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At least 937 records · Page 52

High-throughput native mass spectrometry as experimental validation for in silico drug design

In this project, we developed automated workflows for both experimental validation and computational prediction of protein-ligand interactions. The ultimate goal is to establish an integrated pipeline for high throughput design of inhibitors to enzymes relevant to all areas of biological research. Our experimental approach is based on native mass spectrometry (native MS), which measures accurate masses and quantify the relative abundance of protein-ligand complexes to define binding affinity. We set up an in-house built autosampler with highly flexible configurations to minimize the manual steps for high throughput native MS. In parallel, we also performed manual native MS to characterize the binding of substrates and inhibitors of SARS-Cov-2 nonstructural protein nsp10/16 in order to optimize the experimental parameters for future automation. On the computational side, we streamlined the pipeline to achieve minimal manual intervention for predicting enzyme inhibitors via simulation, using the same nsp10/16 system as an example. Using the native MS method we examined 8 top-ranked designed compounds, 2 of which showed weak binding of ~50 µM. The information from native MS experiment provided critical insights and the foundation for a fully integrated workflow for enzyme inhibitor design.

59 BASIC BIOLOGICAL SCIENCES↗

Spectral solution of the incompressible Navier-Stokes equations on the Connection Machine2

The issue of solving the time-dependent incompressible Navier-Stokes equations on the Connection Machine 2 is addressed, for the problem of transition to turbulence of the steady flow in a channel. The spectral algorithm used serially requires O(N4) operations when solving the equations on an N x N x N grid; using the massive parallelism of the CM, it becomes an O(N2) problem. Preliminary timings of the code, written in LISP, are included and compared with a corresponding code optimized for the Cray-2 for a 128 x 128 x 101 grid.

Tomboulian, Sherryl↗

Recursive dynamics for flexible multibody systems using spatial operators

Due to their structural flexibility, spacecraft and space manipulators are multibody systems with complex dynamics and possess a large number of degrees of freedom. Here the spatial operator algebra methodology is used to develop a new dynamics formulation and spatially recursive algorithms for such flexible multibody systems. A key feature of the formulation is that the operator description of the flexible system dynamics is identical in form to the corresponding operator description of the dynamics of rigid multibody systems. A significant advantage of this unifying approach is that it allows ideas and techniques for rigid multibody systems to be easily applied to flexible multibody systems. The algorithms use standard finite-element and assumed modes models for the individual body deformation. A Newton-Euler Operator Factorization of the mass matrix of the multibody system is first developed. It forms the basis for recursive algorithms such as for the inverse dynamics, the computation of the mass matrix, and the composite body forward dynamics for the system. Subsequently, an alternative Innovations Operator Factorization of the mass matrix, each of whose factors is invertible, is developed. It leads to an operator expression for the inverse of the mass matrix, and forms the basis for the recursive articulated body forward dynamics algorithm for the flexible multibody system. For simplicity, most of the development here focuses on serial chain multibody systems. However, extensions of the algorithms to general topology flexible multibody systems are described. While the computational cost of the algorithms depends on factors such as the topology and the amount of flexibility in the multibody system, in general, it appears that in contrast to the rigid multibody case, the articulated body forward dynamics algorithm is the more efficient algorithm for flexible multibody systems containing even a small number of flexible bodies. The variety of algorithms described here permits a user to choose the algorithm which is optimal for the multibody system at hand. The availability of a number of algorithms is even more important for real-time applications, where implementation on parallel processors or custom computing hardware is often necessary to maximize speed.

Jain, A.↗

User's and test case manual for FEMATS

The FEMATS program incorporates first-order edge-based finite elements and vector absorbing boundary conditions into the scattered field formulation for computation of the scattering from three-dimensional geometries. The code has been validated extensively for a large class of geometries containing inhomogeneities and satisfying transition conditions. For geometries that are too large for the workstation environment, the FEMATS code has been optimized to run on various supercomputers. Currently, FEMATS has been configured to run on the HP 9000 workstation, vectorized for the Cray Y-MP, and parallelized to run on the Kendall Square Research (KSR) architecture and the Intel Paragon.

Chatterjee, Arindam↗

Excursion-Set-Mediated Genetic Algorithm

Excursion-set-mediated genetic algorithm (ESMGA) is embodiment of method of searching for and optimizing computerized mathematical models. Incorporates powerful search and optimization techniques based on concepts analogous to natural selection and laws of genetics. In comparison with other genetic algorithms, this one achieves stronger condition for implicit parallelism. Includes three stages of operations in each cycle, analogous to biological generation.

