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At least 181 records · Page 10

Accelerating crystal structure determination with iterative AlphaFold prediction

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

59 BASIC BIOLOGICAL SCIENCES↗

Computational architecture for integrated controls and structures design

To facilitate the development of control structure interaction (CSI) design methodology, a computational architecture for interdisciplinary design of active structures is presented. The emphasis of the computational procedure is to exploit existing sparse matrix structural analysis techniques, in-core data transfer with control synthesis programs, and versatility in the optimization methodology to avoid unnecessary structural or control calculations. The architecture is designed such that all required structure, control and optimization analyses are performed within one program. Hence, the optimization strategy is not unduly constrained by cold starts of existing structural analysis and control synthesis packages.

Belvin, W. Keith↗

Polarization Aberrations

The analysis of the polarization characteristics displayed by optical systems can be divided into two categories: geometrical and physical. Geometrical analysis calculates the change in polarization of a wavefront between pupils in an optical instrument. Physical analysis propagates the polarized fields wherever the geometrical analysis is not valid, i.e., near the edges of stops, near images, in anisotropic media, etc. Polarization aberration theory provides a starting point for geometrical design and facilitates subsequent optimization. The polarization aberrations described arise from differences in the transmitted (or reflected) amplitudes and phases at interfaces. The polarization aberration matrix (PAM) is calculated for isotropic rotationally symmetric systems through fourth order and includes the interface phase, amplitude, linear diattenuation, and linear retardance aberrations. The exponential form of Jones matrices used are discussed. The PAM in Jones matrix is introduced. The exact calculation of polarization aberrations through polarization ray tracing is described. The report is divided into three sections: I. Rotationally Symmetric Optical Systems; II. Tilted and Decentered Optical Systems; and Polarization Analysis of LIDARs.

Mcguire, James P., Jr.↗

Advanced integrated life support system update

The Advanced Integrated Life Support System Program (AILSS) is an advanced development effort to integrate the life support and protection requirements using the U.S. Navy's fighter/attack mission as a starting point. The goal of AILSS is to optimally mate protection from altitude, acceleration, chemical/biological agent, thermal environment (hot, cold, and cold water immersion) stress as well as mission enhancement through improved restraint, night vision, and head-mounted reticules and displays to ensure mission capability. The primary emphasis to date has been to establish garment design requirements and tradeoffs for protection. Here the garment and the human interface are treated as a system. Twelve state-off-the-art concepts from government and industry were evaluated for design versus performance. On the basis of a combination of centrifuge, thermal manikin data, thermal modeling, and mobility studies, some key design parameters have been determined. Future efforts will concentrate on the integration of protection through garment design and the use of a single layer, multiple function concept to streamline the garment system.

Whitley, Phillip E.↗

Testing New Programming Paradigms with NAS Parallel Benchmarks

Over the past decade, high performance computing has evolved rapidly, not only in hardware architectures but also with increasing complexity of real applications. Technologies have been developing to aim at scaling up to thousands of processors on both distributed and shared memory systems. Development of parallel programs on these computers is always a challenging task. Today, writing parallel programs with message passing (e.g. MPI) is the most popular way of achieving scalability and high performance. However, writing message passing programs is difficult and error prone. Recent years new effort has been made in defining new parallel programming paradigms. The best examples are: HPF (based on data parallelism) and OpenMP (based on shared memory parallelism). Both provide simple and clear extensions to sequential programs, thus greatly simplify the tedious tasks encountered in writing message passing programs. HPF is independent of memory hierarchy, however, due to the immaturity of compiler technology its performance is still questionable. Although use of parallel compiler directives is not new, OpenMP offers a portable solution in the shared-memory domain. Another important development involves the tremendous progress in the internet and its associated technology. Although still in its infancy, Java promisses portability in a heterogeneous environment and offers possibility to "compile once and run anywhere." In light of testing these new technologies, we implemented new parallel versions of the NAS Parallel Benchmarks (NPBs) with HPF and OpenMP directives, and extended the work with Java and Java-threads. The purpose of this study is to examine the effectiveness of alternative programming paradigms. NPBs consist of five kernels and three simulated applications that mimic the computation and data movement of large scale computational fluid dynamics (CFD) applications. We started with the serial version included in NPB2.3. Optimization of memory and cache usage was applied to several benchmarks, noticeably BT and SP, resulting in better sequential performance. In order to overcome the lack of an HPF performance model and guide the development of the HPF codes, we employed an empirical performance model for several primitives found in the benchmarks. We encountered a few limitations of HPF, such as lack of supporting the "REDISTRIBUTION" directive and no easy way to handle irregular computation. The parallelization with OpenMP directives was done at the outer-most loop level to achieve the largest granularity. The performance of six HPF and OpenMP benchmarks is compared with their MPI counterparts for the Class-A problem size in the figure in next page. These results were obtained on an SGI Origin2000 (195MHz) with MIPSpro-f77 compiler 7.2.1 for OpenMP and MPI codes and PGI pghpf-2.4.3 compiler with MPI interface for HPF programs.

