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International audience; Understanding the generation and evolution of defects induced in matter by ion irradiation is of fundamental importance to estimate the degradation of functional properties of materials. Computational approaches used in different communities, from space radiation effects to nuclear energy experiments, are based on a number of approximations that, among others, traditionally neglect the coupling between electronic and ionic degrees of freedom in the description of displacements. In this work, we study collision cascades in GaAs, including the electronic stopping power for self-projectiles in different directions obtained via real-time time-dependent density functional theory in molecular dynamics simulations of collision cascades, using the recent electron-phonon model and the previously developed two-temperature model. We show that the former can be well applied to describe the effects of electronic stopping in molecular dynamics simulations of collision cascades in a multielement semiconductor and that the number of defects is considerably affected by electronic stopping effects. The results are also discussed in the wider context of the commonly used nonionizing energy loss model to estimate degradation of materials by cumulative displacements.

A recently proposed theoretical framework for the description of electronic quantum friction for constant-velocity nuclear projectiles traversing periodic crystals is here implemented using a local basis representation. The theory requires a change of reference frame to that of the projectile, and a basis set transformation for the target basis functions to a gliding basis is presented, which is time-periodic but does not displace in space with respect to the projectile, allowing a local-basis Floquet impurity-scattering formalism to be used. It is illustrated for a one-dimensional single-band tight-binding model, as the simplest paradigmatic example, displaying the qualitative behaviour of the formalism. The time-dependent non-orthogonality of the gliding basis requires care in the proper (simplest) definition of a local projectile perturbation. The Fermi level is tilted with a slope given by the projectile velocity, which complicates integration over occupied states. It is solved by a recurrent application of the Lippmann-Schwinger equation, in analogy with previous non-equilibrium treatment of electron ballistic transport. Aiming towards a first-principles mean-field-like implementation, the final result is the time-periodic particle density in the region around the projectile, describing the stroboscopically stationary perturbation cloud around the projectile, out of which other quantities can be obtained, such as the electronic stopping power.

The computational study of DNA and its interaction with ligands is a highly relevant area of research, with significant consequences for developing new therapeutic strategies. However, the computational description of such large and complex systems requires considering interactions of different types simultaneously in a balanced way, such as non-covalent weak interactions (namely hydrogen bonds and stacking), metal–ligand interactions, polarisation and charge transfer effects. All these considerations imply a real challenge for computational chemistry. The possibility of studying large biological systems using quantum methods for the entire system requires significant computational resources, with improvements in parallelisation and optimisation of theoretical strategies. Computational methods, such as Linear-Scaling Density Functional Theory (LS-DFT) and DLPNO-CCSD(T), may allow performing ab initio quantum mechanics calculations, including the electronic structure for large biological systems, in a reasonable computing time. In this work, we study the interaction of small molecules and cations with DNA (both duplex DNA and G-quadruplexes), comparing different computational methods: a LS-DFT method at the LMKLL/DZDP level of theory, semi-empirical methods (PM6-DH2 and PM7), mixed QM/MM, and DLPNO-CCSD(T). Our goal is to demonstrate the adequacy of LS-DFT to treat the different types of interactions present in DNA-dependent systems. We show that LMKLL/DZDP using SIESTA can yield very accurate geometries and energetics in all the different systems considered in this work: duplex DNA (dDNA), phenanthroline intercalating dDNA, G-quadruplexes, and metal-G-tetrads considering alkaline metals of different sizes. As far as we know, this is the first time that full G-quadruplex geometry optimisations have been carried out using a DFT method thanks to its linear-scaling capabilities. Moreover, we show that LS-DFT provides high-quality structures, and some semi-empirical Hamiltonians can also yield suitable geometries. However, DLPNO-CCSD(T) and LS-DFT are the only methods that accurately describe interaction energies for all the systems considered in our study., This research was financially supported by Diputación Foral de Gipuzkoa through the Gipuzkoa Fellows Program to A. G. This research was also financially supported by the Fundação para a Ciência e a Tecnologia (FCT) by means of Projects PTDC/QUI-QFI/29236/2017, UIDB/04046/2020, and UIDP/04046/2020 and by the Spanish Ministry of Economy, Industry and Competitiveness under the Maria de Maeztu Units of Excellence Program/MDM-2016-0618). A. G. is thankful to ARAID – Fundación Agencia Aragonesa para la Investigación y el Desarrollo for current funding in the frame of ARAID researchers. The authors also thank for technical and human support provided by IZO-SGI (SGIker) of UPV/EHU and European funding (ERDF and ESF). Financial support comes also from Eusko Jaurlaritza (Basque Government) through the project IT1254-19 and IT1584-22, from Spanish MICINN through Grant No. PID2019-107338RB-C61/AEI/10.13039/501100011033, and grant PGC2018-099321-B-100 from the Ministry of Science, Innovation and Universities through the Office of Science Research (MINECO/FEDER). Pseudopotentials and Numerical Atomic Orbitals Basis Dataset for SIESTA were provided by Simune Atomistics S. L. (www.simuneatomistics.com). S. E. thanks the Ministry of Higher Education and Scientific Research of Tunisia for the funding of intership carried out in Portugal and Spain. I. O. D. L. is also very grateful to CICnanoGUNE BRTA for his PhD grant.

