Michigan State University

LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different materials, that it runs on any platform from a single CPU core to the largest supercomputers with accelerators, and that it gives users control over simulation details, either via the input script or by adding code for new interatomic potentials, constraints, diagnostics, or other features needed for their models. As a result, hundreds of people have contributed new capabilities to LAMMPS and it has grown from fifty thousand lines of code in 2004 to a million lines today. In this paper several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers. We also highlight some capabilities recently added to the code which were enabled by this flexibility, including dynamic load balancing, on-the-fly visualization, magnetic spin dynamics models, and quantum-accuracy machine learning interatomic potentials. Program Title: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) CPC Library link to program files: https://doi.org/10.17632/cxbxs9btsv.1 Developer's repository link: https://github.com/lammps/lammps Licensing provisions: GPLv2 Programming language: C++, Python, C, Fortran Supplementary material: https://www.lammps.org Nature of problem: Many science applications in physics, chemistry, materials science, and related fields require parallel, scalable, and efficient generation of long, stable classical particle dynamics trajectories. Within this common problem definition, there lies a great diversity of use cases, distinguished by different particle interaction models, external constraints, as well as timescales and lengthscales ranging from atomic to mesoscale to macroscopic. Solution method: The LAMMPS code uses parallel spatial decomposition, distributed neighbor lists, and parallel FFTs for long-range Coulombic interactions [1]. The time integration algorithm is based on the Størmer-Verlet symplectic integrator [2], which provides better stability than higher-order non-symplectic methods. In addition, LAMMPS supports a wide range of interatomic potentials, constraints, diagnostics, software interfaces, and pre- and post-processing features. Additional comments including restrictions and unusual features: This paper serves as the definitive reference for the LAMMPS code. S. Plimpton, Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117 (1995) 1–19. L. Verlet, Computer experiments on classical fluids: I. Thermodynamical properties of Lennard–Jones molecules, Phys. Rev. 159 (1967) 98–103.

Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

Most current speech recognition systems use hidden Markov models (HMMs) to deal with the temporal variability of speech and Gaussian mixture models (GMMs) to determine how well each state of each HMM fits a frame or a short window of frames of coefficients that represents the acoustic input. An alternative way to evaluate the fit is to use a feed-forward neural network that takes several frames of coefficients as input and produces posterior probabilities over HMM states as output. Deep neural networks (DNNs) that have many hidden layers and are trained using new methods have been shown to outperform GMMs on a variety of speech recognition benchmarks, sometimes by a large margin. This article provides an overview of this progress and represents the shared views of four research groups that have had recent successes in using DNNs for acoustic modeling in speech recognition.

Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010

Free Radicals in Biology and Medicine

The new edition of this well-established book is thoroughly revised and gives a comprehensive account of the role of free radicals, other reactive species (RS), and antioxidants in life, health, and disease. Chapter 1 reviews how oxygen (O2) is used by living organisms, why it can be toxic, and introduces the concept of oxygen radicals and other RS; their chemistry is detailed in Chapter 2, especially for superoxide, hydroxyl radical (including Fenton chemistry), peroxynitrite, nitric oxide, ozone, and singlet O2, with emphasis on their redox properties. Subsequent chapters detail what antioxidants can be made in vivo (e.g. superoxide dismutases, peroxiredoxins) and which can come from diet (e.g. vitamins E and C, carotenoids, and polyphenols such as the flavonoids) and how they work in vivo. The role of RS in cell proliferation, senescence, and death (e.g. by apoptosis, necrosis, or intermediate forms) is presented. Methods for measuring RS are described in detail, including electron paramagnetic resonance and biomarker determination. Useful roles for RS (e.g. cell signalling, phagocyte action), as well as systems in which they cause particular problems (e.g. premature babies, the eye, the ear) are presented. Acute and chronic inflammation are used to illustrate both roles There is a comprehensive description of the role of RS in human diseases, from cancer to heart disease to dementia, in the ageing process, and in the toxicity of many agents, from ethanol to carbon tetrachloride to paraquat. Therapeutic agents active against RS are reviewed in detail, including NADPH oxidase inhibitors, N-acetylcysteine, and Ebselen.

Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010

Review of Particle Physics

The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 2,873 new measurements from 758 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 118 reviews are many that are new or heavily revised, including a new review on Neutrinos in Cosmology.Starting with this edition, the Review is divided into two volumes. Volume 1 includes the Summary Tables and all review articles. Volume 2 consists of the Particle Listings. Review articles that were previously part of the Listings are now included in volume 1.The complete Review (both volumes) is published online on the website of the Particle Data Group (http://pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is also available.The 2018 edition of the Review of Particle Physics should be cited as: M. Tanabashi et al. (Particle Data Group), Phys. Rev. D 98, 030001 (2018).

Review of Particle Physics

Review of Particle Physics

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 2,143 new measurements from 709 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on Machine Learning, and one on Spectroscopy of Light Meson Resonances. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 97 review articles. Volume 2 consists of the Particle Listings and contains also 23 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print, as a web version optimized for use on phones, and as an Android app.

Review of Particle Physics

This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2658 new measurements from 644 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 112 reviews are many that are new or heavily revised including those on Heavy-Quark and Soft-Collinear Effective Theory, Neutrino Cross Section Measurements, Monte Carlo Event Generators, Lattice QCD, Heavy Quarkonium Spectroscopy, Top Quark, Dark Matter, ${V}_{\mathit{cb}}$ ${V}_{\mathit{ub}}$, Quantum Chromodynamics, High-Energy Collider Parameters, Astrophysical Constants, Cosmological Parameters, and Dark Matter.A booklet is available containing the Summary Tables and abbreviated versions of some of the other sections of this full Review. All tables, listings, and reviews (and errata) are also available on the Particle Data Group website: http://pdg.lbl.gov/.The 2012 edition of Review of Particle Physics is published for the Particle Data Group as article 010001 in volume 86 of Physical Review D.This edition should be cited as: J. Beringer et al. (Particle Data Group), Phys. Rev. D 86, 010001 (2012).

Review of Particle Physics

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,324 new measurements from 878 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on High Energy Soft QCD and Diffraction and one on the Determination of CKM Angles from B Hadrons. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 98 review articles. Volume 2 consists of the Particle Listings and contains also 22 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print and as a web version optimized for use on phones as well as an Android app.

Review of Particle Physics

The DSSAT cropping system model

<i>The Physics of Rubber Elasticity</i>

1. General Physical Properties of Rubber 2. Internal Energy and Entropy Changes on Deformation 3. The Elasticity of Long-Chain Molecules 4. The Elasticity of a Molecular Network 5Ex5 Experimental Examination of the Statistical Theory 6. Non-Gaussian Chain Statistics and Network Theory 7. Swelling Phenomena 8. Cross-linking and Modulus 9. Photoelastic Properties of Rubbers 10. The General Strain: Phenomenological Theory 11. Alternative Forms of Strain-Energy Function 12. Large-Deformation Theory: Shear and Torsion 13. Thermodynamic Analysis of Gaussian Network

Review of Particle Physics

The summarizes much of particle physics and cosmology. Using data from previous editions, plus 2,717 new measurements from 869 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Most of the 120 reviews are updated, including many that are heavily revised. The is divided into two volumes. Volume 1 includes the Summary Tables and 97 review articles. Volume 2 consists of the Particle Listings and contains also 23 reviews that address specific aspects of the data presented in the Listings. The complete (both volumes) is published online on the website of the Particle Data Group () and in a journal. Volume 1 is available in print as the . A with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print, as a web version optimized for use on phones, and as an Android app. The 2024 edition of the Review of Particle Physics should be cited as: S. Navas et al. (Particle Data Group), Phys. Rev. D 110, 030001 (2024) © 2024 2024

