Photogrammetry and Videogrammetry Methods for Solar Sails and Other Gossamer Structures

NASA Technical Reports Server (NTRS)

Black, Jonathan T.; Pappa, Richard S.

2004-01-01

Ultra-lightweight and inflatable gossamer space structures are designed to be tightly packaged for launch, then deploy or inflate once in space. These properties will allow for in-space construction of very large structures 10 to 1000 meters in size such as solar sails, inflatable antennae, and space solar power stations using a single launch. Solar sails are of particular interest because of their potential for propellantless propulsion. Gossamer structures do, however, have significant complications. Their low mass and high flexibility make them very difficult to test on the ground. The added mass and stiffness of attached measurement devices can significantly alter the static and dynamic properties of the structure. This complication necessitates an alternative approach for characterization. This paper discusses the development and application of photogrammetry and videogrammetry methods for the static and dynamic characterization of gossamer structures, as four specific solar sail applications demonstrate. The applications prove that high-resolution, full-field, non-contact static measurements of solar sails using dot projection photogrammetry are possible as well as full-field, noncontact, dynamic characterization using dot projection videogrammetry.

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle.

PubMed

Salorinne, Kirsi; Malola, Sami; Wong, O Andrea; Rithner, Christopher D; Chen, Xi; Ackerson, Christopher J; Häkkinen, Hannu

2016-01-21

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of (1)H and (13)C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications.

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle

PubMed Central

Salorinne, Kirsi; Malola, Sami; Wong, O. Andrea; Rithner, Christopher D.; Chen, Xi; Ackerson, Christopher J.; Häkkinen, Hannu

2016-01-01

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications. PMID:26791253

Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy.

PubMed

McHaourab, Hassane S; Steed, P Ryan; Kazmier, Kelli

2011-11-09

Trapping membrane proteins in the confines of a crystal lattice obscures dynamic modes essential for interconversion between multiple conformations in the functional cycle. Moreover, lattice forces could conspire with detergent solubilization to stabilize a minor conformer in an ensemble thus confounding mechanistic interpretation. Spin labeling in conjunction with electron paramagnetic resonance (EPR) spectroscopy offers an exquisite window into membrane protein dynamics in the native-like environment of a lipid bilayer. Systematic application of spin labeling and EPR identifies sequence-specific secondary structures, defines their topology and their packing in the tertiary fold. Long range distance measurements (60 Å-80 Å) between pairs of spin labels enable quantitative analysis of equilibrium dynamics and triggered conformational changes. This review highlights the contribution of spin labeling to bridging structure and mechanism. Efforts to develop methods for determining structures from EPR restraints and to increase sensitivity and throughput promise to expand spin labeling applications in membrane protein structural biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

Application of holographic interferometry for analysis of the dynamic and modal characteristics of an advanced exotic metal airfoil structure

NASA Astrophysics Data System (ADS)

Fein, Howard

1999-03-01

Holographic Interferometry has been successfully employed to characterize the materials and behavior of diverse types of structures under stress. Specialized variations of this technology have also been applied to define dynamic and vibration related structural behavior. Such applications of holographic technique offer some of the most effective methods of modal and dynamic analysis available. Real-time dynamic testing of the modal and mechanical behavior of aerodynamic control and airfoil structures for advanced aircraft has always required advanced instrumentation for data collection in either actual flight test or wind-tunnel simulations. Advanced optical holography techniques are alternate methods which result in actual full-field behavioral data on the ground in a noninvasive environment. These methods offer significant insight in both the development and subsequent operational test and modeling of advanced exotic metal control structures and their integration with total vehicle system dynamics. Structures and materials can be analyzed with very low amplitude excitation and the resultant data can be used to adjust the accuracy mathematically derived structural and behavioral models. Holographic Interferometry offers a powerful tool to aid in the developmental engineering of exotic metal structures for high stress applications. Advanced Titanium alloy is a significant example of these sorts of materials which has found continually increased use in advanced aerodynamic, undersea, and other highly mobil platforms. Aircraft applications in particular must consider environments where extremes in vibration and impulsive mechanical stress can affect both operation and structural stability. These considerations present ideal requisites for analysis using advanced holographic methods in the initial design and test of structures made with such advanced materials. Holographic techniques are nondestructive, real- time, and definitive in allowing the identification of vibrational modes, displacements, and motion geometries. Such information can be crucial to the determination of mechanical configurations and designs as well as operational parameters of structural components fabricated from advanced and exotic materials. Anomalous behavioral characteristics can be directly related to hidden structural or mounting anomalies and defects. Deriving such information can be crucial to the determination of mechanical configurations and designs, as well as critical operational parameters of structural components fabricated from advanced and exotic materials.

A curved piezo-structure model: implications on active structural acoustic control.

PubMed

Henry, J K; Clark, R L

1999-09-01

Current research in Active Structural Acoustic Control (ASAC) relies heavily upon accurately capturing the application physics associated with the structure being controlled. The application of ASAC to aircraft interior noise requires a greater understanding of the dynamics of the curved panels which compose the skin of an aircraft fuselage. This paper presents a model of a simply supported curved panel with attached piezoelectric transducers. The model is validated by comparison to previous work. Further, experimental results for a simply supported curved panel test structure are presented in support of the model. The curvature is shown to affect substantially the dynamics of the panel, the integration of transducers, and the bandwidth required for structural acoustic control.

Advances in engineering science, volume 2

NASA Technical Reports Server (NTRS)

1976-01-01

Papers are presented dealing with structural dynamics; structural synthesis; and the nonlinear analysis of structures, structural members, and composite structures and materials. Applications of mathematics and computer science are included.

NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

PubMed Central

Konrat, Robert

2014-01-01

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

Impedance measures in analysis and characterization of multistable structures subjected to harmonic excitation

NASA Astrophysics Data System (ADS)

Harne, Ryan L.; Goodpaster, Benjamin A.

2018-01-01

Structural components susceptible to adverse, post-buckled dynamic behaviors have long challenged the success of applications requiring lightweight, slender curved structures, while researchers have begun to leverage such bistable systems in emerging applications for novel energy attenuation and shape-changing properties. To expedite development and deployment of these built-up platforms containing post-buckled constituents, efficient approaches are required to complement time-consuming full-field models in the prediction of the near- and far-from-equilibrium dynamics. This research meets the need by introducing a semi-analytical model framework to enable the characterization of steady-state responses in multi degree-of-freedom (DOF) and multistable structural systems subjected to harmonic excitation. In so doing, the pathway for assessing impedance measures is created here so as to identify how energy travels and returns within built-up multistable structures. Verified by simulations and qualitatively validated by experiments, the analysis is shown to accurately reproduce both near- and far-from-equilibrium responses including different classes of energetic snap-through dynamics that only exist in such multistable structures. A first look at the impedance measures of different dynamic regimes reveals a connection between damping in multistable structures and the sustainability of far-from-equilibrium oscillations.

Dynamic social community detection and its applications.

PubMed

Nguyen, Nam P; Dinh, Thang N; Shen, Yilin; Thai, My T

2014-01-01

Community structure is one of the most commonly observed features of Online Social Networks (OSNs) in reality. The knowledge of this feature is of great advantage: it not only provides helpful insights into developing more efficient social-aware solutions but also promises a wide range of applications enabled by social and mobile networking, such as routing strategies in Mobile Ad Hoc Networks (MANETs) and worm containment in OSNs. Unfortunately, understanding this structure is very challenging, especially in dynamic social networks where social interactions are evolving rapidly. Our work focuses on the following questions: How can we efficiently identify communities in dynamic social networks? How can we adaptively update the network community structure based on its history instead of recomputing from scratch? To this end, we present Quick Community Adaptation (QCA), an adaptive modularity-based framework for not only discovering but also tracing the evolution of network communities in dynamic OSNs. QCA is very fast and efficient in the sense that it adaptively updates and discovers the new community structure based on its history together with the network changes only. This flexible approach makes QCA an ideal framework applicable for analyzing large-scale dynamic social networks due to its lightweight computing-resource requirement. To illustrate the effectiveness of our framework, we extensively test QCA on both synthesized and real-world social networks including Enron, arXiv e-print citation, and Facebook networks. Finally, we demonstrate the applicability of QCA in real applications: (1) A social-aware message forwarding strategy in MANETs, and (2) worm propagation containment in OSNs. Competitive results in comparison with other methods reveal that social-based techniques employing QCA as a community detection core outperform current available methods.

Dynamic Social Community Detection and Its Applications

PubMed Central

Nguyen, Nam P.; Dinh, Thang N.; Shen, Yilin; Thai, My T.

2014-01-01

Community structure is one of the most commonly observed features of Online Social Networks (OSNs) in reality. The knowledge of this feature is of great advantage: it not only provides helpful insights into developing more efficient social-aware solutions but also promises a wide range of applications enabled by social and mobile networking, such as routing strategies in Mobile Ad Hoc Networks (MANETs) and worm containment in OSNs. Unfortunately, understanding this structure is very challenging, especially in dynamic social networks where social interactions are evolving rapidly. Our work focuses on the following questions: How can we efficiently identify communities in dynamic social networks? How can we adaptively update the network community structure based on its history instead of recomputing from scratch? To this end, we present Quick Community Adaptation (QCA), an adaptive modularity-based framework for not only discovering but also tracing the evolution of network communities in dynamic OSNs. QCA is very fast and efficient in the sense that it adaptively updates and discovers the new community structure based on its history together with the network changes only. This flexible approach makes QCA an ideal framework applicable for analyzing large-scale dynamic social networks due to its lightweight computing-resource requirement. To illustrate the effectiveness of our framework, we extensively test QCA on both synthesized and real-world social networks including Enron, arXiv e-print citation, and Facebook networks. Finally, we demonstrate the applicability of QCA in real applications: (1) A social-aware message forwarding strategy in MANETs, and (2) worm propagation containment in OSNs. Competitive results in comparison with other methods reveal that social-based techniques employing QCA as a community detection core outperform current available methods. PMID:24722164

Application of design sensitivity analysis for greater improvement on machine structural dynamics

NASA Technical Reports Server (NTRS)

Yoshimura, Masataka

1987-01-01

Methodologies are presented for greatly improving machine structural dynamics by using design sensitivity analyses and evaluative parameters. First, design sensitivity coefficients and evaluative parameters of structural dynamics are described. Next, the relations between the design sensitivity coefficients and the evaluative parameters are clarified. Then, design improvement procedures of structural dynamics are proposed for the following three cases: (1) addition of elastic structural members, (2) addition of mass elements, and (3) substantial charges of joint design variables. Cases (1) and (2) correspond to the changes of the initial framework or configuration, and (3) corresponds to the alteration of poor initial design variables. Finally, numerical examples are given for demonstrating the availability of the methods proposed.

High-rate RTK and PPP multi-GNSS positioning for small-scale dynamic displacements monitoring

NASA Astrophysics Data System (ADS)

Paziewski, Jacek; Sieradzki, Rafał; Baryła, Radosław; Wielgosz, Pawel

2017-04-01

The monitoring of dynamic displacements and deformations of engineering structures such as buildings, towers and bridges is of great interest due to several practical and theoretical reasons. The most important is to provide information required for safe maintenance of the constructions. High temporal resolution and precision of GNSS observations predestine this technology to be applied to most demanding application in terms of accuracy, availability and reliability. GNSS technique supported by appropriate processing methodology may meet the specific demands and requirements of ground and structures monitoring. Thus, high-rate multi-GNSS signals may be used as reliable source of information on dynamic displacements of ground and engineering structures, also in real time applications. In this study we present initial results of application of precise relative GNSS positioning for detection of small scale (cm level) high temporal resolution dynamic displacements. Methodology and algorithms applied in self-developed software allowing for relative positioning using high-rate dual-frequency phase and pseudorange GPS+Galileo observations are also given. Additionally, an approach was also made to use the Precise Point Positioning technique to such application. In the experiment were used the observations obtained from high-rate (20 Hz) geodetic receivers. The dynamic displacements were simulated using specially constructed device moving GNSS antenna with dedicated amplitude and frequency. The obtained results indicate on possibility of detection of dynamic displacements of the GNSS antenna even at the level of few millimetres using both relative and Precise Point Positioning techniques after suitable signals processing.

Order reduction, identification and localization studies of dynamical systems

NASA Astrophysics Data System (ADS)

Ma, Xianghong

In this thesis methods are developed for performing order reduction, system identification and induction of nonlinear localization in complex mechanical dynamic systems. General techniques are proposed for constructing low-order models of linear and nonlinear mechanical systems; in addition, novel mechanical designs are considered for inducing nonlinear localization phenomena for the purpose of enhancing their dynamical performance. The thesis is in three major parts. In the first part, the transient dynamics of an impulsively loaded multi-bay truss is numerically computed by employing the Direct Global Matrix (DGM) approach. The approach is applicable to large-scale flexible structures with periodicity. Karhunen-Loeve (K-L) decomposition is used to discretize the dynamics of the truss and to create the low-order models of the truss. The leading order K-L modes are recovered by an experiment, which shows the feasibility of K-L based order reduction technique. In the second part of the thesis, nonlinear localization in dynamical systems is studied through two applications. In the seismic base isolation study, it is shown that the dynamics are sensitive to the presence of nonlinear elements and that passive motion confinement can be induced under proper design. In the coupled rod system, numerical simulation of the transient dynamics shows that a nonlinear backlash spring can induce either nonlinear localization or delocalization in the form of beat phenomena. K-L decomposition and poincare maps are utilized to study the nonlinear effects. The study shows that nonlinear localization can be induced in complex structures through backlash. In the third and final part of the thesis, a new technique based on Green!s function method is proposed to identify the dynamics of practical bolted joints. By modeling the difference between the dynamics of the bolted structure and the corresponding unbolted one, one constructs a nonparametric model for the joint dynamics. Two applications are given with a bolted beam and a truss joint in order to show the applicability of the technique.

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

PubMed

Wiebrands, Michael; Malajczuk, Chris J; Woods, Andrew J; Rohl, Andrew L; Mancera, Ricardo L

2018-06-21

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

NASA Astrophysics Data System (ADS)

Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

2017-01-01

Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

"Structure and dynamics in complex chemical systems: Gaining new insights through recent advances in time-resolved spectroscopies.” ACS Division of Physical Chemistry Symposium presented at the Fall National ACS Meeting in Boston, MA, August 2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, Daniel

8-Session Symposium on STRUCTURE AND DYNAMICS IN COMPLEX CHEMICAL SYSTEMS: GAINING NEW INSIGHTS THROUGH RECENT ADVANCES IN TIME-RESOLVED SPECTROSCOPIES. The intricacy of most chemical, biochemical, and material processes and their applications are underscored by the complex nature of the environments in which they occur. Substantial challenges for building a global understanding of a heterogeneous system include (1) identifying unique signatures associated with specific structural motifs within the heterogeneous distribution, and (2) resolving the significance of each of multiple time scales involved in both small- and large-scale nuclear reorganization. This symposium focuses on the progress in our understanding of dynamics inmore » complex systems driven by recent innovations in time-resolved spectroscopies and theoretical developments. Such advancement is critical for driving discovery at the molecular level facilitating new applications. Broad areas of interest include: Structural relaxation and the impact of structure on dynamics in liquids, interfaces, biochemical systems, materials, and other heterogeneous environments.« less

Closed Loop Vibrational Control: Theory and Applications

DTIC Science & Technology

1993-10-01

the open loop system dynamics will be close to that of Bit. However, in general, in a closed loop system with a specified feedback co-’ - oller , for...Juang, and G. Rodriguez , "Formulations and Applications of Large Structure Actuator and Sensor Placements," Second VPI & SU/AIAA Symposium on Dynamics

Nonlinear Dynamics and Control of Flexible Structures

DTIC Science & Technology

1991-03-01

of which might be used for space applications. This project was a collaborative one involving structural, electrical and mechanical engineers and...methods for vibration analysis and new models to analyze chaotic dynamics in nonlinear structures with large deformations and friction forces. Finally... electrical and mechanical engineers and resulted in nine doctoral dissertations and two masters theses wholly or partially supported by this grant

Structures and Dynamics Division research and technology plans for FY 1986 and accomplishments for FY 1985

NASA Technical Reports Server (NTRS)

Bales, K. S.

1986-01-01

Presented are the Objectives, FY 1986 Plans, Approach, and FY 1986 Milestones for the Structures and Dynamics Division's research programs. FY 1985 Accomplishments are presented where applicable. This information is useful in program coordination with other governmental organizations in areas of mutual interest.

Applications of fiber optics sensors in weigh-in-motion (WIM) systems for monitoring truck weights on pavements and structures.

DOT National Transportation Integrated Search

2003-04-01

The main objective of this project was to investigate emerging technologies and to establish criteria for evaluating fiber optic sensors used to measure actual dynamic loads on pavements and structures. The dynamic load of particular interest for thi...

Photogrammetry and optical methods in structural dynamics - A review

NASA Astrophysics Data System (ADS)

Baqersad, Javad; Poozesh, Peyman; Niezrecki, Christopher; Avitabile, Peter

2017-03-01

In the last few decades, there has been a surge of research in the area of non-contact measurement techniques. Photogrammetry has received considerable attention due to its ability to achieve full-field measurement and its robustness to work in testing environments and on testing articles in which using other measurement techniques may not be practical. More recently, researchers have used this technique to study transient phenomena and to perform measurements on vibrating structures. The current paper reviews the most current trends in the photogrammetry technique (point tracking, digital image correlation, and target-less approaches) and compares the applications of photogrammetry to other measurement techniques used in structural dynamics (e.g. laser Doppler vibrometry and interferometry techniques). The paper does not present the theoretical background of the optical techniques, but instead presents the general principles of each approach and highlights the novel structural dynamic measurement concepts and applications that are enhanced by utilizing optical techniques.

Using directed information for influence discovery in interconnected dynamical systems

NASA Astrophysics Data System (ADS)

Rao, Arvind; Hero, Alfred O.; States, David J.; Engel, James Douglas

2008-08-01

Structure discovery in non-linear dynamical systems is an important and challenging problem that arises in various applications such as computational neuroscience, econometrics, and biological network discovery. Each of these systems have multiple interacting variables and the key problem is the inference of the underlying structure of the systems (which variables are connected to which others) based on the output observations (such as multiple time trajectories of the variables). Since such applications demand the inference of directed relationships among variables in these non-linear systems, current methods that have a linear assumption on structure or yield undirected variable dependencies are insufficient. Hence, in this work, we present a methodology for structure discovery using an information-theoretic metric called directed time information (DTI). Using both synthetic dynamical systems as well as true biological datasets (kidney development and T-cell data), we demonstrate the utility of DTI in such problems.

Modeling structural change in spatial system dynamics: A Daisyworld example.

PubMed

Neuwirth, C; Peck, A; Simonović, S P

2015-03-01

System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed.

Structural stability of nonlinear population dynamics.

PubMed

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Structural stability of nonlinear population dynamics

NASA Astrophysics Data System (ADS)

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Quantum theory for the dynamic structure factor in correlated two-component systems in nonequilibrium: Application to x-ray scattering.

PubMed

Vorberger, J; Chapman, D A

2018-01-01

We present a quantum theory for the dynamic structure factors in nonequilibrium, correlated, two-component systems such as plasmas or warm dense matter. The polarization function, which is needed as the input for the calculation of the structure factors, is calculated in nonequilibrium based on a perturbation expansion in the interaction strength. To make our theory applicable for x-ray scattering, a generalized Chihara decomposition for the total electron structure factor in nonequilibrium is derived. Examples are given and the influence of correlations and exchange on the structure and the x-ray-scattering spectrum are discussed for a model nonequilibrium distribution, as often encountered during laser heating of materials, as well as for two-temperature systems.

Quantum theory for the dynamic structure factor in correlated two-component systems in nonequilibrium: Application to x-ray scattering

NASA Astrophysics Data System (ADS)

Vorberger, J.; Chapman, D. A.

2018-01-01

We present a quantum theory for the dynamic structure factors in nonequilibrium, correlated, two-component systems such as plasmas or warm dense matter. The polarization function, which is needed as the input for the calculation of the structure factors, is calculated in nonequilibrium based on a perturbation expansion in the interaction strength. To make our theory applicable for x-ray scattering, a generalized Chihara decomposition for the total electron structure factor in nonequilibrium is derived. Examples are given and the influence of correlations and exchange on the structure and the x-ray-scattering spectrum are discussed for a model nonequilibrium distribution, as often encountered during laser heating of materials, as well as for two-temperature systems.

Dynamic Analyses Including Joints Of Truss Structures

NASA Technical Reports Server (NTRS)

Belvin, W. Keith

1991-01-01

Method for mathematically modeling joints to assess influences of joints on dynamic response of truss structures developed in study. Only structures with low-frequency oscillations considered; only Coulomb friction and viscous damping included in analysis. Focus of effort to obtain finite-element mathematical models of joints exhibiting load-vs.-deflection behavior similar to measured load-vs.-deflection behavior of real joints. Experiments performed to determine stiffness and damping nonlinearities typical of joint hardware. Algorithm for computing coefficients of analytical joint models based on test data developed to enable study of linear and nonlinear effects of joints on global structural response. Besides intended application to large space structures, applications in nonaerospace community include ground-based antennas and earthquake-resistant steel-framed buildings.

Development and evaluation of a dynamic web-based application.

PubMed

Hsieh, Yichuan; Brennan, Patricia Flatley

2007-10-11

Traditional consumer health informatics (CHI) applications that were developed for lay public on the Web were commonly written in a Hypertext Markup Language (HTML). As genetics knowledge rapidly advances and requires updating information in a timely fashion, a different content structure is therefore needed to facilitate information delivery. This poster will present the process of developing a dynamic database-driven Web CHI application.

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

PubMed Central

Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

2016-01-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts. PMID:27124275

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

PubMed

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

Two key areas of crucial importance to the computer-based simulation of large space structures are discussed. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area involves massively parallel computers.

49 CFR Appendix F to Part 238 - Alternative Dynamic Performance Requirements for Front End Structures of Cab Cars and MU Locomotives

Code of Federal Regulations, 2010 CFR

2010-10-01

... Front End Structures of Cab Cars and MU Locomotives F Appendix F to Part 238 Transportation Other... Performance Requirements for Front End Structures of Cab Cars and MU Locomotives As specified in § 238.209(b... and allow for the application of dynamic performance criteria to cab cars and MU locomotives as an...

Structures and Dynamics Division research and technology plans for FY 1988 and accomplishments for FY 1987

NASA Technical Reports Server (NTRS)

Bales, Kay S.

1988-01-01

Presented are the Objectives, FY 1988 Plans, Approach, and FY 1988 Milestones for the Structures and Dynamics Division (Langley Research Center) research programs. FY 1987 Accomplishments are presented where applicable. This information is useful in program coordination with other governmental organizations in areas of mutual interest.

Structures and Dynamics Division research and technology plans for FY 1987 and accomplishments for FY 1986

NASA Technical Reports Server (NTRS)

Bales, Kay S.

1987-01-01

This paper presents the Objectives, FY 1987 Plans, Approach, and FY 1987 Milestones for the Structures and Dynamics Division's research programs. FY 1986 Accomplishments are presented where applicable. This information is useful in program coordination with other governmental organizations in areas of mutual interest.

Structures and Dynamics Division research and technology plans for FY 1985 and accomplishments for FY 1984

NASA Technical Reports Server (NTRS)

Bales, K. S.

1985-01-01

The objectives, FY 1985 plans, approach, and FY 1985 milestones for the Structures and Dynamics Division's research programs are presented. The FY 1984 accomplishments are presented where applicable. This information is useful in program coordination with other government organizations in areas of mutual interest.

Seventh NASTRAN User's Colloquium

NASA Technical Reports Server (NTRS)

1978-01-01

The general application of finite element methodology and the specific application of NASTRAN to a wide variety of static and dynamic structural problems are described. Topics include: fluids and thermal applications, NASTRAN programming, substructuring methods, unique new applications, general auxiliary programs, specific applications, and new capabilities.

ER fluid applications to vibration control devices and an adaptive neural-net controller

NASA Astrophysics Data System (ADS)

Morishita, Shin; Ura, Tamaki

1993-07-01

Four applications of electrorheological (ER) fluid to vibration control actuators and an adaptive neural-net control system suitable for the controller of ER actuators are described: a shock absorber system for automobiles, a squeeze film damper bearing for rotational machines, a dynamic damper for multidegree-of-freedom structures, and a vibration isolator. An adaptive neural-net control system composed of a forward model network for structural identification and a controller network is introduced for the control system of these ER actuators. As an example study of intelligent vibration control systems, an experiment was performed in which the ER dynamic damper was attached to a beam structure and controlled by the present neural-net controller so that the vibration in several modes of the beam was reduced with a single dynamic damper.

Multidisciplinary analysis of actively controlled large flexible spacecraft

NASA Technical Reports Server (NTRS)

Cooper, Paul A.; Young, John W.; Sutter, Thomas R.

1986-01-01

The control of Flexible Structures (COFS) program has supported the development of an analysis capability at the Langley Research Center called the Integrated Multidisciplinary Analysis Tool (IMAT) which provides an efficient data storage and transfer capability among commercial computer codes to aid in the dynamic analysis of actively controlled structures. IMAT is a system of computer programs which transfers Computer-Aided-Design (CAD) configurations, structural finite element models, material property and stress information, structural and rigid-body dynamic model information, and linear system matrices for control law formulation among various commercial applications programs through a common database. Although general in its formulation, IMAT was developed specifically to aid in the evaluation of the structures. A description of the IMAT system and results of an application of the system are given.

Dynamic Structural Health Monitoring of slender structures using optical sensors.

PubMed

Antunes, Paulo; Travanca, Rui; Rodrigues, Hugo; Melo, José; Jara, José; Varum, Humberto; André, Paulo

2012-01-01

In this paper we summarize the research activities at the Instituto de Telecomunicações--Pólo de Aveiro and University of Aveiro, in the field of fiber Bragg grating based sensors and their applications in dynamic measurements for Structural Health Monitoring of slender structures such as towers. In this work we describe the implementation of an optical biaxial accelerometer based on fiber Bragg gratings inscribed on optical fibers. The proof-of-concept was done with the dynamic monitoring of a reinforced concrete structure and a slender metallic telecommunication tower. Those structures were found to be suitable to demonstrate the feasibility of FBG accelerometers to obtain the structures' natural frequencies, which are the key parameters in Structural Health Monitoring and in the calibration of numerical models used to simulate the structure behavior.

A Fluid Structure Interaction Strategy with Application to Low Reynolds Number Flapping Flight

DTIC Science & Technology

2010-01-01

using a predictor - corrector strategy. Dynamic fluid grid adaptation is implemented to reduce the number of grid points and computation costs...governing the dynamics of the ow and the structure are simultaneously advanced in time by using a predictor - corrector strategy. Dynamic uid grid...colleague Patrick Rabenold, the math-guy, who provided the seminal work on adaptive mesh refine- ment for incompressible flow using the Paramesh c

Sodars and their application for investigation of the turbulent structure of the lower atmosphere

NASA Astrophysics Data System (ADS)

Krasnenko, N. P.; Shamanaeva, L. G.

2016-11-01

Possibilities of sodar application for investigation of the spatiotemporal dynamics of three components of wind velocity vector, longitudinal and transverse structural functions of wind velocity field, structural characteristics of temperature and wind velocity, turbulent kinetic energy dissipation rate, and outer scales of temperature and dynamic turbulence in the atmospheric boundary layer are analyzed. The original closed iterative algorithm of sodar data processing taking into account the classical and molecular absorption and the turbulent sound attenuation on the propagation path is used that allows the vertical profiles of the characteristics of temperature and wind velocity field to be reconstructed simultaneously and their interrelations to be investigated. It is demonstrated how the structure of temperature and wind turbulence is visualised in real time.

Virtual-pulse time integral methodology: A new explicit approach for computational dynamics - Theoretical developments for general nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Chen, Xiaoqin; Tamma, Kumar K.; Sha, Desong

1993-01-01

The present paper describes a new explicit virtual-pulse time integral methodology for nonlinear structural dynamics problems. The purpose of the paper is to provide the theoretical basis of the methodology and to demonstrate applicability of the proposed formulations to nonlinear dynamic structures. Different from the existing numerical methods such as direct time integrations or mode superposition techniques, the proposed methodology offers new perspectives and methodology of development, and possesses several unique and attractive computational characteristics. The methodology is tested and compared with the implicit Newmark method (trapezoidal rule) through a nonlinear softening and hardening spring dynamic models. The numerical results indicate that the proposed explicit virtual-pulse time integral methodology is an excellent alternative for solving general nonlinear dynamic problems.

Three-Dimensional, Inelastic Response of Single-Edge Notch Bend Specimens Subjected to Impact Loading

DTIC Science & Technology

1993-08-01

measure the inherent fracture toughness of a material. A thor- ough understanding of the test specimen behavior is a prerequisite to the application of...measured material properties in structural applications . Three- dimensional dynamic analyses are performed for three different specimen configurations...derstanding of the test specimen behavior is a prerequisite to the application of measured ma- terial properties in structural applications . Three

Study on embedding fiber Bragg grating sensor into the 3D printing structure for health monitoring

NASA Astrophysics Data System (ADS)

Li, Ruiya; Tan, Yuegang; Zhou, Zude; Fang, Liang; Chen, Yiyang

2016-10-01

3D printing technology is a rapidly developing manufacturing technology, which is known as a core technology in the third industrial revolution. With the continuous improvement of the application of 3D printing products, the health monitoring of the 3D printing structure is particularly important. Fiber Bragg grating (FBG) sensing technology is a new type of optical sensing technology with unique advantages comparing to traditional sensing technology, and it has great application prospects in structural health monitoring. In this paper, the FBG sensors embedded in the internal structure of the 3D printing were used to monitor the static and dynamic strain variation of 3D printing structure during loading process. The theoretical result and experimental result has good consistency and the characteristic frequency detected by FBG sensor is consistent with the testing results of traditional accelerator in the dynamic experiment. The results of this paper preliminary validate that FBG embedded in the 3D printing structure can effectively detecting the static and dynamic stain change of the 3D printing structure, which provide some guidance for the health monitoring of 3D printing structure.

Proceedings of Damping 1993, volume 3

NASA Astrophysics Data System (ADS)

Portis, Bonnie L.

1993-06-01

Presented are individual papers of Damping '93, held 24-26 February 1993 in San Francisco. The subjects included: passive damping concepts; passive damping analysis and design techniques; optimization; damped control/structure interaction; viscoelastic material testing and characterization; highly damped materials; vibration suppression techniques; damping identification and dynamic testing; applications to aircraft; space structures; Marine structures; and commercial products; defense applications; and payoffs of vibration suppression.

Proceedings of Damping 1993, volume 1

NASA Astrophysics Data System (ADS)

Portis, Bonnie L.

1993-06-01

Presented are individual papers of Damping '93 held 24-26 February, 1993, in San Francisco. The subjects included: passive damping concepts; passive damping analysis and design techniques; optimization; damped control/structure interaction; viscoelastic material testing and characterization; highly damped materials; vibration suppression techniques; damping identification and dynamic testing; application to aircraft; space structures; marine structures; commercial products; defense applications; and payoffs of vibration suppression.

Sixteenth NASTRAN (R) Users' Colloquium

NASA Technical Reports Server (NTRS)

1988-01-01

These are the proceedings of the Sixteenth NASTRAN Users' Colloquium held in Arlington, Virginia from 25 to 29 April, 1988. Technical papers contributed by participants review general application of finite element methodology and the specific application of the NASA Structural Analysis System (NASTRAN) to a variety of static and dynamic structural problems.

Dynamic Adaptive Neural Network Arrays: A Neuromorphic Architecture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Disney, Adam; Reynolds, John

2015-01-01

Dynamic Adaptive Neural Network Array (DANNA) is a neuromorphic hardware implementation. It differs from most other neuromorphic projects in that it allows for programmability of structure, and it is trained or designed using evolutionary optimization. This paper describes the DANNA structure, how DANNA is trained using evolutionary optimization, and an application of DANNA to a very simple classification task.

Morphology and dynamics of galaxies; Proceedings of the Twelfth Advanced Course, Saas-Fee, Switzerland, March 29-April 3, 1982

NASA Astrophysics Data System (ADS)

Martinet, L.; Mayor, M.

The basic problems and analysis techniques in examining the morphology, dynamics, and interactions between star systems, galaxies, and galactic clusters are detailed. Attention is devoted to the dynamics of hot stellar systems, with note taken of the derivation and application of the Vlasov equation, Jean's theorem, and the virial equations. Observations of galactic structure and dynamics are reviewed, and consideration is directed toward environmental influences on galactic structure. For individual items see A84-15503 to A84-15505

Characterizing RNA Dynamics at Atomic Resolution Using Solution-state NMR Spectroscopy

PubMed Central

Bothe, Jameson R.; Nikolova, Evgenia N.; Eichhorn, Catherine D.; Chugh, Jeetender; Hansen, Alexandar L.; Al-Hashimi, Hashim M.

2012-01-01

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering. PMID:22036746

Some design constraints required for the use of generic software in embedded systems: Packages which manage abstract dynamic structures without the need for garbage collection

NASA Technical Reports Server (NTRS)

Johnson, Charles S.

1986-01-01

The embedded systems running real-time applications, for which Ada was designed, require their own mechanisms for the management of dynamically allocated storage. There is a need for packages which manage their own internalo structures to control their deallocation as well, due to the performance implications of garbage collection by the KAPSE. This places a requirement upon the design of generic packages which manage generically structured private types built-up from application-defined input types. These kinds of generic packages should figure greatly in the development of lower-level software such as operating systems, schedulers, controllers, and device driver; and will manage structures such as queues, stacks, link-lists, files, and binary multary (hierarchical) trees. Controlled to prevent inadvertent de-designation of dynamic elements, which is implicit in the assignment operation A study was made of the use of limited private type, in solving the problems of controlling the accumulation of anonymous, detached objects in running systems. The use of deallocator prodecures for run-down of application-defined input types during deallocation operations during satellites.

Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog

PubMed Central

Spring-Connell, Alexander M.; Evich, Marina G.; Debelak, Harald; Seela, Frank; Germann, Markus W.

2016-01-01

A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2′deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. PMID:27566150

Structured population dynamics: continuous size and discontinuous stage structures.

PubMed

Buffoni, Giuseppe; Pasquali, Sara

2007-04-01

A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

Measurements of Acoustic Properties of Porous and Granular Materials and Application to Vibration Control

NASA Technical Reports Server (NTRS)

Park, Junhong; Palumbo, Daniel L.

2004-01-01

For application of porous and granular materials to vibro-acoustic controls, a finite dynamic strength of the solid component (frame) is an important design factor. The primary goal of this study was to investigate structural vibration damping through this frame wave propagation for various poroelastic materials. A measurement method to investigate the vibration characteristics of the frame was proposed. The measured properties were found to follow closely the characteristics of the viscoelastic materials - the dynamic modulus increased with frequency and the degree of the frequency dependence was determined by its loss factor. The dynamic stiffness of hollow cylindrical beams containing porous and granular materials as damping treatment was measured also. The data were used to extract the damping materials characteristics using the Rayleigh-Ritz method. The results suggested that the acoustic structure interaction between the frame and the structure enhances the dissipation of the vibration energy significantly.

Automatic Dynamic Aircraft Modeler (ADAM) for the Computer Program NASTRAN

NASA Technical Reports Server (NTRS)

Griffis, H.

1985-01-01

Large general purpose finite element programs require users to develop large quantities of input data. General purpose pre-processors are used to decrease the effort required to develop structural models. Further reduction of effort can be achieved by specific application pre-processors. Automatic Dynamic Aircraft Modeler (ADAM) is one such application specific pre-processor. General purpose pre-processors use points, lines and surfaces to describe geometric shapes. Specifying that ADAM is used only for aircraft structures allows generic structural sections, wing boxes and bodies, to be pre-defined. Hence with only gross dimensions, thicknesses, material properties and pre-defined boundary conditions a complete model of an aircraft can be created.

Dynamic Structural Health Monitoring of Slender Structures Using Optical Sensors

PubMed Central

Antunes, Paulo; Travanca, Rui; Rodrigues, Hugo; Melo, José; Jara, José; Varum, Humberto; André, Paulo

2012-01-01

In this paper we summarize the research activities at the Instituto de Telecomunicações—Pólo de Aveiro and University of Aveiro, in the field of fiber Bragg grating based sensors and their applications in dynamic measurements for Structural Health Monitoring of slender structures such as towers. In this work we describe the implementation of an optical biaxial accelerometer based on fiber Bragg gratings inscribed on optical fibers. The proof-of-concept was done with the dynamic monitoring of a reinforced concrete structure and a slender metallic telecommunication tower. Those structures were found to be suitable to demonstrate the feasibility of FBG accelerometers to obtain the structures' natural frequencies, which are the key parameters in Structural Health Monitoring and in the calibration of numerical models used to simulate the structure behavior. PMID:22778661

Application of the Spectral Element Method to Acoustic Radiation

NASA Technical Reports Server (NTRS)

Doyle, James F.; Rizzi, Stephen A. (Technical Monitor)

2000-01-01

This report summarizes research to develop a capability for analysis of interior noise in enclosed structures when acoustically excited by an external random source. Of particular interest was the application to the study of noise and vibration transmission in thin-walled structures as typified by aircraft fuselages. Three related topics are focused upon. The first concerns the development of a curved frame spectral element, the second shows how the spectral element method for wave propagation in folded plate structures is extended to problems involving curved segmented plates. These are of significance because by combining these curved spectral elements with previously presented flat spectral elements, the dynamic response of geometrically complex structures can be determined. The third topic shows how spectral elements, which incorporate the effect of fluid loading on the structure, are developed for analyzing acoustic radiation from dynamically loaded extended plates.

Large Space Antenna Systems Technology, 1984

NASA Technical Reports Server (NTRS)

Boyer, W. J. (Compiler)

1985-01-01

Mission applications for large space antenna systems; large space antenna structural systems; materials and structures technology; structural dynamics and control technology, electromagnetics technology, large space antenna systems and the Space Station; and flight test and evaluation were examined.

Proceedings of Damping 1993, volume 2

NASA Astrophysics Data System (ADS)

Portis, Bonnie L.

1993-06-01

Presented are individual papers of Damping '93, held 24-26 Feb. 1993 in San Francisco. The subjects included the following: passive damping concepts; passive damping analysis and design techniques; optimization; damped control/structure interaction; viscoelastic material testing and characterization; highly damped materials; vibration suppression techniques; damping identification and dynamic testing; applications to aircraft; space structures; marine structures; and commercial products; defense applications; and payoffs of vibration suppression.

New applications of a model of electromechanical impedance for SHM

NASA Astrophysics Data System (ADS)

Pavelko, Vitalijs

2014-03-01

The paper focuses on the further development of the model of the electromechanical impedance (EMI) of the piezoceramics transducer (PZT) and its application for aircraft structural health monitoring (SHM). There was obtained an expression of the electromechanical impedance common to any dimension of models (1D, 2D, 3D), and directly independent from imposed constraints. Determination of the dynamic response of the system "host structure - PZT", which is crucial for the practical application supposes the use of modal analysis. This allows to get a general tool to determine EMI regardless of the specific features of a particular application. Earlier there was considered the technology of separate determination of the dynamic response for the PZT and the structural element". Here another version that involves the joint modal analysis of the entire system "host structure - PZT" is presented. As a result, the dynamic response is obtained in the form of modal decomposition of transducer mechanical strains. The use of models for the free and constrained transducer, analysis of the impact of the adhesive layer to the EMI is demonstrated. In all cases there was analyzed the influence of the dimension of the model (2D and 3D). The validity of the model is confirmed by experimental studies. Correlation between the fatigue crack length in a thin-walled Al plate and EMI of embedded PZT was simulated and compared with test result.

Knowledge Base for Automatic Generation of Online IMS LD Compliant Course Structures

ERIC Educational Resources Information Center

Pacurar, Ecaterina Giacomini; Trigano, Philippe; Alupoaie, Sorin

2006-01-01

Our article presents a pedagogical scenarios-based web application that allows the automatic generation and development of pedagogical websites. These pedagogical scenarios are represented in the IMS Learning Design standard. Our application is a web portal helping teachers to dynamically generate web course structures, to edit pedagogical content…

Structural crashworthiness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, N.; Wierzbicki, T.

1983-01-01

Behind the quest for safety in all forms of transport lies a complex technology of which structural crashworthiness forms an important part. This volume contains the work of over twenty experts whose interests range from the fundamental principles of structural collapse to the application of those principles to the design of ships, aircraft, road vehicles, and rail vehicles. The text focuses on the application of analytical and experimental techniques to predict energy dissipation characteristics of thin-walled structures and structural members under quasi-static and dynamic loadings.

Evolution of Excited-State Dynamics in Periodic Au 28, Au 36, Au 44, and Au 52 Nanoclusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Meng; Zeng, Chenjie; Sfeir, Matthew Y.

An understanding of the correlation between the atomic structure and optical properties of gold nanoclusters is essential for exploration of their functionalities and applications involving light harvesting and electron transfer. We report the femto-nanosecond excited state dynamics of a periodic series of face-centered cubic (FCC) gold nanoclusters (including Au 28, Au 36, Au 44, and Au 52), which exhibit a set of unique features compared with other similar sized clusters. Molecular-like ultrafast S n → S 1 internal conversions (i.e., radiationless electronic transitions) are observed in the relaxation dynamics of FCC periodic series. Excited-state dynamics with near-HOMO–LUMO gap excitation lacksmore » ultrafast decay component, and only the structural relaxation dominates in the dynamical process, which proves the absence of core–shell relaxation. Interestingly, both the relaxation of the hot carriers and the band-edge carrier recombination become slower as the size increases. The evolution in excited-state properties of this FCC series offers new insight into the structure-dependent properties of metal nanoclusters, which will benefit their optical energy harvesting and photocatalytic applications.« less

Evolution of Excited-State Dynamics in Periodic Au 28, Au 36, Au 44, and Au 52 Nanoclusters

DOE PAGES

Zhou, Meng; Zeng, Chenjie; Sfeir, Matthew Y.; ...

2017-08-10

An understanding of the correlation between the atomic structure and optical properties of gold nanoclusters is essential for exploration of their functionalities and applications involving light harvesting and electron transfer. We report the femto-nanosecond excited state dynamics of a periodic series of face-centered cubic (FCC) gold nanoclusters (including Au 28, Au 36, Au 44, and Au 52), which exhibit a set of unique features compared with other similar sized clusters. Molecular-like ultrafast S n → S 1 internal conversions (i.e., radiationless electronic transitions) are observed in the relaxation dynamics of FCC periodic series. Excited-state dynamics with near-HOMO–LUMO gap excitation lacksmore » ultrafast decay component, and only the structural relaxation dominates in the dynamical process, which proves the absence of core–shell relaxation. Interestingly, both the relaxation of the hot carriers and the band-edge carrier recombination become slower as the size increases. The evolution in excited-state properties of this FCC series offers new insight into the structure-dependent properties of metal nanoclusters, which will benefit their optical energy harvesting and photocatalytic applications.« less

An efficient predictor-corrector-based dynamic mesh method for multi-block structured grid with extremely large deformation and its applications

NASA Astrophysics Data System (ADS)

Guo, Tongqing; Chen, Hao; Lu, Zhiliang

2018-05-01

Aiming at extremely large deformation, a novel predictor-corrector-based dynamic mesh method for multi-block structured grid is proposed. In this work, the dynamic mesh generation is completed in three steps. At first, some typical dynamic positions are selected and high-quality multi-block grids with the same topology are generated at those positions. Then, Lagrange interpolation method is adopted to predict the dynamic mesh at any dynamic position. Finally, a rapid elastic deforming technique is used to correct the small deviation between the interpolated geometric configuration and the actual instantaneous one. Compared with the traditional methods, the results demonstrate that the present method shows stronger deformation ability and higher dynamic mesh quality.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raymond, David W.; Blankenship, Douglas A.; Buerger, Stephen

The dynamic stability of deep drillstrings is challenged by an inability to impart controllability with ever-changing conditions introduced by geology, depth, structural dynamic properties and operating conditions. A multi-organizational LDRD project team at Sandia National Laboratories successfully demonstrated advanced technologies for mitigating drillstring vibrations to improve the reliability of drilling systems used for construction of deep, high-value wells. Using computational modeling and dynamic substructuring techniques, the benefit of controllable actuators at discrete locations in the drillstring is determined. Prototype downhole tools were developed and evaluated in laboratory test fixtures simulating the structural dynamic response of a deep drillstring. A laboratory-basedmore » drilling applicability demonstration was conducted to demonstrate the benefit available from deployment of an autonomous, downhole tool with self-actuation capabilities in response to the dynamic response of the host drillstring. A concept is presented for a prototype drilling tool based upon the technical advances. The technology described herein is the subject of U.S. Patent Application No. 62219481, entitled "DRILLING SYSTEM VIBRATION SUPPRESSION SYSTEMS AND METHODS", filed September 16, 2015.« less

Versatile and declarative dynamic programming using pair algebras.

PubMed

Steffen, Peter; Giegerich, Robert

2005-09-12

Dynamic programming is a widely used programming technique in bioinformatics. In sharp contrast to the simplicity of textbook examples, implementing a dynamic programming algorithm for a novel and non-trivial application is a tedious and error prone task. The algebraic dynamic programming approach seeks to alleviate this situation by clearly separating the dynamic programming recurrences and scoring schemes. Based on this programming style, we introduce a generic product operation of scoring schemes. This leads to a remarkable variety of applications, allowing us to achieve optimizations under multiple objective functions, alternative solutions and backtracing, holistic search space analysis, ambiguity checking, and more, without additional programming effort. We demonstrate the method on several applications for RNA secondary structure prediction. The product operation as introduced here adds a significant amount of flexibility to dynamic programming. It provides a versatile testbed for the development of new algorithmic ideas, which can immediately be put to practice.

