Computing the Many-Body Green’s Function with Adaptive Variational Quantum Dynamics
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Nonequilibrium Electrochemical Phase Maps: Beyond Butler–Volmer Kinetics
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Alumina(0001)/Water Interface: Structural Properties and Infrared Spectra from First-Principles Molecular Dynamics Simulations
We investigated the atomic structure and infrared spectra of the alumina(0001)/water interface, using first-principles molecular dynamics simulations based on density functional theory within the generalized gradient approximation. The computed structural properties of the interface are in good agreement with the results of synchrotron X-ray experiments. In this work detailed analyses of the computed infrared spectra revealed two types of water molecules at the hydrophilic oxide/water interface: molecules participating in strong “ice-like” hydrogen bonding with the oxide surface and molecules involved in weaker “liquid-like” hydrogen bonding. Our results provide a molecular interpretation of the “ice-like” and “liquid-like” bands observed in sum-frequency vibrational spectroscopy experiments and underscore the significance of strong hydrogen-bonding interactions in determining the orientation of interfacial water molecules.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Volume Flow Rate Estimation for Small Explosions at Mt. Etna, Italy, From Acoustic Waveform Inversion
Rapid assessment of the volume and the rate at which gas and pyroclasts are injected into the atmosphere during volcanic explosions is key to effective eruption hazard mitigation. Here, we use data from a dense infrasound network deployed in 2017 on Mt. Etna, Italy, to estimate eruptive volume flow rates (VFRs) during small gas-and-ash explosions. We use a finite-difference time-domain approximation to compute the acoustic Green's functions and perform a full waveform inversion for a multipole source, combining monopole and horizontal dipole terms. The inversion produces realistic estimates of VFR, on the order of 4 × 10 4 m 3 /s and well-defined patterns of source directivity. This is the first application of acoustic waveform inversion at Mt. Etna. Our results demonstrate that acoustic waveform inversion is a mature and robust tool for assessment of source parameters and holds potential as a tool to provide rapid estimates of VFR in near real time.
58 GEOSCIENCES↗
Physics based model for online fault detection in autonomous cryogenic loading system
We report the progress in the development of the chilldown model for a rapid cryogenic loading system developed at NASA-Kennedy Space Center. The nontrivial characteristic feature of the analyzed chilldown regime is its active control by dump valves. The two-phase flow model of the chilldown is approximated as one-dimensional homogeneous fluid flow with no slip condition for the interphase velocity. The model is built using commercial SINDA/FLUINT software. The results of numerical predictions are in good agreement with the experimental time traces. The obtained results pave the way to the application of the SINDA/FLUINT model as a verification tool for the design and algorithm development required for autonomous loading operation.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
An automated miniature robotic vehicle inspection system
A novel, autonomous reconfigurable robotic inspection system for quantitative NDE mapping is presented. The system consists of a fleet of wireless (802.11g) miniature robotic vehicles, each approximately 175 × 125 × 85 mm with magnetic wheels that enable them to inspect industrial structures such as storage tanks, chimneys and large diameter pipe work. The robots carry one of a number of payloads including a two channel MFL sensor, a 5 MHz dry coupled UT thickness wheel probe and a machine vision camera that images the surface. The system creates an NDE map of the structure overlaying results onto a 3D model in real time. The authors provide an overview of the robot design, data fusion algorithms (positioning and NDE) and visualization software.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Embedding potentials for excited states of embedded species
Frozen-Density-Embedding Theory (FDET) is a formalism to obtain the upper bound of the ground-state energy of the total system and the corresponding embedded wavefunction by means of Euler-Lagrange equations [T. A. Wesolowski, Phys. Rev. A 77(1), 012504 (2008)]. FDET provides the expression for the embedding potential as a functional of the electron density of the embedded species, electron density of the environment, and the field generated by other charges in the environment. Under certain conditions, FDET leads to the exact ground-state energy and density of the whole system. Following Perdew-Levy theorem on stationary states of the ground-state energy functional, the other-than-ground-state stationary states of the FDET energy functional correspond to excited states. In the present work, we analyze such use of other-than-ground-state embedded wavefunctions obtained in practical calculations, i.e., when the FDET embedding potential is approximated. Three computational approaches based on FDET, that assure self-consistent excitation energy and embedded wavefunction dealing with the issue of orthogonality of embedded wavefunctions for different states in a different manner, are proposed and discussed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Investigation of structural stability and elastic properties of Zrh and Zrh{sub 2}: A first principles study
The electronic, structural and mechanical properties of ZrH and ZrH{sub 2} are investigated by means of first principles calculation based on density functional theory as implemented in VASP code with generalized gradient approximation. The calculated ground state properties are in good agreement with previous experimental and other theoretical results. Among the six crystallographic structures considered for ZrH, ZB phase is found to be the most stable phase, whereas ZrH{sub 2} is energetically stable in tetragonal structure at ambient condition. A structural phase transition from ZB→NaCl at a pressure 10 GPa is predicted for ZrH.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
The effect of large amplitude motions on the transition frequency redshift in hydrogen bonded complexes: A physical picture
