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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records

Exponential Decay in the Sensitivity Analysis of Nonlinear Dynamic Programming

In this report, we study the sensitivity of discrete-time dynamic programs with nonlinear dynamics and objective to perturbations in the initial conditions and reference parameters. Under uniform controllability and boundedness assumptions for the problem data, we prove that the directional derivative of the optimal state and control at time $k$, $x^*_k$, and $u^*_k$, with respect to the reference signal at time $i$, $d_i$, will have exponential decay in terms of $|k-i|$ with a decay rate $\rho$ independent of the temporal horizon length. The key technical step is to prove that a version of the convexification approach proposed by Verschueren et al. can be applied to the KKT conditions and results in a convex quadratic program with uniformly bounded data. In turn, Riccati techniques can be further employed to obtain the sensitivity result, borne from the observation that the directional derivatives are solutions of quadratic programs with structure similar to the KKT conditions themselves. We validate our findings with numerical experiments on a small nonlinear, nonconvex, dynamic program.

97 MATHEMATICS AND COMPUTING↗

Improving Dose Modeling With Dynamic Modeling Tools [Slides]

Utilities aiming for higher fuel enrichment for power uprates or extended operation times before refueling must conduct a new dose analysis. Current conservative dose estimation standards may cause utilities to exceed regulatory limits for proposed increased fuel enrichment. A more accurate modeling of doses from reactor accidents can lower these conservative assumptions. Prescott et al. (2022) demonstrated that the Event Modeling Risk Assessment using Linked Diagrams (EMRALD) software tool, developed at Idaho National Laboratory (INL), can be coupled with the Modular Accident Analysis Program (MAAP5) for dynamic accident analysis in reactor plants. EMRALD forms models of potential accident scenarios, while MAAP5 simulates the accident progression and dose consequences. By integrating these software tools with utility-specific data, a more precise estimation of dose consequences from plant accidents can be achieved. Preliminary findings indicate that EMRALD provides accurate mean core damage frequencies for generalized accident scenarios. Future work includes expanding the model to account for plant-specific data and mitigation factors.

97 - MATHEMATICS AND COMPUTING↗

A Program Analysis Tool to Query Static and Dynamic Characteristics of HPC Applications

Emerging HPC platforms are becoming extraordinarily difficult to program as a result of complex, deep and heterogeneous memory hierarchies, heterogeneous cores, and the need to divide work and data among them. New programming models and libraries are being developed to aid in porting efforts of application developers, but substantial code restructuring is still necessary to fully make use of these new technologies. To do this effectively, these developers need information about their source code characteristics, including static and dynamic (e.g. performance) information to direct their optimisation efforts and make key decisions. On the other hand, system administrators need to understand how users are using the software stack and resources on their systems to understand what software they need to provide to improve the productivity of the users on a platform.In this paper we describe a tool that combines compiler and profiler information to query performance characteristics within an application or across multiple applications on a given platform. Static and dynamic data about applications are collected and stored together in an SQL database that can be queried by either a developer or a system administrator. We will demonstrate the capabilities of this tool via a real-world example from application-driven case studies that aims at understanding the use of scientific libraries on a routine from the molecular simulation application CP2K.

Welch, Aaron↗

An application of different dioids in public key cryptography

Dioids provide a natural framework for analyzing a broad class of discrete event dynamical systems such as the design and analysis of bus and railway timetables, scheduling of high-throughput industrial processes, solution of combinatorial optimization problems, the analysis and improvement of flow systems in communication networks. They have appeared in several branches of mathematics such as functional analysis, optimization, stochastic systems and dynamic programming, tropical geometry, fuzzy logic. In this paper we show how to involve dioids in public key cryptography. The main goal is to create key – exchange protocols based on dioids. Additionally the digital signature scheme is presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quasi-Optimal Elimination Trees for 2D Grids with Singularities

We construct quasi-optimal elimination trees for 2D finite element meshes with singularities. These trees minimize the complexity of the solution of the discrete system. The computational cost estimates of the elimination process model the execution of the multifrontal algorithms in serial and in parallel shared-memory executions. Since the meshes considered are a subspace of all possible mesh partitions, we call these minimizers quasi-optimal. We minimize the cost functionals using dynamic programming. Finding these minimizers is more computationally expensive than solving the original algebraic system. Nevertheless, from the insights provided by the analysis of the dynamic programming minima, we propose a heuristic construction of the elimination trees that has cost O N e log ⁡ N e , where N e is the number of elements in the mesh. We show that this heuristic ordering has similar computational cost to the quasi-optimal elimination trees found with dynamic programming and outperforms state-of-the-art alternatives in our numerical experiments.

Paszyńska, A.↗

A Polyhedral Transformation Framework for Compiler Optimization (Final Project Report)

The project developed the polyhedral compiler transformation module PolyOpt/Fortran in the ROSE compiler framework. PolyOpt/Fortran performs automated transformation of affine loop nests within FORTRAN programs for enhanced data locality and parallel execution. A FORTAN version of the Polybench library was also developed by the project. A third development was a dynamic analysis approach to gauge vectorization potential within loops of programs; software (DDVec) for automated instrumentation and dynamic analysis of programs was developed.

