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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

CAML: Commutative Algebra Machine Learning─A Case Study on Protein–Ligand Binding Affinity Prediction

Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein−ligand binding affinities. Specifically, we apply persistent Stanley−Reisner theory, a key concept in combinatorial commutative algebra, to the affinity predictions of protein−ligand binding and metalloprotein−ligand binding. We present three new algorithms, i.e., element-specific commutative algebra, category-specific commutative algebra, and commutative algebra on bipartite complexes, to tackle the complexity of data involved in (metallo) protein−ligand complexes. We show that the proposed CAML outperforms other state-of-theart methods in (metallo) protein−ligand binding affinity predictions, indicating the great potential of commutative algebra learning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Multilevel elliptic smoothing of large three-dimensional grids

Elliptic grid generation methods have been used for many years to smooth and improve grids generated by algebraic interpolation schemes. However, the elliptic system that must be solved is nonlinear and convergence is generally very slow for large grids. In an attempt to make elliptic methods practical for large three-dimensional grids, a two-stage implementation is developed where the overall grid point locations are set using a coarse grid generated by the elliptic system. The coarse grid is then interpolated to generate a finer grid which is smoothed using only a few iterations of the elliptic system.

Mastin, C. Wayne↗
NASA NTRS1992

Variable-complexity aerodynamic-structural design of a high-speed civil transport wing

A variable-complexity strategy of combining simple and detailed analysis methods is presented for the design optimization of a high-speed civil transport (HSCT) wing. Two sets of results are shown: the aerodynamic design of the wing using algebraic weight equations for structural considerations, and optimization results of the internal wing structure for a fixed wing configuration. We show example results indicating that using simple analysis methods alone for the calculation of a critical constraint can allow an optimizer to exploit weaknesses in the analysis. The structural optimization results provide a valuable check for the weight equations used in the aerodynamic design. In addition, these results confirm the need for using simple, algebraic models in conjunction with more detailed analysis methods. A strategy of interlaced aerodynanic-structural design is proposed.

Hutchison, M. G.↗
NASA NTRS1993

Accuracy of least-squares methods for the Navier-Stokes equations

Recently there has been substantial interest in least-squares finite element methods for velocity-vorticity-pressure formulations of the incompressible Navier-Stokes equations. The main cause for this interest is the fact that algorithms for the resulting discrete equations can be devised which require the solution of only symmetric, positive definite systems of algebraic equations. On the other hand, it is well-documented that methods using the vorticity as a primary variable often yield very poor approximations. Thus, here we study the accuracy of these methods through a series of computational experiments, and also comment on theoretical error estimates. It is found, despite the failure of standard methods for deriving error estimates, that computational evidence suggests that these methods are, at the least, nearly optimally accurate. Thus, in addition to the desirable matrix properties yielded by least-squares methods, one also obtains accurate approximations.

Bochev, Pavel B.↗
NASA NTRS1993

Accuracy of least-squares methods for the Navier-Stokes equations

Recently there has been substantial interest in least-squares finite element methods for velocity-vorticity-pressure formulations of the incompressible Navier-Stokes equations. The main cause for this interest is the fact that algorithms for the resulting discrete equations can be devised which require the solution of only symmetric, positive definite systems of algebraic equations. On the other hand, it is well-documented that methods using the vorticity as a primary variable often yield very poor approximations. Thus, here we study the accuracy of these methods through a series of computational experiments, and also comment on theoretical error estimates. It is found, despite the failure of standard methods for deriving error estimates, that computational evidence suggests that these methods are, at the least, nearly optimally accurate. Thus, in addition to the desirable matrix properties yielded by least-squares methods, one also obtains accurate approximations.