We describe the vibrational transitions of the donor unit in water dimer with an approach that is based on a three-dimensional local mode model. We perform a perturbative treatment of the intermolecular vibrational modes to improve the transition wavenumber of the hydrogen bonded OH-stretching transition. The model accurately predicts the transition wavenumbers of the vibrations in water dimer compared to experimental values and provides a physical picture that explains the redshift of the hydrogen bonded OH-oscillator. We find that it is unnecessary to include all six intermolecular modes in the vibrational model and that their effect can, to a good approximation, be computed using a potential energy surface calculated at a lower level electronic structure method than that used for the unperturbed model.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A minimal model of self-sustaining turbulence
In this work, we examine the turbulence maintained in a Restricted Nonlinear (RNL) model of plane Couette flow. This model is a computationally efficient approximation of the second order statistical state dynamics obtained by partitioning the flow into a streamwise averaged mean flow and perturbations about that mean, a closure referred to herein as the RNL{sub ∞} model. The RNL model investigated here employs a single member of the infinite ensemble that comprises the covariance of the RNL{sub ∞} dynamics. The RNL system has previously been shown to support self-sustaining turbulence with a mean flow and structural features that are consistent with direct numerical simulations (DNS). Regardless of the number of streamwise Fourier components used in the simulation, the RNL system’s self-sustaining turbulent state is supported by a small number of streamwise varying modes. Remarkably, further truncation of the RNL system’s support to as few as one streamwise varying mode can suffice to sustain the turbulent state. The close correspondence between RNL simulations and DNS that has been previously demonstrated along with the results presented here suggest that the fundamental mechanisms underlying wall-turbulence can be analyzed using these highly simplified RNL systems.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
First-principles Hubbard U approach for small molecule binding in metal-organic frameworks
We apply first-principles approaches with Hubbard U corrections for calculation of small molecule binding energetics to open-shell transition metal atoms in metal-organic frameworks (MOFs). Using density functional theory with van der Waals dispersion-corrected functionals, we determine Hubbard U values ab initio through an established linear response procedure for M-MOF-74, for a number of different metal centers (M = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu). While our ab initio U values differ from those used in previous work, we show that they result in lattice parameters and electronic contributions to CO{sub 2}-MOF binding energies that lead to excellent agreement with experiments and previous results, yielding lattice parameters within 3%. In addition, U-dependent calculations for an example system, Co-MOF-74, suggest that the CO{sub 2} binding energy grows monotonically with the value of Hubbard U, with the binding energy shifting 4 kJ/mol (or 0.041 eV) over the range of U = 0-5.4 eV. These results provide insight into an approximate but computationally efficient means for calculation of small molecule binding energies to open-shell transition metal atoms in MOFs and suggest that the approach can be predictive with good accuracy, independent of the cations used and the availability of experimental data.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
M. Riesz-Schur-type inequalities for entire functions of exponential type
We prove a general M. Riesz-Schur-type inequality for entire functions of exponential type.
97 MATHEMATICS AND COMPUTING↗
Evolution of homologous recombination rates across bacteria
Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as “quasi-sexual.” However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate—as a trait—remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate—as a trait—is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.
59 BASIC BIOLOGICAL SCIENCES↗
Probabilistic inference of reaction rate parameters from summary statistics
Here, this investigation tackles the probabilistic parameter estimation problem involving the Arrhenius parameters for the rate coefficient of the chain branching reaction H + O 2 → OH + O. This is achieved in a Bayesian inference framework that uses indirect data from the literature in the form of summary statistics by approximating the maximum entropy solution with the aid of approximate bayesian computation. The summary statistics include nominal values and uncertainty factors of the rate coefficient, obtained from shock-tube experiments performed at various initial temperatures. The Bayesian framework allows for the incorporation of uncertainty in the rate coefficient of a secondary reaction, namely OH + H 2 → H 2 O + H, resulting in a consistent joint probability density on Arrhenius parameters for the two rate coefficients. It also allows for uncertainty quantification in numerical ignition predictions while conforming with the published summary statistics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Modeling neutrino-induced scale-dependent galaxy clustering for photometric galaxy surveys
Abstract The increasing statistical precision of photometric redshift surveys requires improved accuracy of theoretical predictions for large-scale structure observables to obtain unbiased cosmological constraints. In ΛCDM cosmologies, massive neutrinos stream freely at small cosmological scales, suppressing the small-scale power spectrum. In massive neutrino cosmologies, galaxy bias modeling needs to accurately relate the scale-dependent growth of the underlying matter field to observed galaxy clustering statistics. In this work, we implement a computationally efficient approximation of the neutrino-induced scale-dependent bias (NISDB). Through simulated likelihood analyses of Dark Energy Survey Year 3 (DESY3) and Legacy Survey of Space and Time Year 1 (LSSTY1) synthetic data that contain an appreciable NISDB, we examine the impact of linear galaxy bias and neutrino mass modeling choices on cosmological parameter inference. We find model misspecification of the NISDB approximation and neutrino mass models to decrease the constraining power of photometric galaxy surveys and cause parameter biases in the cosmological interpretation of future surveys. We quantify these biases and devise mitigation strategies.
Astronomy & Astrophysics↗
Homologous recombination shapes the architecture and evolution of bacterial genomes
Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotspots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.
Torrance, Ellis L [University of North Carolina, G↗
Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies
Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.
59 BASIC BIOLOGICAL SCIENCES↗