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CSPlib - A Software Toolkit for the Analysis of Dynamical Systems and Chemical Kinetic Models
CSPlib is an open source software library for analyzing general ordinary differential equation (ODE) systems and detailed chemical kinetic ODE systems. It relies on the computational singular perturbation (CSP) method for the analysis of these systems. The software provides support for: General ODE models (gODE model class) for computing source terms and Jacobians for a generic ODE system; TChem model (ChemElemODETChem model class) for computing source term, Jacobian, other necessary chemical reaction data, as well as the rates of progress for a homogenous batch reactor using an elementary step detailed chemical kinetic reaction mechanism. This class relies on the TChem [2] library; A set of functions to compute essential elements of CSP analysis (Kernel class). This includes computations of the eigensolution of the Jacobian matrix, CSP basis vectors and co-vectors, time scales (reciprocals of the magnitudes of the Jacobian eigenvalues), mode amplitudes, CSP pointers, and the number of exhausted modes. This class relies on the Tines library; A set of functions to compute the eigensolution of the Jacobian matrix using Tines library GPU eigensolver; A set of functions to compute CSP indices (Index Class). This includes participation indices and both slow and fast importance indices.
CSPlib - A Toolkit for the Analysis of ODE/DAE Dynamical Systems and Chemical Kinetic Models
CSPlib is an open source software library for analyzing general ordinary differential equation (ODE) systems and detailed chemical kinetic ODE/DAE systems. It relies on the computational singular perturbation (CSP) method for the analysis of these systems.
Three-Dimensional Simulations of Machined Perturbation Profiles Subjected to the Richtmyer-Meshkov Instability: Mix Metrics Analysis and Comparison to Experiments
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Three-Dimensional Simulations of Machined Perturbation Profiles Subjected to the Richtmyer-Meshkov Instability: Mix Metrics Analysis and Comparison to Experiments
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Competition between Hydrogen and Chalcogen Bonding in Homodimers of Chalcogen Hydrides (H 2 X) 2 , X = O, S, Se, Te
The structural and chemical bonding motifs manifested by the competition between hydrogen and chalcogen bonding in the homodimers of chalcogen hydrides (H 2 X) 2 , where X = O, S, Se, Te have been characterized using high-level electronic structure calculations and analysis of the electron density based on Quasi-atomic orbital (QUAO) and the Symmetry-adapted perturbation theory (SAPT) methods. The QUAO analysis clearly identifies a three-center interaction responsible for either hydrogen or chalcogen bonds: in the former, the σ-bond connecting the donor and hydrogen atom participating in the hydrogen bond interacts with the lone pair on the nucleophile acceptor via the hydrogen atom, while in the latter this same σ-bond interacts with the nucleophile lone pair via the donor chalcogen. The number of minimum energy structures increase dramatically from one for (H 2 O) 2 , three for (H 2 S) 2 , four for (H 2 Se) 2 , and finally six for (H 2 Te) 2 . Furthermore, the emergence of the chalcogen-bonded arrangements appears for (H 2 S) 2 with their subsequent energetic stabilization over the hydrogen-bonded minima manifesting in (H 2 Se) 2 and (H 2 Te) 2 . In particular, one of the (H 2 S) 2 , two of the (H 2 Se) 2 , and three of the (H 2 Te) 2 dimers are chalcogen bonded. Induction plays a small but important role in stabilizing hydrogen over chalcogen-bonded structures, while dispersion is more important for chalcogen bonds.
A Uniform Analysis of Debris Disks with the Gemini Planet Imager. I. An Empirical Search for Perturbations from Planetary Companions in Polarized Light Images
The Gemini Planet Imager (GPI) has excelled in imaging debris disks in the near-infrared. The GPI Exoplanet Survey imaged 24 debris disks in polarized H-band light, while other programs observed half of these disks in polarized J and/or K1 bands. Using these data, we present a uniform analysis of the morphology of each disk to find asymmetries suggestive of perturbations, particularly those due to planet–disk interactions. The multiwavelength surface brightness, disk color, and geometry permit the identification of any asymmetries such as warps or disk offsets from the central star. We find that 19 of the disks in this sample exhibit asymmetries in surface brightness, disk color, disk geometry, or a combination of the three, suggesting that for this sample, perturbations, as seen in scattered light, are common. The relationship between these perturbations and potential planets in the system is discussed. We also explore correlations among stellar temperatures, ages, disk properties, and observed perturbations. We find significant trends between the vertical aspect ratio and the stellar temperature, disk radial extent, and the dust grain size distribution power law, q. We also confirm a trend between the disk color and stellar effective temperature, where the disk becomes increasingly red/neutral with increasing temperature. Such results have important implications for the evolution of debris disk systems around stars of various spectral types.