Bochev, Pavel B.↗
NASA NTRSDate not supplied

Towards Formalization of Advanced Linear Algebra with Applications to Dynamical Systems using PVS

Linear Algebra is essential for numerous aerospace problems of interest. Formal reasoning about hybrid systems that contain variables modeled by differential equations rely on concepts from Linear Algebra such as eigenvalues, matrix decompositions, and matrix valued functions. For example, the long-term dynamics of a system of differential equations depend on the stability/instability of its equilibrium points, which often reduces to an eigenvalue problem. This talk will embark on a quest to formalize theorems and results about eigenvalues and eigenvectors using PVS. We shall start our journey with 2 x 2 complex matrices, where we will apply our PVS code to a simple example of a dynamical system. Since it can be difficult or impossible to give simple expressions of eigenvalues for larger matrices (i.e. 5 x 5 or higher), we then move towards specifying the power method for verified computation of eigenvalue approximations in PVS. This effort requires development of multivariate complex arithmetic. At the end of the day, having such additions to the PVS NASA libraries will help move towards the use of formal methods to verify concepts of control theory and system level verification.

Linear Algebra↗
NASA NTRS1999

A Textbook for a First Course in Computational Fluid Dynamics

This paper describes and discusses the textbook, Fundamentals of Computational Fluid Dynamics by Lomax, Pulliam, and Zingg, which is intended for a graduate level first course in computational fluid dynamics. This textbook emphasizes fundamental concepts in developing, analyzing, and understanding numerical methods for the partial differential equations governing the physics of fluid flow. Its underlying philosophy is that the theory of linear algebra and the attendant eigenanalysis of linear systems provides a mathematical framework to describe and unify most numerical methods in common use in the field of fluid dynamics. Two linear model equations, the linear convection and diffusion equations, are used to illustrate concepts throughout. Emphasis is on the semi-discrete approach, in which the governing partial differential equations (PDE's) are reduced to systems of ordinary differential equations (ODE's) through a discretization of the spatial derivatives. The ordinary differential equations are then reduced to ordinary difference equations (O(Delta)E's) using a time-marching method. This methodology, using the progression from PDE through ODE's to O(Delta)E's, together with the use of the eigensystems of tridiagonal matrices and the theory of O(Delta)E's, gives the book its distinctiveness and provides a sound basis for a deep understanding of fundamental concepts in computational fluid dynamics.

Zingg, D. W.↗
NASA NTRS1987

Petrov-Galerkin methods for natural convection in directional solidification of binary alloys

A Petrov-Galerkin finite element method is presented for calculation of the steady, axisymmetric thermosolutal convection and interface morphology in a model for vertical Bridgman crystal growth of nondilute binary alloys. The Petrov-Galerkin method is based on the formulation for biquadratic elements developed by Heinrich and Zienkiewicz and is introduced into the calculation of the velocity, temperature and concentration fields. The algebraic system is solved simultaneously for the field variables and interface shape by Newton's method. The results of the Petrov-Galerkin method are compared critically with those of Galerkin's method using the same finite element grids. Significant improvements in accuracy are found with the Petrov-Galerkin method only when the mesh is refined and when the formulation of the residual equations is modified to account for the mixed boundary conditions that arise at the solidification interface. Calculations for alloys with stable and unstable solute gradients show the occurrence of classical flow transitions and morphological instabilities in the solidification system.

Adornato, Peter M.↗
NASA NTRS1987

Estimation of blade airloads from rotor blade bending moments

This paper presents a method for the estimation of blade airloads, based on the measurements of flap bending moments. In this procedure, the blade rotation in vacuum modes is calculated, and the airloads are expressed as an algebraic sum of the mode shapes, modal amplitudes, mass distribution, and frequency properties. The method was validated by comparing the calculated airload distribution with the original wind tunnel measurements which were made using ten modes and twenty measurement stations. Good agreement between the predicted and the measured airloads was found up to 0.90 R, but the agreement degraded towards the blade tip. The method is shown to be quite robust to the type of experimental problems that could be expected to occur in the testing of full-scale and model-scale rotors.

