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At least 919 records · Page 51

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗

Extension-torsion coupling behavior of advanced composite tilt-rotor blades

An analytic model was developed to study the extension-bend-twist coupling behavior of an advanced composite helicopter or tilt-rotor blade. The outer surface of the blade is defined by rotating an arbitrary cross section about an initial twist axis. The cross section can be nonhomogeneous and composed of generally anisotropic materials. The model is developed based upon a three dimensional elasticity approach that is recast as a coupled two-dimensional boundary value problem defined in a curvilinear coordinate system. Displacement solutions are written in terms of known functions that represent extension, bending, and twisting and unknown functions for local cross section deformations. The unknown local deformation functions are determined by applying the principle of minimum potential energy to the discretized two-dimensional cross section. This is an application of the Ritz method, where the trial function family is the displacement field associated with a finite element (8-node isoparametric quadrilaterals) representation of the section. A computer program was written where the cross section is discretized into 8-node quadrilateral subregions. Initially the program was verified using previously published results (both three-dimensional elasticity and technical beam theory) for pretwisted isotropic bars with an elliptical cross section. In addition, solid and thin-wall multi-cell NACA-0012 airfoil sections were analyzed to illustrate the pronounced effects that pretwist, initial twist axis location, and spar location has on coupled behavior. Currently, a series of advanced composite airfoils are being modeled in order to assess how the use of laminated composite materials interacts with pretwist to alter the coupling behavior of the blade. These studies will investigate the use of different ply angle orientations and the use of symmetric versus unsymmetric laminates.

Kosmatka, J. B.↗

Precision and radiosonde validation of satellite gridpoint temperature anomalies. I - MSU channel 2. II - A tropospheric retrieval and trends during 1979-90

Monthly 2.5-deg gridpoint anomalies in the Tiros-N satellite series Microwave Sounding Unit channel 2 brightness temperatures during 1979-1988 are evaluated with multiple satellites and radiosonde data for their climate temperature monitoring capability. The MSU anomalies are computed about a 10-yr mean annual cycle at each gridpoint, with the MSUs intercalibrated to a common arbitrary level. The monthly gridpoint anomaly agreement between concurrently operating satellites reveals single-satellite precision generally better than 0.07 C in the tropics and better than 0.15 C at higher latitudes. The removal from channel 2 of the temperature influence above the 30-kPa level is addressed, providing a sharper and thus potentially more useful weighting function for monitoring lower tropospheric temperatures.

Spencer, Roy W.↗

Refraction of Sound Emitted Near Solid Boundaries from a Sheared Jet

A mathematical model is developed to describe the sound emitted from an arbitrary point within a turbulent flow near solid boundaries. A unidirectional, transversely sheared mean flow is assumed, and the cross-section of the cold jet is of arbitrary shape. The analysis begins with Lilley's formulation of aerodynamic noise and, depending upon the specific model of turbulence used, leads via Fourier analysis to an expression for the spectral density of the intensity of the far-field sound emitted from a unit volume of turbulence. The expressions require solution of a reduced Green's function of Lilley's equation as well as certain moving axis velocity correlations of the turbulence. Integration over the entire flow field is required in order to predict the sound emitted by the complete flow. Calculations are presented for sound emitted from a plugflow jet exiting a semi-infinite flat duct. Polar plots of the far-field directivity show the dependence upon frequency and source position within the duct. Certain model problems are suggested to investigate the effect of duct termination, duct geometry, and mean flow shear upon the far-field sound.

