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Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis
Not provided.
Ecological information and approaches needed for risk communication dialogs for acute or chronic environmental crises
Scientists, social scientists, risk communicators, and many others are often thrust into a crisis situation where they need to interact with a range of stakeholders, including governmental personnel (tribal, U.S. federal, state, local), local residents, and other publics, as well as other scientists and other risk communicators in situations where information is incomplete and evolving. This paper provides: (1) an overall framework for thinking about communication during crises, from acute to chronic, and local to widespread, (2) a template for the types of ecological information needed to address public and environmental concerns, and (3) examples to illustrate how this information will aid risk communicators. The main goal is providing an approach to the knowledge needed by communicators to address the challenges of protecting ecological resources during an environmental crisis, or for an on-going, chronic environmental issue. To understand the risk to these ecological resources, it is important to identify the type of event, whether it is acute or chronic (or some combination of these), what receptors are at risk, and what stressors are involved (natural, biological, chemical, radiological). For ecological resources, the key information a communicator needs for a crisis is whether any of the following are present: threatened or endangered species, species of special concern, species groups of concern (e.g., neotropical bird migrants, breeding frogs in vernal ponds, rare plant assemblages), unique or rare habitats, species of commercial and recreational interest, and species/habitats of especial interest for medicinal, cultural, or religious activities. Communication among stakeholders is complicated with respect to risk to ecological receptors because of differences in trust, credibility, empathy, perceptions, world view valuation of the resources, and in many cases, a history of misinformation, disinformation, or no information. Exposure of salmon spawning in the Columbia River to hexavalent chromium from the Hanford Site is used as an example of communication challenges with different stakeholders, including Native Americans with Tribal Treaty rights to the land.
Trust and consequences: Role of community science, perceptions, values, and environmental justice in risk communication
Risk communication is often viewed as imparting information and perhaps as a two-way dialogue. Risk communication inadequacies on the part of both “communicator” and “community members” can lead to adverse consequences and amplify environmental justice disparities. The paper suggests a transformational approach where risk communicators must learn to trust community experts and their knowledge base (and act upon it), where risk information imparted by risk communicators addresses what communities are most concerned about (as well as risk from specific chemicals or radionuclides), and where risk information and assessments address underlying issues and disparities, as well as cultural traditions (among others). Providing risk probabilities is no longer sufficient; western science may not be enough, and community and native scientific knowledge is needed. Risk communication (or information transfer) for environmental risks that are ongoing usually applies to low-income, minority communities—people living in dense inner cities, rural communities, Native American communities—or to people living near a risky facility. Communication within this context requires mutual trust, listening and respect, as well as acceptance of indigenous and community knowledge as equally valuable. Examples are given to illustrate a community perspective.
Nonlinear instabilities of multi-site breathers in Klein-Gordon lattices
Here, we explore the possibility of multi-site breather states in a nonlinear Klein–Gordon lattice to become nonlinearly unstable, even if they are found to be spectrally stable. The mechanism for this nonlinear instability is through the resonance with the wave continuum of a multiple of an internal mode eigenfrequency in the linearization of excited breather states. For the nonlinear instability, the internal mode must have its Krein signature opposite to that of the wave continuum. This mechanism is not only theoretically proposed, but also numerically corroborated through two concrete examples of the Klein–Gordon lattice with a soft (Morse) and a hard (Φ 4 ) potential. Compared to the case of the nonlinear Schrödinger lattice, the Krein signature of the internal mode relative to that of the wave continuum may change depending on the period of the multi-site breather state. For the periods for which the Krein signatures of the internal mode and the wave continuum coincide, multi-site breather states are observed to be nonlinearly stable.
The Pele Simulation Suite for Reacting Flows at Exascale
In this work, we present the Pele suite of software tools for compressible and incompressible reacting flows. The Pele suite leverages several different libraries, notably AMReX and SUNDIALS, to achieve performance portability on heterogeneous computing architectures across the supercomputing landscape. The Pele suite is comprised of PeleC, a compressible reacting flow block-structured adaptive mesh refinement solver, PeleLMeX, a low-Mach number reacting flow block-structured adaptive mesh refinement solver, Pele-Physics, a library for transport, thermodynamics, finite rate chemistry, soot, spray and radiation physics. The objective of this paper is (i) to present the code development efforts necessary to achieve highly effective and scalable applications for exascale machines and (ii) to detail the performance results of the Combustion-Pele project applications on Oak Ridge National Laboratory's Frontier. We show good weak and strong scaling results for both PeleC and PeleLMeX up to more than 50 billion cells on more than 4096 Frontier graphics processing unit nodes. We also present a capability demonstration simulation of a dual-fuel pulse compression ignition engine (six adaptive mesh refinement levels, and 60 billion cells or 2.1 trillion degrees of freedom) on Frontier, to date one of the largest simulations performed on the first exascale-class supercomputer.
