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At least 973 records · Page 54

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↗

Faster than Real-Time Dynamic Simulation for Large-Size Power System with Detailed Dynamic Models using High-Performance Computing Platform

This paper presents a faster-than-real-time dynamic simulation software package that is designed for large-size power system dynamic simulation. It was developed on the GridPACKTM high-performance computing (HPC) framework. The key features of the developed software package include (1) faster-than-real-time dynamic simulation for a WECC system (17,000 buses) with different types of detailed generator, controller, and relay dynamic models, (2) a decoupled parallel dynamic simulation algorithm with optimized computation architecture to better leverage HPC resources and technologies, (3) options for HPC-based linear and iterative solvers, (4) hidden HPC details, such as data communication and distribution, to enable development centered on mathematical models and algorithms rather than on computational details for power system researchers, and (5) easy integration of new dynamic models and related algorithms into the software package.

Huang, Renke↗

Data-Driven Learning for the Mori--Zwanzig Formalism: A Generalization of the Koopman Learning Framework

A theoretical framework which unifies the conventional Mori--Zwanzig formalism and the approximate Koopman learning of deterministic dynamical systems from noiseless observation is presented. In this framework, the Mori--Zwanzig formalism, developed in statistical mechanics to tackle the hard problem of construction of reduced-order dynamics for high-dimensional dynamical systems, can be considered as a natural generalization of the Koopman description of the dynamical system. We next show that, similar to the approximate Koopman learning methods, data-driven methods can be developed for the Mori--Zwanzig formalism with Mori's linear projection operator. We have developed two algorithms to extract the key operators, the Markov and the memory kernel, using time series of a reduced set of observables in a dynamical system. We have adopted the Lorenz `96 system as a test problem and solved for the above operators. These operators exhibit complex behaviors, which are unlikely to be captured by traditional modeling approaches in Mori--Zwanzig analysis. The nontrivial generalized fluctuation-dissipation relationship, which relates the memory kernel with the two-time correlation statistics of the orthogonal dynamics, was numerically verified as a validation of the solved operators. Here we present numerical evidence that the generalized Langevin equation, a key construct in the Mori--Zwanzig formalism, is more advantageous in predicting the evolution of the reduced set of observables than the conventional approximate Koopman operators.

97 MATHEMATICS AND COMPUTING↗

Dynamic Covalent Chemistry for Synthetic Molecular Machines

The first and only exhaustive review of the theory, thermodynamic fundamentals, mechanisms, and design principles of dynamic covalent systems Dynamic Covalent Chemistry: Principles, Reactions, and Applications presents a comprehensive ...

Liu, Yi↗

Shaker-structure interaction modeling and analysis for nonlinear force appropriation testing

Nonlinear force appropriation is an extension of its linear counterpart where sinusoidal excitation is applied to a structure with a modal shaker and phase quadrature is achieved between the excitation and response. While a standard practice in modal testing, modal shaker excitation has the potential to alter the dynamics of the structure under test. Previous studies have been conducted to address several concerns, but this work specifically focuses on a shaker-structure interaction phenomenon which arises during the force appropriation testing of a nonlinear structure. Under pure-tone sinusoidal forcing, a nonlinear structure may respond not only at the fundamental harmonic but also potentially at sub- or superharmonics, or it can even produce aperiodic and chaotic motion in certain cases. Shaker-structure interaction occurs when the response physically pushes back against the shaker attachment, producing non-fundamental harmonic content in the force measured by the load cell, even for pure tone voltage input to the shaker. This work develops a model to replicate these physics and investigates their influence on the response of a nonlinear normal mode of the structure. Experimental evidence is first provided that demonstrates the generation of harmonic content in the measured load cell force during a force appropriation test. This interaction is replicated by developing an electromechanical model of a modal shaker attached to a nonlinear, three-mass dynamical system. Several simulated experiments are conducted both with and without the shaker model in order to identify which effects are specifically due to the presence of the shaker. Finally, the results of these simulations are then compared to the undamped nonlinear normal modes of the structure under test to evaluate the influence of shaker-structure interaction on the identified system’s dynamics.