The phenomenological theory for the polar instability giving rise to a two-dimensional electron gas at perovskite interfaces is hereby extended to include the coupling to perovskite tilts. A Landau theory for homogeneous tilts is first explored, setting the scene for the further, more realistic Landau-Ginzburg theory describing varying tilt amplitudes across a thin film. The theory is also generalized to account for the response to an applied electric field normal to the interface, which allows a finer control on phase transitions. The conventionally described physics of a single metal-insulator transition is substantially enriched by the coupling, the model describing various scenarios with one or two transitions, possibly continuous or discontinuous. First-principles calculations permit the estimation of the parameters defining the model, which have been calculated for the interface between lanthanum aluminate and strontium titanate., Comment: Accepted version

The electronic stopping power ($S_e$) of water vapor (H$_2$O), hydrogen (H$_2$) and oxygen (O$_2$) gases for protons in a broad range of energies, centered in the Bragg peak, was calculated using real-time time-dependent density functional theory (rt-TDDFT) simulations with Gaussian basis sets. This was done for a kinetic energy of incident protons ($E_k$) ranging from 1.56 keV/amu to 1.6 MeV/amu. $S_e$ was calculated as the average over geometrically pre-sampled short ion trajectories. The average $S_e(E_k)$ values were found to rapidly converge with 25-30 pre-sampled, 2 nm-long ion trajectories. The rt-TDDFT $S_e(E_k)$ curves were compared to experimental and SRIM data, and used to validate the Bragg's Additivity Rule (BAR). Discrepancies were analyzed in terms of basis set effects and omitted nuclear stopping at low energies. At variance with SRIM, we found that BAR is applicable to our rt-TDDFT simulations of $\mathrm{2H_2+O_2}$ $\mathrm{\rightarrow 2H_2O}$ without scaling for $E_k>40$ keV/amu. The hydrogen and oxygen Core and Bond (CAB) contributions to electronic stopping were calculated and found to be slightly smaller than SRIM values as a result of a red-shift in our rt-TDDFT $S_e(E_k)$ curves and a re-distribution of weights due to some bond contributions being neglected in SRIM., 15 pages 5 figures, 1 table

