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Motif statistics and spike correlations in neuronal networks

BMC Neuroscience 2012年第1期13卷 1-2页

作者： Yu Hu Eric Shea-Brown James Trousdale Krĕsimir Josić Department of Applied Mathematics University of Washington Seattle WA 98195 USA Program in Neurobiology and Behavior University of Washington Seattle WA 98195 USA Department of Mathematics University of Houston Houston TX 77204-5001 USA Department of Biology and Biochemistry University of Houston Houston TX 77204-5001 USA

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Origin of the Energy Barrier to Chemical Reactions of O2 on Al(111): Evidence for Charge Transfer, Not Spin Selection

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Physical Review Letters 2012年第19期109卷 198303-198303页

作者： Florian Libisch Chen Huang Peilin Liao Michele Pavone Emily A. Carter Departments of Mechanical and Aerospace Engineering and Chemistry Program in Applied and Computational Mathematics and Andlinger Center for Energy and the Environment Princeton University Princeton New Jersey 08544 USA Theoretical Division Los Alamos National Laboratory New Mexico 87544 USA

Dissociative adsorption of molecular oxygen on the Al(111) surface exhibits mechanistic complexity that remains surprisingly poorly understood in terms of the underlying physics. Experiments clearly indicate substantial energy barriers and a mysteriously large number of adsorbed single oxygen atoms instead of pairs. Conventional first principles quantum mechanics (density functional theory) predicts no energy barrier at all; instead, spin selection rules have been invoked to explain the barrier. In this Letter, we show that correct barriers arise naturally when embedded correlated electron wave functions are used to capture the physics of the interaction of O2 with the metal surface. The barrier originates from an abrupt charge transfer (from metal to oxygen), which is properly treated within correlated wave function theory but not within conventional density functional theory. Our potential energy surfaces also identify oxygen atom abstraction as the dominant reaction pathway at low incident energies, consistent with measurements, and show that charge transfer occurs in a stepwise fashion.

关键词： CHEMICAL reactions CHARGE transfer ADSORPTION SURFACE chemistry WAVE mechanics QUANTUM theory

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Spectral Dynamics of Spatially Incoherent Modulation Instability

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Physical Review Letters 2012年第26期108卷 263902-263902页

作者： Can Sun Laura Waller Dmitry V. Dylov Jason W. Fleischer Department of Electrical Engineering Princeton University Princeton New Jersey 08544 USA General Electric Global Research Center Niskayuna New York 12309 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

To date, all experiments in nonlinear statistical optics have relied on beams whose transverse spatial statistics were Gaussian. Here, we present a new technique to generalize these studies by using a spatial light modulator to create spatially incoherent beams with arbitrary spectral distributions. As a specific example of the new dynamics possible, we consider the spatial modulation instability of a partially coherent beam. We show that, for statistical beams of uniform intensity and equal correlation length, the underlying spectral shape determines the threshold and visibility of intensity modulations as well as the spectral profile of the growing sidebands. We demonstrate the behavior using statistical light, but the results will hold for any wave-kinetic system, such as plasma, ultracold gases, and turbulent acoustic waves.

关键词： NONLINEAR optics MODULATION theory SPECTRUM analysis BEAM optics GAUSSIAN processes LIGHT modulators SOUND waves COLD gases

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Optical shock and blow-up of ultrashort pulses in transparent media

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Physical Review A 2012年第3期86卷 033806-033806页

作者： P. Whalen J. V. Moloney A. C. Newell K. Newell M. Kolesik Program in Applied Mathematics University of Arizona Tucson AZ 85721-0089 USA Arizona Center for Mathematical Sciences University of Arizona Tucson AZ 85721-0089 USA Department of Mathematics University of Arizona Tucson AZ 85721-0089 USA College of Optical Sciences University of Arizona Tucson AZ 85721-0089 USA Department of Physics Constantine the Philosopher University Nitra 94974 Slovakia

Ultrashort pulses can exhibit two distinctive types of singularity: self-focusing collapse and self-steepening shock. We examine various ultrashort pulse propagation models and their relative effectiveness in explaining these phenomena. In particular, the modified Kadomtsev-Petviashvilli equation of type 1 (MKP1) is examined in some detail. We show that MKP1 is not simply a few-cycle pulse model but is valid in a more general broad spectrum setting. Furthermore, we emphasize that the dispersion of the MKP1 model can result in poor estimation of frequency-dependent phenomena, such as harmonic generation, which occur far away from the carrier frequency. Some of this loss of accuracy can be removed by using a more general MKP1 dispersion relation.