97 MATHEMATICS AND COMPUTING↗

The Structural Evaluation Test Unit (SETU) Benchmark Test Results

A series of extensively instrumented tests was performed on the Structural Evaluation Test Unit in the early 1990s. The purpose of these tests was to determine the response of a minimally designed cask to impacts that were more severe than the design basis impact. This test series provides an excellent opportunity for benchmarking explicit dynamic finite element analysis programs for behaviors that may be experienced by casks during regulatory and extra-regulatory impact events. This report provides the results of the four tests that were conducted. It is meant to go along with a companion report that defines the benchmark problem and gives the locations for the instrumentation and inspection points.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

The Structural Evaluation Test Unit (SETU) Benchmark Problem Statement

A series of extensively instrumented tests was performed on the Structural Evaluation Test Unit in the early 1990s. The purpose of these tests was to determine the response of a minimally designed cask to impacts that were more severe than the design basis impact. This test series provides an excellent opportunity for benchmarking explicit dynamic finite element analysis programs for behaviors that may be experienced by casks during regulatory and extra-regulatory impact events. This report provides the parameters of the test unit, the locations of instrumentation, the locations of inspection points, and the parameters of the four tests that were conducted. A companion report provides the results of the tests.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Dynamic programming algorithms within the NUPACK software suite enable analysis of equilibrium base-pairing properties for complex and test tube ensembles containing arbitrary numbers of interacting nucleic acid strands. Currently, calculations are limited to single-material systems that are either all-RNA or all-DNA. Here, to enable analysis of mixed-material systems that are critical for modern applications in vitro, in situ, and in vivo, we develop physical models and dynamic programming algorithms that allow the material of the system to be specified at nucleotide resolution. Free energy parameter sets are constructed for both RNA/DNA and RNA/2'OMe-RNA mixed-material systems by combining available empirical mixed-material parameters with single-material parameter sets to enable treatment of the full complex and test tube ensembles. New dynamic programming recursions account for the material of each nucleotide throughout the recursive process. For a complex with N nucleotides, the mixed-material dynamic programming algorithms maintain the O(N 3 ) time complexity of the single-material algorithms, enabling efficient calculation of diverse physical quantities over complex and test tube ensembles (e.g., complex partition function, equilibrium complex concentrations, equilibrium base-pairing probabilities, minimum free energy secondary structure(s), and Boltzmann-sampled secondary structures) at a cost increase of roughly 2.0-3.5×. The results of existing single-material algorithms are exactly reproduced when applying the new mixed-material algorithms to single-material systems. Accuracy is significantly enhanced using mixed-material models and algorithms to predict RNA/DNA and RNA/2'OMe-RNA duplex melting temperatures from the experimental literature as well as RNA/DNA melt profiles from new experiments. In conclusion, mixed-material analyses can be performed online using the NUPACK web app (www.nupack.org) or locally using the NUPACK Python module.

2′OMe-RNA↗

Estimating Arrhenius parameters using temperature programmed molecular dynamics

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms, In: ISC High Performance 2016: High Performance Computing

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.

Computer Science↗

Solving differential‐algebraic equations in power system dynamic analysis with quantum computing

Abstract Power system dynamics are generally modeled by high dimensional non‐linear differential‐algebraic equations (DAEs) given a large number of components forming the network. These DAEs' complexity can grow exponentially due to the increasing penetration of distributed energy resources, whereas their computation time becomes sensitive due to the increasing interconnection of the power grid with other energy systems. This paper demonstrates the use of quantum computing algorithms to solve DAEs for power system dynamic analysis. We leverage a symbolic programming framework to equivalently convert the power system's DAEs into ordinary differential equations (ODEs) using index reduction methods and then encode their data into qubits using amplitude encoding. The system non‐linearity is captured by Hamiltonian simulation with truncated Taylor expansion so that state variables can be updated by a quantum linear equation solver. Our results show that quantum computing can solve the power system's DAEs accurately with a computational complexity polynomial in the logarithm of the system dimension. We also illustrate the use of recent advanced tools in scientific machine learning for implementing complex computing concepts, that is, Taylor expansion, DAEs/ODEs transformation, and quantum computing solver with abstract representation for power engineering applications.

computational complexity↗

Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini

R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. We investigated the space sampled by the disordered N-termini of R67 DHFR using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE (http://www.smallangles.net/sassie/SASSIE_HOME.html), the apoenzyme displays a radius of gyration (Rg) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the Rg increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ~900 waters indicates the N-termini are well-hydrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superconvergence of Online Optimization for Model Predictive Control

We develop a one-Newton-step-per-horizon, online, lag-L, model predictive control (MPC) algorithm for solving discrete-time, equality-constrained, nonlinear dynamic programs. Based on recent sensitivity analysis results for the target problems class, we prove that the approach exhibits a behavior that we call superconvergence; that is, the tracking error with respect to the full horizon solution is not only stable for successive horizon shifts, but also decreases with increasing shift order to a minimum value that decays exponentially in the length of the receding horizon. The key analytical step is the decomposition of the one-step error recursion of our algorithm into algorithmic error and perturbation error. We show that the perturbation error decays exponentially with the lag between two consecutive receding horizons, while the algorithmic error, determined by Newton’s method, achieves quadratic convergence instead. Overall this approach induces our local exponential convergence result in terms of the receding horizon length for suitable values of L. In conclusion, numerical experiments validate our theoretical findings.

97 MATHEMATICS AND COMPUTING↗