Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “dynamic”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Water foraging with dynamic roots in E3SM; The role of roots in terrestrial ecosystem memory on intermediate timescales (Final Technical Report)

Terrestrial ecosystems can show sustained responses to stress events that may last for years after the initial perturbation. This phenomenon is referred to as legacy or memory and it emerges from a set of ecosystem processes that are poorly captured by Earth System and Land Surface Models. Consequently, these models struggle to predict the impact that extreme climate events have on surface energy, carbon and hydrological exchange once a stressor such as drought has relaxed or in response to repeated exposure to stress. In this project, we set out to test how the addition of dynamic root profiles in land surface models impact the capacity for Earth System Models, such as the Department of Energy’s E3SM, to capture realistic legacy effects. Observations have shown that vegetation shifts their root profiles during stress events to forage for water and these altered root profiles may take years to relax back to the initial state. We hypothesized that the alteration of the belowground root structures may be a source of terrestrial ecosystem legacy that is missing from models. To test this idea we undertook three core activities. (1) We developed a global-scale analysis of the impact of dynamic roots on ecosystem legacy building from a recently developed dynamic root module. (2) We developed new root dynamics in the DOE’s Energy Land Model (ELM) that allowed not only root profiles to shift their profile but also simultaneously alter carbon allocation to fine root pools. We then tested the impact of these new dynamics with intensive sensitivity analysis at four long-term AmeriFlux sites. (3) We undertook detailed isotopic analysis of tree rings from these AmeriFlux sites to assess ecophysiological and ecohydrological legacy to stress events that can be used to benchmark the sensitivity experiments with ELM. From these core activities, we report the following key findings. Firstly, on a global scale, the addition of dynamic roots led to chronically water-stressed ecosystems recovering faster to climate stress while wetter ecosystem showed enhanced legacy. This is because across ecosystems, stress events were almost universally associated with water shortages that led to the development of deeper root profiles. These deeper root profiles proved beneficial for recovery from drought stress. While the root dynamics did not universally improve the modeled representation of legacy it showed complex transient dynamics that emerge from the addition of dynamic roots. Secondly, the sensitivity analysis illustrated long term shifts in rooting depths away from the prescribed default profile suggesting that initializing of root profiles could benefit from spin-up simulations that converge on locally optimized root profiles. In addition, by enabling dynamic allocation some of the sites predicted unrealistically low allocation to roots (and high allocation to leaves). While these changes did not dramatically alter modeled gross primary productivity, they illustrated that without more sophisticated root processes in models, there is little penalty to dramatically disinvest in roots. Thirdly, the isotopic analysis of tree rings showed highly distinct legacy responses across species and sites. For example, T. canadensis showed reduced transpiration the year after stress events illustrated by sustained elevated $\delta^{18}$O. In contrast, A saccharum displayed elevated $\delta^{13}$C associated with reduced stomatal conductance in response to the previous years’ stress event. These geochemical signatures of legacy were present despite tree growth returning to normal the year after the stress. The results show the importance of species-level dynamics in legacy that are absent in modeling that assumes common traits within plant functional types. In summary, the work here established new avenues to explore root dynamics in models while illustrating how additional root processes are needed before dynamic carbon allocation can be implemented. Lastly, this project provided mentorship to a postdoctoral fellow, training for an early career scientist and multiple undergraduate students recruited from a minority serving institution.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Dynamic Stability Analysis Using Free-Flight CFD