Course Modules on Structural Health Monitoring with Smart Materials

ERIC Educational Resources Information Center

Shih, Hui-Ru; Walters, Wilbur L.; Zheng, Wei; Everett, Jessica

2009-01-01

Structural Health Monitoring (SHM) is an emerging technology that has multiple applications. SHM emerged from the wide field of smart structures, and it also encompasses disciplines such as structural dynamics, materials and structures, nondestructive testing, sensors and actuators, data acquisition, signal processing, and possibly much more. To…

Verification of nonlinear dynamic structural test results by combined image processing and acoustic analysis

NASA Astrophysics Data System (ADS)

Tene, Yair; Tene, Noam; Tene, G.

1993-08-01

An interactive data fusion methodology of video, audio, and nonlinear structural dynamic analysis for potential application in forensic engineering is presented. The methodology was developed and successfully demonstrated in the analysis of heavy transportable bridge collapse during preparation for testing. Multiple bridge elements failures were identified after the collapse, including fracture, cracks and rupture of high performance structural materials. Videotape recording by hand held camcorder was the only source of information about the collapse sequence. The interactive data fusion methodology resulted in extracting relevant information form the videotape and from dynamic nonlinear structural analysis, leading to full account of the sequence of events during the bridge collapse.

CDOCKER and lambda λ -dynamics for prospective prediction in D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Ding, Xinqiang; Hayes, Ryan L.; Vilseck, Jonah Z.; Charles, Murchtricia K.; Brooks, Charles L.

2018-01-01

The opportunity to prospectively predict ligand bound poses and free energies of binding to the Farnesoid X Receptor in the D3R Grand Challenge 2 provided a useful exercise to evaluate CHARMM based docking (CDOCKER) and λ-dynamics methodologies for use in "real-world" applications in computer aided drug design. In addition to measuring their current performance, several recent methodological developments have been analyzed retrospectively to highlight best procedural practices in future applications. For pose prediction with CDOCKER, when the protein structure used for rigid receptor docking was close to the crystallographic holo structure, reliable poses were obtained. Benzimidazoles, with a known holo receptor structure, were successfully docked with an average RMSD of 0.97 Å. Other non-benzimidazole ligands displayed less accuracy largely because the receptor structures we chose for docking were too different from the experimental holo structures. However, retrospective analysis has shown that when these ligands were re-docked into their holo structures, the average RMSD dropped to 1.18 Å for all ligands. When sulfonamides and spiros were docked with the apo structure, which agrees more with their holo structure than the structures we chose, five out of six ligands were correctly docked. These docking results emphasize the need for flexible receptor docking approaches. For λ-dynamics techniques, including multisite λ-dynamics (MSλD), reasonable agreement with experiment was observed for the 33 ligands investigated; root mean square errors of 2.08 and 1.67 kcal/mol were obtained for free energy sets 1 and 2, respectively. Retrospectively, soft-core potentials, adaptive landscape flattening, and biasing potential replica exchange (BP-REX) algorithms were critical to model large substituent perturbations with sufficient precision and within restrictive timeframes, such as was required with participation in Grand Challenge 2. These developments, their associated benefits, and proposed procedures for their use in future applications are discussed.

CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.

PubMed

Ding, Xinqiang; Hayes, Ryan L; Vilseck, Jonah Z; Charles, Murchtricia K; Brooks, Charles L

2018-01-01

The opportunity to prospectively predict ligand bound poses and free energies of binding to the Farnesoid X Receptor in the D3R Grand Challenge 2 provided a useful exercise to evaluate CHARMM based docking (CDOCKER) and [Formula: see text]-dynamics methodologies for use in "real-world" applications in computer aided drug design. In addition to measuring their current performance, several recent methodological developments have been analyzed retrospectively to highlight best procedural practices in future applications. For pose prediction with CDOCKER, when the protein structure used for rigid receptor docking was close to the crystallographic holo structure, reliable poses were obtained. Benzimidazoles, with a known holo receptor structure, were successfully docked with an average RMSD of 0.97 [Formula: see text]. Other non-benzimidazole ligands displayed less accuracy largely because the receptor structures we chose for docking were too different from the experimental holo structures. However, retrospective analysis has shown that when these ligands were re-docked into their holo structures, the average RMSD dropped to 1.18 [Formula: see text] for all ligands. When sulfonamides and spiros were docked with the apo structure, which agrees more with their holo structure than the structures we chose, five out of six ligands were correctly docked. These docking results emphasize the need for flexible receptor docking approaches. For [Formula: see text]-dynamics techniques, including multisite [Formula: see text]-dynamics (MS[Formula: see text]D), reasonable agreement with experiment was observed for the 33 ligands investigated; root mean square errors of 2.08 and 1.67 kcal/mol were obtained for free energy sets 1 and 2, respectively. Retrospectively, soft-core potentials, adaptive landscape flattening, and biasing potential replica exchange (BP-REX) algorithms were critical to model large substituent perturbations with sufficient precision and within restrictive timeframes, such as was required with participation in Grand Challenge 2. These developments, their associated benefits, and proposed procedures for their use in future applications are discussed.

Development of a thick film PZT foil sensor for use in structural health monitoring applications.

PubMed

Pickwell, Andrew J; Dorey, Robert A; Mba, David

2013-02-01

Acoustic emission (AE) monitoring is a technique of growing interest in the field of nondestructive testing (NDT). The use of AE devices to monitor the health of structural components is currently limited by the cost of AE equipment, which prohibits the permanent placement of AE devices on structures for the purposes of continuous monitoring and the monitoring of areas with limited access. Micro electromechanical systems (MEMS) can provide solutions to these problems. We present the manufacture of a 4.4-μm-thick lead zirconate titanate (PZT) film on a 110-μm-thick titanium foil substrate for use as an AE sensor. The thick-film sensor is benchmarked against commercially available AE sensors in static and dynamic monitoring applications. The thick-film AE device is found to perform well in the detection of AE in static applications. A low signal-to-noise ratio is found to prohibit the detection of AE in a dynamic application.

A Galerkin method for linear PDE systems in circular geometries with structural acoustic applications

NASA Technical Reports Server (NTRS)

Smith, Ralph C.

1994-01-01

A Galerkin method for systems of PDE's in circular geometries is presented with motivating problems being drawn from structural, acoustic, and structural acoustic applications. Depending upon the application under consideration, piecewise splines or Legendre polynomials are used when approximating the system dynamics with modifications included to incorporate the analytic solution decay near the coordinate singularity. This provides an efficient method which retains its accuracy throughout the circular domain without degradation at singularity. Because the problems under consideration are linear or weakly nonlinear with constant or piecewise constant coefficients, transform methods for the problems are not investigated. While the specific method is developed for the two dimensional wave equations on a circular domain and the equation of transverse motion for a thin circular plate, examples demonstrating the extension of the techniques to a fully coupled structural acoustic system are used to illustrate the flexibility of the method when approximating the dynamics of more complex systems.

Dynamic tests of composite panels of an aircraft wing

NASA Astrophysics Data System (ADS)

Splichal, Jan; Pistek, Antonin; Hlinka, Jiri

2015-10-01

The paper describes the analysis of aerospace composite structures under dynamic loading. Today, it is common to use design procedures based on assumption of static loading only, and dynamic loading is rarely assumed and applied in design and certification of aerospace structures. The paper describes the application of dynamic loading for the design of aircraft structures, and the validation of the procedure on a selected structure. The goal is to verify the possibility of reducing the weight through improved design/modelling processes using dynamic loading instead of static loading. The research activity focuses on the modelling and testing of a composite panel representing a local segment of an aircraft wing section, investigating in particular the buckling behavior under dynamic loading. Finite Elements simulation tools are discussed, as well as the advantages of using a digital optical measurement system for the evaluation of the tests. The comparison of the finite element simulations with the results of the tests is presented.

Leveraging natural dynamical structures to explore multi-body systems

NASA Astrophysics Data System (ADS)

Bosanac, Natasha

Multi-body systems have become the target of an increasing number of mission concepts and observations, supplying further information about the composition, origin and dynamical environment of bodies within the solar system and beyond. In many of these scenarios, identification and characterization of the particular solutions that exist in a circular restricted three-body model is valuable. This insight into the underlying natural dynamical structures is achieved via the application of dynamical systems techniques. One application of such analysis is trajectory design for CubeSats, which are intended to explore cislunar space and other planetary systems. These increasingly complex mission objectives necessitate innovative trajectory design strategies for spacecraft within our solar system, as well as the capability for rapid and well-informed redesign. Accordingly, a trajectory design framework is constructed using dynamical systems techniques and demonstrated for the Lunar IceCube mission. An additional application explored in this investigation involves the motion of an exoplanet near a binary star system. Due to the strong gravitational field near a binary star, physicists have previously leveraged these systems as testbeds for examining the validity of gravitational and relativistic theories. In this investigation, a preliminary analysis into the effect of an additional three-body interaction on the dynamical environment near a large mass ratio binary system is conducted. As demonstrated through both of these sample applications, identification and characterization of the natural particular solutions that exist within a multi-body system supports a well-informed and guided analysis.

Dynamically variable negative stiffness structures.

PubMed

Churchill, Christopher B; Shahan, David W; Smith, Sloan P; Keefe, Andrew C; McKnight, Geoffrey P

2016-02-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness-based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators.

Similitude design for the vibration problems of plates and shells: A review

NASA Astrophysics Data System (ADS)

Zhu, Yunpeng; Wang, You; Luo, Zhong; Han, Qingkai; Wang, Deyou

2017-06-01

Similitude design plays a vital role in the analysis of vibration and shock problems encountered in large engineering equipment. Similitude design, including dimensional analysis and governing equation method, is founded on the dynamic similitude theory. This study reviews the application of similitude design methods in engineering practice and summarizes the major achievements of the dynamic similitude theory in structural vibration and shock problems in different fields, including marine structures, civil engineering structures, and large power equipment. This study also reviews the dynamic similitude design methods for thin-walled and composite material plates and shells, including the most recent work published by the authors. Structure sensitivity analysis is used to evaluate the scaling factors to attain accurate distorted scaling laws. Finally, this study discusses the existing problems and the potential of the dynamic similitude theory for the analysis of vibration and shock problems of structures.

Tribute to the contribution of Gerard Lallenment to structural dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Los Alamos National Laboratory

The Society for Experimental Mechanics and the International Modal Analysis Conference recognize the remarkable contribution to experimental mechanics, mechanical engineering and structural dynamics of Professor Gerard Lallement, from the University of Franche-Comte, France. A special session is organized during the IMAC-XX to outline the many achievements of Gerard Lallement in the fields of modal analysis, structural system identification, the theory and practice of structural modification, component mode synthesis and finite element model updating. The purpose of this publication is not to provide an exhaustive account of Gerard Lallement's contribution to structural dynamics. Numerous references are provided that should help themore » interested reader learn more about the many aspects of his work. Instead, the significance of this work is illustrated by discussing the role of structural dynamics in industrial applications and its future challenges. The technical aspects of Gerard Lallement's work are illustrated with a discussion of structural modification, modeling error localization and model updating.« less

Coupled orbit-attitude mission design in the circular restricted three-body problem

NASA Astrophysics Data System (ADS)

Guzzetti, Davide

Trajectory design increasingly leverages multi-body dynamical structures that are based on an understanding of various types of orbits in the Circular Restricted Three-Body Problem (CR3BP). Given the more complex dynamical environment, mission applications may also benefit from deeper insight into the attitude motion. In this investigation, the attitude dynamics are coupled with the trajectories in the CR3BP. In a highly sensitive dynamical model, such as the orbit-attitude CR3BP, periodic solutions allow delineation of the fundamental dynamical structures. Periodic solutions are also a subset of motions that are bounded over an infinite time-span (assuming no perturbing factors), without the necessity to integrate over an infinite time interval. Euler equations of motion and quaternion kinematics describe the rotational behavior of the spacecraft, whereas the translation of the center of mass is modeled in the CR3BP equations. A multiple shooting and continuation procedure are employed to target orbit-attitude periodic solutions in this model. Application of Floquet theory, Poincare mapping, and grid search to identify initial guesses for the targeting algorithm is described. In the Earth-Moon system, representative scenarios are explored for axisymmetric vehicles with various inertia characteristics, assuming that the vehicles move along Lyapunov, halo as well as distant retrograde orbits. A rich structure of possible periodic behaviors appears to pervade the solution space in the coupled problem. The stability analysis of the attitude dynamics for the selected families is included. Among the computed solutions, marginally stable and slowly diverging rotational behaviors exist and may offer interesting mission applications. Additionally, the solar radiation pressure is included and a fully coupled orbit-attitude model is developed. With specific application to solar sails, various guidance algorithms are explored to direct the spacecraft along a desired path, when the mutual interaction between orbit and attitude dynamics is considered. Each strategy implements a different form of control input, ranging from instantaneous reorientation of the sail pointing direction to the application of control torques, and it is demonstrated within a simple station keeping scenario.

Medical applications of model-based dynamic thermography

NASA Astrophysics Data System (ADS)

Nowakowski, Antoni; Kaczmarek, Mariusz; Ruminski, Jacek; Hryciuk, Marcin; Renkielska, Alicja; Grudzinski, Jacek; Siebert, Janusz; Jagielak, Dariusz; Rogowski, Jan; Roszak, Krzysztof; Stojek, Wojciech

2001-03-01

The proposal to use active thermography in medical diagnostics is promising in some applications concerning investigation of directly accessible parts of the human body. The combination of dynamic thermograms with thermal models of investigated structures gives attractive possibility to make internal structure reconstruction basing on different thermal properties of biological tissues. Measurements of temperature distribution synchronized with external light excitation allow registration of dynamic changes of local temperature dependent on heat exchange conditions. Preliminary results of active thermography applications in medicine are discussed. For skin and under- skin tissues an equivalent thermal model may be determined. For the assumed model its effective parameters may be reconstructed basing on the results of transient thermal processes. For known thermal diffusivity and conductivity of specific tissues the local thickness of a two or three layer structure may be calculated. Results of some medical cases as well as reference data of in vivo study on animals are presented. The method was also applied to evaluate the state of the human heart during the open chest cardio-surgical interventions. Reference studies of evoked heart infarct in pigs are referred, too. We see the proposed new in medical applications technique as a promising diagnostic tool. It is a fully non-invasive, clean, handy, fast and affordable method giving not only qualitative view of investigated surfaces but also an objective quantitative measurement result, accurate enough for many applications including fast screening of affected tissues.

Photogrammetry and Videogrammetry Methods Development for Solar Sail Structures. Masters Thesis awarded by George Washington Univ.

NASA Technical Reports Server (NTRS)

Pappa, Richard S. (Technical Monitor); Black, Jonathan T.

2003-01-01

This report discusses the development and application of metrology methods called photogrammetry and videogrammetry that make accurate measurements from photographs. These methods have been adapted for the static and dynamic characterization of gossamer structures, as four specific solar sail applications demonstrate. The applications prove that high-resolution, full-field, non-contact static measurements of solar sails using dot projection photogrammetry are possible as well as full-field, non-contact, dynamic characterization using dot projection videogrammetry. The accuracy of the measurement of the resonant frequencies and operating deflection shapes that were extracted surpassed expectations. While other non-contact measurement methods exist, they are not full-field and require significantly more time to take data.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience.

PubMed

Corradi, Luca; Porro, Ivan; Schenone, Andrea; Momeni, Parastoo; Ferrari, Raffaele; Nobili, Flavio; Ferrara, Michela; Arnulfo, Gabriele; Fato, Marco M

2012-10-08

Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of "meta" data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a "meta" data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

PubMed Central

2012-01-01

Background Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. Methods A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of “meta” data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. Results The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a “meta” data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Conclusions Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. PMID:23043673

Scaling of membrane-type locally resonant acoustic metamaterial arrays.

PubMed

Naify, Christina J; Chang, Chia-Ming; McKnight, Geoffrey; Nutt, Steven R

2012-10-01

Metamaterials have emerged as promising solutions for manipulation of sound waves in a variety of applications. Locally resonant acoustic materials (LRAM) decrease sound transmission by 500% over acoustic mass law predictions at peak transmission loss (TL) frequencies with minimal added mass, making them appealing for weight-critical applications such as aerospace structures. In this study, potential issues associated with scale-up of the structure are addressed. TL of single-celled and multi-celled LRAM was measured using an impedance tube setup with systematic variation in geometric parameters to understand the effects of each parameter on acoustic response. Finite element analysis was performed to predict TL as a function of frequency for structures with varying complexity, including stacked structures and multi-celled arrays. Dynamic response of the array structures under discrete frequency excitation was investigated using laser vibrometry to verify negative dynamic mass behavior.

Methods for evaluating the predictive accuracy of structural dynamic models

NASA Technical Reports Server (NTRS)

Hasselman, T. K.; Chrostowski, Jon D.

1990-01-01

Uncertainty of frequency response using the fuzzy set method and on-orbit response prediction using laboratory test data to refine an analytical model are emphasized with respect to large space structures. Two aspects of the fuzzy set approach were investigated relative to its application to large structural dynamics problems: (1) minimizing the number of parameters involved in computing possible intervals; and (2) the treatment of extrema which may occur in the parameter space enclosed by all possible combinations of the important parameters of the model. Extensive printer graphics were added to the SSID code to help facilitate model verification, and an application of this code to the LaRC Ten Bay Truss is included in the appendix to illustrate this graphics capability.

Formation and field-driven dynamics of nematic spheroids.

PubMed

Fu, Fred; Abukhdeir, Nasser Mohieddin

2017-07-19

Unlike the canonical application of liquid crystals (LCs), LC displays, emerging technologies based on LC materials are increasingly leveraging the presence of nanoscale defects. The inherent nanoscale characteristics of LC defects present both significant opportunities as well as barriers for the application of this fascinating class of materials. Simulation-based approaches to the study of the effects of confinement and interface anchoring conditions on LC domains has resulted in significant progress over the past decade, where simulations are now able to access experimentally-relevant length scales while simultaneously capturing nanoscale defect structures. In this work, continuum simulations were performed in order to study the dynamics of micron-scale nematic LC spheroids of varying shape. Nematic spheroids are one of the simplest inherently defect-containing LC structures and are relevant to polymer-dispersed LC-based "smart" window technology. Simulation results include nematic phase formation and external field-switching dynamics of nematic spheroids ranging in shape from oblate to prolate. Results include both qualitative and quantitative insight into the complex coupling of nanoscale defect dynamics and structure transitions to micron-scale reorientation. Dynamic mechanisms are presented and related to structural transitions in LC defects present in the nematic domain. Domain-averaged metrics including order parameters and response times are determined for a range of experimentally-accessible electric field strengths. These results have both fundamental and technological relevance, in that increased understanding of LC dynamics in the presence of defects is a key barrier to continued advancement in the field.

Parameter and Structure Inference for Nonlinear Dynamical Systems

NASA Technical Reports Server (NTRS)

Morris, Robin D.; Smelyanskiy, Vadim N.; Millonas, Mark

2006-01-01

A great many systems can be modeled in the non-linear dynamical systems framework, as x = f(x) + xi(t), where f() is the potential function for the system, and xi is the excitation noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications.

Single walled boron nitride nanotube-based biosensor: an atomistic finite element modelling approach.

PubMed

Panchal, Mitesh B; Upadhyay, Sanjay H

2014-09-01

The unprecedented dynamic characteristics of nanoelectromechanical systems make them suitable for nanoscale mass sensing applications. Owing to superior biocompatibility, boron nitride nanotubes (BNNTs) are being increasingly used for such applications. In this study, the feasibility of single walled BNNT (SWBNNT)-based bio-sensor has been explored. Molecular structural mechanics-based finite element (FE) modelling approach has been used to analyse the dynamic behaviour of SWBNNT-based biosensors. The application of an SWBNNT-based mass sensing for zeptogram level of mass has been reported. Also, the effect of size of the nanotube in terms of length as well as different chiral atomic structures of SWBNNT has been analysed for their sensitivity analysis. The vibrational behaviour of SWBNNT has been analysed for higher-order modes of vibrations to identify the intermediate landing position of biological object of zeptogram scale. The present molecular structural mechanics-based FE modelling approach is found to be very effectual to incorporate different chiralities of the atomic structures. Also, different boundary conditions can be effectively simulated using the present approach to analyse the dynamic behaviour of the SWBNNT-based mass sensor. The presented study has explored the potential of SWBNNT, as a nanobiosensor having the capability of zeptogram level mass sensing.

Nonlinear Synergistic Emergence and Predictability in Complex Systems: Theory and Hydro-Climatic Applications

NASA Astrophysics Data System (ADS)

Perdigão, Rui A. P.; Hall, Julia; Pires, Carlos A. L.; Blöschl, Günter

2017-04-01

Classical and stochastic dynamical system theories assume structural coherence and dynamic recurrence with invariants of motion that are not necessarily so. These are grounded on the unproven assumption of universality in the dynamic laws derived from statistical kinematic evaluation of non-representative empirical records. As a consequence, the associated formulations revolve around a restrictive set of configurations and intermittencies e.g. in an ergodic setting, beyond which any predictability is essentially elusive. Moreover, dynamical systems are fundamentally framed around dynamic codependence among intervening processes, i.e. entail essentially redundant interactions such as couplings and feedbacks. That precludes synergistic cooperation among processes that, whilst independent from each other, jointly produce emerging dynamic behaviour not present in any of the intervening parties. In order to overcome these fundamental limitations, we introduce a broad class of non-recursive dynamical systems that formulate dynamic emergence of unprecedented states in a fundamental synergistic manner, with fundamental principles in mind. The overall theory enables innovations to be predicted from the internal system dynamics before any a priori information is provided about the associated dynamical properties. The theory is then illustrated to anticipate, from non-emergent records, the spatiotemporal emergence of multiscale hyper chaotic regimes, critical transitions and structural coevolutionary changes in synthetic and real-world complex systems. Example applications are provided within the hydro-climatic context, formulating and dynamically forecasting evolving hydro-climatic distributions, including the emergence of extreme precipitation and flooding in a structurally changing hydro-climate system. Validation is then conducted with a posteriori verification of the simulated dynamics against observational records. Agreement between simulations and observations is confirmed with robust nonlinear information diagnostics.

Seeing with the nano-eye: accessing structure, function, and dynamics of matter on its natural length and time scales

NASA Astrophysics Data System (ADS)

Raschke, Markus

2015-03-01

To understand and ultimately control the properties of most functional materials, from molecular soft-matter to quantum materials, requires access to the structure, coupling, and dynamics on the elementary time and length scales that define the microscopic interactions in these materials. To gain the desired nanometer spatial resolution with simultaneous spectroscopic specificity we combine scanning probe microscopy with different optical, including coherent, nonlinear, and ultrafast spectroscopies. The underlying near-field interaction mediated by the atomic-force or scanning tunneling microscope tip provides the desired deep-sub wavelength nano-focusing enabling few-nm spatial resolution. I will introduce our generalization of the approach in terms of the near-field impedance matching to a quantum system based on special optical antenna-tip designs. The resulting enhanced and qualitatively new forms of light-matter interaction enable measurements of quantum dynamics in an interacting environment or to image the electromagnetic local density of states of thermal radiation. Other applications include the inter-molecular coupling and dynamics in soft-matter hetero-structures, surface plasmon interferometry as a probe of electronic structure and dynamics in graphene, and quantum phase transitions in correlated electron materials. These examples highlight the general applicability of the new near-field microscopy approach, complementing emergent X-ray and electron imaging tools, aiming towards the ultimate goal of probing matter on its most elementary spatio-temporal level.

Designing for aircraft structural crashworthiness

NASA Technical Reports Server (NTRS)

Thomson, R. G.; Caiafa, C.

1981-01-01

This report describes structural aviation crash dynamics research activities being conducted on general aviation aircraft and transport aircraft. The report includes experimental and analytical correlations of load-limiting subfloor and seat configurations tested dynamically in vertical drop tests and in a horizontal sled deceleration facility. Computer predictions using a finite-element nonlinear computer program, DYCAST, of the acceleration time-histories of these innovative seat and subfloor structures are presented. Proposed application of these computer techniques, and the nonlinear lumped mass computer program KRASH, to transport aircraft crash dynamics is discussed. A proposed FAA full-scale crash test of a fully instrumented radio controlled transport airplane is also described.

Structure Detection of Nonlinear Aeroelastic Systems with Application to Aeroelastic Flight Test Data. Part 2

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.; Brenner, martin J.

2006-01-01

This viewgraph presentation reviews the 1. Motivation for the study 2. Nonlinear Model Form 3. Structure Detection 4. Least Absolute Shrinkage and Selection Operator (LASSO) 5. Objectives 6. Results 7. Assess LASSO as a Structure Detection Tool: Simulated Nonlinear Models 8. Applicability to Complex Systems: F/A-18 Active Aeroelastic Wing Flight Test Data. The authors conclude that 1. this is a novel approach for detecting the structure of highly over-parameterised nonlinear models in situations where other methods may be inadequate 2. that it is a practical significance in the analysis of aircraft dynamics during envelope expansion and could lead to more efficient control strategies and 3. this could allow greater insight into the functionality of various systems dynamics, by providing a quantitative model which is easily interpretable

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

PubMed

Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

2016-01-21

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

Model-Based Heterogeneous Data Fusion for Reliable Force Estimation in Dynamic Structures under Uncertainties

PubMed Central

Khodabandeloo, Babak; Melvin, Dyan; Jo, Hongki

2017-01-01

Direct measurements of external forces acting on a structure are infeasible in many cases. The Augmented Kalman Filter (AKF) has several attractive features that can be utilized to solve the inverse problem of identifying applied forces, as it requires the dynamic model and the measured responses of structure at only a few locations. But, the AKF intrinsically suffers from numerical instabilities when accelerations, which are the most common response measurements in structural dynamics, are the only measured responses. Although displacement measurements can be used to overcome the instability issue, the absolute displacement measurements are challenging and expensive for full-scale dynamic structures. In this paper, a reliable model-based data fusion approach to reconstruct dynamic forces applied to structures using heterogeneous structural measurements (i.e., strains and accelerations) in combination with AKF is investigated. The way of incorporating multi-sensor measurements in the AKF is formulated. Then the formulation is implemented and validated through numerical examples considering possible uncertainties in numerical modeling and sensor measurement. A planar truss example was chosen to clearly explain the formulation, while the method and formulation are applicable to other structures as well. PMID:29149088

Structural Mechanics and Dynamics Branch

NASA Technical Reports Server (NTRS)

Stefko, George

2003-01-01

The 2002 annual report of the Structural Mechanics and Dynamics Branch reflects the majority of the work performed by the branch staff during the 2002 calendar year. Its purpose is to give a brief review of the branch s technical accomplishments. The Structural Mechanics and Dynamics Branch develops innovative computational tools, benchmark experimental data, and solutions to long-term barrier problems in the areas of propulsion aeroelasticity, active and passive damping, engine vibration control, rotor dynamics, magnetic suspension, structural mechanics, probabilistics, smart structures, engine system dynamics, and engine containment. Furthermore, the branch is developing a compact, nonpolluting, bearingless electric machine with electric power supplied by fuel cells for future "more electric" aircraft. An ultra-high-power-density machine that can generate projected power densities of 50 hp/lb or more, in comparison to conventional electric machines, which generate usually 0.2 hp/lb, is under development for application to electric drives for propulsive fans or propellers. In the future, propulsion and power systems will need to be lighter, to operate at higher temperatures, and to be more reliable in order to achieve higher performance and economic viability. The Structural Mechanics and Dynamics Branch is working to achieve these complex, challenging goals.

Super-resolution optical microscopy for studying membrane structure and dynamics.

PubMed

Sezgin, Erdinc

2017-07-12

Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.

Structure-based control of complex networks with nonlinear dynamics.

PubMed

Zañudo, Jorge Gomez Tejeda; Yang, Gang; Albert, Réka

2017-07-11

What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system toward any of its natural long-term dynamic behaviors, regardless of the specific functional forms and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of structural controllability in control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case but not in specific model instances.

CEAS/AIAA/ICASE/NASA Langley International Forum on Aeroelasticity and Structural Dynamics 1999. Pt. 2

NASA Technical Reports Server (NTRS)

Whitlow, Jr., Woodrow (Editor); Todd, Emily N. (Editor)

1999-01-01

The proceedings of a workshop sponsored by the Confederation of European Aerospace Societies (CEAS), the American Institute of Aeronautics and Astronautics (AIAA), the National Aeronautics and Space Administration (NASA), Washington, D.C., and the Institute for Computer Applications in Science and Engineering (ICASE), Hampton, Virginia, and held in Williamsburg, Virginia June 22-25, 1999 represent a collection of the latest advances in aeroelasticity and structural dynamics from the world community. Research in the areas of unsteady aerodynamics and aeroelasticity, structural modeling and optimization, active control and adaptive structures, landing dynamics, certification and qualification, and validation testing are highlighted in the collection of papers. The wide range of results will lead to advances in the prediction and control of the structural response of aircraft and spacecraft.

Application of Lanczos vectors to control design of flexible structures, part 2

NASA Technical Reports Server (NTRS)

Craig, Roy R., Jr.; Su, Tzu-Jeng

1992-01-01

This report covers the period of the grant from January 1991 until its expiration in June 1992. Together with an Interim Report (Ref. 9), it summarizes the research conducted under NASA Grant NAG9-357 on the topic 'Application of Lanczos Vectors to Control Design of Flexible Structures.' The research concerns various ways to obtain reduced-order mathematical models of complex structures for use in dynamics analysis and in the design of control systems for these structures. This report summarizes the research.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

Ninth NASTRAN (R) Users' Colloquium

NASA Technical Reports Server (NTRS)

1980-01-01

The general application of finite element methodology and the specific application of NASTRAN to a wide variety of static and dynamic structural problems is addressed. Comparison with other approaches and new methods of analysis with nastran are included.

Mid-frequency Band Dynamics of Large Space Structures

NASA Technical Reports Server (NTRS)

Coppolino, Robert N.; Adams, Douglas S.

2004-01-01

High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

Application of ESPI techniques for the study of dynamic vibrations

NASA Astrophysics Data System (ADS)

Krupka, Rene

2004-06-01

Full field optical measurement techniques have already entered into various fields of industrial applications covering static as well as dynamic phenomena. The electronic speckle pattern interferometry (ESPI) allows the non contact, sensitive and three dimensional measurement of displacements in the sub micron range of objects with dimensions from mm2 to m2. For dynamic and transient phenomena, the use of pulsed laser have already been reported for various applications and successfully proven for the determination of the structural response of different components. In this paper we would like to present recent developments in the field of pulsed ESPI applications where emphasis is put onto the full field measurement result. The use of a completely computer controlled system allows easy access to mode shape characterization, deformation measurements and the characterization of transient events like shock wave propagation. Recent developments of the 3D-PulseESPI technique led to a very compact and complete system with improved characteristics regarding robustness and operation. The integrated design of the illumination laser and sensors for image acquisition allows easy aiming and adjustments with respect to the object of inspection. The laser is completely computer controlled which is advantageously used in a completely automatic brake squeal inspection system, which captures the squealing signal, automatically fires the laser and provides the complete deformation map of the component under test. Examples of recent applications in the field of dynamic structure response, with an emphasis in the field of automotive applications are given.

Guest-Induced Two-Way Structural Transformation in a Layered Metal-Organic Framework Thin Film.

PubMed

Haraguchi, Tomoyuki; Otsubo, Kazuya; Sakata, Osami; Fujiwara, Akihiko; Kitagawa, Hiroshi

2016-12-28

Fabrication of thin films made of metal-organic frameworks (MOFs) has been intensively pursued for practical applications that use the structural response of MOFs. However, to date, only physisorption-induced structural response has been studied in these films. Chemisorption can be expected to provide a remarkable structural response because of the formation of bonds between guest molecules and reactive metal sites in host MOFs. Here, we report that chemisorption-induced two-way structural transformation in a nanometer-sized MOF thin film. We prepared a two-dimensional layered-type MOF Fe[Pt(CN) 4 ] thin film using a step-by-step approach. Although the as-synthesized film showed poor crystallinity, the dehydrated form of this thin film had a highly oriented crystalline nature (Film-D) as confirmed by synchrotron X-ray diffraction (XRD). Surprisingly, under water and pyridine vapors, Film-D showed chemisorption-induced dynamic structural transformations to Fe(L) 2 [Pt(CN) 4 ] thin films [L = H 2 O (Film-H), pyridine (Film-P)], where water and pyridine coordinated to the open Fe 2+ site. Dynamic structural transformations were also confirmed by in situ XRD, sorption measurement, and infrared reflection absorption spectroscopy. This is the first report of chemisorption-induced dynamic structural response in a MOF thin film, and it provides useful insights, which would lead to future practical applications of MOFs utilizing chemisorption-induced structural responses.

Dynamic characteristics and simplified numerical methods of an all-vertical-piled wharf in offshore deep water

NASA Astrophysics Data System (ADS)

Zhang, Hua-qing; Sun, Xi-ping; Wang, Yuan-zhan; Yin, Ji-long; Wang, Chao-yang

2015-10-01

There has been a growing trend in the development of offshore deep-water ports in China. For such deep sea projects, all-vertical-piled wharves are suitable structures and generally located in open waters, greatly affected by wave action. Currently, no systematic studies or simplified numerical methods are available for deriving the dynamic characteristics and dynamic responses of all-vertical-piled wharves under wave cyclic loads. In this article, we compare the dynamic characteristics of an all-vertical-piled wharf with those of a traditional inshore high-piled wharf through numerical analysis; our research reveals that the vibration period of an all-vertical-piled wharf under cyclic loading is longer than that of an inshore high-piled wharf and is much closer to the period of the loading wave. Therefore, dynamic calculation and analysis should be conducted when designing and calculating the characteristics of an all-vertical-piled wharf. We establish a dynamic finite element model to examine the dynamic response of an all-vertical-piled wharf under wave cyclic loads and compare the results with those under wave equivalent static load; the comparison indicates that dynamic amplification of the structure is evident when the wave dynamic load effect is taken into account. Furthermore, a simplified dynamic numerical method for calculating the dynamic response of an all-vertical-piled wharf is established based on the P-Y curve. Compared with finite element analysis, the simplified method is more convenient to use and applicable to large structural deformation while considering the soil non-linearity. We confirmed that the simplified method has acceptable accuracy and can be used in engineering applications.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

This final report on computational methods and software systems for dynamics and control of large space structures covers progress to date, projected developments in the final months of the grant, and conclusions. Pertinent reports and papers that have not appeared in scientific journals (or have not yet appeared in final form) are enclosed. The grant has supported research in two key areas of crucial importance to the computer-based simulation of large space structure. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area, as reported here, involves massively parallel computers.

Hierarchical structure and dynamics of oligocarbonate-functionalized PEG block copolymer gels

NASA Astrophysics Data System (ADS)

Prabhu, Vivek; Wei, Guangmin; Ali, Samim; Venkataraman, Shrinivas; Yang, Yi Yan; Hedrick, James

Hierarchical, self-assembled block copolymers in aqueous solutions provide advanced materials for biomaterial applications. Recent advancements in the synthesis of aliphatic polycarbonates have shown nontraditional micellar and hierarchical structures driven by the supramolecular assembly of the carbonate block functionality that includes cholesterol, vitamin D, and fluorene. This presentation shall describe the supramolecular assembly structure and dynamics observed by static and dynamic light scattering, small-angle neutron scattering and transmission electron microscopy in a model pi-pi stacking driven fluorene system. The combination of real-space and reciprocal space methods to develop appropriate models that quantify the structure from the micelle to transient gel network will be discussed. 1) Biomedical Research Council, Agency for Science, Technology and Research, Singapore, 2) NIST Materials Genome Initiative.

Seismology in civil engineering

NASA Astrophysics Data System (ADS)

Dvorak, A.

Properties of soils and rocks exposed to vibrations in the practice of civil engineering are examined. Seismic and dynamic field investigations, determination of seismic and dynamic modulus of elasticity, coefficients of damping and absorption are studied. Seismic effects of blasting and of other sources of vibrations on structures and persons, application of rock-noise and dynamic tests of piles are studied.

Evaluation of experimental methods for determining dynamic stiffness and damping of composite materials

NASA Technical Reports Server (NTRS)

Bert, C. W.; Clary, R. R.

1974-01-01

Various methods potentially usable for determining dynamic stiffness and damping of composite materials are reviewed. Of these, the following most widely used techniques are singled out for more detailed discussion: free vibration, pulse propagation, and forced vibration response. To illustrate the usefulness and validity of dynamic property data, their application in dynamic analyses and comparison with measured structural response are described for the following composite-material structures: free-free sandwich beam with glass-epoxy facings, clamped-edge sandwich plate with similar facings, free-end sandwich conical shell with similar facings, and boron-epoxy free plate with layers arranged at various orientations.

New Millenium Inflatable Structures Technology

NASA Technical Reports Server (NTRS)

Mollerick, Ralph

1997-01-01

Specific applications where inflatable technology can enable or enhance future space missions are tabulated. The applicability of the inflatable technology to large aperture infra-red astronomy missions is discussed. Space flight validation and risk reduction are emphasized along with the importance of analytical tools in deriving structurally sound concepts and performing optimizations using compatible codes. Deployment dynamics control, fabrication techniques, and system testing are addressed.

The NASA/industry Design Analysis Methods for Vibrations (DAMVIBS) program: McDonnell-Douglas Helicopter Company achievements

NASA Technical Reports Server (NTRS)

Toossi, Mostafa; Weisenburger, Richard; Hashemi-Kia, Mostafa

1993-01-01

This paper presents a summary of some of the work performed by McDonnell Douglas Helicopter Company under NASA Langley-sponsored rotorcraft structural dynamics program known as DAMVIBS (Design Analysis Methods for VIBrationS). A set of guidelines which is applicable to dynamic modeling, analysis, testing, and correlation of both helicopter airframes and a large variety of structural finite element models is presented. Utilization of these guidelines and the key features of their applications to vibration modeling of helicopter airframes are discussed. Correlation studies with the test data, together with the development and applications of a set of efficient finite element model checkout procedures, are demonstrated on a large helicopter airframe finite element model. Finally, the lessons learned and the benefits resulting from this program are summarized.

Recursive formulae and performance comparisons for first mode dynamics of periodic structures

NASA Astrophysics Data System (ADS)

Hobeck, Jared D.; Inman, Daniel J.

2017-05-01

Periodic structures are growing in popularity especially in the energy harvesting and metastructures communities. Common types of these unique structures are referred to in the literature as zigzag, orthogonal spiral, fan-folded, and longitudinal zigzag structures. Many of these studies on periodic structures have two competing goals in common: (a) minimizing natural frequency, and (b) minimizing mass or volume. These goals suggest that no single design is best for all applications; therefore, there is a need for design optimization and comparison tools which first require efficient easy-to-implement models. All available structural dynamics models for these types of structures do provide exact analytical solutions; however, they are complex requiring tedious implementation and providing more information than necessary for practical applications making them computationally inefficient. This paper presents experimentally validated recursive models that are able to very accurately and efficiently predict the dynamics of the four most common types of periodic structures. The proposed modeling technique employs a combination of static deflection formulae and Rayleigh’s Quotient to estimate the first mode shape and natural frequency of periodic structures having any number of beams. Also included in this paper are the results of an extensive experimental validation study which show excellent agreement between model prediction and measurement. Lastly, the proposed models are used to evaluate the performance of each type of structure. Results of this performance evaluation reveal key advantages and disadvantages associated with each type of structure.

Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

PubMed Central

Hocking, Henry G; Zangger, Klaus; Madl, Tobias

2013-01-01

Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes. PMID:23836693

Brownian dynamics of sterically-stabilized colloidal suspensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

TeGrotenhuis, W.E.; Radke, C.J.; Denn, M.M.

1994-02-01

One application where microstructure plays a critical role is in the production of specialty ceramics, where colloidal suspensions act as precursors; here the microstructure influences the structural, thermal, optical and electrical properties of the ceramic products. Using Brownian dynamics, equilibrium and dynamic properties are calculated for colloidal suspensions that are stabilized through the Milner, Witten and Cates (1988) steric potential. Results are reported for osmotic pressures, radial distributions functions, static structure factors, and self-diffusion coefficients. The sterically-stabilized systems are also approximated by equivalent hard spheres, with good agreement for osmotic pressure and long-range structure. The suitability of the potential tomore » model the behavior of a real system is explored by comparing static structure factors calculated from Brownian dynamics simulations to those measured using SANS. Finally, the effects of Hamaker and hydrodynamic forces on calculated properties are investigated.« less

Multi-scale compositionality: identifying the compositional structures of social dynamics using deep learning.

PubMed

Peng, Huan-Kai; Marculescu, Radu

2015-01-01

Social media exhibit rich yet distinct temporal dynamics which cover a wide range of different scales. In order to study this complex dynamics, two fundamental questions revolve around (1) the signatures of social dynamics at different time scales, and (2) the way in which these signatures interact and form higher-level meanings. In this paper, we propose the Recursive Convolutional Bayesian Model (RCBM) to address both of these fundamental questions. The key idea behind our approach consists of constructing a deep-learning framework using specialized convolution operators that are designed to exploit the inherent heterogeneity of social dynamics. RCBM's runtime and convergence properties are guaranteed by formal analyses. Experimental results show that the proposed method outperforms the state-of-the-art approaches both in terms of solution quality and computational efficiency. Indeed, by applying the proposed method on two social network datasets, Twitter and Yelp, we are able to identify the compositional structures that can accurately characterize the complex social dynamics from these two social media. We further show that identifying these patterns can enable new applications such as anomaly detection and improved social dynamics forecasting. Finally, our analysis offers new insights on understanding and engineering social media dynamics, with direct applications to opinion spreading and online content promotion.

Multi-Scale Compositionality: Identifying the Compositional Structures of Social Dynamics Using Deep Learning

PubMed Central

Peng, Huan-Kai; Marculescu, Radu

2015-01-01

Objective Social media exhibit rich yet distinct temporal dynamics which cover a wide range of different scales. In order to study this complex dynamics, two fundamental questions revolve around (1) the signatures of social dynamics at different time scales, and (2) the way in which these signatures interact and form higher-level meanings. Method In this paper, we propose the Recursive Convolutional Bayesian Model (RCBM) to address both of these fundamental questions. The key idea behind our approach consists of constructing a deep-learning framework using specialized convolution operators that are designed to exploit the inherent heterogeneity of social dynamics. RCBM’s runtime and convergence properties are guaranteed by formal analyses. Results Experimental results show that the proposed method outperforms the state-of-the-art approaches both in terms of solution quality and computational efficiency. Indeed, by applying the proposed method on two social network datasets, Twitter and Yelp, we are able to identify the compositional structures that can accurately characterize the complex social dynamics from these two social media. We further show that identifying these patterns can enable new applications such as anomaly detection and improved social dynamics forecasting. Finally, our analysis offers new insights on understanding and engineering social media dynamics, with direct applications to opinion spreading and online content promotion. PMID:25830775

Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

NASA Technical Reports Server (NTRS)

Noor, A. K. (Editor); Hayduk, R. J. (Editor)

1985-01-01

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

NASA Astrophysics Data System (ADS)

Faini, Marco; Stengel, Florian; Aebersold, Ruedi

2016-06-01

Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

Joint nonlinearity effects in the design of a flexible truss structure control system

NASA Technical Reports Server (NTRS)

Mercadal, Mathieu

1986-01-01

Nonlinear effects are introduced in the dynamics of large space truss structures by the connecting joints which are designed with rather important tolerances to facilitate the assembly of the structures in space. The purpose was to develop means to investigate the nonlinear dynamics of the structures, particularly the limit cycles that might occur when active control is applied to the structures. An analytical method was sought and derived to predict the occurrence of limit cycles and to determine their stability. This method is mainly based on the quasi-linearization of every joint using describing functions. This approach was proven successful when simple dynamical systems were tested. Its applicability to larger systems depends on the amount of computations it requires, and estimates of the computational task tend to indicate that the number of individual sources of nonlinearity should be limited. Alternate analytical approaches, which do not account for every single nonlinearity, or the simulation of a simplified model of the dynamical system should, therefore, be investigated to determine a more effective way to predict limit cycles in large dynamical systems with an important number of distributed nonlinearities.

Layerwise Mechanics and Finite Elements for Smart Composite Structures with Piezoelectric Actuators and Sensors

NASA Technical Reports Server (NTRS)

Saravanos, Dimitris A.; Heyliger, Paul R.; Hopkins, Dale A.

1996-01-01

Recent developments on layerwise mechanics for the analysis of composite laminates and structures with piezoelectric actuators and sensors are reviewed. The mechanics implement layerwise representations of displacements and electric potential, and can model both the global and local electromechanical response of smart composite structures. The corresponding finite-element implementations for the static and dynamic analysis of smart piezoelectric composite structures are also summarized. Select application illustrate the accuracy, robustness and capability of the developed mechanics to capture the global and local dynamic response of thin and/or thick laminated piezoelectric plates.

Application of singular value decomposition to structural dynamics systems with constraints

NASA Technical Reports Server (NTRS)

Juang, J.-N.; Pinson, L. D.

1985-01-01

Singular value decomposition is used to construct a coordinate transformation for a linear dynamic system subject to linear, homogeneous constraint equations. The method is compared with two commonly used methods, namely classical Gaussian elimination and Walton-Steeves approach. Although the classical method requires fewer numerical operations, the singular value decomposition method is more accurate and convenient in eliminating the dependent coordinates. Numerical examples are presented to demonstrate the application of the method.