Jin, H.↗

Hubble Systems Optimize Hospital Schedules

Don Rosenthal, a former Ames Research Center computer scientist who helped design the Hubble Space Telescope's scheduling software, co-founded Allocade Inc. of Menlo Park, California, in 2004. Allocade's OnCue software helps hospitals reclaim unused capacity and optimize constantly changing schedules for imaging procedures. After starting to use the software, one medical center soon reported noticeable improvements in efficiency, including a 12 percent increase in procedure volume, 35 percent reduction in staff overtime, and significant reductions in backlog and technician phone time. Allocade now offers versions for outpatient and inpatient magnetic resonance imaging (MRI), ultrasound, interventional radiology, nuclear medicine, Positron Emission Tomography (PET), radiography, radiography-fluoroscopy, and mammography.

Source record↗

Phase and Pupil Amplitude Recovery for JWST Space-Optics Control

This slide presentation reviews the phase and pupil amplitude recovery for the James Webb Space Telescope (JWST) Near Infrared Camera (NIRCam). It includes views of the Integrated Science Instrument Module (ISIM), the NIRCam, examples of Phase Retrieval Data, Ghost Irradiance, Pupil Amplitude Estimation, Amplitude Retrieval, Initial Plate Scale Estimation using the Modulation Transfer Function (MTF), Pupil Amplitude Estimation vs lambda, Pupil Amplitude Estimation vs. number of Images, Pupil Amplitude Estimation vs Rotation (clocking), and Typical Phase Retrieval Results Also included is information about the phase retrieval approach, Non-Linear Optimization (NLO) Optimized Diversity Functions, and Least Square Error vs. Starting Pupil Amplitude.

Dean, B. H.↗

Starting-point-independent quantum Monte Carlo calculations of iron oxide

Quantum Monte Carlo (QMC) methods are useful for studies of strongly correlated materials because they are many body in nature and use the physical Hamiltonian. Typical calculations assume as a starting point a wave function constructed from single-particle orbitals obtained from one-body methods, e.g., density functional theory. However, mean-field-derived wave functions can sometimes lead to systematic QMC biases if the mean-field result poorly describes the true ground state. In this study, we examine the accuracy and flexibility of QMC trial wave functions using variational and fixed-node diffusion QMC estimates of the total spin density and lattice distortion of antiferromagnetic iron oxide (FeO) in the ground state B1 crystal structure. We found that for relatively simple wave functions the predicted lattice distortion was controlled by the choice of single-particle orbitals used to construct the wave function, rather than by subsequent wave function optimization techniques within QMC. By optimizing the orbitals with QMC, we then demonstrate starting-point independence of the trial wave function with respect to the method by which the orbitals were constructed by demonstrating convergence of the energy, spin density, and predicted lattice distortion for two qualitatively different sets of orbitals. The results suggest that orbital optimization is a promising method for accurate many-body calculations of strongly correlated condensed phases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Transferable Reinforcement Learning for Smart Homes: Preprint

To harness the great amount of untapped resources at the demand side, smart home technology plays a vital role in solving the "last mile" problem in smart grid. Reinforcement learning (RL), which has demonstrated an outstanding performance in solving many sequential decision-making problems, can be a great candidate to be used in smart home control. For instance, many studies have started investigating the load scheduling problem under dynamic pricing scheme. Based on those, this study aims at providing an affordable solution to encourage a higher smart home adoption rate. Specifically, we investigate combining transfer learning (TL) with RL to reduce the training cost of an optimal RL control policy. Given an optimal policy for a benchmark home, TL can jump-start the RL training of a policy for a new home, which has different appliances and user preferences. Simulation results show that by leveraging TL, RL training converges faster and requires much less computing time for new homes that are similar to the benchmark home. In all, this study proposes a cost-effective approach for training RL control policies for homes at scale, which ultimately reduces the controller's implementation costs, increases the adoption rate of RL controllers, and makes more homes grid-interactive.

ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATION,↗

Optimizing Desalination Operations for Energy Flexibility

Despite the value of energy optimization in desalination processes, modeling dynamic operations for monthly billing periods has remained a computational challenge. This work proposes a framework for energy flexibility optimization, which includes new modeling features for independent operation of parallel skids, start-up delays associated with chemical stabilization, the consideration of industrial energy tariff structures, and inclusion of hourly electrical carbon intensities. This is done using a modular and computationally efficient formulation that guarantees a globally optimal solution with standard optimization solvers. In this study, the approach is demonstrated in two distinct case studies: a seawater desalination plant in Santa Barbara, CA, and an indirect potable reuse facility in San Jose, CA. Trends predicted from the model are validated against operational facility measurements from a demand response shutdown event. Preliminary results show that optimizing energy flexibility can result in 18.51% monthly cost savings over energy efficiency-optimized operation. The value extracted from a facility-wide shutdown during peak electricity price hours is hampered by start-up delays in post-treatment chemical stabilization. In cases in which a facility does not have much excess capacity, using a flow equalization tank or operating over a wide recovery range may be cost-effective.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Leveraging Automated Fiber Placement Computer Aided Process Planning Framework for Defect Validation and Dynamic Layup Strategies

Process planning represents an essential stage of the Automated Fiber Placement (AFP) workflow. It develops useful and efficient machine processes based upon the working material, composite design, and manufacturing resources. The current state of process planning requires a high degree of interaction from the process planner and could greatly benefit from increased automation. Therefore, a list of key steps and functions are created to identify the more difficult and time-consuming phases of process planning. Additionally, a set of metrics must exist by which to evaluate the effectiveness of the manufactured laminate from the machine code created during the Process Planning stage. Layup strategies, in addition to dog ears, stagger shifts, steering constraints, and starting points, represented the group of functions labeled as process optimization and ranked the highest in terms of priority for automation. The laminates resulting from the selected parameters are evaluated through the occurrences of principal defect metrics such as fiber gaps, overlaps, angle deviation and steering violations. This document presents an automated software solution to the layup strategy and starting point selection phase of process planning. A series of ply scenarios are generated with variations of these ply parameters and evaluated according to a set of metrics entered by the Process Planner. These metrics are generated through use of the Analytical Hierarchy Process (AHP), where relative importance between each of the fiber features are defined. The ply scenarios are selected which reduce the overall fiber feature scores based on the defects the Process Planner wishes to minimize.

HiCAM↗

Wing-section optimization for supersonic viscous flows

The recent interest in High Speed Civil Transport (HSCT) has resulted in renewed research studies of optimized supersonic cruise transport configurations. Incorporation of flow viscosity effects in the design process of such a supersonic wing is currently under investigation. This may lead to more accurate problem formulations and, in turn, greater aerodynamic efficiency than can be obtained by the traditional, inviscid, linear theories. In this context, for a design code to be a candidate for a complex optimization problem, such as three-dimensional viscous supersonic wing design, it should be validated using simpler building-block shapes. To optimize the shape of a supersonic wing, an automated method that also includes higher fidelity to the flow physics is desirable. With this impetus, an aerodynamic optimization methodology incorporating Navier-Stokes equations and sensitivity analysis had been previously developed. Prior to embarking upon the wing design task, the present investigation concentrated on testing the flexibility of the methodology, and the identification of adequate problem formulations, by defining two-dimensional, cost-effective test cases. Starting with two distinctly different initial airfoils, two independent shape optimizations resulted in shapes with very similar features. Secondly, the normal section to the subsonic portion of the leading edge, which had a high normal angle-of-attack, was considered. The optimization resulted in a shape with twist and camber, which eliminated the adverse pressure gradient, hence, exploiting the leading-edge thrust. The wing section shapes obtained in all the test cases had the features predicted by previous studies. Therefore, it was concluded that the flowfield analyses and the sensitivity coefficients were computed and fed to the present gradient-based optimizer correctly. Also, as a result of the present two-dimensional study, suggestions were made for problem formulations which should contribute to an effective wing shape optimization.

Item, Cem C.↗

Wing-section optimization for supersonic viscous flow

To improve the shape of a supersonic wing, an automated method that also includes higher fidelity to the flow physics is desirable. With this impetus, an aerodynamic optimization methodology incorporating thin-layer Navier-Stokes equations and sensitivity analysis had been previously developed. Prior to embarking upon the wind design task, the present investigation concentrated on testing the feasibility of the methodology, and the identification of adequate problem formulations, by defining two-dimensional, cost-effective test cases. Starting with two distinctly different initial airfoils, two independent shape optimizations resulted in shapes with similar features: slightly cambered, parabolic profiles with sharp leading- and trailing-edges. Secondly, the normal section to the subsonic portion of the leading edge, which had a high normal angle-of-attack, was considered. The optimization resulted in a shape with twist and camber which eliminated the adverse pressure gradient, hence, exploiting the leading-edge thrust. The wing section shapes obtained in all the test cases had the features predicted by previous studies. Therefore, it was concluded that the flowfield analyses and sensitivity coefficients were computed and fed to the present gradient-based optimizer correctly. Also, as a result of the present two-dimensional study, suggestions were made for the problem formulations which should contribute to an effective wing shape optimization.