Free radicals in biology and medicine

Cyclooxygenases: Structural, Cellular, and Molecular Biology

The prostaglandin endoperoxide H synthases-1 and 2 (PGHS-1 and PGHS-2; also cyclooxygenases-1 and 2, COX-1 and COX-2) catalyze the committed step in prostaglandin synthesis. PGHS-1 and 2 are of particular interest because they are the major targets of nonsteroidal anti-inflammatory drugs (NSAIDs) including aspirin, ibuprofen, and the new COX-2 inhibitors. Inhibition of the PGHSs with NSAIDs acutely reduces inflammation, pain, and fever, and long-term use of these drugs reduces fatal thrombotic events, as well as the development of colon cancer and Alzheimer's disease. In this review, we examine how the structures of these enzymes relate mechanistically to cyclooxygenase and peroxidase catalysis, and how differences in the structure of PGHS-2 confer on this isozyme differential sensitivity to COX-2 inhibitors. We further examine the evidence for independent signaling by PGHS-1 and PGHS-2, and the complex mechanisms for regulation of PGHS-2 gene expression.

New parton distributions for collider physics

We extract new parton distribution functions (PDFs) of the proton by global analysis of hard scattering data in the general-mass framework of perturbative quantum chromodynamics. Our analysis includes new theoretical developments together with the most recent collider data from deep-inelastic scattering, vector boson production, and single-inclusive jet production. Because of the difficulty in fitting both the D0 Run-II $W$ lepton asymmetry data and some fixed-target DIS data, we present two families of PDFs, CT10 and CT10W, without and with these high-luminosity $W$ lepton asymmetry data included in the global analysis. With both sets of PDFs, we study theoretical predictions and uncertainties for a diverse selection of processes at the Fermilab Tevatron and the CERN Large Hadron Collider.

VAIM-CFF: a variational autoencoder inverse mapper solution to Compton form factor extraction from deeply virtual exclusive reactions

Abstract We develop a new methodology for extracting Compton form factors (CFFs) from deeply virtual exclusive reactions such as the unpolarized DVCS cross section using a specialized inverse problem solver, a variational autoencoder inverse mapper (VAIM). The VAIM-CFF framework not only allows us access to a fitted solution set possibly containing multiple solutions in the extraction of all 8 CFFs from a single cross section measurement, but also accesses the lost information contained in the forward mapping from CFFs to cross section. We investigate various assumptions and their effects on the predicted CFFs such as cross section organization, number of extracted CFFs, use of uncertainty quantification technique, and inclusion of prior physics information. We then use dimensionality reduction techniques such as principal component analysis to visualize the missing physics information tracked in the latent space of the VAIM framework. Through re-framing the extraction of CFFs as an inverse problem, we gain access to fundamental properties of the problem not comprehensible in standard fitting methodologies: exploring the limits of the information encoded in deeply virtual exclusive experiments.

Exploring physics teacher identity: Pathways toward equitable instruction among teachers

Physics teacher identity encompasses teachers’ beliefs and views toward being a physics teacher. Physics teacher identity is influenced by teachers’ perspectives on physics teaching and learning. Previous studies on teacher identity in general suggest that the construct is complex and malleable. Studies further suggest that it influences instructional methods, student engagement, and classroom environment. However, within physics education, there has yet to be an examination of how physics teacher identity influences “equitable” teaching approaches. This qualitative study sought to identify various dimensions of physics teacher identity and its implications for physics education research. We interviewed secondary and postsecondary physics teachers ( n = 1 0 ) from different regions of the country with varying years of experience. We searched for consistent themes regarding the influence of physics teacher identity on equitable instruction using a conceptual framework that examines conceptions of self, others, knowledge, and pedagogy. Findings showed that teachers held a variety of conceptions of self and others, while many struggled to describe their conceptions of knowledge and pedagogy. Our findings are significant for physics teachers, educators, and researchers aiming to employ equitable teaching strategies. Ultimately, this study fostered a deeper understanding of the relationship between physics teacher identity and equitable instruction.