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At least 109 records · Page 6

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DOE OSTI2025

In silico λ-dynamics predicts protein binding specificities to modified RNAs

Abstract RNA modifications shape gene expression through a variety of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.

Biochemistry & Molecular Biology↗

NASA NTRS1972

Numerical method for the solution of large systems of differential equations of the boundary layer type

A numerical method for the solution of large systems of nonlinear differential equations of the boundary-layer type is described. The method is a modification of the technique for satisfying asymptotic boundary conditions. The present method employs inverse interpolation instead of the Newton method to adjust the initial conditions of the related initial-value problem. This eliminates the so-called perturbation equations. The elimination of the perturbation equations not only reduces the user's preliminary work in the application of the method, but also reduces the number of time-consuming initial-value problems to be numerically solved at each iteration. For further ease of application, the solution of the overdetermined system for the unknown initial conditions is obtained automatically by applying Golub's linear least-squares algorithm. The relative ease of application of the proposed numerical method increases directly as the order of the differential-equation system increases. Hence, the method is especially attractive for the solution of large-order systems. After the method is described, it is applied to a fifth-order problem from boundary-layer theory.

Green, M. J.↗

NASA NTRS1978

A computational scheme usable for calculating the plume backflow region

The effects of the nozzle wall boundary layer on the plume flowfield are neglected in the majority of computational schemes which exist for the calculation of rocket engine exhaust plume flowfields. This neglect, which is unimportant in many applications, becomes unacceptable for applications where a surface which can be adversely affected by plume impingement forces, heating, or contamination is located behind the nozzle exit plane in what is called the 'plume backflow region'. The flow in this region originates in, and is highly affected by, the nozzle wall boundary layer. The inclusion of the effects of the boundary layer in the calculations is required for an appropriate determination of the flowfield properties within this region. A description is presented of the results of modifications of a method-of-characteristics computer program. The modifications were made to include the effects of the nozzle wall boundary layer on the plume flowfield. A comparison of computed and experimental data indicates that the employed computer program may be a useful tool for calculating the entire plume flowfield for liquid propellant rocket engines.

Cooper, B. P., Jr.↗

NASA NTRS1979

A three-dimensional viscous/potential flow interaction analysis method for multi-element wings: Modifications to the potential flow code to allow part-span, high-lift devices and close-interference calculations

The description of the modified code includes details of a doublet subpanel technique in which panels that are close to a velocity calculation point are replaced by a subpanel set. This treatment gives the effect of a higher panel density without increasing the number of unknowns. In particular, the technique removes the close approach problem of the earlier singularity model in which distortions occur in the detailed pressure calculation near panel corners. Removal of this problem allowed a complete wake relaxation and roll-up iterative procedure to be installed in the code. The geometry package developed for the new technique and also for the more general configurations is based on a multiple patch scheme. Each patch has a regular array of panels, but arbitrary relationships are allowed between neighboring panels at the edges of adjacent patches. This provides great versatility for treating general configurations.

Maskew, B.↗

NASA NTRS1998

Assessment of Uncertainty in the Determination of Activation Energy for Polymeric Materials

An assessment of the experimental uncertainty in obtaining the kinetic activation energy from thermogravimetric analysis (TGA) data is presented. A neat phenolic resin, Borden SC1O08, was heated at three heating rates to obtain weight loss vs temperature data. Activation energy was calculated by two methods: the traditional Flynn and Wall method based on the slope of log(q) versus 1/T, and a modification of this method where the ordinate and abscissa are reversed in the linear regression. The modified method produced a more accurate curve fit of the data, was more sensitive to data nonlinearity, and gave a value of activation energy 75 percent greater than the original method. An uncertainty analysis using the modified method yielded a 60 percent uncertainty in the average activation energy. Based on this result, the activation energy for a carbon-phenolic material was doubled and used to calculate the ablation rate In a typical solid rocket environment. Doubling the activation energy increased surface recession by 3 percent. Current TGA data reduction techniques that use the traditional Flynn and Wall approach to calculate activation energy should be changed to the modified method.

Darby, Stephania P.↗

NASA NTRS1983

A new calibration of the extragalactic distance scale using Cepheids and RR Lyrae stars

Visual absolute magnitudes of classical Cepheids, metal-poor RR Lyrae stars and short-period type II Cepheids have been determined with very high precision by combining a large number of old and new astrophysical data. Five independent methods (four observational and one theoretical) have been successfully used: (1) secular and statistical parallaxes; (2) moving-group parallaxes; (3) cluster main-sequence fitting; (4) the Baade-Wesselink method and its modifications; and (5) light-curve and velocity-curve fitting (the theoretical method). With these five adopted methods, the zero point of the galactic and extragalactic distance scale can be set on a relatively firm and self-consistent basis. Classical Cepheids and RR Lyrae stars now provide essentially identical distances to nearby galaxies: the distance modulus to the Large Magellanic Cloud is 18.5 and to the Small Magellanic Cloud is 18.8, both with an uncertainty of 0.1. The distance to the center of our Galaxy is 8.6 plus or minus 0.5 kiloparsecs. The major uncertainty in these values lies in the correction for interstellar extinction.

