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© 2019, Springer Nature America, Inc. The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations.

Diboron trioxide (B2O3) assumes critical importance as an effective oxidation inhibitor in prominent chemical applications. For instance, it has been extensively used in electrolysis and ceramic/glass technology. Results are presented of accurate quantum mechanical calculations using the PW1PW hybrid HF/DFT functional of four low-index surfaces of the low-pressure phase of B2O3: (101), (100), (011), and (001). Bond lengths, bond angles, and net Mulliken charges of the surface atoms are analyzed in detail. Total and projected density of states as well as surface energies are discussed. The occurrence of tetrahedral BO4 units on the lowest energy structures of two of these surfaces has been demonstrated for the first time. The corresponding surface orientations incur larger energies in reference to the two orientations featuring only BO3 units. All of the four investigated lowest energy structures have no dangling bonds, which reasonably relates to the experimentally observed low reactivity of this compound. Findings in this paper pave the way for potential interest in the perspective of future studies on the surfaces of amorphous B2O3, as well as on the hydroxylation of both crystalline and amorphous B2O3.

Our aims were to design a reproducible method of measuring life-time alcohol consumption in patients with cirrhosis, and to assess the risk of liver decompensation associated with alcohol intake using a case-control design and a multivariate analysis. We studied 439 patients ("cases") with decompensated cirrhosis, and 233 with compensated cirrhosis ("controls"). Mean life-time daily amount and duration of alcohol intake were measured by a standardized questionnaire, whose reproducibility, assessed by interviewing 75 relatives, was 70% for daily alcohol intake and 84% for duration of intake. Better reproducibility was found by re-interviewing patients at discharge from hospital. Daily alcohol intake was significantly higher in males, younger patients and patients with liver decompensation. After stratification according to the average life-time daily alcohol intake, we found a significant increase in the risk of liver decompensation from 125 g ethanol intake per day onwards. No association was found between duration of alcohol intake and risk of liver decompensation. We conclude that alcohol intake can be reliably and reproducibly measured: in patients with cirrhosis, increased alcohol intake is associated with increased risk of liver decompensation, with a significant dose-effect above a daily intake of 125 g ethanol

The properties of the (n,n) icosahedral family of carbon fullerenes up to n = 10 (6000 atoms) have been investigated through ab initio quantum-mechanical simulation by using a Gaussian type basis set of double zeta quality with polarization functions (84 000 atomic orbitals for the largest case), the hybrid B3LYP functional and the CRYSTAL14 code featuring generalization of symmetry treatment. The geometry of giant fullerenes shows hybrid features, between a polyhedron and a sphere; as n increases, it approaches the former. Hexagon rings at face centres take a planar, graphene-like configuration; the 12 pentagon rings at vertices impose, however, a severe structural constraint to which hexagon rings at the edges must adapt smoothly, adopting a bent (rather than sharp) transversal profile and an inward longitudinal curvature. The HOMO and LUMO electronic levels, as well as the band gap, are well described using power laws. The gap is predicted to become zero for n ≥ 34 (69 360 atoms). The atomic excess energy with respect to the ideal graphene sheet goes to zero following the log(Nat)/Nat law, which is well described through the continuum elastic theory applied to graphene; the limits for the adopted model are briefly outlined. Compared to larger fullerenes of the series, C60 shows unique features with respect to all the considered properties; C240 presents minor structural and energetic peculiarities, too.

The capabilities of the CRYSTAL14 program are presented, and the improvements made with respect to the previous CRYSTAL09 version discussed. CRYSTAL14 is an ab initio code that uses a Gaussian-type basis set: both pseudopotential and all-electron strategies are permitted; the latter is not much more expensive than the former up to the first-second transition metal rows of the periodic table. A variety of density functionals is available, including as an extreme case Hartree–Fock; hybrids of various nature (global, range-separated, double) can be used. In particular, a very efficient implementation of global hybrids, such as popular B3LYP and PBE0 prescriptions, allows for such calculations to be performed at relatively low computational cost. The program can treat on the same grounds zero-dimensional (molecules), one-dimensional (polymers), two-dimensional (slabs), as well as three-dimensional (3D; crystals) systems. No spurious 3D periodicity is required for low-dimensional systems as happens when plane-waves are used as a basis set. Symmetry is fully exploited at all steps of the calculation; this permits, for example, to investigate nanotubes of increasing radius at a nearly constant cost (better than linear scaling!) or to perform self-consistent-field (SCF) calculations on fullerenes as large as (10,10), with 6000 atoms, 84,000 atomic orbitals, and 20 SCF cycles, on a single core in one day. Three versions of the code exist, serial, parallel, and massive-parallel. In the second one, the most relevant matrices are duplicated, whereas in the third one the matrices in reciprocal space are distributed for diagonalization. All the relevant vectors are now dynamically allocated and deallocated after use, making CRYSTAL14 much more agile than the previous version, in which they were statically allocated.The program now fits more easily in low-memory machines (as many supercomputers nowadays are). CRYSTAL14 can be used on parallel machines up to a high number of cores