Tau neurofibrillary tangle (NFT) pathology in the medial temporal lobe (MTL) is closely linked to neurodegeneration, and is the early pathological change associated with Alzheimer’s disease (AD). To elucidate patterns of structural change in the MTL specifically associated with tau pathology, we compared high-resolution ex vivo MRI scans of human postmortem MTL specimens with histology-based pathological assessments of the MTL. MTL specimens were obtained from twenty-nine brain donors, including patients with AD, other dementias, and individuals with no known history of neurological disease. Ex vivo MRI scans were combined using a customized groupwise diffeomorphic registration approach to construct a 3D probabilistic atlas that captures the anatomical variability of the MTL. Using serial histology imaging in eleven specimens, we labelled the MTL subregions in the atlas based on cytoarchitecture. Leveraging the atlas and neuropathological ratings of tau and TAR DNA-binding protein 43 (TDP-43) pathology severity, morphometric analysis was performed to correlate regional MTL thickness with the severity of tau pathology, after correcting for age and TDP-43 pathology. We found significant correlations between tau pathology and thickness in the entorhinal cortex (ERC) and stratum radiatum lacunosum moleculare (SRLM). When focusing on cases with low levels of TDP-43 pathology, we found strong associations between tau pathology and thickness in the ERC, SRLM and the subiculum/cornu ammonis 1 (CA1) subfields of the hippocampus, consistent with early Braak stages. Supplementary Information The online version contains supplementary material available at 10.1186/s40478-021-01275-7.

The medial temporal lobe (MTL) is a nidus for neurodegenerative pathologies and therefore an important region in which to study polypathology. We investigated associations between neurodegenerative pathologies and the thickness of different MTL subregions measured using high-resolution post-mortem MRI. Tau, TAR DNA-binding protein 43 (TDP-43), amyloid-β and α-synuclein pathology were rated on a scale of 0 (absent)—3 (severe) in the hippocampus and entorhinal cortex (ERC) of 58 individuals with and without neurodegenerative diseases (median age 75.0 years, 60.3% male). Thickness measurements in ERC, Brodmann Area (BA) 35 and 36, parahippocampal cortex, subiculum, cornu ammonis (CA)1 and the stratum radiatum lacunosum moleculare (SRLM) were derived from 0.2 × 0.2 × 0.2 mm3 post-mortem MRI scans of excised MTL specimens from the contralateral hemisphere using a semi-automated approach. Spearman’s rank correlations were performed between neurodegenerative pathologies and thickness, correcting for age, sex and hemisphere, including all four proteinopathies in the model. We found significant associations of (1) TDP-43 with thickness in all subregions (r = − 0.27 to r = − 0.46), and (2) tau with BA35 (r = − 0.31) and SRLM thickness (r = − 0.33). In amyloid-β and TDP-43 negative cases, we found strong significant associations of tau with ERC (r = − 0.40), BA35 (r = − 0.55), subiculum (r = − 0.42) and CA1 thickness (r = − 0.47). This unique dataset shows widespread MTL atrophy in relation to TDP-43 pathology and atrophy in regions affected early in Braak stageing and tau pathology. Moreover, the strong association of tau with thickness in early Braak regions in the absence of amyloid-β suggests a role of Primary Age-Related Tauopathy in neurodegeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s40478-021-01225-3.

Tau protein neurofibrillary tangles (NFT) are closely linked to neuronal/synaptic loss and cognitive decline in Alzheimer's disease (AD) and related dementias. Our knowledge of the pattern of NFT progression in the human brain, critical to the development of imaging biomarkers and interpretation of in vivo imaging studies in AD, is based on conventional 2D histology studies that only sample the brain sparsely. To address this limitation, ex vivo MRI and dense serial histological imaging in 18 human medial temporal lobe (MTL) specimens were used to construct 3D quantitative maps of NFT burden in the MTL at individual and group levels. These maps reveal significant variation in NFT burden along the anterior-posterior axis. While early NFT pathology is thought to be confined to the transentorhinal region, we find similar levels of NFT burden in this region and other MTL subregions, including amygdala, temporopolar cortex, and subiculum/CA1.