关键词： SHOCK waves BLOWING up (Algebraic geometry) ULTRASHORT laser pulses TRANSPARENCY (Optics) OPTICAL materials PARTIAL differential equations DISPERSION SECOND harmonic generation

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Efficient coarse simulation of a growing avascular tumor

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Physical Review E 2012年第3期85卷 031912-031912页

作者： Michail E. Kavousanakis Ping Liu Andreas G. Boudouvis John Lowengrub Ioannis G. Kevrekidis School of Chemical Engineering National Technical University of Athens 9 Heroon Polytechniou St. Zographos Athens GR-15780 Greece Department of Chemical and Biological Engineering Princeton University Princeton New Jersey 08544 USA Department of Mathematics University of California 103 MSTB Irvine California 92697 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

The subject of this work is the development and implementation of algorithms which accelerate the simulation of early stage tumor growth models. Among the different computational approaches used for the simulation of tumor progression, discrete stochastic models (e.g., cellular automata) have been widely used to describe processes occurring at the cell and subcell scales (e.g., cell-cell interactions and signaling processes). To describe macroscopic characteristics (e.g., morphology) of growing tumors, large numbers of interacting cells must be simulated. However, the high computational demands of stochastic models make the simulation of large-scale systems impractical. Alternatively, continuum models, which can describe behavior at the tumor scale, often rely on phenomenological assumptions in place of rigorous upscaling of microscopic models. This limits their predictive power. In this work, we circumvent the derivation of closed macroscopic equations for the growing cancer cell populations; instead, we construct, based on the so-called “equation-free” framework, a computational superstructure, which wraps around the individual-based cell-level simulator and accelerates the computations required for the study of the long-time behavior of systems involving many interacting cells. The microscopic model, e.g., a cellular automaton, which simulates the evolution of cancer cell populations, is executed for relatively short time intervals, at the end of which coarse-scale information is obtained. These coarse variables evolve on slower time scales than each individual cell in the population, enabling the application of forward projection schemes, which extrapolate their values at later times. This technique is referred to as coarse projective integration. Increasing the ratio of projection times to microscopic simulator execution times enhances the computational savings. Crucial accuracy issues arising for growing tumors with radial symmetry are addressed by applying th

关键词： SIMULATION methods & models TUMORS -- Growth MATHEMATICAL models CANCER invasiveness STOCHASTIC models COMPUTATIONAL biology BIONICS PHENOMENOLOGY

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Density-decomposed orbital-free density functional theory for covalently bonded molecules and materials

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Physical Review B 2012年第23期86卷 235109-235109页

作者： Junchao Xia Emily A. Carter Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544-5263 USA Program in Applied and Computational Mathematics and Andlinger Center for Energy and the Environment Princeton University Princeton New Jersey 08544-5263 USA

We propose a density decomposition scheme using a Wang-Govind-Carter- (WGC-) based kinetic energy density functional (KEDF) to accurately and efficiently simulate various covalently bonded molecules and materials within orbital-free (OF) density functional theory (DFT). By using a local, density-dependent scale function, the total density is decomposed into a highly localized density within covalent bond regions and a flattened delocalized density, with the former described by semilocal KEDFs and the latter treated by the WGC KEDF. The new model predicts reasonable equilibrium volumes, bulk moduli, and phase-ordering energies for various semiconductors compared to Kohn-Sham (KS) DFT benchmarks. The decomposition formalism greatly improves numerical stability and accuracy, while retaining computational speed compared to simply applying the original WGC KEDF to covalent materials. The surface energy of Si(100) and various diatomic molecule properties can be stably calculated and also agree well with KSDFT benchmarks. This linear-scaled, computationally efficient, density-partitioned, multi-KEDF scheme opens the door to large-scale simulations of molecules, semiconductors, and insulators with OFDFT.