Unitarity bounds on effective field theories at the LHC
Effective Field Theory (EFT) extensions of the Standard Model are tools to compute observables (e.g. cross sections with partonic center-of-mass energy √s^) as a systematically improvable expansion suppressed by a new physics scale M. If one is interested in EFT predictions in the parameter space where M < √s^, concerns of self-consistency emerge, which can manifest as a violation of perturbative partial-wave unitarity. However, when we search for the effects of an EFT at a hadron collider with center-of-mass energy √s using an inclusive strategy, we typically do not have access to the event-by-event value of √s^. This motivates the need for a formalism that incorporates parton distribution functions into the perturbative partial-wave unitarity analysis. Developing such a framework and initiating an exploration of its implications is the goal of this work. Our approach opens up a potentially valid region of the EFT parameter space where M << √s. We provide evidence that there exist valid EFTs in this parameter space. The perturbative unitarity bounds are sensitive to the details of a given search, an effect we investigate by varying kinematic cuts.
Linear stability analysis via simulated annealing and accelerated relaxation
Simulated annealing (SA) is a kind of relaxation method for finding equilibria of Hamiltonian systems. A set of evolution equations is solved with SA, which is derived from the original Hamiltonian system so that the energy of the system changes monotonically while preserving Casimir invariants inherent to noncanonical Hamiltonian systems. The energy extremum reached by SA is an equilibrium. Since SA searches for an energy extremum, it can also be used for stability analysis when initiated from a state where a perturbation is added to an equilibrium. The procedure of the stability analysis is explained, and some examples are shown. Because the time evolution is computationally time consuming, efficient relaxation is necessary for SA to be practically useful. An acceleration method is developed by introducing time dependence in the symmetric kernel used in the double bracket, which is part of the SA formulation described here. An explicit formulation for low-beta reduced magnetohydrodynamics (MHD) in cylindrical geometry is presented. In conclusion, since SA for low-beta reduced MHD has two advection fields that relax, it is important to balance the orders of magnitude of these advection fields.
Transverse energy–energy correlations of jets in the electron–proton deep inelastic scattering at HERA
We study the event shape variables, transverse energy–energy correlation TEEC (cosφ) and its asymmetry ATEEC (cosφ) in deep inelastic scattering (DIS) at the electron–proton collider HERA, where φ is the angle between two jets defined using a transverse-momentum (k T ) jet algorithm. At HERA, jets are defined in the Breit frame, and the leading nontrivial transverse energy–energy correlations arise from the 3-jet configurations. With the help of the NLOJET++, these functions are calculated in the leading order (LO) and the next-to-leading order (NLO) approximations in QCD at the electron–proton center-of-mass energy $\sqrt{s}$ = 314 GeV. We restrict the angular region to -0.8 ≤ cosφ ≤ 0.8, as the forward- and backward-angular regions require resummed logarithmic corrections, which we have neglected in this work. Following experimental jet-analysis at HERA, we restrict the DIS-variables x, y = Q 2 /(xs), where Q 2 = -q 2 is the negative of the momentum transfer squared q 2 , to 0 ≤ x ≤ 1, 0.2 ≤ y ≤ 0.6, and the pseudo-rapidity variable in the laboratory frame (η lab ) to the range -1 ≤ η lab ≤ 2.5. The TEEC and ATEEC functions are worked out for two ranges in Q 2 , defined by 5.5GeV 2 ≤ Q 2 ≤ 80GeV 2 , called the low-Q 2 -range, and 150GeV 2 ≤ Q 2 ≤ 1000GeV 2 , called the high-Q 2 -range. We show the sensitivity of these functions on the parton distribution functions (PDFs), the factorization (μ F ) and renormalization (μ R ) scales, and on α s (M$^2_Z$). Of these the correlations are stable against varying the scale μ F and the PDFs, but they do depend on μ R . For the choice of the scale μ R =$\sqrt{\langle ET \rangle^2+Q^2}$, advocated in earlier jet analysis at HERA, the shape variables TEEC and ATEEC are found perturbatively robust. These studies are useful in the analysis of the HERA data, including the determination of α s (M$^2_Z$) from the shape variables.