Bousman, William G.↗
NASA NTRS1995

Three-dimensional aerodynamic shape optimization using discrete sensitivity analysis

An aerodynamic shape optimization procedure based on discrete sensitivity analysis is extended to treat three-dimensional geometries. The function of sensitivity analysis is to directly couple computational fluid dynamics (CFD) with numerical optimization techniques, which facilitates the construction of efficient direct-design methods. The development of a practical three-dimensional design procedures entails many challenges, such as: (1) the demand for significant efficiency improvements over current design methods; (2) a general and flexible three-dimensional surface representation; and (3) the efficient solution of very large systems of linear algebraic equations. It is demonstrated that each of these challenges is overcome by: (1) employing fully implicit (Newton) methods for the CFD analyses; (2) adopting a Bezier-Bernstein polynomial parameterization of two- and three-dimensional surfaces; and (3) using preconditioned conjugate gradient-like linear system solvers. Whereas each of these extensions independently yields an improvement in computational efficiency, the combined effect of implementing all the extensions simultaneously results in a significant factor of 50 decrease in computational time and a factor of eight reduction in memory over the most efficient design strategies in current use. The new aerodynamic shape optimization procedure is demonstrated in the design of both two- and three-dimensional inviscid aerodynamic problems including a two-dimensional supersonic internal/external nozzle, two-dimensional transonic airfoils (resulting in supercritical shapes), three-dimensional transport wings, and three-dimensional supersonic delta wings. Each design application results in realistic and useful optimized shapes.

Burgreen, Gregory W.↗
DOE OSTI2024

Connected Traffic Signal Coordination Optimization Framework through Network-Wide Adaptive Linear Quadratic Regulator–Based Control Strategy

Traffic congestion in metropolitan areas causes several significant challenges, such as longer travel times, decreased productivity, increased fuel consumption and vehicle emissions, and even severe injuries during crashes. Traffic signal control is a management approach to reduce traffic congestion and allocate the appropriate right of way for safety and mobility efficiency, both in temporal and spatial domains. Here, this study proposes a network-wide adaptive signal control coordination optimization framework based on the linear quadratic regulator algorithm. The traffic flow conditions driven by signal control inputs are formulated based on their network-wide state-space representation. After modeling traffic control regulation constraints, an adaptive linear quadratic regulator algorithm is designed to maximize the network-wide total throughput under the current conditions. Optimal signal control split time durations for multiple intersections in the network are derived by solving the algebraic Riccati equation. Furthermore, the recursive least square parameter estimation method is employed to quantify dynamic traffic condition changes. To verify the effectiveness of this proposed signal control framework, both simulation and real-world experimental tests are conducted for multiple intersections in downtown Chattanooga, Tennessee, United States. In preparation for real-world experimental tests, pipelines for real-time data processing implementation and historical traffic flow data analysis are conducted. The test results demonstrate that the proposed control framework achieves a decrease in travel time by up to 19.4%, total time spent (TTS) by up to 11.9%, and relative queue balance (RQB) by up to 15.6%. The research findings indicate that the proposed signal control framework can be generalized to handle large scale signal control optimization network-wide.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

cppTPSA/pyTPSA: a C++/Python package for truncated power series algebra

The truncated power series algebra (TPSA), also referred to as differential algebra (DA), is a well-established and widely used method in particle accelerator physics and astronomy. The most straightforward usage of TPSA/DA is to calculate the Taylor expansion of a given function at a specific point up to order ?. In recent years, as the application of TPSA/TA has been extended to other fields, a reusable implementation of TPSA/DA as a modern C++ library or other high level programming language like Python has become desirable. The cppTPSA package implements TPSA/DA in C++11 and provides developers a convenient library with which to build advanced TPSA/DA-based methods. A Python 3 library, pyTPSA, has also been developed based on the C++ lib.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Beam Dynamics of the Muon $g\textrm{-}2$ Experiment