Blunt body probes are the primary design for atmospheric entry. The blunted capsule shape, while desirable for the decreased forebody heating, typically experiences dynamic instability at low supersonic and transonic flight. At moderate to low supersonic conditions, the unsteady wake begins to adversely interact with the vehicle in free-flight resulting in attitude oscillations which can grow in time and result in tumbling. Understanding vehicle dynamics is thus important when considering vehicle entry design and guidance navigation and control (GN&C) considerations. Historically, dynamic stability has been carried out exclusively using experimental techniques. The wide range of experimental approaches provide reasonable coverage in Mach and dynamic pressure space for a given trajectory, however achieving flight similitude is often difficult or impossible. Advancements in Computational Fluid Dynamics (CFD) techniques allow for dynamic motion of the vehicle surface during the simulation with either forced/prescribed motion or free motion in response to fluid forces. Several examples of CFD software with the ability to simulate fluid dynamics and vehicle motion are available in literature. The Free-Flight CFD (FF-CFD) capability developed by NASA Ames within the US3D flow solver has shown extensive validation and verification (V&V) efforts from moderate to low supersonic flow across a range of vehicle architectures. The solver is able to simulate full rotational and translation motion resulting in full 6 degrees-of-freedom (DoF) motion. The validation and verification efforts the solver's ability to predict the motion of a ballistic range model as compared to experimental results. Similar to other computational capabilities in literature, FF-CFD relied on heritage data reduction methodologies and processes for reducing dynamic data into aerodynamic coefficients intended for use in design and trajectory codes. These heritage approaches, initially developed with the assumptions (and restrictions) of ground test facilities, resulted in the significant culling of the full 6-DoF dynamic data set to discrete values which are then fit using an aerodynamic model. Recent development of simulation and data reduction methodologies has resulted in an improved approach to FF-CFD simulations of vehicle dynamics which leverage the control of dynamic constraints within a simulation set-up. The presentation of this work will cover the constrained dynamic simulation approach for deriving dynamic coefficients for a Genesis capsule. The methodology will be outlined and a discussion of implications in motion restriction will be discussed. Finally, reconstructed vehicle trajectories using FF-CFD derived aerodynamic coefficients will be presented.

Joseph M Brock↗
DOE OSTI2015

A concurrent multiscale micromorphic molecular dynamics

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Dynamic Event Tree advancements and control logic improvements

The RAVEN code has been under development at the Idaho National Laboratory since 2012. Its main goal is to create a multi-purpose platform for the deploying of all the capabilities needed for Probabilistic Risk Assessment, uncertainty quantification, data mining analysis and optimization studies. RAVEN is currently equipped with three different sampling categories: Forward samplers (Monte Carlo, Latin Hyper Cube, Stratified, Grid Sampler, Factorials, etc.), Adaptive Samplers (Limit Surface search, Adaptive Polynomial Chaos, etc.) and Dynamic Event Tree (DET) samplers (Deterministic and Adaptive Dynamic Event Trees). The main subject of this document is to report the activities that have been done in order to: start the migration of the RAVEN/RELAP-7 control logic system into MOOSE, and develop advanced dynamic sampling capabilities based on the Dynamic Event Tree approach. In order to provide to all MOOSE-based applications a control logic capability, in this Fiscal Year an initial migration activity has been initiated, moving the control logic system, designed for RELAP-7 by the RAVEN team, into the MOOSE framework. In this document, a brief explanation of what has been done is going to be reported. The second and most important subject of this report is about the development of a Dynamic Event Tree (DET) sampler named “Hybrid Dynamic Event Tree” (HDET) and its Adaptive variant “Adaptive Hybrid Dynamic Event Tree” (AHDET). As other authors have already reported, among the different types of uncertainties, it is possible to discern two principle types: aleatory and epistemic uncertainties. The classical Dynamic Event Tree is in charge of treating the first class (aleatory) uncertainties; the dependence of the probabilistic risk assessment and analysis on the epistemic uncertainties are treated by an initial Monte Carlo sampling (MCDET). From each Monte Carlo sample, a DET analysis is run (in total, N trees). The Monte Carlo employs a pre-sampling of the input space characterized by epistemic uncertainties. The consequent Dynamic Event Tree performs the exploration of the aleatory space. In the RAVEN code, a more general approach has been developed, not limiting the exploration of the epistemic space through a Monte Carlo method but using all the forward sampling strategies RAVEN currently employs. The user can combine a Latin Hyper Cube, Grid, Stratified and Monte Carlo sampling in order to explore the epistemic space, without any limitation. From this pre-sampling, the Dynamic Event Tree sampler starts its aleatory space exploration. As reported by the authors, the Dynamic Event Tree is a good fit to develop a goal-oriented sampling strategy. The DET is used to drive a Limit Surface search. The methodology that has been developed by the authors last year, performs a Limit Surface search in the aleatory space only. This report documents how this approach has been extended in order to consider the epistemic space interacting with the Hybrid Dynamic Event Tree methodology.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this “on-the-fly” approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. Furthermore, this approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH 2 O → H 2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Modeling starch dynamics from seasonal variations of photosynthesis, growth and respiration