Comment on “Nonlocal nucleon matrix elements in the rest frame”
In a recent paper, “Nonlocal nucleon matrix elements in the rest frame” [1], it was observed that the next-to-leading order calculations of the renormalization factor can describe, to a few percent accuracy, the logarithm of the lattice quantum chromodynamics (QCD) rest frame matrix elements with separations up to distances of 0.6 fm on multiple lattice spacings. We argue that perturbative QCD breaks down at such a distance scale after resumming the associated large logarithms, while the Ansatz used in the analysis there is not justified in perturbation theory. Besides, we explain the observation in Ref. [1] and demonstrate that the Ansatz fails to describe the data for 𝑧 > 0.3 fm, showing an opposite trend. Finally, although Ref. [1] proposes multiplying the Ansatz by a Gaussian correction model, which is shown to reduce the discrepancy with the data, this does not legitimize the use of perturbative QCD at such distance scales.
Ensuring statistical reproducibility of ocean model simulations in the age of hybrid computing
Novel high performance computing systems that feature hybrid architectures require large scale code refactoring to unravel underlying exploitable parallelism. Such redesign can often be accompanied with machine-precision changes as the order of computation cannot always be maintained. For chaotic systems like climate models, these round-off level differences can grow rapidly. Systematic errors may also manifest initially as machine-precision differences. Isolating genuine round off level differences from such errors remains a challenge. Here, we apply two-sample equality of distribution tests to evaluate statistical reproducibility of the ocean model component of US Department of Energy's Energy Exascale Earth System Model (E3SM). A 2-year control simulation ensemble is compared to a modified ensemble as a test case - after a known non-bit-for-bit change in a model component is introduced - to evaluate the null hypothesis that the two ensembles are statistically indistinguishable. To quantify the false negative rates of these tests, we conduct a formal power analysis using a targeted suite of short simulation ensembles. The ensemble suite contains several perturbed ensembles, each with a progressively different climate than the baseline ensemble - obtained by perturbing the magnitude of a single model tuning parameter, the Gent and McWilliams κ, in a controlled manner. The null hypothesis is evaluated for each of perturbed ensembles using these tests. The power analysis informs on the detection limits of the tests for given ensemble size allowing model developers to evaluate the impact of an introduced non-bit-for-bit change to the model.
Non-perturbative production of fermionic dark matter from fast preheating
We investigate non-perturbative production of fermionic dark matter in the early universe. We study analytically the gravitational production mechanism accompanied by the coupling of fermions to the background inflaton field. The latter leads to the variation of effective fermion mass during preheating and makes the resulting spectrum and abundance sensitive to its parameters. Assuming fast preheating that completes in less than the inflationary Hubble time and no oscillations of the inflaton field after inflation, we find an abundant production of particles with energies ranging from the inflationary Hubble rate to the inverse duration of preheating. The produced fermions can account for all observed dark matter in a broad range of parameters. As an application of our analysis, we study non-perturbative production of fermionic dark matter in the model of Palatini Higgs inflation.
On the interaction of a wind turbine wake with a conventionally neutral atmospheric boundary layer
In this work, we investigate the dynamics of wind turbine tip-vortex breakdown in a conventionally neutral atmospheric boundary layer (ABL). To this end, high-resolution data are collected from large-eddy simulations of a wind turbine operating within a neutral ABL and studied by means of proper orthogonal decomposition (POD) and Fourier analysis. The high resolution of the generated data in both space and time allows us to gain insight into the tip-vortex breakdown mechanisms by (i) capturing the energy modes of the coherent structures, (ii) studying their contribution to the tip-vortex breakdown through their power spectra functions and mean kinetic energy (MKE) flux, and (iii) analysing the growth rate of each contributing perturbation frequency along tip vortices. Our analysis shows that under a fully turbulent scenario, the growth rate of perturbations along the tip vortices is largest for low wave numbers, i.e. long-wave perturbations. Additionally, the MKE flux reaches its highest value at two diameters downstream of the rotor plane, a behaviour that can be attributed to the coexistence of multiple interacting POD modes, with the streamwise vortex roller mode being the primary contributor to the total MKE flux budget, contributing approximately . Finally, comparisons with a laminar, uniform flow scenario subject to a single-frequency perturbation highlight the differences between the two ambient flow conditions. In the non-turbulent, uniform flow scenario, the growth rate attains its maximum value at a wave number corresponding to the out-of-phase mutual-inductance mechanism, whereas the MKE flux exhibits local minima and maxima along the wake and at different downstream locations depending on the perturbation frequency. Our analyses suggest that the breakdown of the wind turbine tip vortices under a fully turbulent neutral ABL inflow is due to complex interactions across a range of excitation frequencies, in which the mutual-inductance instability may not be the dominant one.