Operationalizing Dynamic Ocean Management (DOM): Understanding the Incentive Structure, Policy and Regulatory Context for DOM in Practice

NASA Astrophysics Data System (ADS)

Lewison, R. L.; Saumweber, W. J.; Erickson, A.; Martone, R. G.

2016-12-01

Dynamic ocean management, or management that uses near real-time data to guide the spatial distribution of commercial activities, is an emerging approach to balance ocean resource use and conservation. Employing a wide range of data types, dynamic ocean management in a fisheries context can be used to meet multiple objectives - managing target quota, bycatch reduction, and reducing interactions with species of conservation concern. There is a growing list of DOM applications currently in practice in fisheries around the world, yet the approach is new enough that both fishers and fisheries managers are unclear how DOM can be applied to their fishery. Here, we use the experience from dynamic ocean management applications that are currently in practice to address the commonly asked question "How can dynamic management approaches be implemented in a traditionally managed fishery?". Combining knowledge from the DOM participants with a review of regulatory frameworks and incentive structures, stakeholder participation, and technological requirements of DOM in practice, we identify ingredients that have supported successful implementation of this new management approach.

Inverse load calculation procedure for offshore wind turbines and application to a 5-MW wind turbine support structure: Inverse load calculation procedure for offshore wind turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pahn, T.; Rolfes, R.; Jonkman, J.

A significant number of wind turbines installed today have reached their designed service life of 20 years, and the number will rise continuously. Most of these turbines promise a more economical performance if they operate for more than 20 years. To assess a continued operation, we have to analyze the load-bearing capacity of the support structure with respect to site-specific conditions. Such an analysis requires the comparison of the loads used for the design of the support structure with the actual loads experienced. This publication presents the application of a so-called inverse load calculation to a 5-MW wind turbine supportmore » structure. The inverse load calculation determines external loads derived from a mechanical description of the support structure and from measured structural responses. Using numerical simulations with the software fast, we investigated the influence of wind-turbine-specific effects such as the wind turbine control or the dynamic interaction between the loads and the support structure to the presented inverse load calculation procedure. fast is used to study the inverse calculation of simultaneously acting wind and wave loads, which has not been carried out until now. Furthermore, the application of the inverse load calculation procedure to a real 5-MW wind turbine support structure is demonstrated. In terms of this practical application, setting up the mechanical system for the support structure using measurement data is discussed. The paper presents results for defined load cases and assesses the accuracy of the inversely derived dynamic loads for both the simulations and the practical application.« less

Analysis of passive damping in thick composite structures

NASA Technical Reports Server (NTRS)

Saravanos, D. A.

1993-01-01

Computational mechanics for the prediction of damping and other dynamic characteristics in composite structures of general thicknesses and laminations are presented. Discrete layer damping mechanics that account for the representation of interlaminar shear effects in the material are summarized. Finite element based structural mechanics for the analysis of damping are described, and a specialty finite element is developed. Applications illustrate the quality of the discrete layer damping mechanics in predicting the damped dynamic characteristics of composite structures with thicker sections and/or laminate configurations that induce interlaminar shear. The results also illustrate and quantify the significance of interlaminar shear damping in such composite structures.

Mechanical design of DNA nanostructures

NASA Astrophysics Data System (ADS)

Castro, Carlos E.; Su, Hai-Jun; Marras, Alexander E.; Zhou, Lifeng; Johnson, Joshua

2015-03-01

Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07153k

Correlation of finite-element structural dynamic analysis with measured free vibration characteristics for a full-scale helicopter fuselage

NASA Technical Reports Server (NTRS)

Kenigsberg, I. J.; Dean, M. W.; Malatino, R.

1974-01-01

The correlation achieved with each program provides the material for a discussion of modeling techniques developed for general application to finite-element dynamic analyses of helicopter airframes. Included are the selection of static and dynamic degrees of freedom, cockpit structural modeling, and the extent of flexible-frame modeling in the transmission support region and in the vicinity of large cut-outs. The sensitivity of predicted results to these modeling assumptions are discussed. Both the Sikorsky Finite-Element Airframe Vibration analysis Program (FRAN/Vibration Analysis) and the NASA Structural Analysis Program (NASTRAN) have been correlated with data taken in full-scale vibration tests of a modified CH-53A helicopter.

Discrete and continuous dynamics modeling of a mass moving on a flexible structure

NASA Technical Reports Server (NTRS)

Herman, Deborah Ann

1992-01-01

A general discrete methodology for modeling the dynamics of a mass that moves on the surface of a flexible structure is developed. This problem was motivated by the Space Station/Mobile Transporter system. A model reduction approach is developed to make the methodology applicable to large structural systems. To validate the discrete methodology, continuous formulations are also developed. Three different systems are examined: (1) simply-supported beam, (2) free-free beam, and (3) free-free beam with two points of contact between the mass and the flexible beam. In addition to validating the methodology, parametric studies were performed to examine how the system's physical properties affect its dynamics.

A Framework for the Specification of the Semantics and the Dynamics of Instructional Applications

ERIC Educational Resources Information Center

Buendia-Garcia, Felix; Diaz, Paloma

2003-01-01

An instructional application consists of a set of resources and activities to implement interacting, interrelated, and structured experiences oriented towards achieving specific educational objectives. The development of computer-based instructional applications has to follow a well defined process, so models for computer-based instructional…

Allosteric effects of gold nanoparticles on human serum albumin.

PubMed

Shao, Qing; Hall, Carol K

2017-01-07

The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions.

Dynamically variable negative stiffness structures

PubMed Central

Churchill, Christopher B.; Shahan, David W.; Smith, Sloan P.; Keefe, Andrew C.; McKnight, Geoffrey P.

2016-01-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness–based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators. PMID:26989771

Accurate Structural Correlations from Maximum Likelihood Superpositions

PubMed Central

Theobald, Douglas L; Wuttke, Deborah S

2008-01-01

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

ORATOS: ESA's future flight dynamics operations system

NASA Astrophysics Data System (ADS)

Dreger, Frank; Fertig, Juergen; Muench, Rolf

The Orbit and Attitude Operations System (ORATOS -- the European Space Agency's future orbit and attitude operations system -- will be in use from the mid-nineties until well beyond the year 2000. The ORATOS design is based on the experience from flight dynamics support to all past ESA missions. The ORATOS computer hardware consists of a network of powerful UNIX workstations. ORATOS resides on several hardware platforms, each comprising one or more fileservers, several client workstations and the associated communications interface hardware. The ORATOS software is structured into three layers. The flight dynamics applications layer, the support layer and the operating system layer. This architectural design separates the flight dynamics application software from the support tools and operating system facilities. It allows upgrading and replacement of operating system facilities with a minimum (or no) effect on the application layer.

Modelling Ni-mH battery using Cauer and Foster structures

NASA Astrophysics Data System (ADS)

Kuhn, E.; Forgez, C.; Lagonotte, P.; Friedrich, G.

This paper deals with dynamic models of Ni-mH battery and focuses on the development of the equivalent electric models. We propose two equivalent electric models, using Cauer and Foster structures, able to relate both dynamic and energetic behavior of the battery. These structures are well adapted to real time applications (e.g. Battery Management Systems) or system simulations. A special attention will be brought to the influence of the complexity of the equivalent electric scheme on the precision of the model. Experimental validations allow to discuss about performances of proposed models.

Coupling of electromagnetics and structural/fluid dynamics - application to the dual coolant blanket subjected to plasma disruptions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jordan, T.

Some aspects concerning the coupling of quasi-stationary electromagnetics and the dynamics of structure and fluid are investigated. The necessary equations are given in a dimensionless form. The dimensionless parameters in these equations are used to evaluate the importance of the different coupling effects. A finite element formulation of the eddy-current damping in solid structures is developed. With this formulation, an existing finite element method (FEM) structural dynamics code is extended and coupled to an FEM eddy-current code. With this program system, the influence of the eddy-current damping on the dynamic loading of the dual coolant blanket during a centered plasmamore » disruption is determined. The analysis proves that only in loosely fixed or soft structures will eddy-current damping considerably reduce the resulting stresses. Additionally, the dynamic behavior of the liquid metal in the blankets` poloidal channels is described with a simple two-dimensional magnetohydrodynamic approach. The analysis of the dimensionless parameters shows that for small-scale experiments, which are designed to model the coupled electromagnetic and structural/fluid dynamic effects in such a blanket, the same magnetic fields must be applied as in the real fusion device. This will be the easiest way to design experiments that produce transferable results. 10 refs., 7 figs.« less

CFA Films in Amorphous Substrate: Structural Phase Induction and Magnetization Dynamics

NASA Astrophysics Data System (ADS)

Correa, M. A.; Bohn, F.; Escobar, V. M.

We report a systematic study of the structural and quasi-static magnetic properties, as well as of the dynamic magnetic response through MI effect, in Co2FeAl and MgO//Co2FeAl single layers and a MgO//Co2FeAl/Ag/Co2FeAl trilayered film, all grown onto an amorphous substrate. We present a new route to induce the crystalline structure in the Co2FeAl alloy and verify that changes in the structural phase of this material leads to remarkable modifications of the magnetic anisotropy and, consequently, dynamic magnetic behavior. Considering the electrical and magnetic properties of the Co2FeAl, our results open new possibilities for technological applications of this full-Heusler alloy in rigid and flexible spintronic devices.

Supercomputer optimizations for stochastic optimal control applications

NASA Technical Reports Server (NTRS)

Chung, Siu-Leung; Hanson, Floyd B.; Xu, Huihuang

1991-01-01

Supercomputer optimizations for a computational method of solving stochastic, multibody, dynamic programming problems are presented. The computational method is valid for a general class of optimal control problems that are nonlinear, multibody dynamical systems, perturbed by general Markov noise in continuous time, i.e., nonsmooth Gaussian as well as jump Poisson random white noise. Optimization techniques for vector multiprocessors or vectorizing supercomputers include advanced data structures, loop restructuring, loop collapsing, blocking, and compiler directives. These advanced computing techniques and superconducting hardware help alleviate Bellman's curse of dimensionality in dynamic programming computations, by permitting the solution of large multibody problems. Possible applications include lumped flight dynamics models for uncertain environments, such as large scale and background random aerospace fluctuations.

Recent advances in reduction methods for nonlinear problems. [in structural mechanics

NASA Technical Reports Server (NTRS)

Noor, A. K.

1981-01-01

Status and some recent developments in the application of reduction methods to nonlinear structural mechanics problems are summarized. The aspects of reduction methods discussed herein include: (1) selection of basis vectors in nonlinear static and dynamic problems, (2) application of reduction methods in nonlinear static analysis of structures subjected to prescribed edge displacements, and (3) use of reduction methods in conjunction with mixed finite element models. Numerical examples are presented to demonstrate the effectiveness of reduction methods in nonlinear problems. Also, a number of research areas which have high potential for application of reduction methods are identified.

Stochastic formation of magnetic vortex structures in asymmetric disks triggered by chaotic dynamics

DOE PAGES

Im, Mi-Young; Lee, Ki-Suk; Vogel, Andreas; ...

2014-12-17

The non-trivial spin configuration in a magnetic vortex is a prototype for fundamental studies of nanoscale spin behaviour with potential applications in magnetic information technologies. Arrays of magnetic vortices interfacing with perpendicular thin films have recently been proposed as enabler for skyrmionic structures at room temperature, which has opened exciting perspectives on practical applications of skyrmions. An important milestone for achieving not only such skyrmion materials but also general applications of magnetic vortices is a reliable control of vortex structures. However, controlling magnetic processes is hampered by stochastic behaviour, which is associated with thermal fluctuations in general. Here we showmore » that the dynamics in the initial stages of vortex formation on an ultrafast timescale plays a dominating role for the stochastic behaviour observed at steady state. Our results show that the intrinsic stochastic nature of vortex creation can be controlled by adjusting the interdisk distance in asymmetric disk arrays.« less

Resting-state functional connectivity emerges from structurally and dynamically shaped slow linear fluctuations.

PubMed

Deco, Gustavo; Ponce-Alvarez, Adrián; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-07-03

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure-function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure-function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu; Yang, Mo

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heatmore » transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.« less

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Structure-based control of complex networks with nonlinear dynamics

NASA Astrophysics Data System (ADS)

Zanudo, Jorge G. T.; Yang, Gang; Albert, Reka

What can we learn about controlling a system solely from its underlying network structure? Here we use a framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors, regardless of the dynamic details and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of classical structural control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case, but not in specific model instances. This work was supported by NSF Grants PHY 1205840 and IIS 1160995. JGTZ is a recipient of a Stand Up To Cancer - The V Foundation Convergence Scholar Award.

Dynamic Imbalance Would Counter Offcenter Thrust

NASA Technical Reports Server (NTRS)

Mccanna, Jason

1994-01-01

Dynamic imbalance generated by offcenter thrust on rotating body eliminated by shifting some of mass of body to generate opposing dynamic imbalance. Technique proposed originally for spacecraft including massive crew module connected via long, lightweight intermediate structure to massive engine module, such that artificial gravitation in crew module generated by rotating spacecraft around axis parallel to thrust generated by engine. Also applicable to dynamic balancing of rotating terrestrial equipment to which offcenter forces applied.

MODELING MICROBUBBLE DYNAMICS IN BIOMEDICAL APPLICATIONS*

PubMed Central

CHAHINE, Georges L.; HSIAO, Chao-Tsung

2012-01-01

Controlling microbubble dynamics to produce desirable biomedical outcomes when and where necessary and avoid deleterious effects requires advanced knowledge, which can be achieved only through a combination of experimental and numerical/analytical techniques. The present communication presents a multi-physics approach to study the dynamics combining viscous- in-viscid effects, liquid and structure dynamics, and multi bubble interaction. While complex numerical tools are developed and used, the study aims at identifying the key parameters influencing the dynamics, which need to be included in simpler models. PMID:22833696

SSME structural dynamic model development

NASA Technical Reports Server (NTRS)

Foley, M. J.; Tilley, D. M.; Welch, C. T.

1983-01-01

A mathematical model of the Space Shuttle Main Engine (SSME) as a complete assembly, with detailed emphasis on LOX and High Fuel Turbopumps is developed. The advantages of both complete engine dynamics, and high fidelity modeling are incorporated. Development of this model, some results, and projected applications are discussed.

Plasmonic- and dielectric-based structural coloring: from fundamentals to practical applications

NASA Astrophysics Data System (ADS)

Lee, Taejun; Jang, Jaehyuck; Jeong, Heonyeong; Rho, Junsuk

2018-01-01

Structural coloring is production of color by surfaces that have microstructure fine enough to interfere with visible light; this phenomenon provides a novel paradigm for color printing. Plasmonic color is an emergent property of the interaction between light and metallic surfaces. This phenomenon can surpass the diffraction limit and achieve near unlimited lifetime. We categorize plasmonic color filters according to their designs (hole, rod, metal-insulator-metal, grating), and also describe structures supported by Mie resonance. We discuss the principles, and the merits and demerits of each color filter. We also discuss a new concept of color filters with tunability and reconfigurability, which enable printing of structural color to yield dynamic coloring at will. Approaches for dynamic coloring are classified as liquid crystal, chemical transition and mechanical deformation. At the end of review, we highlight a scale-up of fabrication methods, including nanoimprinting, self-assembly and laser-induced process that may enable real-world application of structural coloring.

Fourteenth NASTRAN (R) Users' Colloquium

NASA Technical Reports Server (NTRS)

1986-01-01

The proceedings of a colloquium are presented along with technical papers contributed during the conference. Reviewed are general applications of finite element methodology and the specific application of the NASA Structural Analysis System, NASTRAN, to a variety of static and dynamic sturctural problems.

Structure and dynamics of biomembranes in room-temperature ionic liquid water solutions studied by neutron scattering and by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Benedetto, Antonio; Ballone, Pietro

2018-05-01

Increasing attention is being devoted to the interaction of a new class of organic ionic liquids known as room-temperature ionic liquids (RTILs) with biomolecules, partly because of health and environment concerns, and, even more, for the prospect of exciting new applications in biomedicine, sensing and energy technologies. Here we focus on the interaction between RTILs and phospholipid bilayers that are well-accepted models for bio-membranes. We discuss how neutron scattering has been used to probe both the structure and the dynamics of these systems, and how its integration with molecular dynamics simulation has allowed the determination of the microscopic details of their interaction.

Shockwave dynamics: a comparison between stochastic and periodic porous architectures

NASA Astrophysics Data System (ADS)

Branch, Brittany; Ionite, Axinte; Clements, Bradford; Montgomery, David; Schmalzer, Andrew; Patterson, Brian; Mueller, Alexander; Jensen, Brian; Dattelbaum, Dana

Polymeric foams are used extensively as structural supports and load mitigating materials in which they are subjected to compressive loading at a range of strain rates, up to the high strain rates encountered in blast and shockwave loading. To date, there have been few insights into compaction phenomena in porous structures at the mesoscale, and the influence of structure on shockwave localization. Of particular interest is when the properties of the inherent mesoscopic, periodic structure begin to emerge, versus the discrete behavior of the individual cell. Here, we illustrate, for the first time, modulation of shockwave dynamics controlled at micron-length scales in additively manufactured periodic porous structures measured using in situ, time-resolved x-ray phase contrast imaging at the Advanced Photon Source. Further, we demonstrate how the shockwave dynamics in periodic structures differ from stochastic foams of similar density and we conclude that microstructural control in elastomer foams has a dramatic effect on shockwave dynamics and can be tailored towards a variety of applications. Laboratory Directed Research and Development (LDRD) program at Los Alamos National Laboratory (project# 20160103DR) and DOE/NNSA Campaign 2.

Total-energy Assisted Tight-binding Method Based on Local Density Approximation of Density Functional Theory

NASA Astrophysics Data System (ADS)

Fujiwara, Takeo; Nishino, Shinya; Yamamoto, Susumu; Suzuki, Takashi; Ikeda, Minoru; Ohtani, Yasuaki

2018-06-01

A novel tight-binding method is developed, based on the extended Hückel approximation and charge self-consistency, with referring the band structure and the total energy of the local density approximation of the density functional theory. The parameters are so adjusted by computer that the result reproduces the band structure and the total energy, and the algorithm for determining parameters is established. The set of determined parameters is applicable to a variety of crystalline compounds and change of lattice constants, and, in other words, it is transferable. Examples are demonstrated for Si crystals of several crystalline structures varying lattice constants. Since the set of parameters is transferable, the present tight-binding method may be applicable also to molecular dynamics simulations of large-scale systems and long-time dynamical processes.

Hybrid state vector methods for structural dynamic and aeroelastic boundary value problems

NASA Technical Reports Server (NTRS)

Lehman, L. L.

1982-01-01

A computational technique is developed that is suitable for performing preliminary design aeroelastic and structural dynamic analyses of large aspect ratio lifting surfaces. The method proves to be quite general and can be adapted to solving various two point boundary value problems. The solution method, which is applicable to both fixed and rotating wing configurations, is based upon a formulation of the structural equilibrium equations in terms of a hybrid state vector containing generalized force and displacement variables. A mixed variational formulation is presented that conveniently yields a useful form for these state vector differential equations. Solutions to these equations are obtained by employing an integrating matrix method. The application of an integrating matrix provides a discretization of the differential equations that only requires solutions of standard linear matrix systems. It is demonstrated that matrix partitioning can be used to reduce the order of the required solutions. Results are presented for several example problems in structural dynamics and aeroelasticity to verify the technique and to demonstrate its use. These problems examine various types of loading and boundary conditions and include aeroelastic analyses of lifting surfaces constructed from anisotropic composite materials.

How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships From Coarse-Grained Simulations.

PubMed

Torchi, Andrea; Bochicchio, Davide; Pavan, Giovanni M

2018-04-12

The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in a controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at an experimental level. Here we show coarse-grained molecular dynamics simulations (<5 Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers. As a representative case, we focus on a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers, experimentally seen to undergo dynamic clustering following the superselective binding to a multivalent recruiter. Our simulations show that the dynamic reorganization of the supramolecular structure proceeds via monomer diffusion on the dynamic fiber surface (exchange within the fiber). Rationally changing the structure of the monomers to make the fiber surface more or less dynamic allows tuning the rate of response to the stimulus and of supramolecular reconfiguration. Simple in silico experiments draw a structure-dynamics-property relationship revealing the key factors underpinning the dynamic adaptivity and stimuli-responsiveness of these supramolecular polymers. We come out with clear evidence that to master the bioinspired properties of these fibers, it is necessary to control their intrinsic dynamics, while the high-resolution of our molecular models permits us to show how.

The dynamic properties of sandwich structures based on metal-ceramic foams.

DOT National Transportation Integrated Search

2014-01-01

The present research program has studied the fracture properties of closed pore metal-ceramic foams for their potential applications as core systems in sandwich structures. The composite foams were created at Fireline, Inc. (Youngstown, OH) using the...

Land Application of Wastes: An Educational Program - Introduction and Script.

ERIC Educational Resources Information Center

Clarkson, W. W.; And Others

This is the introductory module to the Land Application of Wastes educational program. The module contains information on the content, structure, and dynamics of the program. Also included with the module is a script to accompany a slide presentation. The Land Application of Wastes program consists of twenty-five modules and audio-visual…

Identification of dynamic load for prosthetic structures.

PubMed

Zhang, Dequan; Han, Xu; Zhang, Zhongpu; Liu, Jie; Jiang, Chao; Yoda, Nobuhiro; Meng, Xianghua; Li, Qing

2017-12-01

Dynamic load exists in numerous biomechanical systems, and its identification signifies a critical issue for characterizing dynamic behaviors and studying biomechanical consequence of the systems. This study aims to identify dynamic load in the dental prosthetic structures, namely, 3-unit implant-supported fixed partial denture (I-FPD) and teeth-supported fixed partial denture. The 3-dimensional finite element models were constructed through specific patient's computerized tomography images. A forward algorithm and regularization technique were developed for identifying dynamic load. To verify the effectiveness of the identification method proposed, the I-FPD and teeth-supported fixed partial denture structures were investigated to determine the dynamic loads. For validating the results of inverse identification, an experimental force-measuring system was developed by using a 3-dimensional piezoelectric transducer to measure the dynamic load in the I-FPD structure in vivo. The computationally identified loads were presented with different noise levels to determine their influence on the identification accuracy. The errors between the measured load and identified counterpart were calculated for evaluating the practical applicability of the proposed procedure in biomechanical engineering. This study is expected to serve as a demonstrative role in identifying dynamic loading in biomedical systems, where a direct in vivo measurement may be rather demanding in some areas of interest clinically. Copyright © 2017 John Wiley & Sons, Ltd.

Complex Dynamic Systems View on Conceptual Change: How a Picture of Students' Intuitive Conceptions Accrue from Dynamically Robust Task Dependent Learning Outcomes

ERIC Educational Resources Information Center

Koponen, Ismo T.; Kokkonen, Tommi; Nousiainen, Maiji

2017-01-01

We discuss here conceptual change and the formation of robust learning outcomes from the viewpoint of complex dynamic systems (CDS). The CDS view considers students' conceptions as context dependent and multifaceted structures which depend on the context of their application. In the CDS view the conceptual patterns (i.e. intuitive conceptions…

Integration of dynamic, aerodynamic, and structural optimization of helicopter rotor blades

NASA Technical Reports Server (NTRS)

Peters, David A.

1991-01-01

Summarized here is the first six years of research into the integration of structural, dynamic, and aerodynamic considerations in the design-optimization process for rotor blades. Specifically discussed here is the application of design optimization techniques for helicopter rotor blades. The reduction of vibratory shears and moments at the blade root, aeroelastic stability of the rotor, optimum airframe design, and an efficient procedure for calculating system sensitivities with respect to the design variables used are discussed.

Application of dynamic recurrent neural networks in nonlinear system identification

NASA Astrophysics Data System (ADS)

Du, Yun; Wu, Xueli; Sun, Huiqin; Zhang, Suying; Tian, Qiang

2006-11-01

An adaptive identification method of simple dynamic recurrent neural network (SRNN) for nonlinear dynamic systems is presented in this paper. This method based on the theory that by using the inner-states feed-back of dynamic network to describe the nonlinear kinetic characteristics of system can reflect the dynamic characteristics more directly, deduces the recursive prediction error (RPE) learning algorithm of SRNN, and improves the algorithm by studying topological structure on recursion layer without the weight values. The simulation results indicate that this kind of neural network can be used in real-time control, due to its less weight values, simpler learning algorithm, higher identification speed, and higher precision of model. It solves the problems of intricate in training algorithm and slow rate in convergence caused by the complicate topological structure in usual dynamic recurrent neural network.

Development of structural health monitoring techniques using dynamics testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

James, G.H. III

Today`s society depends upon many structures (such as aircraft, bridges, wind turbines, offshore platforms, buildings, and nuclear weapons) which are nearing the end of their design lifetime. Since these structures cannot be economically replaced, techniques for structural health monitoring must be developed and implemented. Modal and structural dynamics measurements hold promise for the global non-destructive inspection of a variety of structures since surface measurements of a vibrating structure can provide information about the health of the internal members without costly (or impossible) dismantling of the structure. In order to develop structural health monitoring for application to operational structures, developments inmore » four areas have been undertaken within this project: operational evaluation, diagnostic measurements, information condensation, and damage identification. The developments in each of these four aspects of structural health monitoring have been exercised on a broad range of experimental data. This experimental data has been extracted from structures from several application areas which include aging aircraft, wind energy, aging bridges, offshore structures, structural supports, and mechanical parts. As a result of these advances, Sandia National Laboratories is in a position to perform further advanced development, operational implementation, and technical consulting for a broad class of the nation`s aging infrastructure problems.« less

Solution NMR views of dynamical ordering of biomacromolecules.

PubMed

Ikeya, Teppei; Ban, David; Lee, Donghan; Ito, Yutaka; Kato, Koichi; Griesinger, Christian

2018-02-01

To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Unsymmetric Lanczos model reduction and linear state function observer for flexible structures

NASA Technical Reports Server (NTRS)

Su, Tzu-Jeng; Craig, Roy R., Jr.

1991-01-01

This report summarizes part of the research work accomplished during the second year of a two-year grant. The research, entitled 'Application of Lanczos Vectors to Control Design of Flexible Structures' concerns various ways to use Lanczos vectors and Krylov vectors to obtain reduced-order mathematical models for use in the dynamic response analyses and in control design studies. This report presents a one-sided, unsymmetric block Lanczos algorithm for model reduction of structural dynamics systems with unsymmetric damping matrix, and a control design procedure based on the theory of linear state function observers to design low-order controllers for flexible structures.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

PubMed Central

Brodie, Nicholas I.; Popov, Konstantin I.; Petrotchenko, Evgeniy V.; Dokholyan, Nikolay V.; Borchers, Christoph H.

2017-01-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein—models for α helix–rich and β sheet–rich proteins, respectively—and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures. PMID:28695211

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

PubMed

Brodie, Nicholas I; Popov, Konstantin I; Petrotchenko, Evgeniy V; Dokholyan, Nikolay V; Borchers, Christoph H

2017-07-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures.

Structural kinematics based damage zone prediction in gradient structures using vibration database

NASA Astrophysics Data System (ADS)

Talha, Mohammad; Ashokkumar, Chimpalthradi R.

2014-05-01

To explore the applications of functionally graded materials (FGMs) in dynamic structures, structural kinematics based health monitoring technique becomes an important problem. Depending upon the displacements in three dimensions, the health of the material to withstand dynamic loads is inferred in this paper, which is based on the net compressive and tensile displacements that each structural degree of freedom takes. These net displacements at each finite element node predicts damage zones of the FGM where the material is likely to fail due to a vibration response which is categorized according to loading condition. The damage zone prediction of a dynamically active FGMs plate have been accomplished using Reddy's higher-order theory. The constituent material properties are assumed to vary in the thickness direction according to the power-law behavior. The proposed C0 finite element model (FEM) is applied to get net tensile and compressive displacement distributions across the structures. A plate made of Aluminum/Ziconia is considered to illustrate the concept of structural kinematics-based health monitoring aspects of FGMs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez, Mario E.

An area in earthquake risk reduction that needs an urgent examination is the selection of earthquake records for nonlinear dynamic analysis of structures. An often-mentioned shortcoming from results of nonlinear dynamic analyses of structures is that these results are limited to the type of records that these analyses use as input data. This paper proposes a procedure for selecting earthquake records for nonlinear dynamic analysis of structures. This procedure uses a seismic damage index evaluated using the hysteretic energy dissipated by a Single Degree of Freedom System (SDOF) representing a multi-degree-of freedom structure responding to an earthquake record, and themore » plastic work capacity of the system at collapse. The type of structural system is considered using simple parameters. The proposed method is based on the evaluation of the damage index for a suite of earthquake records and a selected type of structural system. A set of 10 strong ground motion records is analyzed to show an application of the proposed procedure for selecting earthquake records for structural design.« less

Advanced Plasmonic Materials for Dynamic Color Display.

PubMed

Shao, Lei; Zhuo, Xiaolu; Wang, Jianfang

2018-04-01

Plasmonic structures exhibit promising applications in high-resolution and durable color generation. Research on advanced hybrid plasmonic materials that allow dynamically reconfigurable color control has developed rapidly in recent years. Some of these results may give rise to practically applicable reflective displays in living colors with high performance and low power consumption. They will attract broad interest from display markets, compared with static plasmonic color printing, for example, in applications such as digital signage, full-color electronic paper, and electronic device screens. In this progress report, the most promising recent examples of utilizing advanced plasmonic materials for the realization of dynamic color display are highlighted and put into perspective. The performances, advantages, and disadvantages of different technologies are discussed, with emphasis placed on both the potential and possible limitations of various hybrid materials for dynamic plasmonic color display. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tracking the Dynamic Folding and Unfolding of RNA G-Quadruplexes in Live Cells.

PubMed

Chen, Xiu-Cai; Chen, Shuo-Bin; Dai, Jing; Yuan, Jia-Hao; Ou, Tian-Miao; Huang, Zhi-Shu; Tan, Jia-Heng

2018-04-16

Because of the absence of methods for tracking RNA G-quadruplex dynamics, especially the folding and unfolding of this attractive structure in live cells, understanding of the biological roles of RNA G-quadruplexes is so far limited. Herein, we report a new red-emitting fluorescent probe, QUMA-1, for the selective, continuous, and real-time visualization of RNA G-quadruplexes in live cells. The applications of QUMA-1 in several previously intractable applications, including live-cell imaging of the dynamic folding, unfolding, and movement of RNA G-quadruplexes and the visualization of the unwinding of RNA G-quadruplexes by RNA helicase have been demonstrated. Notably, our real-time results revealed the complexity of the dynamics of RNA G-quadruplexes in live cells. We anticipate that the further application of QUMA-1 in combination with appropriate biological and imaging methods to explore the dynamics of RNA G-quadruplexes will uncover more information about the biological roles of RNA G-quadruplexes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct observation of a single nanoparticle-ubiquitin corona formation

NASA Astrophysics Data System (ADS)

Ding, Feng; Radic, Slaven; Chen, Ran; Chen, Pengyu; Geitner, Nicholas K.; Brown, Jared M.; Ke, Pu Chun

2013-09-01

The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation.The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation. Electronic supplementary information (ESI) available: Experimental and computational methods as well as supporting figures. See DOI: 10.1039/c3nr02147e

Integrated analysis and design of thick composite structures for optimal passive damping characteristics

NASA Technical Reports Server (NTRS)

Saravanos, D. A.

1993-01-01

The development of novel composite mechanics for the analysis of damping in composite laminates and structures and the more significant results of this effort are summarized. Laminate mechanics based on piecewise continuous in-plane displacement fields are described that can represent both intralaminar stresses and interlaminar shear stresses and the associated effects on the stiffness and damping characteristics of a composite laminate. Among other features, the mechanics can accurately model the static and damped dynamic response of either thin or thick composite laminates, as well as, specialty laminates with embedded compliant damping layers. The discrete laminate damping theory is further incorporated into structural analysis methods. In this context, an exact semi-analytical method for the simulation of the damped dynamic response of composite plates was developed. A finite element based method and a specialty four-node plate element were also developed for the analysis of composite structures of variable shape and boundary conditions. Numerous evaluations and applications demonstrate the quality and superiority of the mechanics in predicting the damped dynamic characteristics of composite structures. Finally, additional development was focused on the development of optimal tailoring methods for the design of thick composite structures based on the developed analytical capability. Applications on composite plates illustrated the influence of composite mechanics in the optimal design of composites and the potential for significant deviations in the resultant designs when more simplified (classical) laminate theories are used.

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

NASA Astrophysics Data System (ADS)

Alba, Josephine; Marcaida, Maria Jose; Prieto, Jesus; Montoya, Guillermo; Molina, Rafael; D'Abramo, Marco

2017-12-01

I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.

Comparisons of several aerodynamic methods for application to dynamic loads analyses

NASA Technical Reports Server (NTRS)

Kroll, R. I.; Miller, R. D.

1976-01-01

The results of a study are presented in which the applicability at subsonic speeds of several aerodynamic methods for predicting dynamic gust loads on aircraft, including active control systems, was examined and compared. These aerodynamic methods varied from steady state to an advanced unsteady aerodynamic formulation. Brief descriptions of the structural and aerodynamic representations and of the motion and load equations are presented. Comparisons of numerical results achieved using the various aerodynamic methods are shown in detail. From these results, aerodynamic representations for dynamic gust analyses are identified. It was concluded that several aerodynamic methods are satisfactory for dynamic gust analyses of configurations having either controls fixed or active control systems that primarily affect the low frequency rigid body aircraft response.

Structured Ionomer Thin Films at Water Interface: Molecular Dynamics Simulation Insight

DOE PAGES

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; ...

2017-08-23

Controlling the structure and dynamics of thin films of ionizable polymers at water interfaces is critical to their many applications. As the chemical diversity within one polymer is increased, controlling the structure and dynamics of the polymer, which is a key to their use, becomes a challenge. Here molecular dynamics simulations (MD) are used to obtain molecular insight into the structure and dynamics of thin films of one such macromolecule at the interface with water. The polymer consists of an ABCBA topology with randomly sulfonated polystyrene (C), tethered symmetrically to flexible poly(ethylene- r-propylene) blocks (B), and end-capped by a poly(more » t-butylstyrene) block (A). The compositions of the interfacial and bulk regions of thin films of the ABCBA polymers are followed as a function of exposure time to water. We find that interfacial rearrangements take place where buried ionic segments migrate toward the water interface. The hydrophobic blocks collapse and rearrange to minimize their exposure to water. In conclusion, the water that initially drives interfacial reengagements breaks the ionic clusters within the film, forming a dynamic hydrophilic internal network within the hydrophobic segments.« less

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2005-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook are solicited from the spacecraft structural dynamics testing community.

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2004-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook is solicited from the spacecraft structural dynamics testing community.

Fluorescence-based strategies to investigate the structure and dynamics of aptamer-ligand complexes

NASA Astrophysics Data System (ADS)

Perez-Gonzalez, Cibran; Lafontaine, Daniel; Penedo, J.

2016-08-01

In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labelling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labelled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.

Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes

PubMed Central

Perez-Gonzalez, Cibran; Lafontaine, Daniel A.; Penedo, J. Carlos

2016-01-01

In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques. PMID:27536656

Preserving Lagrangian Structure in Nonlinear Model Reduction with Application to Structural Dynamics

DOE PAGES

Carlberg, Kevin; Tuminaro, Ray; Boggs, Paul

2015-03-11

Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with thesemore » quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.« less

Preserving Lagrangian Structure in Nonlinear Model Reduction with Application to Structural Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlberg, Kevin; Tuminaro, Ray; Boggs, Paul

Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with thesemore » quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.« less

Criteria for structural test

NASA Technical Reports Server (NTRS)

1973-01-01

The results of a study to define criteria and techniques of design, analysis and test which permit the use of a single major structural test article for performing dynamic, fatigue, and static testing are presented. The criteria developed is applicable to both space vehicles and aircraft structures operating in the subsonic or supersonic regime. The feasibility of such an approach was demonstrated by defining test interactions, compatibilities and incompatibilities between the three different types of tests. The results of the study indicate that the single test article concept is feasible with a testing sequence of dynamic test followed by a fatigue and static test.

Applications of solid-state NMR to membrane proteins.

PubMed

Ladizhansky, Vladimir

2017-11-01

Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

On the Use of Material-Dependent Damping in ANSYS for Mode Superposition Transient Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nie, J.; Wei, X.

The mode superposition method is often used for dynamic analysis of complex structures, such as the seismic Category I structures in nuclear power plants, in place of the less efficient full method, which uses the full system matrices for calculation of the transient responses. In such applications, specification of material-dependent damping is usually desirable because complex structures can consist of multiple types of materials that may have different energy dissipation capabilities. A recent review of the ANSYS manual for several releases found that the use of material-dependent damping is not clearly explained for performing a mode superposition transient dynamic analysis.more » This paper includes several mode superposition transient dynamic analyses using different ways to specify damping in ANSYS, in order to determine how material-dependent damping can be specified conveniently in a mode superposition transient dynamic analysis.« less

Dynamically tunable implementation of electromagnetically induced transparency with two coupling graphene-nanostrips in terahertz region

NASA Astrophysics Data System (ADS)

Shu, Chang; Chen, Qing-Guo; Mei, Jin-Shuo; Yin, Jing-Hua

2018-03-01

In this paper, we numerically demonstrated a dynamically tunable implementation of electromagnetically induced transparency (EIT) response with two coupling graphene-nanostrips in terahertz region. Compared to the metal-based structures or separated graphene structures, the Fermi energies of proposed two coupling graphene-nanostrips can be independently tuned by changing bias voltage between the metallic pads and substrate, the EIT window which appears from the near-field coupling between two resonators can be dynamically tuned without reoptimizing and refabricating the structures. As a result, the EIT window has a significant tunable capacity which can realize a higher frequency modulation depth and control the amplitude of transmission peak at a fixed frequency; moreover, the group delay of transmission peak at a fixed frequency with the amplitude of over 0.95 could be dynamically tuned. These results would exhibit potential applications in modulators and tunable slow light devices.

Super-integrable Calogero-type systems admit maximal number of Poisson structures

NASA Astrophysics Data System (ADS)

Gonera, C.; Nutku, Y.

2001-07-01

We present a general scheme for constructing the Poisson structure of super-integrable dynamical systems of which the rational Calogero-Moser system is the most interesting one. This dynamical system is 2 N-dimensional with 2 N-1 first integrals and our construction yields 2 N-1 degenerate Poisson tensors that each admit 2( N-1) Casimirs. Our results are quite generally applicable to all super-integrable systems and form an alternative to the traditional bi-Hamiltonian approach.

Quasielastic neutron scattering with in situ humidity control: Water dynamics in uranyl fluoride

DOE PAGES

Miskowiec, A.; Kirkegaard, M. C.; Herwig, K. W.; ...

2016-03-04

The authors confirm that water vapor pressure is the driving thermodynamic force for the conversion of the anhydrous structure to [(UO 2F 2)(H 2O)] 7 ∙ (H 2O) 4, and they demonstrate the feasibility of extending this approach to aqueous forms of UO 2F 2+ xH 2O. This method has general applicability to systems in which water content itself is a driving variable for structural or dynamical phase transitions.

The harmonic oscillator and nuclear physics

NASA Technical Reports Server (NTRS)

Rowe, D. J.

1993-01-01

The three-dimensional harmonic oscillator plays a central role in nuclear physics. It provides the underlying structure of the independent-particle shell model and gives rise to the dynamical group structures on which models of nuclear collective motion are based. It is shown that the three-dimensional harmonic oscillator features a rich variety of coherent states, including vibrations of the monopole, dipole, and quadrupole types, and rotations of the rigid flow, vortex flow, and irrotational flow types. Nuclear collective states exhibit all of these flows. It is also shown that the coherent state representations, which have their origins in applications to the dynamical groups of the simple harmonic oscillator, can be extended to vector coherent state representations with a much wider range of applicability. As a result, coherent state theory and vector coherent state theory become powerful tools in the application of algebraic methods in physics.

Parallel Processing of Adaptive Meshes with Load Balancing

NASA Technical Reports Server (NTRS)

Das, Sajal K.; Harvey, Daniel J.; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

Many scientific applications involve grids that lack a uniform underlying structure. These applications are often also dynamic in nature in that the grid structure significantly changes between successive phases of execution. In parallel computing environments, mesh adaptation of unstructured grids through selective refinement/coarsening has proven to be an effective approach. However, achieving load balance while minimizing interprocessor communication and redistribution costs is a difficult problem. Traditional dynamic load balancers are mostly inadequate because they lack a global view of system loads across processors. In this paper, we propose a novel and general-purpose load balancer that utilizes symmetric broadcast networks (SBN) as the underlying communication topology, and compare its performance with a successful global load balancing environment, called PLUM, specifically created to handle adaptive unstructured applications. Our experimental results on an IBM SP2 demonstrate that the SBN-based load balancer achieves lower redistribution costs than that under PLUM by overlapping processing and data migration.

Optimal estimation of recurrence structures from time series

NASA Astrophysics Data System (ADS)

beim Graben, Peter; Sellers, Kristin K.; Fröhlich, Flavio; Hutt, Axel

2016-05-01

Recurrent temporal dynamics is a phenomenon observed frequently in high-dimensional complex systems and its detection is a challenging task. Recurrence quantification analysis utilizing recurrence plots may extract such dynamics, however it still encounters an unsolved pertinent problem: the optimal selection of distance thresholds for estimating the recurrence structure of dynamical systems. The present work proposes a stochastic Markov model for the recurrent dynamics that allows for the analytical derivation of a criterion for the optimal distance threshold. The goodness of fit is assessed by a utility function which assumes a local maximum for that threshold reflecting the optimal estimate of the system's recurrence structure. We validate our approach by means of the nonlinear Lorenz system and its linearized stochastic surrogates. The final application to neurophysiological time series obtained from anesthetized animals illustrates the method and reveals novel dynamic features of the underlying system. We propose the number of optimal recurrence domains as a statistic for classifying an animals' state of consciousness.

Surface Modeling, Grid Generation, and Related Issues in Computational Fluid Dynamic (CFD) Solutions

NASA Technical Reports Server (NTRS)

Choo, Yung K. (Compiler)

1995-01-01

The NASA Steering Committee for Surface Modeling and Grid Generation (SMAGG) sponsored a workshop on surface modeling, grid generation, and related issues in Computational Fluid Dynamics (CFD) solutions at Lewis Research Center, Cleveland, Ohio, May 9-11, 1995. The workshop provided a forum to identify industry needs, strengths, and weaknesses of the five grid technologies (patched structured, overset structured, Cartesian, unstructured, and hybrid), and to exchange thoughts about where each technology will be in 2 to 5 years. The workshop also provided opportunities for engineers and scientists to present new methods, approaches, and applications in SMAGG for CFD. This Conference Publication (CP) consists of papers on industry overview, NASA overview, five grid technologies, new methods/ approaches/applications, and software systems.

Functional supramolecular polymers for biomedical applications.

PubMed

Dong, Ruijiao; Zhou, Yongfeng; Huang, Xiaohua; Zhu, Xinyuan; Lu, Yunfeng; Shen, Jian

2015-01-21

As a novel class of dynamic and non-covalent polymers, supramolecular polymers not only display specific structural and physicochemical properties, but also have the ability to undergo reversible changes of structure, shape, and function in response to diverse external stimuli, making them promising candidates for widespread applications ranging from academic research to industrial fields. By an elegant combination of dynamic/reversible structures with exceptional functions, functional supramolecular polymers are attracting increasing attention in various fields. In particular, functional supramolecular polymers offer several unique advantages, including inherent degradable polymer backbones, smart responsiveness to various biological stimuli, and the ease for the incorporation of multiple biofunctionalities (e.g., targeting and bioactivity), thereby showing great potential for a wide range of applications in the biomedical field. In this Review, the trends and representative achievements in the design and synthesis of supramolecular polymers with specific functions are summarized, as well as their wide-ranging biomedical applications such as drug delivery, gene transfection, protein delivery, bio-imaging and diagnosis, tissue engineering, and biomimetic chemistry. These achievements further inspire persistent efforts in an emerging interdisciplin-ary research area of supramolecular chemistry, polymer science, material science, biomedical engineering, and nanotechnology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative analysis of on-orbit dynamic performance of several large antenna concepts

NASA Technical Reports Server (NTRS)

Andersen, G. C.; Garrett, L. B.; Calleson, R. E.

1985-01-01

A comparative analysis of the on-orbit dynamic performance of four large anetanna concepts is presented. Among the antenna concepts evaluated are: the box truss; tetrahedral truss; warp-radial rib; and the hoop and column antenna designs. The characteristics and magnitudes of the antennas' dynamic response were evaluated in terms of structural displacements and member loads incurred during various slew-rate maneuvers. The results of the dynamic response analysis are compared to the design requirements of the Land Mobile Satellite System (LMSS) with respect to surface accuracy, decenter, defocus, and angular rocking. Comments are made on the effectiveness of structural damping and the application of active controls for vibrational response reduction. Schematic illustrations of the antenna design concepts are provided.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

PubMed

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

Dynamic Structure Factor: An Introduction

NASA Astrophysics Data System (ADS)

Sturm, K.

1993-02-01

The doubly differential cross-section for weak inelastic scattering of waves or particles by manybody systems is derived in Born approximation and expressed in terms of the dynamic structure factor according to van Hove. The application of this very general scheme to scattering of neutrons, x-rays and high-energy electrons is discussed briefly. The dynamic structure factor, which is the space and time Fourier transform of the density-density correlation function, is a property of the many-body system independent of the external probe and carries information on the excitation spectrum of the system. The relation of the electronic structure factor to the density-density response function defined in linear-response theory is shown using the fluctuation-dissipation theorem. This is important for calculations, since the response function can be calculated approximately from the independent-particle response function in self-consistent field approximations, such as the random-phase approximation or the local-density approximation of the density functional theory. Since the density-density response function also determines the dielectric function, the dynamic structure can be expressed by the dielectric function.