关键词： PHYSICAL sciences research MOLECULES SEMICONDUCTORS BENCHMARKING (Management) CRYSTALS SURFACE energy COVALENT bonds (Chemistry)

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Improving parallel scalability for edge plasma transport simulations with neutral gas species

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Computational Science and Discovery 2012年第1期5卷

作者： McCourt, M. Rognlien, T.D. McInnes, L.C. Zhang, H. Center for Applied Mathematics 657 Rhodes Hall Cornell University Ithaca NY 14853 United States Fusion Energy Sciences Program Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550 United States Argonne National Laboratory Mathematics and Computer Science Division 9700 South Cass Avenue Argonne IL 60439 United States

Simulating the transport of multi-species plasma and neutral species in the edge region of a tokamak magnetic fusion energy device is computationally intensive and difficult due to coupling among various components, strong nonlinearities and a broad range of temporal scales. In addition to providing boundary conditions for the core plasma, such models aid in the understanding and control of the associated plasma/material-wall interactions, a topic that is essential for the development of a viable fusion power plant. The governing partial differential equations are discretized to form a large nonlinear system that typically must be evolved in time to obtain steady-state solutions. Fully implicit techniques using preconditioned Jacobian-free Newton-Krylov methods with parallel domain-based preconditioners are shown to be robust and efficient for the plasma components. Inclusion of neutral gas components, however, increases the condition number of the system to the point where improved parallel preconditioning is needed. Standard algebraic preconditioners that provide sufficient coupling throughout the global domain to handle the neutrals are not generally scalable. We present a new preconditioner, termed FieldSplit, which exploits the character of the neutral equations to improve the scalability of the combined plasma/neutral system. © 2012 IOP Publishing Ltd.

关键词： Scalability

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Density of States for a Specified Correlation Function and the Energy Landscape

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Physical Review Letters 2012年第8期108卷 080601-080601页

作者： C. J. Gommes Y. Jiao S. Torquato Department of Chemical Engineering University of Liège B-4000 Liège Belgium Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics and Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA

The degeneracy of two-phase disordered microstructures consistent with a specified correlation function is analyzed by mapping it to a ground-state degeneracy. We determine for the first time the associated density of states via a Monte Carlo algorithm. Our results are explained in terms of the roughness of an energy landscape, defined on a hypercubic configuration space. The use of a Hamming distance in this space enables us to define a roughness metric, which is calculated from the correlation function alone and related quantitatively to the structural degeneracy. This relation is validated for a wide variety of disordered structures.

关键词： ENERGY levels (Quantum mechanics) CORRELATION (Statistics) MICROSTRUCTURE GROUND state (Quantum mechanics) MONTE Carlo method CONFIGURATION space QUANTITATIVE research

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Proceedings of the 3rd IPLeiria's International Health Congress Abstracts

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BMC HEALTH SERVICES RESEARCH 2016年第3期16卷 111-242页

作者： [Anonymous] Health Sciences Research Unit: Nursing Collegue of College of Health Technology of Coimbra Coimbra Portugal Sisters Hospitallers of the Sacred Heart of Jesus Casa de Saúde Rainha Santa Isabel Coimbra Portugal Research Unit for Sport and Physical Activity Faculty of Sport Sciences and Physical Education University of Coimbra Coimbra Portugal Complementary Sciences- INESCC Coimbra Portugal CUF Hospitals Lisbon Portugal Breast Unit Champalimaud Clinical Center Lisbon Portugal Swiss Centre for Medical Simulation & Swiss Association of Simulation in Healthcare Basel Switzerland Basel University Hospital Basel Switzerland HELPO Association Cascais Portugal Centro de Linguística Universidade de Lisboa Lisboa Portugal Centro Superior de Estudios Universitarios La Salle Madrid Spain Universidade da Madeira Funchal Portugal Serviço de Saúde da Região Autónoma da Madeira E.P.E. Funchal Portugal Escola Superior de Enfermagem de Lisboa Lisboa Portugal Instituto Superior Miguel Torga Coimbra Portugal Centro de Investigação do Núcleo de Estudos e Intervenção Cognitivo Comportamental Universidade de Coimbra Coimbra Portugal Escola Superior de Saúde de Leiria & Unidade de Investigação em Saúde Instituto Politécnico de Leiria Leiria Portugal National School of Public Health & Centro de Investigação em Saúde Pública Universidade Nova de Lisboa Lisboa Portugal Agrarian Superior School Polytechnic Institute of Viseu Viseu Portugal Laboratory of Microbiology Department of Biological Sciences Faculty of Pharmacy University of Porto Porto Portugal Unit for Multidisciplinary Biomedical Research Institute of Biomedical Sciences Abel Salazar University of Porto Porto Portugal Agrupamento de Centros de Saúde (ACES) Baixo Mondego Figueira da Foz Portugal Universidade de Trás-os-Montes e Alto Douro Vila Real Portugal Centro de Salud La Paz Badajoz España Centro de Salud San Fernando Badajoz España Complejo Hospitalario Universitario de Badajoz Badajoz España Hospital Don Beni

