Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

PubMed Central

Han, Nanyu; Mu, Yuguang

2013-01-01

Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147–150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus. PMID:23593372

Shape Morphing Adaptive Radiator Technology (SMART) Updates to Techport Entry

NASA Technical Reports Server (NTRS)

Erickson, Lisa; Bertagne, Christopher; Hartl, Darren; Witcomb, John; Cognata, Thomas

2017-01-01

The Shape-Morphing Adaptive Radiator Technology (SMART) project builds off the FY16 research effort that developed a flexible composite radiator panel and demonstrated its ability to actuate from SMA's attached to it. The proposed FY17 Shape-Morphing Adaptive Radiator Technology (SMART) project's goal is to 1) develop a practical radiator design with shape memory alloys (SMAs) bonded to the radiator's panel, and 2) build a multi-panel radiator prototype for subsequent system level thermal vacuum tests. The morphing radiator employs SMA materials to passively change its shape to adapt its rate of heat rejection to vehicle requirements. Conceptually, the radiator panel has a naturally closed position (like a cylinder) in a cold environment. Whenever the radiator's temperature gradually rises, SMA's affixed to the face sheet will pull the face sheet open a commensurate amount - increasing the radiators view to space and causing it to reject more heat. In a vehicle, the radiator's variable heat rejection capabilities would reduce the number of additional heat rejection devices in a vehicle's thermal control system. This technology aims to help achieve the required maximum to minimum heat rejection ratio required for manned space vehicles to adopt a lighter, simpler, single loop thermal control architecture (ATCS). Single loop architectures are viewed as an attractive means to reduce mass and complexity over traditional dual-loop solutions. However, fluids generally considered safe enough to flow within crewed cabins (e.g. propylene glycol-water mixtures) have much higher freezing points and viscosities than those used in the external sides of dual loop ATCSs (e.g. Ammonia and HFE7000).

Functional Loop Dynamics of the Streptavidin-Biotin Complex

PubMed Central

Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

2015-01-01

Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer. PMID:25601277

Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP.

PubMed

Yang, Rong; Lee, Matthew C; Yan, Honggao; Duan, Yong

2005-07-01

Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding to its first substrate, ATP. Two of the three surface loops (loop 2 and loop 3) accounting for most of the conformational differences appear to be confined by crystal contacts, raising questions about the putative large-scale induced-fit conformational change of HPPK and the functional roles of the conserved side-chain residues on the loops. To investigate the loop dynamics in crystal-free environment, we carried out molecular dynamics and locally enhanced sampling simulations of the apo-enzyme and the HPPK.MgATP complex. Our simulations showed that the crystallographic B-factors underestimated the loop dynamics considerably. We found that the open-conformation of loop 3 in the binary complex is accessible to the apo-enzyme and is the favored conformation in solution phase. These results revise our previous view of HPPK-substrate interactions and the associated functional mechanism of conformational change. The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design.

Dynamical transitions of a driven Ising interface

NASA Astrophysics Data System (ADS)

Sahai, Manish K.; Sengupta, Surajit

2008-03-01

We study the structure of an interface in a three-dimensional Ising system created by an external nonuniform field H(r,t) . H changes sign over a two-dimensional plane of arbitrary orientation. When the field is pulled with velocity ve , [i.e., H(r,t)=H(r-vet) ], the interface undergoes several dynamical transitions. For low velocities it is pinned by the field profile and moves along with it, the distribution of local slopes undergoing a series of commensurate-incommensurate transitions. For large ve the interface depins and grows with Kardar-Parisi-Zhang exponents.

Research on the Dynamic Hysteresis Loop Model of the Residence Times Difference (RTD)-Fluxgate

PubMed Central

Wang, Yanzhang; Wu, Shujun; Zhou, Zhijian; Cheng, Defu; Pang, Na; Wan, Yunxia

2013-01-01

Based on the core hysteresis features, the RTD-fluxgate core, while working, is repeatedly saturated with excitation field. When the fluxgate simulates, the accurate characteristic model of the core may provide a precise simulation result. As the shape of the ideal hysteresis loop model is fixed, it cannot accurately reflect the actual dynamic changing rules of the hysteresis loop. In order to improve the fluxgate simulation accuracy, a dynamic hysteresis loop model containing the parameters which have actual physical meanings is proposed based on the changing rule of the permeability parameter when the fluxgate is working. Compared with the ideal hysteresis loop model, this model has considered the dynamic features of the hysteresis loop, which makes the simulation results closer to the actual output. In addition, other hysteresis loops of different magnetic materials can be explained utilizing the described model for an example of amorphous magnetic material in this manuscript. The model has been validated by the output response comparison between experiment results and fitting results using the model. PMID:24002230

Trajectory tracking control for underactuated stratospheric airship

NASA Astrophysics Data System (ADS)

Zheng, Zewei; Huo, Wei; Wu, Zhe

2012-10-01

Stratospheric airship is a new kind of aerospace system which has attracted worldwide developing interests for its broad application prospects. Based on the trajectory linearization control (TLC) theory, a novel trajectory tracking control method for an underactuated stratospheric airship is presented in this paper. Firstly, the TLC theory is described sketchily, and the dynamic model of the stratospheric airship is introduced with kinematics and dynamics equations. Then, the trajectory tracking control strategy is deduced in detail. The designed control system possesses a cascaded structure which consists of desired attitude calculation, position control loop and attitude control loop. Two sub-loops are designed for the position and attitude control loops, respectively, including the kinematics control loop and dynamics control loop. Stability analysis shows that the controlled closed-loop system is exponentially stable. Finally, simulation results for the stratospheric airship to track typical trajectories are illustrated to verify effectiveness of the proposed approach.

Well-observed dynamics of flaring and peripheral coronal magnetic loops during an M-class limb flare

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

Shen, Jinhua; Zhou, Tuanhui; Ji, Haisheng

2014-08-20

In this paper, we present a variety of well-observed dynamic behaviors for the flaring and peripheral magnetic loops of the M6.6 class extreme limb flare that occurred on 2011 February 24 (SOL2011-02-24T07:20) from EUV observations by the Atmospheric Imaging Assembly on the Solar Dynamics Observatory and X-ray observations by RHESSI. The flaring loop motion confirms the earlier contraction-expansion picture. We find that the U-shaped trajectory delineated by the X-ray corona source of the flare roughly follows the direction of a filament eruption associated with the flare. Different temperature structures of the coronal source during the contraction and expansion phases stronglymore » suggest different kinds of magnetic reconnection processes. For some peripheral loops, we discover that their dynamics are closely correlated with the filament eruption. During the slow rising to abrupt, fast rising of the filament, overlying peripheral magnetic loops display different responses. Two magnetic loops on the elbow of the active region had a slow descending motion followed by an abrupt successive fast contraction, while magnetic loops on the top of the filament were pushed outward, slowly being inflated for a while and then erupting as a moving front. We show that the filament activation and eruption play a dominant role in determining the dynamics of the overlying peripheral coronal magnetic loops.« less

Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

NASA Astrophysics Data System (ADS)

Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

2009-03-01

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

Dynamic loop gain increases upon adopting the supine body position during sleep in patients with obstructive sleep apnoea.

PubMed

Joosten, Simon A; Landry, Shane A; Sands, Scott A; Terrill, Philip I; Mann, Dwayne; Andara, Christopher; Skuza, Elizabeth; Turton, Anthony; Berger, Philip; Hamilton, Garun S; Edwards, Bradley A

2017-11-01

Obstructive sleep apnoea (OSA) is typically worse in the supine versus lateral sleeping position. One potential factor driving this observation is a decrease in lung volume in the supine position which is expected by theory to increase a key OSA pathogenic factor: dynamic ventilatory control instability (i.e. loop gain). We aimed to quantify dynamic loop gain in OSA patients in the lateral and supine positions, and to explore the relationship between change in dynamic loop gain and change in lung volume with position. Data from 20 patients enrolled in previous studies on the effect of body position on OSA pathogenesis were retrospectively analysed. Dynamic loop gain was calculated from routinely collected polysomnographic signals using a previously validated mathematical model. Lung volumes were measured in the awake state with a nitrogen washout technique. Dynamic loop gain was significantly higher in the supine than in the lateral position (0.77 ± 0.15 vs 0.68 ± 0.14, P = 0.012). Supine functional residual capacity (FRC) was significantly lower than lateral FRC (81.0 ± 15.4% vs 87.3 ± 18.4% of the seated FRC, P = 0.021). The reduced FRC we observed on moving to the supine position was predicted by theory to increase loop gain by 10.2 (0.6, 17.1)%, a value similar to the observed increase of 8.4 (-1.5, 31.0)%. Dynamic loop gain increased by a small but statistically significant amount when moving from the lateral to supine position and this may, in part, contribute to the worsening of OSA in the supine sleeping position. © 2017 Asian Pacific Society of Respirology.

Quantum incommensurate skyrmion crystals and commensurate to in-commensurate transitions in cold atoms and materials with spin-orbit couplings in a Zeeman field

NASA Astrophysics Data System (ADS)

Sun, Fadi; Ye, Jinwu; Liu, Wu-Ming

2017-08-01

In this work, we study strongly interacting spinor atoms in a lattice subject to a two dimensional (2d) anisotropic Rashba type of spin orbital coupling (SOC) and an Zeeman field. We find the interplay between the Zeeman field and the SOC provides a new platform to host rich and novel classes of quantum commensurate and in-commensurate phases, excitations and phase transitions. These commensurate phases include two collinear states at low and high Zeeman field, two co-planar canted states at mirror reflected SOC parameters respectively. Most importantly, there are non-coplanar incommensurate Skyrmion (IC-SkX) crystal phases surrounded by the four commensurate phases. New excitation spectra above all the five phases, especially on the IC-SKX phase are computed. Three different classes of quantum commensurate to in-commensurate transitions from the IC-SKX to its four neighboring commensurate phases are identified. Finite temperature behaviors and transitions are discussed. The critical temperatures of all the phases can be raised above that reachable by current cold atom cooling techniques simply by tuning the number of atoms N per site. In view of recent impressive experimental advances in generating 2d SOC for cold atoms in optical lattices, these new many-body phenomena can be explored in the current and near future cold atom experiments. Applications to various materials such as MnSi, {Fe}}0.5 {Co}}0.5Si, especially the complex incommensurate magnetic ordering in Li2IrO3 are given.

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains.

PubMed

Krieger, Florian; Möglich, Andreas; Kiefhaber, Thomas

2005-03-16

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.

Man-in-the-control-loop simulation of manipulators

NASA Technical Reports Server (NTRS)

Chang, J. L.; Lin, Tsung-Chieh; Yae, K. Harold

1989-01-01

A method to achieve man-in-the-control-loop simulation is presented. Emerging real-time dynamics simulation suggests a potential for creating an interactive design workstation with a human operator in the control loop. The recursive formulation for multibody dynamics simulation is studied to determine requirements for man-in-the-control-loop simulation. High speed computer graphics techniques provides realistic visual cues for the simulator. Backhoe and robot arm simulations are implemented to demonstrate the capability of man-in-the-control-loop simulation.

Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis

PubMed Central

Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

2014-01-01

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements. PMID:24403092

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

Similarity Metrics for Closed Loop Dynamic Systems

NASA Technical Reports Server (NTRS)

Whorton, Mark S.; Yang, Lee C.; Bedrossian, Naz; Hall, Robert A.

2008-01-01

To what extent and in what ways can two closed-loop dynamic systems be said to be "similar?" This question arises in a wide range of dynamic systems modeling and control system design applications. For example, bounds on error models are fundamental to the controller optimization with modern control design methods. Metrics such as the structured singular value are direct measures of the degree to which properties such as stability or performance are maintained in the presence of specified uncertainties or variations in the plant model. Similarly, controls-related areas such as system identification, model reduction, and experimental model validation employ measures of similarity between multiple realizations of a dynamic system. Each area has its tools and approaches, with each tool more or less suited for one application or the other. Similarity in the context of closed-loop model validation via flight test is subtly different from error measures in the typical controls oriented application. Whereas similarity in a robust control context relates to plant variation and the attendant affect on stability and performance, in this context similarity metrics are sought that assess the relevance of a dynamic system test for the purpose of validating the stability and performance of a "similar" dynamic system. Similarity in the context of system identification is much more relevant than are robust control analogies in that errors between one dynamic system (the test article) and another (the nominal "design" model) are sought for the purpose of bounding the validity of a model for control design and analysis. Yet system identification typically involves open-loop plant models which are independent of the control system (with the exception of limited developments in closed-loop system identification which is nonetheless focused on obtaining open-loop plant models from closed-loop data). Moreover the objectives of system identification are not the same as a flight test and hence system identification error metrics are not directly relevant. In applications such as launch vehicles where the open loop plant is unstable it is similarity of the closed-loop system dynamics of a flight test that are relevant.

Molecular dynamics simulation of hepatitis C virus IRES IIId domain: structural behavior, electrostatic and energetic analysis.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Di-Giorgio, Audrey; Condom, Roger; Cabrol-Bass, Daniel

2004-02-01

The dynamic behavior of the HCV IRES IIId domain is analyzed by means of a 2.6-ns molecular dynamics simulation, starting from an NMR structure. The simulation is carried out in explicit water with Na+ counterions, and particle-mesh Ewald summation is used for the electrostatic interactions. In this work, we analyze selected patterns of the helix that are crucial for IRES activity and that could be considered as targets for the intervention of inhibitors, such as the hexanucleotide terminal loop (more particularly its three consecutive guanines) and the loop-E motif. The simulation has allowed us to analyze the dynamics of the loop substructure and has revealed a behavior among the guanine bases that might explain the different role of the third guanine of the GGG triplet upon molecular recognition. The accessibility of the loop-E motif and the loop major and minor groove is also examined, as well as the effect of Na+ or Mg2+ counterion within the simulation. The electrostatic analysis reveals several ion pockets, not discussed in the experimental structure. The positions of these ions are useful for locating specific electrostatic recognition sites for potential inhibitor binding.

A Dynamic Model of Sustainment Investment

DTIC Science & Technology

2015-02-01

Sustainment System Dynamics Model 11 Figure 7: Core Structure of Sustainment Work 12 Figure 8: Bandwagon Effect Loop 13 Figure 9: Limits to Growth Loop 14...Dynamics Model sustainment capacity sustainment performance gap Bandwagon Effect R1 Limits to Growth B1 S Work Smarter B3 Work Bigger B2 desired...which is of concern primarily when using the model as a vehicle for research. Figure 8 depicts a reinforcing loop called the “ Bandwagon Effect

Feedback control laws for highly maneuverable aircraft

NASA Technical Reports Server (NTRS)

Garrard, William L.; Balas, Gary J.

1994-01-01

During the first half of the year, the investigators concentrated their efforts on completing the design of control laws for the longitudinal axis of the HARV. During the second half of the year they concentrated on the synthesis of control laws for the lateral-directional axes. The longitudinal control law design efforts can be briefly summarized as follows. Longitudinal control laws were developed for the HARV using mu synthesis design techniques coupled with dynamic inversion. An inner loop dynamic inversion controller was used to simplify the system dynamics by eliminating the aerodynamic nonlinearities and inertial cross coupling. Models of the errors resulting from uncertainties in the principal longitudinal aerodynamic terms were developed and included in the model of the HARV with the inner loop dynamic inversion controller. This resulted in an inner loop transfer function model which was an integrator with the modeling errors characterized as uncertainties in gain and phase. Outer loop controllers were then designed using mu synthesis to provide robustness to these modeling errors and give desired response to pilot inputs. Both pitch rate and angle of attack command following systems were designed. The following tasks have been accomplished for the lateral-directional controllers: inner and outer loop dynamic inversion controllers have been designed; an error model based on a linearized perturbation model of the inner loop system was derived; controllers for the inner loop system have been designed, using classical techniques, that control roll rate and Dutch roll response; the inner loop dynamic inversion and classical controllers have been implemented on the six degree of freedom simulation; and lateral-directional control allocation scheme has been developed based on minimizing required control effort.

Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics.

PubMed

Campbell, Zachary T; Baldwin, Thomas O; Miyashita, Osamu

2010-12-15

Bacterial luciferase contains an extended 29-residue mobile loop. Movements of this loop are governed by binding of either flavin mononucleotide (FMNH2) or polyvalent anions. To understand this process, loop dynamics were investigated using replica-exchange molecular dynamics that yielded conformational ensembles in either the presence or absence of FMNH2. The resulting data were analyzed using clustering and network analysis. We observed the closed conformations that are visited only in the simulations with the ligand. Yet the mobile loop is intrinsically flexible, and FMNH2 binding modifies the relative populations of conformations. This model provides unique information regarding the function of a crystallographically disordered segment of the loop near the binding site. Structures at or near the fringe of this network were compatible with flavin binding or release. Finally, we demonstrate that the crystallographically observed conformation of the mobile loop bound to oxidized flavin was influenced by crystal packing. Thus, our study has revealed what we believe are novel conformations of the mobile loop and additional context for experimentally determined structures. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Dynamic simulation of perturbation responses in a closed-loop virtual arm model.

PubMed

Du, Yu-Fan; He, Xin; Lan, Ning

2010-01-01

A closed-loop virtual arm (VA) model has been developed in SIMULINK environment by adding spinal reflex circuits and propriospinal neural networks to the open-loop VA model developed in early study [1]. An improved virtual muscle model (VM4.0) is used to speed up simulation and to generate more precise recruitment of muscle force at low levels of muscle activation. Time delays in the reflex loops are determined by their synaptic connections and afferent transmission back to the spinal cord. Reflex gains are properly selected so that closed-loop responses are stable. With the closed-loop VA model, we are developing an approach to evaluate system behaviors by dynamic simulation of perturbation responses. Joint stiffness is calculated based on simulated perturbation responses by a least-squares algorithm in MATLAB. This method of dynamic simulation will be essential for further evaluation of feedforward and reflex control of arm movement and position.

Interaction of 〈1 0 0〉 dislocation loops with dislocations studied by dislocation dynamics in α-iron

NASA Astrophysics Data System (ADS)

Shi, X. J.; Dupuy, L.; Devincre, B.; Terentyev, D.; Vincent, L.

2015-05-01

Interstitial dislocation loops with Burgers vector of 〈1 0 0〉 type are formed in α-iron under neutron or heavy ion irradiation. As the density and size of these loops increase with radiation dose and temperature, these defects are thought to play a key role in hardening and subsequent embrittlement of iron-based steels. The aim of the present work is to study the pinning strength of the loops on mobile dislocations. Prior to run massive Dislocation Dynamics (DD) simulations involving experimentally representative array of radiation defects and dislocations, the DD code and its parameterization are validated by comparing the individual loop-dislocation reactions with those obtained from direct atomistic Molecular Dynamics (MD) simulations. Several loop-dislocation reaction mechanisms are successfully reproduced as well as the values of the unpinning stress to detach mobile dislocations from the defects.

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

PubMed

Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

2018-04-01

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

Gross-Pitaevski map as a chaotic dynamical system.

PubMed

Guarneri, Italo

2017-03-01

The Gross-Pitaevski map is a discrete time, split-operator version of the Gross-Pitaevski dynamics in the circle, for which exponential instability has been recently reported. Here it is studied as a classical dynamical system in its own right. A systematic analysis of Lyapunov exponents exposes strongly chaotic behavior. Exponential growth of energy is then shown to be a direct consequence of rotational invariance and for stationary solutions the full spectrum of Lyapunov exponents is analytically computed. The present analysis includes the "resonant" case, when the free rotation period is commensurate to 2π, and the map has countably many constants of the motion. Except for lowest-order resonances, this case exhibits an integrable-chaotic transition.

A uniform LMI formulation for tuning PID, multi-term fractional-order PID, and Tilt-Integral-Derivative (TID) for integer and fractional-order processes.

PubMed

Merrikh-Bayat, Farshad

2017-05-01

In this paper first the Multi-term Fractional-Order PID (MFOPID) whose transfer function is equal to [Formula: see text] , where k j and α j are unknown and known real parameters respectively, is introduced. Without any loss of generality, a special form of MFOPID with transfer function k p +k i /s+k d1 s+k d2 s μ where k p , k i , k d1 , and k d2 are unknown real and μ is a known positive real parameter, is considered. Similar to PID and TID, MFOPID is also linear in its parameters which makes it possible to study all of them in a same framework. Tuning the parameters of PID, TID, and MFOPID based on loop shaping using Linear Matrix Inequalities (LMIs) is discussed. For this purpose separate LMIs for closed-loop stability (of sufficient type) and adjusting different aspects of the open-loop frequency response are developed. The proposed LMIs for stability are obtained based on the Nyquist stability theorem and can be applied to both integer and fractional-order (not necessarily commensurate) processes which are either stable or have one unstable pole. Numerical simulations show that the performance of the four-variable MFOPID can compete the trivial five-variable FOPID and often excels PID and TID. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Nonequilibrium phase transitions in isotropic Ashkin-Teller model

NASA Astrophysics Data System (ADS)

Akıncı, Ümit

2017-03-01

Dynamic behavior of an isotropic Ashkin-Teller model in the presence of a periodically oscillating magnetic field has been analyzed by means of the mean field approximation. The dynamic equation of motion has been constructed with the help of a Glauber type stochastic process and solved for a square lattice. After defining the possible dynamical phases of the system, phase diagrams have been given and the behavior of the hysteresis loops has been investigated in detail. The hysteresis loop for specific order parameter of isotropic Ashkin-Teller model has been defined and characteristics of this loop in different dynamical phases have been given.

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

NASA Astrophysics Data System (ADS)

Dodani, Sheel C.; Kiss, Gert; Cahn, Jackson K. B.; Su, Ye; Pande, Vijay S.; Arnold, Frances H.

2016-05-01

The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate.

A class of optimum digital phase locked loops

NASA Technical Reports Server (NTRS)

Kumar, R.; Hurd, W. J.

1986-01-01

This paper presents a class of optimum digital filters for digital phase locked loops, for the important case in which the maximum update rate of the loop filter and numerically controlled oscillator (NCO) is limited. This case is typical when the loop filter is implemented in a microprocessor. In these situations, pure delay is encountered in the loop transfer function and thus the stability and gain margin of the loop are of crucial interest. The optimum filters designed for such situations are evaluated in terms of their gain margin for stability, dynamic error, and steady-state error performance. For situations involving considerably high phase dynamics an adaptive and programmable implementation is also proposed to obtain an overall optimum strategy.

Efficient dynamic coherence transfer relying on offset locking using optical phase-locked loop

NASA Astrophysics Data System (ADS)

Xie, Weilin; Dong, Yi; Bretenaker, Fabien; Shi, Hongxiao; Zhou, Qian; Xia, Zongyang; Qin, Jie; Zhang, Lin; Lin, Xi; Hu, Weisheng

2018-01-01

We design and experimentally demonstrate a highly efficient coherence transfer based on composite optical phaselocked loop comprising multiple feedback servo loops. The heterodyne offset-locking is achieved by conducting an acousto-optic frequency shifter in combination with the current tuning and the temperature controlling of the semiconductor laser. The adaptation of the composite optical phase-locked loop enables the tight coherence transfer from a frequency comb to a semiconductor laser in a fully dynamic manner.

Extended molecular dynamics of a c-kit promoter quadruplex

PubMed Central

Islam, Barira; Stadlbauer, Petr; Krepl, Miroslav; Koca, Jaroslav; Neidle, Stephen; Haider, Shozeb; Sponer, Jiri

2015-01-01

The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex. PMID:26245347

High frequency, high temperature specific core loss and dynamic B-H hysteresis loop characteristics of soft magnetic alloys

NASA Technical Reports Server (NTRS)

Wieserman, W. R.; Schwarze, G. E.; Niedra, J. M.

1990-01-01

Limited experimental data exists for the specific core loss and dynamic B-H loops for soft magnetic materials for the combined conditions of high frequency and high temperature. This experimental study investigates the specific core loss and dynamic B-H loop characteristics of Supermalloy and Metglas 2605SC over the frequency range of 1 to 50 kHz and temperature range of 23 to 300 C under sinusoidal voltage excitation. The experimental setup used to conduct the investigation is described. The effects of the maximum magnetic flux density, frequency, and temperature on the specific core loss and on the size and shape of the B-H loops are examined.

Flow volume loops in patients with goiters.