Data Intensive Systems (DIS) Benchmark Performance Summary

DTIC Science & Technology

2003-08-01

models assumed by today’s conventional architectures. Such applications include model- based Automatic Target Recognition (ATR), synthetic aperture...radar (SAR) codes, large scale dynamic databases/battlefield integration, dynamic sensor- based processing, high-speed cryptanalysis, high speed...distributed interactive and data intensive simulations, data-oriented problems characterized by pointer- based and other highly irregular data structures

High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision

Treesearch

Jonathan P. Dandois; Erle C. Ellis

2013-01-01

High spatial resolution three-dimensional (3D) measurements of vegetation by remote sensing are advancing ecological research and environmental management. However, substantial economic and logistical costs limit this application, especially for observing phenological dynamics in ecosystem structure and spectral traits. Here we demonstrate a new aerial remote sensing...

Teaching Group Dynamics through an Application-Based Learning Approach

ERIC Educational Resources Information Center

Harper, Melinda S.; Allegretti, Christine L.

2015-01-01

The purpose of this study was to demonstrate how a structured experiential course can be used to teach students to lead group discussions. Group dynamics and leadership skills were taught through two teaching strategies in the course: the first method required junior- and senior-level undergraduate students to participate in a process-oriented…

Constraint elimination in dynamical systems

NASA Technical Reports Server (NTRS)

Singh, R. P.; Likins, P. W.

1989-01-01

Large space structures (LSSs) and other dynamical systems of current interest are often extremely complex assemblies of rigid and flexible bodies subjected to kinematical constraints. A formulation is presented for the governing equations of constrained multibody systems via the application of singular value decomposition (SVD). The resulting equations of motion are shown to be of minimum dimension.

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

Evaluation of Structural Robustness against Column Loss: Methodology and Application to RC Frame Buildings.

PubMed

Bao, Yihai; Main, Joseph A; Noh, Sam-Young

2017-08-01

A computational methodology is presented for evaluating structural robustness against column loss. The methodology is illustrated through application to reinforced concrete (RC) frame buildings, using a reduced-order modeling approach for three-dimensional RC framing systems that includes the floor slabs. Comparisons with high-fidelity finite-element model results are presented to verify the approach. Pushdown analyses of prototype buildings under column loss scenarios are performed using the reduced-order modeling approach, and an energy-based procedure is employed to account for the dynamic effects associated with sudden column loss. Results obtained using the energy-based approach are found to be in good agreement with results from direct dynamic analysis of sudden column loss. A metric for structural robustness is proposed, calculated by normalizing the ultimate capacities of the structural system under sudden column loss by the applicable service-level gravity loading and by evaluating the minimum value of this normalized ultimate capacity over all column removal scenarios. The procedure is applied to two prototype 10-story RC buildings, one employing intermediate moment frames (IMFs) and the other employing special moment frames (SMFs). The SMF building, with its more stringent seismic design and detailing, is found to have greater robustness.

Optical methods for non-contact measurements of membranes

NASA Astrophysics Data System (ADS)

Roose, S.; Stockman, Y.; Rochus, P.; Kuhn, T.; Lang, M.; Baier, H.; Langlois, S.; Casarosa, G.

2009-11-01

Structures for space applications very often suffer stringent mass constraints. Lightweight structures are developed for this purpose, through the use of deployable and/or inflatable beams, and thin-film membranes. Their inherent properties (low mass and small thickness) preclude the use of conventional measurement methods (accelerometers and displacement transducers for example) during on-ground testing. In this context, innovative non-contact measurement methods need to be investigated for these stretched membranes. The object of the present project is to review existing measurement systems capable of measuring characteristics of membrane space-structures such as: dot-projection videogrammetry (static measurements), stereo-correlation (dynamic and static measurements), fringe projection (wrinkles) and 3D laser scanning vibrometry (dynamic measurements). Therefore, minimum requirements were given for the study in order to have representative test articles covering a wide range of applications. We present test results obtained with the different methods on our test articles.

Self-assembly of polyelectrolyte surfactant complexes using large scale MD simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby

2014-03-01

Polyelectrolytes (PE) and surfactants are known to form interesting structures with varied properties in aqueous solutions. The morphological details of the PE-surfactant complexes depend on a combination of polymer backbone, electrostatic interactions and hydrophobic interactions. We study the self-assembly of cationic PE and anionic surfactants complexes in dilute condition. The importance of such complexes of PE with oppositely charged surfactants can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate which has applications in industry. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered pearl-necklace structures that have been observed experimentally in biological systems. We investigate many different properties of PE-surfactant complexation for different parameter ranges that are useful for pharmaceutical, engineering and biological applications.

Concept of dynamic memory in economics

NASA Astrophysics Data System (ADS)

Tarasova, Valentina V.; Tarasov, Vasily E.

2018-02-01

In this paper we discuss a concept of dynamic memory and an application of fractional calculus to describe the dynamic memory. The concept of memory is considered from the standpoint of economic models in the framework of continuous time approach based on fractional calculus. We also describe some general restrictions that can be imposed on the structure and properties of dynamic memory. These restrictions include the following three principles: (a) the principle of fading memory; (b) the principle of memory homogeneity on time (the principle of non-aging memory); (c) the principle of memory reversibility (the principle of memory recovery). Examples of different memory functions are suggested by using the fractional calculus. To illustrate an application of the concept of dynamic memory in economics we consider a generalization of the Harrod-Domar model, where the power-law memory is taken into account.

PREFACE: Topics in the application of scattering methods to investigate the structure and dynamics of soft condensed matter

NASA Astrophysics Data System (ADS)

Chen, Sow-Hsin; Baglioni, Piero

2006-09-01

This special issue of Journal of Physics: Condensed Matter gathers together a series of contributions presented at the workshop entitled `Topics in the Application of Scattering Methods to Investigate the Structure and Dynamics of Soft Condensed Matter' held at Pensione Bencista, Fiesole, Italy, a wonderful Italian jewel tucked high in the hills above Florence. This immaculate 14th century villa is a feast for the eyes with antiques and original artwork everywhere you turn, and a stunning view of Florence, overlooking numerous villas and groves of olive trees. The meeting consisted of about 40 invited talks delivered by a selected group of prominent physicists and chemists from the USA, Mexico, Europe and Asia working in the fields of complex and glassy liquids. The topics covered by the talks included: simulations on the liquid-liquid transition phenomenon dynamic crossover in deeply supercooled confined water thermodynamics and dynamics of complex fluids dynamics of interfacial water structural arrest transitions in colloidal systems structure and dynamics in complex systems structure of supramolecular assemblies The choice of topics is obviously heavily biased toward the current interests of the two organizers of the workshop, in view of the fact that one of the incentives for organizing the meeting was to celebrate Sow-Hsin Chen’s life-long scientific activities on the occasion of his 70th birthday. The 21 articles presented in this issue are a state-of-the-art description of the different aspects reported at the workshop from all points of view---experimental, theoretical and numerical. The interdisciplinary nature of the talks should make this special issue of interest to a broad community of scientists involved in the study of the properties of complex fluids, soft condensed matter and disordered glassy systems. We are grateful to the Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Florence, Italy and to the Materials Science Program of the US Department of Energy for their support of the workshop.

Magnetic and optical holonomic manipulation of colloids, structures and topological defects in liquid crystals for characterization of mesoscale self-assembly and dynamics

NASA Astrophysics Data System (ADS)

Varney, Michael C. M.

Colloidal systems find important applications ranging from fabrication of photonic crystals to direct probing of phenomena encountered in atomic crystals and glasses; topics of great interest for physicists exploring a broad range of scientific, industrial and biomedical fields. The ability to accurately control particles of mesoscale size in various liquid host media is usually accomplished through optical trapping methods, which suffer limitations intrinsic to trap laser intensity and force generation. Other limitations are due to colloid properties, such as optical absorptivity, and host properties, such as viscosity, opacity and structure. Therefore, alternative and/or novel methods of colloidal manipulation are of utmost importance in order to advance the state of the art in technical applications and fundamental science. In this thesis, I demonstrate a magnetic-optical holonomic control system to manipulate magnetic and optical colloids in liquid crystals and show that the elastic structure inherent to nematic and cholesteric liquid crystals may be used to assist in tweezing of particles in a manner impossible in other media. Furthermore, I demonstrate the utility of this manipulation in characterizing the structure and microrheology of liquid crystals, and elucidating the energetics and dynamics of colloids interacting with these structures. I also demonstrate the utility of liquid crystal systems as a table top model system to probe topological defects in a manner that may lead to insights into topologically related phenomena in other fields, such as early universe cosmology, sub-atomic and high energy systems, or Skrymionic structures. I explore the interaction of colloid surface anchoring with the structure inherent in cholesteric liquid crystals, and how this affects the periodic dynamics and localization metastability of spherical colloids undergoing a "falling" motion within the sample. These so called "metastable states" cause colloidal dynamics to deviate from Stokes-like behavior at very low Reynolds numbers and is understood by accounting for periodic landscapes of elastic interaction potential between the particle and cholesteric host medium due to surface anchoring. This work extends our understanding of how colloids interact with liquid crystals and topological defects, and introduces a powerful method of colloidal manipulation with many potential applications.

Structure and dynamics of protein waters revealed by radiolysis and mass spectrometry

PubMed Central

Gupta, Sayan; D’Mello, Rhijuta; Chance, Mark R.

2012-01-01

Water is critical for the structure, stability, and functions of macromolecules. Diffraction and NMR studies have revealed structure and dynamics of bound waters at atomic resolution. However, localizing the sites and measuring the dynamics of bound waters, particularly on timescales relevant to catalysis and macromolecular assembly, is quite challenging. Here we demonstrate two techniques: first, temperature-dependent radiolytic hydroxyl radical labeling with a mass spectrometry (MS)-based readout to identify sites of bulk and bound water interactions with surface and internal residue side chains, and second, H218O radiolytic exchange coupled MS to measure the millisecond dynamics of bound water interactions with various internal residue side chains. Through an application of the methods to cytochrome c and ubiquitin, we identify sites of water binding and measure the millisecond dynamics of bound waters in protein crevices. As these MS-based techniques are very sensitive and not protein size limited, they promise to provide unique insights into protein–water interactions and water dynamics for both small and large proteins and their complexes. PMID:22927377

Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction

PubMed Central

Lynch, Diane L.; Hurst, Dow P.; Shore, Derek M.; Pitman, Mike C.; Reggio, Patricia H.

2018-01-01

The cannabinoid type 1 and 2 G-protein-coupled receptors are currently important pharmacological targets with significant drug discovery potential. These receptors have been shown to display functional selectivity or biased agonism, a property currently thought to have substantial therapeutic potential. Although recent advances in crystallization techniques have provided a wealth of structural information about this important class of membrane-embedded proteins, these structures lack dynamical information. In order to fully understand the interplay of structure and function for this important class of proteins, complementary techniques that address the dynamical aspects of their function are required such as NMR as well as a variety of other spectroscopies. Complimentary to these experimental approaches is molecular dynamics, which has been effectively used to help unravel, at the atomic level, the dynamics of ligand binding and activation of these membrane-bound receptors. Here, we discuss and present several representative examples of the application of molecular dynamics simulations to the understanding of the signatures of ligand-binding and -biased signaling at the cannabinoid type 1 and 2 receptors. PMID:28750815

APPLICATION OF CFD SIMULATIONS FOR SHORT-RANGE ATMOSPHERIC DISPERSION OVER OPEN FIELDS AND WITHIN ARRAYS OF BUILDINGS

EPA Science Inventory

Computational Fluid Dynamics (CFD) techniques are increasingly being applied to air quality modeling of short-range dispersion, especially the flow and dispersion around buildings and other geometrically complex structures. The proper application and accuracy of such CFD techniqu...

Analysis of shell-type structures subjected to time-dependent mechanical and thermal loading

NASA Technical Reports Server (NTRS)

Simitses, George J.

1990-01-01

The development of a general mathematical model and solution methodologies for analyzing structural response of thin, metallic shell-like structures under dynamic and/or static thermomechanical loads is examined. In the mathematical model, geometric as well as material-type of nonlinearities are considered. Traditional as well as novel approaches are reported and detailed applications are presented in the appendices. The emphasis for the mathematical model, the related solution schemes, and the applications, is on thermal viscoelastic and viscoplastic phenomena, which can predict creep and ratchetting.

Analysis of shell-type structures subjected to time-dependent mechanical and thermal loading

NASA Technical Reports Server (NTRS)

Simitses, G. J.

1991-01-01

This report deals with the development of a general mathematical model and solution methodology for analyzing the structural response of thin, metallic shell-like structures under dynamic and/or static thermomechanical loads. In the mathematical model, geometric as well as the material-type of nonlinearities are considered. Traditional as well as novel approaches are reported and detailed applications are presented in the appendices. The emphasis for the mathematical model, the related solution schemes, and the applications, is on thermal viscoelastic and viscoplastic phenomena, which can predict creep and ratchetting.

Flexible Animation Computer Program

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.

1990-01-01

FLEXAN (Flexible Animation), computer program animating structural dynamics on Evans and Sutherland PS300-series graphics workstation with VAX/VMS host computer. Typical application is animation of spacecraft undergoing structural stresses caused by thermal and vibrational effects. Displays distortions in shape of spacecraft. Program displays single natural mode of vibration, mode history, or any general deformation of flexible structure. Written in FORTRAN 77.

A preliminary look at control augmented dynamic response of structures

NASA Technical Reports Server (NTRS)

Ryan, R. S.; Jewell, R. E.

1983-01-01

The augmentation of structural characteristics, mass, damping, and stiffness through the use of control theory in lieu of structural redesign or augmentation was reported. The standard single-degree-of-freedom system was followed by a treatment of the same system using control augmentation. The system was extended to elastic structures using single and multisensor approaches and concludes with a brief discussion of potential application to large orbiting space structures.

An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

NASA Technical Reports Server (NTRS)

Lemke, Max; Witsch, Kristian; Quinlan, Daniel

1993-01-01

Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.

CABS-flex: Server for fast simulation of protein structure fluctuations.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

Crashworthy airframe design concepts: Fabrication and testing

NASA Technical Reports Server (NTRS)

Cronkhite, J. D.; Berry, V. L.

1982-01-01

Crashworthy floor concepts applicable to general aviation aircraft metal airframe structures were investigated. Initially several energy absorbing lower fuselage structure concepts were evaluated. Full scale floor sections representative of a twin engine, general aviation airplane lower fuselage structure were designed and fabricated. The floors featured an upper high strength platform with an energy absorbing, crushable structure underneath. Eighteen floors were fabricated that incorporated five different crushable subfloor concepts. The floors were then evaluated through static and dynamic testing. Computer programs NASTRAN and KRASH were used for the static and dynamic analysis of the floor section designs. Two twin engine airplane fuselages were modified to incorporate the most promising crashworthy floor sections for test evaluation.

NASTRAN: User's Experiences

NASA Technical Reports Server (NTRS)

1976-01-01

The application of NASTRAN to a wide variety of static and dynamic structural problems is discussed. The following topics are focused upon: (1) methods of analysis; (2) hydroelastic methods; (3) complete analysis of structures; (4) elements and material studies; (5) critical comparisons with other programs; and (6) pre- and post-processor operations.

2D Automatic body-fitted structured mesh generation using advancing extraction method

USDA-ARS?s Scientific Manuscript database

This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like...

2D automatic body-fitted structured mesh generation using advancing extraction method

USDA-ARS?s Scientific Manuscript database

This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like...

Elucidating Peptide and Protein Structure and Dynamics: UV Resonance Raman Spectroscopy

PubMed Central

Oladepo, Sulayman A.; Xiong, Kan; Hong, Zhenmin; Asher, Sanford A.

2011-01-01

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III3 band and the Cα-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 310- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures. PMID:21379371

Application of Dynamic Mode Decomposition: Temporal Evolution of Flow Structures in an Aneurysm

NASA Astrophysics Data System (ADS)

Conlin, William; Yu, Paulo; Durgesh, Vibhav

2017-11-01

An aneurysm is an enlargement of a weakened arterial wall that can be fatal or debilitating on rupture. Aneurysm hemodynamics is integral to developing an understanding of aneurysm formation, growth, and rupture. The flow in an aneurysm exhibits complex fluid dynamics behavior due to an inherent unsteady inflow condition and its interactions with large-scale flow structures present in the aneurysm. The objective of this study is to identify the large-scale structures in the aneurysm, study temporal behavior, and quantify their interaction with the inflow condition. For this purpose, detailed Particle Image Velocimetry (PIV) measurements were performed at the center plane of an idealized aneurysm model for a range of inflow conditions. Inflow conditions were precisely controlled using a ViVitro SuperPump system. Dynamic Modal Decomposition (DMD) of the velocity field was used to identify coherent structures and their temporal behavior. DMD was successful in capturing the large-scale flow structures and their temporal behavior. A low dimensional approximation to the flow field was obtained with the most relevant dynamic modes and was used to obtain temporal information about the coherent structures and their interaction with the inflow, formation, evolution, and growth.

pH-Driven Reversible Self-Assembly of Micron-Scale DNA Scaffolds.

PubMed

Green, Leopold N; Amodio, Alessia; Subramanian, Hari K K; Ricci, Francesco; Franco, Elisa

2017-12-13

Inspired by cytoskeletal scaffolds that sense and respond dynamically to environmental changes and chemical inputs with a unique capacity for reconfiguration, we propose a strategy that allows the dynamic and reversible control of the growth and breakage of micron-scale synthetic DNA structures upon pH changes. We do so by rationally designing a pH-responsive system composed of synthetic DNA strands that act as pH sensors, regulators, and structural elements. Sensor strands can dynamically respond to pH changes and route regulatory strands to direct the self-assembly of structural elements into tubular structures. This example represents the first demonstration of the reversible assembly and disassembly of micron-scale DNA scaffolds using an external chemical input other than DNA. The capacity to reversibly modulate nanostructure size may promote the development of smart devices for catalysis or drug-delivery applications.

Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space.

PubMed

Schenk, Emily R; Nau, Frederic; Fernandez-Lima, Francisco

2015-06-01

The ability to correlate experimental ion mobility data with candidate structures from theoretical modeling provides a powerful analytical and structural tool for the characterization of biomolecules. In the present paper, a theoretical workflow is described to generate and assign candidate structures for experimental trapped ion mobility and H/D exchange (HDX-TIMS-MS) data following molecular dynamics simulations and statistical filtering. The applicability of the theoretical predictor is illustrated for a peptide and protein example with multiple conformations and kinetic intermediates. The described methodology yields a low computational cost and a simple workflow by incorporating statistical filtering and molecular dynamics simulations. The workflow can be adapted to different IMS scenarios and CCS calculators for a more accurate description of the IMS experimental conditions. For the case of the HDX-TIMS-MS experiments, molecular dynamics in the "TIMS box" accounts for a better sampling of the molecular intermediates and local energy minima.

Dynamic functional connectivity using state-based dynamic community structure: method and application to opioid analgesia.

PubMed

Robinson, Lucy F; Atlas, Lauren Y; Wager, Tor D

2015-03-01

We present a new method, State-based Dynamic Community Structure, that detects time-dependent community structure in networks of brain regions. Most analyses of functional connectivity assume that network behavior is static in time, or differs between task conditions with known timing. Our goal is to determine whether brain network topology remains stationary over time, or if changes in network organization occur at unknown time points. Changes in network organization may be related to shifts in neurological state, such as those associated with learning, drug uptake or experimental conditions. Using a hidden Markov stochastic blockmodel, we define a time-dependent community structure. We apply this approach to data from a functional magnetic resonance imaging experiment examining how contextual factors influence drug-induced analgesia. Results reveal that networks involved in pain, working memory, and emotion show distinct profiles of time-varying connectivity. Copyright © 2014 Elsevier Inc. All rights reserved.

Engineering science and mechanics; Proceedings of the International Symposium, Tainan, Republic of China, December 29-31, 1981. Parts 1 & 2

NASA Astrophysics Data System (ADS)

Hsia, H.-M.; Chou, Y.-L.; Longman, R. W.

1983-07-01

The topics considered are related to measurements and controls in physical systems, the control of large scale and distributed parameter systems, chemical engineering systems, aerospace science and technology, thermodynamics and fluid mechanics, and computer applications. Subjects in structural dynamics are discussed, taking into account finite element approximations in transient analysis, buckling finite element analysis of flat plates, dynamic analysis of viscoelastic structures, the transient analysis of large frame structures by simple models, large amplitude vibration of an initially stressed thick plate, nonlinear aeroelasticity, a sensitivity analysis of a combined beam-spring-mass structure, and the optimal design and aeroelastic investigation of segmented windmill rotor blades. Attention is also given to dynamics and control of mechanical and civil engineering systems, composites, and topics in materials. For individual items see A83-44002 to A83-44061

Incubation under fluid dynamic conditions markedly improves the structural preservation in vitro of explanted skeletal muscles.

PubMed

Carton, Flavia; Calderan, Laura; Malatesta, Manuela

2017-11-28

Explanted organs and tissues represent suitable experimental systems mimicking the functional and structural complexity of the living organism, with positive ethical and economic impact on research activities. However, their preservation in culture is generally limited, thus hindering their application as experimental models for biomedical research. In the present study, we investigated the potential of an innovative fluid dynamic culture system to improve the structural preservation in vitro of explanted mouse skeletal muscles (soleus). We used light and transmission electron microscopy to compare the morphological features of muscles maintained either in multiwell plates under conventional conditions or in a bioreactor mimicking the flow of physiological fluids. Our results demonstrate that fluid dynamic conditions markedly slowed the progressive structural deterioration of the muscle tissue occurring during the permanence in the culture medium, prolonging the preservation of some organelles such as mitochondria up to 48 h.

Incubation under fluid dynamic conditions markedly improves the structural preservation in vitro of explanted skeletal muscles

PubMed Central

Carton, Flavia; Calderan, Laura; Malatesta, Manuela

2017-01-01

Explanted organs and tissues represent suitable experimental systems mimicking the functional and structural complexity of the living organism, with positive ethical and economic impact on research activities. However, their preservation in culture is generally limited, thus hindering their application as experimental models for biomedical research. In the present study, we investigated the potential of an innovative fluid dynamic culture system to improve the structural preservation in vitro of explanted mouse skeletal muscles (soleus). We used light and transmission electron microscopy to compare the morphological features of muscles maintained either in multiwell plates under conventional conditions or in a bioreactor mimicking the flow of physiological fluids. Our results demonstrate that fluid dynamic conditions markedly slowed the progressive structural deterioration of the muscle tissue occurring during the permanence in the culture medium, prolonging the preservation of some organelles such as mitochondria up to 48 h. PMID:29313601

System approach to distributed sensor management

NASA Astrophysics Data System (ADS)

Mayott, Gregory; Miller, Gordon; Harrell, John; Hepp, Jared; Self, Mid

2010-04-01

Since 2003, the US Army's RDECOM CERDEC Night Vision Electronic Sensor Directorate (NVESD) has been developing a distributed Sensor Management System (SMS) that utilizes a framework which demonstrates application layer, net-centric sensor management. The core principles of the design support distributed and dynamic discovery of sensing devices and processes through a multi-layered implementation. This results in a sensor management layer that acts as a System with defined interfaces for which the characteristics, parameters, and behaviors can be described. Within the framework, the definition of a protocol is required to establish the rules for how distributed sensors should operate. The protocol defines the behaviors, capabilities, and message structures needed to operate within the functional design boundaries. The protocol definition addresses the requirements for a device (sensors or processes) to dynamically join or leave a sensor network, dynamically describe device control and data capabilities, and allow dynamic addressing of publish and subscribe functionality. The message structure is a multi-tiered definition that identifies standard, extended, and payload representations that are specifically designed to accommodate the need for standard representations of common functions, while supporting the need for feature-based functions that are typically vendor specific. The dynamic qualities of the protocol enable a User GUI application the flexibility of mapping widget-level controls to each device based on reported capabilities in real-time. The SMS approach is designed to accommodate scalability and flexibility within a defined architecture. The distributed sensor management framework and its application to a tactical sensor network will be described in this paper.

An Evaluation of the Applicability of Damage Tolerance to Dynamic Systems

NASA Technical Reports Server (NTRS)

Forth, Scott C.; Le, Dy; Turnberg, Jay

2005-01-01

The Federal Aviation Administration, the National Aeronautics and Space Administration and the aircraft industry have teamed together to develop methods and guidance for the safe life-cycle management of dynamic systems. Based on the success of the United States Air Force damage tolerance initiative for airframe structure, a crack growth based damage tolerance approach is being examined for implementation into the design and management of dynamic systems. However, dynamic systems accumulate millions of vibratory cycles per flight hour, more than 12,000 times faster than an airframe system. If a detectable crack develops in a dynamic system, the time to failure is extremely short, less than 100 flight hours in most cases, leaving little room for error in the material characterization, life cycle analysis, nondestructive inspection and maintenance processes. In this paper, the authors review the damage tolerant design process focusing on uncertainties that affect dynamic systems and evaluate the applicability of damage tolerance on dynamic systems.

Modeling and Characterization of Electrical Resistivity of Carbon Composite Laminates

NASA Astrophysics Data System (ADS)

Yasuda, Hiromi

Origami has recently received significant interest from the scientific and engineering communities as a method for designing building blocks of engineered structures to enhance their mechanical properties. However, the primary focus has been placed on their kinematic applications by leveraging the compactness and auxeticity of planar origami platforms. In this thesis, we study two different types of volumetric origami structures, Tachi-Miura Polyhedron (TMP) and Triangulated Cylindrical Origami (TCO), hierarchically from a single unit cell level to an assembly of multi-origami cells. We strategically assemble these origami cells into mechanical metamaterials and demonstrate their unique static/dynamic mechanical responses. In particular, these origami structures exhibit tailorable stiffness and strain softening/hardening behaviors, which leads to rich wave dynamics in origami-based architectures such as tunable frequency bands and new types of nonlinear wave propagations. One of the novel waveforms investigated in this thesis is the rarefaction solitary wave arising from strain-softening nature of origami unit cell. This unique wave dynamic mechanism is analyzed in numerical, analytical, and experimental approaches. By leveraging their tailorable folding mechanisms, the origami-based mechanical metamaterials can be used for designing new types of engineering devices and structures, not only for deployable space and disaster relief applications, but also for vibration filtering, impact mitigation, and energy harvesting.

Pressure Studies of Protein Dynamics.

DTIC Science & Technology

1987-02-20

applicable ) Office of Naval Research ONR N00014-86-K-0270 kc. ADDRESS (City, State,and ZIP Code) 10. SOURCE OF FUNDING NUMBERS - PROGRAM PROJECT I TASK IWORK...Pressure Studies of Protein Dynamics 12. PERSONAL AUTHOR(S) Hans Frauenfelder and Robert D. Young 13a. TYPE OF REPORT |13b. TIME COVERED 114 DATE OF...relatioihbetween dynamic structure and function of protein protein dyna -bsey observing the phenomena induced by flash photolysis using near ultravfilet

76 FR 20953 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-14

...., 9700 South Cass Ave., Lemont, IL 60439. Instrument: Mythen 1K Detector System. Manufacturer: Dectris... (RIXS) to study the electronic structure of highly correlated systems. This instrument is unique in that... dynamic range; and a small, lightweight and compact design. Justification for Duty-Free Entry: There are...

EXAMPLE APPLICATION OF CFD SIMULATIONS FOR SHORT-RANGE ATMOSPHERIC DISPERSION OVER THE OPEN FIELDS OF PROJECT PRAIRIE GRASS

EPA Science Inventory

Computational Fluid Dynamics (CFD) techniques are increasingly being applied to air quality modeling of short-range dispersion, especially the flow and dispersion around buildings and other geometrically complex structures. The proper application and accuracy of such CFD techniqu...

A domain decomposition approach to implementing fault slip in finite-element models of quasi-static and dynamic crustal deformation

USGS Publications Warehouse

Aagaard, Brad T.; Knepley, M.G.; Williams, C.A.

2013-01-01

We employ a domain decomposition approach with Lagrange multipliers to implement fault slip in a finite-element code, PyLith, for use in both quasi-static and dynamic crustal deformation applications. This integrated approach to solving both quasi-static and dynamic simulations leverages common finite-element data structures and implementations of various boundary conditions, discretization schemes, and bulk and fault rheologies. We have developed a custom preconditioner for the Lagrange multiplier portion of the system of equations that provides excellent scalability with problem size compared to conventional additive Schwarz methods. We demonstrate application of this approach using benchmarks for both quasi-static viscoelastic deformation and dynamic spontaneous rupture propagation that verify the numerical implementation in PyLith.

Kentucky geotechnical database.

DOT National Transportation Integrated Search

2005-03-01

Development of a comprehensive dynamic, geotechnical database is described. Computer software selected to program the client/server application in windows environment, components and structure of the geotechnical database, and primary factors cons...

Handling of subpixel structures in the application of satellite derived irradiance data for solar energy system analysis - a review

NASA Astrophysics Data System (ADS)

Beyer, Hans Georg

2016-04-01

With the increasing availability of satellite derived irradiance information, this type of data set is more and more in use for the design and operation of solar energy systems, most notably PV- and CSP-systems. By this, the need for data measured on-site is reduced. However, due to basic limitations of the satellite-derived data, several requirements put by the intended application cannot be coped with this data type directly. Traw satellite information has to be enhanced in both space and time resolution by additional information to be fully applicable for all aspects of the modelling od solar energy systems. To cope with this problem, several individual and collaborative projects had been performed in the recent years or are ongoing. Approaches are on one hand based on pasting synthesized high-resolution data into the low-resolution original sets. Pre-requite is an appropriate model, validated against real world data. For the case of irradiance data, these models can be extracted either directly from ground measured data sets or from data referring to the cloud situation as gained from the images of sky cameras or from monte -carlo initialized physical models. The current models refer to the spatial structure of the cloud fields. Dynamics are imposed by moving the cloud structures according to a large scale cloud motion vector, either extracted from the dynamics interfered from consecutive satellite images or taken from a meso-scale meteorological model. Dynamic irradiance information is then derived from the cloud field structure and the cloud motion vector. This contribution, which is linked to subtask A - Solar Resource Applications for High Penetration of Solar Technologies - of IEA SHC task 46, will present the different approaches and discuss examples in view of validation, need for auxiliary information and respective general applicability.

MSTV Mini-Symposium Preview

DTIC Science & Technology

2009-08-12

Man-In- The-Loop Simulation Integration & Demonstrators FTTS JLTV Future Force MRAP Thermal / CFD Crew Safety Structures/Durability Blast Dynamics ...Scott Stilson – General Dynamics Land Systems Chief Engineer, Stryker Modernization (S-Mod) Program The Application of Modeling and Simulation to the S...Military Ground Vehicles Nammalwar Purushothaman, Paramsothy Jayakumar & James Critchley – BAE Systems Sandip Datta & Venkat Pisipati – TAC World Wide

Dynamic Pattern Formation in Electron-Beam-Induced Etching [Emergent formation of dynamic topographic patterns in electron beam induced etching

DOE PAGES

Martin, Aiden A.; Bahm, Alan; Bishop, James; ...

2015-12-15

Here, we report highly ordered topographic patterns that form on the surface of diamond, span multiple length scales, and have a symmetry controlled by the precursor gas species used in electron-beam-induced etching (EBIE). The pattern formation dynamics reveals an etch rate anisotropy and an electron energy transfer pathway that is overlooked by existing EBIE models. Therefore, we, modify established theory such that it explains our results and remains universally applicable to EBIE. Furthermore, the patterns can be exploited in controlled wetting, optical structuring, and other emerging applications that require nano- and microscale surface texturing of a wide band-gap material.

A Novel Shape Parameterization Approach

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

1999-01-01

This paper presents a novel parameterization approach for complex shapes suitable for a multidisciplinary design optimization application. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft objects animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in a similar manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminated plate structures) and high-fidelity analysis tools (e.g., nonlinear computational fluid dynamics and detailed finite element modeling). This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, and camber. The results are presented for a multidisciplinary design optimization application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, performance, and a simple propulsion module.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

Chemically Patterned Inverse Opal Created by a Selective Photolysis Modification Process.

PubMed

Tian, Tian; Gao, Ning; Gu, Chen; Li, Jian; Wang, Hui; Lan, Yue; Yin, Xianpeng; Li, Guangtao

2015-09-02

Anisotropic photonic crystal materials have long been pursued for their broad applications. A novel method for creating chemically patterned inverse opals is proposed here. The patterning technique is based on selective photolysis of a photolabile polymer together with postmodification on released amine groups. The patterning method allows regioselective modification within an inverse opal structure, taking advantage of selective chemical reaction. Moreover, combined with the unique signal self-reporting feature of the photonic crystal, the fabricated structure is capable of various applications, including gradient photonic bandgap and dynamic chemical patterns. The proposed method provides the ability to extend the structural and chemical complexity of the photonic crystal, as well as its potential applications.

Architectural Visualization of C/C++ Source Code for Program Comprehension

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panas, T; Epperly, T W; Quinlan, D

2006-09-01

Structural and behavioral visualization of large-scale legacy systems to aid program comprehension is still a major challenge. The challenge is even greater when applications are implemented in flexible and expressive languages such as C and C++. In this paper, we consider visualization of static and dynamic aspects of large-scale scientific C/C++ applications. For our investigation, we reuse and integrate specialized analysis and visualization tools. Furthermore, we present a novel layout algorithm that permits a compressive architectural view of a large-scale software system. Our layout is unique in that it allows traditional program visualizations, i.e., graph structures, to be seen inmore » relation to the application's file structure.« less

Non-Invasive Visualization and Quantitation of Cardiovascular Structure and Function.

ERIC Educational Resources Information Center

Ritman, E. L.; And Others

1979-01-01

Described is a new approach to investigative physiology based on computerized transaxial tomography, in which visualization and measurement of the internal structure of the cardiopulmonary system is possible without postmortem, biopsy, or vivisection procedures. Examples are given for application of the Dynamic Spatial Reconstructor (DSR). (CS)

Research in nonlinear structural and solid mechanics

NASA Technical Reports Server (NTRS)

Mccomb, H. G., Jr. (Compiler); Noor, A. K. (Compiler)

1980-01-01

Nonlinear analysis of building structures and numerical solution of nonlinear algebraic equations and Newton's method are discussed. Other topics include: nonlinear interaction problems; solution procedures for nonlinear problems; crash dynamics and advanced nonlinear applications; material characterization, contact problems, and inelastic response; and formulation aspects and special software for nonlinear analysis.

Experimental validation of docking and capture using space robotics testbeds

NASA Technical Reports Server (NTRS)

Spofford, John; Schmitz, Eric; Hoff, William

1991-01-01

This presentation describes the application of robotic and computer vision systems to validate docking and capture operations for space cargo transfer vehicles. Three applications are discussed: (1) air bearing systems in two dimensions that yield high quality free-flying, flexible, and contact dynamics; (2) validation of docking mechanisms with misalignment and target dynamics; and (3) computer vision technology for target location and real-time tracking. All the testbeds are supported by a network of engineering workstations for dynamic and controls analyses. Dynamic simulation of multibody rigid and elastic systems are performed with the TREETOPS code. MATRIXx/System-Build and PRO-MATLAB/Simulab are the tools for control design and analysis using classical and modern techniques such as H-infinity and LQG/LTR. SANDY is a general design tool to optimize numerically a multivariable robust compensator with a user-defined structure. Mathematica and Macsyma are used to derive symbolically dynamic and kinematic equations.

Impact of Hydrologic Variability on Ecosystem Dynamics and the Sustainable Use of Soil and Water Resources

NASA Astrophysics Data System (ADS)

Porporato, A. M.

2013-05-01

We discuss the key processes by which hydrologic variability affects the probabilistic structure of soil moisture dynamics in water-controlled ecosystems. These in turn impact biogeochemical cycling and ecosystem structure through plant productivity and biodiversity as well as nitrogen availability and soil conditions. Once the long-term probabilistic structure of these processes is quantified, the results become useful to understand the impact of climatic changes and human activities on ecosystem services, and can be used to find optimal strategies of water and soil resources management under unpredictable hydro-climatic fluctuations. Particular applications regard soil salinization, phytoremediation and optimal stochastic irrigation.

Structural drift: the population dynamics of sequential learning.

PubMed

Crutchfield, James P; Whalen, Sean

2012-01-01

We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream "teacher" and then pass samples from the model to their downstream "student". It extends the population dynamics of genetic drift, recasting Kimura's selectively neutral theory as a special case of a generalized drift process using structured populations with memory. We examine the diffusion and fixation properties of several drift processes and propose applications to learning, inference, and evolution. We also demonstrate how the organization of drift process space controls fidelity, facilitates innovations, and leads to information loss in sequential learning with and without memory.

Structure and dynamics of mica-confined films of [C10C1Pyrr][NTf2] ionic liquid

NASA Astrophysics Data System (ADS)

Freitas, Adilson Alves de; Shimizu, Karina; Smith, Alexander M.; Perkin, Susan; Canongia Lopes, José Nuno

2018-05-01

The structure of the ionic liquid 1-decyl-1-methylpyrrolidinium bis[(trifluoromethane)sulfonyl]imide, [C10C1Pyrr][NTf2], has been probed using Molecular Dynamics (MD) simulations. The simulations endeavour to model the behaviour of the ionic liquid in bulk isotropic conditions and also at interfaces and in confinement. The MD results have been confronted and validated with scattering and surface force experiments reported in the literature. The calculated structure factors, distribution functions, and density profiles were able to provide molecular and mechanistic insights into the properties of these long chain ionic liquids under different conditions, in particular those that lead to the formation of multi-layered ionic liquid films in confinement. Other properties inaccessible to experiment such as in-plane structures and relaxation rates within the films have also been analysed. Overall the work contributes structural and dynamic information relevant to many applications of ionic liquids with long alkyl chains, ranging from nanoparticle synthesis to lubrication.

Broad frequency band full field measurements for advanced applications: Point-wise comparisons between optical technologies

NASA Astrophysics Data System (ADS)

Zanarini, Alessandro

2018-01-01

The progress of optical systems gives nowadays at disposal on lightweight structures complex dynamic measurements and modal tests, each with its own advantages, drawbacks and preferred usage domains. It is thus more easy than before to obtain highly spatially defined vibration patterns for many applications in vibration engineering, testing and general product development. The potential of three completely different technologies is here benchmarked on a common test rig and advanced applications. SLDV, dynamic ESPI and hi-speed DIC are here first deployed in a complex and unique test on the estimation of FRFs with high spatial accuracy from a thin vibrating plate. The latter exhibits a broad band dynamics and high modal density in the common frequency domain where the techniques can find an operative intersection. A peculiar point-wise comparison is here addressed by means of discrete geometry transforms to put all the three technologies on trial at each physical point of the surface. Full field measurement technologies cannot estimate only displacement fields on a refined grid, but can exploit the spatial consistency of the results through neighbouring locations by means of numerical differentiation operators in the spatial domain to obtain rotational degrees of freedom and superficial dynamic strain distributions, with enhanced quality, compared to other technologies in literature. Approaching the task with the aid of superior quality receptance maps from the three different full field gears, this work calculates and compares rotational and dynamic strain FRFs. Dynamic stress FRFs can be modelled directly from the latter, by means of a constitutive model, avoiding the costly and time-consuming steps of building and tuning a numerical dynamic model of a flexible component or a structure in real life conditions. Once dynamic stress FRFs are obtained, spectral fatigue approaches can try to predict the life of a component in many excitation conditions. Different spectral shaping of the excitation can easily be used to enhance the comparison in the framework of any of the spectral approaches for fatigue life calculations, highlighting benefits and drawbacks of a direct experimental approach to failure and risk assessment in structural dynamics when dealing with complex patterns in real-life testing. Are optical measurements and spatially dense datasets really effective in advanced model updating of lightweight structures with complex structural dynamics? The noise shown in the raw signal of some experiments may pose issues in proficiently exploiting the added data in a fruitful model updating procedure. Model updating results are here compared between scanning and native full field technologies, with comments and details on the test rig, on the advantages and drawbacks of the approaches. The identification of EMA models highlights the increasing quality of shapes that can be obtained from native full field high resolution gears, against that (some time unexpectedly poor) of SLDV tested.

Modelling and Simulation of the Dynamics of the Antigen-Specific T Cell Response Using Variable Structure Control Theory.

PubMed

Anelone, Anet J N; Spurgeon, Sarah K

2016-01-01

Experimental and mathematical studies in immunology have revealed that the dynamics of the programmed T cell response to vigorous infection can be conveniently modelled using a sigmoidal or a discontinuous immune response function. This paper hypothesizes strong synergies between this existing work and the dynamical behaviour of engineering systems with a variable structure control (VSC) law. These findings motivate the interpretation of the immune system as a variable structure control system. It is shown that dynamical properties as well as conditions to analytically assess the transition from health to disease can be developed for the specific T cell response from the theory of variable structure control. In particular, it is shown that the robustness properties of the specific T cell response as observed in experiments can be explained analytically using a VSC perspective. Further, the predictive capacity of the VSC framework to determine the T cell help required to overcome chronic Lymphocytic Choriomeningitis Virus (LCMV) infection is demonstrated. The findings demonstrate that studying the immune system using variable structure control theory provides a new framework for evaluating immunological dynamics and experimental observations. A modelling and simulation tool results with predictive capacity to determine how to modify the immune response to achieve healthy outcomes which may have application in drug development and vaccine design.

Lessons from bacterial homolog of tubulin, FtsZ for microtubule dynamics.

PubMed

Battaje, Rachana Rao; Panda, Dulal

2017-09-01

FtsZ, a homolog of tubulin, is found in almost all bacteria and archaea where it has a primary role in cytokinesis. Evidence for structural homology between FtsZ and tubulin came from their crystal structures and identification of the GTP box. Tubulin and FtsZ constitute a distinct family of GTPases and show striking similarities in many of their polymerization properties. The differences between them, more so, the complexities of microtubule dynamic behavior in comparison to that of FtsZ, indicate that the evolution to tubulin is attributable to the incorporation of the complex functionalities in higher organisms. FtsZ and microtubules function as polymers in cell division but their roles differ in the division process. The structural and partial functional homology has made the study of their dynamic properties more interesting. In this review, we focus on the application of the information derived from studies on FtsZ dynamics to study microtubule dynamics and vice versa. The structural and functional aspects that led to the establishment of the homology between the two proteins are explained to emphasize the network of FtsZ and microtubule studies and how they are connected. © 2017 Society for Endocrinology.

Application of Lanczos vectors to control design of flexible structures

NASA Technical Reports Server (NTRS)

Craig, Roy R., Jr.; Su, Tzu-Jeng

1990-01-01

This report covers research conducted during the first year of the two-year grant. The research, entitled 'Application of Lanczos Vectors to Control Design of Flexible Structures' concerns various ways to obtain reduced-order mathematical models for use in dynamic response analyses and in control design studies. This report summarizes research described in several reports and papers that were written under this contract. Extended abstracts are presented for technical papers covering the following topics: controller reduction by preserving impulse response energy; substructuring decomposition and controller synthesis; model reduction methods for structural control design; and recent literature on structural modeling, identification, and analysis.

Evaluation of the temporal structure of postural sway fluctuations based on a comprehensive set of analysis tools

NASA Astrophysics Data System (ADS)

Kirchner, M.; Schubert, P.; Schmidtbleicher, D.; Haas, C. T.

2012-10-01

The analysis of postural control has a long history. Traditionally, the amount of body sway is solely used as an index of postural stability. Although this leads to some extent to an effective evaluation of balance performance, the control mechanisms involved have not yet been fully understood. The concept of nonlinear dynamics suggests that variability in the motor output is not randomness but structure, providing the stimulus to reveal the functionality of postural sway. The present work evaluates sway dynamics by means of COP excursions in a quiet standing task versus a dual-task condition in three different test times (30, 60, 300 s). Besides the application of traditional methods-which estimate the overall size of sway-the temporal pattern of body sway was quantified via wavelet transform, multiscale entropy and fractal analysis. We found higher sensitivity of the structural parameters to modulations of postural control strategies and partly an improved evaluation of sway dynamics in longer recordings. It could be shown that postural control modifications take place on different timescales corresponding to the interplay of the sensory systems. A continued application of nonlinear analysis can help to better understand postural control mechanisms.

Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins.

PubMed

Kirubakaran, Palani; Pfeiferová, Lucie; Boušová, Kristýna; Bednarova, Lucie; Obšilová, Veronika; Vondrášek, Jiří

2016-10-01

Artificial multidomain proteins with enhanced structural and functional properties can be utilized in a broad spectrum of applications. The design of chimeric fusion proteins utilizing protein domains or one-domain miniproteins as building blocks is an important advancement for the creation of new biomolecules for biotechnology and medical applications. However, computational studies to describe in detail the dynamics and geometry properties of two-domain constructs made from structurally and functionally different proteins are lacking. Here, we tested an in silico design strategy using all-atom explicit solvent molecular dynamics simulations. The well-characterized PDZ3 and SH3 domains of human zonula occludens (ZO-1) (3TSZ), along with 5 artificial domains and 2 types of molecular linkers, were selected to construct chimeric two-domain molecules. The influence of the artificial domains on the structure and dynamics of the PDZ3 and SH3 domains was determined using a range of analyses. We conclude that the artificial domains can function as allosteric modulators of the PDZ3 and SH3 domains. Proteins 2016; 84:1358-1374. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

High frequency flow-structural interaction in dense subsonic fluids

NASA Technical Reports Server (NTRS)

Liu, Baw-Lin; Ofarrell, J. M.