Noever, David↗

Multichannel Analysis of Surface Waves Accelerated (MASWAccelerated): Software for efficient surface wave inversion using MPI and GPUs

Multichannel Analysis of Surface Waves (MASW) is a technique frequently used in geotechnical engineering and engineering geophysics to infer 1D layered models of seismic shear wave velocities in the top tens to hundreds of meters of the subsurface. We aim to accelerate MASW calculations by capitalizing on modern computer hardware available in the workstations of most engineers: multiple cores and graphics processing units (GPUs). We propose new parallel and GPU accelerated algorithms for computing 1D MASW inversion, and provide software implementations in C using Message Passing Interface (MPI) and CUDA. These algorithms take advantage of sparsity that arises in the problem, and the work balance between processes considers typical data trends. We compare our methods to an existing open source Matlab MASW tool. Our serial C implementation achieves a 2x speedup over the Matlab software, and we continue to see improvements by parallelizing the problem with MPI. Here we see nearly perfect strong and weak scaling for uniform data, and improve strong scaling for realistic data by repartitioning the problem to process mapping. By utilizing GPUs available on most modern workstations, we observe an additional 1.3x speedup over the serial C implementation on the first use of the method. We typically repeatedly evaluate theoretical dispersion curves as part of an optimization procedure, and on the GPU the kernel can be cached for faster reuse on later runs. We observe a 3.2x speedup on the cached GPU runs compared to the serial C runs. This work is the first open-source parallel or GPU-accelerated software tool for MASW imaging, and should enable geotechnical engineers to fully utilize all computer hardware at their disposal.

58 GEOSCIENCES↗

Co-synthesis of Hydrogen and High-Value Carbon Products from Methane Pyrolysis

The ARPA-E Methane Pyrolysis Project successfully developed a scalable technology for hydrogen production with low-CO x emission through methane pyrolysis, co-producing high-value carbon nanotubes (CNTs). The project focused on optimizing reactor design, enhancing catalyst performance, and assessing techno-economic feasibility to create a commercially viable and environmentally sustainable process. The fluidized bed reactor achieved over 90% methane (CH 4 ) conversion by using a 5% CO 2 co-feed, which stabilizes carbon yields and minimizes catalyst deactivation. This setup allowed for continuous operation across ten cycles, each consisting of a 14-minute pyrolysis phase followed by a 10-minute dislodging phase to remove a fraction of the accumulated carbon, resulting in stable performance and high-quality CNT production. In parallel, monolith reactors coated with Fe demonstrated a sustained methane conversion of 73% while producing CNTs with high crystallinity. Although promising for continuous operation, monolith reactors face challenges in coating durability and scalability, highlighting areas for further optimization in commercial applications. Catalyst formulation played a key role in enhancing process efficiency. The core catalyst used was 5%Fe/Al 2 O 3 (wt%), optimized through wet impregnation, which improved CNT morphology, yielding longer and more uniform CNTs. The catalyst's performance was further enhanced by adding promoters: 2.5 wt% Ni increased methane conversion close to the thermodynamic limit, while 2.5 wt% Mn improved CNT alignment and crystallinity, and 1.5 wt% NaCl boosted CNT morphology but slightly lowered methane conversion. These adjustments allowed the reactor to maintain high methane conversion while producing high-quality CNTs, enabling stable performance over multiple cycles. To address carbon buildup and ensure uninterrupted operation, a pneumatic conveying tube was implemented for effective carbon dislodging in the fluidized bed configuration. CO 2 and H 2 O co-feeds were also introduced to enhance carbon removal, with CO 2 boosting CNT yield by approximately 15%. This setup enabled stable reactor operation across multiple cycles, preventing clogging and minimizing catalyst wear, making the process suitable for industrial scaling. Techno-economic analysis (TEA) projected hydrogen production costs between $\$$1.00 and $\$$1.64 per kilogram, with CNT values assumed at $\$$375/ton and $\$$100/ton. The life cycle assessment showed that CO 2 emissions could be as low as 0.64 kg CO 2 e/kg H 2 at 95% methane conversion assuming an electricity input of 50 kg CO 2 e/MWh. Even at 50% methane conversion, emissions remained below 1 kg CO 2 e/kg H 2 , demonstrating the process's low-emission potential and making it a viable alternative to traditional steam methane reforming. Overall, the results from this project demonstrate the feasibility of a pyrolysis process where carbon is continuously removed from the catalyst surface and hydrogen is continuously produced until a catalyst regeneration step is required to fully clean the catalyst surface and renew catalyst performance. Major open challenges are related to avoiding the loss of catalyst material in the dislodged carbon during fluidized bed conditions, since our best result demonstrated a carbon purity of ~70 wt. % (rest being iron and alumina). A monolith reactor was used to favor dislodgement of carbon compared to fluidized bed conditions but our results do not demonstrate an advantage of the monolith configuration. Catalyst performance was similar to fluidized bed conditions with slower deactivation rates overall, but we could not observe carbon dislodging in any of the tens of experiments that were run at Stanford. Our results show that the most relevant areas of improvement are related to the fundamental understanding of the iron-carbon interface for dislodging, and the development of catalyst that can produce CNTs via a base-growth mechanism such that catalyst is not lost in the dislodgement steps. The final report documents all findings and methodologies in detail, providing a valuable resource for the scientific community. By building on these results, researchers can further advance methane pyrolysis technology, moving toward a more sustainable, scalable pathway for hydrogen production. This work lays the foundation for future research and commercial efforts to reduce emissions in hydrogen production while generating valuable carbon products.