Tau protein neurofibrillary tangles are closely linked to neuronal/synaptic loss and cognitive decline in Alzheimer’s disease and related dementias. Our knowledge of the pattern of neurofibrillary tangle progression in the human brain, critical to the development of imaging biomarkers and interpretation of in vivo imaging studies in Alzheimer’s disease, is based on conventional two-dimensional histology studies that only sample the brain sparsely. To address this limitation, ex vivo MRI and dense serial histological imaging in 18 human medial temporal lobe specimens (age 75.3 ± 11.4 years, range 45 to 93) were used to construct three-dimensional quantitative maps of neurofibrillary tangle burden in the medial temporal lobe at individual and group levels. Group-level maps were obtained in the space of an in vivo brain template, and neurofibrillary tangles were measured in specific anatomical regions defined in this template. Three-dimensional maps of neurofibrillary tangle burden revealed significant variation along the anterior-posterior axis. While early neurofibrillary tangle pathology is thought to be confined to the transentorhinal region, we found similar levels of burden in this region and other medial temporal lobe subregions, including amygdala, temporopolar cortex, and subiculum/cornu ammonis 1 hippocampal subfields. Overall, the three-dimensional maps of neurofibrillary tangle burden presented here provide more complete information about the distribution of this neurodegenerative pathology in the region of the cortex where it first emerges in Alzheimer’s disease, and may help inform the field about the patterns of pathology spread, as well as support development and validation of neuroimaging biomarkers.

This article is part of the JCP Special Topic on Electronic Structure Software., A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-1990s, SIESTA’s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a realspace grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin–orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as WANNIER90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various post-processing utilities. SIESTA has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments., Siesta development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Center of Excellence Program [Grant Nos. SEV-2015-0496 (ICMAB) and SEV-2017-0706 (ICN2)], the GenCat (Grant No. 2017SGR1506), and the European Union MaX Center of Excellence (EU-H2020 Grant No. 824143). P.G.-F. acknowledges support from Ramón y Cajal (Grant No. RyC-2013-12515). J.I.C. acknowledges Grant No. RTI2018-097895-B-C41. R.C. acknowledges the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodoswka-Curie Grant Agreement No. 665919. D.S.P, P.K., and P.B. acknowledge Grant No. MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant No. IT1246-19. V. W. Yu was supported by a MolSSI Fellowship (U.S. NSF Award No. 1547580), and V.B. and V.W.Y. were supported by the ELSI Development by the NSF (Award No. 1450280).

Known force terms arising in the Ehrenfest dynamics of quantum electrons and classical nuclei, due to a moving basis set for the former, can be understood in terms of the curvature of the manifold hosting the quantum states of the electronic subsystem. Namely, the velocity-dependent terms appearing in the Ehrenfest forces on the nuclei acquire a geometrical meaning in terms of the intrinsic curvature of the manifold, while Pulay terms relate to its extrinsic curvature., Comment: 4 pages, no figures, as accepted in SciPost Physics

This book collects the lectures presented in the first COST TUMIEE Training School held in Greece in 2019, supplemented with specific applications that illustrate how the multi-scale approach is implemented in specific cases of interest. The book is intended both as a reference in the field and as a textbook for people becoming interested or entering the field. The first part focuses on experimental methods, the second on theoretical approaches, and the third on cases of interest.

The numerical integration of the Schr\"odinger equation by discretization of time is explored for the curved manifolds arising from finite representations based on evolving basis states. In particular, the unitarity of the evolution is assessed, in the sense of the conservation of mutual scalar products in a set of evolving states, and with them the conservation of orthonormality and particle number. Although the adequately represented equation is known to give rise to unitary evolution in spite of curvature, discretized integrators easily break that conservation, thereby deteriorating their stability. The Crank Nicolson algorithm, which offers unitary evolution in Euclidian spaces independent of time-step size $\mathrm{d}t$, can be generalised to curved manifolds in different ways. Here we compare a previously proposed algorithm that is unitary by construction, albeit integrating the wrong equation, with a faithful generalisation of the algorithm, which is, however, not strictly unitary for finite $\mathrm{d}t$., Comment: 12 pages, 5 figures. Accepted in Phys. Rev. Research

