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At least 199 records · Page 11

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NASA NTRS2018

On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences

All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for “repetition”, an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures. The statistics of the occurrences of patterns indicate that short repetitions are sufficient to account for the differences between natural families and randomized groups of sequences by more than 10 standard deviations, while contiguous sequence patterns shorter than 5 residues are effectively random in their occurrences. A small subset of patterns is sufficient to account for a robust ”familiarity” definition between arbitrary sets of sequences.

Pablo Turjanski↗

DOE OSTI2024

Lattice Green’s Functions for High-Order Finite Difference Stencils

Lattice Green's Functions (LGFs) are fundamental solutions to discretized linear operators, and as such they are a useful tool for solving discretized elliptic PDEs on domains that are unbounded in one or more directions. The majority of existing numerical solvers that make use of LGFs rely on a second-order discretization and operate on domains with free-space boundary conditions in all directions. Under these conditions, fast expansion methods are available that enable precomputation of 2D or 3D LGFs in linear time, avoiding the need for brute-force multi-dimensional quadrature of numerically unstable integrals. Here we focus on higher-order discretizations of the Laplace operator on domains with more general boundary conditions, by (1) providing an algorithm for fast and accurate evaluation of the LGFs associated with high-order dimension-split centered finite differences on unbounded domains, and (2) deriving closed-form expressions for the LGFs associated with both dimension-split and Mehrstellen discretizations on domains with one unbounded dimension. Through numerical experiments we demonstrate that these techniques provide LGF evaluations with near machine-precision accuracy, and that the resulting LGFs allow for numerically consistent solutions to high-order discretizations of the Poisson's equation on fully or partially unbounded 3D domains.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Optomechanical self-organization in a mesoscopic atom array

Increasing the number of particles in a system often leads to qualitative changes in its properties, such as breaking of symmetries and the appearance of phase transitions. This renders a macroscopic system fundamentally different from its individual microscopic constituents. Lying between these extremes, mesoscopic systems exhibit microscopic fluctuations that influence behaviour on longer length scales, leading to critical phenomena and dynamics. Therefore, tracing the properties of well-controlled mesoscopic systems can help bridge the gap between an exact description of few-body microscopic systems and the emergent description of many-body systems. Here we explore the mesoscopic signatures of an optomechanical self-organization phase transition using arrays of cold atoms inside an optical cavity. By precisely engineering atom–cavity interactions, we reveal how critical behaviour depends on the atom number, identify characteristic dynamical behaviours in the self-organized regime and observe a finite optomechanical susceptibility at the critical point. These findings advance our understanding of particle-number- and time-resolved properties of phase transitions in mesoscopic systems.

Atomic and molecular interactions with photons↗

DOE OSTI2023

Mean-field limit of a hybrid system for multi-lane multi-class traffic

This article aims to study coupled mean-field equation and ODEs with discrete events motivated by vehicular traffic flow. Precisely, multi-lane traffic flow in presence of human-driven and autonomous vehicles is considered, with autonomous vehicles possibly influenced by external policymakers. First, a finite-dimensional hybrid system is developed based on the continuous Bando-Follow-the-Leader dynamics coupled with discrete events due to lane-change maneuvers. Then the mean-field limit of the finite-dimensional hybrid system is rigorously derived for the dynamics of the human-driven vehicles. The microscopic lane-change maneuvers of the human-driven vehicles generate a source term for the mean-field PDE. This leads to an infinite-dimensional hybrid system described by coupled Vlasov-type PDE, ODEs, and discrete events.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Normalizing Flows for Microscopic Many-Body Calculations: An Application to the Nuclear Equation of State

We report that normalizing flows are a class of machine learning models used to construct a complex distribution through a bijective mapping of a simple base distribution. We demonstrate that normalizing flows are particularly well suited as a Monte Carlo integration framework for quantum many-body calculations that require the repeated evaluation of high-dimensional integrals across smoothly varying integrands and integration regions. As an example, we consider the finite-temperature nuclear equation of state. An important advantage of normalizing flows is the ability to build highly expressive models of the target integrand, which we demonstrate enables precise evaluations of the nuclear free energy and its derivatives. Furthermore, we show that a normalizing flow model trained on one target integrand can be used to efficiently calculate related integrals when the temperature, density, or nuclear force is varied. This work will support future efforts to build microscopic equations of state for numerical simulations of supernovae and neutron star mergers that employ state-of-the-art nuclear forces and many-body methods.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1978

Transmission media effects on precise Doppler tracking

The effects of the transmission media - the earth's troposphere and ionosphere, and the solar wind - on precise Doppler tracking are discussed. The charged particle effects can be largely removed by dual frequency observations; however there are limitations to these corrections (besides system noise and/or finite integration times) including the effects of magnetic fields, diffraction, and differential refraction, all of which must be carefully evaluated. The earth's troposphere can contribute an error of delta f/f approximately 10 to the minus 14th power.