08 HYDROGEN↗

Annual Research Briefs, 2002: Center for Turbulence Research

Turbulent combustion remains the largest component of the CTR's core program. This program and several related activities at CTR are supported by NASA's Ultra Efficient Engine Technology Program. It is also intimately connected with the Department of Energy's ASCI program at Stanford which develops the technology for numerical simulation of realistic aircraft engines using state of the art massively parallel computers. In combustion modeling the attention has been directed to the modeling of higher levels of complexity such as spray dynamics, radiation and soot formation. Major aircraft engine manufacturers have shown considerable interest in this program; in particular, a significant active collaboration exists between CTR and the Pratt & Whitney Corporation. CTR's combustion program is essentially based on the large-eddy simulation technique, LES, which is actively being pursued at CTR for this and many other applications. Important accomplishments in LES included simulations with three-dimensional filters which result in grid independent calculations (that is why we call it "true" LES), and the development of the methodology for integration of LES and Reynolds Averaged computations. Optimization techniques are being studied and used for the important problem of wall boundary conditions for LES as well as for optimal shape design for aeroacoustic and aerodynamic performance gains.

ULTRA EFFICIENT ENGINE TECHNOLOGY↗

Robust multi‐loop control of a floating wind turbine

Abstract A principal challenge facing the control of floating offshore wind turbines (FOWTs) is the problem of instability, or “negative damping,” when using blade pitch feedback to control generator speed. This closed‐loop instability can be attributed to non‐minimum phase zeros in the transfer function from blade pitch to generator speed. Standard approaches to improving stability and performance include robust tuning of control gains and introducing multiple feedback loops to respond to platform motion. Combining these approaches is nontrivial because multiple control loops complicate the impact of coupling in the system dynamics. The single‐loop approach to analyzing stability robustness neglects inter‐loop coupling, while a simplistic multi‐loop approach is highly sensitive to dimensional scaling and overestimates the robustness of the single‐loop controller. This work proposes a sensitivity representation that separates some of the natural FOWT dynamic coupling into a parallel feedback loop in the sensitivity function loop to address both of these concerns. The modified robustness measure is used with a simplified linear FOWT model to optimize scheduled multi‐loop control parameters in an automated tuning procedure. This controller is implemented for the 10‐MW Ultraflexible Smart FLoating Offshore Wind Turbine (USFLOWT) and compared against conventional single‐ and multi‐loop controllers tuned using frequency‐domain analysis and high‐fidelity OpenFAST simulations. The multi‐loop robust controller shows the highest overall performance in generator speed regulation and tower load reduction, though consideration of power quality, actuator usage, and other structural loading leads to additional trade‐offs.

Stockhouse, David↗

Receptance coupling substructure analysis and chatter frequency-informed machine learning for milling stability

This paper describes a milling stability identification approach that simultaneously considers: physics-based models for the tool tip frequency response functions and stability predictions; the binary result from a milling test (automatically labeled as stable or unstable based on frequency content); chatter frequency when an unstable result is obtained; and user risk tolerance. The algorithm applies probabilistic Bayesian machine learning with adaptive, parallelized Markov Chain Monte Carlo sampling to update the probability of stability with each milling test. Furthermore, the result is a robust solution for rapid convergence to optimized milling parameters for maximum metal removal rate using all available information.