1995-01-01

Prediction of the detailed dynamic behavior in rocket propellant feed systems and engines and other such high-energy fluid systems requires precise analysis to assure structural performance. Designs sometimes require placement of bluff bodies in a flow passage. Additionally, there are flexibilities in ducts, liners, and piping systems. A design handbook and interactive data base have been developed for assessing flow/structural interactions to be used as a tool in design and development, to evaluate applicable geometries before problems develop, or to eliminate or minimize problems with existing hardware. This is a compilation of analytical/empirical data and techniques to evaluate detailed dynamic characteristics of both the fluid and structures. These techniques have direct applicability to rocket engine internal flow passages, hot gas drive systems, and vehicle propellant feed systems. Organization of the handbook is by basic geometries for estimating Strouhal numbers, added mass effects, mode shapes for various end constraints, critical onset flow conditions, and possible structural response amplitudes. Emphasis is on dense fluids and high structural loading potential for fatigue at low subsonic flow speeds where high-frequency excitations are possible. Avoidance and corrective measure illustrations are presented together with analytical curve fits for predictions compiled from a comprehensive data base.

Adding dynamic rules to self-organizing fuzzy systems

NASA Technical Reports Server (NTRS)

Buhusi, Catalin V.

1992-01-01

This paper develops a Dynamic Self-Organizing Fuzzy System (DSOFS) capable of adding, removing, and/or adapting the fuzzy rules and the fuzzy reference sets. The DSOFS background consists of a self-organizing neural structure with neuron relocation features which will develop a map of the input-output behavior. The relocation algorithm extends the topological ordering concept. Fuzzy rules (neurons) are dynamically added or released while the neural structure learns the pattern. The DSOFS advantages are the automatic synthesis and the possibility of parallel implementation. A high adaptation speed and a reduced number of neurons is needed in order to keep errors under some limits. The computer simulation results are presented in a nonlinear systems modelling application.

Research on dynamic performance design of mobile phone application based on context awareness

NASA Astrophysics Data System (ADS)

Bo, Zhang

2018-05-01

It aims to explore the dynamic performance of different mobile phone applications and the user's cognitive differences, reduce the cognitive burden, and enhance the sense of experience. By analyzing the dynamic design performance in four different interactive contexts, and constructing the framework of information service process in the interactive context perception and the two perception principles of the cognitive consensus between designer and user, and the two kinds of knowledge in accordance with the perception principles. The analysis of the context will help users sense the dynamic performance more intuitively, so that the details of interaction will be performed more vividly and smoothly, thus enhance user's experience in the interactive process. The common perception experience enables designers and users to produce emotional resonance in different interactive contexts, and help them achieve rapid understanding of interactive content and perceive the logic and hierarchy of the content and the structure, therefore the effectiveness of mobile applications will be improved.

Biophysical EPR Studies Applied to Membrane Proteins

PubMed Central

Sahu, Indra D; Lorigan, Gary A

2015-01-01

Membrane proteins are very important in controlling bioenergetics, functional activity, and initializing signal pathways in a wide variety of complicated biological systems. They also represent approximately 50% of the potential drug targets. EPR spectroscopy is a very popular and powerful biophysical tool that is used to study the structural and dynamic properties of membrane proteins. In this article, a basic overview of the most commonly used EPR techniques and examples of recent applications to answer pertinent structural and dynamic related questions on membrane protein systems will be presented. PMID:26855825

Entering an era of dynamic structural biology….

PubMed

Orville, Allen M

2018-05-31

A recent paper in BMC Biology presents a general method for mix-and-inject serial crystallography, to facilitate the visualization of enzyme intermediates via time-resolved serial femtosecond crystallography (tr-SFX). They apply their method to resolve in near atomic detail the cleavage and inactivation of the antibiotic ceftriaxone by a β-lactamase enzyme from Mycobacterium tuberculosis. Their work demonstrates the general applicability of time-resolved crystallography, from which dynamic structures, at atomic resolution, can be obtained.See research article: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-018-0524-5 .

Dynamic characteristics of specialty composite structures with embedded damping layers

NASA Technical Reports Server (NTRS)

Saravanos, D. A.; Chamis, C. C.

1993-01-01

Damping mechanics for simulating the damped dynamic characteristics in specialty composite structures with compliant interlaminar damping layers are presented. Finite-element based mechanics incorporating a discrete layer (or layer-wise) laminate damping theory are utilized to represent general laminate configurations in terms of lay-up and fiber orientation angles, cross-sectional thickness, shape, and boundary conditions. Evaluations of the method with exact solutions and experimental data illustrate the accuracy of the method. Additional applications investigate the potential for significant damping enhancement in angle-ply composite laminates with cocured interlaminar damping layers.

NASA Sun-Earth Connections Theory Program: The Structure and Dynamics of the Solar Corona and Inner Heliosphere

NASA Technical Reports Server (NTRS)

Mikic, Zoran; Grebowsky, Joseph M. (Technical Monitor)

2001-01-01

This report covers technical progress during the fourth quarter of the second year of NASA Sun-Earth Connections Theory Program (SECTP) contract 'The Structure and Dynamics of the Solar Corona and Inner Heliosphere,' NAS5-99188, between NASA and Science Applications International Corporation, and covers the period May 16,2001 to August 15, 2001. Under this contract SAIC and the University of California, Irvine (UCI) have conducted research into theoretical modeling of active regions, the solar corona, and the inner heliosphere, using the MHD model.

The Structure and Dynamics of the Solar Corona and Inner Heliosphere

NASA Technical Reports Server (NTRS)

Mikic, Zoran; Grebowsky, J. (Technical Monitor)

2002-01-01

This report covers technical progress during the fourth quarter of the second year of NASA Sun-Earth Connections Theory Program (SECTP) contract "The Structure and Dynamics of the Solar Corona and Inner Heliosphere," NAS5-99188, between NASA and Science Applications International Corporation (SAIC), and covers the period May 16, 2001 to August 15, 2001. Under this contract SAIC and the University of California, Irvine (UCI) have conducted research into theoretical modeling of active regions, the solar corona, and the inner heliosphere, using the MHD (magnetohydrodynamic) model.

Workshop on High-Field NMR and Biological Applications

NASA Astrophysics Data System (ADS)

Scientists at the Pacific Northwest Laboratory have been working toward the establishment of a new Molecular Science Research Center (MSRC). The primary scientific thrust of this new research center is in the areas of theoretical chemistry, chemical dynamics, surface and interfacial science, and studies on the structure and interactions of biological macromolecules. The MSRC will provide important new capabilities for studies on the structure of biological macromolecules. The MSRC program includes several types of advanced spectroscopic techniques for molecular structure analysis, and a theory and modeling laboratory for molecular mechanics/dynamics calculations and graphics. It is the goal to closely integrate experimental and theoretical studies on macromolecular structure, and to join these research efforts with those of the molecular biological programs to provide new insights into the structure/function relationships of biological macromolecules. One of the areas of structural biology on which initial efforts in the MSRC will be focused is the application of high field, 2-D NMR to the study of biological macromolecules. First, there is interest in obtaining 3-D structural information on large proteins and oligonucleotides. Second, one of the primary objectives is to closely link theoretical approaches to molecular structure analysis with the results obtained in experimental research using NMR and other spectroscopies.

Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.

PubMed

Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang

2016-09-14

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.

Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Futera, Zdenek; English, Niall J.

2017-07-01

The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

PubMed Central

Paquet, Eric; Viktor, Herna L.

2015-01-01

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262

Revealing networks from dynamics: an introduction

NASA Astrophysics Data System (ADS)

Timme, Marc; Casadiego, Jose

2014-08-01

What can we learn from the collective dynamics of a complex network about its interaction topology? Taking the perspective from nonlinear dynamics, we briefly review recent progress on how to infer structural connectivity (direct interactions) from accessing the dynamics of the units. Potential applications range from interaction networks in physics, to chemical and metabolic reactions, protein and gene regulatory networks as well as neural circuits in biology and electric power grids or wireless sensor networks in engineering. Moreover, we briefly mention some standard ways of inferring effective or functional connectivity.

The relationship between structure and function in locally observed complex networks

NASA Astrophysics Data System (ADS)

Comin, Cesar H.; Viana, Matheus P.; Costa, Luciano da F.

2013-01-01

Recently, studies looking at the small scale interactions taking place in complex networks have started to unveil the wealth of interactions that occur between groups of nodes. Such findings make the claim for a new systematic methodology to quantify, at node level, how dynamics are influenced (or differentiated) by the structure of the underlying system. Here we define a new measure that, based on the dynamical characteristics obtained for a large set of initial conditions, compares the dynamical behavior of the nodes present in the system. Through this measure, we find that the geographic and Barabási-Albert models have a high capacity for generating networks that exhibit groups of nodes with distinct dynamics compared to the rest of the network. The application of our methodology is illustrated with respect to two real systems. In the first we use the neuronal network of the nematode Caenorhabditis elegans to show that the interneurons of the ventral cord of the nematode present a very large dynamical differentiation when compared to the rest of the network. The second application concerns the SIS epidemic model on an airport network, where we quantify how different the distribution of infection times of high and low degree nodes can be, when compared to the expected value for the network.

Control of Flexible Structures (COFS) Flight Experiment Background and Description

NASA Technical Reports Server (NTRS)

Hanks, B. R.

1985-01-01

A fundamental problem in designing and delivering large space structures to orbit is to provide sufficient structural stiffness and static configuration precision to meet performance requirements. These requirements are directly related to control requirements and the degree of control system sophistication available to supplement the as-built structure. Background and rationale are presented for a research study in structures, structural dynamics, and controls using a relatively large, flexible beam as a focus. This experiment would address fundamental problems applicable to large, flexible space structures in general and would involve a combination of ground tests, flight behavior prediction, and instrumented orbital tests. Intended to be multidisciplinary but basic within each discipline, the experiment should provide improved understanding and confidence in making design trades between structural conservatism and control system sophistication for meeting static shape and dynamic response/stability requirements. Quantitative results should be obtained for use in improving the validity of ground tests for verifying flight performance analyses.

Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations

PubMed Central

Deco, Gustavo; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-01-01

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure–function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure–function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications. PMID:23825427

A preliminary structural analysis of space-based inflatable tubular frame structures

NASA Technical Reports Server (NTRS)

Main, John A.; Peterson, Steven W.; Strauss, Alvin M.

1992-01-01

The use of inflatable structures has often been proposed for aerospace and planetary applications. The advantages of such structures include low launch weight and easy assembly. The use of inflatables for applications requiring very large frame structures intended for aerospace use are proposed. In order to consider using an inflated truss, the structural behavior of the inflated frame must be examined. The statics of inflated tubes as beams was discussed in the literature, but the dynamics of these elements has not received much attention. In an effort to evaluate the vibration characteristics of the inflated beam a series of free vibration tests of an inflated fabric cantilevers were performed. Results of the tests are presented and models for system behavior posed.

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications.

PubMed

Du, Likai; Lan, Zhenggang

2015-04-14

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Ultrafast Dynamic Pressure Sensors Based on Graphene Hybrid Structure.

PubMed

Liu, Shanbiao; Wu, Xing; Zhang, Dongdong; Guo, Congwei; Wang, Peng; Hu, Weida; Li, Xinming; Zhou, Xiaofeng; Xu, Hejun; Luo, Chen; Zhang, Jian; Chu, Junhao

2017-07-19

Mechanical flexible electronic skin has been focused on sensing various physical parameters, such as pressure and temperature. The studies of material design and array-accessible devices are the building blocks of strain sensors for subtle pressure sensing. Here, we report a new and facile preparation of a graphene hybrid structure with an ultrafast dynamic pressure response. Graphene oxide nanosheets are used as a surfactant to prevent graphene restacking in aqueous solution. This graphene hybrid structure exhibits a frequency-independent pressure resistive sensing property. Exceeding natural skin, such pressure sensors, can provide transient responses from static up to 10 000 Hz dynamic frequencies. Integrated by the controlling system, the array-accessible sensors can manipulate a robot arm and self-rectify the temperature of a heating blanket. This may pave a path toward the future application of graphene-based wearable electronics.

Study of Nanocomposites of Amino Acids and Organic Polyethers by Means of Mass Spectrometry and Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Zobnina, V. G.; Kosevich, M. V.; Chagovets, V. V.; Boryak, O. A.

A problem of elucidation of structure of nanomaterials based on combination of proteins and polyether polymers is addressed on the monomeric level of single amino acids and oligomers of PEG-400 and OEG-5 polyethers. Efficiency of application of combined approach involving experimental electrospray mass spectrometry and computer modeling by molecular dynamics simulation is demonstrated. It is shown that oligomers of polyethers form stable complexes with amino acids valine, proline, histidine, glutamic, and aspartic acids. Molecular dynamics simulation has shown that stabilization of amino acid-polyether complexes is achieved due to winding of the polymeric chain around charged groups of amino acids. Structural motives revealed for complexes of single amino acids with polyethers can be realized in structures of protein-polyether nanoparticles currently designed for drug delivery.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

PubMed Central

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques. PMID:25721341

Dynamic response mitigation of floating wind turbine platforms using tuned liquid column dampers.

PubMed

Jaksic, V; Wright, C S; Murphy, J; Afeef, C; Ali, S F; Mandic, D P; Pakrashi, V

2015-02-28

In this paper, we experimentally study and compare the effects of three combinations of multiple tuned liquid column dampers (MTLCDs) on the dynamic performance of a model floating tension-leg platform (TLP) structure in a wave basin. The structural stability and safety of the floating structure during operation and maintenance is of concern for the performance of a renewable energy device that it might be supporting. The dynamic responses of the structure should thus be limited for these renewable energy devices to perform as intended. This issue is particularly important during the operation of a TLP in extreme weather conditions. Tuned liquid column dampers (TLCDs) can use the power of sloshing water to reduce surge motions of a floating TLP exposed to wind and waves. This paper demonstrates the potential of MTLCDs in reducing dynamic responses of a scaled TLP model through an experimental study. The potential of using output-only statistical markers for monitoring changes in structural conditions is also investigated through the application of a delay vector variance (DVV) marker for different conditions of control for the experiments. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Structural fluctuation governed dynamic diradical character in pentacene.

PubMed

Yang, Hongfang; Chen, Mengzhen; Song, Xinyu; Bu, Yuxiang

2015-06-07

We unravel intriguing dynamical diradical behavior governed by structural fluctuation in pentacene using ab initio molecular dynamics simulation. In contrast to static equilibrium configuration of pentacene with a closed-shell ground state without diradical character, due to structural fluctuation, some of its dynamical snapshot configurations exhibit an open-shell broken-symmetry singlet ground state with diradical character, and such diradical character presents irregular pulsing behavior in time evolution. Not all structural changes can lead to diradical character, only those involving the shortening of cross-linking C-C bonds and variations of the C-C bonds in polyacetylene chains are the main contributors. This scenario about diradicalization is distinctly different from that in long acenes. The essence is that structural distortion cooperatively raises the HOMO and lowers the LUMO, efficiently reducing the HOMO-LUMO and singlet-triplet energy gaps, which facilitate the formation of a broken-symmetry open-shell singlet state. The irregular pulsing behavior originates from the mixing of normal vibrations in pentacene. This fascinating behavior suggests the potential application of pentacene as a suitable building block in the design of new electronic devices due to its magnetism-controllability through energy induction. This work provides new insight into inherent electronic property fluctuation in acenes.

Stress Intensity Factors for Cracked Metallic Structures Under Rapid Thermal Loading

DTIC Science & Technology

1987-10-01

if applicable ) Flight Dynamics Laboratory (AFWAL/FIBFC) APTECH Engineering Services Air Force Wright Aeronautical Laboratories 6c. ADDRESS (City...SPONSORING Bb OFFICE SYMBOL 9 PROCUREMENT INSTRUMENT IDENTIFICATION NUMBER ORGANIZATION (If applicable ) DOD SBIR Program Office F33615-86-C-3217 8c...flawed components requires the application of fracture mechanics wherein crack tip -tress intensity factors are used to provide a quantitative means

Structure and Dynamics of Water/Methanol Mixtures at Hydroxylated Silica Interfaces Relevant to Chromatography.

PubMed

Gupta, Prashant Kumar; Meuwly, Markus

2016-09-19

The spectroscopy and dynamics of water/methanol (MeOH) mixtures at hydroxylated silica surfaces is investigated from atomistic simulations. The particular focus is on how the structural dynamics of MeOH changes when comparing surface-bound and MeOH in the bulk. From analyzing the frequency frequency correlation functions it is found that the dynamics on the picosecond time scale differs by almost a factor of two. While the relaxation time is 2.0 ps for MeOH in the bulk solvent it is considerably slowed-down to 3.5 ps for surface-bound MeOH. Surface-adsorbed MeOH molecules reside there for several nanoseconds and their H-bonds are strongly oriented towards the surface-OH groups. These results are of particular relevance for chromatographic systems where the solvent may play a central role in their function. The present simulations suggest that surface-sensitive spectroscopic techniques should be useful in better characterizing such heterogeneous systems and provide detailed insight into solvent dynamics and structure relevant in chromatographic applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Local Dynamics of Acid- and Ion-containing Copolymer Melts

NASA Astrophysics Data System (ADS)

Winey, Karen; Middleton, Robert; Tarver, Jacob; Tyagi, Madhusudan; Soles, Christopher; Frischknecht, Amalie

Interest in acid- and ion-containing polymers arises in part from applications as single-ion conductors for selectively transporting a counter ion for battery applications. Structurally, the low dielectric constant of organic polymers and strong ionic interactions leads to ionic aggregation. Here the polymer backbone motion was investigated through quasi-elastic neutron scattering measurements (QENS) and compared with fully atomistic molecular dynamic simulations of precise poly(ethylene-acrylic acid) copolymers and their ionomers (pxAA-y%Li). The effect of carbon spacer length (x =9, 15, 21) between the acid groups and the degree of neutralization (y) with Li on PE backbone dynamics were considered. Systematic slowing in chain dynamics were observed with increasing neutralization where polymer dynamics appear constrained due to anchoring effects. Simulations provide complementary viewpoints indicating a gradient in chain dynamics as a distance away from acid groups. These results indicate that the addition of pendant acid groups inhibit typical PE backbone motion and the neutralized forms strongly suppress the fraction of mobile PE chain.

Overview and major characteristics of future aeronautical and space systems

NASA Technical Reports Server (NTRS)

Venneri, Samuel L.; Noor, Ahmed K.

1992-01-01

A systematic projection is made of prospective materials and structural systems' performance requirements in light of emerging applications. The applications encompass high-speed/long-range rotorcraft, advanced subsonic commercial aircraft, high speed (supersonic) commercial transports, hypersonic aircraft and missiles, extremely high-altitude cruise aircraft and missiles, and aerospace craft and launch vehicles. A tabulation is presented of the materials/structures/dynamics requirements associated with future aerospace systems, as well as the further development needs foreseen in each such case.

Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy.

PubMed

Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy

2018-02-01

A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 3 10 -helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of Structural Robustness against Column Loss: Methodology and Application to RC Frame Buildings

PubMed Central

Bao, Yihai; Main, Joseph A.; Noh, Sam-Young

2017-01-01

A computational methodology is presented for evaluating structural robustness against column loss. The methodology is illustrated through application to reinforced concrete (RC) frame buildings, using a reduced-order modeling approach for three-dimensional RC framing systems that includes the floor slabs. Comparisons with high-fidelity finite-element model results are presented to verify the approach. Pushdown analyses of prototype buildings under column loss scenarios are performed using the reduced-order modeling approach, and an energy-based procedure is employed to account for the dynamic effects associated with sudden column loss. Results obtained using the energy-based approach are found to be in good agreement with results from direct dynamic analysis of sudden column loss. A metric for structural robustness is proposed, calculated by normalizing the ultimate capacities of the structural system under sudden column loss by the applicable service-level gravity loading and by evaluating the minimum value of this normalized ultimate capacity over all column removal scenarios. The procedure is applied to two prototype 10-story RC buildings, one employing intermediate moment frames (IMFs) and the other employing special moment frames (SMFs). The SMF building, with its more stringent seismic design and detailing, is found to have greater robustness. PMID:28890599

Self-similarity in nature

NASA Astrophysics Data System (ADS)

Timashev, S. F.

2000-02-01

A general phenomenological approach to the analysis of experimental temporal, spatial and energetic series for extracting truly physical non-model parameters ("passport data") is presented, which may be used to characterize and distinguish the evolution as well as the spatial and energetic structure of any open nonlinear dissipative system. This methodology is based on a postulate concerning the crucial information contained in the sequences of non-regularities of the measured dynamic variable (temporal, spatial, energetic). In accordance with this approach, multi-parametric formulas for dynamic variable power spectra as well as for structural functions of different orders are identical for every spatial-temporal-energetic level of the system under consideration. In effect, this entails the introduction of a new kind of self-similarity in Nature. An algorithm has been developed for obtaining as many "passport data" as are necessary for the characterization of a dynamic system. Applications of this approach in the analysis of various experimental series (temporal, spatial, energetic) demonstrate its potential for defining adequate phenomenological parameters of different dynamic processes and structures.

Ultrafast Solvation Dynamics and Vibrational Coherences of Halogenated Boron-Dipyrromethene Derivatives Revealed through Two-Dimensional Electronic Spectroscopy.

PubMed

Lee, Yumin; Das, Saptaparna; Malamakal, Roy M; Meloni, Stephen; Chenoweth, David M; Anna, Jessica M

2017-10-18

Boron-dipyrromethene (BODIPY) chromophores have a wide range of applications, spanning areas from biological imaging to solar energy conversion. Understanding the ultrafast dynamics of electronically excited BODIPY chromophores could lead to further advances in these areas. In this work, we characterize and compare the ultrafast dynamics of halogenated BODIPY chromophores through applying two-dimensional electronic spectroscopy (2DES). Through our studies, we demonstrate a new data analysis procedure for extracting the dynamic Stokes shift from 2DES spectra revealing an ultrafast solvent relaxation. In addition, we extract the frequency of the vibrational modes that are strongly coupled to the electronic excitation, and compare the results of structurally different BODIPY chromophores. We interpret our results with the aid of DFT calculations, finding that structural modifications lead to changes in the frequency, identity, and magnitude of Franck-Condon active vibrational modes. We attribute these changes to differences in the electron density of the electronic states of the structurally different BODIPY chromophores.

A Typical Synergy

NASA Astrophysics Data System (ADS)

van Noort, Thomas; Achten, Peter; Plasmeijer, Rinus

We present a typical synergy between dynamic types (dynamics) and generalised algebraic datatypes (GADTs). The former provides a clean approach to integrating dynamic typing in a statically typed language. It allows values to be wrapped together with their type in a uniform package, deferring type unification until run time using a pattern match annotated with the desired type. The latter allows for the explicit specification of constructor types, as to enforce their structural validity. In contrast to ADTs, GADTs are heterogeneous structures since each constructor type is implicitly universally quantified. Unfortunately, pattern matching only enforces structural validity and does not provide instantiation information on polymorphic types. Consequently, functions that manipulate such values, such as a type-safe update function, are cumbersome due to boilerplate type representation administration. In this paper we focus on improving such functions by providing a new GADT annotation via a natural synergy with dynamics. We formally define the semantics of the annotation and touch on novel other applications of this technique such as type dispatching and enforcing type equality invariants on GADT values.

Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2018-01-01

A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules. Furthermore, by constructing a boost potential that follows a Gaussian distribution, accurate reweighting of GaMD simulations is achieved via cumulant expansion to the second order. The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolecular large-scale conformational transitions and biomolecular recognition. PMID:29720925

Integrated structural health monitoring

NASA Astrophysics Data System (ADS)

Farrar, Charles R.; Sohn, Hoon; Fugate, Michael L.; Czarnecki, Jerry J.

2001-07-01

Structural health monitoring is the implementation of a damage detection strategy for aerospace, civil and mechanical engineering infrastructure. Typical damage experienced by this infrastructure might be the development of fatigue cracks, degradation of structural connections, or bearing wear in rotating machinery. The goal of the research effort reported herein is to develop a robust and cost-effective structural health monitoring solution by integrating and extending technologies from various engineering and information technology disciplines. It is the author's opinion that all structural health monitoring systems must be application specific. Therefore, a specific application, monitoring welded moment resisting steel frame connections in structures subjected to seismic excitation, is described along with the motivation for choosing this application. The structural health monitoring solution for this application will integrate structural dynamics, wireless data acquisition, local actuation, micro-electromechanical systems (MEMS) technology, and statistical pattern recognition algorithms. The proposed system is based on an assessment of the deficiencies associated with many current structural health monitoring technologies including past efforts by the authors. This paper provides an example of the integrated approach to structural health monitoring being undertaken at Los Alamos National Laboratory and summarizes progress to date on various aspects of the technology development.

Finite Element Analysis of Wrinkled Membrane Structures for Sunshield Applications

NASA Technical Reports Server (NTRS)

Johnston, John D.; Brodeur, Stephen J. (Technical Monitor)

2002-01-01

The deployable sunshield is an example of a gossamer structure envisioned for use on future space telescopes. The basic structure consists of multiple layers of pretensioned, thin-film membranes supported by deployable booms. The prediction and verification of sunshield dynamics has been identified as an area in need of technology development due to the difficulties inherent in predicting nonlinear structural behavior of the membranes and because of the challenges involved. in ground testing of the full-scale structure. This paper describes a finite element analysis of a subscale sunshield that has been subjected to ground testing in support of the Next Generation Space Telescope (NGST) program. The analysis utilizes a nonlinear material model that accounts for wrinkling of the membranes. Results are presented from a nonlinear static preloading analysis and subsequent dynamics analyses to illustrate baseline sunshield structural characteristics. Studies are then described which provide further insight into the effect of membrane. preload on sunshield dynamics and the performance of different membrane modeling techniques. Lastly, a comparison of analytical predictions and ground test results is presented.

Dynamics of a passive micro-vibration isolator based on a pretensioned plane cable net structure and fluid damper

NASA Astrophysics Data System (ADS)

Chen, Yanhao; Lu, Qi; Jing, Bo; Zhang, Zhiyi

2016-09-01

This paper addresses dynamic modelling and experiments on a passive vibration isolator for application in the space environment. The isolator is composed of a pretensioned plane cable net structure and a fluid damper in parallel. Firstly, the frequency response function (FRF) of a single cable is analysed according to the string theory, and the FRF synthesis method is adopted to establish a dynamic model of the plane cable net structure. Secondly, the equivalent damping coefficient of the fluid damper is analysed. Thirdly, experiments are carried out to compare the plane cable net structure, the fluid damper and the vibration isolator formed by the net and the damper, respectively. It is shown that the plane cable net structure can achieve substantial vibration attenuation but has a great amplification at its resonance frequency due to the light damping of cables. The damping effect of fluid damper is acceptable without taking the poor carrying capacity into consideration. Compared to the plane cable net structure and the fluid damper, the isolator has an acceptable resonance amplification as well as vibration attenuation.

Development and Application of a Structural Health Monitoring System Based on Wireless Smart Aggregates

PubMed Central

Ma, Haoyan; Li, Peng; Song, Gangbing; Wu, Jianxin

2017-01-01

Structural health monitoring (SHM) systems can improve the safety and reliability of structures, reduce maintenance costs, and extend service life. Research on concrete SHMs using piezoelectric-based smart aggregates have reached great achievements. However, the newly developed techniques have not been widely applied in practical engineering, largely due to the wiring problems associated with large-scale structural health monitoring. The cumbersome wiring requires much material and labor work, and more importantly, the associated maintenance work is also very heavy. Targeting a practical large scale concrete crack detection (CCD) application, a smart aggregates-based wireless sensor network system is proposed for the CCD application. The developed CCD system uses Zigbee 802.15.4 protocols, and is able to perform dynamic stress monitoring, structural impact capturing, and internal crack detection. The system has been experimentally validated, and the experimental results demonstrated the effectiveness of the proposed system. This work provides important support for practical CCD applications using wireless smart aggregates. PMID:28714927

Development and Application of a Structural Health Monitoring System Based on Wireless Smart Aggregates.

PubMed

Yan, Shi; Ma, Haoyan; Li, Peng; Song, Gangbing; Wu, Jianxin

2017-07-17

Structural health monitoring (SHM) systems can improve the safety and reliability of structures, reduce maintenance costs, and extend service life. Research on concrete SHMs using piezoelectric-based smart aggregates have reached great achievements. However, the newly developed techniques have not been widely applied in practical engineering, largely due to the wiring problems associated with large-scale structural health monitoring. The cumbersome wiring requires much material and labor work, and more importantly, the associated maintenance work is also very heavy. Targeting a practical large scale concrete crack detection (CCD) application, a smart aggregates-based wireless sensor network system is proposed for the CCD application. The developed CCD system uses Zigbee 802.15.4 protocols, and is able to perform dynamic stress monitoring, structural impact capturing, and internal crack detection. The system has been experimentally validated, and the experimental results demonstrated the effectiveness of the proposed system. This work provides important support for practical CCD applications using wireless smart aggregates.

Computational and experimental studies of microvascular void features for passive-adaptation of structural panel dynamic properties

NASA Astrophysics Data System (ADS)

Sears, Nicholas C.; Harne, Ryan L.

2018-01-01

The performance, integrity, and safety of built-up structural systems are critical to their effective employment in diverse engineering applications. In conflict with these goals, harmonic or random excitations of structural panels may promote large amplitude oscillations that are particularly harmful when excitation energies are concentrated around natural frequencies. This contributes to fatigue concerns, performance degradation, and failure. While studies have considered active or passive damping treatments that adapt material characteristics and configurations for structural control, it remains to be understood how vibration properties of structural panels may be tailored via internal material transitions. Motivated to fill this knowledge gap, this research explores an idea of adapting the static and dynamic material distribution of panels through embedded microvascular channels and strategically placed voids that permit the internal movement of fluids within the panels for structural dynamic control. Finite element model and experimental investigations probe how redistributing material in the form of microscale voids influences the global vibration modes and natural frequencies of structural panels. Through parameter studies, the relationships among void shape, number, size, and location are quantified towards their contribution to the changing structural dynamics. For the panel composition and boundary conditions considered in this report, the findings reveal that transferring material between strategically placed voids may result in eigenfrequency changes as great as 10.0, 5.0, and 7.4% for the first, second, and third modes, respectively.

All-Atom Multiscale Molecular Dynamics Theory and Simulation of Self-Assembly, Energy Transfer and Structural Transition in Nanosystems

NASA Astrophysics Data System (ADS)

Espinosa Duran, John Michael

The study of nanosystems and their emergent properties requires the development of multiscale computational models, theories and methods that preserve atomic and femtosecond resolution, to reveal details that cannot be resolved experimentally today. Considering this, three long time scale phenomena were studied using molecular dynamics and multiscale methods: self-assembly of organic molecules on graphite, energy transfer in nanosystems, and structural transition in vault nanoparticles. Molecular dynamics simulations of the self-assembly of alkoxybenzonitriles with different tail lengths on graphite were performed to learn about intermolecular interactions and phases exhibited by self-organized materials. This is important for the design of ordered self-assembled organic photovoltaic materials with greater efficiency than the disordered blends. Simulations revealed surface dynamical behaviors that cannot be resolved experimentally today due to the lack of spatiotemporal resolution. Atom-resolved structures predicted by simulations agreed with scanning tunneling microscopy images and unit cell measurements. Then, a multiscale theory based on the energy density as a field variable is developed to study energy transfer in nanoscale systems. For applications like photothermal microscopy or cancer phototherapy is required to understand how the energy is transferred to/from nanosystems. This multiscale theory could be applied in this context and here is tested for cubic nanoparticles immersed in water for energy being transferred to/from the nanoparticle. The theory predicts the energy transfer dynamics and reveals phenomena that cannot be described by current phenomenological theories. Finally, temperature-triggered structural transitions were revealed for vault nanoparticles using molecular dynamics and multiscale simulations. Vault is a football-shaped supramolecular assembly very distinct from the commonly observed icosahedral viruses. It has very promising applications in drug delivery and has been extensively studied experimentally. Sub-microsecond multiscale simulations at 310 K on the vault revealed the opening and closing of fractures near the shoulder while preserving the overall structure. This fracture mechanism could explain the uptake and release of small drugs while maintaining the overall structure. Higher temperature simulations show the generation of large fractures near the waist, which enables interaction of the external medium with the inner vault residues. Simulation results agreed with microscopy and spectroscopy measurements, and revealed new structures and mechanisms.

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1981-08-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1980-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1979-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

electronically excited specied are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

RPV application of a globally adaptive rate controlled compressor

NASA Technical Reports Server (NTRS)

Rice, R. F.

1978-01-01

A globally adaptive image compression structure is introduced for use in a tactical RPV environment. The structure described would provide an operator with the flexibility to dynamically maximize the usefulness of a limited and changing data rate. The concepts would potentially simplify system design while at the same time improving overall system performance.

Functionalized lipids and surfactants for specific applications.

PubMed

Kepczynski, Mariusz; Róg, Tomasz

2016-10-01

Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. Copyright © 2016 Elsevier B.V. All rights reserved.

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

PubMed

Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H

2018-05-17

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

Adaptations in Electronic Structure Calculations in Heterogeneous Environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Talamudupula, Sai

Modern quantum chemistry deals with electronic structure calculations of unprecedented complexity and accuracy. They demand full power of high-performance computing and must be in tune with the given architecture for superior e ciency. To make such applications resourceaware, it is desirable to enable their static and dynamic adaptations using some external software (middleware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application. The present work investigates scienti c application interlinking with middleware based on the example of the computational chemistry package GAMESS and middleware NICAN. The existing synchronous model ismore » limited by the possible delays due to the middleware processing time under the sustainable runtime system conditions. Proposed asynchronous and hybrid models aim at overcoming this limitation. When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting statically and dynamically its fragment scheduling policy based on the computing platform conditions. Signi cant execution time and throughput gains have been obtained due to such static adaptations when the compute nodes have very di erent core counts. Dynamic adaptations are based on the main memory availability at run time. NICAN prompts FMO to postpone scheduling certain fragments, if there is not enough memory for their immediate execution. Hence, FMO may be able to complete the calculations whereas without such adaptations it aborts.« less

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Towards Efficient and Accurate Description of Many-Electron Problems: Developments of Static and Time-Dependent Electronic Structure Methods

NASA Astrophysics Data System (ADS)

Ding, Feizhi

Understanding electronic behavior in molecular and nano-scale systems is fundamental to the development and design of novel technologies and materials for application in a variety of scientific contexts from fundamental research to energy conversion. This dissertation aims to provide insights into this goal by developing novel methods and applications of first-principle electronic structure theory. Specifically, we will present new methods and applications of excited state multi-electron dynamics based on the real-time (RT) time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) formalism, and new development of the multi-configuration self-consist field theory (MCSCF) for modeling ground-state electronic structure. The RT-TDHF/TDDFT based developments and applications can be categorized into three broad and coherently integrated research areas: (1) modeling of the interaction between moleculars and external electromagnetic perturbations. In this part we will first prove both analytically and numerically the gauge invariance of the TDHF/TDDFT formalisms, then we will present a novel, efficient method for calculating molecular nonlinear optical properties, and last we will study quantum coherent plasmon in metal namowires using RT-TDDFT; (2) modeling of excited-state charge transfer in molecules. In this part, we will investigate the mechanisms of bridge-mediated electron transfer, and then we will introduce a newly developed non-equilibrium quantum/continuum embedding method for studying charge transfer dynamics in solution; (3) developments of first-principles spin-dependent many-electron dynamics. In this part, we will present an ab initio non-relativistic spin dynamics method based on the two-component generalized Hartree-Fock approach, and then we will generalized it to the two-component TDDFT framework and combine it with the Ehrenfest molecular dynamics approach for modeling the interaction between electron spins and nuclear motion. All these developments and applications will open up new computational and theoretical tools to be applied to the development and understanding of chemical reactions, nonlinear optics, electromagnetism, and spintronics. Lastly, we present a new algorithm for large-scale MCSCF calculations that can utilize massively parallel machines while still maintaining optimal performance for each single processor. This will great improve the efficiency in the MCSCF calculations for studying chemical dissociation and high-accuracy quantum-mechanical simulations.

Large Space Antenna Systems Technology, 1984

NASA Technical Reports Server (NTRS)

Boyer, W. J. (Compiler)

1985-01-01

Papers are presented which provide a comprehensive review of space missions requiring large antenna systems and of the status of key technologies required to enable these missions. Topic areas include mission applications for large space antenna systems, large space antenna structural systems, materials and structures technology, structural dynamics and control technology, electromagnetics technology, large space antenna systems and the space station, and flight test and evaluation.

Molecular dynamics approach to water structure of HII mesophase of monoolein

NASA Astrophysics Data System (ADS)

Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

2012-02-01

The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (HII) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO/water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.

Dynamically tunable interface states in 1D graphene-embedded photonic crystal heterostructure

NASA Astrophysics Data System (ADS)

Huang, Zhao; Li, Shuaifeng; Liu, Xin; Zhao, Degang; Ye, Lei; Zhu, Xuefeng; Zang, Jianfeng

2018-03-01

Optical interface states exhibit promising applications in nonlinear photonics, low-threshold lasing, and surface-wave assisted sensing. However, the further application of interface states in configurable optics is hindered by their limited tunability. Here, we demonstrate a new approach to generate dynamically tunable and angle-resolved interface states using graphene-embedded photonic crystal (GPC) heterostructure device. By combining the GPC structure design with in situ electric doping of graphene, a continuously tunable interface state can be obtained and its tuning range is as wide as the full bandgap. Moreover, the exhibited tunable interface states offer a possibility to study the correspondence between space and time characteristics of light, which is beyond normal incident conditions. Our strategy provides a new way to design configurable devices with tunable optical states for various advanced optical applications such as beam splitter and dynamically tunable laser.

In vivo optical imaging and dynamic contrast methods for biomedical research

PubMed Central

Hillman, Elizabeth M. C.; Amoozegar, Cyrus B.; Wang, Tracy; McCaslin, Addason F. H.; Bouchard, Matthew B.; Mansfield, James; Levenson, Richard M.

2011-01-01

This paper provides an overview of optical imaging methods commonly applied to basic research applications. Optical imaging is well suited for non-clinical use, since it can exploit an enormous range of endogenous and exogenous forms of contrast that provide information about the structure and function of tissues ranging from single cells to entire organisms. An additional benefit of optical imaging that is often under-exploited is its ability to acquire data at high speeds; a feature that enables it to not only observe static distributions of contrast, but to probe and characterize dynamic events related to physiology, disease progression and acute interventions in real time. The benefits and limitations of in vivo optical imaging for biomedical research applications are described, followed by a perspective on future applications of optical imaging for basic research centred on a recently introduced real-time imaging technique called dynamic contrast-enhanced small animal molecular imaging (DyCE). PMID:22006910

Synthetic polymers and biomembranes. How do they interact? Atomistic molecular dynamics simulation study of PEO in contact with a DMPC lipid bilayer.

PubMed

Pal, Sandeep; Milano, Giuseppe; Roccatano, Danilo

2006-12-28

The understanding of interactions of poly(ethylene glycol) (PEG) or poly(ethylene oxide) (PEO) with biological interfaces has important technological application in industry and in medicine. In this paper, structural and dynamical properties of PEO at the dimyristoylphospatidylcholine (DMPC) bilayer/water interface have been investigated by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The structural properties of a PEO chain in bulk water, at the water/vacuum interface, and in the presence of the membrane were compared with available experimental data. The presence of a barrier for the PEO penetration into the DMPC bilayer has been found. A qualitative estimation of the barrier provided a value equal to approximately 19 kJ/mol, that is, 7 times the value of kT at 310 K.

Application and Mechanics Analysis of Multi-Function Construction Platforms in Prefabricated-Concrete Construction

NASA Astrophysics Data System (ADS)

Wang, Meihua; Li, Rongshuai; Zhang, Wenze

2017-11-01

Multi-function construction platforms (MCPs) as an “old construction technology, new application” of the building facade construction equipment, its efforts to reduce labour intensity, improve labour productivity, ensure construction safety, shorten the duration of construction and other aspects of the effect are significant. In this study, the functional analysis of the multi-function construction platforms is carried out in the construction of the assembly building. Based on the general finite element software ANSYS, the static calculation and dynamic characteristics analysis of the MCPs structure are analysed, the simplified finite element model is constructed, and the selection of the unit, the processing and solution of boundary are under discussion and research. The maximum deformation value, the maximum stress value and the structural dynamic characteristic model are obtained. The dangerous parts of the platform structure are analysed, too. Multiple types of MCPs under engineering construction conditions are calculated, so as to put forward the rationalization suggestions for engineering application of the MCPs.

Force fields and scoring functions for carbohydrate simulation.

PubMed

Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

2015-01-12

Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ultra-precise micro-motion stage for optical scanning test

NASA Astrophysics Data System (ADS)

Chen, Wen; Zhang, Jianhuan; Jiang, Nan

2009-05-01

This study aims at the application of optical sensing technology in a 2D flexible hinge test stage. Optical fiber sensor which is manufactured taking advantage of the various unique properties of optical fiber, such as good electric insulation properties, resistance of electromagnetic disturbance, sparkless property and availability in flammable and explosive environment, has lots of good properties, such as high accuracy and wide dynamic range, repeatable, etc. and is applied in 2D flexible hinge stage driven by PZT. Several micro-bending structures are designed utilizing the characteristics of the flexible hinge stage. And through experiments, the optimal micro-bending tooth structure and the scope of displacement sensor trip under this optimal micro-bending tooth structure are derived. These experiments demonstrate that the application of optical fiber displacement sensor in 2D flexible hinge stage driven by PZT substantially broadens the dynamic testing range and improves the sensitivity of this apparatus. Driving accuracy and positioning stability are enhanced as well. [1,2

Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations

NASA Technical Reports Server (NTRS)

Norman, Michael L.

1997-01-01

Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.

1985 Particle Accelerator Conference: Accelerator Engineering and Technology, 11th, Vancouver, Canada, May 13-16, 1985, Proceedings

NASA Astrophysics Data System (ADS)

Strathdee, A.

1985-10-01

The topics discussed are related to high-energy accelerators and colliders, particle sources and electrostatic accelerators, controls, instrumentation and feedback, beam dynamics, low- and intermediate-energy circular accelerators and rings, RF and other acceleration systems, beam injection, extraction and transport, operations and safety, linear accelerators, applications of accelerators, radiation sources, superconducting supercolliders, new acceleration techniques, superconducting components, cryogenics, and vacuum. Accelerator and storage ring control systems are considered along with linear and nonlinear orbit theory, transverse and longitudinal instabilities and cures, beam cooling, injection and extraction orbit theory, high current dynamics, general beam dynamics, and medical and radioisotope applications. Attention is given to superconducting RF structures, magnet technology, superconducting magnets, and physics opportunities with relativistic heavy ion accelerators.

Vibration Damping Analysis of Lightweight Structures in Machine Tools

PubMed Central

Aggogeri, Francesco; Borboni, Alberto; Merlo, Angelo; Pellegrini, Nicola; Ricatto, Raffaele

2017-01-01

The dynamic behaviour of a machine tool (MT) directly influences the machining performance. The adoption of lightweight structures may reduce the effects of undesired vibrations and increase the workpiece quality. This paper aims to present and compare a set of hybrid materials that may be excellent candidates to fabricate the MT moving parts. The selected materials have high dynamic characteristics and capacity to dampen mechanical vibrations. In this way, starting from the kinematic model of a milling machine, this study evaluates a number of prototypes made of Al foam sandwiches (AFS), Al corrugated sandwiches (ACS) and composite materials reinforced by carbon fibres (CFRP). These prototypes represented the Z-axis ram of a commercial milling machine. The static and dynamical properties have been analysed by using both finite element (FE) simulations and experimental tests. The obtained results show that the proposed structures may be a valid alternative to the conventional materials of MT moving parts, increasing machining performance. In particular, the AFS prototype highlighted a damping ratio that is 20 times greater than a conventional ram (e.g., steel). Its application is particularly suitable to minimize unwanted oscillations during high-speed finishing operations. The results also show that the CFRP structure guarantees high stiffness with a weight reduced by 48.5%, suggesting effective applications in roughing operations, saving MT energy consumption. The ACS structure has a good trade-off between stiffness and damping and may represent a further alternative, if correctly evaluated. PMID:28772653

Propellant grain dynamics in aft attach ring of shuttle solid rocket booster

NASA Technical Reports Server (NTRS)

Verderaime, V.

1979-01-01

An analytical technique for implementing simultaneously the temperature, dynamic strain, real modulus, and frequency properties of solid propellant in an unsymmetrical vibrating ring mode is presented. All dynamic parameters and sources are defined for a free vibrating ring-grain structure with initial displacement and related to a forced vibrating system to determine the change in real modulus. Propellant test data application is discussed. The technique was developed to determine the aft attach ring stiffness of the shuttle booster at lift-off.

Tether Dynamics Simulation

NASA Technical Reports Server (NTRS)

1987-01-01

The proceedings of the conference are presented. The objective was to provide a forum for the discussion of the structure and status of existing computer programs which are used to simulate the dynamics of a variety of tether applications in space. A major topic was different simulation models and the process of validating them. Guidance on future work in these areas was obtained from a panel discussion; the panel was composed of resource and technical managers and dynamic analysts in the tether field. The conclusions of this panel are also presented.

Aeroelastic, CFD, and Dynamics Computation and Optimization for Buffet and Flutter Applications

NASA Technical Reports Server (NTRS)

Kandil, Osama A.

1997-01-01

Accomplishments achieved during the reporting period are listed. These accomplishments included 6 papers published in various journals or presented at various conferences; 1 abstract submitted to a technical conference; production of 2 animated movies; and a proposal for use of the National Aerodynamic Simulation Facility at NASA Ames Research Center for further research. The published and presented papers and animated movies addressed the following topics: aeroelasticity, computational fluid dynamics, structural dynamics, wing and tail buffet, vortical flow interactions, and delta wings.