S1 Health literacy and health education in adolescence Catarina Cardoso Tomás S2 The effect of a walking program on the quality of life and well-being of people with schizophrenia Emanuel Oliveira, D. Sousa, M. Uba-Chupel, G. Furtado, C. Rocha, A. Teixeira, P. Ferreira S3 Diagnosis and innovative treatments - the way to a better medical practice Celeste Alves S4 Simulation-based learning and how it is a high contribution Stefan Gisin S5 Formative research about acceptability, utilization and promotion of a home fortification programme with micronutrient powders (MNP) in the Autonomous Region of Príncipe, São Tomé and Príncipe Elisabete Catarino, Nelma Carvalho, Tiago Coucelo, Luís Bonfim, Carina Silva S6 Safety culture of the patient: a reflexion about the therapeutic approach on the patient with vocal pathology Débora Franco S7 About wine, fortune cookies and patient experience Jesús Alcoba González O1 The psychological impact on the emergency crews after the disaster event on February 20, 2010 Helena G. Jardim, Rita Silva O2 Musculoskeletal disorders in midwives Cristina L. Baixinho, Mª Helena Presado, Mª Fátima Marques, Mário E. Cardoso O3 Negative childhood experiences and fears of compassion: Implications for psychological difficulties in adolescence Marina Cunha, Joana Mendes, Ana Xavier, Ana Galhardo, Margarida Couto O4 Optimal age to give the first dose of measles vaccine in Portugal João G. Frade, Carla Nunes, João R. Mesquita, Maria S. Nascimento, Guilherme Gonçalves O5 Functional assessment of elderly in primary care Conceição Castro, Alice Mártires, Mª João Monteiro, Conceição Rainho O6 Smoking and coronary events in a population of Spanish health-care centre: An observational study Francisco P. Caballero, Fatima M. Monago, Jose T. Guerrero, Rocio M. Monago, Africa P. Trigo, Milagros L. Gutierrez, Gemma M. Milanés, Mercedes G. Reina, Ana G. Villanueva, Ana S. Piñero, Isabel R. Aliseda, Francisco B. Ramirez O7 Prevalence of musculoskeletal injuries in Por

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Singularities of quantum control landscapes

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Physical Review A 2012年第1期86卷 013405-013405页

作者： Re-Bing Wu Ruixing Long Jason Dominy Tak-San Ho Herschel Rabitz Department of Automation Tsinghua University Beijing 100084 China and Center for Quantum Information Science and Technology TNList Beijing 100084 China Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Quantum control landscape theory was formulated to assess the ease of finding optimal control fields in simulations and in the laboratory. The landscape is the observable as a function of the controls, and a primary goal of the theory is the analysis of landscape features. In what is referred to as the kinematic picture of the landscape, prior work showed that the landscapes are generally free of traps that could halt the search for an optimal control at a suboptimal observable value. The present paper considers the dynamical picture of the landscape, seeking the existence of singular controls, especially of a nonkinematic nature along with an assessment of whether they correspond to traps. We analyze the necessary and sufficient conditions for singular controls to be kinematic or nonkinematic critical solutions and the likelihood of their being encountered while maximizing an observable. An algorithm is introduced to seek singular controls on the landscape in simulations along with an associated Hessian landscape analysis. Simulations are performed for a large number of model finite-level quantum systems, showing that all the numerically identified kinematic and nonkinematic singular critical controls are not traps, in support of the prior empirical observations on the ease of finding high-quality optimal control fields.

关键词： QUANTUM theory LANDSCAPES COMPUTER simulation OPTIMAL control theory ALGORITHMS

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