The electrostatics arising in ferroelectric/dielectric two-dimensional heterostructures and superlatitices is revisited here within a simplest Kittel model, in order to define a clear paradigmatic reference for domain formation. The screening of the depolarizing field in isolated ferroelectric or polar thin films via the formation of 180$^{\circ}$ domains is well understood, whereby the width of the domains $w$ grows as the square-root of the film thickness $d$, following Kittel's law, for thick enough films ($w\ll d$). This behavior is qualitatively unaltered when the film is deposited on a dielectric substrate, sandwiched between dielectrics, and even in a superlattice setting, with just a suitable renormalisation of Kittel's length. As $d$ decreases, $w(d)$ deviates from Kittel's law, reaching a minimum and then diverging onto the mono-domain limit for thin enough films, always assuming a given spontaneous polarization $P$ of the ferrolectric, only modified by linear response to the depolarizing field. In most cases of experimental relevance $P$ would vanish before reaching that thin-film regime. This is not the case for superlattices. Unlike single films, for which the increase of the dielectric constant of the surrounding medium pushes the deviation from the Kittel's regime to lower values of $d$, there is a critical value of the relative thickness of ferroelectric/dielectric films in superlattices beyond which that behavior is reversed, and which defines the separation between strong and weak ferroelectric coupling in superlattices., 11 pages, 11 figures

Knowledge of the electronic stopping curve for swift ions, $S_e(v)$, particularly around the Bragg peak, is important for understanding radiation damage. Experimentally, however, the determination of such feature for light ions is very challenging, especially in disordered systems such as liquid water and biological tissue. Recent developments in real-time time-dependent density functional theory (rt-TDDFT) have enabled the calculation of $S_e(v)$ along nm-sized trajectories. However, it is still a challenge to obtain a meaningful statistically averaged $S_e(v)$ that can be compared to observations. In this work, taking advantage of the correlation between the local electronic structure probed by the projectile and the distance from the projectile to the atoms in the target, we devise a trajectory pre-sampling scheme to select, geometrically, a small set of short trajectories to accelerate the convergence of the averaged $S_e(v)$ computed via rt-TDDFT. For protons in liquid water, we first calculate the reference probability distribution function (PDF) for the distance from the proton to the closest oxygen atom, $\phi_R(r_{p{\rightarrow}O})$, for a trajectory of a length similar to those sampled experimentally. Then, short trajectories are sequentially selected so that the accumulated PDF reproduces $\phi_R(r_{p{\rightarrow}O})$ to increasingly high accuracy. Using these pre-sampled trajectories, we demonstrate that the averaged $S_e(v_p)$ converges in the whole velocity range with less than eight trajectories, while other averaging methods using randomly and uniformly distributed trajectories require approximately ten times the computational effort. This allows us to compare the $S_e(v_p)$ curve to experimental data, and assess widely used empirical tables based on Bragg's rule.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community., The authors would also like to thank the Psi-k network for having partially funded several of the ESL workshops. A.O., E.A., D.L.-D., S.G., E.K., A.A.M., and M.C.P. received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 676531 (Centre of Excellence project E-CAM). The same project has partly funded the extended software development workshops in which most of the ESL coding effort has happened. A.G., S.M., and E.A. acknowledge support from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 824143 (Centre of Excellence project MaX). M.A.L.M. acknowledges partial support from the DFG through Project No. MA-6786/1. D.G.A.S. was supported by the U.S. National Science Foundation (NSF) (Grant No. ACI1547580). M.C.P. acknowledges support from the EPSRC under Grant No. EP/P034616/1. A.A.M. acknowledges support from the Thomas Young Centre under Grant No. TYC-101, the Wannier Developers Group, and all of the authors and contributors of the wannier90 code (see Ref. 115 for a complete list). A.M.E. acknowledges support from CoSeC, the Computational Science Centre for Research Communities, through CCP5: The Computer Simulation of Condensed Phases (EPSRC Grant Nos. EP/M022617/1 and EP/P022308/1). A.G. and J.M.S. acknowledge Spain’s Ministry of Science (Grant No. PGC2018-096955-B-C42). E.A., A.G., and J.M.S. acknowledge Spain’s Ministry of Science (Grant No. FIS2015-64886- C5). Y.P., D.L.-D., and E.A. acknowledge support from the Spanish MINECO and EU Structural Investment Funds (Grant No. RTC2016-5681-7). M.L. acknowledges support from the EPRSC under Grant No. EP/M022668/1. M.L., M.J.T.O., and Y.P. acknowledge support from the EU COST action (Grant No. MP1306). J.M. was supported by the European Regional Development Fund (ERDF), project CEDAMNF (Reg. No. CZ.02.1.01/0.0/0.0/15-003/0000358). V.W.-Z.Y., W.P.H., Y.L., and V.B. acknowledge support from the National Science Foundation under Award No. ACI-1450280 (the ELSI project). V.W.-Z.Y. also acknowledges a MolSSI fellowship (NSF Award No. ACI-1547580). Simune Atomistics S.L. is thanked for allowing A.H.L. and Y.P. to contribute to the ESL, as is Synopsys, Inc., for the partial availability of F.C.