PubMed Central

Geraghty, J G; Coveney, E C; Kiernan, M; O'Higgins, N J

1992-01-01

Plain radiology is the standard means of assessing upper airway obstruction in patients with goiters. Flow volume loop curves will provide additional information, because they allow a quantitative assessment of airflow dynamics in the respiratory cycle. Fifty-one patients had flow volume loops performed before and after thyroidectomy. There was a significant increase in the maximum inspiratory flow rate (3.9 +/- 0.2 versus 4.9 +/- 0.2 L/second, p less than 0.01) after thyroidectomy. Eight of twelve patients with normal tracheal radiology had improved airflow dynamics in the postoperative period. The flow volume loop curve is a simple noninvasive means of assessing airflow dynamics in patients with goiters and may be superior to conventional radiology. PMID:1731653

Adaptive Sliding Mode Control of Dynamic Systems Using Double Loop Recurrent Neural Network Structure.

PubMed

Fei, Juntao; Lu, Cheng

2018-04-01

In this paper, an adaptive sliding mode control system using a double loop recurrent neural network (DLRNN) structure is proposed for a class of nonlinear dynamic systems. A new three-layer RNN is proposed to approximate unknown dynamics with two different kinds of feedback loops where the firing weights and output signal calculated in the last step are stored and used as the feedback signals in each feedback loop. Since the new structure has combined the advantages of internal feedback NN and external feedback NN, it can acquire the internal state information while the output signal is also captured, thus the new designed DLRNN can achieve better approximation performance compared with the regular NNs without feedback loops or the regular RNNs with a single feedback loop. The new proposed DLRNN structure is employed in an equivalent controller to approximate the unknown nonlinear system dynamics, and the parameters of the DLRNN are updated online by adaptive laws to get favorable approximation performance. To investigate the effectiveness of the proposed controller, the designed adaptive sliding mode controller with the DLRNN is applied to a -axis microelectromechanical system gyroscope to control the vibrating dynamics of the proof mass. Simulation results demonstrate that the proposed methodology can achieve good tracking property, and the comparisons of the approximation performance between radial basis function NN, RNN, and DLRNN show that the DLRNN can accurately estimate the unknown dynamics with a fast speed while the internal states of DLRNN are more stable.

A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: a possible indicator of immunogenicity.

PubMed

Joshi, Harshad; Cheluvaraja, Srinath; Somogyi, Endre; Brown, Darron R; Ortoleva, Peter

2011-11-28

Immunogenicity varies between the human papillomavirus (HPV) L1 monomer assemblies of various sizes (e.g., monomers, pentamers or whole capsids). The hypothesis that this can be attributed to the intensity of fluctuations of important loops containing neutralizing epitopes for the various assemblies is proposed for HPV L1 assemblies. Molecular dynamics simulations were utilized to begin testing this hypothesis. Fluctuations of loops that contain critical neutralizing epitopes (especially FG loop) were quantified via root-mean-square fluctuation and features in the frequency spectrum of dynamic changes in loop conformation. If this fluctuation-immunogenicity hypothesis is a universal aspect of immunogenicity (i.e., immune system recognition of an epitope within a loop is more reliable when it is presented via a more stable delivery structure), then fluctuation measures can serve as one predictor of immunogenicity as part of a computer-aided vaccine design strategy. Copyright © 2011 Elsevier Ltd. All rights reserved.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB.

PubMed

Mansouri, Misagh; Reinbolt, Jeffrey A

2012-05-11

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB's variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1s (OpenSim) to 2.9s (MATLAB). For the closed-loop case, a proportional-integral-derivative controller was used to successfully balance a pole on model's hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB

PubMed Central

Mansouri, Misagh; Reinbolt, Jeffrey A.

2013-01-01

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB’s variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1 s (OpenSim) to 2.9 s (MATLAB). For the closed-loop case, a proportional–integral–derivative controller was used to successfully balance a pole on model’s hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. PMID:22464351

Adler Function, Bjorken Sum Rule, and the Crewther Relation to Order {alpha}{sub s}{sup 4} in a General Gauge Theory

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

Baikov, P. A.; Chetyrkin, K. G.; Kuehn, J. H.

2010-04-02

We compute, for the first time, the order {alpha}{sub s}{sup 4} contributions to the Bjorken sum rule for polarized electron-nucleon scattering and to the (nonsinglet) Adler function for the case of a generic color gauge group. We confirm at the same order a (generalized) Crewther relation which provides a strong test of the correctness of our previously obtained results: the QCD Adler function and the five-loop {beta} function in quenched QED. In particular, the appearance of an irrational contribution proportional to {zeta}{sub 3} in the latter quantity is confirmed. We obtain the commensurate scale equation relating the effective strong couplingmore » constants as inferred from the Bjorken sum rule and from the Adler function at order {alpha}{sub s}{sup 4}.« less

ON THE ROLE OF REPETITIVE MAGNETIC RECONNECTIONS IN EVOLUTION OF MAGNETIC FLUX ROPES IN SOLAR CORONA

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

Kumar, Sanjay; Bhattacharyya, R.; Joshi, Bhuwan

Parker's magnetostatic theorem, extended to astrophysical magnetofluids with large magnetic Reynolds number, supports ceaseless regeneration of current sheets and, hence, spontaneous magnetic reconnections recurring in time. Consequently, a scenario is possible where the repeated reconnections provide an autonomous mechanism governing emergence of coherent structures in astrophysical magnetofluids. In this work, such a scenario is explored by performing numerical computations commensurate with the magnetostatic theorem. In particular, the computations explore the evolution of a flux rope governed by repeated reconnections in a magnetic geometry resembling bipolar loops of solar corona. The revealed morphology of the evolution process—including onset and ascent ofmore » the rope, reconnection locations, and the associated topology of the magnetic field lines—agrees with observations, and thus substantiates physical realizability of the advocated mechanism.« less

Predicting the effects of unmodeled dynamics on an aircraft flight control system design using eigenspace assignment

NASA Technical Reports Server (NTRS)

Johnson, Eric N.; Davidson, John B.; Murphy, Patrick C.

1994-01-01

When using eigenspace assignment to design an aircraft flight control system, one must first develop a model of the plant. Certain questions arise when creating this model as to which dynamics of the plant need to be included in the model and which dynamics can be left out or approximated. The answers to these questions are important because a poor choice can lead to closed-loop dynamics that are unpredicted by the design model. To alleviate this problem, a method has been developed for predicting the effect of not including certain dynamics in the design model on the final closed-loop eigenspace. This development provides insight as to which characteristics of unmodeled dynamics will ultimately affect the closed-loop rigid-body dynamics. What results from this insight is a guide for eigenstructure control law designers to aid them in determining which dynamics need or do not need to be included and a new way to include these dynamics in the flight control system design model to achieve a required accuracy in the closed-loop rigid-body dynamics. The method is illustrated for a lateral-directional flight control system design using eigenspace assignment for the NASA High Alpha Research Vehicle (HARV).

Properties of dynamic magnetic loss of ferrite

NASA Astrophysics Data System (ADS)

Saotome, Hideo; Azuma, Keisuke; Kizuka, Hiroki; Tanaka, Takuma

2018-05-01

The B-H loop of ferrite becomes narrower with a decrease in the excitation frequency. However, even at frequencies lower than 1 kHz, the B-H loop exhibits a certain minimum width, which is referred to as the (DC) hysteresis loop, and its area corresponds to the hysteresis loss. The dynamic magnetic loss is obtained by subtracting the hysteresis loss from the B-H loop area measured at a frequency above 1-10 kHz. The temperature characteristics of the hysteresis and dynamic magnetic losses are determined to be experimentally different, which suggests that the mechanism for the generation of dynamic magnetic loss is not exactly the same as that for the hysteresis loss. The dynamic magnetic loss is expressed using the dynamic magnetic loss parameter, which is a function of B and its time derivative, dB/dt. The dynamic magnetic loss parameter is measured under excitation with a rectangular waveform voltage. A ferrite core of TDK PC47 was used and the maximum magnetic flux density Bm, was set to 350 mT. The measured dynamic magnetic loss parameter was experimentally verified to be one of the intrinsic characteristics of ferrite and was also validated for cases of excitation with sinusoidal waveform voltages.

Micro-Columnated Loop Heat Pipe: The Future of Electronic Substrates

NASA Astrophysics Data System (ADS)

Dhillon, Navdeep Singh

The modern world is run by semiconductor-based electronic systems. Due to continuous improvements in semiconductor device fabrication, there is a clear trend in the market towards the development of electronic devices and components that not only deliver enhanced computing power, but are also more compact. Thermal management has emerged as the primary challenge in this scenario where heat flux dissipation of electronic chips is increasing exponentially, but conventional cooling solutions such as conduction and convection are no longer feasible. To keep device junction temperatures within the safe operating limit, there is an urgent requirement for ultra-high-conductivity thermal substrates that not only absorb and transport large heat fluxes, but can also provide localized cooling to thermal hotspots. This dissertation describes the design, modeling, and fabrication of a phase change-based, planar, ultra-thin, passive thermal transport system that is inspired by the concept of loop heat pipes and capillary pumped loops. Fabricated on silicon and Pyrex wafers using microfabrication techniques, the micro-columnated loop heat pipe (muCLHP) can be integrated directly with densely packed or multiply-stacked electronic substrates, to provide localized high-heat-flux thermal management. The muCLHP employs a dual-scale coherent porous silicon(CPS)-based micro-columnated wicking structure, where the primary CPS wick provides large capillary forces for fluid transport, while a secondary surface-wick maximizes the rate of thin-film evaporation. To overcome the wick thickness limitation encountered in conventional loop heat pipes, strategies based on MEMS surface micromachining techniques were developed to reduce parasitic heat flow from the evaporator to the compensation chamber of the device. Finite element analysis was used to confirm this reduction in a planar evaporator design, thus enabling the generation of a large motive temperature head for continuous device operation. To predict the overall heat carrying capacity of the muCLHP in the capillary pumping limit, an analytical model was developed to account for a steady state pressure balance in the device flow loop. Based on this model, a design optimization study, employing monotonicity analysis and numerical optimization techniques, was undertaken. It was found that an optimized muCLHP device can absorb heat fluxes as large as 1293 W/cm2 when water is used as a working fluid. A finite volume method-based numerical model was also developed to compute the rates of thin-film evaporation from the patterned surface of the secondary wick. The numerical results indicated that, by properly optimizing the dual-scale wick topology, allowable evaporative heat fluxes can be made commensurate with the heat flux performance predicted by the capillary pumping limit. The latter part of the dissertation deals with the fabrication, packaging, and experimental testing of several in-plane-wicking micro loop heat pipe (muLHP) prototypes. These devices were fabricated on silicon and Pyrex substrates and closely resemble the muCLHP design philosophy, with the exception that the CPS wick is substituted with an easier to fabricate in-plane wick. A novel thermal-flux method was developed for the degassing and fluid charging of the muLHP prototypes. Experiments were conducted to study the process of evaporation and dynamics of the liquid and vapor phases in the device flow loop. Using these results, the overall device and individual component topologies critical to the operation of the two-phase flow loop were identified. A continuous two-phase device flow loop was demonstrated for applied evaporator heat fluxes as high as 41 W/cm2. The performance of these devices, currently found to be limited by the motive temperature head requirement, can be significantly improved by implementing the parasitic heat flow-reduction strategies developed in this work. The 3-D thin-film evaporation model, when integrated into the overall device modeling framework, will enable a design optimization of the micro-columnated wick for further device performance enhancements.

Conformational trapping of mismatch recognition complex MSH2/MSH3 on repair-resistant DNA loops.

PubMed

Lang, Walter H; Coats, Julie E; Majka, Jerzy; Hura, Greg L; Lin, Yuyen; Rasnik, Ivan; McMurray, Cynthia T

2011-10-18

Insertion and deletion of small heteroduplex loops are common mutations in DNA, but why some loops are prone to mutation and others are efficiently repaired is unknown. Here we report that the mismatch recognition complex, MSH2/MSH3, discriminates between a repair-competent and a repair-resistant loop by sensing the conformational dynamics of their junctions. MSH2/MSH3 binds, bends, and dissociates from repair-competent loops to signal downstream repair. Repair-resistant Cytosine-Adenine-Guanine (CAG) loops adopt a unique DNA junction that traps nucleotide-bound MSH2/MSH3, and inhibits its dissociation from the DNA. We envision that junction dynamics is an active participant and a conformational regulator of repair signaling, and governs whether a loop is removed by MSH2/MSH3 or escapes to become a precursor for mutation.

Heating and dynamics of two flare loop systems observed by AIA and EIS

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

Li, Y.; Ding, M. D.; Qiu, J., E-mail: yingli@nju.edu.cn

2014-02-01

We investigate heating and evolution of flare loops in a C4.7 two-ribbon flare on 2011 February 13. From Solar Dynamics Observatory/Atmospheric Imaging Assembly (AIA) imaging observations, we can identify two sets of loops. Hinode/EUV Imaging Spectrometer (EIS) spectroscopic observations reveal blueshifts at the feet of both sets of loops. The evolution and dynamics of the two sets are quite different. The first set of loops exhibits blueshifts for about 25 minutes followed by redshifts, while the second set shows stronger blueshifts, which are maintained for about one hour. The UV 1600 observation by AIA also shows that the feet ofmore » the second set of loops brighten twice. These suggest that continuous heating may be present in the second set of loops. We use spatially resolved UV light curves to infer heating rates in the few tens of individual loops comprising the two loop systems. With these heating rates, we then compute plasma evolution in these loops with the 'enthalpy-based thermal evolution of loops' model. The results show that, for the first set of loops, the synthetic EUV light curves from the model compare favorably with the observed light curves in six AIA channels and eight EIS spectral lines, and the computed mean enthalpy flow velocities also agree with the Doppler shift measurements by EIS. For the second set of loops modeled with twice-heating, there are some discrepancies between modeled and observed EUV light curves in low-temperature bands, and the model does not fully produce the prolonged blueshift signatures as observed. We discuss possible causes for the discrepancies.« less

Loop-quantum-gravity vertex amplitude.

PubMed

Engle, Jonathan; Pereira, Roberto; Rovelli, Carlo

2007-10-19

Spin foam models are hoped to provide the dynamics of loop-quantum gravity. However, the most popular of these, the Barrett-Crane model, does not have the good boundary state space and there are indications that it fails to yield good low-energy n-point functions. We present an alternative dynamics that can be derived as a quantization of a Regge discretization of Euclidean general relativity, where second class constraints are imposed weakly. Its state space matches the SO(3) loop gravity one and it yields an SO(4)-covariant vertex amplitude for Euclidean loop gravity.

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.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.

PubMed

Islam, Barira; Stadlbauer, Petr; Gil-Ley, Alejandro; Pérez-Hernández, Guillermo; Haider, Shozeb; Neidle, Stephen; Bussi, Giovanni; Banas, Pavel; Otyepka, Michal; Sponer, Jiri

2017-06-13

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

PubMed Central

2017-01-01

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

Bandwidth controller for phase-locked-loop

NASA Technical Reports Server (NTRS)

Brockman, Milton H. (Inventor)

1992-01-01

A phase locked loop utilizing digital techniques to control the closed loop bandwidth of the RF carrier phase locked loop in a receiver provides high sensitivity and a wide dynamic range for signal reception. After analog to digital conversion, a digital phase locked loop bandwidth controller provides phase error detection with automatic RF carrier closed loop tracking bandwidth control to accommodate several modes of transmission.

Simulating Coronal Loop Implosion and Compressible Wave Modes in a Flare Hit Active Region

NASA Astrophysics Data System (ADS)

Sarkar, Aveek; Vaidya, Bhargav; Hazra, Soumitra; Bhattacharyya, Jishnu

2017-12-01

There is considerable observational evidence of implosion of magnetic loop systems inside solar coronal active regions following high-energy events like solar flares. In this work, we propose that such collapse can be modeled in three dimensions quite accurately within the framework of ideal magnetohydrodynamics. We furthermore argue that the dynamics of loop implosion is only sensitive to the transmitted disturbance of one or more of the system variables, e.g., velocity generated at the event site. This indicates that to understand loop implosion, it is sensible to leave the event site out of the simulated active region. Toward our goal, a velocity pulse is introduced to model the transmitted disturbance generated at the event site. Magnetic field lines inside our simulated active region are traced in real time, and it is demonstrated that the subsequent dynamics of the simulated loops closely resemble observed imploding loops. Our work highlights the role of plasma β in regards to the rigidity of the loop systems and how that might affect the imploding loops’ dynamics. Compressible magnetohydrodynamic modes such as kink and sausage are also shown to be generated during such processes, in accordance with observations.

Robust Adaptive Flight Control Design of Air-breathing Hypersonic Vehicles

DTIC Science & Technology

2016-12-07

dynamic inversion controller design for a non -minimum phase hypersonic vehicle is derived by Kuipers et al. [2008]. Moreover, integrated guidance and...stabilization time for inner loop variables is lesser than the intermediate loop variables because of the three-loop-control design methodology . The control...adaptive design . Control Engineering Practice, 2016. Michael A Bolender and David B Doman. A non -linear model for the longitudinal dynamics of a

A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Gohda, Keigo; Hakoshima, Toshio

2008-11-01

Rho-kinase is a leading player in the regulation of cytoskeletal events involving smooth muscle contraction and neurite growth-cone collapse and retraction, and is a promising drug target in the treatment of both vascular and neurological disorders. Recent crystal structure of Rho-kinase complexed with a small-molecule inhibitor fasudil has revealed structural details of the ATP-binding site, which represents the target site for the inhibitor, and showed that the conserved phenylalanine on the P-loop occupies the pocket, resulting in an increase of protein-ligand contacts. Thus, the P-loop pliability is considered to play an important role in inhibitor binding affinity and specificity. In this study, we carried out a molecular dynamic simulation for Rho-kinase-fasudil complexes with two different P-loop conformations, i.e., the extended and folded conformations, in order to understand the P-loop pliability and dynamics at atomic level. A PKA-fasudil complex was also used for comparison. In the MD simulation, the flip-flop movement of the P-loop conformation starting either from the extended or folded conformation was not able to be observed. However, a significant conformational change in a long loop region covering over the P-loop, and also alteration of ionic interaction-manner of fasudil with acidic residues in the ATP binding site were shown only in the Rho-kinase-fasudil complex with the extended P-loop conformation, while Rho-kinase with the folded P-loop conformation and PKA complexes did not show large fluctuations, suggesting that the Rho-kinase-fasudil complex with the extended P-loop conformation represents a meta-stable state. The information of the P-loop pliability at atomic level obtained in this study could provide valuable clues to designing potent and/or selective inhibitors for Rho-kinase.

A simplified dynamic model of the T700 turboshaft engine

NASA Technical Reports Server (NTRS)

Duyar, Ahmet; Gu, Zhen; Litt, Jonathan S.

1992-01-01

A simplified open-loop dynamic model of the T700 turboshaft engine, valid within the normal operating range of the engine, is developed. This model is obtained by linking linear state space models obtained at different engine operating points. Each linear model is developed from a detailed nonlinear engine simulation using a multivariable system identification and realization method. The simplified model may be used with a model-based real time diagnostic scheme for fault detection and diagnostics, as well as for open loop engine dynamics studies and closed loop control analysis utilizing a user generated control law.

Closed-Loop and Activity-Guided Optogenetic Control

PubMed Central

Grosenick, Logan; Marshel, James H.; Deisseroth, Karl

2016-01-01

Advances in optical manipulation and observation of neural activity have set the stage for widespread implementation of closed-loop and activity-guided optical control of neural circuit dynamics. Closing the loop optogenetically (i.e., basing optogenetic stimulation on simultaneously observed dynamics in a principled way) is a powerful strategy for causal investigation of neural circuitry. In particular, observing and feeding back the effects of circuit interventions on physiologically relevant timescales is valuable for directly testing whether inferred models of dynamics, connectivity, and causation are accurate in vivo. Here we highlight technical and theoretical foundations as well as recent advances and opportunities in this area, and we review in detail the known caveats and limitations of optogenetic experimentation in the context of addressing these challenges with closed-loop optogenetic control in behaving animals. PMID:25856490

Closed-loop spontaneous baroreflex transfer function is inappropriate for system identification of neural arc but partly accurate for peripheral arc: predictability analysis

PubMed Central

Kamiya, Atsunori; Kawada, Toru; Shimizu, Shuji; Sugimachi, Masaru

2011-01-01

Abstract Although the dynamic characteristics of the baroreflex system have been described by baroreflex transfer functions obtained from open-loop analysis, the predictability of time-series output dynamics from input signals, which should confirm the accuracy of system identification, remains to be elucidated. Moreover, despite theoretical concerns over closed-loop system identification, the accuracy and the predictability of the closed-loop spontaneous baroreflex transfer function have not been evaluated compared with the open-loop transfer function. Using urethane and α-chloralose anaesthetized, vagotomized and aortic-denervated rabbits (n = 10), we identified open-loop baroreflex transfer functions by recording renal sympathetic nerve activity (SNA) while varying the vascularly isolated intracarotid sinus pressure (CSP) according to a binary random (white-noise) sequence (operating pressure ± 20 mmHg), and using a simplified equation to calculate closed-loop-spontaneous baroreflex transfer function while matching CSP with systemic arterial pressure (AP). Our results showed that the open-loop baroreflex transfer functions for the neural and peripheral arcs predicted the time-series SNA and AP outputs from measured CSP and SNA inputs, with r2 of 0.8 ± 0.1 and 0.8 ± 0.1, respectively. In contrast, the closed-loop-spontaneous baroreflex transfer function for the neural arc was markedly different from the open-loop transfer function (enhanced gain increase and a phase lead), and did not predict the time-series SNA dynamics (r2; 0.1 ± 0.1). However, the closed-loop-spontaneous baroreflex transfer function of the peripheral arc partially matched the open-loop transfer function in gain and phase functions, and had limited but reasonable predictability of the time-series AP dynamics (r2, 0.7 ± 0.1). A numerical simulation suggested that a noise predominantly in the neural arc under resting conditions might be a possible mechanism responsible for our findings. Furthermore, the predictabilities of the neural arc transfer functions obtained in open-loop and closed-loop conditions were validated by closed-loop pharmacological (phenylephrine and nitroprusside infusions) pressure interventions. Time-series SNA responses to drug-induced AP changes predicted by the open-loop transfer function matched closely the measured responses (r2, 0.9 ± 0.1), whereas SNA responses predicted by closed-loop-spontaneous transfer function deviated greatly and were the inverse of measured responses (r, −0.8 ± 0.2). These results indicate that although the spontaneous baroreflex transfer function obtained by closed-loop analysis has been believed to represent the neural arc function, it is inappropriate for system identification of the neural arc but is essentially appropriate for the peripheral arc under resting conditions, when compared with open-loop analysis. PMID:21486839

Femtosecond visualization of lattice dynamics in shock-compressed matter.

PubMed

Milathianaki, D; Boutet, S; Williams, G J; Higginbotham, A; Ratner, D; Gleason, A E; Messerschmidt, M; Seibert, M M; Swift, D C; Hering, P; Robinson, J; White, W E; Wark, J S

2013-10-11

The ultrafast evolution of microstructure is key to understanding high-pressure and strain-rate phenomena. However, the visualization of lattice dynamics at scales commensurate with those of atomistic simulations has been challenging. Here, we report femtosecond x-ray diffraction measurements unveiling the response of copper to laser shock-compression at peak normal elastic stresses of ~73 gigapascals (GPa) and strain rates of 10(9) per second. We capture the evolution of the lattice from a one-dimensional (1D) elastic to a 3D plastically relaxed state within a few tens of picoseconds, after reaching shear stresses of 18 GPa. Our in situ high-precision measurement of material strength at spatial (<1 micrometer) and temporal (<50 picoseconds) scales provides a direct comparison with multimillion-atom molecular dynamics simulations.