Dill, Loren H.↗

The Area Localized Coupled Model for Analytical Mean Flow Prediction in Arbitrary Wind Farm Geometries

This work introduces the area localized coupled (ALC) model, which extends the applicability of approaches that couple classical wake superposition models and atmospheric boundary layer models to wind farms with arbitrary layouts. Coupling wake and top–down boundary layer models is particularly challenging since the latter requires averaging over planform areas associated with turbine-specific regions of the flow that need to be specified. The ALC model uses Voronoi tessellation to define this local area around each turbine. A top–down description of a developing internal boundary layer is then applied over Voronoi cells upstream of each turbine to estimate the local mean velocity profile. Coupling between the velocity at hub-height based on this localized top–down model and a wake model is achieved by enforcing a minimum least-square-error in mean velocity in each cell. The wake model in the present implementation takes into account variations in wind farm inflow velocity and represents the wake profile behind each turbine as a super-Gaussian function that smoothly transitions between a top-hat shape in the region immediately following the turbine to a Gaussian profile downstream. Detailed comparisons to large-eddy simulation (LES) data from two different wind farms demonstrate the efficacy of the model in accurately predicting both wind farm power output and local turbine hub-height velocity for different wind farm geometries. These validations using data generated from two different LES codes demonstrate the model's versatility with respect to capturing results from different simulation setups and wind farm configurations.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

Modeling Spectralon's Bidirectional Reflectance for In-flight Calibration of Earth-Orbiting Sensors

The in-flight calibration of the EOS Multi-angle Imaging SpectroRadiometer (MISR) will be achieved, in part, by observing deployable Spectralon panels. This material reflects light diffusely, and allows all cameras to view a near constant radiance field. This is particularly true when a panel is illuminated near the surface normal. To meet the challenging MISR calibration requirements, however, very accurate knowledge of the panel reflectance must be known for all utilized angles of illumination, and for all camera and monitoring photodiode view angles. It is believed that model predictions of the panels Bidirectional Reflectance Distribution Function (BRDF) can be used in conjunction with a measurements program to provide the required characterization. This paper describes the results of a model inversion which was conducted using measured Spectralon BRDF data at several illumination angles. Four physical parameters of the material were retrieved, and are available for use with the model to predict reflectance for any arbitrary illumination or view angle. With these data the root mean square difference between the model and the observations is currently of the order of the noise in the data, at about +/- l%. With this success the model will now be used in a variety of future studies, including the development of a measurements test plan, the validation of these data, and the prediction of a new BRDF profile, should the material degrade in space.

Flasse, Stephane P.↗

Tiltrotor Test Rig Aerodynamic Tares

The Tiltrotor Test Rig (TTR) is a NASA facility designed to test full-scale proprotors in the National Full-Scale Aerodynamics Facility (NFAC). The first wind-tunnel entry included measurements of aerodynamic loads (tares) on the spinner without a rotor. The TTR has an onboard balance for direct measurement of rotor loads, so these tares comprise only spinner loads. Spinner tares also affect shaft loads measured independently of the balance. The results show that in axial flow, spinner drag is a linear function of dynamic pressure as expected, but at other flow angles, spinner loads include substantial lift and drag. Furthermore, there is a pronounced Magnus effect when the spinner is sideways to the flow. There is a sharp change in aerodynamic load at 90-deg yaw angle, indicating separation. Equations were developed to characterize the spinner tares at any arbitrary combination of yaw angle and airspeed.

TTR↗

Teaching a neural network to attach and detach electrons from molecules

Abstract Interatomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were parametrized for neutral molecules or closed-shell ions due to architectural limitations. In this work, we propose an improved machine learning framework for simulating open-shell anions and cations. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity with errors of about 2–3 kcal/mol and spin-charges with error errors ~0.01e for small and medium-sized organic molecules, compared to the reference QM simulations. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions.

36 MATERIALS SCIENCE↗

Finite element algorithms for compressible flow computation on a supercomputer

Methods of applying computational fluid dynamics techniques to engineering problems are discussed. The linking factors between theoretical and applied research are the shape and weight functions which produce the Galerkin finite element schemes. The flow is unsteady, viscous, heat conducting and compressible, and steady-state flows are the asymptotic limit of unsteady flows. All flows are described by the time-averaged Navier-Stokes equations (NSE) with mass and energy conservation. Local curvilinear intrinsic coordinates are applied to discretize the NSE in arbitrary geometric domains. A modified weighted residuals approach defines the discrete analogs of the physical systems modeled and a general interpolants method is used to derive families of numerical models, both implicit and explicit, finite difference and finite elemnt, from a single point of departure. Time-dependent element approximations are achieved with a progressive assembly of generalized elements method. Hyperbolic steady-state Euler algorithms and quasi-parabolic are spatial marching algorithms for solving the discretized equations. Application of the techniques is illustrated through calculation of the compressible flow around a hypersonic flight vehicle at 100,000 ft at zero angle of attack at speeds of Mach 4-10.