A general theoretical framework for the study of electronic stopping of particle projectiles in crystalline solids is proposed. It neither relies on perturbative or linear response approximations, nor on an ideal metal host. Instead, it exploits the discrete translational symmetries in a space-time diagonal determined by a projectile with constant velocity moving along a trajectory with crystalline periodicity. This allows for the characterisation of (stroboscopically) stationary solutions, by means of Floquet theory for time-periodic systems. Previous perturbative and non-linear jellium models are recovered from this general theory. An analysis of the threshold velocity effect in insulators is presented based on Floquet quasi-energy conservation., Comment: 6 pages, 4 figures

The variation of the HOMO-LUMO band gap is explored for varying packing arrangements of the 4mod BT-4TIC donor-acceptor molecule pair, by means of a high-throughput ab-initio random structure search of packing possibilities. 350 arrangements of the dimer have been relaxed from initial random dispositions, using non-local density-functional theory. We find that the electronic band gap varies within 0.3 eV, and that this magnitude, the binding energy, and the geometry are not significantly correlated. A clearly favoured structure is found with a binding energy of 1.75±0.07 eV, with all but three other arrangements displaying values of less than one third of this highest binding one, which involves the aliphatic chain of 4TIC.

Uropathogenic Escherichia coli attach to tissues using pili type 1. Each pilus is composed by thousands of coiled FimA domains followed by the domains of the tip fibrillum, FimF-FimG-FimH. The domains are linked by non-covalent β-strands that must resist mechanical forces during attachment. Here, we use single-molecule force spectroscopy to measure the mechanical contribution of each domain to the stability of the pilus and monitor the oxidative folding mechanism of a single Fim domain assisted by periplasmic FimC and the oxidoreductase DsbA. We demonstrate that pilus domains bear high mechanical stability following a hierarchy by which domains close to the tip are weaker than those close to or at the pilus rod. During folding, this remarkable stability is achieved by the intervention of DsbA that not only forms strategic disulfide bonds but also serves as a chaperone assisting the folding of the domains., The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.

