Elastic and vibrational properties of alpha and beta-PbO

The structure, electronic and dynamic properties of the two layered alpha (litharge) and beta (massicot) phases of PbO have been studied by density functional methods. The role of London dispersion interactions as leading component of the total interaction energy between layers has been addressed by using the Grimme's approach, in which new parameters for Pb and O atoms have been developed. Both gradient corrected and hybrid functionals have been adopted using Gaussian-type basis sets of polarized triple zeta quality for O atoms and small core pseudo-potential for the Pb atoms. Basis set superposition error (BSSE) has been accounted for by the Boys-Bernardi correction to compute the interlayer separation. Cross check with calculations adopting plane waves that are BSSE free have also been performed for both structures and vibrational frequencies. With the new set of proposed Grimme's type parameters structures and dynamical parameters for both PbO phases are in good agreement with experimental data.Comment: 8 pages, 5 figure

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives

НАУЧНОЕ ОБОСНОВАНИЕ АЛГОРИТМА ПОДГОТОВКИ БОЛЬНЫХ К ПРОТЕЗИРОВАНИЮ ПОЛОСТИ РТА

The therapeutic and diagnostic activity is a collective work that is carried out jointly by specialists in different directions of dentistry and support units. The main goal of this type of activity is to improve the dental health by preventing dental diseases. It includes the treatment and rehabilitation using various ways of replacement of the lost integrity of the dentition and restoration of the teeth using a prosthetic. In order to do this, it is necessary to prepare the teeth and the pulp of the oral cavity for prosthetics. The sequence of preparatory activities includes a series of steps carried out in sequence: preventive, hygienic, therapeutic (including periodontal), surgical and orthopedic (including orthodontics). Each of these stages includes a series of manipulations, the sequence and number of which is determined by the individual dental status of each patient. The inspection and preparation of a comprehensive plan for the treatment involves a sequence of all these actions carried out by a team of experts in agreement with the patient, evidenced by the «informed consent» subscription. After the preparatory activities, it is possible to go to the final stage, that is to make a prosthetic appliance to the patient. The total duration of all phases of preparatory activities preceding the prosthetics depends on the complexity of the steps themselves, and is determined by the severity of the related dental diseases. The treatment of these diseases is the main part of the preparatory activities.Лечебно-диагностическая деятельность представляет собой коллективную работу, выполняемую совместно специалистами различных направлений стоматологии и вспомогательных подразделений. Основная ее цель - повышение стоматологического здоровья населения путем профилактики стоматологических заболеваний, включающих их лечение и реабилитацию различными способами замещения утраченной целостности зубных рядов и их восстановления с помощью ортопедических конструкций. Для этого необходимо провести мероприятия по подготовке зубов и мягких тканей полости рта к протезированию. Подготовительные мероприятия включают в себя серию последовательно проводимых этапов: профилактического, гигиенического, терапевтического, в том числе пародонтологичес-кого, хирургического, и ортопедического, в том числе ортодонтического. На каждом из указанных этапов прово дится серия манипуляций, количество и последовательность которых определяется индивидуальным стоматологическим статусом конкретного пациента. Осмотр и составление комплексного плана лечения предусматривает последовательность всех этих мероприятий выполняемых коллективом специалистов при согласовании их выполнения с пациентом, о чем свидетельствует заключение информированного согласия. Выполнение подготовительных мероприятий позволяет перейти к заключительному этапу - протезированию пациента. Совокупная продолжительность выполнения всех этапов подготовительных мероприятий, предшествующих протезированию полости рта, зависит от степени сложности выполнения самих этапов и определяется степенью тяжести сопутствующих стоматологических заболеваний, санация которых предполагает основную направленность подготовительных мероприятий

Analysis of Bonding between Conjugated Organic Molecules and Noble Metal Surfaces Using Orbital Overlap Populations

The electronic structure of metal−organic interfaces is of paramount importance for the properties of organic electronic and single-molecule devices. Here, we use so-called orbital overlap populations derived from slab-type band-structure calculations to analyze the covalent contribution to the bonding between an adsorbate layer and a metal. Using two prototypical molecules, the strong acceptor 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) on Ag(111) and the strong donor 1H,1′H-[4,4′]bipyridinylidene (HV0) on Au(111), we present overlap populations as particularly versatile tools for describing the metal−organic interaction. Going beyond traditional approaches, in which overlap populations are represented in an atomic orbital basis, we also explore the use of a molecular orbital basis to gain significant additional insight. On the basis of the derived quantities, it is possible to identify the parts of the molecules responsible for the bonding and to analyze which of the molecular orbitals and metal bands most strongly contribute to the interaction and where on the energy scale they interact in bonding or antibonding fashion

Random-phase approximation and its applications in computational chemistry and materials science

The random-phase approximation (RPA) as an approach for computing the electronic correlation energy is reviewed. After a brief account of its basic concept and historical development, the paper is devoted to the theoretical formulations of RPA, and its applications to realistic systems. With several illustrating applications, we discuss the implications of RPA for computational chemistry and materials science. The computational cost of RPA is also addressed which is critical for its widespread use in future applications. In addition, current correction schemes going beyond RPA and directions of further development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012