42 ENGINEERING↗

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↗

An Analysis of Methanol and Hydrogen Production via High-Temperature Electrolysis Using the Sodium Cooled Advanced Fast Reactor

Integration of an advanced, sodium-cooled fast spectrum reactor into nuclear hybrid energy system (NHES) architectures is the focus of the present study. A techno-economic evaluation of several conceptual system designs was performed for the integration of a sodium-cooled Advanced Fast Reactor (AFR) with the electric grid in conjunction with wind-generated electricity. Cases in which excess thermal and electrical energy would be reapportioned within an integrated energy system to a chemical plant are presented. The process applications evaluated include hydrogen production via high temperature steam electrolysis and methanol production via steam methane reforming to produce carbon monoxide and hydrogen which feed a methanol synthesis reactor. Three power cycles were considered for integration with the AFR, including subcritical and supercritical Rankine cycles and a modified supercritical carbon dioxide modified Brayton cycle. The thermal efficiencies of all of the modeled power conversions units were greater than 40%. A thermal efficiency of 42% was adopted in economic studies because two of the cycles either performed at that level or could potentially do so (subcritical Rankine and S-CO2 Brayton). Each of the evaluated hybrid architectures would be technically feasible but would demonstrate a different internal rate of return (IRR) as a function of multiple parameters; all evaluated configurations showed a positive IRR. As expected, integration of an AFR with a chemical plant increases the IRR when “must-take” wind-generated electricity is added to the energy system. Additional dynamic system analyses are recommended to draw detailed conclusions on the feasibility and economic benefits associated with AFR-hybrid energy system operation.

09 BIOMASS FUELS↗

The solar wind and magnetospheric dynamics

The dynamic processes involved in the interaction between the solar wind and the earth's magnetosphere are reviewed. The evolution of models of the magnetosphere is first surveyed. The existence of the auroral substorm and the cyclical polar magnetic substorm is evidence that the magnetosphere is a dynamic system. The dynamic changes occurring in the magnetosphere, including erosion of the magnetopause, changes in the size of the polar cap, variations in the flaring angle of the tail, neutral point formation, plasma sheet motions, and the inward collapse of the midnight magnetosphere, are discussed. The cyclical variations of geomagnetic activity are explained in terms of the control of the solar wind-magnetosphere interaction by the north-south component of the interplanetary magnetic field. Present phenomenological models allow prediction of geomagnetic activity from interplanetary measurements, but modeling of detailed magnetospheric processes is still in its infancy.

Russell, C. T.↗

An update of engine system research at the Army Propulsion Directorate

The Small Turboshaft Engine Research (STER) program provides a vehicle for evaluating the application of emerging technologies to Army turboshaft engine systems and to investigate related phenomena. Capitalizing on the resources at hand, in the form of both the NASA facilities and the Army personnel, the program goal of developing a physical understanding of engine system dynamics and/or system interactions is being realized. STER entries investigate concepts and components developed both in-house and out-of-house. Emphasis is placed upon evaluations which have evolved from on-going basic research and advanced development programs. Army aviation program managers are also encouraged to make use of STER resources, both people and facilities. The STER personnel have established their reputations as experts in the fields of engine system experimental evaluations and engine system related phenomena. The STER facility has demonstrated its utility in both research and development programs. The STER program provides the Army aviation community the opportunity to perform system level investigations, and then to offer the findings to the entire engine community for their consideration in next generation propulsion systems. In this way results of the fundamental research being conducted to meet small turboshaft engine technology challenges expeditiously find their way into that next generation of propulsion systems.