A study in three-dimensional chaotic dynamics: Granular flow and transport in a bi-axial spherical tumbler
We study three-dimensional (3D) chaotic dynamics through an analysis of transport in a granular flow in a half-full spherical tumbler rotated sequentially about two orthogonal axes (a bi-axial “blinking” tumbler). The flow is essentially quasi-two-dimensional in any vertical slice of the sphere during rotation about a single axis, and we provide an explicit exact solution to the model in this case. Hence, the cross-sectional flow can be represented by a twist map, allowing us to express the 3D flow as a linked twist map (LTM). We prove that if the rates of rotation about each axis are equal, then (in the absence of stochasticity) particle trajectories are restricted to two-dimensional (2D) surfaces consisting of a portion of a hemispherical shell closed by a “cap''; if the rotation rates are unequal, then particles can leave the surface they start on and traverse a volume of the tumbler. The period-one structures of the governing LTM are examined in detail: analytical expressions are provided for the location of period-one curves, their extent into the bulk of the granular material, and their dependence on the protocol parameters (rates and durations of rotations). Exploiting the restriction of trajectories to 2D surfaces in the case of equal rotation rates about the axes, a method is proposed for identifying and constructing 3D Kolmogorov--Arnold--Moser (KAM) tubes around the normally elliptic period-one curves. The invariant manifold structure arising from the normally hyperbolic period-one curves is also examined. When the motion is restricted to 2D surfaces, the structure of manifolds of the hyperbolic points in the bulk differs from that corresponding to hyperbolic points in the flowing layer. Each is reminiscent of a template provided by a non-integrable perturbation to a Hamiltonian system, though the governing LTM is not. This highlights the novel 3D chaotic behaviors observed in this model dynamical system.
The NonConforming Virtual Element Method for the Stokes Equations
In this paper, we present the nonconforming virtual element method (VEM) for the numerical approximation of velocity and pressure in the steady Stokes problem. The pressure is approximated using discontinuous piecewise polynomials, while each component of the velocity is approximated using the nonconforming virtual element space. On each mesh element the local virtual space contains the space of polynomials of up to a given degree, plus suitable nonpolynomial functions. The virtual element functions are implicitly defined as the solution of local Poisson problems with polynomial Neumann boundary conditions. As typical in VEM approaches, the explicit evaluation of the non-polynomial functions is not required. This approach makes it possible to construct nonconforming (virtual) spaces for any polynomial degree regardless of the parity, for two- and three-dimensional problems, and for meshes with very general polygonal and polyhedral elements. We show that the nonconforming VEM is inf-sup stable and establish optimal a priori error estimates for the velocity and pressure approximations. Finally, numerical examples confirm the convergence analysis and the effectiveness of the method in providing high-order accurate approximations.
Algebraic Multigrid Preconditioners for Multiphase Flow in Porous Media
Multiphase flow is a critical process in a wide range of applications, including carbon sequestration, contaminant remediation, and groundwater management. Typically, this process is modeled by a nonlinear system of partial differential equations derived by considering the mass conservation of each phase (e.g., oil, water), along with constitutive laws for the relationship of phase velocity to phase pressure. In this study, we develop and study efficient solution algorithms for solving the algebraic systems of equations derived from a fully coupled and time-implicit treatment of models of multiphase flow. We explore the performance of several preconditioners based on algebraic multigrid (AMG) for solving the linearized problem, including “black-box” AMG applied directly to the system, a new version of constrained pressure residual multigrid (CPR-AMG) preconditioning, and a new preconditioner derived using an approximate Schur complement arising from the block factorization of the Jacobian. Finally, we show that the new methods are the most robust with respect to problem character, as determined by varying effects of capillary pressures, and we show that the block factorization preconditioner both is efficient and scales optimally with problem size.
Maximum Size Intersecting Families of Bounded Minimum Positive Co-degree
Let $\mathcal{H}$ be an $r$-uniform hypergraph. The minimum positive co-degree of $\mathcal{H}$, denoted by $\delta_{r-1}^+(\mathcal{H})$, is the minimum $k$ such that if $S$ is an $(r-1)$-set contained in a hyperedge of $\mathcal{H}$, then $S$ is contained in at least $k$ hyperedges of $\mathcal{H}$. For $r\geq k$ fixed and $n$ sufficiently large, we determine the maximum possible size of an intersecting $r$-uniform $n$-vertex hypergraph with minimum positive co-degree $\delta_{r-1}^+(\mathcal{H}) \geq k$ and characterize the unique hypergraph attaining this maximum. This generalizes the Erd\Hos--Ko--Rado theorem which corresponds to the case $k=1$. Furthermore, our proof is based on the delta-system method.
Adaptive Uncertainty Quantification for Stochastic Hyperbolic Conservation Laws
Here, we propose a predictor-corrector adaptive method for the study of hyperbolic partial differential equations (PDEs) under uncertainty. Constructed around the framework of stochastic finite volume (SFV) methods, our approach circumvents sampling schemes or simulation ensembles while also preserving fundamental properties, in particular hyperbolicity of the resulting systems and conservation of the discrete solutions. Furthermore, we augment the existing SFV theory with a priori convergence results for statistical quantities, in particular push-forward densities, which we demonstrate through numerical experiments. By linking refinement indicators to regions of the physical and stochastic spaces, we drive anisotropic refinements of the discretizations, introducing new degrees of freedom where deemed profitable. To illustrate our proposed method, we consider a series of numerical examples for nonlinear hyperbolic PDEs based on Burgers’ and Euler’s equations.
