering that the model, once matched to the observed abundance of BOSS galaxies, does not have any free parameters. However, we find a deviation (>~10%) in the correlation functions for scales less than ~1 Mpc/h and ~10-40 Mpc/h. A more realistic abundance matching model and better statistics from upcoming observations are needed to clarify the situation. We also estimate that about 12% of the "galaxies" in the abundance-matched sample are satellites inhabiting central haloes with mass M>~1e14 M_sun/h. Using the MultiDark simulation we also study the real space halo bias b(r) of the matched catalogue finding that b=2.00+/-0.07 at large scales, consistent with the one obtained using the measured BOSS projected correlation function. Furthermore, the linear large-scale bias depends on the number density n of the abundance-matched sample as b=-0.048-(0.594+/-0.02)*log(n/(h/Mpc)^3). Extrapolating these results to BAO scales we measure a scale-dependent damping of the acoustic signal produced by non-linear evolution that leads to ~2-4% dips at ~3 sigma level for wavenumbers k>~0.1 h/Mpc in the linear large-scale bias.Comment: Replaced to match published version. Typos corrected; 25 pages, 17 figures, 9 tables. To appear in MNRAS. Correlation functions (projected and redshift-space) and correlation matrices of CMASS presented in Appendix B. Correlation and covariance data for the combined CMASS sample can be downloaded from http://www.sdss3.org/science/boss_publications.ph

Building Simulation Applications BSA 2022 - Proceedings of 5th IBPSA-Italy conference

The participation of about 100 attendees at the fifth Building Simulation Applications BSA2022 Conference, one of the first IBPSA conferences held entirely in presence after the pandemic outbreak, can certainly be claimed as a step forward in the process of overcoming the constraints and limitations imposed by the years of the Covid-19 pandemic. 11 conference sessions in two parallel tracks, 66 presentations reporting the contributions by more than 180 authors are some of the most significant figures of this event. In addition, confirming an international profile and its inclusivity call, the Conference saw a small but significant presence of delegates from abroad, especially from Austria and India. As the previous editions, BSA 2022 focused on providing an overview of the latest applications of building simulation in the following three main fields: the use of simulation for building physics applications, such as building envelope and HVAC system modelling and their design and operation optimization; global performance and multi-domain simulations; the development through simulation of new methodologies, regulations, as well as new calculation and simulation tools. Nonetheless, the times urged to address indoor air quality, the main topic of this edition, emphasizing the role of simulation to assess strategies able to ensure healthy and safe indoor conditions for occupants