Transcriptome-scale similarities between mouse and human skeletal muscles with normal and myopathic phenotypes

BACKGROUND: Mouse and human skeletal muscle transcriptome profiles vary by muscle type, raising the question of which mouse muscle groups have the greatest molecular similarities to human skeletal muscle. METHODS: Orthologous (whole, sub-) transcriptome profiles were compared among four mouse-human transcriptome datasets: (M) six muscle groups obtained from three mouse strains (wildtype, mdx, mdx(5cv)); (H1) biopsied human quadriceps from controls and Duchenne muscular dystrophy patients; (H2) four different control human muscle types obtained at autopsy; and (H3) 12 different control human tissues (ten non-muscle). RESULTS: Of the six mouse muscles examined, mouse soleus bore the greatest molecular similarities to human skeletal muscles, independent of the latters' anatomic location/muscle type, disease state, age and sampling method (autopsy versus biopsy). Significant similarity to any one mouse muscle group was not observed for non-muscle human tissues (dataset H3), indicating this finding to be muscle specific. CONCLUSION: This observation may be partly explained by the higher type I fiber content of soleus relative to the other mouse muscles sampled

Roadmap on Machine learning in electronic structure

AbstractIn recent years, we have been witnessing a paradigm shift in computational materials science. In fact, traditional methods, mostly developed in the second half of the XXth century, are being complemented, extended, and sometimes even completely replaced by faster, simpler, and often more accurate approaches. The new approaches, that we collectively label by machine learning, have their origins in the fields of informatics and artificial intelligence, but are making rapid inroads in all other branches of science. With this in mind, this Roadmap article, consisting of multiple contributions from experts across the field, discusses the use of machine learning in materials science, and share perspectives on current and future challenges in problems as diverse as the prediction of materials properties, the construction of force-fields, the development of exchange correlation functionals for density-functional theory, the solution of the many-body problem, and more. In spite of the already numerous and exciting success stories, we are just at the beginning of a long path that will reshape materials science for the many challenges of the XXIth century

Resolution-of-identity approach to Hartree-Fock, hybrid density functionals, RPA, MP2, and \textit{GW} with numeric atom-centered orbital basis functions

Efficient implementations of electronic structure methods are essential for first-principles modeling of molecules and solids. We here present a particularly efficient common framework for methods beyond semilocal density-functional theory, including Hartree-Fock (HF), hybrid density functionals, random-phase approximation (RPA), second-order M{\o}ller-Plesset perturbation theory (MP2), and the $GW$ method. This computational framework allows us to use compact and accurate numeric atom-centered orbitals (popular in many implementations of semilocal density-functional theory) as basis functions. The essence of our framework is to employ the "resolution of identity (RI)" technique to facilitate the treatment of both the two-electron Coulomb repulsion integrals (required in all these approaches) as well as the linear density-response function (required for RPA and $GW$). This is possible because these quantities can be expressed in terms of products of single-particle basis functions, which can in turn be expanded in a set of auxiliary basis functions (ABFs). The construction of ABFs lies at the heart of the RI technique, and here we propose a simple prescription for constructing the ABFs which can be applied regardless of whether the underlying radial functions have a specific analytical shape (e.g., Gaussian) or are numerically tabulated. We demonstrate the accuracy of our RI implementation for Gaussian and NAO basis functions, as well as the convergence behavior of our NAO basis sets for the above-mentioned methods. Benchmark results are presented for the ionization energies of 50 selected atoms and molecules from the G2 ion test set as obtained with $GW$ and MP2 self-energy methods, and the G2-I atomization energies as well as the S22 molecular interaction energies as obtained with the RPA method.Comment: 58 pages, 15 figures, and 7 table

Synthesis and characterization of triangulene

Triangulene, the smallest triplet-ground-state polybenzenoid (also known as Clar's hydrocarbon), has been an enigmatic molecule ever since its existence was first hypothesized1. Despite containing an even number of carbons (22, in six fused benzene rings), it is not possible to draw Kekulé-style resonant structures for the whole molecule: any attempt results in two unpaired valence electrons2. Synthesis and characterization of unsubstituted triangulene has not been achieved because of its extreme reactivity1, although the addition of substituents has allowed the stabilization and synthesis of the triangulene core3, 4 and verification of the triplet ground state via electron paramagnetic resonance measurements5. Here we show the on-surface generation of unsubstituted triangulene that consists of six fused benzene rings. The tip of a combined scanning tunnelling and atomic force microscope (STM/AFM) was used to dehydrogenate precursor molecules. STM measurements in combination with density functional theory (DFT) calculations confirmed that triangulene keeps its free-molecule properties on the surface, whereas AFM measurements resolved its planar, threefold symmetric molecular structure. The unique topology of such non-Kekulé hydrocarbons results in open-shell π-conjugated graphene fragments6 that give rise to high-spin ground states, potentially useful in organic spintronic devices7, 8. Our generation method renders manifold experiments possible to investigate triangulene and related open-shell fragments at the single-molecule level