Numerical simulation of the stress-strain state of the dental system

We present mathematical models, computational algorithms and software, which can be used for prediction of results of prosthetic treatment. More interest issue is biomechanics of the periodontal complex because any prosthesis is accompanied by a risk of overloading the supporting elements. Such risk can be avoided by the proper load distribution and prediction of stresses that occur during the use of dentures. We developed the mathematical model of the periodontal complex and its software implementation. This model is based on linear elasticity theory and allows to calculate the stress and strain fields in periodontal ligament and jawbone. The input parameters for the developed model can be divided into two groups. The first group of parameters describes the mechanical properties of periodontal ligament, teeth and jawbone (for example, elasticity of periodontal ligament etc.). The second group characterized the geometric properties of objects: the size of the teeth, their spatial coordinates, the size of periodontal ligament etc. The mechanical properties are the same for almost all, but the input of geometrical data is complicated because of their individual characteristics. In this connection, we develop algorithms and software for processing of images obtained by computed tomography (CT) scanner and for constructing individual digital model of the tooth-periodontal ligament-jawbone system of the patient. Integration of models and algorithms described allows to carry out biomechanical analysis on three-dimensional digital model and to select prosthesis design.Comment: 19 pages, 9 figure

OpenFermion: The Electronic Structure Package for Quantum Computers

Quantum simulation of chemistry and materials is predicted to be an important application for both near-term and fault-tolerant quantum devices. However, at present, developing and studying algorithms for these problems can be difficult due to the prohibitive amount of domain knowledge required in both the area of chemistry and quantum algorithms. To help bridge this gap and open the field to more researchers, we have developed the OpenFermion software package (www.openfermion.org). OpenFermion is an open-source software library written largely in Python under an Apache 2.0 license, aimed at enabling the simulation of fermionic models and quantum chemistry problems on quantum hardware. Beginning with an interface to common electronic structure packages, it simplifies the translation between a molecular specification and a quantum circuit for solving or studying the electronic structure problem on a quantum computer, minimizing the amount of domain expertise required to enter the field. The package is designed to be extensible and robust, maintaining high software standards in documentation and testing. This release paper outlines the key motivations behind design choices in OpenFermion and discusses some basic OpenFermion functionality which we believe will aid the community in the development of better quantum algorithms and tools for this exciting area of research.Comment: 22 page

nbodykit: an open-source, massively parallel toolkit for large-scale structure

We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface (MPI), we provide parallel implementations of many commonly used algorithms in LSS. nbodykit is both an interactive and scalable piece of scientific software, performing well in a supercomputing environment while still taking advantage of the interactive tools provided by the Python ecosystem. Existing functionality includes estimators of the power spectrum, 2 and 3-point correlation functions, a Friends-of-Friends grouping algorithm, mock catalog creation via the halo occupation distribution technique, and approximate N-body simulations via the FastPM scheme. The package also provides a set of distributed data containers, insulated from the algorithms themselves, that enable nbodykit to provide a unified treatment of both simulation and observational data sets. nbodykit can be easily deployed in a high performance computing environment, overcoming some of the traditional difficulties of using Python on supercomputers. We provide performance benchmarks illustrating the scalability of the software. The modular, component-based approach of nbodykit allows researchers to easily build complex applications using its tools. The package is extensively documented at http://nbodykit.readthedocs.io, which also includes an interactive set of example recipes for new users to explore. As open-source software, we hope nbodykit provides a common framework for the community to use and develop in confronting the analysis challenges of future LSS surveys.Comment: 18 pages, 7 figures. Feedback very welcome. Code available at https://github.com/bccp/nbodykit and for documentation, see http://nbodykit.readthedocs.i

Extending scientific computing system with structural quantum programming capabilities

We present a basic high-level structures used for developing quantum programming languages. The presented structures are commonly used in many existing quantum programming languages and we use quantum pseudo-code based on QCL quantum programming language to describe them. We also present the implementation of introduced structures in GNU Octave language for scientific computing. Procedures used in the implementation are available as a package quantum-octave, providing a library of functions, which facilitates the simulation of quantum computing. This package allows also to incorporate high-level programming concepts into the simulation in GNU Octave and Matlab. As such it connects features unique for high-level quantum programming languages, with the full palette of efficient computational routines commonly available in modern scientific computing systems. To present the major features of the described package we provide the implementation of selected quantum algorithms. We also show how quantum errors can be taken into account during the simulation of quantum algorithms using quantum-octave package. This is possible thanks to the ability to operate on density matrices