Item, Cem C.↗

Singular-Arc Time-Optimal Trajectory of Aircraft in Two-Dimensional Wind Field

This paper presents a study of a minimum time-to-climb trajectory analysis for aircraft flying in a two-dimensional altitude dependent wind field. The time optimal control problem possesses a singular control structure when the lift coefficient is taken as a control variable. A singular arc analysis is performed to obtain an optimal control solution on the singular arc. Using a time-scale separation with the flight path angle treated as a fast state, the dimensionality of the optimal control solution is reduced by eliminating the lift coefficient control. A further singular arc analysis is used to decompose the original optimal control solution into the flight path angle solution and a trajectory solution as a function of the airspeed and altitude. The optimal control solutions for the initial and final climb segments are computed using a shooting method with known starting values on the singular arc The numerical results of the shooting method show that the optimal flight path angle on the initial and final climb segments are constant. The analytical approach provides a rapid means for analyzing a time optimal trajectory for aircraft performance.

Nguyen, Nhan↗

Adaptive Shape Control for Aerodynamic Design

We present an approach to aerodynamic optimization in which the shape control is adaptively parameterized. Starting from a coarse set of design variables, a sequence of higher-dimensional nested search spaces is automatically generated. Refinement can be either uniform or adaptive, in which case only the most important shape control is added. The relative importance of candidate design variables is determined by comparing objective and constraint gradients, computed at low cost via adjoint solutions. A search procedure for finding an effective ensemble of shape parameters is also given. We first demonstrate this system on a multipoint drag miminization problem in 2D with many constraints, showing that an adaptive parameterization approach consistently achieves smoother, more robust, and faster design improvement than fixed parameterizations. We also establish a 3D shape- matching benchmark, where we demonstrate that our approach automatically discovers the necessary parameters to match a target shape. By largely automating shape parameterization, this work also aims to remove a time-consuming aspect of shape optimization.

Aerodynamic Design↗

Nuclear Power Fault Diagnostics and Preventative Maintenance Optimization

Operation and maintenance costs for nuclear power plants are very large. Reactors are starting to shut down even after their operating licenses have been extended, because they are not price competitive compared to other energy sources. The nuclear industry is witnessing early closure of nuclear power plants due to economic reasons despite excellent safety records. Therefore, it is imperative to reduce costs to prevent these early closures. This paper showcases recent research into advanced fault diagnostics techniques and preventative maintenance optimization to reduce these maintenance costs. This report focuses on the condensate and feedwater system for both pressurized and boiling water reactor systems. The computerized maintenance management system, which contains the plant’s digital record of all the corrective- and preventative-maintenance work orders, was used as a ground truth to locate potential faults and label the process data as healthy or faulty. Various feature extraction techniques were utilized to further differentiate the faults from the healthy data. Support vectors machines were used to categorize other test sets of process data as healthy or faulty through a cross validation procedure. Similar faults were not found within this system leading to preventative maintenance optimization. Unnecessary amounts of preventative maintenance lead to inflated maintenance costs. This paper summarizes the steps for preventative maintenance optimization from component health determination to recommendation for action. This optimization was completed for condensate pumps, condensate booster pumps, and the respective motors that drive them.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

An SCF and MCSCF description of the low-lying states of MgO

The paper presents the multiconfiguration-self-consistent (MCSCF) and configuration state functions (CSF) for the low-lying electronic states of MgO. It was shown that simple description of these states was possible provided the 1 Sigma(+) states are individually optimized at the MCSCF level, noting that the 1(3 Sigma)(+) and 2(1 Sigma)(+) states which nominally result from the same electron occupation are separated energetically. The molecular orbitals obtained at this level of approximation should provide a useful starting point for extended configuration interaction calculations since they have been optimized for the particular states of interest.

Bauschlicher, C. W., Jr.↗

Wing Configuration Impact on Design Optimums for a Subsonic Passenger Transport

This study sought to compare four aircraft wing configurations at a conceptual level using a multi-disciplinary optimization (MDO) process. The MDO framework used was created by Georgia Institute of Technology and Virginia Polytechnic Institute and State University. They created a multi-disciplinary design and optimization environment that could capture the unique features of the truss-braced wing (TBW) configuration. The four wing configurations selected for the study were a low wing cantilever installation, a high wing cantilever, a strut-braced wing, and a single jury TBW. The mission that was used for this study was a 160 passenger transport aircraft with a design range of 2,875 nautical miles at the design payload, flown at a cruise Mach number of 0.78. This paper includes discussion and optimization results for multiple design objectives. Five design objectives were chosen to illustrate the impact of selected objective on the optimization result: minimum takeoff gross weight (TOGW), minimum operating empty weight, minimum block fuel weight, maximum start of cruise lift-to-drag ratio, and minimum start of cruise drag coefficient. The results show that the design objective selected will impact the characteristics of the optimized aircraft. Although minimum life cycle cost was not one of the objectives, TOGW is often used as a proxy for life cycle cost. The low wing cantilever had the lowest TOGW followed by the strut-braced wing.

Wells, Douglas P.↗