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

PubMed Central

Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier

2017-01-01

Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding domains into loop structures, which are widely thought to be stable. Combining genomic and biochemical approaches we show that CTCF and cohesin co-occupy the same sites and physically interact as a biochemically stable complex. However, using single-molecule imaging we find that CTCF binds chromatin much more dynamically than cohesin (~1–2 min vs. ~22 min residence time). Moreover, after unbinding, CTCF quickly rebinds another cognate site unlike cohesin for which the search process is long (~1 min vs. ~33 min). Thus, CTCF and cohesin form a rapidly exchanging 'dynamic complex' rather than a typical stable complex. Since CTCF and cohesin are required for loop domain formation, our results suggest that chromatin loops are dynamic and frequently break and reform throughout the cell cycle. DOI: http://dx.doi.org/10.7554/eLife.25776.001 PMID:28467304

SILHIL Replication of Electric Aircraft Powertrain Dynamics and Inner-Loop Control for V&V of System Health Management Routines

NASA Technical Reports Server (NTRS)

Bole, Brian; Teubert, Christopher Allen; Cuong Chi, Quach; Hogge, Edward; Vazquez, Sixto; Goebel, Kai; George, Vachtsevanos

2013-01-01

Software-in-the-loop and Hardware-in-the-loop testing of failure prognostics and decision making tools for aircraft systems will facilitate more comprehensive and cost-effective testing than what is practical to conduct with flight tests. A framework is described for the offline recreation of dynamic loads on simulated or physical aircraft powertrain components based on a real-time simulation of airframe dynamics running on a flight simulator, an inner-loop flight control policy executed by either an autopilot routine or a human pilot, and a supervisory fault management control policy. The creation of an offline framework for verifying and validating supervisory failure prognostics and decision making routines is described for the example of battery charge depletion failure scenarios onboard a prototype electric unmanned aerial vehicle.

A control system design approach for flexible spacecraft

NASA Technical Reports Server (NTRS)

Silverberg, L. M.

1985-01-01

A control system design approach for flexible spacecraft is presented. The control system design is carried out in two steps. The first step consists of determining the ideal control system in terms of a desirable dynamic performance. The second step consists of designing a control system using a limited number of actuators that possess a dynamic performance that is close to the ideal dynamic performance. The effects of using a limited number of actuators is that the actual closed-loop eigenvalues differ from the ideal closed-loop eigenvalues. A method is presented to approximate the actual closed-loop eigenvalues so that the calculation of the actual closed-loop eigenvalues can be avoided. Depending on the application, it also may be desirable to apply the control forces as impulses. The effect of digitizing the control to produce the appropriate impulses is also examined.

A dynamic flare with anomalously dense flare loops

NASA Technical Reports Server (NTRS)

Svestka, Z.; Fontenla, J. M.; Machado, M. E.; Martin, S. F.; Neidig, D. F.

1986-01-01

The dynamic flare of November 6, 1980 developed a rich system of growing loops which could be followed in H-alpha for 1.5 hours. Throughout the flare, these loops, near the limb, were seen in emission against the disk. Theoretical computations of b-values for a hydrogen atom reveal that this requires electron densities in the loops to be close to 10 to the 12th per cu cm. From measured widths of higher Balmer lines the density at the tops of the loops was found to be 4 x 10 to the 12th per cu cm if no nonthermal motions were present. It is now general knowledge that flare loops are initially observed in X-rays and become visible in H-alpha only after cooling. For such a high density a loop would cool through radiation from 10 to the 7th K to 10 to the 4th K within a few minutes so that the dense H-alpha loops should have heights very close to the heights of the X-ray loops. This, however, contradicts the observations obtained by the HXIS and FCS instruments on board SMM which show the X-ray loops at much higher altitudes than the loops in H-alpha. Therefore, the density must have been significantly smaller when the loops were formed and the flare loops were apparently both shrinking and becoming denser while cooling.

Coronal Loops: Observations and Modeling of Confined Plasma.

PubMed

Reale, Fabio

Coronal loops are the building blocks of the X-ray bright solar corona. They owe their brightness to the dense confined plasma, and this review focuses on loops mostly as structures confining plasma. After a brief historical overview, the review is divided into two separate but not independent parts: the first illustrates the observational framework, the second reviews the theoretical knowledge. Quiescent loops and their confined plasma are considered and, therefore, topics such as loop oscillations and flaring loops (except for non-solar ones, which provide information on stellar loops) are not specifically addressed here. The observational section discusses the classification, populations, and the morphology of coronal loops, its relationship with the magnetic field, and the loop stranded structure. The section continues with the thermal properties and diagnostics of the loop plasma, according to the classification into hot, warm, and cool loops. Then, temporal analyses of loops and the observations of plasma dynamics, hot and cool flows, and waves are illustrated. In the modeling section, some basics of loop physics are provided, supplying fundamental scaling laws and timescales, a useful tool for consultation. The concept of loop modeling is introduced and models are divided into those treating loops as monolithic and static, and those resolving loops into thin and dynamic strands. More specific discussions address modeling the loop fine structure and the plasma flowing along the loops. Special attention is devoted to the question of loop heating, with separate discussion of wave (AC) and impulsive (DC) heating. Large-scale models including atmosphere boxes and the magnetic field are also discussed. Finally, a brief discussion about stellar coronal loops is followed by highlights and open questions.

Generalization of a model of hysteresis for dynamical systems.

PubMed

Piquette, Jean C; McLaughlin, Elizabeth A; Ren, Wei; Mukherjee, Binu K

2002-06-01

A previously described model of hysteresis [J. C. Piquette and S. E. Forsythe, J. Acoust. Soc. Am. 106, 3317-3327 (1999); 106, 3328-3334 (1999)] is generalized to apply to a dynamical system. The original model produces theoretical hysteresis loops that agree well with laboratory measurements acquired under quasi-static conditions. The loops are produced using three-dimensional rotation matrices. An iterative procedure, which allows the model to be applied to a dynamical system, is introduced here. It is shown that, unlike the quasi-static case, self-crossing of the loops is a realistic possibility when inertia and viscous friction are taken into account.

Commensurability condition and hierarchy of fillings for FQHE in higher Landau levels in conventional 2DEG systems and in graphene—monolayer and bilayer

NASA Astrophysics Data System (ADS)

Jacak, Janusz; Jacak, Lucjan

2016-01-01

The structure of the filling rate hierarchy referred to as the fractional quantum Hall effect is studied in higher Landau levels using the commensurability condition. The hierarchy of fillings that are derived in this manner is consistent with the experimental observations of the first three Landau levels in conventional semiconductor Hall systems. The relative poverty of the fractional structure in higher Landau levels compared with the lowest Landau level is explained using commensurability topological arguments. The commensurability criterion for correlated states for higher Landau levels (with n≥slant 1) including the paired states at half fillings of the spin-subbands of these levels is formulated. The commensurability condition is applied to determine the hierarchy of the fractional fillings of Landau levels in the monolayer and bilayer graphene. Good agreement with current experimental observations of fractional quantum Hall effect in the graphene monolayer and bilayer is achieved. The presence of even denominator rates in the hierarchy for fractional quantum Hall effect in the bilayer graphene is also explained.

Direct structural evidence of commensurate-to-incommensurate transition of hydrocarbon adsorption in a microporous metal organic framework

DOE PAGES

Banerjee, Debasis; Wang, Hao; Gong, Qihan; ...

2015-10-27

Here, the efficiency of physisorption-based separation of gas-mixtures depends on the selectivity of adsorbent which is directly linked to size, shape, polarizability and other physical properties of adsorbed molecules. Commensurate adsorption is an interesting and important adsorption phenomenon, where the adsorbed amount, location, and orientation of an adsorbate are commensurate with the crystal symmetry of the adsorbent. Understanding this phenomenon is important and beneficial as it can provide vital information about adsorbate–adsorbent interaction and adsorption–desorption mechanism. So far, only sporadic examples of commensurate adsorption have been reported in porous materials such as zeolites and metal organic frameworks (MOFs). In thismore » work we show for the first time direct structural evidence of commensurate-to-incommensurate transition of linear hydrocarbon molecules (C 2–C7) in a microporous MOF, by employing a number of analytical techniques including single crystal X-ray diffraction (SCXRD), in situ powder X-ray diffraction coupled with differential scanning calorimetry (PXRD-DSC), gas adsorption and molecular simulations.« less

Motor-sensory confluence in tactile perception.

PubMed

Saig, Avraham; Gordon, Goren; Assa, Eldad; Arieli, Amos; Ahissar, Ehud

2012-10-03

Perception involves motor control of sensory organs. However, the dynamics underlying emergence of perception from motor-sensory interactions are not yet known. Two extreme possibilities are as follows: (1) motor and sensory signals interact within an open-loop scheme in which motor signals determine sensory sampling but are not affected by sensory processing and (2) motor and sensory signals are affected by each other within a closed-loop scheme. We studied the scheme of motor-sensory interactions in humans using a novel object localization task that enabled monitoring the relevant overt motor and sensory variables. We found that motor variables were dynamically controlled within each perceptual trial, such that they gradually converged to steady values. Training on this task resulted in improvement in perceptual acuity, which was achieved solely by changes in motor variables, without any change in the acuity of sensory readout. The within-trial dynamics is captured by a hierarchical closed-loop model in which lower loops actively maintain constant sensory coding, and higher loops maintain constant sensory update flow. These findings demonstrate interchangeability of motor and sensory variables in perception, motor convergence during perception, and a consistent hierarchical closed-loop perceptual model.

Investigation of Inner Loop Flight Control Strategies for High-Speed Research

NASA Technical Reports Server (NTRS)

Newman, Brett; Kassem, Ayman

1999-01-01

This report describes the activities and findings conducted under contract NAS1-19858 with NASA Langley Research Center. Subject matter is the investigation of suitable flight control design methodologies and solutions for large, flexible high-speed vehicles. Specifically, methodologies are to address the inner control loops used for stabilization and augmentation of a highly coupled airframe system possibly involving rigid-body motion, structural vibrations, unsteady aerodynamics, and actuator dynamics. Techniques considered in this body of work are primarily conventional-based, and the vehicle of interest is the High-Speed Civil Transport (HSCT). Major findings include 1) current aeroelastic vehicle modeling procedures require further emphasis and refinement, 2) traditional and nontraditional inner loop flight control strategies employing a single feedback loop do not appear sufficient for highly flexible HSCT class vehicles, 3) inner loop flight control systems will, in all likelihood, require multiple interacting feedback loops, and 4) Ref. H HSCT configuration presents major challenges to designing acceptable closed-loop flight dynamics.

HOW GAS-DYNAMIC FLARE MODELS POWERED BY PETSCHEK RECONNECTION DIFFER FROM THOSE WITH AD HOC ENERGY SOURCES

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

Longcope, D. W.; Klimchuk, J. A.

Aspects of solar flare dynamics, such as chromospheric evaporation and flare light curves, have long been studied using one-dimensional models of plasma dynamics inside a static flare loop, subjected to some energy input. While extremely successful at explaining the observed characteristics of flares, all such models so far have specified energy input ad hoc, rather than deriving it self-consistently. There is broad consensus that flares are powered by magnetic energy released through reconnection. Recent work has generalized Petschek’s basic reconnection scenario, topological change followed by field line retraction and shock heating, to permit its inclusion in a one-dimensional flare loop model. Heremore » we compare the gas dynamics driven by retraction and shocking to those from more conventional static loop models energized by ad hoc source terms. We find significant differences during the first minute, when retraction leads to larger kinetic energies and produces higher densities at the loop top, while ad hoc heating tends to rarify the loop top. The loop-top density concentration is related to the slow magnetosonic shock, characteristic of Petschek’s model, but persists beyond the retraction phase occurring in the outflow jet. This offers an explanation for observed loop-top sources of X-ray and EUV emission, with advantages over that provided by ad hoc heating scenarios. The cooling phases of the two models are, however, notably similar to one another, suggesting that observations at that stage will yield little information on the nature of energy input.« less

Phase structure of the Polyakov-quark-meson model

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

Schaefer, B.-J.; Pawlowski, J. M.; Wambach, J.

2007-10-01

The relation between the deconfinement and chiral phase transition is explored in the framework of a Polyakov-loop-extended two-flavor quark-meson (PQM) model. In this model the Polyakov loop dynamics is represented by a background temporal gauge field which also couples to the quarks. As a novelty an explicit quark chemical potential and N{sub f}-dependence in the Polyakov loop potential is proposed by using renormalization group arguments. The behavior of the Polyakov loop as well as the chiral condensate as function of temperature and quark chemical potential is obtained by minimizing the grand canonical thermodynamic potential of the system. The effect ofmore » the Polyakov loop dynamics on the chiral phase diagram and on several thermodynamic bulk quantities is presented.« less

A Culture-Behavior-Brain Loop Model of Human Development.

PubMed

Han, Shihui; Ma, Yina

2015-11-01

Increasing evidence suggests that cultural influences on brain activity are associated with multiple cognitive and affective processes. These findings prompt an integrative framework to account for dynamic interactions between culture, behavior, and the brain. We put forward a culture-behavior-brain (CBB) loop model of human development that proposes that culture shapes the brain by contextualizing behavior, and the brain fits and modifies culture via behavioral influences. Genes provide a fundamental basis for, and interact with, the CBB loop at both individual and population levels. The CBB loop model advances our understanding of the dynamic relationships between culture, behavior, and the brain, which are crucial for human phylogeny and ontogeny. Future brain changes due to cultural influences are discussed based on the CBB loop model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design of Accumulators and Liquid/Gas Charging of Single Phase Mechanically Pumped Fluid Loop Heat Rejection Systems

NASA Technical Reports Server (NTRS)

Bhandari, Pradeep; Dudik, Brenda; Birur, Gajanana; Karlmann, Paul; Bame, David; Mastropietro, A. J.

2012-01-01

For single phase mechanically pumped fluid loops used for thermal control of spacecraft, a gas charged accumulator is typically used to modulate pressures within the loop. This is needed to accommodate changes in the working fluid volume due to changes in the operating temperatures as the spacecraft encounters varying thermal environments during its mission. Overall, the three key requirements on the accumulator to maintain an appropriate pressure range throughout the mission are: accommodation of the volume change of the fluid due to temperature changes, avoidance of pump cavitation and prevention of boiling in the liquid. The sizing and design of such an accumulator requires very careful and accurate accounting of temperature distribution within each element of the working fluid for the entire range of conditions expected, accurate knowledge of volume of each fluid element, assessment of corresponding pressures needed to avoid boiling in the liquid, as well as the pressures needed to avoid cavitation in the pump. The appropriate liquid and accumulator strokes required to accommodate the liquid volume change, as well as the appropriate gas volumes, require proper sizing to ensure that the correct pressure range is maintained during the mission. Additionally, a very careful assessment of the process for charging both the gas side and the liquid side of the accumulator is required to properly position the bellows and pressurize the system to a level commensurate with requirements. To achieve the accurate sizing of the accumulator and the charging of the system, sophisticated EXCEL based spreadsheets were developed to rapidly come up with an accumulator design and the corresponding charging parameters. These spreadsheets have proven to be computationally fast and accurate tools for this purpose. This paper will describe the entire process of designing and charging the system, using a case study of the Mars Science Laboratory (MSL) fluid loops, which is en route to Mars for an August 2012 landing.

A method for reducing sampling jitter in digital control systems

NASA Technical Reports Server (NTRS)

Anderson, T. O.; HURBD W. J.; Hurd, W. J.

1969-01-01

Digital phase lock loop system is designed by smoothing the proportional control with a low pass filter. This method does not significantly affect the loop dynamics when the smoothing filter bandwidth is wide compared to loop bandwidth.

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

PubMed Central

Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

2012-01-01

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

A dynamically reconfigurable multi-functional PLL for SRAM-based FPGA in 65nm CMOS technology

NASA Astrophysics Data System (ADS)

Yang, Mingqian; Chen, Lei; Li, Xuewu; Zhang, Yanlong

2018-04-01

Phase-locked loops (PLL) have been widely utilized in FPGA as an important module for clock management. PLL with dynamic reconfiguration capability is always welcomed in FPGA design as it is able to decrease power consumption and simultaneously improve flexibility. In this paper, a multi-functional PLL with dynamic reconfiguration capability for 65nm SRAM-based FPGA is proposed. Firstly, configurable charge pump and loop filter are utilized to optimize the loop bandwidth. Secondly, the PLL incorporates a VCO with dual control voltages to accelerate the adjustment of oscillation frequency. Thirdly, three configurable dividers are presented for flexible frequency synthesis. Lastly, a configuration block with dynamic reconfiguration function is proposed. Simulation results demonstrate that the proposed multi-functional PLL can output clocks with configurable division ratio, phase shift and duty cycle. The PLL can also be dynamically reconfigured without affecting other parts' running or halting the FPGA device.

A rationale for human operator pulsive control behavior

NASA Technical Reports Server (NTRS)

Hess, R. A.

1979-01-01

When performing tracking tasks which involve demanding controlled elements such as those with K/s-squared dynamics, the human operator often develops discrete or pulsive control outputs. A dual-loop model of the human operator is discussed, the dominant adaptive feature of which is the explicit appearance of an internal model of the manipulator-controlled element dynamics in an inner feedback loop. Using this model, a rationale for pulsive control behavior is offered which is based upon the assumption that the human attempts to reduce the computational burden associated with time integration of sensory inputs. It is shown that such time integration is a natural consequence of having an internal representation of the K/s-squared-controlled element dynamics in the dual-loop model. A digital simulation is discussed in which a modified form of the dual-loop model is shown to be capable of producing pulsive control behavior qualitively comparable to that obtained in experiment.

Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis

PubMed Central

Jordan, Frank; Arjunan, Palaniappa; Kale, Sachin; Nemeria, Natalia S.; Furey, William

2009-01-01

The region encompassing residues 401–413 on the E1 component of the pyruvate dehydrogenase multienzyme complex from Escherichia coli comprises a loop (the inner loop) which was not seen in the X-ray structure in the presence of thiamin diphosphate, the required cofactor for the enzyme. This loop is seen in the presence of a stable analogue of the pre-decarboxylation intermediate, the covalent adduct between the substrate analogue methyl acetylphosphonate and thiamin diphosphate, C2α-phosphonolactylthiamin diphosphate. It has been shown that the residue H407 and several other residues on this loop are required to reduce the mobility of the loop so electron density corresponding to it can be seen once the pre-decarboxylation intermediate is formed. Concomitantly, the loop encompassing residues 541–557 (the outer loop) appears to work in tandem with the inner loop and there is a hydrogen bond between the two loops ensuring their correlated motion. The inner loop was shown to: a) sequester the active center from carboligase side reactions; b) assist the interaction between the E1 and the E2 components, thereby affecting the overall reaction rate of the entire multienzyme complex; c) control substrate access to the active center. Using viscosity effects on kinetics it was shown that formation of the pre-decarboxylation intermediate is specifically affected by loop movement. A cysteine-less variant was created for the E1 component, onto which cysteines were substituted at selected loop positions. Introducing an electron spin resonance spin label and an 19F NMR label onto these engineered cysteines, the loop mobility was examined: a) both methods suggested that in the absence of ligand, the loop exists in two conformations; b) line-shape analysis of the NMR signal at different temperatures, enabled estimation of the rate constant for loop movement, and this rate constant was found to be of the same order of magnitude as the turnover number for the enzyme under the same conditions. Furthermore, this analysis gave important insights into rate-limiting thermal loop dynamics. Overall, the results suggest that the dynamic properties correlate with catalytic events on the E1 component of the pyruvate dehydrogenase complex. PMID:20160956

Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer

PubMed Central

2015-01-01

Plexin-B1 is a single-pass transmembrane receptor. Its Rho GTPase binding domain (RBD) can associate with small Rho GTPases and can also self-bind to form a dimer. In total, more than 400 ns of NAMD molecular dynamics simulations were performed on RBD monomer and dimer. Different analysis methods, such as root mean squared fluctuation (RMSF), order parameters (S2), dihedral angle correlation, transfer entropy, principal component analysis, and dynamical network analysis, were carried out to characterize the motions seen in the trajectories. RMSF results show that after binding, the L4 loop becomes more rigid, but the L2 loop and a number of residues in other regions become slightly more flexible. Calculating order parameters (S2) for CH, NH, and CO bonds on both backbone and side chain shows that the L4 loop becomes essentially rigid after binding, but part of the L1 loop becomes slightly more flexible. Backbone dihedral angle cross-correlation results show that loop regions such as the L1 loop including residues Q25 and G26, the L2 loop including residue R61, and the L4 loop including residues L89–R91, are highly correlated compared to other regions in the monomer form. Analysis of the correlated motions at these residues, such as Q25 and R61, indicate two signal pathways. Transfer entropy calculations on the RBD monomer and dimer forms suggest that the binding process should be driven by the L4 loop and C-terminal. However, after binding, the L4 loop functions as the motion responder. The signal pathways in RBD were predicted based on a dynamical network analysis method using the pathways predicted from the dihedral angle cross-correlation calculations as input. It is found that the shortest pathways predicted from both inputs can overlap, but signal pathway 2 (from F90 to R61) is more dominant and overlaps all of the routes of pathway 1 (from F90 to P111). This project confirms the allosteric mechanism in signal transmission inside the RBD network, which was in part proposed in the previous experimental study. PMID:24901636

Proline Restricts Loop I Conformation of the High Affinity WW Domain from Human Nedd4-1 to a Ligand Binding-Competent Type I β-Turn.

PubMed

Schulte, Marianne; Panwalkar, Vineet; Freischem, Stefan; Willbold, Dieter; Dingley, Andrew J

2018-04-19

Sequence alignment of the four WW domains from human Nedd4-1 (neuronal precursor cell expressed developmentally down-regulated gene 4-1) reveals that the highest sequence diversity exists in loop I. Three residues in this type I β-turn interact with the PPxY motif of the human epithelial Na + channel (hENaC) subunits, indicating that peptide affinity is defined by the loop I sequence. The third WW domain (WW3*) has the highest ligand affinity and unlike the other three hNedd4-1 WW domains or other WW domains studied contains the highly statistically preferred proline at the ( i + 1) position found in β-turns. In this report, molecular dynamics simulations and experimental data were combined to characterize loop I stability and dynamics. Exchange of the proline to the equivalent residue in WW4 (Thr) results in the presence of a predominantly open seven residue Ω loop rather than the type I β-turn conformation for the wild-type apo-WW3*. In the presence of the ligand, the structure of the mutated loop I is locked into a type I β-turn. Thus, proline in loop I ensures a stable peptide binding-competent β-turn conformation, indicating that amino acid sequence modulates local flexibility to tune binding preferences and stability of dynamic interaction motifs.

Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

PubMed

Turcotte, Martin M; Reznick, David N; Daniel Hare, J

2013-05-01

An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

Effects of maneuver dynamics on drag polars of the X-29A forward-swept-wing aircraft with automatic wing camber control

NASA Technical Reports Server (NTRS)

Hicks, John W.; Moulton, Bryan J.

1988-01-01

The camber control loop of the X-29A FSW aircraft was designed to furnish the optimum L/D for trimmed, stabilized flight. A marked difference was noted between automatic wing camber control loop behavior in dynamic maneuvers and in stabilized flight conditions, which in turn affected subsonic aerodynamic performance. The degree of drag level increase was a direct function of maneuver rate. Attention is given to the aircraft flight drag polar effects of maneuver dynamics in light of wing camber control loop schedule. The effect of changing camber scheduling to better track the optimum automatic camber control L/D schedule is discussed.

Two AFC Loops For Low CNR And High Dynamics

NASA Technical Reports Server (NTRS)

Hinedi, Sami M.; Aguirre, Sergio

1992-01-01

Two alternative digital automatic-frequency-control (AFC) loops proposed to acquire (or reacquire) and track frequency of received carrier radio signal. Intended for use where carrier-to-noise ratios (CNR's) low and carrier frequency characterized by high Doppler shift and Doppler rate because of high relative speed and acceleration, respectively, between transmitter and receiver. Either AFC loops used in place of phase-locked loop. New loop concepts integrate ideas from classical spectrum-estimation, digital-phase-locked-loop, and Kalman-Filter theories.

Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

PubMed

Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

2017-12-01

Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

PubMed Central

Chen, Alan A.; García, Angel E.

2013-01-01

We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations. PMID:24043821

Study of the post-flare loops on 29 July 1973. I - Dynamics of the X-ray loops

NASA Technical Reports Server (NTRS)

Nolte, J. T.; Gerassimenko, M.; Krieger, A. S.; Petrasso, R. D.; Svestka, Z.

1979-01-01

We derive an empirical model of the X-ray emitting post-flare loops observed during the decay phase of the 29 July 1973 flare. We find that the loops are elliptical, with the brightest emitting region at the tops. We determine the height, velocity of growth, and ratio of height to width of the loops at times from 3 to 12 hr after the flare onset.