Raman spectroscopy is a standard and powerful investigation technique for minerals, and garnet is one of the most observed and visible minerals, undoubtfully important both as a witness of our planet’s evolution and as a main component in many high-tech applications. This paper presents the Raman spectrum of grossular, the calcium–aluminium end-member of garnets (Ca3Al2Si3O12), as computed by using an ab initio quantum-mechanical approach, an all-electron Gaussian-type basis set and the hybrid B3LYP functional. The wavenumbers of the 25 Raman active modes are in excellent agreement with the available experimental measurements, with the mean absolute difference being between 5 and 8 cm1. The apparent disagreement between a few experimental vs calculated data can be easily justified through the analysis of the corresponding calculated peak intensities, which is very low in all of these cases. The intensities of the Raman active modes of grossular were calculated here for the first time, thanks to a recent implementation by some of the present authors that allow for accurate predictions of the Raman spectra of minerals. To the authors’ knowledge, there are no tabulated data sets for Raman intensities of grossular, although qualitative information can be extracted from the published spectra. This study can then be considered as an accurate reference data set for grossular, other than a clear evidence that quantum-mechanical simulation is an actual tool to predict spectroscopic properties of minerals.

Use of symmetry can dramatically reduce the computational cost (running time and memory allocation) of Self-Consistent-Field ab initio calculations for molecular and crystalline systems. Crucial for running time is symmetry exploitation in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the SACO (Symmetry Adapted Crystalline Orbital) basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. Quantitative examples, referring to the implementation in the Crystal code, are given for high symmetry families of compounds such as carbon fullerenes and nanotubes.

We present an accurate ab initio study of the structure and surface energy at 0 K of the (010), (101), (111), (001), (110), (120), and (021) faces of forsterite (Mg2SiO4) using the hybrid Hartree–Fock/density functional B3LYP Hamiltonian and a localized all-electron Gaussian-type basis set. According to the surface energy values, the stability order of the forsterite faces was found to be (010) < (120) < (001) < (101) < (111) < (021) < (110). Then, the equilibrium shape of forsterite was drawn and compared with the previous ones obtained at an empirical level. Our results were combined with experimental evidence to develop some considerations about the shape and genesis of olivine included in diamond. They provide crucial information on the diamond formation mechanism with respect to its guest inclusions, a topic that is still under strong debate in the scientific community. In particular, we discuss the peculiar crystal morphology of olivine included in diamond, and we demonstrate that it cannot be considered as evidence of syngenesis (i.e., inclusion and host diamond formed at the same time). Furthermore, if the morphology of olivine is modified during its encapsulation in diamond but it does not show a preferential orientation with respect to diamond, we can state that (i) the bulk of olivine is protogenetic (i.e., a piece of previously formed olivine is encapsulated by the host diamond), whereas (ii) its shape is syngenetic, that is, the morphology is rearranged during the encapsulation.

We carried out a hospital-based case-control study to assess the association of both the daily amount and the duration of alcohol intake with the risk of developing non-cirrhotic chronic liver disease (chronic hepatitis) in 121 chronic hepatitis patients diagnosed by laparoscopy and liver biopsy, and in 242 matched 'controls' randomly selected from inpatients of the same hospital. Alcohol intake was quantified in all subjects using a standardized questionnaire administered by two doctors unaware of the aim of the study. The odds ratio (OR) for chronic hepatitis was estimated by conditional logistic regression and increased exponentially from 1.0 for non-drinkers to 11.4 for daily alcohol intake of 325 g or more. Considering duration of alcohol consumption from up to 10 to up to 30 years, the ORs for chronic hepatitis consistently decreased for the daily alcohol intake categories of 25-50 g (from 74.1 to 0.7 respectively), 75-100 g (from 149.7 to 0.7 respectively) and 125 g or more (from 212.0 to 1.8 respectively). Our results suggest the existence of a dose-dependent individual susceptibility to the damaging effect of alcohol on the liver

We carried out a hospital based case-control study involving 655 patients with chronic liver disease encompassing chronic hepatitis, asymptomatic liver cirrhosis and symptomatic liver cirrhosis and 655 pair-matched control individuals in order to estimate the dose-response relationship between alcohol consumption and the occurrence of chronic liver disease. Alcohol intake was measured by a questionnaire and expressed as Daily Alcohol Intake (DAI) during the patient life. DAI estimates from patient interviews were in good agreement with those obtained by interviewing a sample of relatives. We found an exponential positive association between DAI and the risk of chronic hepatitis and cirrhosis. However, consuming less than 100g of alcohol every day did not increase the risk of developing chronic liver disease. For asymptomatic cirrhosis the risk was lower than for chronic hepatitis, especially at high DAI, probably because high consumption carried a high probability of liver decompensation. For symptomatic cirrhosis, the risk function showed a similar pattern as for chronic hepatitis. Chronic hepatitis patients were 6-7 years younger than cirrhotics. Our results suggest that the evolution towards cirrhosis once a chronic liver damage has occurred is probably time-dependent, but not or minimally dependent on alcohol intake