Quantum walks: a comprehensive review

Quantum walks, the quantum mechanical counterpart of classical random walks, is an advanced tool for building quantum algorithms that has been recently shown to constitute a universal model of quantum computation. Quantum walks is now a solid field of research of quantum computation full of exciting open problems for physicists, computer scientists, mathematicians and engineers. In this paper we review theoretical advances on the foundations of both discrete- and continuous-time quantum walks, together with the role that randomness plays in quantum walks, the connections between the mathematical models of coined discrete quantum walks and continuous quantum walks, the quantumness of quantum walks, a summary of papers published on discrete quantum walks and entanglement as well as a succinct review of experimental proposals and realizations of discrete-time quantum walks. Furthermore, we have reviewed several algorithms based on both discrete- and continuous-time quantum walks as well as a most important result: the computational universality of both continuous- and discrete- time quantum walks.Comment: Paper accepted for publication in Quantum Information Processing Journa

The ESCAPE project : Energy-efficient Scalable Algorithms for Weather Prediction at Exascale

In the simulation of complex multi-scale flows arising in weather and climate modelling, one of the biggest challenges is to satisfy strict service requirements in terms of time to solution and to satisfy budgetary constraints in terms of energy to solution, without compromising the accuracy and stability of the application. These simulations require algorithms that minimise the energy footprint along with the time required to produce a solution, maintain the physically required level of accuracy, are numerically stable, and are resilient in case of hardware failure. The European Centre for Medium-Range Weather Forecasts (ECMWF) led the ESCAPE (Energy-efficient Scalable Algorithms for Weather Prediction at Exascale) project, funded by Horizon 2020 (H2020) under the FET-HPC (Future and Emerging Technologies in High Performance Computing) initiative. The goal of ESCAPE was to develop a sustainable strategy to evolve weather and climate prediction models to next-generation computing technologies. The project partners incorporate the expertise of leading European regional forecasting consortia, university research, experienced high-performance computing centres, and hardware vendors. This paper presents an overview of the ESCAPE strategy: (i) identify domain-specific key algorithmic motifs in weather prediction and climate models (which we term Weather & Climate Dwarfs), (ii) categorise them in terms of computational and communication patterns while (iii) adapting them to different hardware architectures with alternative programming models, (iv) analyse the challenges in optimising, and (v) find alternative algorithms for the same scheme. The participating weather prediction models are the following: IFS (Integrated Forecasting System); ALARO, a combination of AROME (Application de la Recherche a l'Operationnel a Meso-Echelle) and ALADIN (Aire Limitee Adaptation Dynamique Developpement International); and COSMO-EULAG, a combination of COSMO (Consortium for Small-scale Modeling) and EULAG (Eulerian and semi-Lagrangian fluid solver). For many of the weather and climate dwarfs ESCAPE provides prototype implementations on different hardware architectures (mainly Intel Skylake CPUs, NVIDIA GPUs, Intel Xeon Phi, Optalysys optical processor) with different programming models. The spectral transform dwarf represents a detailed example of the co-design cycle of an ESCAPE dwarf. The dwarf concept has proven to be extremely useful for the rapid prototyping of alternative algorithms and their interaction with hardware; e.g. the use of a domain-specific language (DSL). Manual adaptations have led to substantial accelerations of key algorithms in numerical weather prediction (NWP) but are not a general recipe for the performance portability of complex NWP models. Existing DSLs are found to require further evolution but are promising tools for achieving the latter. Measurements of energy and time to solution suggest that a future focus needs to be on exploiting the simultaneous use of all available resources in hybrid CPU-GPU arrangements

A Multiresolution Census Algorithm for Calculating Vortex Statistics in Turbulent Flows

The fundamental equations that model turbulent flow do not provide much insight into the size and shape of observed turbulent structures. We investigate the efficient and accurate representation of structures in two-dimensional turbulence by applying statistical models directly to the simulated vorticity field. Rather than extract the coherent portion of the image from the background variation, as in the classical signal-plus-noise model, we present a model for individual vortices using the non-decimated discrete wavelet transform. A template image, supplied by the user, provides the features to be extracted from the vorticity field. By transforming the vortex template into the wavelet domain, specific characteristics present in the template, such as size and symmetry, are broken down into components associated with spatial frequencies. Multivariate multiple linear regression is used to fit the vortex template to the vorticity field in the wavelet domain. Since all levels of the template decomposition may be used to model each level in the field decomposition, the resulting model need not be identical to the template. Application to a vortex census algorithm that records quantities of interest (such as size, peak amplitude, circulation, etc.) as the vorticity field evolves is given. The multiresolution census algorithm extracts coherent structures of all shapes and sizes in simulated vorticity fields and is able to reproduce known physical scaling laws when processing a set of voriticity fields that evolve over time