Review article: closed-loop systems in anesthesia: is there a potential for closed-loop fluid management and hemodynamic optimization?

PubMed

Rinehart, Joseph; Liu, Ngai; Alexander, Brenton; Cannesson, Maxime

2012-01-01

Closed-loop (automated) controllers are encountered in all aspects of modern life in applications ranging from air-conditioning to spaceflight. Although these systems are virtually ubiquitous, they are infrequently used in anesthesiology because of the complexity of physiologic systems and the difficulty in obtaining reliable and valid feedback data from the patient. Despite these challenges, closed-loop systems are being increasingly studied and improved for medical use. Two recent developments have made fluid administration a candidate for closed-loop control. First, the further description and development of dynamic predictors of fluid responsiveness provides a strong parameter for use as a control variable to guide fluid administration. Second, rapid advances in noninvasive monitoring of cardiac output and other hemodynamic variables make goal-directed therapy applicable for a wide range of patients in a variety of clinical care settings. In this article, we review the history of closed-loop controllers in clinical care, discuss the current understanding and limitations of the dynamic predictors of fluid responsiveness, and examine how these variables might be incorporated into a closed-loop fluid administration system.

Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase

PubMed Central

Paës, Gabriel; Cortés, Juan; Siméon, Thierry; O'Donohue, Michael J.; Tran, Vinh

2012-01-01

Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis. PMID:24688637

Commensurability oscillations by snake-orbit magnetotransport in two-dimensional electron gases

NASA Astrophysics Data System (ADS)

Leuschner, A.; Schluck, J.; Cerchez, M.; Heinzel, T.; Pierz, K.; Schumacher, H. W.

2017-04-01

Commensurate magnetoresistance periodic oscillations generated by transversal electron snake orbits are found experimentally. A two-dimensional electron gas is exposed to a magnetic field that changes sign along the current longitudinal direction and is homogeneous in the transverse direction. The change in sign of the magnetic field directs the electron flow along the transversal direction, in snake orbits. This generates resistance oscillations with a predictable periodicity that is commensurate with the width of the electron gas. Numerical simulations are used to reveal the character of the oscillations.

Atomistic Simulations of the pH Induced Functional Rearrangement of Influenza Hemagglutinin

NASA Astrophysics Data System (ADS)

Lin, Xingcheng; Noel, Jeffrey; Wang, Qinghua; Ma, Jianpeng; Onuchic, Jose

Influenza hemagglutinin (HA), a surface glycoprotein responsible for the entry and replication of flu viruses in their host cells, functions by starting a dramatic conformational rearrangement, which leads to a fusion of the viral and endosomal membranes. It has been claimed that a loop-to-coiled-coil transition of the B-loop domain of HA drives the HA-induced membrane fusion. On the lack of dynamical details, however, the microscopic picture for this proposed ``spring-loaded'' movement is missing. To elaborate on the transition of the B-loop, we performed a set of unbiased all-atom molecular dynamics simulations of the full B-loop structure with the CHARMM36 force field. The complete free-energy profile constructed from our simulations reveals a slow transition rate for the B-loop that is incompatible with a downhill process. Additionally, our simulations indicate two potential sources of kinetic traps in the structural switch of the B-loop: Desolvation barriers and non-native secondary structure formation. The slow timescale of the B-loop transition also confirms our previous discovery from simulations using a coarse-grained structure-based model, which identified two competitive pathways both with a slow B-loop transition for HA to guide the membrane fusion.

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains

NASA Astrophysics Data System (ADS)

Zhang, Shuangshuang; Qi, Shuanhu; Klushin, Leonid I.; Skvortsov, Alexander M.; Yan, Dadong; Schmid, Friederike

2018-01-01

We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter ɛ and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force F applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i.e., the mean number of surface contacts in the case of the adsorption transition and the mean position of the chain end in the case of the loop-stretch transition. Close to the transition points, both the static behavior and the dynamic behavior of chains with different length N are very well described by a scaling ansatz with the scaling parameters (ɛ - ɛ*)Nϕ (adsorption transition) and (F - F*)Nν (loop-stretch transition), respectively, where ϕ is the crossover exponent of the adsorption transition and ν is the Flory exponent. We show that both the loop-stretch and the loop adsorption transitions provide an exceptional opportunity to construct explicit analytical expressions for the crossover functions which perfectly describe all simulation results on static properties in the finite-size scaling regime. Explicit crossover functions are based on the ansatz for the analytical form of the order parameter distributions at the respective transition points. In contrast to the close similarity in equilibrium static behavior, the dynamic relaxation at the two transitions shows qualitative differences, especially in the strongly ordered regimes. This is attributed to the fact that the surface contact dynamics in a strongly adsorbed chain is governed by local processes, whereas the end height relaxation of a strongly stretched chain involves the full spectrum of Rouse modes.

GROWING TRANSVERSE OSCILLATIONS OF A MULTISTRANDED LOOP OBSERVED BY SDO/AIA

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

Wang, Tongjiang; Ofman, Leon; Su, Yang

The first evidence of transverse oscillations of a multistranded loop with growing amplitudes and internal coupling observed by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory is presented. The loop oscillation event occurred on 2011 March 8, triggered by a coronal mass ejection (CME). The multiwavelength analysis reveals the presence of multithermal strands in the oscillating loop, whose dynamic behaviors are temperature-dependent, showing differences in their oscillation amplitudes, phases, and emission evolution. The physical parameters of growing oscillations of two strands in 171 A are measured and the three-dimensional loop geometry is determined using STEREO-A/EUVI data. These strandsmore » have very similar frequencies, and between two 193 A strands a quarter-period phase delay sets up. These features suggest the coupling between kink oscillations of neighboring strands and the interpretation by the collective kink mode as predicted by some models. However, the temperature dependence of the multistranded loop oscillations was not studied previously and needs further investigation. The transverse loop oscillations are associated with intensity and loop width variations. We suggest that the amplitude-growing kink oscillations may be a result of continuous non-periodic driving by magnetic deformation of the CME, which deposits energy into the loop system at a rate faster than its loss.« less

Dressed Wilson loops as dual condensates in response to magnetic and electric fields

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

Bruckmann, Falk; Endroedi, Gergely

2011-10-01

We introduce dressed Wilson loops as a novel confinement observable. It consists of closed planar loops of arbitrary geometry but fixed area, and its expectation values decay with the latter. The construction of dressed Wilson loops is based on chiral condensates in response to magnetic and electric fields, thus linking different physical concepts. We present results for generalized condensates and dressed Wilson loops on dynamical lattice configurations and confirm the agreement with conventional Wilson loops in the limit of large probe mass. We comment on the renormalization of dressed Wilson loops.

Fractional compartmental models and multi-term Mittag-Leffler response functions.

PubMed

Verotta, Davide

2010-04-01

Systems of fractional differential equations (SFDE) have been increasingly used to represent physical and control system, and have been recently proposed for use in pharmacokinetics (PK) by (J Pharmacokinet Pharmacodyn 36:165-178, 2009) and (J Phamacokinet Pharmacodyn, 2010). We contribute to the development of a theory for the use of SFDE in PK by, first, further clarifying the nature of systems of FDE, and in particular point out the distinction and properties of commensurate versus non-commensurate ones. The second purpose is to show that for both types of systems, relatively simple response functions can be derived which satisfy the requirements to represent single-input/single-output PK experiments. The response functions are composed of sums of single- (for commensurate) or two-parameters (for non-commensurate) Mittag-Leffler functions, and establish a direct correspondence with the familiar sums of exponentials used in PK.

Superlubric sliding of graphene nanoflakes on graphene.

PubMed

Feng, Xiaofeng; Kwon, Sangku; Park, Jeong Young; Salmeron, Miquel

2013-02-26

The lubricating properties of graphite and graphene have been intensely studied by sliding a frictional force microscope tip against them to understand the origin of the observed low friction. In contrast, the relative motion of free graphene layers remains poorly understood. Here we report a study of the sliding behavior of graphene nanoflakes (GNFs) on a graphene surface. Using scanning tunneling microscopy, we found that the GNFs show facile translational and rotational motions between commensurate initial and final states at temperatures as low as 5 K. The motion is initiated by a tip-induced transition of the flakes from a commensurate to an incommensurate registry with the underlying graphene layer (the superlubric state), followed by rapid sliding until another commensurate position is reached. Counterintuitively, the average sliding distance of the flakes is larger at 5 K than at 77 K, indicating that thermal fluctuations are likely to trigger their transitions from superlubric back to commensurate ground states.

Behaviour of fractional loop delay zero crossing digital phase locked loop (FR-ZCDPLL)

NASA Astrophysics Data System (ADS)

Nasir, Qassim

2018-01-01

This article analyses the performance of the first-order zero crossing digital phase locked loops (FR-ZCDPLL) when fractional loop delay is added to loop. The non-linear dynamics of the loop is presented, analysed and examined through bifurcation behaviour. Numerical simulation of the loop is conducted to proof the mathematical analysis of the loop operation. The results of the loop simulation show that the proposed FR-ZCDPLL has enhanced the performance compared to the conventional zero crossing DPLL in terms of wider lock range, captured range and stable operation region. In addition, extensive experimental simulation was conducted to find the optimum loop parameters for different loop environmental conditions. The addition of the fractional loop delay network in the conventional loop also reduces the phase jitter and its variance especially when the signal-to-noise ratio is low.

Multi-thermal observations of newly formed loops in a dynamic flare

NASA Technical Reports Server (NTRS)

Svestka, Zdenek F.; Fontenla, Juan M.; Machado, Marcos E.; Martin, Sara F.; Neidig, Donald F.

1987-01-01

The dynamic flare of November 6, 1980 (max at about 15:26 UT) developed a rich system of growing loops which could be followed in H-alpha for 1.5 hr. Throughout the flare, these loops, near the limb, were seen in emission against the disk. Theoretical computations of deviations from LTE populations for a hydrogen atom reveal that this requires electron densities in the loops close to, or in excess of 10 to the 12th/cu cm. From measured widths of higher Balmer lines the density at the tops of the loops was found to be 4 x 10 to the 12th/cu cm if no nonthermal motions were present, or 5 x 10 to the 11th/cu cm for a turbulent velocity of about 12 km/s. It is now general knowledge that flare loops are initially observed in X-rays and become visible in H-alpha only after cooling. For such a high density, a loop would cool through radiation from 10 to the 7th to 10 to the 4th K within a few minutes so that the dense H-alpha loops should have heights very close to the heights of the X-ray loops. This, however, contradicts the observations obtained by the HXIS and FCS instruments on board SMM which show the X-ray loops at much higher altitudes than the loops in H-alpha. Therefore, it is suggested that the density must have been significantly lower when the loops were formed, and that the flare loops were apparently both shrinking and increasing in density while cooling.

Radiation from quantum weakly dynamical horizons in loop quantum gravity.

PubMed

Pranzetti, Daniele

2012-07-06

We provide a statistical mechanical analysis of quantum horizons near equilibrium in the grand canonical ensemble. By matching the description of the nonequilibrium phase in terms of weakly dynamical horizons with a local statistical framework, we implement loop quantum gravity dynamics near the boundary. The resulting radiation process provides a quantum gravity description of the horizon evaporation. For large black holes, the spectrum we derive presents a discrete structure which could be potentially observable.

Hidden attractors in dynamical models of phase-locked loop circuits: Limitations of simulation in MATLAB and SPICE

NASA Astrophysics Data System (ADS)

Kuznetsov, N. V.; Leonov, G. A.; Yuldashev, M. V.; Yuldashev, R. V.

2017-10-01

During recent years it has been shown that hidden oscillations, whose basin of attraction does not overlap with small neighborhoods of equilibria, may significantly complicate simulation of dynamical models, lead to unreliable results and wrong conclusions, and cause serious damage in drilling systems, aircrafts control systems, electromechanical systems, and other applications. This article provides a survey of various phase-locked loop based circuits (used in satellite navigation systems, optical, and digital communication), where such difficulties take place in MATLAB and SPICE. Considered examples can be used for testing other phase-locked loop based circuits and simulation tools, and motivate the development and application of rigorous analytical methods for the global analysis of phase-locked loop based circuits.

Urey Prize Lecture - Chaotic dynamics in the solar system

NASA Technical Reports Server (NTRS)

Wisdom, Jack

1987-01-01

Attention is given to solar system cases in which chaotic solutions of Newton's equations are important, as in chaotic rotation and orbital evolution. Hyperion is noted to be tumbling chaotically; chaotic orbital evolution is suggested to be of fundamental importance to an accounting for the Kirkwood gaps in asteroid distribution and for the phase space boundary of the chaotic zone at the 3/1 mean-motion commensurability with Jupiter. In addition, chaotic trajectories in the 2/1 chaotic zone reach very high eccentricities by a route that carries them to high inclinations temporarily.

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.

Dynamic response of a fiber-optic ring resonator: Analysis with influences of light-source parameters

NASA Astrophysics Data System (ADS)

Seraji, Faramarz E.

2009-03-01

In practice, dynamic behavior of fiber-optic ring resonator (FORR) appears as a detrimental factor to influence the transmission response of the FORR. This paper presents dynamic response analysis of the FORR by considering phase modulation of the FORR loop and sinewave modulation of input signal applied to the FORR from a laser diode. The analysis investigates the influences of modulation frequency and amplitude modulation index of laser diode, loop delay time of the FORR, phase angle between FM and AM response of laser diode, and laser diode line-width on dynamic response of the FORR. The analysis shows that the transient response of the FORR strongly depends on the product of modulation frequency and loop delay time, coupling and transmission coefficients of the FORR. The analyses presented here may have applications in optical systems employing an FORR with a laser diode source.

Thrust Control Loop Design for Electric-Powered UAV

NASA Astrophysics Data System (ADS)

Byun, Heejae; Park, Sanghyuk

2018-04-01

This paper describes a process of designing a thrust control loop for an electric-powered fixed-wing unmanned aerial vehicle equipped with a propeller and a motor. In particular, the modeling method of the thrust system for thrust control is described in detail and the propeller thrust and torque force are modeled using blade element theory. A relation between current and torque of the motor is obtained using an experimental setup. Another relation between current, voltage and angular velocity is also obtained. The electric motor and the propeller dynamics are combined to model the thrust dynamics. The associated trim and linearization equations are derived. Then, the thrust dynamics are coupled with the flight dynamics to allow a proper design for the thrust loop in the flight control. The proposed method is validated by an application to a testbed UAV through simulations and flight test.

Dual-loop model of the human controller

NASA Technical Reports Server (NTRS)

Hess, R. A.

1978-01-01

A dual-loop model of the human controller in single-axis compensatory tracking tasks is introduced. This model possesses an inner-loop closure that involves feeding back that portion of controlled element output rate that is due to control activity. A novel feature of the model is the explicit appearance of the human's internal representation of the manipulator-controlled element dynamics in the inner loop. The sensor inputs to the human controller are assumed to be system error and control force. The former can be sensed via visual, aural, or tactile displays, whereas the latter is assumed to be sensed in kinesthetic fashion. A set of general adaptive characteristics for the model is hypothesized, including a method for selecting simplified internal models of the manipulator-controlled element dynamics. It is demonstrated that the model can produce controller describing functions that closely approximate those measured in four laboratory tracking tasks in which the controlled element dynamics vary considerably in terms of ease of control. An empirically derived expression for the normalized injected error remnant spectrum is introduced.

Impact of Eccentricity on East-west Stationkeeping for GPS Class of Orbits

NASA Technical Reports Server (NTRS)

Ely, Todd A.

1999-01-01

There exists a strong relationship between eccentricity and the potential for a repeating groundtrack orbit to exhibit chaotic motion. This is true at all values of eccentricity, but, perhaps most dramatic, is that it is true even for orbits that are nearly circular. These complex motions can have a significant impact on the east-west stationkeeping process for maintaining the repeating groundtrack property of a commensurate orbit. Ely and Howell have shown that traditional stationkeeping (SK) methods are unable to maintain a repeating groundtrack in the presence of complex dynamics, such as with chaotic motion. They developed an alternate SK method that is able to maintain a repeating groundtrack for eccentric, commensurate orbits. The focus of the current study is to investigate orbits with characteristics that are similar to GPS satellites except with modestly larger eccentricities. It will be shown that at eccentricities larger than approx. .01 the chaotic regions become significant, and the need arises for a robust stationkeeping approach, such as developed in. FurtheRmore, the investigation will reveal that the influence of luni-solar perturbations contributes to the growth of eccentricity, thus increasing the probability of encountering chaotic motion during a typical satellite lifetime.

Spatial operator algebra framework for multibody system dynamics

NASA Technical Reports Server (NTRS)

Rodriguez, G.; Jain, Abhinandan; Kreutz, K.

1989-01-01

The Spatial Operator Algebra framework for the dynamics of general multibody systems is described. The use of a spatial operator-based methodology permits the formulation of the dynamical equations of motion of multibody systems in a concise and systematic way. The dynamical equations of progressively more complex grid multibody systems are developed in an evolutionary manner beginning with a serial chain system, followed by a tree topology system and finally, systems with arbitrary closed loops. Operator factorizations and identities are used to develop novel recursive algorithms for the forward dynamics of systems with closed loops. Extensions required to deal with flexible elements are also discussed.

Spatial Operator Algebra for multibody system dynamics

NASA Technical Reports Server (NTRS)

Rodriguez, G.; Jain, A.; Kreutz-Delgado, K.

1992-01-01

The Spatial Operator Algebra framework for the dynamics of general multibody systems is described. The use of a spatial operator-based methodology permits the formulation of the dynamical equations of motion of multibody systems in a concise and systematic way. The dynamical equations of progressively more complex grid multibody systems are developed in an evolutionary manner beginning with a serial chain system, followed by a tree topology system and finally, systems with arbitrary closed loops. Operator factorizations and identities are used to develop novel recursive algorithms for the forward dynamics of systems with closed loops. Extensions required to deal with flexible elements are also discussed.

Super energy saver heat pump with dynamic hybrid phase change material

DOEpatents

Ally, Moonis Raza [Oak Ridge, TN; Tomlinson, John Jager [Knoxville, TN; Rice, Clifford Keith [Clinton, TN

2010-07-20

A heat pump has a refrigerant loop, a compressor in fluid communication with the refrigerant loop, at least one indoor heat exchanger in fluid communication with the refrigerant loop, and at least one outdoor heat exchanger in fluid communication with the refrigerant loop. The at least one outdoor heat exchanger has a phase change material in thermal communication with the refrigerant loop and in fluid communication with an outdoor environment. Other systems, devices, and methods are described.

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

PubMed Central

McDowell, S. Elizabeth; Jun, Jesse M.; Walter, Nils G.

2010-01-01

Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ∼10-fold higher than physiologic concentrations of Mg2+ ions. Extended versions containing native loop–loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg2+ concentrations, for reasons that are still ill-understood. Here, we use Mg2+ titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop–loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop–loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop–loop interactions in extended hammerhead ribozymes—and Mg2+ ions that bind to minimal ribozymes—may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state. PMID:20921269

Shortening a loop can increase protein native state entropy.

PubMed

Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

2015-12-01

Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

Experimental Observation of Classical Dynamical Monodromy

NASA Astrophysics Data System (ADS)

Nerem, M. P.; Salmon, D.; Aubin, S.; Delos, J. B.

2018-03-01

A Hamiltonian system is said to have nontrivial monodromy if its fundamental action-angle loops do not return to their initial topological state at the end of a closed circuit in angular momentum-energy space. This process has been predicted to have consequences which can be seen in dynamical systems, called dynamical monodromy. Using an apparatus consisting of a spherical pendulum subject to magnetic potentials and torques, we observe nontrivial monodromy by the associated topological change in the evolution of a loop of trajectories.

Dynamic formation and magnetic support of loop or arcade prominences

NASA Technical Reports Server (NTRS)

Vanhoven, Gerard; Mok, Y.; Drake, J. F.

1992-01-01

The results of model dynamic simulations of the formation and support of a narrow prominence at the apex of a coronal magnetic loop or arcade are described. The condensation process proceeds via an initial radiative cooling and pressure drop, and a secondary siphon flow from the dense chromospheric ends. The antibuoyancy effect as the prominence forms causes a bending of a confining magnetic field, which propagates toward the semirigid ends of the magnetic loop. Thus, a wide magnetic 'hammock' or well (of a normal polarity Kippenhahn-Schlueter type) is formed, which supports the prominence at or near the field apex.

Influence of the feedback loops in the trp operon of B. subtilis on the system dynamic response and noise amplitude.

PubMed

Zamora-Chimal, Criseida; Santillán, Moisés; Rodríguez-González, Jesús

2012-10-07

In this paper we introduce a mathematical model for the tryptophan operon regulatory pathway in Bacillus subtilis. This model considers the transcription-attenuation, and the enzyme-inhibition regulatory mechanisms. Special attention is paid to the estimation of all the model parameters from reported experimental data. With the aid of this model we investigate, from a mathematical-modeling point of view, whether the existing multiplicity of regulatory feedback loops is advantageous in some sense, regarding the dynamic response and the biochemical noise in the system. The tryptophan operon dynamic behavior is studied by means of deterministic numeric simulations, while the biochemical noise is analyzed with the aid of stochastic simulations. The model feasibility is tested comparing its stochastic and deterministic results with experimental reports. Our results for the wildtype and for a couple of mutant bacterial strains suggest that the enzyme-inhibition feedback loop, dynamically accelerates the operon response, and plays a major role in the reduction of biochemical noise. Also, the transcription-attenuation feedback loop makes the trp operon sensitive to changes in the endogenous tryptophan level, and increases the amplitude of the biochemical noise. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

PubMed

Rysavy, Steven J; Beck, David A C; Daggett, Valerie

2014-11-01

Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼ 25-75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. © 2014 The Protein Society.

Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction

PubMed Central

Rysavy, Steven J; Beck, David AC; Daggett, Valerie

2014-01-01

Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼25–75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. PMID:25142412

Dynamic nesting and the incommensurate magnetic response in superconducting YBa 2Cu 3O 6+ y

NASA Astrophysics Data System (ADS)

Brinckmann, Jan; Lee, Patrick A.

1999-05-01

The dynamic magnetic susceptibility χ″( q, ω) of the t- t‧- J-model for YBCO compounds is studied in slave-boson mean-field theory. Within a renormalized random-phase approximation χ″ is compared for different fixed energies ω in the superconducting state. At the energy ω= ω0, where χ″(( π, π), ω) shows a sharp peak (the `41 meV resonance'), the response is commensurate in wave vector space. At lower energies around ωi=0.7 ω0, however, we find four peaks at q=( π± δ, π) and ( π, π± δ). The results are in agreement with inelastic neutron scattering experiments, in particular with the incommensurate response recently observed in YBa 2Cu 3O 6.6 by Mook et al. We argue that dynamic nesting in the dispersion of quasi particles causes this effect.

The Trade-Off Mechanism in Mammalian Circadian Clock Model with Two Time Delays

NASA Astrophysics Data System (ADS)

Yan, Jie; Kang, Xiaxia; Yang, Ling

Circadian clock is an autonomous oscillator which orchestrates the daily rhythms of physiology and behaviors. This study is devoted to explore how a positive feedback loop affects the dynamics of mammalian circadian clock. We simplify an experimentally validated mathematical model in our previous work, to a nonlinear differential equation with two time delays. This simplified mathematical model incorporates the pacemaker of mammalian circadian clock, a negative primary feedback loop, and a critical positive auxiliary feedback loop, Rev-erbα/Cry1 loop. We perform analytical studies of the system. Delay-dependent conditions for the asymptotic stability of the nontrivial positive steady state of the model are investigated. We also prove the existence of Hopf bifurcation, which leads to self-sustained oscillation of mammalian circadian clock. Our theoretical analyses show that the oscillatory regime is reduced upon the participation of the delayed positive auxiliary loop. However, further simulations reveal that the auxiliary loop can enable the circadian clock gain widely adjustable amplitudes and robust period. Thus, the positive auxiliary feedback loop may provide a trade-off mechanism, to use the small loss in the robustness of oscillation in exchange for adaptable flexibility in mammalian circadian clock. The results obtained from the model may gain new insights into the dynamics of biological oscillators with interlocked feedback loops.

Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations

PubMed Central

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W.; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-01-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. PMID:24792385

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

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

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

PubMed

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-09-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. Copyright © 2014. Published by Elsevier B.V.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 1: Analysis methods

NASA Technical Reports Server (NTRS)

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

1985-01-01

As aircraft become larger and lighter due to design requirements for increased payload and improved fuel efficiency, they will also become more flexible. For highly flexible vehicles, the handling qualities may not be accurately predicted by conventional methods. This study applies two analysis methods 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 model analysis technique. This method considers the effects 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. Volume 1 consists of the development and application of the two analysis methods described above.

The Response of Ω-Loop D Dynamics to Truncation of Trimethyllysine 72 of Yeast Iso-1-cytochrome c Depends on the Nature of Loop Deformation

PubMed Central

McClelland, Levi J.; Seagraves, Sean M.; Khan, Khurshid Alam; Cherney, Melisa M.; Bandi, Swati; Culbertson, Justin E.; Bowler, Bruce E.

2015-01-01

Trimethyllysine 72 (tmK72) has been suggested to play a role in sterically constraining the heme crevice dynamics of yeast iso-1-cytochrome c mediated by the Ω-loop D cooperative substructure (residues 70 to 85). A tmK72A mutation causes a gain in peroxidase activity, a function of cytochrome c that is important early in apoptosis. More than one higher energy state is accessible for the Ω-loop D substructure via tier 0 dynamics. Two of these are alkaline conformers mediated by Lys73 and Lys79. In the current work, the effect of the tmK72A mutation on the thermodynamic and kinetic properties of wild type iso-1-cytochrome c (yWT versus WT*) and on variants carrying a K73H mutation (yWT/K73H versus WT*/K73H) is studied. Whereas the tmK72A mutation confers increased peroxidase activity in wild type yeast iso-1-cytochrome c and increased dynamics for formation of a previously studied His79-heme alkaline conformer, the tmK72A mutation speeds return of the His73-heme alkaline conformer to the native state through destabilization of the His73-heme alkaline conformer relative to the native conformer. These opposing behaviors demonstrate that the response of the dynamics of a protein substructure to mutation depends on the nature of the perturbation to the substructure. For a protein substructure which mediates more than one function of a protein through multiple non-native structures, a mutation could change the partitioning between these functions. The current results suggest that the tier 0 dynamics of Ω-loop D that mediates peroxidase activity has similarities to the tier 0 dynamics required to form the His79-heme alkaline conformer. PMID:25948392

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

PubMed Central

Kurkcuoglu, Zeynep; Bakan, Ahmet; Kocaman, Duygu; Bahar, Ivet; Doruker, Pemra

2012-01-01

Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions. We performed an extensive study on a set of enzymes to assess whether the collective/global dynamics, as predicted by elastic network models (ENMs), facilitates or even defines the local motions undergone by functional loops. Our dataset includes a total of 117 crystal structures for ten enzymes of different sizes and oligomerization states. Each enzyme contains a specific functional/catalytic loop (10–21 residues long) that closes over the active site during catalysis. Principal component analysis (PCA) of the available crystal structures (including apo and ligand-bound forms) for each enzyme revealed the dominant conformational changes taking place in these loops upon substrate binding. These experimentally observed loop reconfigurations are shown to be predominantly driven by energetically favored modes of motion intrinsically accessible to the enzyme in the absence of its substrate. The analysis suggests that robust global modes cooperatively defined by the overall enzyme architecture also entail local components that assist in suitable opening/closure of the catalytic loop over the active site. PMID:23028297

Structure and Dynamics of Cool Flare Loops Observed by the Interface Region Imaging Spectrograph

NASA Astrophysics Data System (ADS)

Mikuła, K.; Heinzel, P.; Liu, W.; Berlicki, A.

2017-08-01

Flare loops were well observed with the Interface Region Imaging Spectrograph (IRIS) during the gradual phase of two solar flares on 2014 March 29 and 2015 June 22. Cool flare loops are visible in various spectral lines formed at chromospheric and transition-region temperatures and exhibit large downflows which correspond to the standard scenario. The principal aim of this work is to analyze the structure and dynamics of cool flare loops observed in Mg II lines. Synthetic profiles of the Mg II h line are computed using the classical cloud model and assuming a uniform background intensity. In this paper, we study novel IRIS NUV observations of such loops in Mg II h and k lines and also show the behavior of hotter lines detected in the FUV channel. We obtained the spatial evolution of the velocities: near the loop top, the flow velocities are small and they are increasing toward the loop legs. Moreover, from slit-jaw image (SJI) movies, we observe some plasma upflows into the loops, which are also detectable in Mg II spectra. The brightness of the loops systematically decreases with increasing flow velocity, and we ascribe this to the effect of Doppler dimming, which works for Mg II lines. Emission profiles of Mg II were found to be extremely broad, and we explain this through the large unresolved non-thermal motions.

Structure and Dynamics of Cool Flare Loops Observed by the Interface Region Imaging Spectrograph

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

Mikuła, K.; Berlicki, A.; Heinzel, P.

Flare loops were well observed with the Interface Region Imaging Spectrograph ( IRIS ) during the gradual phase of two solar flares on 2014 March 29 and 2015 June 22. Cool flare loops are visible in various spectral lines formed at chromospheric and transition-region temperatures and exhibit large downflows which correspond to the standard scenario. The principal aim of this work is to analyze the structure and dynamics of cool flare loops observed in Mg ii lines. Synthetic profiles of the Mg ii h line are computed using the classical cloud model and assuming a uniform background intensity. In thismore » paper, we study novel IRIS NUV observations of such loops in Mg ii h and k lines and also show the behavior of hotter lines detected in the FUV channel. We obtained the spatial evolution of the velocities: near the loop top, the flow velocities are small and they are increasing toward the loop legs. Moreover, from slit-jaw image (SJI) movies, we observe some plasma upflows into the loops, which are also detectable in Mg ii spectra. The brightness of the loops systematically decreases with increasing flow velocity, and we ascribe this to the effect of Doppler dimming, which works for Mg ii lines. Emission profiles of Mg ii were found to be extremely broad, and we explain this through the large unresolved non-thermal motions.« less

All-digital phase-lock loops for noise-free signals

NASA Technical Reports Server (NTRS)

Anderson, T. O.

1973-01-01

Bit-synchronizers utilize all-digital phase-lock loops that are referenced to a high frequency digital clock. Phase-lock loop of first design acquires frequency within nominal range and tracks phase; second design is modified for random binary data by addition of simple transition detector; and third design acquires frequency over wide dynamic range.

Second International Workshop on Grid Simulator Testing of Wind Turbine

Science.gov Websites

, Clemson University, USA Update on the FSU-CAPS Megawatt Scale Power Hardware in the Loop Laboratory Loop Based Anti-Islanding Testing of PV Converters-Michael Steurer, Florida State University, USA Closed-Loop Control of Modern Test Benches Advanced Control Techniques for Dynamic Testing of Wind

Energy Systems Integration News | Energy Systems Integration Facility |

Science.gov Websites

-the-loop" (HIL) to connect physical devices to software models, EdgePower is drawing on NREL's are putting their controller into a synthetic environment that is called 'controller in-the-loop controller-in-the-loop platform allows us to observe the dynamics of these buildings as they implement the

Dislocation dynamics simulations of interactions between gliding dislocations and radiation induced prismatic loops in zirconium

NASA Astrophysics Data System (ADS)

Drouet, Julie; Dupuy, Laurent; Onimus, Fabien; Mompiou, Frédéric; Perusin, Simon; Ambard, Antoine

2014-06-01

The mechanical behavior of Pressurized Water Reactor fuel cladding tubes made of zirconium alloys is strongly affected by neutron irradiation due to the high density of radiation induced dislocation loops. In order to investigate the interaction mechanisms between gliding dislocations and loops in zirconium, a new nodal dislocation dynamics code, adapted to Hexagonal Close Packed metals, has been used. Various configurations have been systematically computed considering different glide planes, basal or prismatic, and different characters, edge or screw, for gliding dislocations with -type Burgers vectors. Simulations show various interaction mechanisms such as (i) absorption of a loop on an edge dislocation leading to the formation of a double super-jog, (ii) creation of a helical turn, on a screw dislocation, that acts as a strong pinning point or (iii) sweeping of a loop by a gliding dislocation. It is shown that the clearing of loops is more favorable when the dislocation glides in the basal plane than in the prismatic plane explaining the easy dislocation channeling in the basal plane observed after neutron irradiation by transmission electron microscopy.

Functional and structural characterization of the pentapeptide insertion of Theileria annulata lactate dehydrogenase by site-directed mutagenesis, comparative modeling and molecular dynamics simulations.

PubMed

Erdemir, Aysegul; Mutlu, Ozal

2017-06-01

Lactate dehydrogenase (LDH) is an important metabolic enzyme in glycolysis and it has been considered as the main energy source in many organisms including apicomplexan parasites. Differences at the active site loop of the host and parasite LDH's makes this enzyme an attractive target for drug inhibitors. In this study, five amino acid insertions in the active site pocket of Theileria annulata LDH (TaLDH) were deleted by PCR-based site-directed mutagenesis, expression and activity analysis of mutant and wild type TaLDH enzymes were performed. Removal of the insertion at the active site loop caused production of an inactive enzyme. Furthermore, structures of wild and mutant enzymes were predicted by comparative modeling and the importance of the insertions at the active site loop were also assigned by molecular docking and dynamics simulations in order to evaluate essential role of this loop for the enzymatic activity. Pentapeptide insertion removal resulted in loss of LDH activity due to deletion of Trp96 and conformational change of Arg98 because of loop instability. Analysis of wild type and mutant enzymes with comparative molecular dynamics simulations showed that the fluctuations of the loop residues increase in mutant enzyme. Together with in silico studies, in vitro results revealed that active site loop has a vital role in the enzyme activity and our findings promise hope for the further drug design studies against theileriosis and other apicomplexan parasite diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Hysteresis losses and specific absorption rate measurements in magnetic nanoparticles for hyperthermia applications.

PubMed

Coïsson, Marco; Barrera, Gabriele; Celegato, Federica; Martino, Luca; Kane, Shashank N; Raghuvanshi, Saroj; Vinai, Franco; Tiberto, Paola

2017-06-01

Magnetic hysteresis loops areas and hyperthermia on magnetic nanoparticles have been studied with the aim of providing reliable and reproducible methods of measuring the specific absorption rate (SAR). The SAR of Fe 3 O 4 nanoparticles with two different mean sizes, and Ni 1-x Zn x Fe 2 O 4 ferrites with 0 ≤ x ≤ 0.8 has been measured with three approaches: static hysteresis loops areas, dynamic hysteresis loops areas and hyperthermia of a water solution. For dynamic loops and thermometric measurements, specific experimental setups have been developed, that operate at comparable frequencies (≈ 69kHz and ≈ 100kHz respectively) and rf magnetic field peak values (up to 100mT). The hyperthermia setup has been fully modelled to provide a direct measurement of the SAR of the magnetic nanoparticles by taking into account the heat exchange with the surrounding environment in non-adiabatic conditions and the parasitic heating of the water due to ionic currents. Dynamic hysteresis loops are shown to provide an accurate determination of the SAR except for superparamagnetic samples, where the boundary with a blocked regime could be crossed in dynamic conditions. Static hysteresis loops consistently underestimate the specific absorption rate but can be used to select the most promising samples. A means of reliably measure SAR of magnetic nanoparticles by different approaches for hyperthermia applications is presented and its validity discussed by comparing different methods. This work fits within the general subject of metrological traceability in medicine with a specific focus on magnetic hyperthermia. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editor: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamics of nonlinear feedback control.

PubMed

Snippe, H P; van Hateren, J H

2007-05-01

Feedback control in neural systems is ubiquitous. Here we study the mathematics of nonlinear feedback control. We compare models in which the input is multiplied by a dynamic gain (multiplicative control) with models in which the input is divided by a dynamic attenuation (divisive control). The gain signal (resp. the attenuation signal) is obtained through a concatenation of an instantaneous nonlinearity and a linear low-pass filter operating on the output of the feedback loop. For input steps, the dynamics of gain and attenuation can be very different, depending on the mathematical form of the nonlinearity and the ordering of the nonlinearity and the filtering in the feedback loop. Further, the dynamics of feedback control can be strongly asymmetrical for increment versus decrement steps of the input. Nevertheless, for each of the models studied, the nonlinearity in the feedback loop can be chosen such that immediately after an input step, the dynamics of feedback control is symmetric with respect to increments versus decrements. Finally, we study the dynamics of the output of the control loops and find conditions under which overshoots and undershoots of the output relative to the steady-state output occur when the models are stimulated with low-pass filtered steps. For small steps at the input, overshoots and undershoots of the output do not occur when the filtering in the control path is faster than the low-pass filtering at the input. For large steps at the input, however, results depend on the model, and for some of the models, multiple overshoots and undershoots can occur even with a fast control path.

Generalized characteristic ratios assignment for commensurate fractional order systems with one zero.

PubMed

Tabatabaei, Mohammad

2017-07-01

In this paper, a new method for determination of the desired characteristic equation and zero location of commensurate fractional order systems is presented. The concept of the characteristic ratio is extended for zero-including commensurate fractional order systems. The generalized version of characteristic ratios is defined such that the time-scaling property of characteristic ratios is also preserved. The monotonicity of the magnitude frequency response is employed to assign the generalized characteristic ratios for commensurate fractional order transfer functions with one zero. A simple pattern for characteristic ratios is proposed to reach a non-overshooting step response. Then, the proposed pattern is revisited to reach a low overshoot (say for example 2%) step response. Finally, zero-including controllers such as fractional order PI or lag (lead) controllers are designed using generalized characteristic ratios assignment method. Numerical simulations are provided to show the efficiency of the so designed controllers. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Alpha-canonical form representation of the open loop dynamics of the Space Shuttle main engine

NASA Technical Reports Server (NTRS)

Duyar, Almet; Eldem, Vasfi; Merrill, Walter C.; Guo, Ten-Huei

1991-01-01

A parameter and structure estimation technique for multivariable systems is used to obtain a state space representation of open loop dynamics of the space shuttle main engine in alpha-canonical form. The parameterization being used is both minimal and unique. The simplified linear model may be used for fault detection studies and control system design and development.

Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus.

PubMed

Balmith, Marissa; Soliman, Mahmoud E S

2017-02-28

The first account of the dynamic features of the loop region of VP40 of the Ebola virus (EboV) using accelerated molecular dynamics (aMD) simulations is reported herein. Due to its major role in the Ebola life cycle, VP40 is considered a promising therapeutic target. The available experimental data on the N-terminal domain (NTD) loop indicates that mutations K127A, T129A and N130A demonstrate an unrecognized role for NTD-plasma membrane (PM) interaction for efficient VP40-PM localization, oligomerization, matrix assembly and egress. Despite experimental results, the molecular description of VP40 and the information it can provide still remain vague. Therefore, to gain further molecular insight into the effect of mutations on the loop region of VP40 and its effects on the overall protein conformation and VP40 dimerization, aMD simulations and post-dynamic analyses were employed for wildtype (WT) and mutant systems. The results showed significant variations in the presence of mutations as per RMSF, RMSD, R g , PCA and distance calculations in comparison to the WT. These results could provide researchers with insight with regards to the conformational aspects concerning VP40 and its close relation to the experimental data. We believe that the results presented in this study will ultimately provide a useful understanding of the structural landscape of the loop region of VP40, which would contribute towards the discovery of novel EboV inhibitors.

Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation.

PubMed

Villa, Elizabeth; Balaeff, Alexander; Schulten, Klaus

2005-05-10

A multiscale simulation of a complex between the lac repressor protein (LacI) and a 107-bp-long DNA segment is reported. The complex between the repressor and two operator DNA segments is described by all-atom molecular dynamics; the size of the simulated system comprises either 226,000 or 314,000 atoms. The DNA loop connecting the operators is modeled as a continuous elastic ribbon, described mathematically by the nonlinear Kirchhoff differential equations with boundary conditions obtained from the coordinates of the terminal base pairs of each operator. The forces stemming from the looped DNA are included in the molecular dynamics simulations; the loop structure and the forces are continuously recomputed because the protein motions during the simulations shift the operators and the presumed termini of the loop. The simulations reveal the structural dynamics of the LacI-DNA complex in unprecedented detail. The multiple domains of LacI exhibit remarkable structural stability during the simulation, moving much like rigid bodies. LacI is shown to absorb the strain from the looped DNA mainly through its mobile DNA-binding head groups. Even with large fluctuating forces applied, the head groups tilt strongly and keep their grip on the operator DNA, while the remainder of the protein retains its V-shaped structure. A simulated opening of the cleft of LacI by 500-pN forces revealed the interactions responsible for locking LacI in the V-conformation.

Hydrodynamically induced oscillations and traffic dynamics in 1D microfludic networks

NASA Astrophysics Data System (ADS)

Bartolo, Denis; Jeanneret, Raphael

2011-03-01

We report on the traffic dynamics of particles driven through a minimal microfluidic network. Even in the minimal network consisting in a single loop, the traffic dynamics has proven to yield complex temporal patterns, including periodic, multi-periodic or chaotic sequences. This complex dynamics arises from the strongly nonlinear hydrodynamic interactions between the particles, that takes place at a junction. To better understand the consequences of this nontrivial coupling, we combined theoretical, numerical and experimental efforts and solved the 3-body problem in a 1D loop network. This apparently simple dynamical system revealed a rich and unexpected dynamics, including coherent spontaneous oscillations along closed orbits. Striking similarities between Hamiltonian systems and this driven dissipative system will be explained.

Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays

PubMed Central

Suzuki, Yoko; Lu, Mingyang; Ben-Jacob, Eshel; Onuchic, José N.

2016-01-01

Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations, and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer. PMID:26876008

Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays

NASA Astrophysics Data System (ADS)

Suzuki, Yoko; Lu, Mingyang; Ben-Jacob, Eshel; Onuchic, José N.

2016-02-01

Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations, and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer.

7 CFR 1400.7 - Commensurate contributions and risk.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Commensurate contributions and risk. 1400.7 Section 1400.7 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT... contributions and risk. (a) In order to be considered eligible to receive payments under the programs specified...

SMART materials: Surfaces, transforms and interfaces. The commensurate engineering dimension

NASA Astrophysics Data System (ADS)

McDonach, Alaster; Gardiner, Peter T.; McEwen, Ron S.; Culshaw, Brian

1994-11-01

The future of molecularly based smart materials hinges on the development of integrated technologies addressing synthesis, assembly, shaping, etc. and some of these are now becoming clear. Even in the bolt on era new technologies will allow issues of commensurate engineering to be addressed.

Proteins with Novel Structure, Function and Dynamics

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Dynamic order in a surface process

NASA Astrophysics Data System (ADS)

Eiswirth, M.; Ertl, G.

1988-09-01

Under certain well-defined conditions ( p co,p_{{text{O}}_{text{2}} } , T) the rate of catalytic oxidation of CO on a Pt(110) surface may exhibit sustained temporal oscillations with an autonomous frequency v 0. Small amplitude modulation ofp_{{text{O}}_{text{2}} } with frequency v p causes a variety of phenomena characteristic for systems of nonlinear dynamics which may be identified with temporal order and show formal similarities to spatial order of surface phases: Periodic behavior for certain rational numbers of v p/v0 — corresponding to commensurate surface structures; quasiperiodic behavior characterized by an irrational ratio of the periods of perturbation and response — corresponding to incommensurate structures; and critical slowing down near the boundary of a transition to quasiperiodicity which has its counterpart in the critical fluctuations near a (spatial) phase transition.

Revealing mesoscopic structural universality with diffusion.

PubMed

Novikov, Dmitry S; Jensen, Jens H; Helpern, Joseph A; Fieremans, Els

2014-04-08

Measuring molecular diffusion is widely used for characterizing materials and living organisms noninvasively. This characterization relies on relations between macroscopic diffusion metrics and structure at the mesoscopic scale commensurate with the diffusion length. Establishing such relations remains a fundamental challenge, hindering progress in materials science, porous media, and biomedical imaging. Here we show that the dynamical exponent in the time dependence of the diffusion coefficient distinguishes between the universality classes of the mesoscopic structural complexity. Our approach enables the interpretation of diffusion measurements by objectively selecting and modeling the most relevant structural features. As an example, the specific values of the dynamical exponent allow us to identify the relevant mesoscopic structure affecting MRI-measured water diffusion in muscles and in brain, and to elucidate the structural changes behind the decrease of diffusion coefficient in ischemic stroke.

Design and Implementation of an RTK-Based Vector Phase Locked Loop

PubMed Central

Shafaati, Ahmad; Lin, Tao; Broumandan, Ali; Lachapelle, Gérard

2018-01-01

This paper introduces a novel double-differential vector phase-locked loop (DD-VPLL) for Global Navigation Satellite Systems (GNSS) that leverages carrier phase position solutions as well as base station measurements in the estimation of rover tracking loop parameters. The use of double differencing alleviates the need for estimating receiver clock dynamics and atmospheric delays; therefore, the navigation filter consists of the baseline dynamic states only. It is shown that using vector processing for carrier phase tracking leads to a significant enhancement in the receiver sensitivity compared to using the conventional scalar-based tracking loop (STL) and vector frequency locked loop (VFLL). The sensitivity improvement of 8 to 10 dB compared to STL, and 7 to 8 dB compared to VFLL, is obtained based on the test cases reported in the paper. Also, an increased probability of ambiguity resolution in the proposed method results in better availability for real time kinematic (RTK) applications. PMID:29533994

Dynamics and unfolding pathway of chimeric azurin variants: insights from molecular dynamics simulation.

PubMed

Evoli, Stefania; Guzzi, Rita; Rizzuti, Bruno

2013-10-01

The spectroscopic, thermal, and functional properties of blue copper proteins can be modulated by mutations in the metal binding loop. Molecular dynamics simulation was used to compare the conformational properties of azurin and two chimeric variants, which were obtained by inserting into the azurin scaffold the copper binding loop of amicyanin and plastocyanin, respectively. Simulations at room temperature show that the proteins retain their overall structure and exhibit concerted motions among specific inner regions, as revealed by principal component analysis. Molecular dynamics at high temperature indicates that the first events in the unfolding pathway are structurally similar in the three proteins and unfolding starts from the region of the α-helix that is far from the metal binding loop. The results provide details of the denaturation process that are consistent with experimental data and in close agreement with other computational approaches, suggesting a distinct mechanism of unfolding of azurin and its chimeric variants. Moreover, differences observed in the dynamics of specific regions in the three proteins correlate with their thermal behavior, contributing to the determination of the basic factors that influence the stability.

Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein.

PubMed

Eberini, Ivano; Guerini Rocco, Alessandro; Ientile, Anna Rita; Baptista, António M; Gianazza, Elisabetta; Tomaselli, Simona; Molinari, Henriette; Ragona, Laura

2008-06-01

The correlation between protein motions and function is a central problem in protein science. Several studies have demonstrated that ligand binding and protein dynamics are strongly correlated in intracellular lipid binding proteins (iLBPs), in which the high degree of flexibility, principally occurring at the level of helix-II, CD, and EF loops (the so-called portal area), is significantly reduced upon ligand binding. We have recently investigated by NMR the dynamic properties of a member of the iLBP family, chicken liver bile acid binding protein (cL-BABP), in its apo and holo form, as a complex with two bile salts molecules. Binding was found to be regulated by a dynamic process and a conformational rearrangement was associated with this event. We report here the results of molecular dynamics (MD) simulations performed on apo and holo cL-BABP with the aim of further characterizing the protein regions involved in motion propagation and of evaluating the main molecular interactions stabilizing bound ligands. Upon binding, the root mean square fluctuation values substantially decrease for CD and EF loops while increase for the helix-loop-helix region, thus indicating that the portal area is the region mostly affected by complex formation. These results nicely correlate with backbone dynamics data derived from NMR experiments. Essential dynamics analysis of the MD trajectories indicates that the major concerted motions involve the three contiguous structural elements of the portal area, which however are dynamically coupled in different ways whether in the presence or in the absence of the ligands. Motions of the EF loop and of the helical region are part of the essential space of both apo and holo-BABP and sample a much wider conformational space in the apo form. Together with NMR results, these data support the view that, in the apo protein, the flexible EF loop visits many conformational states including those typical of the holo state and that the ligand acts stabilizing one of these pre-existing conformations. The present results, in agreement with data reported for other iLBPs, sharpen our knowledge on the binding mechanism for this protein family. (c) 2008 Wiley-Liss, Inc.