Spradley, L. W.↗

The Senior Executive Service

A major innovation of the Civil Service Reform Act of 1978 was the creation of a Senior Executive Service (SES). The purpose of the SES is both simple and bold: to attract executives of the highest quality into Federal service and to retain them by providing outstanding opportunities for career growth and reward. The SES is intended to: provide greater authority in managing executive resources; attract and retain highly competent executives, and assign them where they will effectively accomplish their missions and best use their talents; provide for systematic development of executives; hold executives accountable for individual and organizational performance; reward outstanding performers and remove poor performers; and provide for an executive merit system free of inappropriate personnel practices and arbitrary actions. This Handbook summarizes the key features of the SES at NASA. It is intended as a special welcome to new appointees and also as a general reference document. It contains an overview of SES management at NASA, including the Executive Resources Board and the Performance Review Board, which are mandated by law to carry out key SES functions. In addition, assistance is provided by a Senior Executive Committee in certain reviews and decisions and by Executive Position Managers in day-to-day administration and oversight.

Source record↗

Strategy-Enhanced Interactive Proving and Arithmetic Simplification for PVS

We describe an approach to strategy-based proving for improved interactive deduction in specialized domains. An experimental package of strategies (tactics) and support functions called Manip has been developed for PVS to reduce the tedium of arithmetic manipulation. Included are strategies aimed at algebraic simplification of real-valued expressions. A general deduction architecture is described in which domain-specific strategies, such as those for algebraic manipulation, are supported by more generic features, such as term-access techniques applicable in arbitrary settings. An extended expression language provides access to subterms within a sequent.

diVito, Ben L.↗

Strategy-Enhanced Interactive Proving and Arithmetic Simplification for PVS

We describe an approach to strategy-based proving for improved interactive deduction in specialized domains. An experimental package of strategies (tactics) and support functions called Manip has been developed for PVS to reduce the tedium of arithmetic manipulation. Included are strategies aimed at algebraic simplification of real-valued expressions. A general deduction architecture is described in which domain-specific strategies, such as those for algebraic manipulation, are supported by more generic features, such as term-access techniques applicable in arbitrary settings. An extended expression language provides access to subterms within a sequent.

DiVito, Ben L.↗

Design of Neural Networks for Fast Convergence and Accuracy: Dynamics and Control

A procedure for the design and training of artificial neural networks, used for rapid and efficient controls and dynamics design and analysis for flexible space systems, has been developed. Artificial neural networks are employed, such that once properly trained, they provide a means of evaluating the impact of design changes rapidly. Specifically, two-layer feedforward neural networks are designed to approximate the functional relationship between the component/spacecraft design changes and measures of its performance or nonlinear dynamics of the system/components. A training algorithm, based on statistical sampling theory, is presented, which guarantees that the trained networks provide a designer-specified degree of accuracy in mapping the functional relationship. Within each iteration of this statistical-based algorithm, a sequential design algorithm is used for the design and training of the feedforward network to provide rapid convergence to the network goals. Here, at each sequence a new network is trained to minimize the error of previous network. The proposed method should work for applications wherein an arbitrary large source of training data can be generated. Two numerical examples are performed on a spacecraft application in order to demonstrate the feasibility of the proposed approach.