Bobula, George A.↗

An update of engine system research at the Army Propulsion Directorate

The Small Turboshaft Engine Research (STER) program provides a vehicle for evaluating the application of emerging technologies to Army turboshaft engine systems and to investigate related phenomena. Capitalizing on the resources at hand, in the form of both the NASA facilities and the Army personnel, the program goal of developing a physical understanding of engine system dynamics and/or system interactions is being realized. STER entries investigate concepts and components developed both in-house and out-of-house. Emphasis is placed upon evaluations which evolved from on-going basic research and advanced development programs. Army aviation program managers are also encouraged to make use of STER resources, both people and facilities. The STER personnel have established their reputations as experts in the fields of engine system experimental evaluations and engine system related phenomena. The STER facility has STER program provides the Army aviation community the opportunity to perform system level investigations, and then to offer the findings to the entire engine community for their consideration in next generation propulsion systems. In this way results of the fundamental research being conducted to meet small turboshaft engine technology challenges expeditiously find their way into that next generation of propulsion systems.

Bobula, George A.↗

Introduction to Fuzzy Set Theory

An introduction to fuzzy set theory is described. Topics covered include: neural networks and fuzzy systems; the dynamical systems approach to machine intelligence; intelligent behavior as adaptive model-free estimation; fuzziness versus probability; fuzzy sets; the entropy-subsethood theorem; adaptive fuzzy systems for backing up a truck-and-trailer; product-space clustering with differential competitive learning; and adaptive fuzzy system for target tracking.

Kosko, Bart↗

Dynamics of Numerics and CFD

This lecture attempts to illustrate the basic ideas of how the recent advances in nonlinear dynamical systems theory (dynamics) can provide new insights into the understanding of numerical algorithms used in solving nonlinear differential equations (DEs). Examples will be given of the use of dynamics to explain unusual phenomena that occur in numerics. The inadequacy of the use of linearized analysis for the understanding of long time behavior of nonlinear problems will be illustrated, and the role of dynamics in studying the nonlinear stability, accuracy, convergence property and efficiency of using time- dependent approaches to obtaining steady-state numerical solutions in computational fluid dynamics (CFD) will briefly be explained.

Yee, H. C.↗

A Methodology for Flight-Time Identification of Helicopter-Slung Load Frequency Response Characteristics Using CIFER

Helicopter slung load operations are common in both military and civil contexts. The slung load adds load rigid body modes, sling stretching, and load aerodynamics to the system dynamics, which can degrade system stability and handling qualities, and reduce the operating envelope of the combined system below that of the helicopter alone. Further, the effects of the load on system dynamics vary significantly among the large range of loads, slings, and flight conditions that a utility helicopter will encounter in its operating life. In this context, military helicopters and loads are often qualified for slung load operations via flight tests which can be time consuming and expensive. One way to reduce the cost and time required to carry out these tests and generate quantitative data more readily is to provide an efficient method for analysis during the flight, so that numerous test points can be evaluated in a single flight test, with evaluations performed in near real time following each test point and prior to clearing the aircraft to the next point. Methodology for this was implemented at Ames and demonstrated in slung load flight tests in 1997 and was improved for additional flight tests in 1999. The parameters of interest for the slung load tests are aircraft handling qualities parameters (bandwidth and phase delay), stability margins (gain and phase margin), and load pendulum roots (damping and natural frequency). A procedure for the identification of these parameters from frequency sweep data was defined using the CIFER software package. CIFER is a comprehensive interactive package of utilities for frequency domain analysis previously developed at Ames for aeronautical flight test applications. It has been widely used in the US on a variety of aircraft, including some primitive flight time analysis applications.

Sahai, Ranjana↗

GSFC Technology Thrusts and Partnership Opportunities

This slide presentation reviews the technology thrusts and the opportunities to partner in developing software in support of the technological advances at the Goddard Space Flight Center (GSFC). There are thrusts in development of end-to-end software systems for mission data systems in areas of flight software, ground data systems, flight dynamic systems and science data systems. The required technical expertise is reviewed, and the supported missions are shown for the various areas given.