Dynamics of knotted flexible loops settling under a constant force in a viscous fluid

NASA Astrophysics Data System (ADS)

Gruziel, Magdalena; Thyagarajan, Krishnan; Dietler, Giovanni; Szymczak, Piotr; Ekiel-Jezewska, Maria

2017-11-01

Sedimenting chains of metal beads knotted to a topology of a torus knot tend to stabilize in the form of extended, flat, tightly interwound loops. In this configuration they perform an oscillatory motion of the loops swirling periodically around each other. Stokesian dynamics simulations of elastic fibers confirm the long-lasting character of the traveling wave-like swirling motion and show also the accompanying rotation of the system. Moreover, the periodic motion shows striking resemblance to the stable solutions for the evolution of vortices of torus knot topology. Using the results of the simulations we study the dependence of the frequencies and sedimentation velocities on the length of the fiber. We also notice the dependence of the knot dynamics on the bending stiffness of the fiber and the knot rank. NCN-2015/19/D/ST8/03199.

Study of a Simulation Tool to Determine Achievable Control Dynamics and Control Power Requirements with Perfect Tracking

NASA Technical Reports Server (NTRS)

Ostroff, Aaron J.

1998-01-01

This paper contains a study of two methods for use in a generic nonlinear simulation tool that could be used to determine achievable control dynamics and control power requirements while performing perfect tracking maneuvers over the entire flight envelope. The two methods are NDI (nonlinear dynamic inversion) and the SOFFT(Stochastic Optimal Feedforward and Feedback Technology) feedforward control structure. Equivalent discrete and continuous SOFFT feedforward controllers have been developed. These equivalent forms clearly show that the closed-loop plant model loop is a plant inversion and is the same as the NDI formulation. The main difference is that the NDI formulation has a closed-loop controller structure whereas SOFFT uses an open-loop command model. Continuous, discrete, and hybrid controller structures have been developed and integrated into the formulation. Linear simulation results show that seven different configurations all give essentially the same response, with the NDI hybrid being slightly different. The SOFFT controller gave better tracking performance compared to the NDI controller when a nonlinear saturation element was added. Future plans include evaluation using a nonlinear simulation.

Spatiotemporal Dynamics of a Network of Coupled Time-Delay Digital Tanlock Loops

NASA Astrophysics Data System (ADS)

Paul, Bishwajit; Banerjee, Tanmoy; Sarkar, B. C.

The time-delay digital tanlock loop (TDTLs) is an important class of phase-locked loop that is widely used in electronic communication systems. Although nonlinear dynamics of an isolated TDTL has been studied in the past but the collective behavior of TDTLs in a network is an important topic of research and deserves special attention as in practical communication systems separate entities are rarely isolated. In this paper, we carry out the detailed analysis and numerical simulations to explore the spatiotemporal dynamics of a network of a one-dimensional ring of coupled TDTLs with nearest neighbor coupling. The equation representing the network is derived and we carry out analytical calculations using the circulant matrix formalism to obtain the stability criteria. An extensive numerical simulation reveals that with the variation of gain parameter and coupling strength the network shows a variety of spatiotemporal dynamics such as frozen random pattern, pattern selection, spatiotemporal intermittency and fully developed spatiotemporal chaos. We map the distinct dynamical regions of the system in two-parameter space. Finally, we quantify the spatiotemporal dynamics by using quantitative measures like Lyapunov exponent and the average quadratic deviation of the full network.

Sampling-based real-time motion planning under state uncertainty for autonomous micro-aerial vehicles in GPS-denied environments.

PubMed

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-11-18

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints.

Sampling-Based Real-Time Motion Planning under State Uncertainty for Autonomous Micro-Aerial Vehicles in GPS-Denied Environments

PubMed Central

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-01-01

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints. PMID:25412217

Application of the Tool for Turbine Engine Closed-loop Transient Analysis (TTECTrA) for Dynamic Systems Analysis

NASA Technical Reports Server (NTRS)

Csank, Jeffrey; Zinnecker, Alicia

2014-01-01

Systems analysis involves steady-state simulations of combined components to evaluate the steady-state performance, weight, and cost of a system; dynamic considerations are not included until later in the design process. The Dynamic Systems Analysis task, under NASAs Fixed Wing project, is developing the capability for assessing dynamic issues at earlier stages during systems analysis. To provide this capability the Tool for Turbine Engine Closed-loop Transient Analysis (TTECTrA) has been developed to design a single flight condition controller (defined as altitude and Mach number) and, ultimately, provide an estimate of the closed-loop performance of the engine model. This tool has been integrated with the Commercial Modular Aero-Propulsion System Simulation 40,000(CMAPSS40k) engine model to demonstrate the additional information TTECTrA makes available for dynamic systems analysis. This dynamic data can be used to evaluate the trade-off between performance and safety, which could not be done with steady-state systems analysis data. TTECTrA has been designed to integrate with any turbine engine model that is compatible with the MATLABSimulink (The MathWorks, Inc.) environment.

Application of the Tool for Turbine Engine Closed-loop Transient Analysis (TTECTrA) for Dynamic Systems Analysis

NASA Technical Reports Server (NTRS)

Csank, Jeffrey Thomas; Zinnecker, Alicia Mae

2014-01-01

Systems analysis involves steady-state simulations of combined components to evaluate the steady-state performance, weight, and cost of a system; dynamic considerations are not included until later in the design process. The Dynamic Systems Analysis task, under NASAs Fixed Wing project, is developing the capability for assessing dynamic issues at earlier stages during systems analysis. To provide this capability the Tool for Turbine Engine Closed-loop Transient Analysis (TTECTrA) has been developed to design a single flight condition controller (defined as altitude and Mach number) and, ultimately, provide an estimate of the closed-loop performance of the engine model. This tool has been integrated with the Commercial Modular Aero-Propulsion System Simulation 40,000 (CMAPSS 40k) engine model to demonstrate the additional information TTECTrA makes available for dynamic systems analysis. This dynamic data can be used to evaluate the trade-off between performance and safety, which could not be done with steady-state systems analysis data. TTECTrA has been designed to integrate with any turbine engine model that is compatible with the MATLAB Simulink (The MathWorks, Inc.) environment.

X-38 Experimental Controls Laws

NASA Technical Reports Server (NTRS)

Munday, Steve; Estes, Jay; Bordano, Aldo J.

2000-01-01

X-38 Experimental Control Laws X-38 is a NASA JSC/DFRC experimental flight test program developing a series of prototypes for an International Space Station (ISS) Crew Return Vehicle, often called an ISS "lifeboat." X- 38 Vehicle 132 Free Flight 3, currently scheduled for the end of this month, will be the first flight test of a modem FCS architecture called Multi-Application Control-Honeywell (MACH), originally developed by the Honeywell Technology Center. MACH wraps classical P&I outer attitude loops around a modem dynamic inversion attitude rate loop. The dynamic inversion process requires that the flight computer have an onboard aircraft model of expected vehicle dynamics based upon the aerodynamic database. Dynamic inversion is computationally intensive, so some timing modifications were made to implement MACH on the slower flight computers of the subsonic test vehicles. In addition to linear stability margin analyses and high fidelity 6-DOF simulation, hardware-in-the-loop testing is used to verify the implementation of MACH and its robustness to aerodynamic and environmental uncertainties and disturbances.

Improvements in flight table dynamic transparency for hardware-in-the-loop facilities

NASA Astrophysics Data System (ADS)

DeMore, Louis A.; Mackin, Rob; Swamp, Michael; Rusterholtz, Roger

2000-07-01

Flight tables are a 'necessary evil' in the Hardware-In-The- Loop (HWIL) simulation. Adding the actual or prototypic flight hardware to the loop, in order to increase the realism of the simulation, forces us to add motion simulation to the process. Flight table motion bases bring unwanted dynamics, non- linearities, transport delays, etc to an already difficult problem sometimes requiring the simulation engineer to compromise the results. We desire that the flight tables be 'dynamically transparent' to the simulation scenario. This paper presents a State Variable Feedback (SVF) control system architecture with feed-forward techniques that improves the flight table's dynamic transparency by significantly reducing the table's low frequency phase lag. We offer some actual results with existing flight tables that demonstrate the improved transparency. These results come from a demonstration conducted on a flight table in the KHILS laboratory at Eglin AFB and during a refurbishment of a flight table for the Boeing Company of St. Charles, Missouri.

7 CFR 1400.206 - Estates.

Code of Federal Regulations, 2010 CFR

2010-01-01

... labor or active personal management or (ii) The combination of active personal labor and active personal management; and (3) The estate has a share of the profits or losses from the farming operation commensurate... farming operation that are at risk for a loss, with the level of risk being commensurate with the legal...

24 CFR 954.502 - Applicability of uniform administrative requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., 85.36, 85.43, 85.44, 85.51, and 85.52. (b) Non-profit organizations. The requirements of OMB Circular... 20 percent of the total contract price, subject to reduction during the warranty period, commensurate... payable upon demand of the grantee, subject to reduction during the warranty period commensurate with...

24 CFR 954.502 - Applicability of uniform administrative requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., 85.36, 85.43, 85.44, 85.51, and 85.52. (b) Non-profit organizations. The requirements of OMB Circular... 20 percent of the total contract price, subject to reduction during the warranty period, commensurate... payable upon demand of the grantee, subject to reduction during the warranty period commensurate with...

A Feel for Numbers: Affect, Data and Education Policy

ERIC Educational Resources Information Center

Sellar, Sam

2015-01-01

This article explores the relationship between commensuration and affect in various contexts of education policy. Commensuration is the process through which disparate qualities are transformed into a common metric and is central to the production of performance data. The rise of governance through numbers in education has resulted in a…

A loop-based neural architecture for structured behavior encoding and decoding.

PubMed

Gisiger, Thomas; Boukadoum, Mounir

2018-02-01

We present a new type of artificial neural network that generalizes on anatomical and dynamical aspects of the mammal brain. Its main novelty lies in its topological structure which is built as an array of interacting elementary motifs shaped like loops. These loops come in various types and can implement functions such as gating, inhibitory or executive control, or encoding of task elements to name a few. Each loop features two sets of neurons and a control region, linked together by non-recurrent projections. The two neural sets do the bulk of the loop's computations while the control unit specifies the timing and the conditions under which the computations implemented by the loop are to be performed. By functionally linking many such loops together, a neural network is obtained that may perform complex cognitive computations. To demonstrate the potential offered by such a system, we present two neural network simulations. The first illustrates the structure and dynamics of a single loop implementing a simple gating mechanism. The second simulation shows how connecting four loops in series can produce neural activity patterns that are sufficient to pass a simplified delayed-response task. We also show that this network reproduces electrophysiological measurements gathered in various regions of the brain of monkeys performing similar tasks. We also demonstrate connections between this type of neural network and recurrent or long short-term memory network models, and suggest ways to generalize them for future artificial intelligence research. Copyright © 2017 Elsevier Ltd. All rights reserved.

Movement Forms: A Graph-Dynamic Perspective

PubMed Central

Saltzman, Elliot; Holt, Ken

2014-01-01

The focus of this paper is on characterizing the physical movement forms (e.g., walk, crawl, roll, etc.) that can be used to actualize abstract, functionally-specified behavioral goals (e.g., locomotion). Emphasis is placed on how such forms are distinguished from one another, in part, by the set of topological patterns of physical contact between agent and environment (i.e., the set of physical graphs associated with each form) and the transitions among these patterns displayed over the course of performance (i.e., the form’s physical graph dynamics). Crucial in this regard is the creation and dissolution of loops in these graphs, which can be related to the distinction between open and closed kinematic chains. Formal similarities are described within the theoretical framework of task-dynamics between physically-closed kinematic chains (physical loops) that are created during various movement forms and functionally-closed kinematic chains (functional loops) that are associated with task-space control of end-effectors; it is argued that both types of loop must be flexibly incorporated into the coordinative structures that govern skilled action. Final speculation is focused on the role of graphs and their dynamics, not only in processes of coordination and control for individual agents, but also in processes of inter-agent coordination and the coupling of agents with (non-sentient) environmental objects. PMID:24910507

Movement Forms: A Graph-Dynamic Perspective.

PubMed

Saltzman, Elliot; Holt, Ken

2014-01-01

The focus of this paper is on characterizing the physical movement forms (e.g., walk, crawl, roll, etc.) that can be used to actualize abstract, functionally-specified behavioral goals (e.g., locomotion). Emphasis is placed on how such forms are distinguished from one another, in part, by the set of topological patterns of physical contact between agent and environment (i.e., the set of physical graphs associated with each form) and the transitions among these patterns displayed over the course of performance (i.e., the form's physical graph dynamics ). Crucial in this regard is the creation and dissolution of loops in these graphs, which can be related to the distinction between open and closed kinematic chains. Formal similarities are described within the theoretical framework of task-dynamics between physically-closed kinematic chains (physical loops) that are created during various movement forms and functionally-closed kinematic chains (functional loops) that are associated with task-space control of end-effectors; it is argued that both types of loop must be flexibly incorporated into the coordinative structures that govern skilled action. Final speculation is focused on the role of graphs and their dynamics, not only in processes of coordination and control for individual agents, but also in processes of inter-agent coordination and the coupling of agents with (non-sentient) environmental objects.

3D-Stereoscopic Analysis of Solar Active Region Loops: I: SoHo/EIT Observations at Temperatures of 1.0-1.5 MK

NASA Technical Reports Server (NTRS)

Aschwanden, Markus J.; Newmark, Jeff; Delaboudiniere, Jean-Pierre; Neupert, Werner M.; Portier-Fozzani, Fabrice; Gary, G. Allen; Zucker, Arik

1998-01-01

The three-dimensional (3D) structure of solar active region NOAA 7986 observed on 1996 August 30 with the Extrem-ultraviolet Imaging Telescope (EIT) onboard the Solar and Heliospheric Observatory (SoHO) is analyzed. We develop a new method of Dynamic Stereoscopy to reconstruct the 3D geometry of dynamically changing loops, which allows us to determine the orientation of the loop plane with respect to the line-of-sight, a prerequisite to correct properly for projection effects in 3D loop models. With this method and the filter-ratio technique applied to EIT 171 A and 195 A images we determine the 3D coordinates (x(s), y(s), z(s)), the loop width) w(s), the electron density n(sub e)(s), and the electron temperature T(sub e)(s) as function of the loop length s for 30 loop segments. Fitting the loop densities with an exponential density model n(sub e)(h) we find that the so inferred scale height temperatures, T(sub e)(sup lambda) = 1.22 +/- 0.23 MK, match closely the EIT filter-ratio temperatures, T(sub e)(sup FIT) = 1.21 +/- 0.06 MK. We conclude that these rather large-scale loops (with heights of h approx. equals 50 - 200 Mm) that dominate EIT 171 A images are close to thermal equilibrium. Most of the loops show no significant thickness variation w(s), but many exhibit a trend of increasing temperature (dT/ds greater than 0) above the footpoint.

Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

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

Chen, Youxing; Zhang, Xinghang; Wang, Jian

Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacentmore » to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.« less

Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

DOE PAGES

Chen, Youxing; Zhang, Xinghang; Wang, Jian

2016-11-01

Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacentmore » to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.« less

Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin.

PubMed

Peacock, Riley B; Davis, Jessie R; Markwick, Phineus R L; Komives, Elizabeth A

2018-05-08

Thrombin normally cleaves fibrinogen to promote coagulation; however, binding of thrombomodulin to thrombin switches the specificity of thrombin toward protein C, triggering the anticoagulation pathway. The W215A thrombin mutant was reported to have decreased activity toward fibrinogen without significant loss of activity toward protein C. To understand how mutation of Trp215 may alter thrombin specificity, hydrogen-deuterium exchange experiments (HDXMS), accelerated molecular dynamics (AMD) simulations, and activity assays were carried out to compare the dynamics of Trp215 mutants with those of wild type (WT) thrombin. Variation in NaCl concentration had no detectable effect on the sodium-binding (220s CT ) loop, but appeared to affect other surface loops. Trp215 mutants showed significant increases in amide exchange in the 170s CT loop consistent with a loss of H-bonding in this loop identified by the AMD simulations. The W215A thrombin showed increased amide exchange in the 220s CT loop and in the N-terminus of the heavy chain. The AMD simulations showed that a transient conformation of the W215A thrombin has a distorted catalytic triad. HDXMS experiments revealed that mutation of Phe227, which engages in a π-stacking interaction with Trp215, also caused significantly increased amide exchange in the 170s CT loop. Activity assays showed that only the F227V mutant had wild type catalytic activity, whereas all other mutants showed markedly lower activity. Taken together, the results explain the reduced pro-coagulant activity of the W215A mutant and demonstrate the allosteric connection between Trp215, the sodium-binding loop, and the active site.

Dynamics of safety performance and culture: a group model building approach.

PubMed

Goh, Yang Miang; Love, Peter E D; Stagbouer, Greg; Annesley, Chris

2012-09-01

The management of occupational health and safety (OHS) including safety culture interventions is comprised of complex problems that are often hard to scope and define. Due to the dynamic nature and complexity of OHS management, the concept of system dynamics (SD) is used to analyze accident prevention. In this paper, a system dynamics group model building (GMB) approach is used to create a causal loop diagram of the underlying factors influencing the OHS performance of a major drilling and mining contractor in Australia. While the organization has invested considerable resources into OHS their disabling injury frequency rate (DIFR) has not been decreasing. With this in mind, rich individualistic knowledge about the dynamics influencing the DIFR was acquired from experienced employees with operations, health and safety and training background using a GMB workshop. Findings derived from the workshop were used to develop a series of causal loop diagrams that includes a wide range of dynamics that can assist in better understanding the causal influences OHS performance. The causal loop diagram provides a tool for organizations to hypothesize the dynamics influencing effectiveness of OHS management, particularly the impact on DIFR. In addition the paper demonstrates that the SD GMB approach has significant potential in understanding and improving OHS management. Copyright © 2011 Elsevier Ltd. All rights reserved.

Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study

PubMed Central

Zhang, Tong; Mu, Yuguang

2012-01-01

Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg2+ ions with binding free energy −7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation. PMID:22952795

Closed-Loop HIRF Experiments Performed on a Fault Tolerant Flight Control Computer

NASA Technical Reports Server (NTRS)

Belcastro, Celeste M.

1997-01-01

ABSTRACT Closed-loop HIRF experiments were performed on a fault tolerant flight control computer (FCC) at the NASA Langley Research Center. The FCC used in the experiments was a quad-redundant flight control computer executing B737 Autoland control laws. The FCC was placed in one of the mode-stirred reverberation chambers in the HIRF Laboratory and interfaced to a computer simulation of the B737 flight dynamics, engines, sensors, actuators, and atmosphere in the Closed-Loop Systems Laboratory. Disturbances to the aircraft associated with wind gusts and turbulence were simulated during tests. Electrical isolation between the FCC under test and the simulation computer was achieved via a fiber optic interface for the analog and discrete signals. Closed-loop operation of the FCC enabled flight dynamics and atmospheric disturbances affecting the aircraft to be represented during tests. Upset was induced in the FCC as a result of exposure to HIRF, and the effect of upset on the simulated flight of the aircraft was observed and recorded. This paper presents a description of these closed- loop HIRF experiments, upset data obtained from the FCC during these experiments, and closed-loop effects on the simulated flight of the aircraft.

77 FR 38569 - Information Collection; Application for Permit for Use of Roads, Trails, or Areas Restricted by...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-28

... investments in NFS roads; and require commercial users to perform road maintenance commensurate with their use... commercial users to perform maintenance commensurate with their road use. Section 261.10 contains a national... appropriate investment sharing arrangements, require commercial users of NFS roads to perform maintenance...

14 CFR 139.317 - Aircraft rescue and firefighting: Equipment and agents.

Code of Federal Regulations, 2011 CFR

2011-01-01

... pounds of potassium-based dry chemical and water with a commensurate quantity of AFFF to total 100 gallons for simultaneous dry chemical and AFFF application. (b) Index B. Either of the following: (1) One... gallons of water and the commensurate quantity of AFFF for foam production. (2) Two vehicles— (i) One...

14 CFR 139.317 - Aircraft rescue and firefighting: Equipment and agents.

Code of Federal Regulations, 2012 CFR

2012-01-01

... pounds of potassium-based dry chemical and water with a commensurate quantity of AFFF to total 100 gallons for simultaneous dry chemical and AFFF application. (b) Index B. Either of the following: (1) One... gallons of water and the commensurate quantity of AFFF for foam production. (2) Two vehicles— (i) One...

14 CFR 139.317 - Aircraft rescue and firefighting: Equipment and agents.

Code of Federal Regulations, 2010 CFR

2010-01-01

... pounds of potassium-based dry chemical and water with a commensurate quantity of AFFF to total 100 gallons for simultaneous dry chemical and AFFF application. (b) Index B. Either of the following: (1) One... gallons of water and the commensurate quantity of AFFF for foam production. (2) Two vehicles— (i) One...

14 CFR 139.317 - Aircraft rescue and firefighting: Equipment and agents.

Code of Federal Regulations, 2014 CFR

2014-01-01

... pounds of potassium-based dry chemical and water with a commensurate quantity of AFFF to total 100 gallons for simultaneous dry chemical and AFFF application. (b) Index B. Either of the following: (1) One... gallons of water and the commensurate quantity of AFFF for foam production. (2) Two vehicles— (i) One...

14 CFR 139.317 - Aircraft rescue and firefighting: Equipment and agents.

Code of Federal Regulations, 2013 CFR

2013-01-01

... pounds of potassium-based dry chemical and water with a commensurate quantity of AFFF to total 100 gallons for simultaneous dry chemical and AFFF application. (b) Index B. Either of the following: (1) One... gallons of water and the commensurate quantity of AFFF for foam production. (2) Two vehicles— (i) One...

Flux quantization in aperiodic and periodic networks

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

Behrooz, A.

1987-01-01

The phase boundary of quasicrystalline, quasi-periodic, and random networks, was studied. It was found that if a network is composed of two different tiles, whose areas are relatively irrational, then the T/sub c/ (H) curve shows large-scale structure at fields that approximate flux quantization around the tiles, i.e., when the ratio of fluxoids contained in the large tiles to those in the small tiles is a rational approximant to the irrational area ratio. The phase boundaries of quasi-crystalline and quasi-periodic networks show fine structure indicating the existence of commensurate vortex superlattices on these networks. No such fine structure is foundmore » on the random array. For a quasi-crystal whose quasi-periodic long-range order is characterized by the irrational number of tau, the commensurate vortex lattices are all found at H = H/sub 0/ absolute value n + m tau (n,m integers). It was found that the commensurate superlattices on quasicrystalline as well as on crystalline networks are related to the inflation symmetry. A general definition of commensurability is proposed.« less

The commensurate-to-incommensurate phase transition of an organic monolayer: A high resolution LEED analysis of the superstructures of NTCDA on Ag(1 1 1)

NASA Astrophysics Data System (ADS)

Kilian, L.; Stahl, U.; Kossev, I.; Sokolowski, M.; Fink, R.; Umbach, E.

2008-07-01

The structural order of 1,4,9,10-naphthalene-tetracarboxylicacid-dianhydride (NTCDA) monolayers on Ag(1 1 1) has been investigated by spot profile analysis low energy electron diffraction (SPA-LEED). For increasing coverage, we find a sequence of three highly ordered structures: a commensurate structure (α), a uniaxially incommensurate structure (α 2), and an incommensurate structure (β) with coverages of 0.9 ML, 0.95 ML, and 1 (saturated) monolayer (ML), respectively. In the high coverage regime, the structures coexist and a coverage increase causes a change of their relative fractions. The α and β structures were known before [U. Stahl, D. Gador, A. Soukopp, R. Fink, E. Umbach, Surf. Sci. 414 (1998) 423], but the β structure was proposed as commensurate, since its very small misfit with respect to a commensurate structure could not be resolved. This misfit leads to a periodic modulation, causing additional Moiré satellites in the diffraction pattern. This finding demonstrates the importance of high resolution methods for the geometry determination of large organic adsorbates.

Implementation of Push Recovery Strategy Using Triple Linear Inverted Pendulum Model in “T-FloW” Humanoid Robot

NASA Astrophysics Data System (ADS)

Dimas Pristovani, R.; Raden Sanggar, D.; Dadet, Pramadihanto.