Stothers, R. B.↗

DOE OSTI2025

An extension of the localized artificial diffusivity method for immiscible and high density ratio flows

The localized artificial diffusivity (LAD) method is widely regarded as the preferred multi-material regularization scheme for the compact finite difference method, because it is conservative, easy to implement, and generally robust for a wide range of multi-material problems. However, traditional LAD methods face significant challenges when applied to flows with large density ratios and when maintaining thermodynamic equilibrium across material interfaces. These limitations arise from the formulation of the artificial diffusivity flux and the reliance on enthalpy diffusion for interface regularization. Additionally, traditional LAD methods struggle to ensure stability under large density ratio conditions, fail to maintain a finite interface thickness, and are therefore unsuitable for modeling immiscible interfaces. Here, in this work, we discuss the origins of these issues in traditional LAD methods and propose modifications which enable the simulation of large density ratio and immiscible flows. The proposed method targets the artificial diffusion fluxes at gradients and ringing in the volume fraction, rather than the mass fraction in traditional methods, to consistently regularize large density ratio interfaces. Furthermore, the proposed method introduces an artificial bulk density diffusion term to enforce equilibrium conditions across interfaces. To address the challenge of modeling immiscible flows, a conservative diffuse interface term is incorporated into the formulation to ensure a finite interface thickness. Specific consideration is taken in the design of the method to ensure that these crucial properties are maintained for N -material flows. The effectiveness of the proposed method is demonstrated through a series of canonical test cases, and its accuracy is validated by comparison with experimental data on micro-bubble collapse in water. These results highlight the method’s robustness and its ability to overcome the limitations of traditional LAD approaches.

Artificial diffusivity↗

NASA NTRS2011

Interaction of microwaves with carbon nanotubes to facilitate modification

The present invention is directed toward methods of crosslinking carbon nanotubes to each other using microwave radiation, articles of manufacture produced by such methods, compositions produced by such methods, and applications for such compositions and articles of manufacture. The present invention is also directed toward methods of radiatively modifying composites and/or blends comprising carbon nanotubes with microwaves, and to the compositions produced by such methods. In some embodiments, the modification comprises a crosslinking process, wherein the carbon nanotubes serve as a conduit for thermally and photolytically crosslinking the host matrix with microwave radiation.

Tour, James M.↗

NASA NTRS1948

The experimental determination of the moments of inertia of airplanes by a simplified compound-pendulum method

A simplified compound-pendulum method for the experimental determination of the moments of inertia of airplanes about the x and y axes is described. The method is developed as a modification of the standard pendulum method reported previously in NACA report, NACA-467. A brief review of the older method is included to form a basis for discussion of the simplified method. (author)

MOMENTS OF INERTIA↗

NASA NTRS2005

Faster Evolution of More Multifunctional Logic Circuits

A modification in a method of automated evolutionary synthesis of voltage-controlled multifunctional logic circuits makes it possible to synthesize more circuits in less time. Prior to the modification, the computations for synthesizing a four-function logic circuit by this method took about 10 hours. Using the method as modified, it is possible to synthesize a six-function circuit in less than half an hour. The concepts of automated evolutionary synthesis and voltage-controlled multifunctional logic circuits were described in a number of prior NASA Tech Briefs articles. To recapitulate: A circuit is designed to perform one of several different logic functions, depending on the value of an applied control voltage. The circuit design is synthesized following an automated evolutionary approach that is so named because it is modeled partly after the repetitive trial-and-error process of biological evolution. In this process, random populations of integer strings that encode electronic circuits play a role analogous to that of chromosomes. An evolved circuit is tested by computational simulation (prior to testing in real hardware to verify a final design). Then, in a fitness-evaluation step, responses of the circuit are compared with specifications of target responses and circuits are ranked according to how close they come to satisfying specifications. The results of the evaluation provide guidance for refining designs through further iteration.

Stoica, Adrian↗

NASA NTRS1981

The effect of inflow velocity profiles on the performance of supersonic ejector nozzles

The design of supersonic nozzles is becoming increasingly complex as conflicting requirements for low noise, higher efficiency, and wider operating range are driving the designer toward more variable geometry and multiple stream flows. Analysis techniques must be modified and expanded to take into account these additional complexities and still retain the rapid computational rate necessary for optimization and design studies. A nozzle analysis must handle more flow streams, more complex geometries, and more highly distorted initial profiles. This paper discusses some modifications to a method for calculating the performance characteristics of supersonic ejector nozzles and demonstrates the improvement in results the modifications provide.