Callahan, P. S.↗

NASA NTRS1980

Pressure data for four analytically defined arrow wings in supersonic flow

In order to provide experimental data for comparison with newly developed finite difference methods for computing supersonic flows over aircraft configurations, wind tunnel tests were conducted on four arrow wing models. The models were machined under numeric control to precisely duplicate analytically defined shapes. They were heavily instrumented with pressure orifices at several cross sections ahead of and in the region where there is a gap between the body and the wing trailing edge. The test Mach numbers were 2.36, 2.96, and 4.63. Tabulated pressure data for the complete test series are presented along with selected oil flow photographs. Comparisons of some preliminary numerical results at zero angle of attack show good to excellent agreement with the experimental pressure distributions.

Townsend, J. C.↗

NASA NTRS1993

Computing Vibration-Mode Matrices From Finite-Element Output

Postprocessing algorithms devised to facilitate vibrational-mode analyses of dynamics of complicated structures. Yields inertia matrices and elastic/rigid-coupling matrices. Such analyses important in simulation and control in active suppression of vibrations in large building or in precise aiming of large antenna.

Levy, Roy↗

NASA NTRS1989

Domain decomposition methods for systems of conservation laws: Spectral collocation approximations

Hyperbolic systems of conversation laws are considered which are discretized in space by spectral collocation methods and advanced in time by finite difference schemes. At any time-level a domain deposition method based on an iteration by subdomain procedure was introduced yielding at each step a sequence of independent subproblems (one for each subdomain) that can be solved simultaneously. The method is set for a general nonlinear problem in several space variables. The convergence analysis, however, is carried out only for a linear one-dimensional system with continuous solutions. A precise form of the error reduction factor at each iteration is derived. Although the method is applied here to the case of spectral collocation approximation only, the idea is fairly general and can be used in a different context as well. For instance, its application to space discretization by finite differences is straight forward.

Quarteroni, Alfio↗

DOE OSTI2024

A self-consistent Hamiltonian model of the ponderomotive force and its structure preserving discretization

In the presence of an inhomogeneous oscillatory electric field, charged particles experience a net force, averaged over the oscillatory timescale, known as the ponderomotive force. We derive a one-dimensional Hamiltonian model which self-consistently couples the electromagnetic field to a plasma which experiences the ponderomotive force. We derive a family of structure preserving discretizations of the model of varying order in space and time using conforming and broken finite element exterior calculus spectral element methods. In all variants of our discretization framework, the method is found to conserve the Casimir invariants of the continuous model to machine precision and the energy to the order of the splitting method used.

Physics↗

DOE OSTI2025

Toward quantum tunneling from excited states: Recovering imaginary-time instantons from a real-time analysis

We revisit the path integral description of quantum tunneling and its generalization to excited states. For clarity, we focus on the simple toy model of a point particle in a double-well potential, for which we perform all steps explicitly. Instead of performing the familiar Wick rotation from physical to imaginary time—which is inconsistent with the requisite boundary conditions when treating tunneling from excited states—we regularize the path integral by adding an infinitesimal complex contribution to the Hamiltonian, while keeping time strictly real. We find that this gives rise to a complex stationary-phase solution, in agreement with recent insights from Picard-Lefshetz theory. We then show that there exists a class of analytic solutions for the corresponding equations of motion, which can be made to match the appropriate boundary conditions in the physically relevant limits of a vanishing regulator and an infinite physical time. We provide a detailed discussion of this nontrivial limit. We find that, for systems without an explicit time-dependence, our approach reproduces the picture of an instantonlike solution defined on a finite Euclidean-time interval. Lastly, we discuss the generalization of our approach to broader classes of systems, for which it serves as a reliable framework for high-precision calculations. Published by the American Physical Society 2025