Le Moigne, Jacqueline↗

A Robust Hybrid Deep Learning Model for Spatiotemporal Image Fusion

Dense time-series remote sensing data with detailed spatial information are highly desired for the monitoring of dynamic earth systems. Due to the sensor tradeoff, most remote sensing systems cannot provide images with both high spatial and temporal resolutions. Spatiotemporal image fusion models provide a feasible solution to generate such a type of satellite imagery, yet existing fusion methods are limited in predicting rapid and/or transient phenological changes. Additionally, a systematic approach to assessing and understanding how varying levels of temporal phenological changes affect fusion results is lacking in spatiotemporal fusion research. The objective of this study is to develop an innovative hybrid deep learning model that can effectively and robustly fuse the satellite imagery of various spatial and temporal resolutions. The proposed model integrates two types of network models: super-resolution convolutional neural network (SRCNN) and long short-term memory (LSTM). SRCNN can enhance the coarse images by restoring degraded spatial details, while LSTM can learn and extract the temporal changing patterns from the time-series images. To systematically assess the effects of varying levels of phenological changes, we identify image phenological transition dates and design three temporal phenological change scenarios representing rapid, moderate, and minimal phenological changes. The hybrid deep learning model, alongside three benchmark fusion models, is assessed in different scenarios of phenological changes. Results indicate the hybrid deep learning model yields significantly better results when rapid or moderate phenological changes are present. It holds great potential in generating high-quality time-series datasets of both high spatial and temporal resolutions, which can further benefit terrestrial system dynamic studies. The innovative approach to understanding phenological changes’ effect will help us better comprehend the strengths and weaknesses of current and future fusion models.

spatiotemporal fusion↗

Transition Dynamics in the Nascent Bioproducts Industry

Bioproducts are chemicals derived from a biomass feedstock that can be produced on their own or as biofuel co-products. Historically, bioproduct developers have faced significant barriers in scaling up bioproduct technologies and in bringing bioproducts to market, resulting in a high failure rate for bioproduct development projects. To date, there has been essentially no research done on the factors that lead to a bioproduct successfully capturing market share and why bioproduct projects fail. We address this knowledge gap with a model of the transition dynamics involved in taking a bioproduct technology from applied research to commercial production and the interactions between bioproduct developers, investors providing private funds, and federal government agencies which may provide cost-sharing and production incentives. This model incorporates several novel techniques including stochastic submodels and forecasts of market shares and company performance. Our research objectives are to identify relevant factors and mechanisms that impact bioproduct success and to develop a decision support tool, the Bioproduct Transition Dynamics (BTD) system dynamics model, that can be used by investors, bioproduct developers and government agencies to bring more bioproducts to market and to grow the nascent bioproducts industry.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Constraining dark matter sub-structure with the dynamics of astrophysical systems

The accuracy of the measurements of some astrophysical dynamical systems allows to constrain the existence of incredibly small gravitational perturbations. In particular, the internal Solar System dynamics (planets, Earth-Moon) opens up the possibility, for the first time, to prove the abundance, mass and size, of dark sub-structures at the Earth vicinity. We find that adopting the standard dark matter density, its local distribution can be composed by sub-solar mass halos with no currently measurable dynamical consequences, regardless of the mini-halo fraction. On the other hand, it is possible to exclude the presence of dark streams with linear mass densities higher than λ{sub st} > 10{sup −10}M{sub ☉}/AU (about the Earth mass spread along the diameter of the SS up to the Kuiper belt). In addition, we review the dynamics of wide binaries inside the dwarf spheroidal galaxies in the Milky Way. The dynamics of such kind of binaries seem to be compatible with the presence of a huge fraction of dark sub-structure, thus their existence is not a sharp discriminant of the dark matter hypothesis as been claimed before. However, there are regimes where the constraints from different astrophysical systems may reveal the sub-structure mass function cut-off scale.

79 ASTRONOMY AND ASTROPHYSICS↗