2018-04-01

Push recovery is one of humanbehaviorwhich is a strategy to defend the body from anexternal force in any environment. This paper describes push recovery strategy which usesMIMO decoupled control system method. The dynamics system uses aquasi-dynamic system based on triple linear inverted pendulum model (TLIPM). The analysis of TLIPMuses zero moment point (ZMP) calculation from ZMP simplification in last research. By using this simplification of dynamics system, the control design can be simplified into 3 serial SISOwith known and uncertain disturbance models in each inverted pendulum. Each pendulum has different plan to damp the external force effect. In this experiment, PID controller (closed- loop)is used to arrange the damp characteristic.The experiment result shows thatwhen using push recovery control strategy (closed-loop control) is about 85.71% whilewithout using push recovery control strategy (open-loop control) it is about 28.57%.

Hybrid automata models of cardiac ventricular electrophysiology for real-time computational applications.

PubMed

Andalam, Sidharta; Ramanna, Harshavardhan; Malik, Avinash; Roop, Parthasarathi; Patel, Nitish; Trew, Mark L

2016-08-01

Virtual heart models have been proposed for closed loop validation of safety-critical embedded medical devices, such as pacemakers. These models must react in real-time to off-the-shelf medical devices. Real-time performance can be obtained by implementing models in computer hardware, and methods of compiling classes of Hybrid Automata (HA) onto FPGA have been developed. Models of ventricular cardiac cell electrophysiology have been described using HA which capture the complex nonlinear behavior of biological systems. However, many models that have been used for closed-loop validation of pacemakers are highly abstract and do not capture important characteristics of the dynamic rate response. We developed a new HA model of cardiac cells which captures dynamic behavior and we implemented the model in hardware. This potentially enables modeling the heart with over 1 million dynamic cells, making the approach ideal for closed loop testing of medical devices.

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation.

PubMed

Ruff, Emily F; Muretta, Joseph M; Thompson, Andrew R; Lake, Eric W; Cyphers, Soreen; Albanese, Steven K; Hanson, Sonya M; Behr, Julie M; Thomas, David D; Chodera, John D; Levinson, Nicholas M

2018-02-21

Many eukaryotic protein kinases are activated by phosphorylation on a specific conserved residue in the regulatory activation loop, a post-translational modification thought to stabilize the active DFG-In state of the catalytic domain. Here we use a battery of spectroscopic methods that track different catalytic elements of the kinase domain to show that the ~100 fold activation of the mitotic kinase Aurora A (AurA) by phosphorylation occurs without a population shift from the DFG-Out to the DFG-In state, and that the activation loop of the activated kinase remains highly dynamic. Instead, molecular dynamics simulations and electron paramagnetic resonance experiments show that phosphorylation triggers a switch within the DFG-In subpopulation from an autoinhibited DFG-In substate to an active DFG-In substate, leading to catalytic activation. This mechanism raises new questions about the functional role of the DFG-Out state in protein kinases. © 2018, Ruff et al.

Dynamics for a 2-vertex quantum gravity model

NASA Astrophysics Data System (ADS)

Borja, Enrique F.; Díaz-Polo, Jacobo; Garay, Iñaki; Livine, Etera R.

2010-12-01

We use the recently introduced U(N) framework for loop quantum gravity to study the dynamics of spin network states on the simplest class of graphs: two vertices linked with an arbitrary number N of edges. Such graphs represent two regions, in and out, separated by a boundary surface. We study the algebraic structure of the Hilbert space of spin networks from the U(N) perspective. In particular, we describe the algebra of operators acting on that space and discuss their relation to the standard holonomy operator of loop quantum gravity. Furthermore, we show that it is possible to make the restriction to the isotropic/homogeneous sector of the model by imposing the invariance under a global U(N) symmetry. We then propose a U(N)-invariant Hamiltonian operator and study the induced dynamics. Finally, we explore the analogies between this model and loop quantum cosmology and sketch some possible generalizations of it.

System identification of dynamic closed-loop control of total peripheral resistance by arterial and cardiopulmonary baroreceptors

NASA Astrophysics Data System (ADS)

Nikolai Aljuri, A.; Bursac, Nenad; Marini, Robert; Cohen, Richard J.

2001-08-01

Prolonged exposure to microgravity in space flight missions (days) impairs the mechanisms responsible for defense of arterial blood pressure (ABP) and cardiac output (CO) against orthostatic stress in the post-flight period. The mechanisms responsible for the observed orthostatic intolerance are not yet completely understood. Additionally, effective counter measures to attenuate this pathophysiological response are not available. The aim of this study was to investigate the ability of our proposed system identification method to predict closed-loop dynamic changes in TPR induced by changes in mean arterial pressure (MAP) and right atrial pressure (RAP). For this purpose we designed and employed a novel experimental animal model for the examination of arterial and cardiopulmonary baroreceptors in the dynamic closed-loop control of total peripheral resistance (TPR), and applied system identification to the analysis of beat-to-beat fluctuations in the measured signals.

HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase.

PubMed

La Sala, Giuseppina; Riccardi, Laura; Gaspari, Roberto; Cavalli, Andrea; Hantschel, Oliver; De Vivo, Marco

2016-11-08

A number of structural factors modulate the activity of Abelson (Abl) tyrosine kinase, whose deregulation is often related to oncogenic processes. First, only the open conformation of the Abl kinase domain's activation loop (A-loop) favors ATP binding to the catalytic cleft. In this regard, the trans-autophosphorylation of the Y412 residue, which is located along the A-loop, favors the stability of the open conformation, in turn enhancing Abl activity. Another key factor for full Abl activity is the formation of active conformations of the catalytic DFG motif in the Abl kinase domain. Furthermore, binding of the SH2 domain to the N-lobe of the Abl kinase was recently demonstrated to have a long-range allosteric effect on the stabilization of the A-loop open state. Intriguingly, these distinct structural factors imply a complex signal transmission network for controlling the A-loop's flexibility and conformational preference for optimal Abl function. However, the exact dynamical features of this signal transmission network structure remain unclear. Here, we report on microsecond-long molecular dynamics coupled with enhanced sampling simulations of multiple Abl model systems, in the presence or absence of the SH2 domain and with the DFG motif flipped in two ways (in or out conformation). Through comparative analysis, our simulations augment the interpretation of the existing Abl experimental data, revealing a dynamical network of interactions that interconnect SH2 domain binding with A-loop plasticity and Y412 autophosphorylation in Abl. This signaling network engages the DFG motif and, importantly, other conserved structural elements of the kinase domain, namely, the EPK-ELK H-bond network and the HRD motif. Our results show that the signal propagation for modulating the A-loop spatial localization is highly dependent on the HRD motif conformation, which thus acts as the central hub of this (allosteric) signaling network controlling Abl activation and function.

Dynamically limiting energy consumed by cooling apparatus

DOEpatents

Chainer, Timothy J.; David, Milnes P.; Iyengar, Madhusudan K.; Parida, Pritish R.; Schmidt, Roger R.; Schultz, Mark D.

2015-05-26

Cooling apparatuses and methods are provided which include one or more coolant-cooled structures associated with an electronics rack, a coolant loop coupled in fluid communication with one or more passages of the coolant-cooled structure(s), one or more heat exchange units coupled to facilitate heat transfer from coolant within the coolant loop, and N controllable components associated with the coolant loop or the heat exchange unit(s), wherein N.gtoreq.1. The N controllable components facilitate circulation of coolant through the coolant loop or transfer of heat from the coolant via the heat exchange unit(s). A controller is coupled to the N controllable components, and dynamically adjusts operation of the N controllable components, based on Z input parameters and one or more specified constraints, to provide a specified cooling to the coolant-cooled structure(s), while limiting energy consumed by the N controllable components, wherein Z.gtoreq.1.

Dynamically limiting energy consumed by cooling apparatus

DOEpatents

Chainer, Timothy J.; David, Milnes P.; Iyengar, Madhusudan K.; Parida, Pritish R.; Schmidt, Roger R.; Schultz, Mark D.

2015-06-09

Cooling methods are provided which include providing: one or more coolant-cooled structures associated with an electronics rack, a coolant loop coupled in fluid communication with one or more passages of the coolant-cooled structure(s), one or more heat exchange units coupled to facilitate heat transfer from coolant within the coolant loop, and N controllable components associated with the coolant loop or the heat exchange unit(s), wherein N.gtoreq.1. The N controllable components facilitate circulation of coolant through the coolant loop or transfer of heat from the coolant via the heat exchange unit(s). A controller is also provided to dynamically adjust operation of the N controllable components, based on Z input parameters and one or more specified constraints, and provide a specified cooling to the coolant-cooled structure(s), while limiting energy consumed by the N controllable components, wherein Z.gtoreq.1.

The Solar Dynamic radiator with a historical perspective

NASA Technical Reports Server (NTRS)

Mclallin, K. L.; Fleming, M. L.; Hoehn, F. W.; Howerton, R.

1988-01-01

A historical perspective on pumped loop space radiators provides a basis for the design of the Space Station Solar Dynamic (SD) power module radiator. SD power modules, capable of generating 25 kWe each, are planned for growth Station power requirements. The Brayton (cycle) SD module configuration incorporates a pumped loop radiator that must reject up to 99 kW. The thermal/hydraulic design conditions in combination with required radiator orientation and packaging envelope form a unique set of constraints as compared to previous pumped loop radiator systems. Nevertheless, past program successes have demonstrated a technology base which can be applied to the SD radiator development program to ensure a low risk, low cost system.

Growth rate effects on the formation of dislocation loops around deep helium bubbles in Tungsten

DOE PAGES

Sandoval, Luis; Perez, Danny; Uberuaga, Blas P.; ...

2016-11-15

Here, the growth process of spherical helium bubbles located 6 nm below a (100) surface is studied using molecular dynamics and parallel replica dynamics simulations, over growth rates from 10 6 to 10 12 helium atoms per second. Slower growth rates lead to a release of pressure and lower helium content as compared with fast growth cases. In addition, at slower growth rates, helium bubbles are not decorated by multiple dislocation loops, as these tend to merge or emit given sufficient time. At faster rates, dislocation loops nucleate faster than they can emit, leading to a more complicated dislocation structuremore » around the bubble.« less

Incommensurate and commensurate modulations of Ba{sub 5}RTi{sub 3}Nb{sub 7}O{sub 30} (R = La, Nd) tungsten bronzes and the ferroelectric domain structures

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

Mao, Min Min; Li, Kun; Zhu, Xiao Li

2015-04-07

Incommensurate and commensurate structural modulations of Ba{sub 5}RTi{sub 3}Nb{sub 7}O{sub 30} (R = La, Nd) tungsten bronze ceramics were investigated by using a cooling holder equipped transmission electron microscopy in the temperature range from 100 K to 363 K. The incommensurate modulation was observed in both Ba{sub 5}LaTi{sub 3}Nb{sub 7}O{sub 30} and Ba{sub 5}NdTi{sub 3}Nb{sub 7}O{sub 30} at room temperature, while there was a transition from incommensurate tilted structure to commensurate superstructure for Ba{sub 5}NdTi{sub 3}Nb{sub 7}O{sub 30} with decreasing temperature. The incommensurate and commensurate modulations were determined by the A-site occupancy of Ba and R cations. The A-site disorder resulted in larger incommensurabilitymore » parameter δ and the diffusion of the satellite reflection spots. The effect of A-site disorder on the coupling between long-range dipolar order and the commensurate modulation was also discussed. The obvious ferroelectric 180° domains with spike-like shape parallel to c axis were observed for Ba{sub 5}NdTi{sub 3}Nb{sub 7}O{sub 30}, while no macro ferroelectric domain was determined for Ba{sub 5}LaTi{sub 3}Nb{sub 7}O{sub 30}.« less

Flux Quantization in Aperiodic and Periodic Networks

NASA Astrophysics Data System (ADS)

Behrooz, Angelika

The normal - superconducting phase boundary, T_{c}(H), of a periodic wire network shows periodic oscillations with period H _{o} = phi_ {o}/A due to flux quantization around the individual plaquettes (of area A) of the network. The magnetic flux quantum is phi_{o } = hc/2e. The phase boundary also shows fine structure at fields H = (p/q)H_{o} (p,q integers), where the flux vortices can form commensurate superlattices on the periodic substrate. We have studied the phase boundary of quasicrystalline, quasiperiodic and random networks. We have found that if a network is composed of two different tiles, whose areas are relatively irrational then the T_ {c}(H) curve shows large scale structure at fields that approximate flux quantization around the tiles, i.e. when the ratio of fluxoids contained in the large tiles to those in the small tiles is a rational approximant to the irrational area ratio. The phase boundaries of quasicrystalline and quasiperiodic networks show fine structure indicating the existence of commensurate vortex superlattices on these networks. No such fine structure is found on the random array. For a quasicrystal whose quasiperiodic long-range order is characterized by the irrational number tau the commensurate vortex lattices are all found at H = H_{o}| n + mtau| (n,m integers). We have found that the commensurate superlattices on quasicrystalline as well as on crystalline networks are related to the inflation symmetry. We propose a general definition of commensurability.

Emergent quasicrystals in strongly correlated systems

NASA Astrophysics Data System (ADS)

Sagi, Eran; Nussinov, Zohar

2016-07-01

Commensurability is of paramount importance in numerous strongly interacting electronic systems. In the fractional quantum Hall effect, a rich cascade of increasingly narrow plateaux appear at larger denominator filling fractions. Rich commensurate structures also emerge, at certain filling fractions, in high temperature superconductors and other electronic systems. A natural question concerns the character of these and other electronic systems at irrational filling fractions. Here we demonstrate that quasicrystalline structures naturally emerge in these situations, and trigger behaviors not typically expected of periodic systems. We first show that irrationally filled quantum Hall systems cross over into quasiperiodically ordered configuration in the thin-torus limit. Using known properties of quasicrystals, we argue that these states are unstable against the effects of disorder, in agreement with the existence of quantum Hall plateaux. We then study analogous physical situations in a system of cold Rydberg atoms placed on an optical lattice. Such an experimental setup is generally disorder free, and can therefore be used to detect the emergent quasicrystals we predict. We discuss similar situations in the Falicov-Kimball model, where known exact results can be used to establish quasicrystalline structures in one and two dimensions. We briefly speculate on possible relations between our theoretical findings and the existence of glassy dynamics and other features of strongly correlated electronic systems.

Commensurability effects in the critical forces of a superconducting film with Kagomé pinning array at submatching fields

NASA Astrophysics Data System (ADS)

Vizarim, Nicolas P.; Carlone, Maicon; Verga, Lucas G.; Venegas, Pablo A.

2017-09-01

Using molecular dynamics simulations, we find the commensurability force peaks in a two-dimensional superconducting thin-film with a Kagomé pinning array. A transport force is applied in two mutually perpendicular directions, and the magnetic field is increased up to the first matching field. Usually the condition to have pronounced force peaks in systems with periodic pinning is associated to the rate between the applied magnetic field and the first matching field, it must be an integer or a rational fraction. Here, we show that another condition must be satisfied, the vortex ground state must be ordered. Our calculations show that the pinning size and strength may dramatically change the vortex ground state. Small pinning radius and high values of pinning strength may lead to disordered vortex configurations, which fade the critical force peaks. The critical forces show anisotropic behavior, but the same dependence on pinning strength and radius is observed for both driven force directions. Different to cases where the applied magnetic field is higher than the first matching field, here the depinning process begins with vortices weakly trapped on top of a pinning site and not with interstitial vortices. Our results are in good agreement with recent experimental results.

Commensurate Superstructure of the {Cu(NO3)(H2O)}(HTae)(Bpy) Coordination Polymer: An Example of 2D Hydrogen-Bonding Networks as Magnetic Exchange Pathway.

PubMed

Fernández de Luis, Roberto; Larrea, Edurne S; Orive, Joseba; Lezama, Luis; Arriortua, María I

2016-11-21

The average and commensurate superstructures of the one-dimensional coordination polymer {Cu(NO 3 )(H 2 O)}(HTae)(Bpy) (H 2 Tae = 1,1,2,2-tetraacetylethane, Bpy = 4,4'-bipyridine) were determined by single-crystal X-ray diffraction, and the possible symmetry relations between the space group of the average structure and the superstructure were checked. The crystal structure consists in parallel and oblique {Cu(HTae)(Bpy)} zigzag metal-organic chains stacked along the [100] crystallographic direction. The origin of the fivefold c axis in the commensurate superstructure is ascribed to a commensurate modulation of the coordination environment of the copper atoms. The commensurately ordered nitrate groups and coordinated water molecules establish a two-dimensional hydrogen-bonding network. Moreover, the crystal structure shows a commensurate to incommensurate transition at room temperature. The release of the coordination water molecules destabilizes the crystal framework, and the compound shows an irreversible structure transformation above 100 °C. Despite the loss of crystallinity, the spectroscopic studies indicate that the main building blocks of the crystal framework are retained after the transformation. The hydrogen-bonding network not only plays a crucial role stabilizing the crystal structure but also is an important pathway for magnetic exchange transmission. In fact, the magnetic susceptibility curves indicate that after the loss of coordinated water molecules, and hence the collapse of the hydrogen-bonding network, the weak anti-ferromagnetic coupling observed in the initial compound is broken. The electron paramagnetic resonance spectra are the consequence of the average signals from Cu(II) with different orientations, indicating that the magnetic coupling is effective between them. In fact, X- and Q-band data are reflecting different situations; the X-band spectra show the characteristics of an exchange g-tensor, while the Q-band signals are coming from both the exchange and the molecular g-tensors.

Silicon photonic dynamic optical channel leveler with external feedback loop.

PubMed

Doylend, J K; Jessop, P E; Knights, A P

2010-06-21

We demonstrate a dynamic optical channel leveler composed of a variable optical attenuator (VOA) integrated monolithically with a defect-mediated photodiode in a silicon photonic waveguide device. An external feedback loop mimics an analog circuit such that the photodiode directly controls the VOA to provide blind channel leveling within +/-1 dB across a 7-10 dB dynamic range for wavelengths from 1530 nm to 1570 nm. The device consumes approximately 50 mW electrical power and occupies a 6 mm x 0.1 mm footprint per channel. Dynamic leveling is accomplished without tapping optical power from the output path to the photodiode and thus the loss penalty is minimized.

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.

Dynamic magnetic hysteresis properties of two-dimensional ferrimagnetic structures containing high-spin (S = 5/2) and low-spin (S = 1/2)

NASA Astrophysics Data System (ADS)

Batı, Mehmet; Ertaş, Mehmet

2017-09-01

The dynamic hysteresis behaviors of a containing high spin-5/2 and low spin-1/2 Ising ferrimagnetic system on a square lattice are studied by using the dynamic mean-field approximation. The influences of the temperature, the single-ion anisotropy and the frequency on dynamic hysteresis behaviors are investigated in detail. Somewhat characteristic behaviors are found, such as the presence of triple hysteresis loop for appropriate values of the crystal field or temperature. Besides, we observed that, hysteresis loop area and phase transition points are very sensitive to changes in frequency and thus have profound importance in device application.

Depression as a systemic syndrome: mapping the feedback loops of major depressive disorder.

PubMed

Wittenborn, A K; Rahmandad, H; Rick, J; Hosseinichimeh, N

2016-02-01

Depression is a complex public health problem with considerable variation in treatment response. The systemic complexity of depression, or the feedback processes among diverse drivers of the disorder, contribute to the persistence of depression. This paper extends prior attempts to understand the complex causal feedback mechanisms that underlie depression by presenting the first broad boundary causal loop diagram of depression dynamics. We applied qualitative system dynamics methods to map the broad feedback mechanisms of depression. We used a structured approach to identify candidate causal mechanisms of depression in the literature. We assessed the strength of empirical support for each mechanism and prioritized those with support from validation studies. Through an iterative process, we synthesized the empirical literature and created a conceptual model of major depressive disorder. The literature review and synthesis resulted in the development of the first causal loop diagram of reinforcing feedback processes of depression. It proposes candidate drivers of illness, or inertial factors, and their temporal functioning, as well as the interactions among drivers of depression. The final causal loop diagram defines 13 key reinforcing feedback loops that involve nine candidate drivers of depression. Future research is needed to expand upon this initial model of depression dynamics. Quantitative extensions may result in a better understanding of the systemic syndrome of depression and contribute to personalized methods of evaluation, prevention and intervention.

Depression as a systemic syndrome: mapping the feedback loops of major depressive disorder

PubMed Central

Wittenborn, A. K.; Rahmandad, H.; Rick, J.; Hosseinichimeh, N.

2016-01-01

Background Depression is a complex public health problem with considerable variation in treatment response. The systemic complexity of depression, or the feedback processes among diverse drivers of the disorder, contribute to the persistence of depression. This paper extends prior attempts to understand the complex causal feedback mechanisms that underlie depression by presenting the first broad boundary causal loop diagram of depression dynamics. Method We applied qualitative system dynamics methods to map the broad feedback mechanisms of depression. We used a structured approach to identify candidate causal mechanisms of depression in the literature. We assessed the strength of empirical support for each mechanism and prioritized those with support from validation studies. Through an iterative process, we synthesized the empirical literature and created a conceptual model of major depressive disorder. Results The literature review and synthesis resulted in the development of the first causal loop diagram of reinforcing feedback processes of depression. It proposes candidate drivers of illness, or inertial factors, and their temporal functioning, as well as the interactions among drivers of depression. The final causal loop diagram defines 13 key reinforcing feedback loops that involve nine candidate drivers of depression. Conclusions Future research is needed to expand upon this initial model of depression dynamics. Quantitative extensions may result in a better understanding of the systemic syndrome of depression and contribute to personalized methods of evaluation, prevention and intervention. PMID:26621339

[Deletion of a dynamic surface loop improves thermostability of (R)-selective amine transaminase from Aspergillus terreus].

PubMed

Xie, Dongfang; Lv, Changjiang; Fang, Hui; Yang, Weikang; Hu, Sheng; Zhao, Weirui; Huang, Jun; Mei, Lehe

2017-12-25

Chiral amines are important building blocks for the synthesis of pharmaceutical products and fine chemicals. Highly stereoselective synthesis of chiral amines compounds through asymmetric amination has attracted more and more attention. ω-transaminases (ω-TAs) are a promising class of natural biocatalysts which provide an efficient and environment-friendly access to production of chiral amines with stringent enantioselectivity and excellent catalytic efficiency. Compared with (S)-ω-TA, the research focused on (R)-ω-TA was relatively less. However, increasing demand for chiral (R)-amines as pharmaceutical intermediates has rendered industrial applications of (R)-ω-TA more attractive. Improving the thermostability of (R)-ω-TA with potential biotechnological application will facilitate the preparation of chiral amines. In this study, the dynamic surface loop with higher B-factor from Aspergillus terreus (R)-ω-TA was predicted by two computer softwares (PyMOL and YASARA). Then mutant enzymes were obtained by deleting amino acid residues of a dynamic surface loop using site-directed mutagenesis. The results showed that the best two mutants R131del and P132-E133del improved thermostability by 2.6 ℃ and 0.9 ℃ in T₅₀¹⁰ (41.1 ℃ and 39.4 ℃, respectively), and 2.2-fold and 1.5-fold in half-life (t1/2) at 40 ℃ (15.0 min and 10.0 min, respectively), compared to that of wild type. Furtherly, the thermostability mechanism of the mutant enzymes was investigated by molecular dynamics (MD) simulation and intermolecular interaction analysis. R131del in the loop region has lower root mean square fluctuation (RMSF) than the wild type at 400 K for 10 ns, and mutant enzyme P132-E133del increases four hydrogen bonds in the loop region. In this study, we obtain two stability-increased mutants of (R)-ω-TA from A. terreus by deleting its dynamic surface loop and also provide methodological guidance for the use of rational design to enhance the thermal stability of other enzymes.