Adaptive control of structural balance for complex dynamical networks based on dynamic coupling of nodes

NASA Astrophysics Data System (ADS)

Gao, Zilin; Wang, Yinhe; Zhang, Lili

2018-02-01

In the existing research results of the complex dynamical networks controlled, the controllers are mainly used to guarantee the synchronization or stabilization of the nodes’ state, and the terms coupled with connection relationships may affect the behaviors of nodes, this obviously ignores the dynamic common behavior of the connection relationships between the nodes. In fact, from the point of view of large-scale system, a complex dynamical network can be regarded to be composed of two time-varying dynamic subsystems, which can be called the nodes subsystem and the connection relationships subsystem, respectively. Similar to the synchronization or stabilization of the nodes subsystem, some characteristic phenomena can be also emerged in the connection relationships subsystem. For example, the structural balance in the social networks and the synaptic facilitation in the biological neural networks. This paper focuses on the structural balance in dynamic complex networks. Generally speaking, the state of the connection relationships subsystem is difficult to be measured accurately in practical applications, and thus it is not easy to implant the controller directly into the connection relationships subsystem. It is noted that the nodes subsystem and the relationships subsystem are mutually coupled, which implies that the state of the connection relationships subsystem can be affected by the controllable state of nodes subsystem. Inspired by this observation, by using the structural balance theory of triad, the controller with the parameter adaptive law is proposed for the nodes subsystem in this paper, which may ensure the connection relationship matrix to approximate a given structural balance matrix in the sense of the uniformly ultimately bounded (UUB). That is, the structural balance may be obtained by employing the controlling state of the nodes subsystem. Finally, the simulations are used to show the validity of the method in this paper.

Modelling, simulation and applications of longitudinal train dynamics

NASA Astrophysics Data System (ADS)

Cole, Colin; Spiryagin, Maksym; Wu, Qing; Sun, Yan Quan

2017-10-01

Significant developments in longitudinal train simulation and an overview of the approaches to train models and modelling vehicle force inputs are firstly presented. The most important modelling task, that of the wagon connection, consisting of energy absorption devices such as draft gears and buffers, draw gear stiffness, coupler slack and structural stiffness is then presented. Detailed attention is given to the modelling approaches for friction wedge damped and polymer draft gears. A significant issue in longitudinal train dynamics is the modelling and calculation of the input forces - the co-dimensional problem. The need to push traction performances higher has led to research and improvement in the accuracy of traction modelling which is discussed. A co-simulation method that combines longitudinal train simulation, locomotive traction control and locomotive vehicle dynamics is presented. The modelling of other forces, braking propulsion resistance, curve drag and grade forces are also discussed. As extensions to conventional longitudinal train dynamics, lateral forces and coupler impacts are examined in regards to interaction with wagon lateral and vertical dynamics. Various applications of longitudinal train dynamics are then presented. As an alternative to the tradition single wagon mass approach to longitudinal train dynamics, an example incorporating fully detailed wagon dynamics is presented for a crash analysis problem. Further applications of starting traction, air braking, distributed power, energy analysis and tippler operation are also presented.

Interaction of N-vortex structures in a continuum, including atmosphere, hydrosphere and plasma

NASA Astrophysics Data System (ADS)

Belashov, Vasily Yu.

2017-10-01

The results of analysis and numerical simulation of evolution and interaction of the N-vortex structures of various configuration and different vorticities in the continuum including atmosphere, hydrosphere and plasma are presented. It is found that in dependence on initial conditions the regimes of weak interaction with quasi-stationary evolution and active interaction with the "phase intermixing", when the evolution can lead to formation of complex forms of vorticity regions, are realized in the N-vortex systems. For the 2-vortex interaction the generalized critical parameter determining qualitative character of interaction of vortices is introduced. It is shown that for given initial conditions its value divides modes of active interaction and quasi-stationary evolution. The results of simulation of evolution and interaction of the two-dimensional and three-dimensional vortex structures, including such phenomena as dynamics of the atmospheric synoptic vortices of cyclonic types and tornado, hydrodynamic 4-vortex interaction and also interaction in the systems of a type of "hydrodynamic vortex - dust particles" are presented. The applications of undertaken approach to the problems of such plasma systems as streams of charged particles in a uniform magnetic field B and plasma clouds in the ionosphere are considered. It is shown that the results obtained have obvious applications in studies of the dynamics of the vortex structures dynamics in atmosphere, hydrosphere and plasma.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

Dynamic Characterization of an Inflatable Concentrator for Solar Thermal Propulsion

NASA Technical Reports Server (NTRS)

Leigh, Larry; Hamidzadeh, Hamid; Tinker, Michael L.; Rodriguez, Pedro I. (Technical Monitor)

2001-01-01

An inflatable structural system that is a technology demonstrator for solar thermal propulsion and other applications is characterized for structural dynamic behavior both experimentally and computationally. The inflatable structure is a pressurized assembly developed for use in orbit to support a Fresnel lens or inflatable lenticular element for focusing sunlight into a solar thermal rocket engine. When the engine temperature reaches a pre-set level, the propellant is injected into the engine, absorbs heat from an exchanger, and is expanded through the nozzle to produce thrust. The inflatable structure is a passively adaptive system in that a regulator and relief valve are utilized to maintain pressure within design limits during the full range of orbital conditions. Modeling and test activities are complicated by the fact that the polyimide film material used for construction of the inflatable is nonlinear, with modulus varying as a function of frequency, temperature, and level of excitation. Modal vibration testing and finite element modeling are described in detail in this paper. The test database is used for validation and modification of the model. This work is highly significant because of the current interest in inflatable structures for space application, and because of the difficulty in accurately modeling such systems.

Experimental and Numerical Evaluation of the Mechanical Behavior of Strongly Anisotropic Light-Weight Metallic Fiber Structures under Static and Dynamic Compressive Loading

PubMed Central

Andersen, Olaf; Vesenjak, Matej; Fiedler, Thomas; Jehring, Ulrike; Krstulović-Opara, Lovre

2016-01-01

Rigid metallic fiber structures made from a variety of different metals and alloys have been investigated mainly with regard to their functional properties such as heat transfer, pressure drop, or filtration characteristics. With the recent advent of aluminum and magnesium-based fiber structures, the application of such structures in light-weight crash absorbers has become conceivable. The present paper therefore elucidates the mechanical behavior of rigid sintered fiber structures under quasi-static and dynamic loading. Special attention is paid to the strongly anisotropic properties observed for different directions of loading in relation to the main fiber orientation. Basically, the structures show an orthotropic behavior; however, a finite thickness of the fiber slabs results in moderate deviations from a purely orthotropic behavior. The morphology of the tested specimens is examined by computed tomography, and experimental results for different directions of loading as well as different relative densities are presented. Numerical calculations were carried out using real structural data derived from the computed tomography data. Depending on the direction of loading, the fiber structures show a distinctively different deformation behavior both experimentally and numerically. Based on these results, the prevalent modes of deformation are discussed and a first comparison with an established polymer foam and an assessment of the applicability of aluminum fiber structures in crash protection devices is attempted. PMID:28773522

Experimental and Numerical Evaluation of the Mechanical Behavior of Strongly Anisotropic Light-Weight Metallic Fiber Structures under Static and Dynamic Compressive Loading.

PubMed

Andersen, Olaf; Vesenjak, Matej; Fiedler, Thomas; Jehring, Ulrike; Krstulović-Opara, Lovre

2016-05-21

Rigid metallic fiber structures made from a variety of different metals and alloys have been investigated mainly with regard to their functional properties such as heat transfer, pressure drop, or filtration characteristics. With the recent advent of aluminum and magnesium-based fiber structures, the application of such structures in light-weight crash absorbers has become conceivable. The present paper therefore elucidates the mechanical behavior of rigid sintered fiber structures under quasi-static and dynamic loading. Special attention is paid to the strongly anisotropic properties observed for different directions of loading in relation to the main fiber orientation. Basically, the structures show an orthotropic behavior; however, a finite thickness of the fiber slabs results in moderate deviations from a purely orthotropic behavior. The morphology of the tested specimens is examined by computed tomography, and experimental results for different directions of loading as well as different relative densities are presented. Numerical calculations were carried out using real structural data derived from the computed tomography data. Depending on the direction of loading, the fiber structures show a distinctively different deformation behavior both experimentally and numerically. Based on these results, the prevalent modes of deformation are discussed and a first comparison with an established polymer foam and an assessment of the applicability of aluminum fiber structures in crash protection devices is attempted.

A dynamic clinical dental relational database.

PubMed

Taylor, D; Naguib, R N G; Boulton, S

2004-09-01

The traditional approach to relational database design is based on the logical organization of data into a number of related normalized tables. One assumption is that the nature and structure of the data is known at the design stage. In the case of designing a relational database to store historical dental epidemiological data from individual clinical surveys, the structure of the data is not known until the data is presented for inclusion into the database. This paper addresses the issues concerned with the theoretical design of a clinical dynamic database capable of adapting the internal table structure to accommodate clinical survey data, and presents a prototype database application capable of processing, displaying, and querying the dental data.

Stress Analyzer

NASA Technical Reports Server (NTRS)

1990-01-01

SPATE 900 Dynamic Stress Analyzer is an acronym for Stress Pattern Analysis by Thermal Emission. It detects stress-induced temperature changes in a structure and indicates the degree of stress. Ometron, Inc.'s SPATE 9000 consists of a scan unit and a data display. The scan unit contains an infrared channel focused on the test structure to collect thermal radiation, and a visual channel used to set up the scan area and interrogate the stress display. Stress data is produced by detecting minute temperature changes, down to one-thousandth of a degree Centigrade, resulting from the application to the structure of dynamic loading. The electronic data processing system correlates the temperature changes with a reference signal to determine stress level.

The Lamb wave bandgap variation of a locally resonant phononic crystal subjected to thermal deformation

NASA Astrophysics Data System (ADS)

Zhu, Yun; Li, Zhen; Li, Yue-ming

2018-05-01

A study on dynamical characteristics of a ternary locally resonant phononic crystal (PC) plate (i.e., hard scatterer with soft coating periodically disperse in stiff host matrix) is carried out in this paper. The effect of thermal deformation on the structure stiffness, which plays an important role in the PC's dynamical characteristics, is considered. Results show that both the start and the stop frequency of bandgap shift to higher range with the thermal deformation. In particular, the characteristics of band structure change suddenly at critical buckling temperature. The effect of thermal deformation could be utilized for tuning of phononic band structures, which can promote their design and further applications.

2D automatic body-fitted structured mesh generation using advancing extraction method

NASA Astrophysics Data System (ADS)

Zhang, Yaoxin; Jia, Yafei

2018-01-01

This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like topography with extrusion-like structures (i.e., branches or tributaries) and intrusion-like structures (i.e., peninsula or dikes). With the AEM, the hierarchical levels of sub-domains can be identified, and the block boundary of each sub-domain in convex polygon shape in each level can be extracted in an advancing scheme. In this paper, several examples were used to illustrate the effectiveness and applicability of the proposed algorithm for automatic structured mesh generation, and the implementation of the method.

Development of dynamic Bayesian models for web application test management

NASA Astrophysics Data System (ADS)

Azarnova, T. V.; Polukhin, P. V.; Bondarenko, Yu V.; Kashirina, I. L.

2018-03-01

The mathematical apparatus of dynamic Bayesian networks is an effective and technically proven tool that can be used to model complex stochastic dynamic processes. According to the results of the research, mathematical models and methods of dynamic Bayesian networks provide a high coverage of stochastic tasks associated with error testing in multiuser software products operated in a dynamically changing environment. Formalized representation of the discrete test process as a dynamic Bayesian model allows us to organize the logical connection between individual test assets for multiple time slices. This approach gives an opportunity to present testing as a discrete process with set structural components responsible for the generation of test assets. Dynamic Bayesian network-based models allow us to combine in one management area individual units and testing components with different functionalities and a direct influence on each other in the process of comprehensive testing of various groups of computer bugs. The application of the proposed models provides an opportunity to use a consistent approach to formalize test principles and procedures, methods used to treat situational error signs, and methods used to produce analytical conclusions based on test results.

Gas Dynamic Spray Technology Demonstration

NASA Technical Reports Server (NTRS)

Burford, Pattie Lewis

2011-01-01

Zinc primer systems are currently used across NASA and AFSPC for corrosion protection of steel. AFSPC and NASA have approved the use of Thermal Spray Coatings (TSCs) as an environmentally preferable alternative. TSCs are approved in NASA-STD-5008 and AFSPC and KSC is currently looking for additional applications in which TSC can be used. Gas Dynamic Spray (GDS, also known as Cold Spray) is being evaluated as a means of repairing TSCs and for areas such as corners and edges where TSCs do not work as well. Other applications could include spot repair/maintenance of steel on structures, facilities, and ground support equipment.

Symmetric linear systems - An application of algebraic systems theory

NASA Technical Reports Server (NTRS)

Hazewinkel, M.; Martin, C.

1983-01-01

Dynamical systems which contain several identical subsystems occur in a variety of applications ranging from command and control systems and discretization of partial differential equations, to the stability augmentation of pairs of helicopters lifting a large mass. Linear models for such systems display certain obvious symmetries. In this paper, we discuss how these symmetries can be incorporated into a mathematical model that utilizes the modern theory of algebraic systems. Such systems are inherently related to the representation theory of algebras over fields. We will show that any control scheme which respects the dynamical structure either implicitly or explicitly uses the underlying algebra.

Polymer Physics Prize Talk

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

Polymer electrolytes have been particularly difficult to describe theoretically given the large number of disparate length scales involved in determining their physical properties. The Debye length, the Bjerrum length, the ion size, the chain length, and the distance between the charges along their backbones determine their structure and their response to external fields. We have developed an approach that uses multi-scale calculations with the capability of demonstrating the phase behavior of polymer electrolytes and of providing a conceptual understanding of how charge dictates nano-scale structure formation. Moreover, our molecular dynamics simulations have provided an understanding of the coupling of their conformation to their dynamics, which is crucial to design self-assembling materials, as well as to explore the dynamics of complex electrolytes for energy storage and conversion applications.

Vision-based system identification technique for building structures using a motion capture system

NASA Astrophysics Data System (ADS)

Oh, Byung Kwan; Hwang, Jin Woo; Kim, Yousok; Cho, Tongjun; Park, Hyo Seon

2015-11-01

This paper presents a new vision-based system identification (SI) technique for building structures by using a motion capture system (MCS). The MCS with outstanding capabilities for dynamic response measurements can provide gage-free measurements of vibrations through the convenient installation of multiple markers. In this technique, from the dynamic displacement responses measured by MCS, the dynamic characteristics (natural frequency, mode shape, and damping ratio) of building structures are extracted after the processes of converting the displacement from MCS to acceleration and conducting SI by frequency domain decomposition. A free vibration experiment on a three-story shear frame was conducted to validate the proposed technique. The SI results from the conventional accelerometer-based method were compared with those from the proposed technique and showed good agreement, which confirms the validity and applicability of the proposed vision-based SI technique for building structures. Furthermore, SI directly employing MCS measured displacements to FDD was performed and showed identical results to those of conventional SI method.

Influence of wing tip morphology on vortex dynamics of flapping flight

NASA Astrophysics Data System (ADS)

Krishna, Swathi; Mulleners, Karen

2013-11-01

The mechanism of flapping wing flight provides insects with extraordinary flight capabilities. The uniquely shaped wing tips give insects an edge in flight performance and the interaction between the leading edge vortices and wing tip vortices enhance their propelling efficiencies and manoeuvrability. These are qualities that are sought after in current-day Micro Air Vehicles. A detailed understanding of the vortex dynamics of flapping flight and the influence of the wing tip planform is imperative for technical application. An experimental study is conducted to investigate the effects of different wing tip planforms on the formation, evolution and interaction of vortical structures. We thereby focus on the interaction between the coherent structures evolving from the leading edge and the wing tip during pitching and flapping motions.The spatial and temporal evolution of the three-dimensional flow structures are determined using Scanning (Stereo) Particle Image Velocimetry and an in-depth coherent structure analysis. By comparing the vortex dynamics, the aerodynamic performance of various wing tip planforms are evaluated.

Dynamics of psychological crisis experience with psychological consulting by gestalt therapy methods.

PubMed

Fahrutdinova, Liliya Raifovna; Nugmanova, Dzhamilia Renatovna

2015-01-01

Dynamics of experience as such and its corporeal, emotional and cognitive elements in the situation of psychological consulting provisioning is covered. The aim of research was to study psychological crisis experience dynamics in the situation when psychological consulting by gestalt therapy methods is provided. Theoretical analysis of the problem of crisis situations, phenomenon and structural, and dynamic organization of experience of the subject of consulting have been carried out. To fulfill research project test subjects experience crisis situation have been selected, studied in the situation when they provided psychological consulting by methods of gestalt therapy, and methodology of study of crisis situations experience has been prepared. Specifics of psychological crisis experience have been revealed and its elements in different stages of psychological consulting by gestalt therapy methods. Dynamics of experience of psychological crisis and its structural elements have been revealed and reliable changes in it have been revealed. Dynamics of psychological crisis experience and its structural elements have been revealed and reliable changes in it have been revealed. "Desiccation" of experience is being observed, releasing its substantiality of negative impression to the end of consulting and development of the new experience of control over crisis situation. Interrelations of structural elements of experience in the process of psychological consulting have been shown. Effecting one structure causes reliable changes in all others structural elements of experience. Giving actual psychological help to clients in crisis situation by methods of gestalt therapy is possible as it was shown in psychological consulting sessions. Structure of client's request has been revealed - problems of personal sense are fixed as the most frequent cause of clients' applications, as well as absence of choices, obtrusiveness of negative thoughts, tend to getting stuck on events took place in the past, drawing into oneself, etc.

Structural topology optimization with fuzzy constraint

NASA Astrophysics Data System (ADS)

Rosko, Peter

2011-12-01

The paper deals with the structural topology optimization with fuzzy constraint. The optimal topology of structure is defined as a material distribution problem. The objective is the weight of the structure. The multifrequency dynamic loading is considered. The optimal topology design of the structure has to eliminate the danger of the resonance vibration. The uncertainty of the loading is defined with help of fuzzy loading. Special fuzzy constraint is created from exciting frequencies. Presented study is applicable in engineering and civil engineering. Example demonstrates the presented theory.

Framework for Evaluating Loop Invariant Detection Games in Relation to Automated Dynamic Invariant Detectors

DTIC Science & Technology

2015-09-01

Detectability ...............................................................................................37 Figure 20. Excel VBA Codes for Checker...National Vulnerability Database OS Operating System SQL Structured Query Language VC Verification Condition VBA Visual Basic for Applications...checks each of these assertions for detectability by Daikon. The checker is an Excel Visual Basic for Applications ( VBA ) script that checks the

Molecular dynamics study of the structural and dynamic characteristics of the polyextremophilic short-chain dehydrogenase from the Thermococcus sibiricus archaeon and its homologues

NASA Astrophysics Data System (ADS)

Popinako, Anna V.; Antonov, Mikhail Yu.; Bezsudnova, Ekaterina Yu.; Prokopiev, Georgiy A.; Popov, Vladimir O.

2017-11-01

The study of structural adaptations of proteins from polyextremophilic organisms using computational molecular dynamics method is appealing because the obtained knowledge can be applied to construction of synthetic proteins with high activity and stability in polyextreme media which is useful for many industrial applications. To investigate molecular adaptations to high temperature, we have focused on a superthermostable short-chain dehydrogenase TsAdh319 from the Thermococcus sibiricus polyextremophilic archaeon and its closest structural homologues. Molecular dynamics method is widely used for molecular structure refinement, investigation of biological macromolecules motion, and, consequently, for interpreting the results of certain biophysical experiments. We performed molecular dynamics simulations of the proteins at different temperatures. Comparison of root mean square fluctuations (RMSF) of the atoms in thermophilic alcohol dehydrogenases (ADHs) at 300 K and 358 K revealed the existence of stable residues at 358 K. These residues surround the active site and form a "nucleus of rigidity" in thermophilic ADHs. The results of our studies suggest that the existence of the "nucleus of rigidity" is crucial for the stability of TsAdh319. Absence of the "nucleus of rigidity" in non-thermally stable proteins causes fluctuations throughout the protein, especially on the surface, triggering the process of denaturation at high temperatures.

Numerical Analysis of Constrained Dynamical Systems, with Applications to Dynamic Contact of Solids, Nonlinear Elastodynamics and Fluid-Structure Interactions

DTIC Science & Technology

2000-12-01

Numerical Simulations ..... ................. .... 42 1.4.1. Impact of a rod on a rigid wall ..... ................. .... 42 1.4.2. Impact of two...dissipative properties of the proposed scheme . . . . 81 II.4. Representative Numerical Simulations ...... ................. ... 84 11.4.1. Forging of...Representative numerical simulations ...... ............. .. 123 111.3. Model Problem II: a Simplified Model of Thin Beams ... ......... ... 127 III

Uncertain dynamical systems: A differential game approach

NASA Technical Reports Server (NTRS)

Gutman, S.

1976-01-01

A class of dynamical systems in a conflict situation is formulated and discussed, and the formulation is applied to the study of an important class of systems in the presence of uncertainty. The uncertainty is deterministic and the only assumption is that its value belongs to a known compact set. Asymptotic stability is fully discussed with application to variable structure and model reference control systems.

Nonlinear Structural Analysis Methodology and Dynamics Scaling of Inflatable Parabolic Reflector Antenna Concepts

NASA Technical Reports Server (NTRS)

Sreekantamurthy, Tham; Gaspar, James L.; Mann, Troy; Behun, Vaughn; Pearson, James C., Jr.; Scarborough, Stephen

2007-01-01

Ultra-light weight and ultra-thin membrane inflatable antenna concepts are fast evolving to become the state-of-the-art antenna concepts for deep-space applications. NASA Langley Research Center has been involved in the structural dynamics research on antenna structures. One of the goals of the research is to develop structural analysis methodology for prediction of the static and dynamic response characteristics of the inflatable antenna concepts. This research is focused on the computational studies to use nonlinear large deformation finite element analysis to characterize the ultra-thin membrane responses of the antennas. Recently, structural analyses have been performed on a few parabolic reflector antennas of varying size and shape, which are referred in the paper as 0.3 meters subscale, 2 meters half-scale, and 4 meters full-scale antenna. The various aspects studied included nonlinear analysis methodology and solution techniques, ways to speed convergence in iterative methods, the sensitivities of responses with respect to structural loads, such as inflation pressure, gravity, and pretension loads in the ground and in-space conditions, and the ultra-thin membrane wrinkling characteristics. Several such intrinsic aspects studied have provided valuable insight into evaluation of structural characteristics of such antennas. While analyzing these structural characteristics, a quick study was also made to assess the applicability of dynamics scaling of the half-scale antenna. This paper presents the details of the nonlinear structural analysis results, and discusses the insight gained from the studies on the various intrinsic aspects of the analysis methodology. The predicted reflector surface characteristics of the three inflatable ultra-thin membrane parabolic reflector antenna concepts are presented as easily observable displacement fringe patterns with associated maximum values, and normal mode shapes and associated frequencies. Wrinkling patterns are presented to show how surface wrinkle progress with increasing tension loads. Antenna reflector surface accuracies were found to be very much dependent on the type and size of the antenna, the reflector surface curvature, reflector membrane supports in terms of spacing of catenaries, as well as the amount of applied load.

From Two‐ to Three‐Dimensional Structures of a Supertetrahedral Boran Using Density Functional Calculations

PubMed Central

Getmanskii, Iliya V.; Steglenko, Dmitrii V.; Koval, Vitaliy V.; Zaitsev, Stanislav A.

2017-01-01

Abstract With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two‐ and three‐dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two‐ and three‐layer systems resulted in the construction of a three‐dimensional supertetrahedral borane crystal structure. The two‐dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three‐dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm−3) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. PMID:28402596

Finite-difference simulation and visualization of elastodynamics in time-evolving generalized curvilinear coordinates

NASA Technical Reports Server (NTRS)

Kaul, Upender K. (Inventor)

2009-01-01

Modeling and simulation of free and forced structural vibrations is essential to an overall structural health monitoring capability. In the various embodiments, a first principles finite-difference approach is adopted in modeling a structural subsystem such as a mechanical gear by solving elastodynamic equations in generalized curvilinear coordinates. Such a capability to generate a dynamic structural response is widely applicable in a variety of structural health monitoring systems. This capability (1) will lead to an understanding of the dynamic behavior of a structural system and hence its improved design, (2) will generate a sufficiently large space of normal and damage solutions that can be used by machine learning algorithms to detect anomalous system behavior and achieve a system design optimization and (3) will lead to an optimal sensor placement strategy, based on the identification of local stress maxima all over the domain.

Development of a rotorcraft. Propulsion dynamics interface analysis, volume 2

NASA Technical Reports Server (NTRS)

Hull, R.

1982-01-01

A study was conducted to establish a coupled rotor/propulsion analysis that would be applicable to a wide range of rotorcraft systems. The effort included the following tasks: (1) development of a model structure suitable for simulating a wide range of rotorcraft configurations; (2) defined a methodology for parameterizing the model structure to represent a particular rotorcraft; (3) constructing a nonlinear coupled rotor/propulsion model as a test case to use in analyzing coupled system dynamics; and (4) an attempt to develop a mostly linear coupled model derived from the complete nonlinear simulations. Documentation of the computer models developed is presented.

Investigating the Structure of Paramagnetic Aggregates from Colloidal Emulsions - 2

NASA Technical Reports Server (NTRS)

Furst, Eric M.; Gast, Alice P.

2008-01-01

Particle dynamics of magnetorheological fluids (fluids that change properties in response to magnetic fields) are studied to help understand adaptable new fluids for use in such applications as brake systems and robotics.

Machine learning for quantum dynamics: deep learning of excitation energy transfer properties

DOE PAGES

Häse, Florian; Kreisbeck, Christoph; Aspuru-Guzik, Alán

2017-01-01

Understanding the relationship between the structure of light-harvesting systems and their excitation energy transfer properties is of fundamental importance in many applications including the development of next generation photovoltaics.

Beam dynamics design of the muon linac high-beta section

NASA Astrophysics Data System (ADS)

Kondo, Y.; Hasegawa, K.; Otani, M.; Mibe, T.; Yoshida, M.; Kitamura, R.

2017-07-01

A muon linac development for a new muon g-2 experiment is now going on at J-PARC. Muons from the muon beam line (H line) at the J-PARC muon science facility are once stopped in a silica-aerogel target, and room temperature muoniums are evaporated from the aerogel. They are dissociated with lasers, then accelerated up to 212 MeV using a linear accelerator. For the accelerating structure from 40 MeV, disk-loaded traveling-wave structure is applicable because the particle beta is more than 0.7. The structure itself is similar to that for electron linacs, however, the cell length should be harmonic to the increase of the particle velocity. In this paper, the beam dynamics design of this muon linac using the disk-loaded structure (DLS) is described.

From Geometry Optimization to Time Dependent Molecular Structure Modeling: Method Developments, ab initio Theories and Applications

NASA Astrophysics Data System (ADS)

Liang, Wenkel

This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the characteristics of ultrafast dynamics in photoexcited fullerene derivatives, and aids in the rational design for pre-dissociative exciton in the intramolecular CT process in organic solar cells.

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox.

PubMed

Weidmann, Chase A; Mustoe, Anthony M; Weeks, Kevin M

2016-09-01

While a variety of powerful tools exists for analyzing RNA structure, identifying long-range and intermolecular base-pairing interactions has remained challenging. Recently, three groups introduced a high-throughput strategy that uses psoralen-mediated crosslinking to directly identify RNA-RNA duplexes in cells. Initial application of these methods highlights the preponderance of long-range structures within and between RNA molecules and their widespread structural dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Graph-based linear scaling electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Structure and dynamics of European sports science textual contents: Analysis of ECSS abstracts (1996-2014).

PubMed

Hristovski, Robert; Aceski, Aleksandar; Balague, Natalia; Seifert, Ludovic; Tufekcievski, Aleksandar; Cecilia, Aguirre

2017-02-01

The article discusses general structure and dynamics of the sports science research content as obtained from the analysis of 21998 European College of Sport Science abstracts belonging to 12 science topics. The structural analysis showed intertwined multidisciplinary and unifying tendencies structured along horizontal (scope) and vertical (level) axes. Methodological (instrumental and mode of inquiry) integrative tendencies are dominant. Theoretical integrative tendencies are much less detectable along both horizontal and vertical axes. The dynamic analysis of written abstracts text content over the 19 years reveals the contextualizing and guiding role of thematic skeletons of each sports science topic in forming more detailed contingent research ideas and the role of the latter in stabilizing and procreating the former. This circular causality between both hierarchical levels and functioning on separate characteristic time scales is crucial for understanding how stable research traditions self-maintain and self-procreate through innovative contingencies. The structure of sports science continuously rebuilds itself through use and re-use of contingent research ideas. The thematic skeleton ensures its identity and the contingent conceptual sets its flexibility and adaptability to different research or applicative problems.

Virtual sensors for active noise control in acoustic-structural coupled enclosures using structural sensing: robust virtual sensor design.

PubMed

Halim, Dunant; Cheng, Li; Su, Zhongqing

2011-03-01

The work was aimed to develop a robust virtual sensing design methodology for sensing and active control applications of vibro-acoustic systems. The proposed virtual sensor was designed to estimate a broadband acoustic interior sound pressure using structural sensors, with robustness against certain dynamic uncertainties occurring in an acoustic-structural coupled enclosure. A convex combination of Kalman sub-filters was used during the design, accommodating different sets of perturbed dynamic model of the vibro-acoustic enclosure. A minimax optimization problem was set up to determine an optimal convex combination of Kalman sub-filters, ensuring an optimal worst-case virtual sensing performance. The virtual sensing and active noise control performance was numerically investigated on a rectangular panel-cavity system. It was demonstrated that the proposed virtual sensor could accurately estimate the interior sound pressure, particularly the one dominated by cavity-controlled modes, by using a structural sensor. With such a virtual sensing technique, effective active noise control performance was also obtained even for the worst-case dynamics. © 2011 Acoustical Society of America

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Nanomotor dynamics in a chemically oscillating medium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robertson, Bryan, E-mail: bryan.robertson@mail.utoronto.ca; Kapral, Raymond, E-mail: rkapral@chem.utoronto.ca

2015-04-21

Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give risemore » to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media.« less

Slippery liquid-infused porous surface bio-inspired by pitcher plant for marine anti-biofouling application.

PubMed

Wang, Peng; Zhang, Dun; Lu, Zhou

2015-12-01

Marine biofouling, caused by the adhesion of microorganism, is a worldwide problem in marine systems. In this research work, slippery liquid-infused porous surface (SLIPS), inspired by Nepenthes pitcher plant, was constructed over aluminum for marine anti-biofouling application. The as-fabricated SLIPS was characterized with SEM, AFM, and contact angle meter. Its anti-biofouling performance was evaluated with settlement experiment of a typical marine biofouling organism Chlorella vulgaris in both static and dynamic conditions. The effect of solid substrate micro-structure on anti-biofouling property of SLIPS was studied. It was suggested that the micro-structure with low length scale and high degree of regularity should be considered for designing stable SLIPS with exceptional anti-biofouling property. The liquid-like property is proven to be the main contributor for the exceptional anti-biofouling performance of SLIPS in both static and dynamic conditions. The low roughness, which facilitates removing the settled C. vulgaris under shear force, is also a main contributor for the anti-biofouling performance of SLIPS in dynamic condition. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular dynamics simulations and novel drug discovery.

PubMed

Liu, Xuewei; Shi, Danfeng; Zhou, Shuangyan; Liu, Hongli; Liu, Huanxiang; Yao, Xiaojun

2018-01-01

Molecular dynamics (MD) simulations can provide not only plentiful dynamical structural information on biomacromolecules but also a wealth of energetic information about protein and ligand interactions. Such information is very important to understanding the structure-function relationship of the target and the essence of protein-ligand interactions and to guiding the drug discovery and design process. Thus, MD simulations have been applied widely and successfully in each step of modern drug discovery. Areas covered: In this review, the authors review the applications of MD simulations in novel drug discovery, including the pathogenic mechanisms of amyloidosis diseases, virtual screening and the interaction mechanisms between drugs and targets. Expert opinion: MD simulations have been used widely in investigating the pathogenic mechanisms of diseases caused by protein misfolding, in virtual screening, and in investigating drug resistance mechanisms caused by mutations of the target. These issues are very difficult to solve by experimental methods alone. Thus, in the future, MD simulations will have wider application with the further improvement of computational capacity and the development of better sampling methods and more accurate force fields together with more efficient analysis methods.

Harnessing graphical structure in Markov chain Monte Carlo learning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stolorz, P.E.; Chew P.C.

1996-12-31

The Monte Carlo method is recognized as a useful tool in learning and probabilistic inference methods common to many datamining problems. Generalized Hidden Markov Models and Bayes nets are especially popular applications. However, the presence of multiple modes in many relevant integrands and summands often renders the method slow and cumbersome. Recent mean field alternatives designed to speed things up have been inspired by experience gleaned from physics. The current work adopts an approach very similar to this in spirit, but focusses instead upon dynamic programming notions as a basis for producing systematic Monte Carlo improvements. The idea is tomore » approximate a given model by a dynamic programming-style decomposition, which then forms a scaffold upon which to build successively more accurate Monte Carlo approximations. Dynamic programming ideas alone fail to account for non-local structure, while standard Monte Carlo methods essentially ignore all structure. However, suitably-crafted hybrids can successfully exploit the strengths of each method, resulting in algorithms that combine speed with accuracy. The approach relies on the presence of significant {open_quotes}local{close_quotes} information in the problem at hand. This turns out to be a plausible assumption for many important applications. Example calculations are presented, and the overall strengths and weaknesses of the approach are discussed.« less

Structure and Dynamics of the Quasi-Biennial Oscillation in MERRA-2.

PubMed

Coy, Lawrence; Wargan, Krzysztof; Molod, Andrea M; McCarty, William R; Pawson, Steven

2016-07-01

The structure, dynamics, and ozone signal of the Quasi-Biennial Oscillation produced by the 35-year NASA MERRA-2 (Modern-Era Retrospective Analysis for Research and Applications) reanalysis are examined based on monthly mean output. Along with the analysis of the QBO in assimilation winds and ozone, the QBO forcings created by assimilated observations, dynamics, parameterized gravity wave drag, and ozone chemistry parameterization are examined and compared with the original MERRA system. Results show that the MERRA-2 reanalysis produces a realistic QBO in the zonal winds, mean meridional circulation, and ozone over the 1980-2015 time period. In particular, the MERRA-2 zonal winds show improved representation of the QBO 50 hPa westerly phase amplitude at Singapore when compared to MERRA. The use of limb ozone observations creates improved vertical structure and realistic downward propagation of the ozone QBO signal during times when the MLS ozone limb observations are available (October 2004 to present). The increased equatorial GWD in MERRA-2 has reduced the zonal wind data analysis contribution compared to MERRA so that the QBO mean meridional circulation can be expected to be more physically forced and therefore more physically consistent. This can be important for applications in which MERRA-2 winds are used to drive transport experiments.

Structure and Dynamics of the Quasi-Biennial Oscillation in MERRA-2

PubMed Central

Coy, Lawrence; Wargan, Krzysztof; Molod, Andrea M.; McCarty, William R.; Pawson, Steven

2018-01-01

The structure, dynamics, and ozone signal of the Quasi-Biennial Oscillation produced by the 35-year NASA MERRA-2 (Modern-Era Retrospective Analysis for Research and Applications) reanalysis are examined based on monthly mean output. Along with the analysis of the QBO in assimilation winds and ozone, the QBO forcings created by assimilated observations, dynamics, parameterized gravity wave drag, and ozone chemistry parameterization are examined and compared with the original MERRA system. Results show that the MERRA-2 reanalysis produces a realistic QBO in the zonal winds, mean meridional circulation, and ozone over the 1980–2015 time period. In particular, the MERRA-2 zonal winds show improved representation of the QBO 50 hPa westerly phase amplitude at Singapore when compared to MERRA. The use of limb ozone observations creates improved vertical structure and realistic downward propagation of the ozone QBO signal during times when the MLS ozone limb observations are available (October 2004 to present). The increased equatorial GWD in MERRA-2 has reduced the zonal wind data analysis contribution compared to MERRA so that the QBO mean meridional circulation can be expected to be more physically forced and therefore more physically consistent. This can be important for applications in which MERRA-2 winds are used to drive transport experiments. PMID:29551854

Mechanical design of DNA nanostructures.

PubMed

Castro, Carlos E; Su, Hai-Jun; Marras, Alexander E; Zhou, Lifeng; Johnson, Joshua

2015-04-14

Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.

Modal testing with Asher's method using a Fourier analyzer and curve fitting

NASA Technical Reports Server (NTRS)

Gold, R. R.; Hallauer, W. L., Jr.

1979-01-01

An unusual application of the method proposed by Asher (1958) for structural dynamic and modal testing is discussed. Asher's method has the capability, using the admittance matrix and multiple-shaker sinusoidal excitation, of separating structural modes having indefinitely close natural frequencies. The present application uses Asher's method in conjunction with a modern Fourier analyzer system but eliminates the necessity of exciting the test structure simultaneously with several shakers. Evaluation of this approach with numerically simulated data demonstrated its effectiveness; the parameters of two modes having almost identical natural frequencies were accurately identified. Laboratory evaluation of this approach was inconclusive because of poor experimental input data.

Analytical investigation of the dynamics of tethered constellations in Earth orbit, phase 2

NASA Technical Reports Server (NTRS)

Lorenzini, Enrico C.; Gullahorn, Gordon E.; Cosmo, Mario L.; Estes, Robert D.; Grossi, Mario D.

1994-01-01

This final report covers nine years of research on future tether applications and on the actual flights of the Small Expendable Deployment System (SEDS). Topics covered include: (1) a description of numerical codes used to simulate the orbital and attitude dynamics of tethered systems during station keeping and deployment maneuvers; (2) a comparison of various tethered system simulators; (3) dynamics analysis, conceptual design, potential applications and propagation of disturbances and isolation from noise of a variable gravity/microgravity laboratory tethered to the Space Station; (4) stability of a tethered space centrifuge; (5) various proposed two-dimensional tethered structures for low Earth orbit for use as planar array antennas; (6) tethered high gain antennas; (7) numerical calculation of the electromagnetic wave field on the Earth's surface on an electrodynamically tethered satellite; (8) reentry of tethered capsules; (9) deployment dynamics of SEDS-1; (10) analysis of SEDS-1 flight data; and (11) dynamics and control of SEDS-2.

The HART II International Workshop: An Assessment of the State-of-the-Art in Comprehensive Code Prediction

NASA Technical Reports Server (NTRS)

vanderWall, Berend G.; Lim, Joon W.; Smith, Marilyn J.; Jung, Sung N.; Bailly, Joelle; Baeder, James D.; Boyd, D. Douglas, Jr.

2013-01-01

Significant advancements in computational fluid dynamics (CFD) and their coupling with computational structural dynamics (CSD, or comprehensive codes) for rotorcraft applications have been achieved recently. Despite this, CSD codes with their engineering level of modeling the rotor blade dynamics, the unsteady sectional aerodynamics and the vortical wake are still the workhorse for the majority of applications. This is especially true when a large number of parameter variations is to be performed and their impact on performance, structural loads, vibration and noise is to be judged in an approximate yet reliable and as accurate as possible manner. In this article, the capabilities of such codes are evaluated using the HART II International Workshop database, focusing on a typical descent operating condition which includes strong blade-vortex interactions. A companion article addresses the CFD/CSD coupled approach. Three cases are of interest: the baseline case and two cases with 3/rev higher harmonic blade root pitch control (HHC) with different control phases employed. One setting is for minimum blade-vortex interaction noise radiation and the other one for minimum vibration generation. The challenge is to correctly predict the wake physics-especially for the cases with HHC-and all the dynamics, aerodynamics, modifications of the wake structure and the aero-acoustics coming with it. It is observed that the comprehensive codes used today have a surprisingly good predictive capability when they appropriately account for all of the physics involved. The minimum requirements to obtain these results are outlined.

An Assessment of Comprehensive Code Prediction State-of-the-Art Using the HART II International Workshop Data

NASA Technical Reports Server (NTRS)

vanderWall, Berend G.; Lim, Joon W.; Smith, Marilyn J.; Jung, Sung N.; Bailly, Joelle; Baeder, James D.; Boyd, D. Douglas, Jr.

2012-01-01

Despite significant advancements in computational fluid dynamics and their coupling with computational structural dynamics (= CSD, or comprehensive codes) for rotorcraft applications, CSD codes with their engineering level of modeling the rotor blade dynamics, the unsteady sectional aerodynamics and the vortical wake are still the workhorse for the majority of applications. This is especially true when a large number of parameter variations is to be performed and their impact on performance, structural loads, vibration and noise is to be judged in an approximate yet reliable and as accurate as possible manner. In this paper, the capabilities of such codes are evaluated using the HART II Inter- national Workshop data base, focusing on a typical descent operating condition which includes strong blade-vortex interactions. Three cases are of interest: the baseline case and two cases with 3/rev higher harmonic blade root pitch control (HHC) with different control phases employed. One setting is for minimum blade-vortex interaction noise radiation and the other one for minimum vibration generation. The challenge is to correctly predict the wake physics - especially for the cases with HHC - and all the dynamics, aerodynamics, modifications of the wake structure and the aero-acoustics coming with it. It is observed that the comprehensive codes used today have a surprisingly good predictive capability when they appropriately account for all of the physics involved. The minimum requirements to obtain these results are outlined.

Unraveling DNA dynamics using atomic force microscopy.

PubMed

Suzuki, Yuki; Yoshikawa, Yuko; Yoshimura, Shige H; Yoshikawa, Kenichi; Takeyasu, Kunio

2011-01-01

The elucidation of structure-function relationships of biological samples has become important issue in post-genomic researches. In order to unveil the molecular mechanisms controlling gene regulations, it is essential to understand the interplay between fundamental DNA properties and the dynamics of the entire molecule. The wide range of applicability of atomic force microscopy (AFM) has allowed us to extract physicochemical properties of DNA and DNA-protein complexes, as well as to determine their topographical information. Here, we review how AFM techniques have been utilized to study DNA and DNA-protein complexes and what types of analyses have accelerated the understanding of the DNA dynamics. We begin by illustrating the application of AFM to investigate the fundamental feature of DNA molecules; topological transition of DNA, length dependent properties of DNA molecules, flexibility of double-stranded DNA, and capability of the formation of non-Watson-Crick base pairing. These properties of DNA are critical for the DNA folding and enzymatic reactions. The technical advancement in the time-resolution of AFM and sample preparation methods enabled visual analysis of DNA-protein interactions at sub-second time region. DNA tension-dependent enzymatic reaction and DNA looping dynamics by restriction enzymes were examined at a nanoscale in physiological environments. Contribution of physical properties of DNA to dynamics of nucleosomes and transition of the higher-order structure of reconstituted chromatin are also reviewed. Copyright © 2011 John Wiley & Sons, Inc.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

NASA Astrophysics Data System (ADS)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding. Electronic supplementary information (ESI) is available: Fluorescence spectra, ITC, CD spectra and other data as described in the text. See DOI: 10.1039/c4nr01544d

Sea loads on ships and offshore structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faltinsen, O.

1990-01-01

The book introduces the theory of the structural loading on ships and offshore structures caused by wind, waves and currents, and goes on to describe the applications of this theory in terms of real structures. The main topics described are linear-wave induced motions, loads on floating structures, numerical methods for ascertaining wave induced motions and loads, viscous wave loads and damping, stationkeeping and water impact and entry. The applications of the theoretical principles are introduced with extensive use of exercises and examples. Applications covered include conventional ships, barges, high speed marine vehicles, semisubmersibles, tension leg platforms, moored or dynamic positionedmore » ships, risers, buoys, fishing nets, jacket structures and gravity platforms. One aim of the book is to provide a physical understanding through simplified mathematical models. In this way one can develop analytical tools to evaluate results from test models, full scale trials or computer simulation, and learns which parameters represent the major contributions and influences on sea loads.« less

Attitude Dynamics, Stability, and Control of a Heliogyro Solar Sail

NASA Astrophysics Data System (ADS)

Pimienta-Penalver, Adonis Reinier

A heliogyro solar sail concept, dubbed `HELIOS', is proposed as an alternative to deep space missions without the need for on-board propellant. Although this type of solar sail has existed in concept for several decades, and some previous studies have investigated certain aspects of its operation, a significant amount of research is still needed to analyze the dynamic and control characteristics of the structure under the projected range of orbital conditions. This work presents an improvement upon the existing discrete-mass models of the heliogyro blade, and the extension of its application from a single membrane blade to a fully-coupled approximation of the dynamics of the HELIOS system with multiple spinning membrane blades around a central hub. The incorporation of structural stiffness and external forcing effects into the model is demonstrated to add a further degree of fidelity in simulating the stability properties of the system. Additionally, the approximated dynamics of multiple-blade heliogyro structures are examined under the effect of solar radiation pressure. Lastly, this study evaluates a control algorithm at each blade root to impose structural integrity and attitude control by coordinating well-known helicopter blade pitching profiles.