42 ENGINEERING↗

Fusion pilot plant performance and the role of a sustained high power density tokamak

Here, recent U.S. fusion development strategy reports all recommend that the U.S. should pursue innovative science and technology to enable construction of a fusion pilot plant (FPP) that produces net electricity from fusion at low capital cost. Compact tokamaks have been proposed as a means of potentially reducing the capital cost of a FPP. However, compact steady-state tokamak FPPs face the challenge of integrating a high fraction of self-driven current with high core confinement, plasma pressure, and high divertor parallel heat flux. This integration is sufficiently challenging that a dedicated sustained-high-power-density (SHPD) tokamak facility is proposed by the U.S. community as the optimal way to close this integration gap. Performance projections for the steady-state tokamak FPP regime are presented and a preliminary SHPD device with substantial flexibility in lower aspect ratio (A = 2–2.5), shaping, and divertor configuration to narrow gaps to an FPP is described.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Virtual Log-Structured Storage for High-Performance Streaming

Over the past decade, given the higher number of data sources (e.g., Cloud applications, Internet of things) and critical business demands, Big Data transitioned from batch-oriented to real-time analytics. Stream storage systems, such as Apache Kafka, are well known for their increasing role in real-time Big Data analytics. For scalable stream data ingestion and processing, they logically split a data stream topic into multiple partitions. Stream storage systems keep multiple data stream copies to protect against data loss while implementing a stream partition as a replicated log. This architectural choice enables simplified development while trading cluster size with performance and the number of streams optimally managed. This paper introduces a shared virtual log-structured storage approach for improving the cluster throughput when multiple producers and consumers write and consume in parallel data streams. Stream partitions are associated with shared replicated virtual logs transparently to the user, effectively separating the implementation of stream partitioning (and data ordering) from data replication (and durability). We implement the virtual log technique in the KerA stream storage system. When comparing with Apache Kafka, KerA improves the cluster ingestion throughput by up to 4x when multiple producers write over hundreds of data streams.

consistent stream ordering↗

O3BNN-R: An Out-Of-Order Architecture for High-Performance and Regularized BNN Inference

Binarized Neural Networks (BNN) have drawn tremendous attention due to significantly reduced computational complexity and memory demand. They have especially shown great potential in cost- and power-restricted domains, such as IoT and smart edge-devices, where reaching a certain accuracy bar is often sufficient, and real-time is highly desired.In this work, we demonstrate that the highly-condensed BNN model can be shrunk significantly further by dynamically pruning irregular redundant edges. Based on two new observations on BNN-specific properties, an out-of-order (OoO) architecture – O3BNN-R, can curtail edge evaluation in cases where the binary output of a neuron can be determined early. Similar to Instruction-Level-Parallelism(ILP), these fine-grained, irregular, runtime pruning opportunities are traditionally presumed to be difficult to exploit. In order to increase the pruning opportunities, we also optimize the training process by adding 2 regularization items in the loss function (1) for pooling pruning and (2) for threshold pruning. We evaluate our design on an FPGA platform using three well-known networks, including VggNet-16, AlexNet for ImageNet, and a VGG-like network for Cifar-10.

Geng, Tong↗

Dictionary Learning with Accumulator Neurons

The Locally Competitive Algorithm (LCA) uses local competition between non-spiking leaky integrator neurons to infer sparse representations, allowing for potentially real-time execution on massively parallel neuromorphic architectures such as Intel's Loihi processor. Here, we focus on the problem of inferring sparse representations from streaming video using dictionaries of spatiotemporal features optimized in an unsupervised manner for sparse reconstruction. Non-spiking LCA has previously been used to achieve unsupervised learning of spatiotemporal dictionaries composed of convolutional kernels from raw, unlabeled video. We demonstrate how unsupervised dictionary learning with spiking LCA (\hbox{S-LCA}) can be efficiently implemented using accumulator neurons, which combine a conventional leaky-integrate-and-fire (\hbox{LIF}) spike generator with an additional state variable that is used to minimize the difference between the integrated input and the spiking output. We demonstrate dictionary learning across a wide range of dynamical regimes, from graded to intermittent spiking, for inferring sparse representations of both static images drawn from the CIFAR database as well as video frames captured from a DVS camera. On a classification task that requires identification of the suite from a deck of cards being rapidly flipped through as viewed by a DVS camera, we find essentially no degradation in performance as the LCA model used to infer sparse spatiotemporal representations migrates from graded to spiking. We conclude that accumulator neurons are likely to provide a powerful enabling component of future neuromorphic hardware for implementing online unsupervised learning of spatiotemporal dictionaries optimized for sparse reconstruction of streaming video from event based DVS cameras.