We assess several recently developed dispersion-corrected exchange-correlation functionals [PBE + VV10L of H. Peng and J. P. Perdew, Phys. Rev. B 95, 081105 (2017); SG4 + VV10m of A. V. Terentjev et al., Computation 6, 7 (2018); and PBEsol+VV10s of A. V. Terentjev et al., Phys. Rev. B 98, 214108 (2018)] for the adsorption of a noble-gas atom/monolayer as well as a graphene on the Cu(111), Pt(111), Pd(111), and Ag(111) close-packed surfaces. Most of these systems are characterized by weak interactions between the surface and the atom/monolayer, where the van der Waals interaction dominates. Here we investigate the above mentioned dispersion-corrected exchange-correlation functionals using atomic orbitals instead of plane waves applied in earlier works. We find that PBEsol+VV10s is an optimal functional for such hybrid interfaces, being accurate for both the equilibrium distance and the adsorption energy and providing realistic potential-energy curves. Moreover, we also show that PBEsol+VV10s and SG4+VV10m are both very accurate for the investigation of surface formation energies of all transition metals under consideration, A.V.T. acknowledges Dr. Federico Marchesin for fruitful discussion. E.A. would like to acknowledge financial support from MINECO-Spain through Plan Nacional Grant No. FIS2015-64886.

The hippocampal formation (HF) has an important role in different human capacities, such as memory processing and emotional expression. Both extensive changes and limited variations of its components can cause clinically expressed dysfunctions. Although there remains no effective treatment for diseases caused by pathological changes in this brain region, detection of these changes, even minimally, could allow us to develop early interventions and establish corrective measures. This study analysed the neuronal islands of layer II of the entorhinal cortex (EC), the neuronal clumps of the external principal layer of the presubiculum (PrS) and the dentate granule cells of the dentate gyrus (DG), which represent the prominent structural regions within the HF circuit. Subjects from two age groups (younger or older than 65 years) were studied and their neuronal size assessed by the point-sampled intercepts stereological method. The quantitative v ¯ v ( s o m a ) estimate was a volume of roughly 8,500 µm3 for EC layer II neurons, and DG granule neurons and presubicular neurons were five and 10 times smaller, respectively. The older age group showed a v ¯ v ( s o m a ) increase of 2%, 18% and 28% with respect to the younger group in the PrS, DG and EC regions, respectively. None of these regions showed interhemispheric differences. This quantitative estimation is relevant because the observed variance in the v ¯ v ( s o m a ) estimates suggests that biological variation is the main contributory factor, with intercepts and measurements having a smaller impact. Therefore, we suggest that age has a limited influence on neuronal volume variation in these HF regions, which needs to be compared with similar measurements in neurodegenerative disorders such as Alzheimer's.

© 2019 American Physical Society. The twoerature model (TTM) is commonly used to represent the energy exchange between atoms and electrons in materials under irradiation. In this work we use the TTM coupled to molecular dynamics (TTM-MD) to study swift heavy ion irradiation of Au and W finite nanowires. While no permanent structural modifications are observed in bulk, nanowires behave in a different way depending on thermal conductivity and the electron-phonon coupling parameter. Au is a good heat conductor and it does not transfer energy from electrons to phonons too efficiently. Therefore, energy is quickly carried away from the track so that both electronic and lattice temperatures remain quite uniform across the sample at all times. W has a lower thermal conductivity and a larger electron-phonon coupling, thus supporting an inhomogeneous lattice temperature profile with temperatures well above melting lasting several picoseconds in the irradiated region. Both W and Au nanowires display radiation-induced surface roughening. However, in the case of W there is also sputtering and the formation of a hole in the central part of the wire, purely due to the energy transferred to the atoms by the electrons. The physical mechanisms underlying these findings are rationalized in terms of a combination of sputtering, vacancy formation, and melt flow phenomena. The role of the electron-phonon coupling parameter g is analyzed.