Bishop, A. R.↗

NASA NTRS1987

Survey of methods for calculating sensitivity of general eigenproblems

A survey of methods for sensitivity analysis of the algebraic eigenvalue problem for non-Hermitian matrices is presented. In addition, a modification of one method based on a better normalizing condition is proposed. Methods are classified as Direct or Adjoint and are evaluated for efficiency. Operation counts are presented in terms of matrix size, number of design variables and number of eigenvalues and eigenvectors of interest. The effect of the sparsity of the matrix and its derivatives is also considered, and typical solution times are given. General guidelines are established for the selection of the most efficient method.

Murthy, Durbha V.↗

NASA NTRS1988

Derivatives of eigenvalues and eigenvectors of a general complex matrix

Murthy, Durbha V.↗

NASA NTRS1986

Controller design via structural reduced modeling by FETM

The Finite Element - Transfer Matrix (FETM) method has been developed to reduce the computations involved in analysis of structures. This widely accepted method, however, has certain limitations, and does not directly produce reduced models for control design. To overcome these shortcomings, a modification of FETM method has been developed. The modified FETM method easily produces reduced models that are tailored toward subsequent control design. Other features of this method are its ability to: (1) extract open loop frequencies and mode shapes with less computations, (2) overcome limitations of the original FETM method, and (3) simplify the procedures for output feedback, constrained compensation, and decentralized control. This semi annual report presents the development of the modified FETM, and through an example, illustrates its applicability to an output feedback and a decentralized control design.

Yousuff, A.↗

NASA NTRS1973

The Lyapunov stabilization of satellite equations of motion using integrals

A method is introduced that weakens the Lyapunov or in track instability of satellite equations of motion. The method utilizes a linearized energy integral of satellite motion as a constraint on solutions obtained by numerical integration. The procedure prevents local numerical error from altering the frequency associated with the fast angular variable and thereby reduces the Lyapunov instability and the global numerical error. Applications of the method to satellite motion show accuracy improvements of two to three orders of magnitude in position and velocity after 50 revolutions. A modification of the method is presented that allows the use of slowly varying integrals of motion.

Nacozy, P. E.↗

NASA NTRS1951

On the turbulent friction layer for rising pressure

Among the information presented are included displacement, momentum, and kinetic energy thicknesses, shearing stress distributions across boundary layer, and surface friction coefficients. The Gruschwitz method and its modifications are examined and tested. An energy theorem for the turbulent boundary layer is introduced and discussed but does not lead to a method for the prediction of the behavior of the turbulent boundary layer because relations for the shearing stress and the surface friction are lacking.

SKIN FRICTION - PLATES↗

NASA NTRS2004

On the Methods of Determining the Radio Emission Geometry in Pulsar Magnetospheres

We present a modification of the relativistic phase shift method of determining the radio emission geometry from pulsar magnetospheres proposed by Gangadhara & Gupta (2001). Our modification provides a method of determining radio emission altitudes which does not depend on the viewing geometry and does not require polarization measurements. We suggest application of the method to the outer edges of averaged radio pulse profiles to identify magnetic field lines associated with'the edges of the pulse and, thereby, to test the geometric method based on the measurement of the pulse width at the lowest intensity level. We show that another relativistic method proposed by Blaskiewicz et al. (1991) provides upper limits for emission altitudes associated with the outer edges of pulse profiles. A comparison of these limits with the altitudes determined with the geometric method may be used to probe the importance of rotational distortions of magnetic field and refraction effects in the pulsar magnetosphere. We provide a comprehensive discussion of the assumptions used in the relativistic methods.

Dyks, J.↗

NASA NTRS1989

An Approximate Model for the Performance and Acoustic Predictions of Counterrotating Propeller Configurations

An approximate method was developed to analyze and predict the acoustics of a counterrotating propeller configuration. The method employs the analytical techniques of Lock and Theodorsen as described by Davidson to predict the steady performance of a counterrotating configuration. Then, a modification of the method of Lesieutre is used to predict the unsteady forces on the blades. Finally, the steady and unsteady loads are used in the numerical method of Succi to predict the unsteady acoustics of the propeller. The numerical results are compared with experimental acoustic measurements of a counterrotating propeller configuration by Gazzaniga operating under several combinations of advance ratio, blade pitch, and number of blades. In addition, a constant-speed commuter-class propeller configuration was designed with the Davidson method and the acoustics analyzed at three advance ratios. Noise levels and frequency spectra were calculated at a number of locations around the configuration. The directivity patterns of the harmonics in both the horizontal and vertical planes were examined, with the conclusion that the noise levels of the even harmonics are relatively independent of direction whereas the noise levels of the odd harmonics are extremely dependent on azimuthal direction in the horizontal plane. The equations of Succi are examined to explain this behavior.

Denner, Brett William↗