Modelface: an Application Programming Interface (API) for Homology Modeling Studies Using Modeller Software

PubMed Central

Sakhteman, Amirhossein; Zare, Bijan

2016-01-01

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures are also implemented inside Modelface. The API is a simple batch based application with no memory occupation and is free of charge for academic use. The application is also able to repair missing atom types in the PDB structures making it suitable for many molecular modeling studies such as docking and molecular dynamic simulation. Some successful instances of modeling studies using Modelface are also reported. PMID:28243276

An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back

PubMed Central

Chiappori, Federica; Merelli, Ivan; Milanesi, Luciano; Colombo, Giorgio; Morra, Giulia

2016-01-01

The Hsp70 is an allosterically regulated family of molecular chaperones. They consist of two structural domains, NBD and SBD, connected by a flexible linker. ATP hydrolysis at the NBD modulates substrate recognition at the SBD, while peptide binding at the SBD enhances ATP hydrolysis. In this study we apply Molecular Dynamics (MD) to elucidate the molecular determinants underlying the allosteric communication from the NBD to the SBD and back. We observe that local structural and dynamical modulation can be coupled to large-scale rearrangements, and that different combinations of ligands at NBD and SBD differently affect the SBD domain mobility. Substituting ADP with ATP in the NBD induces specific structural changes involving the linker and the two NBD lobes. Also, a SBD-bound peptide drives the linker docking by increasing the local dynamical coordination of its C-terminal end: a partially docked DnaK structure is achieved by combining ATP in the NBD and peptide in the SBD. We propose that the MD-based analysis of the inter domain dynamics and structure modulation could be used as a tool to computationally predict the allosteric behaviour and functional response of Hsp70 upon introducing mutations or binding small molecules, with potential applications for drug discovery. PMID:27025773

Emergence, evolution and scaling of online social networks.

PubMed

Wang, Le-Zhi; Huang, Zi-Gang; Rong, Zhi-Hai; Wang, Xiao-Fan; Lai, Ying-Cheng

2014-01-01

Online social networks have become increasingly ubiquitous and understanding their structural, dynamical, and scaling properties not only is of fundamental interest but also has a broad range of applications. Such networks can be extremely dynamic, generated almost instantaneously by, for example, breaking-news items. We investigate a common class of online social networks, the user-user retweeting networks, by analyzing the empirical data collected from Sina Weibo (a massive twitter-like microblogging social network in China) with respect to the topic of the 2011 Japan earthquake. We uncover a number of algebraic scaling relations governing the growth and structure of the network and develop a probabilistic model that captures the basic dynamical features of the system. The model is capable of reproducing all the empirical results. Our analysis not only reveals the basic mechanisms underlying the dynamics of the retweeting networks, but also provides general insights into the control of information spreading on such networks.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. K.

1985-01-01

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

The dynamics of discrete-time computation, with application to recurrent neural networks and finite state machine extraction.

PubMed

Casey, M

1996-08-15

Recurrent neural networks (RNNs) can learn to perform finite state computations. It is shown that an RNN performing a finite state computation must organize its state space to mimic the states in the minimal deterministic finite state machine that can perform that computation, and a precise description of the attractor structure of such systems is given. This knowledge effectively predicts activation space dynamics, which allows one to understand RNN computation dynamics in spite of complexity in activation dynamics. This theory provides a theoretical framework for understanding finite state machine (FSM) extraction techniques and can be used to improve training methods for RNNs performing FSM computations. This provides an example of a successful approach to understanding a general class of complex systems that has not been explicitly designed, e.g., systems that have evolved or learned their internal structure.

A Historical Perspective on Dynamics Testing at the Langley Research Center

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Kvaternik, Raymond G.; Hanks, Brantley R.

2000-01-01

The experience and advancement of Structural dynamics testing for space system applications at the Langley Research Center of the National Aeronautics and Space Administration (NASA) over the past four decades is reviewed. This experience began in the 1960's with the development of a technology base using a variety of physical models to explore dynamic phenomena and to develop reliable analytical modeling capability for space systems. It continued through the 1970's and 80's with the development of rapid, computer-aided test techniques, the testing of low-natural frequency, gravity-sensitive systems, the testing of integrated structures with active flexible motion control, and orbital flight measurements, It extended into the 1990's where advanced computerized system identification methods were developed for estimating the dynamic states of complex, lightweight, flexible aerospace systems, The scope of discussion in this paper includes ground and flight tests and summarizes lessons learned in both successes and failures.

Exploring RNA structure and dynamics through enhanced sampling simulations.

PubMed

Mlýnský, Vojtěch; Bussi, Giovanni

2018-04-01

RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided. Copyright © 2018 Elsevier Ltd. All rights reserved.

Using the dynamic bond to access macroscopically responsive structurally dynamic polymers

NASA Astrophysics Data System (ADS)

Wojtecki, Rudy J.; Meador, Michael A.; Rowan, Stuart J.

2011-01-01

New materials that have the ability to reversibly adapt to their environment and possess a wide range of responses ranging from self-healing to mechanical work are continually emerging. These adaptive systems have the potential to revolutionize technologies such as sensors and actuators, as well as numerous biomedical applications. We will describe the emergence of a new trend in the design of adaptive materials that involves the use of reversible chemistry (both non-covalent and covalent) to programme a response that originates at the most fundamental (molecular) level. Materials that make use of this approach - structurally dynamic polymers - produce macroscopic responses from a change in the material's molecular architecture (that is, the rearrangement or reorganization of the polymer components, or polymeric aggregates). This design approach requires careful selection of the reversible/dynamic bond used in the construction of the material to control its environmental responsiveness.

Nonlinear control of linear parameter varying systems with applications to hypersonic vehicles

NASA Astrophysics Data System (ADS)

Wilcox, Zachary Donald

The focus of this dissertation is to design a controller for linear parameter varying (LPV) systems, apply it specifically to air-breathing hypersonic vehicles, and examine the interplay between control performance and the structural dynamics design. Specifically a Lyapunov-based continuous robust controller is developed that yields exponential tracking of a reference model, despite the presence of bounded, nonvanishing disturbances. The hypersonic vehicle has time varying parameters, specifically temperature profiles, and its dynamics can be reduced to an LPV system with additive disturbances. Since the HSV can be modeled as an LPV system the proposed control design is directly applicable. The control performance is directly examined through simulations. A wide variety of applications exist that can be effectively modeled as LPV systems. In particular, flight systems have historically been modeled as LPV systems and associated control tools have been applied such as gain-scheduling, linear matrix inequalities (LMIs), linear fractional transformations (LFT), and mu-types. However, as the type of flight environments and trajectories become more demanding, the traditional LPV controllers may no longer be sufficient. In particular, hypersonic flight vehicles (HSVs) present an inherently difficult problem because of the nonlinear aerothermoelastic coupling effects in the dynamics. HSV flight conditions produce temperature variations that can alter both the structural dynamics and flight dynamics. Starting with the full nonlinear dynamics, the aerothermoelastic effects are modeled by a temperature dependent, parameter varying state-space representation with added disturbances. The model includes an uncertain parameter varying state matrix, an uncertain parameter varying non-square (column deficient) input matrix, and an additive bounded disturbance. In this dissertation, a robust dynamic controller is formulated for a uncertain and disturbed LPV system. The developed controller is then applied to a HSV model, and a Lyapunov analysis is used to prove global exponential reference model tracking in the presence of uncertainty in the state and input matrices and exogenous disturbances. Simulations with a spectrum of gains and temperature profiles on the full nonlinear dynamic model of the HSV is used to illustrate the performance and robustness of the developed controller. In addition, this work considers how the performance of the developed controller varies over a wide variety of control gains and temperature profiles and are optimized with respect to different performance metrics. Specifically, various temperature profile models and related nonlinear temperature dependent disturbances are used to characterize the relative control performance and effort for each model. Examining such metrics as a function of temperature provides a potential inroad to examine the interplay between structural/thermal protection design and control development and has application for future HSV design and control implementation.

Some Considerations on Short Crack Growth Behaviour in Aircraft Structures,

DTIC Science & Technology

1983-03-01

Aerospace Applications Studies Programme. The results of AGARI) work are reported to the member nations and the NATO Authorities through the AGARI) series...AEROSPACE ENGINFFR AIR FORCE WRIGHT AFRONAUTICAL LABORATORIES (FIBFC) WRIGHT-PATTERSON AFB, OHIO, USA Small crack technology applications to airframe...rowth at Fastener Holes," AFFD,-TR-77-83, Air Force Flight Dynamics Laboratory, April 1q78. 1’-5 8. Rudd, J.L., " Applications of The Equivalent

Investigations into the Structure and Dynamics of Chalcogenide Glasses using High-Resolution Nuclear Magnetic Resonance Spectroscopy

NASA Astrophysics Data System (ADS)

Kaseman, Derrick Charles

Chalcogenide glasses constitute an important class of materials that are sulfides, selenides or tellurides of group IV and/or V elements, namely Ge, As, P and Si with minor concentrations of other elements such as Ga, Sb, In. Because of their infrared transparency that can be tuned by changing chemistry and can be actively altered by exposure to band gap irradiation, chalcogenide glasses find use in passive and active optical devices for applications in the areas of photonics, remote sensing and memory technology. Therefore, it is important to establish predictive models of structure-property relationships for these materials for optimization of their physical properties for various applications. Structural elucidation of chalcogenide glasses is experimentally challenging and in order to make predictive structural models, structural units at both short and intermediate -range length scales must be identified and quantified. Nuclear Magnetic Resonance (NMR) spectroscopy is an element-specific structural probe that is uniquely suited for this task, but resolution and sensitivity issues have severely limited the applications of such techniques in the past. The recent development of multi-dimensional solid-state NMR techniques, such as Phase Adjusted Spinning Sidebands (PASS) and Magic Angle Turning (MAT) can potentially alleviate such issues. In this study novel two-dimensional, high-resolution 77Se and 125Te MATPASS NMR spectroscopic techniques are utilized to elucidate quantitatively the compositional evolution of the short- and intermediate- range atomic structure in three binary chalcogenide glass-forming systems, namely: GexSe100-x, AsxSe100-x , and AsxTe100-x. The spectroscopic results provide unambiguous site speciation and quantification for short- and intermediate-range structural motifs present in these glasses. In turn, for all systems, robust structural models and the corresponding structure-property relationships are successfully established as a function of composition. The results indicate that the physical properties are intimately tied to the topology and chemical order present in each system. Finally, a dynamic version of the two-dimensional 31P PASS NMR spectroscopy is used to study the molecular motion in a supercooled chalcogenide liquid of composition P5Se3. The results clearly display the presence of isotropic rotational reorientation of the constituent molecules at timescales significantly decoupled from that of the structural relaxation near and above Tg. This behavior is atypical of conventional molecular glasses in organic systems in which rotational and translational dynamics remain coupled near Tg. When taken together with previous reports on the dynamics of other globular inorganic molecules, the results support the existence of a "plastic glass" phase where the molecules perform rapid rotation without significant translation.

Structural damage identification using damping: a compendium of uses and features

NASA Astrophysics Data System (ADS)

Cao, M. S.; Sha, G. G.; Gao, Y. F.; Ostachowicz, W.

2017-04-01

The vibration responses of structures under controlled or ambient excitation can be used to detect structural damage by correlating changes in structural dynamic properties extracted from responses with damage. Typical dynamic properties refer to modal parameters: natural frequencies, mode shapes, and damping. Among these parameters, natural frequencies and mode shapes have been investigated extensively for their use in damage characterization by associating damage with reduction in local stiffness of structures. In contrast, the use of damping as a dynamic property to represent structural damage has not been comprehensively elucidated, primarily due to the complexities of damping measurement and analysis. With advances in measurement technologies and analysis tools, the use of damping to identify damage is becoming a focus of increasing attention in the damage detection community. Recently, a number of studies have demonstrated that damping has greater sensitivity for characterizing damage than natural frequencies and mode shapes in various applications, but damping-based damage identification is still a research direction ‘in progress’ and is not yet well resolved. This situation calls for an overall survey of the state-of-the-art and the state-of-the-practice of using damping to detect structural damage. To this end, this study aims to provide a comprehensive survey of uses and features of applying damping in structural damage detection. First, we present various methods for damping estimation in different domains including the time domain, the frequency domain, and the time-frequency domain. Second, we investigate the features and applications of damping-based damage detection methods on the basis of two predominant infrastructure elements, reinforced concrete structures and fiber-reinforced composites. Third, we clarify the influential factors that can impair the capability of damping to characterize damage. Finally, we recommend future research directions for advancing damping-based damage detection. This work holds the promise of (a) helping researchers identify crucial components in damping-based damage detection theories, methods, and technologies, and (b) leading practitioners to better implement damping-based structural damage identification.

A dynamic model of the marriage market-Part 2: simulation of marital states and application to empirical data.

PubMed

Matthews, A P; Garenne, M L

2013-09-01

A dynamic, two-sex, age-structured marriage model is presented. Part 1 focused on first marriage only and described a marriage market matching algorithm. In Part 2 the model is extended to include divorce, widowing, and remarriage. The model produces a self-consistent set of marital states distributed by age and sex in a stable population by means of a gender-symmetric numerical method. The model is compared with empirical data for the case of Zambia. Furthermore, a dynamic marriage function for a changing population is demonstrated in simulations of three hypothetical scenarios of elevated mortality in young to middle adulthood. The marriage model has its primary application to simulation of HIV-AIDS epidemics in African countries. Copyright © 2013 Elsevier Inc. All rights reserved.

System Dynamics

NASA Astrophysics Data System (ADS)

Morecroft, John

System dynamics is an approach for thinking about and simulating situations and organisations of all kinds and sizes by visualising how the elements fit together, interact and change over time. This chapter, written by John Morecroft, describes modern system dynamics which retains the fundamentals developed in the 1950s by Jay W. Forrester of the MIT Sloan School of Management. It looks at feedback loops and time delays that affect system behaviour in a non-linear way, and illustrates how dynamic behaviour depends upon feedback loop structures. It also recognises improvements as part of the ongoing process of managing a situation in order to achieve goals. Significantly it recognises the importance of context, and practitioner skills. Feedback systems thinking views problems and solutions as being intertwined. The main concepts and tools: feedback structure and behaviour, causal loop diagrams, dynamics, are practically illustrated in a wide variety of contexts from a hot water shower through to a symphony orchestra and the practical application of the approach is described through several real examples of its use for strategic planning and evaluation.

Enhanced dynamics of hydrated tRNA on nanodiamond surfaces: A combined neutron scattering and MD simulation study

DOE PAGES

Dhindsa, Gurpreet K.; Bhowmik, Debsindhu; Goswami, Monojoy; ...

2016-09-01

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on NDmore » surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. As a result, our new findings may provide new design principles for safer, improved drug delivery platforms.« less

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Model structure of the stream salmonid simulator (S3)—A dynamic model for simulating growth, movement, and survival of juvenile salmonids

USGS Publications Warehouse

Perry, Russell W.; Plumb, John M.; Jones, Edward C.; Som, Nicholas A.; Hetrick, Nicholas J.; Hardy, Thomas B.

2018-04-06

Fisheries and water managers often use population models to aid in understanding the effect of alternative water management or restoration actions on anadromous fish populations. We developed the Stream Salmonid Simulator (S3) to help resource managers evaluate the effect of management alternatives on juvenile salmonid populations. S3 is a deterministic stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and usable habitat area or carrying capacity. The physical characteristics of each habitat unit and the number of fish occupying each unit, in turn, drive survival and growth within each habitat unit and movement of fish among habitat units.The purpose of this report is to outline the underlying general structure of the S3 model that is common among different applications of the model. We have developed applications of the S3 model for juvenile fall Chinook salmon (Oncorhynchus tshawytscha) in the lower Klamath River. Thus, this report is a companion to current application of the S3 model to the Trinity River (in review). The general S3 model structure provides a biological and physical framework for the salmonid freshwater life cycle. This framework captures important demographics of juvenile salmonids aimed at translating management alternatives into simulated population responses. Although the S3 model is built on this common framework, the model has been constructed to allow much flexibility in application of the model to specific river systems. The ability for practitioners to include system-specific information for the physical stream structure, survival, growth, and movement processes ensures that simulations provide results that are relevant to the questions asked about the population under study.

Applications of the BIOPHYS Algorithm for Physically-Based Retrieval of Biophysical, Structural and Forest Disturbance Information

NASA Technical Reports Server (NTRS)

Peddle, Derek R.; Huemmrich, K. Fred; Hall, Forrest G.; Masek, Jeffrey G.; Soenen, Scott A.; Jackson, Chris D.

2011-01-01

Canopy reflectance model inversion using look-up table approaches provides powerful and flexible options for deriving improved forest biophysical structural information (BSI) compared with traditional statistical empirical methods. The BIOPHYS algorithm is an improved, physically-based inversion approach for deriving BSI for independent use and validation and for monitoring, inventory and quantifying forest disturbance as well as input to ecosystem, climate and carbon models. Based on the multiple-forward mode (MFM) inversion approach, BIOPHYS results were summarized from different studies (Minnesota/NASA COVER; Virginia/LEDAPS; Saskatchewan/BOREAS), sensors (airborne MMR; Landsat; MODIS) and models (GeoSail; GOMS). Applications output included forest density, height, crown dimension, branch and green leaf area, canopy cover, disturbance estimates based on multi-temporal chronosequences, and structural change following recovery from forest fires over the last century. Good correspondences with validation field data were obtained. Integrated analyses of multiple solar and view angle imagery further improved retrievals compared with single pass data. Quantifying ecosystem dynamics such as the area and percent of forest disturbance, early regrowth and succession provide essential inputs to process-driven models of carbon flux. BIOPHYS is well suited for large-area, multi-temporal applications involving multiple image sets and mosaics for assessing vegetation disturbance and quantifying biophysical structural dynamics and change. It is also suitable for integration with forest inventory, monitoring, updating, and other programs.

A fitting empirical potential for NiTi alloy and its application

NASA Astrophysics Data System (ADS)

Ren, Guowu; Tang, Tiegang; Sehitoglu, Huseyin

Due to its superelastic behavior, NiTi shape memory alloy receives considerable attentions over a wide range of industrial and commercial applications. Limited to its complex structural transformation and multiple variants, semiempirical potentials for performing large-scale molecular dynamics simulations to investigate the atomistic mechanical process, are very few. In this work, we construct a new interatomic potential for the NiTi alloy by fitting to experimental or ab initio data. The fitting potential correctly predicts the lattice parameter, structural stability, equation of state for cubic B2(austenite) and monoclinic B19'(martensite) phases. In particular the elastic properties(three elastic constants for B2 and thirteen ones for B19') are in satisfactory agreement with the experiments or ab initio calculations. Furthermore, we apply this potential to conduct the molecular dynamics simulations of the mechanical behavior for NiTi alloy and the results capture its reversible transformation.

Controlled Synthesis and Fluorescence Tracking of Highly Uniform Poly(N-isopropylacrylamide) Microgels.

PubMed

Virtanen, Otto L J; Purohit, Ashvini; Brugnoni, Monia; Wöll, Dominik; Richtering, Walter

2016-09-08

Stimuli-sensitive poly(N-isopropylacrylamide) (PNIPAM) microgels have various prospective practical applications and uses in fundamental research. In this work, we use single particle tracking of fluorescently labeled PNIPAM microgels as a showcase for tuning microgel size by a rapid non-stirred precipitation polymerization procedure. This approach is well suited for prototyping new reaction compositions and conditions or for applications that do not require large amounts of product. Microgel synthesis, particle size and structure determination by dynamic and static light scattering are detailed in the protocol. It is shown that the addition of functional comonomers can have a large influence on the particle nucleation and structure. Single particle tracking by wide-field fluorescence microscopy allows for an investigation of the diffusion of labeled tracer microgels in a concentrated matrix of non-labeled microgels, a system not easily investigated by other methods such as dynamic light scattering.

Hydrolyzable Polyureas Bearing Hindered Urea Bonds

PubMed Central

2015-01-01

Hydrolyzable polymers are widely used materials that have found numerous applications in biomedical, agricultural, plastic, and packaging industrials. They usually contain ester and other hydrolyzable bonds, such as anhydride, acetal, ketal, or imine, in their backbone structures. Here, we report the first design of hydrolyzable polyureas bearing dynamic hindered urea bonds (HUBs) that can reversibly dissociate to bulky amines and isocyanates, the latter of which can be further hydrolyzed by water, driving the equilibrium to facilitate the degradation of polyureas. Polyureas bearing 1-tert-butyl-1-ethylurea bonds that show high dynamicity (high bond dissociation rate), in the form of either linear polymers or cross-linked gels, can be completely degraded by water under mild conditions. Given the simplicity and low cost for the production of polyureas by simply mixing multifunctional bulky amines and isocyanates, the versatility of the structures, and the tunability of the degradation profiles of HUB-bearing polyureas, these materials are potentially of very broad applications. PMID:25406025

Elucidating the design principles of photosynthetic electron-transfer proteins by site-directed spin labeling EPR spectroscopy.

PubMed

Ishara Silva, K; Jagannathan, Bharat; Golbeck, John H; Lakshmi, K V

2016-05-01

Site-directed spin labeling electron paramagnetic resonance (SDSL EPR) spectroscopy is a powerful tool to determine solvent accessibility, side-chain dynamics, and inter-spin distances at specific sites in biological macromolecules. This information provides important insights into the structure and dynamics of both natural and designed proteins and protein complexes. Here, we discuss the application of SDSL EPR spectroscopy in probing the charge-transfer cofactors in photosynthetic reaction centers (RC) such as photosystem I (PSI) and the bacterial reaction center (bRC). Photosynthetic RCs are large multi-subunit proteins (molecular weight≥300 kDa) that perform light-driven charge transfer reactions in photosynthesis. These reactions are carried out by cofactors that are paramagnetic in one of their oxidation states. This renders the RCs unsuitable for conventional nuclear magnetic resonance spectroscopy investigations. However, the presence of native paramagnetic centers and the ability to covalently attach site-directed spin labels in RCs makes them ideally suited for the application of SDSL EPR spectroscopy. The paramagnetic centers serve as probes of conformational changes, dynamics of subunit assembly, and the relative motion of cofactors and peptide subunits. In this review, we describe novel applications of SDSL EPR spectroscopy for elucidating the effects of local structure and dynamics on the electron-transfer cofactors of photosynthetic RCs. Because SDSL EPR Spectroscopy is uniquely suited to provide dynamic information on protein motion, it is a particularly useful method in the engineering and analysis of designed electron transfer proteins and protein networks. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson. Copyright © 2016. Published by Elsevier B.V.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Chemical structure of the Chromophoric Dissolved Organic Matter (CDOM) fluorescent matter.

NASA Astrophysics Data System (ADS)

Blough, N. V.; Del Vecchio, R.; Cartisano, C. M.; Bianca, M.

2017-12-01

The structure(s), distribution and dynamics of CDOM have been investigated over the last several decades largely through optical spectroscopy (including both absorption and fluorescence) due to the fairly inexpensive instrumentation and the easy-to-gather data (over thousands published papers from 1990-2016). Yet, the chemical structure(s) of the light absorbing and emitting species or constituents within CDOM has only recently being proposed and tested through chemical manipulation of selected functional groups (such as carbonyl and carboxylic/phenolic containing molecules) naturally occurring within the organic matter pool. Similarly, fitting models (among which the PArallel FACtor analysis, PARAFAC) have been developed to better understand the nature of a subset of DOM, the CDOM fluorescent matter (FDOM). Fluorescence spectroscopy coupled with chemical tests and PARAFAC analyses could potentially provide valuable insights on CDOM sources and chemical nature of the FDOM pool. However, despite that applications (and publications) of PARAFAC model to FDOM have grown exponentially since its first application/publication (2003), a large fraction of such publications has misinterpreted the chemical meaning of the delivered PARAFAC `components' leading to more confusion than clarification on the nature, distribution and dynamics of the FDOM pool. In this context, we employed chemical manipulation of selected functional groups to gain further insights on the chemical structure of the FDOM and we tested to what extent the PARAFAC `components' represent true fluorophores through a controlled chemical approach with the ultimate goal to provide insights on the chemical nature of such `components' (as well as on the chemical nature of the FDOM) along with the advantages and limitations of the PARAFAC application.

Dynamics of a gravity-gradient stabilized flexible spacecraft

NASA Technical Reports Server (NTRS)

Meirovitch, L.; Juang, J. N.

1974-01-01

The dynamics of gravity-gradient stabilized flexible satellite in the neighborhood of a deformed equilibrium configuration are discussed. First the equilibrium configuration was determined by solving a set of nonlinear differential equations. Then stability of motion about the deformed equilibrium was tested by means of the Liapunov direct method. The natural frequencies of oscillation of the complete structure were calculated. The analysis is applicable to the RAE/B satellite.

Application of TOPEX/Poseidon altimetry to ocean dynamics and geophysics

NASA Technical Reports Server (NTRS)

Douglas, Bruce; Cheney, R.; Miller, L.; Mcadoo, D.; Leetmaa, A.; Schopf, P.; Schwiderski, E. W.

1991-01-01

We will analyze the TOPEX/POSEIDON data using techniques developed for Geosat, although the more accurate TOPEX/POSEIDON data will enable a wider range of problems to be addressed. Our proposed investigations will have five distinct areas: (1) a description of global sea level variability; (2) tropical ocean dynamics; (3) coupled models for El Nino prediction; (4) structure of the lithosphere; and (5) global tide model improvement.

Use of Molecular Dynamics Data in Biochemistry Courses: An Amphipathy Scale to Determine Protein [alpha]-Helix Transmembrane Segments

ERIC Educational Resources Information Center

Mazze, Fernanda M.; Fuzo, Carlos A.; Degreve, Leo; Ciancaglini, Pietro

2008-01-01

The aim of this manuscript is to explain the application of an amphipathy scale obtained from molecular dynamics simulations and to demonstrate how it can be useful in the protein structure field. It is shown that this scale is easy to be used with the advantage of revealing domains of transmembrane [alpha]-helix of proteins without the need of…

Interactive Structure (EUCLID) For Static And Dynamic Representation Of Human Body

NASA Astrophysics Data System (ADS)

Renaud, Ch.; Steck, R.

1983-07-01

A specific software (EUCLID) for static and dynamic representation of human models is described. The data processing system is connected with ERGODATA and used in interactive mode by intrinsic or specific functions. More or less complex representations in 3-D view of models of the human body are developed. Biostereometric and conventional anthropometric raw data from the data bank are processed for different applications in ergonomy.

Single-particle tracking: applications to membrane dynamics.

PubMed

Saxton, M J; Jacobson, K

1997-01-01

Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.

The Emergence of Temporal Structures in Dynamical Systems

NASA Astrophysics Data System (ADS)

Mainzer, Klaus

2010-10-01

Dynamical systems in classical, relativistic and quantum physics are ruled by laws with time reversibility. Complex dynamical systems with time-irreversibility are known from thermodynamics, biological evolution, growth of organisms, brain research, aging of people, and historical processes in social sciences. Complex systems are systems that compromise many interacting parts with the ability to generate a new quality of macroscopic collective behavior the manifestations of which are the spontaneous emergence of distinctive temporal, spatial or functional structures. But, emergence is no mystery. In a general meaning, the emergence of macroscopic features results from the nonlinear interactions of the elements in a complex system. Mathematically, the emergence of irreversible structures is modelled by phase transitions in non-equilibrium dynamics of complex systems. These methods have been modified even for chemical, biological, economic and societal applications (e.g., econophysics). Emergence of irreversible structures can also be simulated by computational systems. The question arises how the emergence of irreversible structures is compatible with the reversibility of fundamental physical laws. It is argued that, according to quantum cosmology, cosmic evolution leads from symmetry to complexity of irreversible structures by symmetry breaking and phase transitions. Thus, arrows of time and aging processes are not only subjective experiences or even contradictions to natural laws, but they can be explained by quantum cosmology and the nonlinear dynamics of complex systems. Human experiences and religious concepts of arrows of time are considered in a modern scientific framework. Platonic ideas of eternity are at least understandable with respect to mathematical invariance and symmetry of physical laws. Heraclit’s world of change and dynamics can be mapped onto our daily real-life experiences of arrows of time.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE PAGES

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

2018-03-22

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Classification of Dynamical Diffusion States in Single Molecule Tracking Microscopy

PubMed Central

Bosch, Peter J.; Kanger, Johannes S.; Subramaniam, Vinod

2014-01-01

Single molecule tracking of membrane proteins by fluorescence microscopy is a promising method to investigate dynamic processes in live cells. Translating the trajectories of proteins to biological implications, such as protein interactions, requires the classification of protein motion within the trajectories. Spatial information of protein motion may reveal where the protein interacts with cellular structures, because binding of proteins to such structures often alters their diffusion speed. For dynamic diffusion systems, we provide an analytical framework to determine in which diffusion state a molecule is residing during the course of its trajectory. We compare different methods for the quantification of motion to utilize this framework for the classification of two diffusion states (two populations with different diffusion speed). We found that a gyration quantification method and a Bayesian statistics-based method are the most accurate in diffusion-state classification for realistic experimentally obtained datasets, of which the gyration method is much less computationally demanding. After classification of the diffusion, the lifetime of the states can be determined, and images of the diffusion states can be reconstructed at high resolution. Simulations validate these applications. We apply the classification and its applications to experimental data to demonstrate the potential of this approach to obtain further insights into the dynamics of cell membrane proteins. PMID:25099798

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

NASA Astrophysics Data System (ADS)

Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

2018-05-01

One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

Colloquium: Non-Markovian dynamics in open quantum systems

NASA Astrophysics Data System (ADS)

Breuer, Heinz-Peter; Laine, Elsi-Mari; Piilo, Jyrki; Vacchini, Bassano

2016-04-01

The dynamical behavior of open quantum systems plays a key role in many applications of quantum mechanics, examples ranging from fundamental problems, such as the environment-induced decay of quantum coherence and relaxation in many-body systems, to applications in condensed matter theory, quantum transport, quantum chemistry, and quantum information. In close analogy to a classical Markovian stochastic process, the interaction of an open quantum system with a noisy environment is often modeled phenomenologically by means of a dynamical semigroup with a corresponding time-independent generator in Lindblad form, which describes a memoryless dynamics of the open system typically leading to an irreversible loss of characteristic quantum features. However, in many applications open systems exhibit pronounced memory effects and a revival of genuine quantum properties such as quantum coherence, correlations, and entanglement. Here recent theoretical results on the rich non-Markovian quantum dynamics of open systems are discussed, paying particular attention to the rigorous mathematical definition, to the physical interpretation and classification, as well as to the quantification of quantum memory effects. The general theory is illustrated by a series of physical examples. The analysis reveals that memory effects of the open system dynamics reflect characteristic features of the environment which opens a new perspective for applications, namely, to exploit a small open system as a quantum probe signifying nontrivial features of the environment it is interacting with. This Colloquium further explores the various physical sources of non-Markovian quantum dynamics, such as structured environmental spectral densities, nonlocal correlations between environmental degrees of freedom, and correlations in the initial system-environment state, in addition to developing schemes for their local detection. Recent experiments addressing the detection, quantification, and control of non-Markovian quantum dynamics are also briefly discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Jincheng; Rimsza, Jessica

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Layerwise mechanics and finite element for the dynamic analysis of piezoelectric composite plates

NASA Technical Reports Server (NTRS)

Saravanos, Dimitris A.; Heyliger, Paul R.; Hopkins, Dale A.

1996-01-01

Laminate and structural mechanics for the analysis of laminated composite plate structures with piezoelectric actuators and sensors are presented. The theories implement layerwise representations of displacements and electric potential, and can model both the global and local electromechanical response of smart composite laminates. Finite-element formulations are developed for the quasi-static and dynamic analysis of smart composite structures containing piezoelectric layers. Comparisons with an exact solution illustrate the accuracy, robustness and capability of the developed mechanics to capture the global and local response of thin and/or thick laminated piezoelectric plates. Additional correlations and numerical applications demonstrate the unique capabilities of the mechanics in analyzing the static and free-vibration response of composite plates with distributed piezoelectric actuators and sensors.

Surfactant mediated polyelectrolyte self-assembly

DOE PAGES

Goswami, Monojoy; Borreguero Calvo, Jose M.; Pincus, Phillip A.; ...

2015-11-25

Self-assembly and dynamics of polyelectrolyte (PE) surfactant complex (PES) is investigated using molecular dynamics simulations. The complexation is systematically studied for five different PE backbone charge densities. At a fixed surfactant concentration the PES complexation exhibits pearl-necklace to agglomerated double spherical structures with a PE chain decorating the surfactant micelles. The counterions do not condense on the complex, but are released in the medium with a random distribution. The relaxation dynamics for three different length scales, polymer chain, segmental and monomer, show distinct features of the charge and neutral species; the counterions are fastest followed by the PE chain andmore » surfactants. The surfactant heads and tails have the slowest relaxation due to their restricted movement inside the agglomerated structure. At the shortest length scale, all the charge and neutral species show similar relaxation dynamics confirming Rouse behavior at monomer length scales. Overall, the present study highlights the structure-property relationship for polymer-surfactant complexation. These results will help improve the understanding of PES complex and should aid in the design of better materials for future applications.« less

A structured overview of trends and technologies used in dynamic hand orthoses.

PubMed

Bos, Ronald A; Haarman, Claudia J W; Stortelder, Teun; Nizamis, Kostas; Herder, Just L; Stienen, Arno H A; Plettenburg, Dick H

2016-06-29

The development of dynamic hand orthoses is a fast-growing field of research and has resulted in many different devices. A large and diverse solution space is formed by the various mechatronic components which are used in these devices. They are the result of making complex design choices within the constraints imposed by the application, the environment and the patient's individual needs. Several review studies exist that cover the details of specific disciplines which play a part in the developmental cycle. However, a general collection of all endeavors around the world and a structured overview of the solution space which integrates these disciplines is missing. In this study, a total of 165 individual dynamic hand orthoses were collected and their mechatronic components were categorized into a framework with a signal, energy and mechanical domain. Its hierarchical structure allows it to reach out towards the different disciplines while connecting them with common properties. Additionally, available arguments behind design choices were collected and related to the trends in the solution space. As a result, a comprehensive overview of the used mechatronic components in dynamic hand orthoses is presented.

Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System's Dynamics: The Life Cycle of the Insulin Receptor.

PubMed

Scheidel, Jennifer; Lindauer, Klaus; Ackermann, Jörg; Koch, Ina

2015-12-17

The insulin-dependent activation and recycling of the insulin receptor play an essential role in the regulation of the energy metabolism, leading to a special interest for pharmaceutical applications. Thus, the recycling of the insulin receptor has been intensively investigated, experimentally as well as theoretically. We developed a time-resolved, discrete model to describe stochastic dynamics and study the approximation of non-linear dynamics in the context of timed Petri nets. Additionally, using a graph-theoretical approach, we analyzed the structure of the regulatory system and demonstrated the close interrelation of structural network properties with the kinetic behavior. The transition invariants decomposed the model into overlapping subnetworks of various sizes, which represent basic functional modules. Moreover, we computed the quasi-steady states of these subnetworks and demonstrated that they are fundamental to understand the dynamic behavior of the system. The Petri net approach confirms the experimental results of insulin-stimulated degradation of the insulin receptor, which represents a common feature of insulin-resistant, hyperinsulinaemic states.

Casting Control of Floating-films into Ribbon-shape Structure by modified Dynamic FTM

NASA Astrophysics Data System (ADS)

Tripathi, A.; Pandey, M.; Nagamatsu, S.; Pandey, S. S.; Hayase, S.; Takashima, W.

2017-11-01

We have developed a new method to obtain Ribbon-shaped floating films via dynamic casting of floating-film and transfer method (dynamic-FTM). Dynamic-FTM is a unique method to prepare oriented thin-film of conjugated polymers (CPs) which is quick and easy. This method has several advantages as compared to the other conventional casting procedure to prepare oriented CP films. In the conventional dynamic FTM appearance of large scale circular orientation poses difficulty not only for practical applications but also hinders the detailed analysis of the orientation mechanism. In this present work, pros and cons of this newly proposed ribbon-shaped floating-film have been discussed in detail from those of the conventional floating-film prepared by dynamic-FTM.

Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

PubMed Central

2017-01-01

Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular biodynamers are commonly produced in aqueous media under mild or even physiological conditions to suit their biorelated applications. In contrast to static biopolymers emphasizing structural stability and unity by using irreversible covalent bonds, molecular biodynamers are seeking relative structural adaptability and diversity through the formation of reversible covalent bonds. Based on these considerations, molecular biodynamers are capable of reorganizing their monomers, generating, identifying, and amplifying the fittest structures in response to environmental factors. Hence, molecular biodynamers have received considerable research attention over the past decades. Accordingly, the construction of molecular biodynamers through equilibrium polymerization of nucleobase-, carbohydrate- or amino-acid-based monomers can lead to the fabrication of dynamic analogues of nucleic acids (DyNAs), polysaccharides (glycodynamers), or proteins (dynamic proteoids), respectively. In this Account, we summarize recent advances in developing different types of molecular biodynamers as structural or functional biomimetics of biopolymers, including DyNAs, glycodynamers, and dynamic proteoids. We introduce how chemists utilize various reversible reactions to generate molecular biodynamers with specific sequences and well-ordered structures in aqueous medium. We also discuss and list their potential applications in various research fields, such as drug delivery, drug discovery, gene sensing, cancer diagnosis, and treatment. PMID:28169527

Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study.

PubMed

Das, Atanu; Mukhopadhyay, Chaitali

2007-10-28

We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide-ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.

Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Das, Atanu; Mukhopadhyay, Chaitali

2007-10-01

We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide—ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.

Molecular dynamics simulations of large macromolecular complexes.

PubMed

Perilla, Juan R; Goh, Boon Chong; Cassidy, C Keith; Liu, Bo; Bernardi, Rafael C; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

2015-04-01

Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

Tensor of effective susceptibility in random magnetic composites: Application to two-dimensional and three-dimensional cases

NASA Astrophysics Data System (ADS)

Posnansky, Oleg P.

2018-05-01

The measuring of dynamic magnetic susceptibility by nuclear magnetic resonance is used for revealing information about the internal structure of various magnetoactive composites. The response of such material on the applied external static and time-varying magnetic fields encodes intrinsic dynamic correlations and depends on links between macroscopic effective susceptibility and structure on the microscopic scale. In the current work we carried out computational analysis of the frequency dependent dynamic magnetic susceptibility and demonstrated its dependence on the microscopic architectural elements while also considering Euclidean dimensionality. The proposed numerical method is efficient in the simulation of nuclear magnetic resonance experiments in two- and three-dimensional random magnetic media by choosing and modeling the influence of the concentration of components and internal hierarchical characteristics of physical parameters.

Microbial Community Structures and Dynamics in the O3/BAC Drinking Water Treatment Process

PubMed Central

Tian, Jian; Lu, Jun; Zhang, Yu; Li, Jian-Cheng; Sun, Li-Chen; Hu, Zhang-Li

2014-01-01

Effectiveness of drinking water treatment, in particular pathogen control during the water treatment process, is always a major public health concern. In this investigation, the application of PCR-DGGE technology to the analysis of microbial community structures and dynamics in the drinking water treatment process revealed several dominant microbial populations including: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Actinobacteria Firmicutes and Cyanobacteria. α-Proteobacteria and β-Proteobacteria were the dominant bacteria during the whole process. Bacteroidetes and Firmicutes were the dominant bacteria before and after treatment, respectively. Firmicutes showed season-dependent changes in population dynamics. Importantly, γ-Proteobacteria, which is a class of medically important bacteria, was well controlled by the O3/biological activated carbon (BAC) treatment, resulting in improved effluent water bio-safety. PMID:24937529

Stochastic modeling and control system designs of the NASA/MSFC Ground Facility for large space structures: The maximum entropy/optimal projection approach

NASA Technical Reports Server (NTRS)

Hsia, Wei-Shen

1986-01-01

In the Control Systems Division of the Systems Dynamics Laboratory of the NASA/MSFC, a Ground Facility (GF), in which the dynamics and control system concepts being considered for Large Space Structures (LSS) applications can be verified, was designed and built. One of the important aspects of the GF is to design an analytical model which will be as close to experimental data as possible so that a feasible control law can be generated. Using Hyland's Maximum Entropy/Optimal Projection Approach, a procedure was developed in which the maximum entropy principle is used for stochastic modeling and the optimal projection technique is used for a reduced-order dynamic compensator design for a high-order plant.

Automated dynamic analytical model improvement for damped structures

NASA Technical Reports Server (NTRS)

Fuh, J. S.; Berman, A.

1985-01-01

A method is described to improve a linear nonproportionally damped analytical model of a structure. The procedure finds the smallest changes in the analytical model such that the improved model matches the measured modal parameters. Features of the method are: (1) ability to properly treat complex valued modal parameters of a damped system; (2) applicability to realistically large structural models; and (3) computationally efficiency without involving eigensolutions and inversion of a large matrix.

Recent Advances in Multidisciplinary Analysis and Optimization, part 3

NASA Technical Reports Server (NTRS)

Barthelemy, Jean-Francois M. (Editor)

1989-01-01

This three-part document contains a collection of technical papers presented at the Second NASA/Air Force Symposium on Recent Advances in Multidisciplinary Analysis and Optimization, held September 28-30, 1988 in Hampton, Virginia. The topics covered include: aircraft design, aeroelastic tailoring, control of aeroelastic structures, dynamics and control of flexible structures, structural design, design of large engineering systems, application of artificial intelligence, shape optimization, software development and implementation, and sensitivity analysis.

Recent Advances in Multidisciplinary Analysis and Optimization, part 2

NASA Technical Reports Server (NTRS)

Barthelemy, Jean-Francois M. (Editor)

1989-01-01

This three-part document contains a collection of technical papers presented at the Second NASA/Air Force Symposium on Recent Advances in Multidisciplinary Analysis and Optimization, held September 28-30, 1988 in Hampton, Virginia. The topics covered include: helicopter design, aeroelastic tailoring, control of aeroelastic structures, dynamics and control of flexible structures, structural design, design of large engineering systems, application of artificial intelligence, shape optimization, software development and implementation, and sensitivity analysis.

Recent Advances in Multidisciplinary Analysis and Optimization, part 1

NASA Technical Reports Server (NTRS)

Barthelemy, Jean-Francois M. (Editor)

1989-01-01

This three-part document contains a collection of technical papers presented at the Second NASA/Air Force Symposium on Recent Advances in Multidisciplinary Analysis and Optimization, held September 28-30, 1988 in Hampton, Virginia. The topics covered include: helicopter design, aeroelastic tailoring, control of aeroelastic structures, dynamics and control of flexible structures, structural design, design of large engineering systems, application of artificial intelligence, shape optimization, software development and implementation, and sensitivity analysis.

Model verification of large structural systems. [space shuttle model response

NASA Technical Reports Server (NTRS)

Lee, L. T.; Hasselman, T. K.

1978-01-01

A computer program for the application of parameter identification on the structural dynamic models of space shuttle and other large models with hundreds of degrees of freedom is described. Finite element, dynamic, analytic, and modal models are used to represent the structural system. The interface with math models is such that output from any structural analysis program applied to any structural configuration can be used directly. Processed data from either sine-sweep tests or resonant dwell tests are directly usable. The program uses measured modal data to condition the prior analystic model so as to improve the frequency match between model and test. A Bayesian estimator generates an improved analytical model and a linear estimator is used in an iterative fashion on highly nonlinear equations. Mass and stiffness scaling parameters are generated for an improved finite element model, and the optimum set of parameters is obtained in one step.

Reponse dynamique des structures sous charges de vent

NASA Astrophysics Data System (ADS)

Gani, Ferawati

The main purpose of this research is to assemble numerical tools that allows realistic dynamic study of structures under wind loading. The availability of such numerical tools is becoming more important for the industry, following previous experiences in structural damages after extreme wind events. The methodology of the present study involves two main steps: (i) preparing the wind loading according to its spatial and temporal correlations by using digitally generated wind or real measured wind; (ii) preparing the numerical model that captures the characteristics of the real structures and respects all the necessary numerical requirements to pursue transient dynamic analyses. The thesis is presented as an ensemble of four articles written for refereed journals and conferences that showcase the contributions of the present study to the advancement of transient dynamic study of structures under wind loading, on the wind model itself (the first article) and on the application of the wind study on complex structures (the next three articles). The articles presented are as follows: (a) the evaluation of three-dimensional correlations of wind, an important issue for more precise prediction of wind loading for flexible and line-like structures, the results presented in this first article helps design engineers to choose a more suitable models to define three-dimensional wind loading; (b) the refinement of design for solar photovoltaic concentrator-tracker structure developed for utility scale, this study addressed concerns related strict operational criteria and fatigue under wind load for a large parabolic truss structure; (c) the study of guyed towers for TLs, the applicability of the static-equivalent method from the current industry documents for the design of this type of flexible TL support was questioned, a simplified method to improve the wind design was proposed; (d) the fundamental issue of nonlinear behaviour under extreme wind loading for single-degree-of-freedom systems is evaluated here, the use of real measured hurricane and winter storm have highlighted the possible interest of taking into account the ductility in the extreme wind loading design. The present research project has shown the versatility of the use of the developed wind study methodology to solve concerns related to different type of complex structures. In addition, this study proposes simplified methods that are useful for practical engineers when there is the need to solve similar problems. Key words: nonlinear, dynamic, wind, guyed tower, parabolic structure, ductility.

