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At least 1,621 records · Page 90
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI’s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Nonhuman organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype-phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Comprehensive analytical model of the dynamic 𝑍 pinch

In this work we present an analytical 1D axisymmetric model describing the evolution of the dynamic 𝑍 pinch. This model is capable of predicting the trajectories of the imploding sheath's magnetic piston and preceding shock front, along with the velocity, pressure, density, and magnetic field profiles, for any time-dependent current, spatially varying initial density profile, and weak initial axial field. The implosion is divided into stages, with each stage described by a set of coupled ordinary differential equations derived from the ideal MHD equations. Comparisons with experimental data from the COBRA pulsed-power facility are quite promising and imply this model could prove useful in designing and analyzing future pulsed-power experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Analytical expression of a finite, long, conical canted-cosine-theta coil for particle collider interaction regions

Magnets in the accelerator interaction region (IR) present significant challenges because of high field requirements and limited available space. Conical-shaped magnets offer advantages in these environments by allowing closer placement to the interaction point while maintaining clearance from synchrotron radiation. Interestingly, numerical studies have shown that conical canted-cosine-theta (CCT) designs produce a constant field distribution along the axial direction in the IR quadrupoles for the Electron-Ion Collider (EIC) at Brookhaven National Laboratory. However, the field harmonics generated by conical CCT windings are not yet fully understood. This paper presents an analytical approach to describe the magnetic field produced by a conical surface current and proposes a method for designing conical CCT magnets for accelerator applications. First, we begin with a surface current sheet having a general cosine-theta distribution in spherical coordinates and solve the vector potential using the Green’s function. The magnetic fields generated by the conical current sheet are expressed using associated Legendre polynomials. These results are then related to circular field harmonics and integral field harmonics for designing a coil that produces a pure multipole field. Next, a single layer of the conical CCT winding path is produced based on the cosine-theta current distribution. Finally, the magnetic field quality of dipole and quadrupole conical CCT coils with multiple layers is verified using the Biot-Savart law.

Yang, Ye↗
DOE OSTI2019

Heisenberg-scaling measurement protocol for analytic functions with quantum sensor networks

Here we generalize past work on quantum sensor networks to show that, for d input parameters, entanglement can yield a factor O(d) improvement in mean-squared error when estimating an analytic function of these parameters. We show that the protocol is optimal for qubit sensors, and we conjecture an optimal protocol for photons passing through interferometers. Our protocol is also applicable to continuous variable measurements, such as one quadrature of a field operator. We outline a few potential applications, including calibration of laser operations in trapped ion quantum computing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Achieving a large transverse emittance ratio in the Relativistic Heavy Ion Collider: Beam experiments, analytical estimates, and implications for the Electron-Ion Collider

The Electron-Ion Collider (EIC), to be built at Brookhaven National Laboratory, will collide a polarized high-energy electron beam with polarized proton and light ion beams in the center-of-mass energy range of 20–140 GeV, achieving a maximum peak luminosity of up to 1 × 10 34 cm − 2 s − 1 for the proton and electron collisions. To achieve such a high luminosity, the EIC will employ small, flat beams at the interaction point, which requires a transverse emittance ratio of about 11:1. Since 2017, we have carried out a series of beam experiments to test the feasibility of achieving such a large emittance ratio in the Relativistic Heavy Ion Collider (RHIC). Thanks to the existing stochastic cooling and decoupling feedback system in RHIC, we successfully demonstrated a large transverse emittance ratio of 11:1 with gold ion beams in 2023. In this article, we will present more details and data analysis for these experiments, along with analytical estimates and numerical multiparticle simulations, and provide an outlook for future EIC coupling compensation. Published by the American Physical Society 2025

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Analytical WKB theory for high-harmonic generation and its application to massive Dirac electrons

Here we propose an analytical approach to high-harmonic generation (HHG) for nonperturbative low-frequency and high-intensity fields based on the (Jeffreys-)Wentzel-Kramers-Brillouin (WKB) approximation. By properly taking into account Stokes phenomena of WKB solutions, we obtain wave functions that systematically include the repetitive dynamics of production and acceleration of electron-hole pairs and quantum interference due to phase accumulation between different pair production times (Stückelberg phase). Using the obtained wave functions without relying on any phenomenological assumptions, we explicitly compute electric current (including intra- and interband contributions) as the source of HHG for a massive Dirac system in (1+1) dimensions under an ac electric field. We demonstrate that the WKB approximation agrees well with numerical results obtained by solving the time-dependent Schrödinger equation and point out that the quantum interference is important in HHG. We also predict in the deep nonperturbative regime that (1) harmonic intensities oscillate with respect to electric-field amplitude E 0 and frequency Ω with a period determined by the Stückelberg phase, (2) the cutoff order of HHG is determined by 2eE 0 ℏΩ 2 , with e being the electron charge, and that (3) noninteger harmonics, controlled by the Stückelberg phase, appear as a transient effect. Our WKB theory is particularly suited for a parameter regime, where the Keldysh parameter γ = (Δ/2)Ω/eE 0 ,with Δ being the gap size, is small. This parameter regime corresponds to intense lasers in the terahertz regime for realistic massive Dirac materials. Our analysis implies that the so-called HHG plateau can be observed at the terahertz frequency within the current technology.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Analytic calculation of the vison gap in the Kitaev spin liquid