Abstract Nonstructural carbohydrates (NSCs) buffer differences in plant carbon supply (photosynthesis) and demand (respiration, growth, etc.), but the regulation of their dynamics remains unresolved. Seasonal variations in NSCs are well-documented, but differences in the time-average, amplitude, phase and other characteristics across ecosystems and functional types lack explanation; furthermore, observed dynamics do not always match expectations. The failure to match observed and expected dynamics has stimulated debate on whether carbon supply or demand drives NSC dynamics. To gain insight into how carbon supply and demand drive seasonal NSC dynamics, we derive a simple model of NSC dynamics based on carbon mass balance and linearizing the NSC demand to determine how supply-driven and demand-driven seasonal NSC dynamics differ. We find that supply-driven and demand-driven dynamics yield distinct timings of seasonal extrema, and supply overrides demand when carbon supply is low in winter (e.g., at high latitudes). Our results also suggest that NSC dynamics often lag changes carbon mass balance. We also predict differences in NSC dynamics across mass, suggesting that saplings are more dynamic and respond more quickly to the environment than mature trees. Our findings suggest that substrate-dependent regulation with environmental variation is sufficient to generate complex NSC dynamics.

Forestry↗
NASA NTRS1991

The influence of dynamics on two-dimensional model results - Simulations of C-14 and stratospheric aircraft NO(x) injections

The influence of dynamics on model results is investigated via a 2D photochemical model. Three representations of atmospheric transport are tested in order to simulate total ozone and C-14 amounts after nuclear tests in the early 1960s. Three scenarios of NO(x) injections from a proposed fleet of stratospheric aircraft and their effects on ozone are simulated. The three dynamical formulations used are Dynamics A, a base dynamics used in previous work with this model; Dynamics B, a strong circulation dynamics discussed by Jackman et al. (1989); and Dynamics C, the dynamics used by Shia et al. (1989). The advective component of the stratosphere to the troposphere mass exchange rate is largest for Dynamics B (5.8 x 10 exp 17 kg/yr) and smallest for Dynamics C (1.4 x 10 exp 17 kg/yr), with the advective strat/trop exchange rate for Dynamics A (2.4 x 10 exp 17 kg/yr) being these two extremes. Ozone depletion from NO(x) injections of stratospheric aircraft showed a strong sensitivity to dynamics.