Changes in the Coherent Dynamics of Nanoconfined Room Temperature Ionic Liquids

NASA Astrophysics Data System (ADS)

Vallejo, Kevin; Cano, Melissa; Li, Song; Rotner, Gernot; Faraone, Antonio; Banuelos, Jose

Confinement and temperature effects on the coherent dynamics of the room temperature ionic liquid (RTIL) [C10MPy+] [Tf2N-] were investigated using neutron spin-echo (NSE) in two silica matrices with different pore size. Several intermolecular forces give rise to the bulk molecular structure between anions and cations. NSE provided dynamics (via the coherent intermediate scattering function) in the time range of 0.004 to 10 ns, and at Q-values corresponding to intermediate range ordering and inter- and intra-molecular length scales of the RTIL. Pore wall effects were delineated by comparing bulk RTIL dynamics with those of the confined fluid in 2.8 nm and 8 nm pores. Analytical models were applied to the experimental data to extract decay times and amplitudes of each component. We find a fast relaxation outside the experiment time window, a primary relaxation, and slow, surface-induced dynamics, which all speed up with increased temperature, however, the temperature dependence differs between bulk and confinement. This study sheds light on the structure and dynamics of RTILs and is relevant to the optimization of RTILs for green technologies and applications.

Orthogonal Operation of Constitutional Dynamic Networks Consisting of DNA-Tweezer Machines.

PubMed

Yue, Liang; Wang, Shan; Cecconello, Alessandro; Lehn, Jean-Marie; Willner, Itamar

2017-12-26

Overexpression or down-regulation of cellular processes are often controlled by dynamic chemical networks. Bioinspired by nature, we introduce constitutional dynamic networks (CDNs) as systems that emulate the principle of the nature processes. The CDNs comprise dynamically interconvertible equilibrated constituents that respond to external triggers by adapting the composition of the dynamic mixture to the energetic stabilization of the constituents. We introduce a nucleic acid-based CDN that includes four interconvertible and mechanically triggered tweezers, AA', BB', AB' and BA', existing in closed, closed, open, and open configurations, respectively. By subjecting the CDN to auxiliary triggers, the guided stabilization of one of the network constituents dictates the dynamic reconfiguration of the structures of the tweezers constituents. The orthogonal and reversible operations of the CDN DNA tweezers are demonstrated, using T-A·T triplex or K + -stabilized G-quadruplex as structural motifs that control the stabilities of the constituents. The implications of the study rest on the possible applications of input-guided CDN assemblies for sensing, logic gate operations, and programmed activation of molecular machines.

Dynamic Magnification Factor in a Box-Shape Steel Girder

NASA Astrophysics Data System (ADS)

Rahbar-Ranji, A.

2014-01-01

The dynamic effect of moving loads on structures is treated as a dynamic magnification factor when resonant is not imminent. Studies have shown that the calculated magnification factors from field measurements could be higher than the values specified in design codes. It is the main aim of present paper to investigate the applicability and accuracy of a rule-based expression for calculation of dynamic magnification factor for lifting appliances used in marine industry. A steel box shape girder of a crane is considered and transient dynamic analysis using computer code ANSYS is implemented. Dynamic magnification factor is calculated for different loading conditions and compared with rule-based equation. The effects of lifting speeds, acceleration, damping ratio and position of cargo are examined. It is found that rule-based expression underestimate dynamic magnification factor.

On the structure of attractors for discrete, periodically forced systems with applications to population models

Treesearch

James F. Selgrade; James H. Roberds

2001-01-01

This work discusses the effects of periodic forcing on attracting cycles and more complicated attractors for autonomous systems of nonlinear difference equations. Results indicate that an attractor for a periodically forced dynamical system may inherit structure from an attractor of the autonomous (unforced) system and also from the periodicity of the forcing. In...

1997 Technology Applications Report,

DTIC Science & Technology

1997-01-01

handle high -power loads at microwave radio frequencies , microwave vacuum tubes remain the chosen technology to amplify high power. Aria Microwave...structure called the active RF cavity amplifier (ARFCA). With this design , the amplifier handles high -power loads at radio and microwave frequencies ...developed this technology using BMDO-funded modeling methods designed to simulate the dynamics of large space-based structures. Because it increases

Morphology and viscoelastic properties of sealing materials based on EPDM rubber.

PubMed

Milić, J; Aroguz, A; Budinski-Simendić, J; Radicević, R; Prendzov, S

2008-12-01

In this applicative study, the ratio of active and inactive filler loadings was the prime factor for determining the dynamic-mechanical behaviour of ethylene-propylene-diene monomer rubbers. Scanning electron microscopy was used to study the structure of reinforced dense and microcellular elastomeric materials. The effects of filler and blowing agent content on the morphology of composites were investigated. Microcellular samples cured in salt bath show smaller cells and uniform cell size compared with samples cured in hot air. Dynamic-mechanical thermal analysis showed appreciable changes in the viscoelastic properties by increasing active filler content, which could enable tailoring the material properties to suit sealing applications.

Impact compaction of a granular material

DOE PAGES

Fenton, Gregg; Asay, Blaine; Dalton, Devon

2015-05-19

The dynamic behavior of granular materials has importance to a variety of engineering applications. Structural seismic coupling, planetary science, and earth penetration mechanics, are just a few of the application areas. Although the mechanical behavior of granular materials of various types have been studied extensively for several decades, the dynamic behavior of such materials remains poorly understood. High-quality experimental data are needed to improve our general understanding of granular material compaction physics. This study will describe how an instrumented plunger impact system can be used to measure pressure-density relationships for model materials at high and controlled strain rates and subsequentlymore » used for computational modeling.« less

An Assessment of the State-of-the-art in Multidisciplinary Aeromechanical Analyses

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2008-01-01

This paper presents a survey of the current state-of-the-art in multidisciplinary aeromechanical analyses which integrate advanced Computational Structural Dynamics (CSD) and Computational Fluid Dynamics (CFD) methods. The application areas to be surveyed include fixed wing aircraft, turbomachinery, and rotary wing aircraft. The objective of the authors in the present paper, together with a companion paper on requirements, is to lay out a path for a High Performance Computing (HPC) based next generation comprehensive rotorcraft analysis. From this survey of the key technologies in other application areas it is possible to identify the critical technology gaps that stem from unique rotorcraft requirements.

Base reaction optimization of redundant manipulators for space applications

NASA Technical Reports Server (NTRS)

Chung, C. L.; Desa, S.; Desilva, C. W.

1988-01-01

One of the problems associated with redundant manipulators which were proposed for space applications is that the reactions transmitted to the base of the manipulator as a result of the motion of the manipulator will cause undesirable effects on the dynamic behavior of the supporting space structure. It is therefore necessary to minimize the magnitudes of the forces and moments transmitted to the base. It is shown that kinematic redundancy can be used to solve the dynamic problem of minimizing the magnitude of the base reactions. The methodology described is applied to a four degree-of-freedom spatial manipulator with one redundant degree-of-freedom.

An application of nonlinear programming to the design of regulators of a linear-quadratic formulation

NASA Technical Reports Server (NTRS)

Fleming, P.

1983-01-01

A design technique is proposed for linear regulators in which a feedback controller of fixed structure is chosen to minimize an integral quadratic objective function subject to the satisfaction of integral quadratic constraint functions. Application of a nonlinear programming algorithm to this mathematically tractable formulation results in an efficient and useful computer aided design tool. Particular attention is paid to computational efficiency and various recommendations are made. Two design examples illustrate the flexibility of the approach and highlight the special insight afforded to the designer. One concerns helicopter longitudinal dynamics and the other the flight dynamics of an aerodynamically unstable aircraft.

Dynamics and control of twisting bi-stable structures

NASA Astrophysics Data System (ADS)

Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.

2018-02-01

Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states of the bi-stable twisting I-beam structures. The obtained optimal piezoelectric actuator positioning is not necessarily intuitive and when used with the proposed dynamic actuation strategy serve as a blueprint for the actuation of such multi-stable compliant structures to produce fast and large deflections with highly embeddable actuators. This class of structures has potential applications in aerospace systems and soft/compliant robotics.

Efficient Machine Learning Approach for Optimizing Scientific Computing Applications on Emerging HPC Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arumugam, Kamesh

Efficient parallel implementations of scientific applications on multi-core CPUs with accelerators such as GPUs and Xeon Phis is challenging. This requires - exploiting the data parallel architecture of the accelerator along with the vector pipelines of modern x86 CPU architectures, load balancing, and efficient memory transfer between different devices. It is relatively easy to meet these requirements for highly structured scientific applications. In contrast, a number of scientific and engineering applications are unstructured. Getting performance on accelerators for these applications is extremely challenging because many of these applications employ irregular algorithms which exhibit data-dependent control-ow and irregular memory accesses. Furthermore,more » these applications are often iterative with dependency between steps, and thus making it hard to parallelize across steps. As a result, parallelism in these applications is often limited to a single step. Numerical simulation of charged particles beam dynamics is one such application where the distribution of work and memory access pattern at each time step is irregular. Applications with these properties tend to present significant branch and memory divergence, load imbalance between different processor cores, and poor compute and memory utilization. Prior research on parallelizing such irregular applications have been focused around optimizing the irregular, data-dependent memory accesses and control-ow during a single step of the application independent of the other steps, with the assumption that these patterns are completely unpredictable. We observed that the structure of computation leading to control-ow divergence and irregular memory accesses in one step is similar to that in the next step. It is possible to predict this structure in the current step by observing the computation structure of previous steps. In this dissertation, we present novel machine learning based optimization techniques to address the parallel implementation challenges of such irregular applications on different HPC architectures. In particular, we use supervised learning to predict the computation structure and use it to address the control-ow and memory access irregularities in the parallel implementation of such applications on GPUs, Xeon Phis, and heterogeneous architectures composed of multi-core CPUs with GPUs or Xeon Phis. We use numerical simulation of charged particles beam dynamics simulation as a motivating example throughout the dissertation to present our new approach, though they should be equally applicable to a wide range of irregular applications. The machine learning approach presented here use predictive analytics and forecasting techniques to adaptively model and track the irregular memory access pattern at each time step of the simulation to anticipate the future memory access pattern. Access pattern forecasts can then be used to formulate optimization decisions during application execution which improves the performance of the application at a future time step based on the observations from earlier time steps. In heterogeneous architectures, forecasts can also be used to improve the memory performance and resource utilization of all the processing units to deliver a good aggregate performance. We used these optimization techniques and anticipation strategy to design a cache-aware, memory efficient parallel algorithm to address the irregularities in the parallel implementation of charged particles beam dynamics simulation on different HPC architectures. Experimental result using a diverse mix of HPC architectures shows that our approach in using anticipation strategy is effective in maximizing data reuse, ensuring workload balance, minimizing branch and memory divergence, and in improving resource utilization.« less

Thermodynamics of RNA structures by Wang–Landau sampling

PubMed Central

Lou, Feng; Clote, Peter

2010-01-01

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures. Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations. Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/. Contact: clote@bc.edu PMID:20529917

Deployable robotic woven wire structures and joints for space applications

NASA Technical Reports Server (NTRS)

Shahinpoor, MO; Smith, Bradford

1991-01-01

Deployable robotic structures are basically expandable and contractable structures that may be transported or launched to space in a compact form. These structures may then be intelligently deployed by suitable actuators. The deployment may also be done by means of either airbag or spring-loaded typed mechanisms. The actuators may be pneumatic, hydraulic, ball-screw type, or electromagnetic. The means to trigger actuation may be on-board EPROMS, programmable logic controllers (PLCs) that trigger actuation based on some input caused by the placement of the structure in the space environment. The actuation may also be performed remotely by suitable remote triggering devices. Several deployable woven wire structures are examined. These woven wire structures possess a unique form of joint, the woven wire joint, which is capable of moving and changing its position and orientation with respect to the structure itself. Due to the highly dynamic and articulate nature of these joints the 3-D structures built using them are uniquely and highly expandable, deployable, and dynamic. The 3-D structure naturally gives rise to a new generation of deployable three-dimensional spatial structures.

Comparative static curing versus dynamic curing on tablet coating structures.

PubMed

Gendre, Claire; Genty, Muriel; Fayard, Barbara; Tfayli, Ali; Boiret, Mathieu; Lecoq, Olivier; Baron, Michel; Chaminade, Pierre; Péan, Jean Manuel

2013-09-10

Curing is generally required to stabilize film coating from aqueous polymer dispersion. This post-coating drying step is traditionally carried out in static conditions, requiring the transfer of solid dosage forms to an oven. But, curing operation performed directly inside the coating equipment stands for an attractive industrial application. Recently, the use of various advanced physico-chemical characterization techniques i.e., X-ray micro-computed tomography, vibrational spectroscopies (near infrared and Raman) and X-ray microdiffraction, allowed new insights into the film-coating structures of dynamically cured tablets. Dynamic curing end-point was efficiently determined after 4h. The aim of the present work was to elucidate the influence of curing conditions on film-coating structures. Results demonstrated that 24h of static curing and 4h of dynamic curing, both performed at 60°C and ambient relative humidity, led to similar coating layers in terms of drug release properties, porosity, water content, structural rearrangement of polymer chains and crystalline distribution. Furthermore, X-ray microdiffraction measurements pointed out different crystalline coating compositions depending on sample storage time. An aging mechanism might have occur during storage, resulting in the crystallization and the upward migration of cetyl alcohol, coupled to the downward migration of crystalline sodium lauryl sulfate within the coating layer. Interestingly, this new study clearly provided further knowledge into film-coating structures after a curing step and confirmed that curing operation could be performed in dynamic conditions. Copyright © 2013 Elsevier B.V. All rights reserved.

Computational predictions of the new Gallium nitride nanoporous structures

NASA Astrophysics Data System (ADS)

Lien, Le Thi Hong; Tuoc, Vu Ngoc; Duong, Do Thi; Thu Huyen, Nguyen

2018-05-01

Nanoporous structural prediction is emerging area of research because of their advantages for a wide range of materials science and technology applications in opto-electronics, environment, sensors, shape-selective and bio-catalysis, to name just a few. We propose a computationally and technically feasible approach for predicting Gallium nitride nanoporous structures with hollows at the nano scale. The designed porous structures are studied with computations using the density functional tight binding (DFTB) and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications. Their stability is discussed by means of the free energy computed within the lattice-dynamics approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with their parent’s bulk stable phase. The electronic band structures of these nanoporous structures are finally examined in detail.

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

NASA Astrophysics Data System (ADS)

Singh, Krishna P.; Baweja, Lokesh; Wolkenhauer, Olaf; Rahman, Qamar; Gupta, Shailendra K.

2018-03-01

Graphene-based nanomaterials (GBNMs) are widely used in various industrial and biomedical applications. GBNMs of different compositions, size and shapes are being introduced without thorough toxicity evaluation due to the unavailability of regulatory guidelines. Computational toxicity prediction methods are used by regulatory bodies to quickly assess health hazards caused by newer materials. Due to increasing demand of GBNMs in various size and functional groups in industrial and consumer based applications, rapid and reliable computational toxicity assessment methods are urgently needed. In the present work, we investigate the impact of graphene and graphene oxide nanomaterials on the structural conformations of small hepcidin peptide and compare the materials for their structural and conformational changes. Our molecular dynamics simulation studies revealed conformational changes in hepcidin due to its interaction with GBMNs, which results in a loss of its functional properties. Our results indicate that hepcidin peptide undergo severe structural deformations when superimposed on the graphene sheet in comparison to graphene oxide sheet. These observations suggest that graphene is more toxic than a graphene oxide nanosheet of similar area. Overall, this study indicates that computational methods based on structural deformation, using molecular dynamics (MD) simulations, can be used for the early evaluation of toxicity potential of novel nanomaterials.

The Analysis of Crack Growth Initiation, Propagation, and Arrest in Flawed Ship Structures Subjected to Dynamic Loading

DTIC Science & Technology

1984-08-10

most current efforts in EPFM are focused on the application of the J-resistance curve to predict crack initiation and fracture instability. However...element code FRACDYN, which has since been used to solve a variety of problems related to the Navy, NRC, and several industrial applications . Of...that this parameter remains constant during elastic-plastic stable crack growth--see Reference (9). This fact, together with its ease of application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagaoka, Masataka; Core Research for Evolutional Science and Technology; ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520

A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

NERVA dynamic analysis methodology, SPRVIB

NASA Technical Reports Server (NTRS)

Vronay, D. F.

1972-01-01

The general dynamic computer code called SPRVIB (Spring Vib) developed in support of the NERVA (nuclear engine for rocket vehicle application) program is described. Using normal mode techniques, the program computes kinematical responses of a structure caused by various combinations of harmonic and elliptic forcing functions or base excitations. Provision is made for a graphical type of force or base excitation input to the structure. A description of the required input format and a listing of the program are presented, along with several examples illustrating the use of the program. SPRVIB is written in FORTRAN 4 computer language for use on the CDC 6600 or the IBM 360/75 computers.

Numerical and experimental study of bistable plates for morphing structures

NASA Astrophysics Data System (ADS)

Nicassio, F.; Scarselli, G.; Avanzini, G.; Del Core, G.

2017-04-01

This study is concerned with the activation energy threshold of bistable composite plates in order to tailor a bistable system for specific aeronautical applications. The aim is to explore potential configurations of the bistable plates and their dynamic behavior for designing novel morphing structure suitable for aerodynamic surfaces and, as a possible further application, for power harvesters. Bistable laminates have two stable mechanical shapes that can withstand aerodynamic loads without additional constraint forces or locking mechanisms. This kind of structures, when properly loaded, snap-through from one stable configuration to another, causing large strains that can also be used for power harvesting scopes. The transition between the stable states of the composite laminate can be triggered, in principle, simply by aerodynamic loads (pilot, disturbance or passive inputs) without the need of servo-activated control systems. Both numerical simulations based on Finite Element models and experimental testing based on different activating forcing spectra are used to validate this concept. The results show that dynamic activation of bistable plates depend on different parameters that need to be carefully managed for their use as aircraft passive wing flaps.

Development of Test-Analysis Models (TAM) for correlation of dynamic test and analysis results

NASA Technical Reports Server (NTRS)

Angelucci, Filippo; Javeed, Mehzad; Mcgowan, Paul

1992-01-01

The primary objective of structural analysis of aerospace applications is to obtain a verified finite element model (FEM). The verified FEM can be used for loads analysis, evaluate structural modifications, or design control systems. Verification of the FEM is generally obtained as the result of correlating test and FEM models. A test analysis model (TAM) is very useful in the correlation process. A TAM is essentially a FEM reduced to the size of the test model, which attempts to preserve the dynamic characteristics of the original FEM in the analysis range of interest. Numerous methods for generating TAMs have been developed in the literature. The major emphasis of this paper is a description of the procedures necessary for creation of the TAM and the correlation of the reduced models with the FEM or the test results. Herein, three methods are discussed, namely Guyan, Improved Reduced System (IRS), and Hybrid. Also included are the procedures for performing these analyses using MSC/NASTRAN. Finally, application of the TAM process is demonstrated with an experimental test configuration of a ten bay cantilevered truss structure.

A general way for quantitative magnetic measurement by transmitted electrons

NASA Astrophysics Data System (ADS)

Song, Dongsheng; Li, Gen; Cai, Jianwang; Zhu, Jing

2016-01-01

EMCD (electron magnetic circular dichroism) technique opens a new door to explore magnetic properties by transmitted electrons. The recently developed site-specific EMCD technique makes it possible to obtain rich magnetic information from the Fe atoms sited at nonequivalent crystallographic planes in NiFe2O4, however it is based on a critical demand for the crystallographic structure of the testing sample. Here, we have further improved and tested the method for quantitative site-specific magnetic measurement applicable for more complex crystallographic structure by using the effective dynamical diffraction effects (general routine for selecting proper diffraction conditions, making use of the asymmetry of dynamical diffraction for design of experimental geometry and quantitative measurement, etc), and taken yttrium iron garnet (Y3Fe5O12, YIG) with more complex crystallographic structure as an example to demonstrate its applicability. As a result, the intrinsic magnetic circular dichroism signals, spin and orbital magnetic moment of iron with site-specific are quantitatively determined. The method will further promote the development of quantitative magnetic measurement with high spatial resolution by transmitted electrons.

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Building membrane nanopores

NASA Astrophysics Data System (ADS)

Howorka, Stefan

2017-07-01

Membrane nanopores--hollow nanoscale barrels that puncture biological or synthetic membranes--have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.

Precision pointing and control of flexible spacecraft

NASA Technical Reports Server (NTRS)

Bantell, M. H., Jr.

1987-01-01

The problem and long term objectives for the precision pointing and control of flexible spacecraft are given. The four basic objectives are stated in terms of two principle tasks. Under Task 1, robust low order controllers, improved structural modeling methods for control applications and identification methods for structural dynamics are being developed. Under Task 2, a lab test experiment for verification of control laws and system identification algorithms is being developed. For Task 1, work has focused on robust low order controller design and some initial considerations for structural modeling in control applications. For Task 2, work has focused on experiment design and fabrication, along with sensor selection and initial digital controller implementation. Conclusions are given.

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model

PubMed Central

Gordon, J.A.; Freedman, B.R.; Zuskov, A.; Iozzo, R.V.; Birk, D.E.; Soslowsky, L.J.

2015-01-01

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn−/−) and biglycan-null (Bgn−/−) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. PMID:25888014

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model.

PubMed

Gordon, J A; Freedman, B R; Zuskov, A; Iozzo, R V; Birk, D E; Soslowsky, L J

2015-07-16

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn(-/-)) and biglycan-null (Bgn(-/-)) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nouvelles techniques pratiques pour la modelisation du comportement dynamique des systèmes eau-structure

NASA Astrophysics Data System (ADS)

Miquel, Benjamin

The dynamic or seismic behavior of hydraulic structures is, as for conventional structures, essential to assure protection of human lives. These types of analyses also aim at limiting structural damage caused by an earthquake to prevent rupture or collapse of the structure. The particularity of these hydraulic structures is that not only the internal displacements are caused by the earthquake, but also by the hydrodynamic loads resulting from fluid-structure interaction. This thesis reviews the existing complex and simplified methods to perform such dynamic analysis for hydraulic structures. For the complex existing methods, attention is placed on the difficulties arising from their use. Particularly, interest is given in this work on the use of transmitting boundary conditions to simulate the semi infinity of reservoirs. A procedure has been developed to estimate the error that these boundary conditions can introduce in finite element dynamic analysis. Depending on their formulation and location, we showed that they can considerably affect the response of such fluid-structure systems. For practical engineering applications, simplified procedures are still needed to evaluate the dynamic behavior of structures in contact with water. A review of the existing simplified procedures showed that these methods are based on numerous simplifications that can affect the prediction of the dynamic behavior of such systems. One of the main objectives of this thesis has been to develop new simplified methods that are more accurate than those existing. First, a new spectral analysis method has been proposed. Expressions for the fundamental frequency of fluid-structure systems, key parameter of spectral analysis, have been developed. We show that this new technique can easily be implemented in a spreadsheet or program, and that its calculation time is near instantaneous. When compared to more complex analytical or numerical method, this new procedure yields excellent prediction of the dynamic behavior of fluid-structure systems. Spectral analyses ignore the transient and oscillatory nature of vibrations. When such dynamic analyses show that some areas of the studied structure undergo excessive stresses, time history analyses allow a better estimate of the extent of these zones as well as a time notion of these excessive stresses. Furthermore, the existing spectral analyses methods for fluid-structure systems account only for the static effect of higher modes. Thought this can generally be sufficient for dams, for flexible structures the dynamic effect of these modes should be accounted for. New methods have been developed for fluid-structure systems to account for these observations as well as the flexibility of foundations. A first method was developed to study structures in contact with one or two finite or infinite water domains. This new technique includes flexibility of structures and foundations as well as the dynamic effect of higher vibration modes and variations of the levels of the water domains. Extension of this method was performed to study beam structures in contact with fluids. These new developments have also allowed extending existing analytical formulations of the dynamic properties of a dry beam to a new formulation that includes effect of fluid-structure interaction. The method yields a very good estimate of the dynamic behavior of beam-fluid systems or beam like structures in contact with fluid. Finally, a Modified Accelerogram Method (MAM) has been developed to modify the design earthquake into a new accelerogram that directly accounts for the effect of fluid-structure interaction. This new accelerogram can therefore be applied directly to the dry structure (i.e. without water) in order to calculate the dynamic response of the fluid-structure system. This original technique can include numerous parameters that influence the dynamic response of such systems and allows to treat analytically the fluid-structure interaction while keeping the advantages of finite element modeling.

A kinetic theory for age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Chou, Tom; Greenman, Chris

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but they are structurally unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Conversely, current theories that include size-dependent population dynamics (e.g., carrying capacity) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a BBGKY-like hierarchy. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution. NSF.

Exploring space-time structure of human mobility in urban space

NASA Astrophysics Data System (ADS)

Sun, J. B.; Yuan, J.; Wang, Y.; Si, H. B.; Shan, X. M.

2011-03-01

Understanding of human mobility in urban space benefits the planning and provision of municipal facilities and services. Due to the high penetration of cell phones, mobile cellular networks provide information for urban dynamics with a large spatial extent and continuous temporal coverage in comparison with traditional approaches. The original data investigated in this paper were collected by cellular networks in a southern city of China, recording the population distribution by dividing the city into thousands of pixels. The space-time structure of urban dynamics is explored by applying Principal Component Analysis (PCA) to the original data, from temporal and spatial perspectives between which there is a dual relation. Based on the results of the analysis, we have discovered four underlying rules of urban dynamics: low intrinsic dimensionality, three categories of common patterns, dominance of periodic trends, and temporal stability. It implies that the space-time structure can be captured well by remarkably few temporal or spatial predictable periodic patterns, and the structure unearthed by PCA evolves stably over time. All these features play a critical role in the applications of forecasting and anomaly detection.

Analysis and numerical modelling of eddy current damper for vibration problems

NASA Astrophysics Data System (ADS)

Irazu, L.; Elejabarrieta, M. J.

2018-07-01

This work discusses a contactless eddy current damper, which is used to attenuate structural vibration. Eddy currents can remove energy from dynamic systems without any contact and, thus, without adding mass or modifying the rigidity of the structure. An experimental modal analysis of a cantilever beam in the absence of and under a partial magnetic field is conducted in the bandwidth of 01 kHz. The results show that the eddy current phenomenon can attenuate the vibration of the entire structure without modifying the natural frequencies or the mode shapes of the structure itself. In this study, a new inverse method to numerically determine the dynamic properties of the contactless eddy current damper is proposed. The proposed inverse method and the eddy current model based on a lineal viscous force are validated by a practical application. The numerically obtained transfer function correlates with the experimental one, thus showing good agreement in the entire bandwidth of 01 kHz. The proposed method provides an easy and quick tool to model and predict the dynamic behaviour of the contactless eddy current damper, thereby avoiding the use of complex analytical models.

Enhancing Analytical Separations Using Super-Resolution Microscopy

NASA Astrophysics Data System (ADS)

Moringo, Nicholas A.; Shen, Hao; Bishop, Logan D. C.; Wang, Wenxiao; Landes, Christy F.

2018-04-01

Super-resolution microscopy is becoming an invaluable tool to investigate structure and dynamics driving protein interactions at interfaces. In this review, we highlight the applications of super-resolution microscopy for quantifying the physics and chemistry that occur between target proteins and stationary-phase supports during chromatographic separations. Our discussion concentrates on the newfound ability of super-resolved single-protein spectroscopy to inform theoretical parameters via quantification of adsorption-desorption dynamics, protein unfolding, and nanoconfined transport.

Multicore Architecture-aware Scientific Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Srinivasa, Avinash

Modern high performance systems are becoming increasingly complex and powerful due to advancements in processor and memory architecture. In order to keep up with this increasing complexity, applications have to be augmented with certain capabilities to fully exploit such systems. These may be at the application level, such as static or dynamic adaptations or at the system level, like having strategies in place to override some of the default operating system polices, the main objective being to improve computational performance of the application. The current work proposes two such capabilites with respect to multi-threaded scientific applications, in particular a largemore » scale physics application computing ab-initio nuclear structure. The first involves using a middleware tool to invoke dynamic adaptations in the application, so as to be able to adjust to the changing computational resource availability at run-time. The second involves a strategy for effective placement of data in main memory, to optimize memory access latencies and bandwidth. These capabilties when included were found to have a significant impact on the application performance, resulting in average speedups of as much as two to four times.« less

Application of network methods for understanding evolutionary dynamics in discrete habitats.

PubMed

Greenbaum, Gili; Fefferman, Nina H

2017-06-01

In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene-flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population-genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene-flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. © 2017 John Wiley & Sons Ltd.

Initial Results from an Energy-Aware Airborne Dynamic, Data-Driven Application System Performing Sampling in Coherent Boundary-Layer Structures

NASA Astrophysics Data System (ADS)

Frew, E.; Argrow, B. M.; Houston, A. L.; Weiss, C.

2014-12-01

The energy-aware airborne dynamic, data-driven application system (EA-DDDAS) performs persistent sampling in complex atmospheric conditions by exploiting wind energy using the dynamic data-driven application system paradigm. The main challenge for future airborne sampling missions is operation with tight integration of physical and computational resources over wireless communication networks, in complex atmospheric conditions. The physical resources considered here include sensor platforms, particularly mobile Doppler radar and unmanned aircraft, the complex conditions in which they operate, and the region of interest. Autonomous operation requires distributed computational effort connected by layered wireless communication. Onboard decision-making and coordination algorithms can be enhanced by atmospheric models that assimilate input from physics-based models and wind fields derived from multiple sources. These models are generally too complex to be run onboard the aircraft, so they need to be executed in ground vehicles in the field, and connected over broadband or other wireless links back to the field. Finally, the wind field environment drives strong interaction between the computational and physical systems, both as a challenge to autonomous path planning algorithms and as a novel energy source that can be exploited to improve system range and endurance. Implementation details of a complete EA-DDDAS will be provided, along with preliminary flight test results targeting coherent boundary-layer structures.

Spline Approximation of Thin Shell Dynamics

NASA Technical Reports Server (NTRS)

delRosario, R. C. H.; Smith, R. C.

1996-01-01

A spline-based method for approximating thin shell dynamics is presented here. While the method is developed in the context of the Donnell-Mushtari thin shell equations, it can be easily extended to the Byrne-Flugge-Lur'ye equations or other models for shells of revolution as warranted by applications. The primary requirements for the method include accuracy, flexibility and efficiency in smart material applications. To accomplish this, the method was designed to be flexible with regard to boundary conditions, material nonhomogeneities due to sensors and actuators, and inputs from smart material actuators such as piezoceramic patches. The accuracy of the method was also of primary concern, both to guarantee full resolution of structural dynamics and to facilitate the development of PDE-based controllers which ultimately require real-time implementation. Several numerical examples provide initial evidence demonstrating the efficacy of the method.

In-process, non-destructive, dynamic testing of high-speed polymer composite rotors

NASA Astrophysics Data System (ADS)

Kuschmierz, Robert; Filippatos, Angelos; Günther, Philipp; Langkamp, Albert; Hufenbach, Werner; Czarske, Jürgen; Fischer, Andreas

2015-03-01

Polymer composite rotors are lightweight and offer great perspectives in high-speed applications such as turbo machinery. Currently, novel rotor structures and materials are investigated for the purpose of increasing machine efficiency and lifetime, as well as allowing for higher dynamic loads. However, due to the complexity of the composite materials an in-process measurement system is required. This allows for monitoring the evolution of damages under dynamic loads, for testing and predicting the structural integrity of composite rotors in process. In rotor design, it can be used for calibrating and improving models, simulating the dynamic behaviour of polymer composite rotors. The measurement system is to work non-invasive, offer micron uncertainty, as well as a high measurement rate of several tens of kHz. Furthermore, it must be applicable at high surface speeds and under technical vacuum. In order to fulfil these demands a novel laser distance measurement system was developed. It provides the angle resolved measurement of the biaxial deformation of a fibre-reinforced polymer composite rotor with micron uncertainty at surface speeds of more than 300 m/s. Furthermore, a simulation procedure combining a finite element model and a damage mechanics model is applied. A comparison of the measured data and the numerically calculated data is performed to validate the simulation towards rotor expansion. This validating procedure can be used for a model calibration in the future. The simulation procedure could be used to investigate different damage-test cases of the rotor, in order to define its structural behaviour without further experiments.

Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations.

PubMed

Passler, Peter P; Hofer, Thomas S

2017-02-15

Stochastic dynamics is a widely employed strategy to achieve local thermostatization in molecular dynamics simulation studies; however, it suffers from an inherent violation of momentum conservation. Although this short-coming has little impact on structural and short-time dynamic properties, it can be shown that dynamics in the long-time limit such as diffusion is strongly dependent on the respective thermostat setting. Application of the methodically similar dissipative particle dynamics (DPD) provides a simple, effective strategy to ensure the advantages of local, stochastic thermostatization while at the same time the linear momentum of the system remains conserved. In this work, the key parameters to employ the DPD thermostats in the framework of periodic boundary conditions are investigated, in particular the dependence of the system properties on the size of the DPD-region as well as the treatment of forces near the cutoff. Structural and dynamical data for light and heavy water as well as a Lennard-Jones fluid have been compared to simulations executed via stochastic dynamics as well as via use of the widely employed Nose-Hoover chain and Berendsen thermostats. It is demonstrated that a small size of the DPD region is sufficient to achieve local thermalization, while at the same time artifacts in the self-diffusion characteristic for stochastic dynamics are eliminated. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Ultrafast fluorescence upconversion technique and its applications to proteins.

PubMed

Chosrowjan, Haik; Taniguchi, Seiji; Tanaka, Fumio

2015-08-01

The basic principles and main characteristics of the ultrafast time-resolved fluorescence upconversion technique (conventional and space-resolved), including requirements for nonlinear crystals, mixing spectral bandwidth, acceptance angle, etc., are presented. Applications to flavoproteins [wild-type (WT) FMN-binding protein and its W32Y, W32A, E13R, E13K, E13Q and E13T mutants] and photoresponsive proteins [WT photoactive yellow protein and its R52Q mutant in solution and as single crystals] are demonstrated. For flavoproteins, investigations elucidating the effects of ionic charges on ultrafast electron transfer (ET) dynamics are summarized. It is shown that replacement of the ionic amino acid Glu13 and the resulting modification of the electrostatic charge distribution in the protein chromphore-binding pocket substantially alters the ultrafast fluorescence quenching dynamics and ET rate in FMN-binding protein. It is concluded that, together with donor-acceptor distances, electrostatic interactions between ionic photoproducts and other ionic groups in the proteins are important factors influencing the ET rates. In WT photoactive yellow protein and the R52Q mutant, ultrafast photoisomerization dynamics of the chromophore (deprotonated trans-p-coumaric acid) in liquid and crystal phases are investigated. It is shown that the primary dynamics in solution and single-crystal phases are quite similar; hence, the photocycle dynamics and structural differences observed at longer time scales arise mostly from the structural restraints imposed by the crystal lattice rigidity versus the flexibility in solution. © 2014 FEBS.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

NASA Astrophysics Data System (ADS)

Jünger, Felix; Olshausen, Philipp V.; Rohrbach, Alexander

2016-07-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes.

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

PubMed Central

Jünger, Felix; Olshausen, Philipp v.; Rohrbach, Alexander

2016-01-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes. PMID:27465033

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

PubMed

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-07-07

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Multidisciplinary Aerodynamic-Structural Shape Optimization Using Deformation (MASSOUD)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2000-01-01

This paper presents a multidisciplinary shape parameterization approach. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft object animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in the same manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminate plate structures) and high-fidelity (e.g., nonlinear computational fluid dynamics and detailed finite element modeling) analysis tools. This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, camber, and free-form surface. Results are presented for a multidisciplinary application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, and a simple performance module.

Multidisciplinary Aerodynamic-Structural Shape Optimization Using Deformation (MASSOUD)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2000-01-01

This paper presents a multidisciplinary shape parameterization approach. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft object animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in a similar manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminated plate structures) and high-fidelity (e.g., nonlinear computational fluid dynamics and detailed finite element modeling analysis tools. This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, camber, and free-form surface. Results are presented for a multidisciplinary design optimization application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, and a simple performance module.

Research and Applications in Aeroelasticity and Structural Dynamics at the NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Abel, Irving

1997-01-01

An overview of recently completed programs in aeroelasticity and structural dynamics research at the NASA Langley Research Center is presented. Methods used to perform flutter clearance studies in the wind-tunnel on a high performance fighter are discussed. Recent advances in the use of smart structures and controls to solve aeroelastic problems, including flutter and gust response are presented. An aeroelastic models program designed to support an advanced high speed civil transport is described. An extension to transonic small disturbance theory that better predicts flows involving separation and reattachment is presented. The results of a research study to determine the effects of flexibility on the taxi and takeoff characteristics of a high speed civil transport are presented. The use of photogrammetric methods aboard Space Shuttle to measure spacecraft dynamic response is discussed. Issues associated with the jitter response of multi-payload spacecraft are discussed. Finally a Space Shuttle flight experiment that studied the control of flexible spacecraft is described.

Neural control of tuneable skin iridescence in squid

PubMed Central

Wardill, T. J.; Gonzalez-Bellido, P. T.; Crook, R. J.; Hanlon, R. T.

2012-01-01

Fast dynamic control of skin coloration is rare in the animal kingdom, whether it be pigmentary or structural. Iridescent structural coloration results when nanoscale structures disrupt incident light and selectively reflect specific colours. Unlike animals with fixed iridescent coloration (e.g. butterflies), squid iridophores (i.e. aggregations of iridescent cells in the skin) produce dynamically tuneable structural coloration, as exogenous application of acetylcholine (ACh) changes the colour and brightness output. Previous efforts to stimulate iridophores neurally or to identify the source of endogenous ACh were unsuccessful, leaving researchers to question the activation mechanism. We developed a novel neurophysiological preparation in the squid Doryteuthis pealeii and demonstrated that electrical stimulation of neurons in the skin shifts the spectral peak of the reflected light to shorter wavelengths (greater than 145 nm) and increases the peak reflectance (greater than 245%) of innervated iridophores. We show ACh is released within the iridophore layer and that extensive nerve branching is seen within the iridophore. The dynamic colour shift is significantly faster (17 s) than the peak reflectance increase (32 s), revealing two distinct mechanisms. Responses from a structurally altered preparation indicate that the reflectin protein condensation mechanism explains peak reflectance change, while an undiscovered mechanism causes the fast colour shift. PMID:22896651

Vibration energy harvesting based monitoring of an operational bridge undergoing forced vibration and train passage

NASA Astrophysics Data System (ADS)

Cahill, Paul; Hazra, Budhaditya; Karoumi, Raid; Mathewson, Alan; Pakrashi, Vikram

2018-06-01

The application of energy harvesting technology for monitoring civil infrastructure is a bourgeoning topic of interest. The ability of kinetic energy harvesters to scavenge ambient vibration energy can be useful for large civil infrastructure under operational conditions, particularly for bridge structures. The experimental integration of such harvesters with full scale structures and the subsequent use of the harvested energy directly for the purposes of structural health monitoring shows promise. This paper presents the first experimental deployment of piezoelectric vibration energy harvesting devices for monitoring a full-scale bridge undergoing forced dynamic vibrations under operational conditions using energy harvesting signatures against time. The calibration of the harvesters is presented, along with details of the host bridge structure and the dynamic assessment procedures. The measured responses of the harvesters from the tests are presented and the use the harvesters for the purposes of structural health monitoring (SHM) is investigated using empirical mode decomposition analysis, following a bespoke data cleaning approach. Finally, the use of sequential Karhunen Loeve transforms to detect train passages during the dynamic assessment is presented. This study is expected to further develop interest in energy-harvesting based monitoring of large infrastructure for both research and commercial purposes.

Using a Java Dynamic Tree to manage the terminology in a suite of medical applications.

PubMed

Yang, K; Evens, M W; Trace, D A

2008-01-01

Now that the National Library of Medicine has made SNOMED-CT widely available, we are trying to manage the terminology of a whole suite of medical applications and map our terminology into that in SNOMED. This paper describes the design and implementation of the Java Dynamic Tree that provides structure to our medical terminology and explains how it functions as the core of our system. The tree was designed to reflect the stages in a patient interview, so it contains components for identifying the patient and the provider, a large set of chief complaints, review of systems, physical examination, several history modules, medications, laboratory tests, imaging, and special procedures. The tree is mirrored in a commercial DBMS, which also stores multi-encounter patient data, disorder patterns for our Bayesian diagnostic system, and the data and rules for other expert systems. The DBMS facilitates the import and export of large terminology files. Our Java Dynamic Tree allows the health care provider to view the entire terminology along with the structure that supports it, as well as the mechanism for the generation of progress notes and other documents, in terms of a single hierarchical structure. Changes in terminology can be propagated through the system under the control of the expert. The import/ export facility has been a major help by replacing our original terminology by the terminology in SNOMED-CT.

Scaling Irregular Applications through Data Aggregation and Software Multithreading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morari, Alessandro; Tumeo, Antonino; Chavarría-Miranda, Daniel

Bioinformatics, data analytics, semantic databases, knowledge discovery are emerging high performance application areas that exploit dynamic, linked data structures such as graphs, unbalanced trees or unstructured grids. These data structures usually are very large, requiring significantly more memory than available on single shared memory systems. Additionally, these data structures are difficult to partition on distributed memory systems. They also present poor spatial and temporal locality, thus generating unpredictable memory and network accesses. The Partitioned Global Address Space (PGAS) programming model seems suitable for these applications, because it allows using a shared memory abstraction across distributed-memory clusters. However, current PGAS languagesmore » and libraries are built to target regular remote data accesses and block transfers. Furthermore, they usually rely on the Single Program Multiple Data (SPMD) parallel control model, which is not well suited to the fine grained, dynamic and unbalanced parallelism of irregular applications. In this paper we present {\\bf GMT} (Global Memory and Threading library), a custom runtime library that enables efficient execution of irregular applications on commodity clusters. GMT integrates a PGAS data substrate with simple fork/join parallelism and provides automatic load balancing on a per node basis. It implements multi-level aggregation and lightweight multithreading to maximize memory and network bandwidth with fine-grained data accesses and tolerate long data access latencies. A key innovation in the GMT runtime is its thread specialization (workers, helpers and communication threads) that realize the overall functionality. We compare our approach with other PGAS models, such as UPC running using GASNet, and hand-optimized MPI code on a set of typical large-scale irregular applications, demonstrating speedups of an order of magnitude.« less

Dynamic fiber Bragg gratings based health monitoring system of composite aerospace structures

NASA Astrophysics Data System (ADS)

Panopoulou, A.; Loutas, T.; Roulias, D.; Fransen, S.; Kostopoulos, V.

2011-09-01

The main purpose of the current work is to develop a new system for structural health monitoring of composite aerospace structures based on real-time dynamic measurements, in order to identify the structural state condition. Long-gauge Fibre Bragg Grating (FBG) optical sensors were used for monitoring the dynamic response of the composite structure. The algorithm that was developed for structural damage detection utilizes the collected dynamic response data, analyzes them in various ways and through an artificial neural network identifies the damage state and its location. Damage was simulated by slightly varying locally the mass of the structure (by adding a known mass) at different zones of the structure. Lumped masses in different locations upon the structure alter the eigen-frequencies in a way similar to actual damage. The structural dynamic behaviour has been numerically simulated and experimentally verified by means of modal testing on two different composite aerospace structures. Advanced digital signal processing techniques, e.g. the wavelet transform (WT), were used for the analysis of the dynamic response for feature extraction. WT's capability of separating the different frequency components in the time domain without loosing frequency information makes it a versatile tool for demanding signal processing applications. The use of WT is also suggested by the no-stationary nature of dynamic response signals and the opportunity of evaluating the temporal evolution of their frequency contents. Feature extraction is the first step of the procedure. The extracted features are effective indices of damage size and location. The classification step comprises of a feed-forward back propagation network, whose output determines the simulated damage location. Finally, dedicated training and validation activities were carried out by means of numerical simulations and experimental procedures. Experimental validation was performed initially on a flat stiffened panel, representing a section of a typical aeronautical structure, manufactured and tested in the lab and, as a second step, on a scaled up space oriented structure, which is a composite honeycomb plate, used as a deployment base for antenna arrays. An integrated FBG sensor network, based on the advantage of multiplexing, was mounted on both structures and different excitation positions and boundary conditions were used. The analysis of operational dynamic responses was employed to identify both the damage and its position. The system that was designed and tested initially on the thin composite panel, was successfully validated on the larger honeycomb structure. Numerical simulation of both structures was used as a support tool at all the steps of the work providing among others the location of the optical sensors used. The proposed work will be the base for the whole system qualification and validation on an antenna reflector in future work.

Test and Analysis of an Inflatable Parabolic Dish Antenna

NASA Technical Reports Server (NTRS)

Gaspar, james L.; Sreekantamurthy, Tham; Mann, Troy; Behun, Vaughn; Romanofsky, Robert; Lambert, Kevin; Pearson, James

2006-01-01

NASA is developing ultra-lightweight structures technology for large communication antennas for application to space missions. With these goals in mind, SRS Technologies has been funded by NASA Glenn Research Center (GRC) to undertake the development of a subscale ultra-thin membrane inflatable antenna for deep-space applications. One of the research goals is to develop approaches for prediction of the radio frequency and structural characteristics of inflatable and rigidizable membrane antenna structures. GRC has teamed with NASA Langley Research Center (LaRC) to evaluate inflatable and rigidizable antenna concepts for potential space missions. GRC has completed tests to evaluate RF performance, while LaRC completed structural tests and analysis to evaluate the static shape and structural dynamic responses of a laboratory model of a 0.3 meter antenna. This paper presents the details of the tests and analysis completed to evaluate the radio frequency and structural characteristics of the antenna.

From Two- to Three-Dimensional Structures of a Supertetrahedral Boran Using Density Functional Calculations.

PubMed

Getmanskii, Iliya V; Minyaev, Ruslan M; Steglenko, Dmitrii V; Koval, Vitaliy V; Zaitsev, Stanislav A; Minkin, Vladimir I

2017-08-14

With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two- and three-dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two- and three-layer systems resulted in the construction of a three-dimensional supertetrahedral borane crystal structure. The two-dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three-dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm -3 ) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.