Although the ground-state energy of the Kitaev spin liquid can be calculated exactly, the associated vison gap energy has to date only been calculated numerically from finite size diagonalization. Here we show that the phase shift for scattering Majorana fermions off a single bond-flip can be calculated analytically, leading to a closed-form expression for the vison gap energy Δ = 0.2633 J . Generalizations of our approach can be applied to Kitaev spin liquids on more complex lattices such as the three dimensional hyper-octagonal lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Fast and Efficient Stochastic Optimization for Analytic Continuation

In this analytic continuation of imaginary-time quantum Monte Carlo data to extract real-frequency spectra remains a key problem in connecting theory with experiment. Here we present a fast and efficient stochastic optimization method (FESOM) as a more accessible variant of the stochastic optimization method introduced by Mishchenko et al. [Phys. Rev. B 62, 6317 (2000)], and we benchmark the resulting spectra with those obtained by the standard maximum entropy method for three representative test cases, including data taken from studies of the two-dimensional Hubbard model. Genearally, we find that our FESOM approach yields spectra similar to the maximum entropy results. In particular, while the maximum entropy method yields superior results when the quality of the data is strong, we find that FESOM is able to resolve fine structure with more detail when the quality of the data is poor. In addition, because of its stochastic nature, the method provides detailed information on the frequency-dependent uncertainty of the resulting spectra, while the maximum entropy method does so only for the spectral weight integrated over a finite frequency region. Therefore, we believe that this variant of the stochastic optimization approach provides a viable alternative to the routinely used maximum entropy method, especially for data of poor quality.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Analytic insights on the information content of new observables

Uncertainty quantification has emerged as a rapidly growing field in nuclear science. Theoretical predictions of physical observables often involve extrapolations to regions that are poorly constrained by laboratory experi- ments and astrophysical observations. Without properly quantified theoretical errors, such model predictions are of limited value. Also, one often deals with theoretical constructs that involve fundamental quantities that are not accessible to experiment or observation. Particularly relevant in this context is the pressure of pure neutron matter. Furthermore, in this Rapid Communication, we develop an analytic framework to answer the question of “How can new data reduce uncertainties of current theoretical models?” Simple and insightful expressions are obtained to quantify the impact of one or two new observables on theoretical uncertainties in two critical quantities: The slope of the symmetry energy at saturation density and the pressure of pure neutron matter at twice nuclear matter saturation density.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Analytical insights into the interplay of momentum, multiplicity, and the speed of sound in heavy-ion collisions

We introduce a minimal model of ultracentral heavy-ion collisions to study the relation between the speed of sound of the produced plasma and the final particles' energy and multiplicity. We discuss how the particles' multiplicity N tot and average energy E tot / N tot is related to the speed of sound c s by c s 2 = d ln ( E tot / N tot ) / d ln N tot if the fluid is inviscid, its speed of sound is constant and all final particles can be measured. We show that finite rapidity cuts on the particles' multiplicity N and energy E introduce corrections between c s 2 and d ln ( E / N ) / d ln N that depend on the system's lifetime. We study analytically these deviations with the Gubser hydrodynamic solution, finding that, for ultrarelativistic bosons, they scale as the ratio of the freeze-out temperature T FO over the maximum initial temperature of the fluid T 0 ; the nonthermodynamic aspect of these corrections is highlighted through their dependence on the system's initial conditions. Published by the American Physical Society 2024

Physics↗
DOE OSTI2014

Analytical solutions of Landau (1+1)-dimensional hydrodynamics

To help guide our intuition, summarize important features, and point out essential elements, we review the analytical solutions of Landau (1+1)-dimensional hydrodynamics and exhibit the full evolution of the dynamics from the very beginning to subsequent times. Special emphasis is placed on the matching and the interplay between the Khalatnikov solution and the Riemann simple wave solution at the earliest times and in the edge regions at later times.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Analytical continuation from bound to resonant states in the Dirac equation with quadrupole-deformed potentials