Jackman, Charles H.↗
NASA NTRS2012

Cumulative Measurement Errors for Dynamic Testing of Space Flight Hardware

Located at the NASA Johnson Space Center in Houston, TX, the Six-Degree-of-Freedom Dynamic Test System (SDTS) is a real-time, six degree-of-freedom, short range motion base simulator originally designed to simulate the relative dynamics of two bodies in space mating together (i.e., docking or berthing). The SDTS has the capability to test full scale docking and berthing systems utilizing a two body dynamic docking simulation for docking operations and a Space Station Remote Manipulator System (SSRMS) simulation for berthing operations. The SDTS can also be used for nonmating applications such as sensors and instruments evaluations requiring proximity or short range motion operations. The motion base is a hydraulic powered Stewart platform, capable of supporting a 3,500 lb payload with a positional accuracy of 0.03 inches. The SDTS is currently being used for the NASA Docking System testing and has been also used by other government agencies. The SDTS is also under consideration for use by commercial companies. Examples of tests include the verification of on-orbit robotic inspection systems, space vehicle assembly procedures and docking/berthing systems. The facility integrates a dynamic simulation of on-orbit spacecraft mating or de-mating using flight-like mechanical interface hardware. A force moment sensor is used for input during the contact phase, thus simulating the contact dynamics. While the verification of flight hardware presents unique challenges, one particular area of interest involves the use of external measurement systems to ensure accurate feedback of dynamic contact. The measurement systems for the test facility have two separate functions. The first is to take static measurements of facility and test hardware to determine both the static and moving frames used in the simulation and control system. The test hardware must be measured after each configuration change to determine both sets of reference frames. The second function is to take dynamic measurements during hardware motion and contact. While performing dynamic testing of an active docking system, researchers found that the data from the motion platform, test hardware and two external measurement systems exhibited frame offsets and rotational errors. While the errors were relatively small when considering the motion scale overall, they substantially exceeded the individual accuracies for each component. After evaluating both the static and dynamic measurements, researchers found that the static measurements introduced significantly more error into the system than the dynamic measurements even though, in theory, the static measurement errors should be smaller than the dynamic. In several cases, the magnitude of the errors varied widely for the static measurements. Upon further investigation, researchers found the larger errors to be a consequence of hardware alignment issues, frame location and measurement technique whereas the smaller errors were dependent on the number of measurement points. This paper details and quantifies the individual and cumulative errors of the docking system and describes methods for reducing the overall measurement error. The overall quality of the dynamic docking tests for flight hardware verification was improved by implementing these error reductions.

Winnitoy, Susan↗
NASA NTRS2014

Assessing the Risk of Crew Injury Due to Dynamic Loads During Spaceflight

Spaceflight requires tremendous amounts of energy to achieve Earth orbit and to attain escape velocity for interplanetary missions. Although the majority of the energy is managed in such a way as to limit the accelerations on the crew, several mission phases may result in crew exposure to dynamic loads. In the automotive industry, risk of serious injury can be tolerated because the probability of a crash is remote each time a person enters a vehicle, resulting in a low total risk of injury. For spaceflight, the level of acceptable injury risk must be lower to achieve a low total risk of injury because the dynamic loads are expected on each flight. To mitigate the risk of injury due to dynamic loads, the NASA Human Research Program has developed a research plan to inform the knowledge gaps and develop relevant tools for assessing injury risk. The risk of injury due to dynamic loads can be further subdivided into extrinsic and intrinsic risk factors. Extrinsic risk factors include the vehicle dynamic profile, seat and restraint design, and spacesuit design. Human tolerance to loads varies considerably depending on the direction, amplitude, and rise-time of acceleration therefore the orientation of the body to the dynamic vector is critical to determining crew risk of injury. Although a particular vehicle dynamic profile may be safe for a particular design, the seat, restraint, and suit designs can affect the risk of injury due to localized effects. In addition, characteristics intrinsic to the crewmember may also contribute to the risk of injury, such as crewmember sex, age, anthropometry, and deconditioning due to spaceflight, and each astronaut may have a different risk profile because of these factors. The purpose of the research plan is to address any knowledge gaps in the risk factors to mitigate injury risk. Methods for assessing injury risk have been well documented in other analogous industries and include human volunteer testing, human exposure to dynamic environments, post-mortem human subject (PMHS) testing, animal testing, anthropomorphic test devices (ATD), dynamic models of the human, numerical models of ATDs, and numerical models of the human. Each has inherent strengths and limitations. For example, human volunteer testing is advantageous because a population can be selected that is similar to the astronaut corps; however, because of the inherent ethical limitations, only sub-injurious conditions can be tested. PMHSs can be tested in a variety of conditions including injurious levels, but the responses are not completely analogous to living human subjects. In addition, it is exceedingly difficult to select a PMHS population that is similar to the astronaut corps. ATDs are currently widely used in the automotive industry and military because they are highly repeatable and durable. Unfortunately, because they are mechanical models of the human body, the biofidelity of the responses are limited to dynamic conditions used to validate the ATD. Numerical models of the ATD, in addition to the strengths and limitations for ATDs, are easy to use for a variety of designs before a design is fabricated, but also have additional limitations for ATDs, are easy to use for a variety of designs before a design is fabricated, but also have additional uncertainty. Dynamic models are simple and easy to use, but do not account for localized effects of the seat and suit. Finally, numerical models of the human have the potential to have the most advantages; however, the current models are not validated for the conditions expected during spaceflight. To properly assess spaceflight conditions with numerical human models, human data would be needed to optimize the model responses for those conditions. Using the appropriate assessment method with the knowledge gained for each risk factor, an appropriate approach for mitigating the risk of injury due to dynamic loads can be developed ensuring crew safety in future NASA vehicles.