Comment on ''The velocity field due to an oscillating plate in an Oldroyd-B fluid'' by C.C. Hopkins and J.R. de Bruyn [Can. J. Phys. 92 , 533 (2014)]
We correct certain errors and ambiguities in the recent pedagogical article by Hopkins and de Bruyn. The early-time asymptotics of the solution to the transient version of Stokes’ second problem for an Oldroyd-B fluid in a half-space is presented, as Appendix A, to complement the late-time asymptotics given by Hopkins and de Bruyn.
Enhancing disease surveillance with novel data streams: challenges and opportunities
Novel data streams (NDS), such as web search data or social media updates, hold promise for enhancing the capabilities of public health surveillance. In this paper, we outline a conceptual framework for integrating NDS into current public health surveillance. Our approach focuses on two key questions: What are the opportunities for using NDS and what are the minimal tests of validity and utility that must be applied when using NDS? Identifying these opportunities will necessitate the involvement of public health authorities and an appreciation of the diversity of objectives and scales across agencies at different levels (local, state, national, international). We present the case that clearly articulating surveillance objectives and systematically evaluating NDS and comparing the performance of NDS to existing surveillance data and alternative NDS data is critical and has not sufficiently been addressed in many applications of NDS currently in the literature.
Phase separation, edge currents, and Hall effect for active matter with Magnus dynamics
Here we examine run-and-tumble disks in two-dimensional systems where the particles also have a Magnus component to their dynamics. For increased activity, we find that the system forms a motility-induced phase-separated (MIPS) state with chiral edge flow around the clusters, where the direction of the current is correlated with the sign of the Magnus term. The stability of the MIPS state is non-monotonic as a function of increasing Magnus term amplitude, with the MIPS region first extending down to lower activities followed by a break up of MIPS at large Magnus amplitudes into a gel-like state. We examine the dynamics in the presence of quenched disorder and a uniform drive and find that the bulk flow exhibits a drive-dependent Hall angle. This is a result of the side jump effect produced by scattering from the pinning sites and is similar to the behavior found for skyrmions in chiral magnets with quenched disorder.
Peakompactons: Peaked compact nonlinear waves
This paper is meant as an accessible introduction to/tutorial on the analytical construction and numerical simulation of a class of nonstandard solitary waves termed peakompactons. We present that these peaked compactly supported waves arise as solutions to nonlinear evolution equations from a hierarchy of nonlinearly dispersive Korteweg–de Vries-type models. Peakompactons, like the now-well-known compactons and unlike the soliton solutions of the Korteweg–de Vries equation, have finite support, i.e., they are of finite wavelength. However, unlike compactons, peakompactons are also peaked, i.e., a higher spatial derivative suffers a jump discontinuity at the wave’s crest. Here, we construct such solutions exactly by reducing the governing partial differential equation to a nonlinear ordinary differential equation and employing a phase-plane analysis. Lastly, a simple, but reliable, finite-difference scheme is also designed and tested for the simulation of collisions of peakompactons. In addition to the peakompacton class of solutions, the general physical features of the so-called K # (n,m) hierarchy of nonlinearly dispersive Korteweg–de Vries-type models are discussed as well.
Superposed hyperbolic kink and pulse solutions of coupled $φ$ 4 , NLS and mKdV equations
Here, in this paper, we obtain novel solutions of a coupled $φ$ 4 , a coupled nonlinear Schrödinger equation and a coupled modified Korteweg de Vries equation which can be re-expressed as a linear superposition of either the sum or the difference of two hyperbolic pulse solutions or the sum of either a two-kink or a kink and an antikink solution. These results demonstrate that the notion of superposed solutions extends to coupled nonlinear equations as well.
Orthrus: A Framework for Implementing High-performance Collective I/O on Multicore Clusters
Abstract Not Provided
Preparing an Incompressible-Flow Fluid Dynamics Code for Exascale-Class Wind Energy Simulations
The U.S. Department of Energy has identified exascale-class wind farm simulation as critical to wind energy scientific discovery. A primary objective of the ExaWind project is to build high-performance, predictive computational fluid dynamics (CFD) tools that satisfy these modeling needs. GPU accelerators will serve as the computational thoroughbreds of next-generation, exascale-class supercomputers. Here, we report on our efforts in preparing the ExaWind unstructured mesh solver, Nalu-Wind, for exascale-class machines. For computing at this scale, a simple port of the incompressible-flow algorithms to GPUs is insufficient. To achieve high performance, one needs novel algorithms that are application aware, memory efficient, and optimized for the latest-generation GPU devices. The result of our efforts are unstructured-mesh simulations of wind turbines that can effectively leverage thousands of GPUs. In particular, we demonstrate a first-of-its-kind, incompressible-flow simulation using Algebraic Multigrid solvers that strong scales to more than 4000 GPUs on the Summit supercomputer.