Steingasser, Thomas (ORCID:0000000217262117)↗

NASA NTRS1994

Superconducting axisymmetric finite elements based on a gauged potential variational principle. Part 2: Solutions and numerical results

This paper discusses an incremental-iterative nonlinear solution technique for solving the nonlinear finite element equations of the superconducting state of a superconductor. The untreated equations are highly ill-conditioned and are impossible to solve within the typical 16-place double precision supplied by most computers. A combination of matrix scaling and mesh grading techniques is used to reduce the condition number of the tangent stiffness matrix and increase the accuracy of the current carrying boundary layer representation. Numerical results for a one-dimensional model of a time-independent superconductor treated by the Ginzburg-Landau model are presented and discussed. The computed solutions clearly display the Meissner effect of magnetic field expulsion from the central region of the superconductor. These results are compared to the physics of a low-viscosity fluid problem. From this analogy, a physical argument is advanced about the macroscopic behavior of superconductors.

Schuler, James J.↗

NASA NTRS2009

Fused Bead Analysis of Diogenite Meteorites

Bulk rock chemistry is an essential dataset in meteoritics and planetary science [1]. A common method used to obtain the bulk chemistry of meteorites is ICP-MS. While the accuracy, precision and low detection limits of this process are advantageous [2], the sample size used for analysis (approx.70 mg) can be a problem in a field where small and finite samples are the norm. Fused bead analysis is another bulk rock analytical technique that has been used in meteoritics [3]. This technique involves forming a glass bead from ~10 mg of sample and measuring its chemistry using a defocused beam on a microprobe. Though the ICP-MS has lower detection limits than the microprobe, the fused bead method destroys a much smaller sample of the meteorite. Fused bead analysis was initially designed for samples with near-eutectic compositions and low viscosities. Melts generated of this type homogenize at relatively low temperatures and produce primary melts near the sample s bulk composition [3]. The application of fused bead analysis to samples with noneutectic melt compositions has not been validated. The purpose of this study is to test if fused bead analysis can accurately determine the bulk rock chemistry of non-eutectic melt composition meteorites. To determine this, we conduct two examinations of the fused bead. First, we compare ICP-MS and fused bead results of the same samples using statistical analysis. Secondly, we inspect the beads for the presence of crystals and chemical heterogeneity. The presence of either of these would indicate incomplete melting and quenching of the bead.

Mittlefehldt, D.W.↗

NASA NTRSDate not supplied

Coherent Mode Decomposition for Kolmogorov Optical Turbulence in a Finite Aperture

An analysis of the coherent mode decomposition of an optical field after propagation through atmospheric turbulence is presented. The coherent modes represent an ideal basis by which to decompose the field for design of mode-limited optical systems. Due to rotational symmetry of the Fredholm integral operator for Kolmogorov optical turbulence, the coherent modes exhibit separable solutions classified by a radial and azimuthal mode index. The study of the coherent modes is then reduced to that of the radial functions determined by the coherence ratio and obscuration ratio. Analysis of the spectrum of eigenvalues yields sharp bounds on the efficiency of receivers using incoherent or coherent combining with mode-limited photonic devices in the presence of Kolmogorov turbulence. The effective number of modes needed to represent Kolmogorov optical turbulence is studied via the von Neumann entropy, purity, and largest eigenvalue, and the differences in the different definitions is discussed. The similarity of the coherent modes to linearly polarized (LP) fiber modes is quantified yielding a precise characterization of the maximum gain that can be achieved in mode-limited systems via mode shaping techniques. As a final application, a mode sorting technique is presented for optimally splitting power from atmospherically degraded light into a finite number of modes simultaneously maximizing total coupling efficiency and minimizing the difference in average power between channels.

free-space optical communication↗

NASA NTRSDate not supplied

Coherent Mode Decomposition for Kolmogorov Optical Turbulence in a Finite Aperture