Somers, J. T.↗
DOE OSTI2018

Spatiotemporal video-domain high-fidelity simulation and realistic visualization of full-field dynamic responses of structures by a combination of high-spatial-resolution modal model and video motion manipulations

Structures with complex geometries, material properties, and boundary conditions exhibit spatially local dynamic behaviors. A high-spatial-resolution model of the structure is thus required for high-fidelity analysis, assessment, and prediction of the dynamic phenomena of the structure. The traditional approach is to build a highly refined finite element computer model for simulating and analyzing the structural dynamic phenomena based on detailed knowledge and explicit modeling of the structural physics such as geometries, materials properties, and boundary conditions. These physics information of the structure may not be available or accurately modeled in many cases, however. In addition, the simulation on the high-spatial-resolution structural model, with a massive number of degrees of freedom and system parameters, is computationally demanding. Here this study, on a proof-of-principle basis, proposes a novel alternative approach for spatiotemporal video-domain high-fidelity simulation and realistic visualization of full-field structural dynamics by an innovative combination of the fundamentals of structural dynamic modeling and the advanced video motion manipulation techniques. Specifically, a low-modal-dimensional yet high-spatial (pixel)-resolution (as many spatial points as the pixel number on the structure in the video frame) modal model is established in the spatiotemporal video domain with full-field modal parameters first estimated from line-of-sight video measurements of the operating structure. Then in order to simulate new dynamic response of the structure subject to a new force, the force is projected onto each modal domain, and the modal response is computed by solving each individual single-degree-of-freedom system in the modal domain. The simulated modal responses are then synthesized by the full-field mode shapes using modal superposition to obtain the simulated full-field structural dynamic response. Finally, the simulated structural dynamic response is embedded into the original video, replacing the original motion of the video, thus generating a new photo-realistic, physically accurate video that enables a realistic, high-fidelity visualization/animation of the simulated full-field vibration of the structure. Laboratory experiments are conducted to validate the proposed method, and the error sources and limitations in practical implementations are also discussed. Compared with high-fidelity finite element computer model simulations of structural dynamics, the video-based simulation method removes the need to explicitly model the structure's physics. In addition, the photo-realistic, physically accurate simulated video provides a realistic visualization/animation of the full-field structural dynamic response, which was not traditionally available. Lastly, these features of the proposed method should enable a new alternative to the traditional computer-aided finite element model simulation for high-fidelity simulating and realistically visualizing full-field structural dynamics in a relatively efficient and user-friendly manner.