artificial intelligence↗

Fusion Pilot Plant performance and the role of a Sustained High Power Density tokamak

Recent U.S. fusion development strategy reports all recommend that the U.S. should pursue innovative science and technology to enable construction of a Fusion Pilot Plant (FPP) that produces net electricity from fusion at low capital cost. Compact tokamaks have been proposed as a means of potentially reducing the capital cost of a fusion pilot plant. However, compact steady-state tokamak FPPs face the challenge of integrating a high fraction of self-driven current with high core confinement, plasma pressure, and high divertor parallel heat flux. This integration is sufficiently challenging that a dedicated sustained-high-power-density (SHPD) tokamak facility is proposed by the U.S. community as the optimal way to close this integration gap. Performance projections for the steady-state tokamak FPP regime are presented and a preliminary SHPD device with substantial flexibility in lower aspect ratio (A=2-2.5), shaping, and divertor configuration to narrow gaps to a FPP is described.

core-edge integration↗

Performance Enhancement of APW+lo Calculations by Simplest Separation of Concerns

Full-potential linearized augmented plane wave (LAPW) and APW plus local orbital (APW+lo) codes differ widely in both their user interfaces and in capabilities for calculations and analysis beyond their common central task of all-electron solution of the Kohn–Sham equations. However, that common central task opens a possible route to performance enhancement, namely to offload the basic LAPW/APW+lo algorithms to a library optimized purely for that purpose. To explore that opportunity, we have interfaced the Exciting-Plus (“EP”) LAPW/APW+lo DFT code with the highly optimized SIRIUS multi-functional DFT package. This simplest realization of the separation of concerns approach yields substantial performance over the base EP code via additional task parallelism without significant change in the EP source code or user interface. We provide benchmarks of the interfaced code against the original EP using small bulk systems, and demonstrate performance on a spin-crossover molecule and magnetic molecule that are of size and complexity at the margins of the capability of the EP code itself.

Zhang, Long↗

Spectral solution of the incompressible Navier-Stokes equations on the Connection Machine 2

The issue of solving the time-dependent incompressible Navier-Stokes equations on the Connection Machine 2 is addressed, for the problem of transition to turbulence of the steady flow in a channel. The spectral algorithm used serially requires O(N(4)) operations when solving the equations on an N x N x N grid; using the massive parallelism of the CM, it becomes an O(N(2)) problem. Preliminary timings of the code, written in LISP, are included and compared with a corresponding code optimized for the Cray-2 for a 128 x 128 x 101 grid.

Tomboulian, Sherryl↗

A Scalable Interior‐Point Gauss–Newton Method for PDE‐Constrained Optimization With Bound Constraints

Here, we present a scalable approach to solve a class of partial differential equation (PDE)‐constrained optimization problems with bound constraints. This approach utilizes a robust full‐space interior‐point (IP)‐Gauss–Newton optimization method. To cope with the poorly‐conditioned IP‐Gauss–Newton saddle‐point linear systems that need to be solved approximately, once per optimization step, we propose two spectrally related preconditioners. These preconditioners leverage the limited informativeness of data in regularized PDE‐constrained optimization problems. A block Gauss–Seidel preconditioner is proposed for the GMRES‐based solution of the IP‐Gauss–Newton linear systems. It is shown, for a large‐class of PDE‐ and bound‐constrained optimization problems, that the spectrum of the block Gauss–Seidel preconditioned IP‐Gauss–Newton matrix is asymptotically independent of discretization and is not impacted by the ill‐conditioning that notoriously plagues interior‐point methods. We exploit symmetry of the IP‐Gauss–Newton linear systems and propose a regularization and log‐barrier Hessian preconditioner for the preconditioned conjugate gradient (PCG)‐based solution of the equivalent IP‐Gauss–Newton–Schur complement linear systems. The eigenvalues of the block Gauss–Seidel preconditioned IP‐Gauss–Newton matrix, that are not equal to one, are identical to the eigenvalues of the regularization and log‐barrier Hessian preconditioned Schur complement matrix. The scalability of the approach is demonstrated on two example problems. The numerical solution of these optimization problems is shown to require a discretization independent number of IP‐Gauss–Newton linear solves. Furthermore, the linear systems are solved in a discretization and IP ill‐conditioning independent number of preconditioned Krylov subspace iterations. The parallel scalability of the preconditioner, achieved via algebraic multigrid component solvers when applicable, and the aforementioned algorithmic scalability permits a parallel scalable means to compute solutions of a large class of PDE‐ and bound‐constrained problems.

PDE-constrained optimization↗