An analysis of the coherent mode decomposition of an optical field after propagation through atmospheric turbulence is presented. The coherent modes represent an ideal basis by which to decompose the field for design of mode-limited optical systems. Using the rotational symmetry of the Fredholm integral operator for Kolmogorov optical turbulence, it is shown that the coherent modes exhibit separable solutions classified by radial and azimuthal quantum numbers. The study of the coherent modes is then reduced that of the radial functions determined by the aperture-coherence diameter ratio and obscuration ratio. Analysis of the spectrum of eigenvalues yields sharp bounds on the efficiency of receivers using incoherent or coherent combining with mode-limited photonic devices in the presence of Kolmogorov turbulence. The effective number of modes needed to represent Kolmogorov optical turbulence is studied via the von Neumann entropy, purity, and largest eigenvalue, and the differences in the different definitions is discussed. The similarity of the coherent modes to linearly polarized (LP) fiber modes is quantified yielding a precise characterization of the maximum gain that can be achieved in mode-limited systems via mode shaping techniques. As a final application, a mode sorting technique is presented for optimally splitting power from atmospherically degraded light into a finite number of modes simultaneously maximizing total coupling efficiency and minimizing the average and instantaneous power ratio between channels.

free-space optical communication↗

NASA NTRS2019

The NANOGrav 12.5 yr Data Set: The Frequency Dependence of Pulse Jitter in Precision Millisecond Pulsars

Low-frequency gravitational-wave experiments require the highest timing precision from an array of the moststable millisecond pulsars. Several known sources of noise on short timescales in single radio pulsar observationsare well described by a simple model of three components: template fitting from a finite signal-to-noise ratio, pulsephase/amplitude jitter from single-pulse stochasticity, and scintillation errors from short-timescale interstellarscattering variations. Currently template-fitting errors dominate, but as radio telescopes push toward higher signalto-noise ratios, jitter becomes the next dominant term for most millisecond pulsars. Understanding the statistics ofjitter becomes crucial for properly characterizing arrival time uncertainties. We characterize the radio frequencydependence of jitter using data on 48 pulsars in the North American Nanohertz Observatory for GravitationalWaves timing program. We detect significant jitter in 43 of the pulsars and test several functional forms for itsfrequency dependence; we find significant frequency dependence for 30 pulsars. We find moderate correlations ofrms jitter with pulse width (R = 0.62) and number of profile components (R = 0.40); the single-pulse rms jitter istypically 1% of pulse phase. The average frequency dependence for all pulsars using a power-law model hasindex 0.42. We investigate the jitter variations for the interpulse of PSR B1937+21 and find no significantdeviations from the main pulse rms jitter. We also test the time variation of jitter in two pulsars and find thatsystematics likely bias the results for high-precision pulsars. Pulsar timing array analyses must properly modeljitter as a significant component of the noise within the detector.

Lam, M. T.↗

DOE OSTI2022

Non-decoupling new particles

We initiate the study of a new class of beyond the Standard Model states that we call “Loryons.” They have the defining characteristic of being non-decoupling, in the sense that their physical mass is dominated by a contribution from the vacuum expectation value of the Higgs boson. The stakes are high: the discovery of a Loryon would tell us that electroweak symmetry must be non-linearly realized in the effective field theory of the Standard Model. Loryons have their masses bounded from above by perturbative unitarity considerations and thus define a finite parameter space for exploration. After providing a complete catalog of Loryon representations under mild assumptions, we turn to examining the constraints on the parameter space from Higgs couplings measurements, precision electroweak tests, and direct collider searches. We show that most fermionic candidates are already ruled out (with some notable exceptions), while much of the scalar Loryon parameter space is still wide open for discovery.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Solving high-dimensional partial integral differential equations: The finite expression method

Partial integro-differential equations (PIDEs) have broad applications in the sciences, from electro-magnetism to options pricing. Here, in this paper, we introduce a new finite expression method (FEX) to solve PIDEs. This approach builds upon the original FEX and its inherent advantages with new advances: 1) A novel method of parameter grouping is proposed to reduce the number of coefficients in high-dimensional function approximation; 2) A Taylor series approximation method is implemented to significantly improve the computational efficiency and accuracy of the evaluation of the integral terms of PIDEs. The new FEX based method, denoted FEX-PG to indicate the addition of the parameter grouping (PG) step to the algorithm, provides both high accuracy and interpretable numerical solutions, with the outcome being an explicit equation that facilitates intuitive understanding of the underlying solution structures. These features are often absent in traditional methods, such as finite element methods (FEM) and finite difference methods, as well as in deep learning-based approaches. To benchmark our method against recent advances, we apply the new FEX-PG to solve benchmark PIDEs in the literature. In high-dimensional settings, FEX-PG exhibits strong and robust performance, achieving relative errors on the order of single precision machine epsilon, significantly outperforming existing approaches based on neural networks.

Combinatorial optimization↗