42 ENGINEERING↗
DOE OSTI2021

Parallel transport dynamics for mixed quantum states with applications to time-dependent density functional theory

Direct simulation of the von Neumann dynamics for a general (pure or mixed) quantum state can often be expensive. One prominent example is the real-time time-dependent density functional theory (rt-TDDFT), a widely used framework for the first principle description of many-electron dynamics in chemical and materials systems. Practical rt-TDDFT calculations often avoid the direct simulation of the von Neumann equation, and solve instead a set of Schrödinger equations, of which the dynamics is equivalent to that of the von Neumann equation. However, the time step size employed by the Schrödinger dynamics is often much smaller. Here, in order to improve the time step size and the overall efficiency of the simulation, we generalize a recent work of the parallel transport (PT) dynamics for simulating pure states [An, Lin, Multiscale Model. Simul. 18, 612, 2020] to general quantum states. The PT dynamics provides the optimal gauge choice, and can employ a time step size comparable to that of the von Neumann dynamics. Going beyond the linear and near adiabatic regime in previous studies, we find that the error of the PT dynamics can be bounded by certain commutators between Hamiltonians, density matrices, and their derived quantities. Such a commutator structure is not present in the Schrödinger dynamics. We demonstrate that the parallel transport-implicit midpoint (PT-IM) method is a suitable method for simulating the PT dynamics, especially when the spectral radius of the Hamiltonian is large. The commutator structure of the error bound, and numerical results for model rt-TDDFT calculations in both linear and nonlinear regimes, confirm the advantage of the PT dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Dynamical Signatures of Thermotoga maritima Maltose-Binding Proteins Affected by Ligand Binding

Functional segregation among protein isoforms depends on the interplay of their overall structures and the molecular dynamics of these structures. Thermotoga maritima maltose-binding protein (tmMBP) isoforms show size-dependent differential binding of maltose and malto-oligomers while maintaining remarkable fold conservation. This differential behavior needs detailed characterization in native-like aqueous conditions to understand the effects of protein dynamics on ligand binding and recognition. Small-angle neutron scattering (SANS), neutron spin echo (NSE) spectroscopy, and dynamic light scattering (DLS) were used in conjunction with previously published computational molecular dynamics (MD) simulations to understand the dynamic behavior of tmMBPs experimentally. SANS provided information on the overall structure of the molecules, while NSE was used to determine the dynamics in the nanosecond time scale. Both tmMBP2 and tmMBP3 have a bidomain architecture linked with a flexible hinge, with the binding pocket sitting in the cleft between the two domains. tmMBP2 and tmMBP3 showed different solution dynamics, with the translational and rotational components dominating the dynamics of both systems, resulting in a clear differentiation of their diffusion pattern. A faster dynamics component was also observed and was attributed to segmental dynamics. Differences observed between the ligand-free (apo) and ligand-bound (holo) states of the two proteins are attributed to conformational entropy. Our results highlight the intricacies of how structure and dynamics can together shape binding to a repertoire of substrates in structurally similar proteins.

Diffusion↗
DOE OSTI2019

Ab initio molecular dynamics simulation of supercritical aqueous ionic solutions: Spectral diffusion of water in the vicinity of Br¯ and I¯ ions

Supercritical aqueous ionic solutions containing bromide (Br¯) and iodide (I¯) ions have been studied using Car-Parrinello molecular dynamics simulation at two different concentrations and at two different densities. The time dependent trajectory has been used for calculating vibrational spectral diffusion, structural properties and, for other dynamical properties such as hydrogen bond dynamics, orientational relaxation and residence dynamics. The vibrational spectral diffusion of fluctuating OD stretch mode inside the solvation shell of the ions and in the bulk has been studied using frequency-frequency time correlation function. Hydrogen bond dynamics, orientational relaxation and residence dynamics of Sc-water have been investigated using population correlation function approach. The water molecules inside the solvation shell of Br¯ and I¯ ions are found to show complex molecular dynamics in comparison to the water-water dynamics. The concentration dependent spectral diffusion has been observed and it occurs in multiple time scales in the solvation shell of Br¯ and I¯ ions. Here, at supercritical condition, the ion-water hydrogen bond shows faster dynamics with respect to the same at ambient condition and slower dynamics with respect to the water-water hydrogen bond dynamics at supercritical condition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