8 pags., 7 figs., 2 tabs., A method to predict the near-infrared spectra of amorphous solids by means of ab initio molecular dynamics is presented. These solids can simulate molecular ices. To test the method, mixtures of methane, water and nitrogen are generated as amorphous samples of various concentrations. The full theoretical treatment includes as a first step, the optimization of their geometrical structure for a range of densities, after which, the most stable systems are taken as initial structures for molecular dynamics, performed at 200 K in trajectories of 4 ps duration with a 0.2 fs time step. All the dynamics are carried out using the first principles method, solving the quantum problem for the electrons using density-functional theory (DFT), and integrating the DFT forces, following the Born–Oppenheimer dynamics. After the dynamics, near-IR spectra are predicted by the Fourier transform of the macroscopic polarization autocorrelation function. The calculated spectra are compared with the experimental spectra of ice mixtures of CH4 and H2O recorded in our laboratory, and with some spectra recorded by the New Horizons mission on Pluto., The calculations have been carried out at CESGA (CSIC-Xunta de Galicia), Westgrid (Canada) and TCM (Cavendish Laboratory, University of Cambridge). Funds from the Spanish MINECO FIS2016-77726-C3-1P, MINECO/FEDER CTQ2015-65033-P and MECD Sabbatical PRX17/00126 projects are also acknowledged., We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI)

This research was supported by the ERC WIHM Project [#339694] to DAH. The stable isotopes (18O/16O, 17O/16O and 2H/1H) of structurally-bound water (also called hydration water) in gypsum (CaSO4•2H2O) and bassanite (CaSO4•0.5H2O) can be used to reconstruct the isotopic composition of paleo-waters. Understanding the variability of the isotope fractionation factors between the solution and the solid (α17Omineral-water, α18Omineral-water and αDmineral-water) is crucial for applying this proxy to paleoclimatic research. Here we predict the theoretical equilibrium fractionation factors for triple oxygen and hydrogen isotopes in the gypsum-water and bassanite-water systems between 0 °C and 60 °C. We apply first-principles using density functional theory within the harmonic approximation. Our theoretical results for α18Ogypsum-water (1.00347±0.00037) are in agreement with previous experimental studies, whereas αDgypsum-water agrees only at temperatures above 25 °C. At lower temperatures, the experimental values of αDgypsum-water are consistently higher than theoretical values (e.g. 0.9749 and 0.9782, respectively, at 3 °C), which can be explained by kinetic effects that affect gypsum precipitation under laboratory conditions at low temperature. We predict that α18Obassanite-water is similar to α18Ogypsum-water in the temperature range of 0 °C to 60 °C. Both α18Ogypsum-water and α18Obassanite-water show a small temperature dependence of ∼0.0000122 per °C, which is negligible for most paleoclimate studies. The theoretical relationship between α17Ogypsum-water and α18Ogypsum-water (θ =lnα17Olnα18O) from 0 °C to 60 °C is 0.5274±0.00063. The relationship is very insensitive to temperature (0.00002 per °C). The fact that δ18O values of gypsum hydration water are greater than free water (α18Ogypsum-water >1) whereas δD values of gypsum hydration water are less than free water (αDgypsum-water

The rate of energy transfer from ion projectiles onto the electrons of a solid target is hard to determine experimentally in the velocity regime between the adiabatic limit and the Bragg peak. First-principles simulations have lately offered relevant new insights and quantitative information for prototypical homogeneous materials. Here we study the influence of structural anisotropy on electronic stopping power with time-dependent density functional theory simulations of a hydrogen projectile in graphite. The projectile traveled at a range of angles and impact parameters for velocities between 0.1 and 1.4 a.u., and the electronic stopping power was calculated for each simulation. After validation with average experimental data, the anisotropic crystal structure was found to have a strong influence on the stopping power, with a difference between simulations parallel and perpendicular to the graphite plane of up to 25%, more anisotropic than expected based on previous work. The velocity dependence at low velocity displays clear linear behavior in general, except for projectiles traveling perpendicular to graphitic layers, for which a threshold-like behavior is obtained. For projectiles traveling along graphitic planes metallic behaviour is observed with a change of slope when the projectile velocity reaches the Fermi velocity of the electrons., Comment: 8 pages, 6 figures