Here, resonances with pronounced single-particle characteristics are crucial for quantitative descriptions of exotic nuclei near and beyond the drip lines, and often impact halo formation and nucleon decay processes. Since the majority of nuclei are deformed, the interplay between deformation and orbital structure near threshold can lead to improved descriptions of exotic nuclei. Develop a method to study single-particle resonant orbital structure in the Dirac equation with a quadrupole-deformed Woods-Saxon potential. Determine the structure evolution of bound and resonant levels with deformation in this scheme, and examine the impact on halo formation in loosely bound systems, with a focus on the recent halo candidate nucleus 37 Mg. Analytical continuation of the coupling constant (ACCC) method is developed on the basis of the Dirac equation with a deformed Woods-Saxon potential. The scalar and vector terms in the deformed potential are determined by the energies of the valence neutron and nearby orbitals, which are extracted from a self-consistent relativistic Hartree-Bogoliubov (RHB) calculation with the PC-PK1 density functional. As a result, we compare the energies and widths of resonant orbitals in the recent halo nucleus candidate 37 Mg using the ACCC method based on the Dirac coupled-channel equations with those determined from the scattering phase shift (SPS) method. It is found that the results from the two methods agree well for narrow resonances, whereas the SPS method fails for broad resonances. Nilsson levels for bound and resonant orbitals from the ACCC method are calculated over a wide range of deformations and show some decisive hints of halo formation in 37 Mg. In conclusion, in our ACCC model for deformed potentials in the coupled-channel Dirac equations, the crossing of the configuration 1/2[321] and 5/2[312] orbitals at a deformation of approximately 0.5 enhances the probability to occupy the 1/2[321] orbital coming from 2 p3/2 thereby explaining the recent observation of a p-wave one-neutron halo configuration in 37 Mg. The resonant 1/2[301] configuration plays a crucial role in halo formation in the magnesium isotopes beyond A = 40 for a wide range of deformations larger than 0.2.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Construction of wave dark matter halos: Numerical algorithm and analytical constraints

Here we present a wave generalization of the classic Schwarzschild method for constructing self-consistent halos—such a halo consists of a suitable superposition of waves instead of particle orbits, chosen to yield a desired mean density profile. As an illustration, the method is applied to spherically symmetric halos. We derive an analytic relation between the particle distribution function and the wave superposition amplitudes and show how it simplifies in the high-energy (WKB) limit. We verify the stability of such constructed halos by numerically evolving the Schrödinger-Poisson system. The algorithm provides an efficient and accurate way to simulate the time-dependent halo substructures from wave interference. We use this method to construct halos with a variety of density profiles, all of which have a core from the ground-state wave function, though the core-halo relation need not be the standard one.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Analytic continuation of the relativistic three-particle scattering amplitudes

We investigate the relativistic scattering of three identical scalar bosons interacting via pair-wise interactions. Extending techniques from the nonrelativistic three-body scattering theory, we provide a detailed and general prescription for solving and analytically continuing integral equations describing the three-body reactions. We use these techniques to study a system with zero angular momenta described by a single scattering length leading to a bound state in a two-body subchannel. We obtain bound-state-particle and three-particle amplitudes in the previously unexplored kinematical regime; in particular, for real energies below elastic thresholds and complex energies in the physical and unphysical Riemann sheets. We extract positions of three-particle bound-states that agree with previous finite-volume studies, providing further evidence for the consistency of the relativistic finite-volume three-body quantization conditions. We also determine previously unobserved virtual bound states in this theory. Lastly, we find numerical evidence of the breakdown of the two-body finite-volume formalism in the vicinity of the left-hand cuts and argue for the generalization of the existing formalism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

Analytic Evolution of Singular Distribution Amplitudes in QCD

We describe a method of analytic evolution of distribution amplitudes (DA) that have singularities, such as non-zero values at the end-points of the support region, jumps at some points inside the support region and cusps. We illustrate the method by applying it to the evolution of a flat (constant) DA, anti-symmetric at DA and then use it for evolution of the two-photon generalized distribution amplitude. Our approach has advantages over the standard method of expansion in Gegenbauer polynomials, which requires infinite number of terms in order to accurately reproduce functions in the vicinity of singular points, and over a straightforward iteration of an initial distribution with evolution kernel. The latter produces logarithmically divergent terms at each iteration, while in our method the logarithmic singularities are summed from the start, which immediately produces a continuous curve, with only one or two iterations needed afterwards in order to get rather precise results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Analytic pion form factor

The pion electromagnetic form factor and two-pion production in electron-positron collisions are simultaneously fitted by a vector dominance model evolving to perturbative QCD at large momentum transfer. This model was previously successful in simultaneously fitting the nucleon electromagnetic form factors (spacelike region) and the electromagnetic production of nucleon-antinucleon pairs (timelike region). For this pion case dispersion relations are used to produce the analytic connection of the spacelike and timelike regions. The fit to all the data is good, especially for the newer sets of timelike data. The description of high-q2 data, in the timelike region, requires one more meson with ρ quantum numbers than listed in the 2014 Particle Data Group review.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Convenient analytical formula for cluster mean diameter and diameter dispersion after nucleation burst

Here, we propose an alternative method of estimating the mean diameter and dispersion of clusters of particles, formed in a cooling gas, right after the nucleation stage. Using a moment model developed by Friedlander [S. K. Friedlander, Ann. N. Y. Acad. Sci. 404, 354 (1983)], we derive an analytic relationship for both cluster mean diameter and diameter dispersion as a function of two of the characteristic times of the system: the cooling time and the primary constituents collision time. These formulas can be used to predict diameter and dispersion variation with process parameters, such as the initial primary constituents' concentration or cooling rate. It is also possible to use them as an input to the coagulation stage, without the need to compute complex cluster generation during the nucleation burst. We compared our results with a nodal code (NGDE) and got excellent agreement.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