The feasibility of a piecewise-linear dynamic bowtie filter

Purpose: The prepatient attenuator (or 'bowtie filter') in CT is used to modulate the flux as a function of fan angle of the x-ray beam incident on the patient. Traditional, static bowtie filters are tailored only for very generic scans and for the average patient. The authors propose a design for a dynamic bowtie that can produce a time-dependent piecewise-linear attenuation profile. This dynamic bowtie may reduce dynamic range, dose or scatter, but in this work they focus on its ability to reduce dynamic range, which may be particularly important for systems employing photon-counting detectors. Methods: The dynamic bowtie is composed of a set of triangular wedges. Each wedge is independently moved in order to produce a time-dependent piecewise-linear attenuation profile. Simulations of the bowtie are conducted to estimate the dynamic range reduction in six clinical datasets. The control of the dynamic bowtie is determined by solving a convex optimization problem, and the dose is estimated using Monte Carlo techniques. Beam hardening artifacts are also simulated. Results: The dynamic range is reduced by factors ranging from 2.4 to 27 depending on the part of the body studied. With a dynamic range minimization objective, the dose to the patient can be reduced from 6% to 33% while maintaining peak image noise. Further reduction in dose may be possible with a specific dose reduction objective. Beam hardening artifacts are suppressed with a two-pass algorithm. Conclusions: A dynamic bowtie producing a time-dependent, piecewise-linear attenuation profile is possible and can be used to modulate the flux of the scanner to the imaging task. Initial simulations show a large reduction in dynamic range. Several other applications are possible.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1999

MRI Measurements and Granular Dynamics Simulation of Segregation of Granular Mixture

A counter intuitive axial segregation phenomenon in a rotating horizontal cylinder has recently captured attention of many researchers in different disciplines. There is a growing consensus that the interplay between the particle dynamics and the evolution of the internal structure during the segregation process must be carefully investigated. Magnetic resonance imaging (MRI) has been used to non-invasively obtain much needed dynamic/static information such as velocity and concentration profiles, and it has proven to be capable of depicting the evolution of segregation processes. Segregation in a rotating cylinder involves two processes: the first is to transport small particles in the radial direction to form a radial core, and the second is to transform the radial core into axially segregated bands. Percolation and/or "stopping" have been proposed as mechanisms for the radial segregation. As to mechanisms for axial band formation, much less is known. The difference in the dynamic angle of repose has been proposed to segregate different components in the axial direction. Recently, Hill and Kakalios have reported that particles mix or demix depending upon the competition between diffusion and preferential drift whose order can be determined by the dynamic angle of repose through the adjustment of the rotation rate. We claim that the dynamic angle of repose could be one of the causes, however, it fails to offer reasonable explanations for certain aspects of the axial migration. For example, we always observe that the radial segregation precedes the axial segregation and small particles migrate in the radial direction to form an axially extended radial core. It then transforms into axially segregated bands. By definition, the effects of the dynamic angle of repose are restricted near the free surface where the flowing layer is present. However, during the process of transforming from the radially segregated core to axially segregated bands, small particles located in the deep core region, which is untouched by the flowing layer, also completely disappear. Usually, the dynamics angle of repose are uniquely defined for individual species to characterize particle properties, and the dynamic angle of repose thus defined provides little information for the dynamic angle of repose of the mixture since the concentration ratio and the internal packing structure do not remain the same during the segregation processes. Under microgravity environment, the dynamics angle of repose argument does not hold since there is simply no flowing layer to influence/determine the preferred directions of segregation. We have thus designed an experiment so that the effects of the dynamic angle of repose can be minimized by filling the cylinder almost completely full. Small particles still formed a radial core and also migrated to form axial bands. As ground based experiments we have designed and conducted both 2D and 3D segregation experiments. The 2D experiments are performed using a thin cylinder (the gap between two end caps is about 5 mm) filled with different combinations of particles. The 3D experiments are conducted with a long cylinder of its length and diameter of 27cm and 7cm, respectively. Results of 2D experiments indicate that different mechanisms govern particle motion in regions near and far from the axis of rotation. Results of 3D experiments indicate that a series of collapses of microstructures of particle packing (micro-collapses) may be responsible for the creation of voids for small particles to migrate through in the axial direction. We have successfully eliminated the dynamic angle of repose as a cause for segregation, however, by almost completely filling the cylinder with the particles, we have lost an opportunity to investigate a possibility of particle "mobility" being a cause for segregation which requires a flowing surface but not the difference in the angle of repose. This is currently being investigated.