The Muon $g\textrm{-}2$ Experiment (E989) at Fermilab aims to measure the muon anomalous magnetic moment $a_{\mu}$ with unprecedented precision, potentially uncovering physics beyond the Standard Model of particle physics. The result based on Runs 1-3, released in 2023, achieved a precision of 0.20 ppm. The experiment circulates muons in a storage ring, measuring $a_{\mu}$ from decay positron time and energy measurements collected with calorimeters. To achieve the required accuracy, it is crucial to measure and control the magnetic field in the ring with high precision. Beam dynamics corrections are necessary for muons not orbiting exactly in the midplane, for their oscillations, and for electric field effects. Highly accurate beam dynamics simulations are instrumental for quantifying and validating the beam dynamics corrections, ultimately improving the precision of the $a_{\mu}$ measurement and facilitating the achievement of the ambitious $70\:\mathrm{ppb}$ systematic uncertainty goal. The measured field data was incorporated into models for simulations using three codes: \texttt{gm2ringsim} (an internal Geant4-based code), \textit{COSY INFINITY}, and \textit{BMAD}. The advantages of \texttt{gm2ringsim} include using CAD-based geometry and modelling the detector effects. \textit{COSY INFINITY} is a highly accurate and efficient code that uses high-order differential-algebraic transfer maps, precise fringe field calculations, and advanced symplectification methods. Symplectification is important for maintaining the physical correctness of the muon beam behaviour with high precision over the storage time, ensuring conservation of phase space volume and preventing artificial damping or excitation of particle motion. The experiment completed its final Run 6 in July 2023, collecting 21 times more data than the previous BNL experiment. Analyses of data from Runs 4-6 are ongoing, with results planned for release in 2025, potentially resolving the current tension between experiment and theory.

43 PARTICLE ACCELERATORS↗
NASA NTRS1974

Distinguishing between CAT and non-CAT areas by use of discriminant function analysis

The investigation considered is concerned with a method in which a statistical approach is employed to determine algebraic functions involving selected synoptic-scale parameters which would indicate areas and altitudes of CAT in the stratosphere over the western U.S. The statistical approach selected is based on discriminant function analysis. The functions are determined from combinations of synoptic-scale parameters and stratospheric turbulence data. It was found in the investigation that there is a relationship between selected combinations of synoptic-scale parameters of the upper troposphere and lower stratosphere and stratospheric clear-air turbulence.

Clark, T. L.↗
NASA NTRS1974

The application of sensitivity analysis to models of large scale physiological systems

A survey of the literature of sensitivity analysis as it applies to biological systems is reported as well as a brief development of sensitivity theory. A simple population model and a more complex thermoregulatory model illustrate the investigatory techniques and interpretation of parameter sensitivity analysis. The role of sensitivity analysis in validating and verifying models, and in identifying relative parameter influence in estimating errors in model behavior due to uncertainty in input data is presented. This analysis is valuable to the simulationist and the experimentalist in allocating resources for data collection. A method for reducing highly complex, nonlinear models to simple linear algebraic models that could be useful for making rapid, first order calculations of system behavior is presented.

Leonard, J. I.↗
NASA NTRS1983

On the three-dimensional vibrations of the cantilevered rectangular parallelepiped

A solution is presented for the three-dimensional problem of determining the free vibration frequencies and mode shapes for a rectangular parallelepiped which is completely fixed on one face and free on the other five faces. This problem apparently is previously unsolved in the published literature. The Ritz method is used, with displacements assumed in the form of algebraic polynomials. Convergence is studied. Numerical results are given for the first five frequencies of each of the four symmetry classes of vibration, for five thick parallelepiped configurations, including the cube. Contour plots are exhibited for the modal displacements of the cube. The effects of varying Poisson's ratio are also observed.

Leissa, A.↗
NASA NTRS1985

New results on the PLL false lock phenomenon

Conditions, based on the multipliers of a linear differential equation with periodic coefficients, for the occurrence of false lock in a phase lock loop (PLL) are presented. Two new and powerful algorithms are presented for computing the frequency difference between the reference and voltage controlled oscillator when the loop is false locked. The first algorithm expresses omega f sup -1 as a power series in the closed loop gain. The second algorithm expresses omega sup -1 as part of a solution to a nonlinear algebraic system of equations which can be solved by numerical methods. The power of both algorithms is illustrated by application and comparison.

Stensby, J. L.↗