Maghami, Peiman G.↗

Color Histogram Diffusion for Image Enhancement

Various color histogram equalization (CHE) methods have been proposed to extend grayscale histogram equalization (GHE) for color images. In this paper a new method called histogram diffusion that extends the GHE method to arbitrary dimensions is proposed. Ranges in a histogram are specified as overlapping bars of uniform heights and variable widths which are proportional to their frequencies. This diagram is called the vistogram. As an alternative approach to GHE, the squared error of the vistogram from the uniform distribution is minimized. Each bar in the vistogram is approximated by a Gaussian function. Gaussian particles in the vistoram diffuse as a nonlinear autonomous system of ordinary differential equations. CHE results of color images showed that the approach is effective.

Kim, Taemin↗

Methods for Monte Carlo simulation of the exospheres of the moon and Mercury

A general form of the integral equation of exospheric transport on moon-like bodies is derived in a form that permits arbitrary specification of time varying physical processes affecting atom creation and annihilation, atom-regolith collisions, adsorption and desorption, and nonplanetocentric acceleration. Because these processes usually defy analytic representation, the Monte Carlo method of solution of the transport equation, the only viable alternative, is described in detail, with separate discussions of the methods of specification of physical processes as probabalistic functions. Proof of the validity of the Monte Carlo exosphere simulation method is provided in the form of a comparison of analytic and Monte Carlo solutions to three classical, and analytically tractable, exosphere problems. One of the key phenomena in moonlike exosphere simulations, the distribution of velocities of the atoms leaving a regolith, depends mainly on the nature of collisions of free atoms with rocks. It is shown that on the moon and Mercury, elastic collisions of helium atoms with a Maxwellian distribution of vibrating, bound atoms produce a nearly Maxwellian distribution of helium velocities, despite the absence of speeds in excess of escape in the impinging helium velocity distribution.

Hodges, R. R., Jr.↗

A Complexity Agnostic Clustering Engine for Time Projection Chambers and its Implementation in FPGA

A clustering functional block implemented in field-programable-gate-array (FPGA) for time projection chambers (TPC) operating with predictable time regardless the complexity of the event is described in this paper. The clustering functional block reorganizes input data and the hits data belonging to the same clusters are output together for further process in the later stages. The clustering operation consists of two phases, data filling phase and data outputting phase, and the later uses the same number of clock cycles as the data filling phase. The clustering block can accommodate events with arbitrary number of clusters and number of hits per cluster as long as the total number of hits is within a predesigned limit. The operation time is exactly twice of the data filling time with no residual O(n2) term. The clustering block has been implemented with operating frequency of 200 MHz in a low-cost FPGA evaluation module and test results confirm the expected performance.

Wu, Jinyuan [Fermilab] (ORCID:0000000344329521)↗

Multi-matrix correlators and localization

Abstract We study generating functions of$$ \frac{1}{4} $$ 1 4 -BPS states in$$ \mathcal{N} $$ N = 4 super Yang-Mills at finiteNby attempting to generalize the Harish-Chandra-Itzykson-Zuber integral to multiple commuting matrices. This allows us to compute the overlaps of two or more generating functions; such calculations arise in the computation of two-point correlators in the free-field limit. We discuss the four-matrix HCIZ integral in the U(2) context and lay out a prescription for finding a more general formula forN> 2. We then discuss its connections with the restricted Schur polynomial operator basis. Our results generalize readily to arbitrary numbers of matrices, opening up the opportunity to study more generic BPS operators.

Physics↗

blocks_3d: software for general 3d conformal blocks

We introduce the software blocks_3d for computing four-point conformal blocks of operators with arbitrary Lorentz representations in 3d CFTs. It uses Zamolodchikov-like recursion relations to numerically compute derivatives of blocks around a crossing-symmetric configuration. It is implemented as a heavily optimized, multi-threaded, C++ application. We give performance benchmarks for correlators containing scalars, fermions, and stress tensors. As an example application, we recompute bootstrap bounds on four-point functions of fermions and study whether a previously observed sharp jump can be explained using the “fake primary” effect. We conclude that the fake primary effect cannot fully explain the jump and the possible existence of a “dead-end” CFT near the jump merits further study.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