Nakagawa, M.↗
DOE OSTI2025

Long timescale solvation dynamics and confinement: The case of non-ionic deep eutectic solvents of lauric acid and N-methylacetamide

Microscopic segregation and molecular heterogeneities in complex liquids are the result of the interplay between different intermolecular forces, all of which contribute to the energy landscape of the system. A consequence of the intricate energy landscape is the nontrivial effect on the solvation dynamics. Here, the impact of molecular heterogeneities on the solvation dynamics is studied using infrared spectroscopies and molecular dynamics simulations. In particular, this study focuses on the dynamical effect of nanoscopic heterogeneities present in deep eutectic solvents (DESs) composed of lauric acid (LA) and N-methylacetamide (NMA). To this end, a molecular probe containing a carbon triple bond is used as an infrared reporter. The results show that the vibrational probe is likely to be located in the NMA polar domains. Furthermore, the probe solvation dynamics derived from the 2DIR spectra presents a slowdown of its timescale with increasing LA concentration in the DES. Kubo modeling of the probe solvation dynamics shows a correlation between the amplitude of its long time component and the presence of molecular heterogeneities in the sample. Semiclassical modeling of the vibrational line shape of the triple bond stretch demonstrates that the heterogeneities affect the whole solvation dynamics of the system through the amplitudes of the frequency fluctuations. Molecular dynamics simulations confirm the experimental results and their interpretation by showing a slowdown of the solvation dynamics when the LA heterogeneities are present. Overall, the study presents a molecular framework to explain the effect of confinement created by nanoscopic LA heterogeneities on the solvation dynamics of the system.

Chemical compounds↗
NASA NTRS2014

Dissertation Defense Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional "validation by test only" mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions. Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in "Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations". This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics predictions. The method accounts for all uncertainty terms from both numerical and input variables. Objective three is to compile a table of uncertainty parameters that could be used to estimate the error in a Computational Fluid Dynamics model of the Environmental Control System /spacecraft system. Previous studies have looked at the uncertainty in a Computational Fluid Dynamics model for a single output variable at a single point, for example the re-attachment length of a backward facing step. For the flow regime being analyzed (turbulent, three-dimensional, incompressible), the error at a single point can propagate into the solution both via flow physics and numerical methods. Calculating the uncertainty in using Computational Fluid Dynamics to accurately predict airflow speeds around encapsulated spacecraft in is imperative to the success of future missions.

CFD↗
NASA NTRS2014

Dissertation Defense: Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional validation by test only mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions.Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations. This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics predictions. The method accounts for all uncertainty terms from both numerical and input variables. Objective three is to compile a table of uncertainty parameters that could be used to estimate the error in a Computational Fluid Dynamics model of the Environmental Control System spacecraft system.Previous studies have looked at the uncertainty in a Computational Fluid Dynamics model for a single output variable at a single point, for example the re-attachment length of a backward facing step. For the flow regime being analyzed (turbulent, three-dimensional, incompressible), the error at a single point can propagate into the solution both via flow physics and numerical methods. Calculating the uncertainty in using Computational Fluid Dynamics to accurately predict airflow speeds around encapsulated spacecraft in is imperative to the success of future missions.

Fluid Dynamics↗