Unified analysis of finite-size error for periodic Hartree-Fock and second order Møller-Plesset perturbation theory
Despite decades of practice, finite-size errors in many widely used electronic structure theories for periodic systems remain poorly understood. For periodic systems using a general Monkhorst-Pack grid, there has been no comprehensive and rigorous analysis of the finite-size error in the Hartree-Fock theory (HF) and the second order Møller-Plesset perturbation theory (MP2), which are the simplest wavefunction based method, and the simplest post-Hartree-Fock method, respectively. Such calculations can be viewed as a multi-dimensional integral discretized with certain trapezoidal rules. Due to the Coulomb singularity, the integrand has many points of discontinuity in general, and standard error analysis based on the Euler-Maclaurin formula gives overly pessimistic results. The lack of analytic understanding of finite-size errors also impedes the development of effective finite-size correction schemes. We propose a unified analysis to obtain sharp convergence rates of finite-size errors for the periodic HF and MP2 theories. Our main technical advancement is a generalization of the result of Lyness [Math. Comp. 30 (1976), pp. 1–23] for obtaining sharp convergence rates of the trapezoidal rule for a class of non-smooth integrands. Our result is applicable to three-dimensional bulk systems as well as low dimensional systems (such as nanowires and 2D materials). Our unified analysis also allows us to prove the effectiveness of the Madelung-constant correction to the Fock exchange energy, and the effectiveness of a recently proposed staggered mesh method for periodic MP2 calculations (see X. Xing, X. Li, and L. Lin [J. Chem. Theory Comput. 17 (2021), pp. 4733–4745]). In conclusion, our analysis connects the effectiveness of the staggered mesh method with integrands with removable singularities, and suggests a new staggered mesh method for reducing finite-size errors of periodic HF calculations.
Numerical investigation of the influence of shear and thermal stratification on the wind turbine tip‐vortex stability
Summary The interaction between wind turbine wakes and atmospheric turbulence is characterised by complex dynamics. In this study, two major components of the atmospheric boundary layer dynamics have been isolated, namely, the mean velocity profile shear and the thermal stratification, to examine their impact on the near‐wake development by undertaking a series of highly resolved large‐eddy simulations. Subsequently, instantaneous flow fields are extracted from the simulations and used to conduct Fourier analysis and proper orthogonal decomposition (POD) and compute the mean kinetic energy fluxes by different POD modes to better understand the tip‐vortex instability mechanisms. Our findings indicate that shear can significantly affect the breakup of the wind turbine tip‐vortices and the shape and stable length of the wake, whereas thermal stratification seems to only have limited contribution to the spatial development of the near‐wake field. Finally, our analysis shows that the applied perturbation frequency determines the tip‐vortex breakup location as it controls the onset of the mutual inductance instability.
A tale of two saddles
We find a new on-shell replica wormhole in a computation of the generating functional of JT gravity coupled to matter. We show that this saddle has lower action than the disconnected one, and that it is stable under restriction to real Lorentzian sections, but can be unstable otherwise. The behavior of the classical generating functional thus may be strongly dependent on the signature of allowed perturbations. As part of our analysis, we give an LM-style construction for computing the on-shell action of replicated manifolds even as the number of boundaries approaches zero, including a type of one-step replica symmetry breaking that is necessary to capture the contribution of the new saddle. Our results are robust against quantum corrections; in fact, we find evidence that such corrections may sometimes stabilize this new saddle.
Proteogenomic Characterization of Endometrial Carcinoma
We undertook a comprehensive proteogenomic characterization of 95 endometrial carcinomas, of which 83 were endometrioid tumors and 12 were serous tumors. This analysis revealed new consequences of perturbations to the p53 and Wnt/ß-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new insights into proteomic markers of clinical and genomic tumor subgroups, some of which are in known druggable pathways. We performed a broad genome-wide acetylation survey, one of the first of its kind, yielding insights into regulatory mechanisms of histone acetylation. We also characterized the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, further our understanding of the molecular mechanisms underlying endometrial carcinoma, and identify new avenues for investigating potential therapeutic targets.