EVIDENCE FOR COLLAPSING FIELDS IN THE CORONA AND PHOTOSPHERE DURING THE 2011 FEBRUARY 15 X2.2 FLARE: SDO/AIA AND HMI OBSERVATIONS

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

Gosain, S., E-mail: sgosain@nso.edu; Udaipur Solar Observatory, P.O. Box 198, Dewali, Udaipur, Rajasthan 313001

2012-04-10

We use high-resolution Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly observations to study the evolution of the coronal loops in a flaring solar active region, NOAA 11158. We identify three distinct phases of the coronal loop dynamics during this event: (1) slow-rise phase: slow rising motion of the loop-tops prior to the flare in response to the slow rise of the underlying flux rope; (2) collapse phase: sudden contraction of the loop-tops, with the lower loops collapsing earlier than the higher loops; and (3) oscillation phase: the loops exhibit global kink oscillations after the collapse phase at different periods, with themore » period decreasing with the decreasing height of the loops. The period of these loop oscillations is used to estimate the field strength in the coronal loops. Furthermore, we also use SDO/Helioseismic and Magnetic Imager (HMI) observations to study the photospheric changes close to the polarity inversion line (PIL). The longitudinal magnetograms show a stepwise permanent decrease in the magnetic flux after the flare over a coherent patch along the PIL. Furthermore, we examine the HMI Stokes I, Q, U, V profiles over this patch and find that the Stokes-V signal systematically decreases while the Stokes-Q and U signals increase after the flare. These observations suggest that close to the PIL the field configuration became more horizontal after the flare. We also use HMI vector magnetic field observations to quantify the changes in the field inclination angle and find an inward collapse of the field lines toward the PIL by {approx}10 Degree-Sign . These observations are consistent with the 'coronal implosion' scenario and its predictions about flare-related photospheric field changes.« less

All-atomic Molecular Dynamic Studies of Human CDK8: Insight into the A-loop, Point Mutations and Binding with Its Partner CycC

PubMed Central

Xu, Wu; Amire-Brahimi, Benjamin; Xie, Xiao-Jun; Huang, Liying; Ji, Jun-Yuan

2014-01-01

The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable ‘CDK8 submodule’ consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex. Taken together, these analyses will improve our understanding of the exact functions of CDK8 and the interaction with its partner CycC. PMID:24754906

Coronal rain in magnetic bipolar weak fields

NASA Astrophysics Data System (ADS)

Xia, C.; Keppens, R.; Fang, X.

2017-07-01

Aims: We intend to investigate the underlying physics for the coronal rain phenomenon in a representative bipolar magnetic field, including the formation and the dynamics of coronal rain blobs. Methods: With the MPI-AMRVAC code, we performed three dimensional radiative magnetohydrodynamic (MHD) simulation with strong heating localized on footpoints of magnetic loops after a relaxation to quiet solar atmosphere. Results: Progressive cooling and in-situ condensation starts at the loop top due to radiative thermal instability. The first large-scale condensation on the loop top suffers Rayleigh-Taylor instability and becomes fragmented into smaller blobs. The blobs fall vertically dragging magnetic loops until they reach low-β regions and start to fall along the loops from loop top to loop footpoints. A statistic study of the coronal rain blobs finds that small blobs with masses of less than 1010 g dominate the population. When blobs fall to lower regions along the magnetic loops, they are stretched and develop a non-uniform velocity pattern with an anti-parallel shearing pattern seen to develop along the central axis of the blobs. Synthetic images of simulated coronal rain with Solar Dynamics Observatory Atmospheric Imaging Assembly well resemble real observations presenting dark falling clumps in hot channels and bright rain blobs in a cool channel. We also find density inhomogeneities during a coronal rain "shower", which reflects the observed multi-stranded nature of coronal rain. Movies associated to Figs. 3 and 7 are available at http://www.aanda.org

Dynamical behaviour in coronal loops

NASA Technical Reports Server (NTRS)

Haisch, Bernhard M.

1986-01-01

Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

Dynamical behaviour in coronal loops

NASA Astrophysics Data System (ADS)

Haisch, Bernhard M.

Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

NASA Astrophysics Data System (ADS)

Pucheta-Martínez, Encarna; Saladino, Giorgio; Morando, Maria Agnese; Martinez-Torrecuadrada, Jorge; Lelli, Moreno; Sutto, Ludovico; D'Amelio, Nicola; Gervasio, Francesco Luigi

2016-04-01

Phosphorylation of the activation loop is a fundamental step in the activation of most protein kinases. In the case of the Src tyrosine kinase, a prototypical kinase due to its role in cancer and its historic importance, phosphorylation of tyrosine 416 in the activation loop is known to rigidify the structure and contribute to the switch from the inactive to a fully active form. However, whether or not phosphorylation is able per-se to induce a fully active conformation, that efficiently binds ATP and phosphorylates the substrate, is less clear. Here we employ a combination of solution NMR and enhanced-sampling molecular dynamics simulations to fully map the effects of phosphorylation and ATP/ADP cofactor loading on the conformational landscape of Src tyrosine kinase. We find that both phosphorylation and cofactor binding are needed to induce a fully active conformation. What is more, we find a complex interplay between the A-loop and the hinge motion where the phosphorylation of the activation-loop has a significant allosteric effect on the dynamics of the C-lobe.

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

PubMed

Papaleo, Elena; Saladino, Giorgio; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Gervasio, Francesco Luigi; Nussinov, Ruth

2016-06-08

Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as small as the rotation of one or a few side-chain dihedral angles or involve concerted motions in larger portions of the three-dimensional structure; both kinds of motions can be important for biological function and allostery. It is becoming increasingly evident that "connector regions" are important components of the dynamic personality of protein structures. These regions may be either disordered loops, i.e., poorly structured regions connecting secondary structural elements, or linkers that connect entire protein domains. Experimental and computational studies have, however, revealed that these regions are not mere connectors, and their role in allostery and conformational changes has been emerging in the last few decades. Here we provide a detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties. We also describe their importance for protein dynamics and allostery using as examples key proteins in cellular biology and human diseases such as kinases, ubiquitinating enzymes, and transcription factors.

Revealing mesoscopic structural universality with diffusion

PubMed Central

Novikov, Dmitry S.; Jensen, Jens H.; Helpern, Joseph A.; Fieremans, Els

2014-01-01

Measuring molecular diffusion is widely used for characterizing materials and living organisms noninvasively. This characterization relies on relations between macroscopic diffusion metrics and structure at the mesoscopic scale commensurate with the diffusion length. Establishing such relations remains a fundamental challenge, hindering progress in materials science, porous media, and biomedical imaging. Here we show that the dynamical exponent in the time dependence of the diffusion coefficient distinguishes between the universality classes of the mesoscopic structural complexity. Our approach enables the interpretation of diffusion measurements by objectively selecting and modeling the most relevant structural features. As an example, the specific values of the dynamical exponent allow us to identify the relevant mesoscopic structure affecting MRI-measured water diffusion in muscles and in brain, and to elucidate the structural changes behind the decrease of diffusion coefficient in ischemic stroke. PMID:24706873

A study of digital gyro compensation loops. [data conversion routines and breadboard models

NASA Technical Reports Server (NTRS)

1975-01-01

The feasibility is discussed of replacing existing state-of-the-art analog gyro compensation loops with digital computations. This was accomplished by designing appropriate compensation loops for the dry turned TDF gyro, selecting appropriate data conversion and processing techniques and algorithms, and breadboarding the design for laboratory evaluation. A breadboard design was established in which one axis of a Teledyne turned-gimbal TDF gyro was caged digitally while the other was caged using conventional analog electronics. The digital loop was designed analytically to closely resemble the analog loop in performance. The breadboard was subjected to various static and dynamic tests in order to establish the relative stability characteristics and frequency responses of the digital and analog loops. Several variations of the digital loop configuration were evaluated. The results were favorable.

Coronal Loop Evolution Observed with AIA and Hi-C

NASA Technical Reports Server (NTRS)

Mulu-Moore, Fana; Winebarger, A.; Cirtain, J.; Kobayashi, K.; Korreck, K.; Golub, L.; Kuzin. S.; Walsh, R.; DeForest, C.; DePontieu, B.;

It's positive to be negative: Achilles tendon work loops during human locomotion.

PubMed

Zelik, Karl E; Franz, Jason R

2017-01-01

Ultrasound imaging is increasingly used with motion and force data to quantify tendon dynamics during human movement. Frequently, tendon dynamics are estimated indirectly from muscle fascicle kinematics (by subtracting muscle from muscle-tendon unit length), but there is mounting evidence that this Indirect approach yields implausible tendon work loops. Since tendons are passive viscoelastic structures, when they undergo a loading-unloading cycle they must exhibit a negative work loop (i.e., perform net negative work). However, prior studies using this Indirect approach report large positive work loops, often estimating that tendons return 2-5 J of elastic energy for every 1 J of energy stored. More direct ultrasound estimates of tendon kinematics have emerged that quantify tendon elongations by tracking either the muscle-tendon junction or localized tendon tissue. However, it is unclear if these yield more plausible estimates of tendon dynamics. Our objective was to compute tendon work loops and hysteresis losses using these two Direct tendon kinematics estimates during human walking. We found that Direct estimates generally resulted in negative work loops, with average tendon hysteresis losses of 2-11% at 1.25 m/s and 33-49% at 0.75 m/s (N = 8), alluding to 0.51-0.98 J of tendon energy returned for every 1 J stored. We interpret this finding to suggest that Direct approaches provide more plausible estimates than the Indirect approach, and may be preferable for understanding tendon energy storage and return. However, the Direct approaches did exhibit speed-dependent trends that are not consistent with isolated, in vitro tendon hysteresis losses of about 5-10%. These trends suggest that Direct estimates also contain some level of error, albeit much smaller than Indirect estimates. Overall, this study serves to highlight the complexity and difficulty of estimating tendon dynamics non-invasively, and the care that must be taken to interpret biological function from current ultrasound-based estimates.

Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase.

PubMed

Ouedraogo, Daniel; Souffrant, Michael; Vasquez, Sheena; Hamelberg, Donald; Gadda, Giovanni

2017-05-16

Mobile loops located at the active site entrance in enzymes often participate in conformational changes required to shield the reaction from bulk solvent, to control the access of the substrate to the active site, and to position residues for substrate binding and catalysis. In d-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH), previous crystallographic data suggested that residues 45-47 in the FAD-binding domain and residues 50-56 in the substrate-binding domain in loop L1 could adopt two distinct conformations. In this study, we have used molecular dynamics, kinetics, and fluorescence spectroscopy on the S45A and A46G enzyme variants of PaDADH to investigate the impact of mutations in loop L1 on the catalytic function of the enzyme. Molecular dynamics showed that the mutant enzymes have probabilities of being in open conformations that are higher than that of wild-type PaDADH of loop L1, yielding an increased level of solvent exposure of the active site. In agreement, the flavin fluorescence intensity was ∼2-fold higher in the S45A and A46G enzymes than in wild-type PaDADH, with a 9 nm bathochromic shift of the emission band. In the variant enzymes, the k cat /K m values with d-arginine were ∼13-fold lower than in wild-type PaDADH. Moreover, the pH profiles for the k cat value with d-arginine showed a hollow, consistent with restricted proton movements in catalysis, and no saturation was achieved with the alternate substrate d-leucine in the reductive half-reaction of the variant enzymes. Taken together, the computational and experimental data are consistent with the dynamics of loop L1 being important for substrate capture and catalysis in PaDADH.

Neutron scattering studies of the ferroelectric distortion and spin dynamics in the type-1 multiferroic perovskite Sr 0.56 Ba 0.44 MnO 3

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

Pratt, Daniel K.; Lynn, Jeffrey W.; Mais, James

2014-10-01

The magnetic order, spin dynamics, and crystal structure of the multiferroic Sr0.56Ba0.44MnO3 have been investigated using neutron and x-ray scattering. Ferroelectricity develops at T-C = 305 K with a polarization of 4.2 mu C/cm(2) associated with the displacements of the Mn ions, while the Mn4+ spins order below T-N approximate to 200 K into a simple G-type commensurate magnetic structure. Below TN the ferroelectric order decreases dramatically, demonstrating that the two order parameters are strongly coupled. The ground state spin dynamics is characterized by a spin gap of 4.6(5) meV and the magnon density of states peaking at 43 meV.more » Detailed spin wave simulations with a gap and isotropic exchange of J = 4.8(2) meV describe the excitation spectrum well. Above TN strong spin correlations coexist with robust ferroelectric order.« less

Cloud fluid models of gas dynamics and star formation in galaxies

NASA Technical Reports Server (NTRS)

Struck-Marcell, Curtis; Scalo, John M.; Appleton, P. N.

1987-01-01

The large dynamic range of star formation in galaxies, and the apparently complex environmental influences involved in triggering or suppressing star formation, challenges the understanding. The key to this understanding may be the detailed study of simple physical models for the dominant nonlinear interactions in interstellar cloud systems. One such model is described, a generalized Oort model cloud fluid, and two simple applications of it are explored. The first of these is the relaxation of an isolated volume of cloud fluid following a disturbance. Though very idealized, this closed box study suggests a physical mechanism for starbursts, which is based on the approximate commensurability of massive cloud lifetimes and cloud collisional growth times. The second application is to the modeling of colliding ring galaxies. In this case, the driving processes operating on a dynamical timescale interact with the local cloud processes operating on the above timescale. The results is a variety of interesting nonequilibrium behaviors, including spatial variations of star formation that do not depend monotonically on gas density.

Modulation of dynamic modes by interplay between positive and negative feedback loops in gene regulatory networks

NASA Astrophysics Data System (ADS)

Wang, Liu-Suo; Li, Ning-Xi; Chen, Jing-Jia; Zhang, Xiao-Peng; Liu, Feng; Wang, Wei

2018-04-01

A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops. We developed an abstract model of such systems, largely based on the core p53 pathway, to explore the mechanism for the transformation of dynamic behaviors. Our results show that enhancing the positive feedback may promote or suppress oscillations depending on the strength of both feedback loops. We found that the system oscillates with low amplitudes in response to a moderate stimulus and switches to the on state upon a strong stimulus. When the positive feedback is activated much later than the negative one in response to a strong stimulus, the system exhibits long-term oscillations before switching to the on state. We explain this intriguing phenomenon using quasistatic approximation. Moreover, early switching to the on state may occur when the system starts from a steady state in the absence of stimuli. The interplay between the positive and negative feedback plays a key role in the transitions between oscillation and bistability. Of note, our conclusions should be applicable only to some specific gene regulatory networks, especially the p53 network, in which both oscillation and bistability exist in response to a certain type of stimulus. Our work also underscores the significance of transient dynamics in determining cellular outcome.

Formation of prismatic loops from C15 Laves phase interstitial clusters in body-centered cubic iron

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

Zhang, Yongfeng; Bai, Xian-Ming; Tonks, Michael R.

2015-03-01

This Letter reports the transition of C15 phase self-interstitial clusters to loops in body-centered-cubic Iron. Molecular dynamics simulations are performed to evaluate the relative stabilities of difference interstitial cluster configurations including C15 phase structure and <100> and <111>/2 loops. Within a certain size range, C15 cluster are found more stable than loops, and the relative stabilities are reversed beyond that range. In accordance to the crossover in relative stabilities, C15 clusters may grow by absorbing individual interstitials at small sizes and transitions into loops eventually. The transition takes place by nucleation and reaction of <111>/2 loop segments. These observations explainmore » the absence of C15 phase interstitial clusters predicted by density-functional-theory calculations in previous experimental observations. More importantly, the current results provide a new formation mechanism of <100> loops which requires no interaction of loops.« less

An alternative for presenting interactive dynamic data sets in electronic presentations: a scrollable flash movie loop.

PubMed

Yam, Chun-Shan

2007-11-01

The purpose of this article is to describe an alternative for creating scrollable movie loops for electronic presentations including PowerPoint. The alternative provided in this article enables academic radiologists to present scrollable movie loops in PowerPoint. The scrolling capability is created using Flash ActionScript. A Flash template with the required ActionScript code is provided. Users can simply download the template and follow the step-by-step demonstration to create scrollable movie loops. No previous ActionScript programming knowledge is necessary.

Stability of disclination loop in pure twist nematic liquid crystals

NASA Astrophysics Data System (ADS)

Kadivar, Erfan

2018-04-01

In this work, the annihilations dynamics and stability of disclination loop in a bulk pure twist nematic liquid crystal are investigated. This work is based on the Frank free energy and the nematodynamics equations. The energy dissipation is calculated by using two methods. In the first method, the energy dissipation is obtained from the Frank free energy. In the second method, it is calculated by using the nematodynamics equations. Finally, we derive a critical radius of disclination loop that above this radius, loop creation is energetically forbidden.

NMR Studies of the Dynamics of Nitrophorin 2 Bound to Nitric Oxide†

PubMed Central

Muthu, Dhanasekaran; Berry, Robert E.; Zhang, Hongjun; Walker, F. Ann

2013-01-01

The Rhodnius nitrophorins are β-barrel proteins of the lipocalin fold with a heme protruding from the open end of the barrel. They are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands, where NO is bound to iron. NO is released by dilution and pH rise when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect there are four nitrophorins, NP1, NP2, NP3 and NP4. At pH 7.3, NP4 releases NO 17 times faster than does NP2, as measured by stopped-flow kinetics. A number of crystal structures of the least abundant protein, NP4, are available. These structures have been used to propose that two loops between adjacent β-strands at the front opening of the protein, the A-B and G-H loops, determine the rate of NO release. In order to learn how the protein loops contribute to release of NO for each of the nitrophorins, the dynamics of these proteins are being studied in our laboratory. In this work, the NP2-NO complex has been investigated by NMR relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at three pH values, 5.0, 6.5, and 7.3. It is found that at pH 5.0 and 6.5, NP2-NO is rigid and only a few residues in the loop regions show dynamics, while at pH 7.3 somewhat more dynamics, particularly of the A-B loop, are observed. Comparison to other lipocalins shows that all are relatively rigid, and that the dynamics of lipocalins in general are much more subtle than those of mainly α-helical proteins. PMID:24116947

The solar dynamic radiator with a historical perspective

NASA Technical Reports Server (NTRS)

Mclallin, K. L.; Fleming, M. L.; Hoehn, F. W.; Howerton, R. L.

1988-01-01

A historical perspective on pumped-fluid loop space radiators provides a basis for the design of the Space Station Solar Dynamic (SD) power module radiator. SD power modules, capable of generating 25 kW (electrical) each, are planned for growth in Station power requirements. The Brayton cycle SD module configuration incorporates a pumped-fluid loop radiator that must reject up to 99 kW (thermal). The thermal/hydraulic design conditions in combination with required radiator orientation and packaging envelope form a unique set of constraints as compared to previous pumped-fluid loop radiator systems. Nevertheless, past program successes have demonstrated a technology base that can be applied to the SD radiator development program to ensure a low risk, low cost system.

Prominence condensation and magnetic levitation in a coronal loop

NASA Technical Reports Server (NTRS)

Van Hoven, G.; Mok, Y.; Drake, J. F.

1992-01-01

The results of a model dynamic simulation of the formation and support of a narrow prominence at the apex of a coronal magnetic loop or arcade are described. The condensation process proceeds via an initial radiative cooling and pressure drop, and a secondary siphon flow from the dense chromospheric ends. The antibuoyancy effect as the prominence forms causes a bending of the confining magnetic field, which propagates toward the semirigid ends of the magnetic loop. Thus, a wide magnetic 'hammock' or well (of the normal-polarity Kippenhahn-Schlueter-type) is formed, which supports the prominence at or near the field apex. The simplicity of this 1.5-dimensional model, with its accompanying diagnostics, elucidates the various contributions to the nonlinear dynamics of prominence condensation and levitation.

Three flavor Nambu-Jona-Lasinio model with Polyakov loop and competition with nuclear matter

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

Ciminale, M.; Ippolito, N. D.; Nardulli, G.

2008-03-01

We study the phase diagram of the three flavor Polyakov-Nambu-Jona-Lasinio (PNJL) model and, in particular, the interplay between chiral symmetry restoration and deconfinement crossover. We compute chiral condensates, quark densities, and the Polyakov loop at several values of temperature and chemical potential. Moreover we investigate on the role of the Polyakov loop dynamics in the transition from nuclear matter to quark matter.

Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.

PubMed

Kellici, Tahsin F; Mavromoustakos, Thomas; Jendrossek, Dieter; Papageorgiou, Anastassios C

2017-07-01

An open and a closed conformation of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase were identified in two high-resolution crystal structures of a PhaZ7 Y105E mutant. Molecular dynamics (MD) simulations revealed high root mean square fluctuations (RMSF) of the 281-295 loop, in particular at residue Asp289 (RMSF 7.62 Å). Covalent docking between a 3-hydroxybutyric acid trimer and the catalytic residue Ser136 showed that the binding energy of the substrate is significantly more favorable in the open loop conformation compared to that in the closed loop conformation. MD simulations with the substrate covalently bound depicted 1 Å RMSF higher values for the residues 281-295 in comparison to the apo (substrate-free) form. In addition, the presence of the substrate in the active site enhanced the ability of the loop to adopt a closed form. Taken together, the analysis suggests that the flexible loop 281-295 of PhaZ7 depolymerase can act as a lid domain to control substrate access to the active site of the enzyme. Proteins 2017; 85:1351-1361. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Plasma dynamics above solar flare soft x-ray loop tops

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

Doschek, G. A.; Warren, H. P.; McKenzie, D. E.

2014-06-10

We measure non-thermal motions in flare loop tops and above the loop tops using profiles of highly ionized spectral lines of Fe XXIV and Fe XXIII formed at multimillion-degree temperatures. Non-thermal motions that may be due to turbulence or multiple flow regions along the line of sight are extracted from the line profiles. The non-thermal motions are measured for four flares seen at or close to the solar limb. The profile data are obtained using the Extreme-ultraviolet Imaging Spectrometer on the Hinode spacecraft. The multimillion-degree non-thermal motions are between 20 and 60 km s{sup –1} and appear to increase withmore » height above the loop tops. Motions determined from coronal lines (i.e., lines formed at about 1.5 MK) tend to be smaller. The multimillion-degree temperatures in the loop tops and above range from about 11 MK to 15 MK and also tend to increase with height above the bright X-ray-emitting loop tops. The non-thermal motions measured along the line of sight, as well as their apparent increase with height, are supported by Solar Dynamics Observatory Atmospheric Imaging Assembly measurements of turbulent velocities in the plane of the sky.« less

A time domain inverse dynamic method for the end point tracking control of a flexible manipulator

NASA Technical Reports Server (NTRS)

Kwon, Dong-Soo; Book, Wayne J.

1991-01-01

The inverse dynamic equation of a flexible manipulator was solved in the time domain. By dividing the inverse system equation into the causal part and the anticausal part, we calculated the torque and the trajectories of all state variables for a given end point trajectory. The interpretation of this method in the frequency domain was explained in detail using the two-sided Laplace transform and the convolution integral. The open loop control of the inverse dynamic method shows an excellent result in simulation. For real applications, a practical control strategy is proposed by adding a feedback tracking control loop to the inverse dynamic feedforward control, and its good experimental performance is presented.

Mass gap in the weak coupling limit of (2 +1 )-dimensional SU(2) lattice gauge theory

NASA Astrophysics Data System (ADS)

Anishetty, Ramesh; Sreeraj, T. P.

2018-04-01

We develop the dual description of (2 +1 )-dimensional SU(2) lattice gauge theory as interacting "Abelian-like" electric loops by using Schwinger bosons. "Point splitting" of the lattice enables us to construct explicit Hilbert space for the gauge invariant theory which in turn makes dynamics more transparent. Using path integral representation in phase space, the interacting closed loop dynamics is analyzed in the weak coupling limit to get the mass gap.

Dynamic stability and handling qualities tests on a highly augmented, statically unstable airplane

NASA Technical Reports Server (NTRS)

Gera, Joseph; Bosworth, John T.

1987-01-01

This paper describes some novel flight tests and analysis techniques in the flight dynamics and handling qualities area. These techniques were utilized during the initial flight envelope clearance of the X-29A aircraft and were largely responsible for the completion of the flight controls clearance program without any incidents or significant delays. The resulting open-loop and closed-loop frequency responses and the time history comparison using flight and linear simulation data are discussed.

Thermoelectric power generator with intermediate loop

DOEpatents

Bell, Lon E; Crane, Douglas Todd

2013-05-21

A thermoelectric power generator is disclosed for use to generate electrical power from heat, typically waste heat. An intermediate heat transfer loop forms a part of the system to permit added control and adjustability in the system. This allows the thermoelectric power generator to more effectively and efficiently generate power in the face of dynamically varying temperatures and heat flux conditions, such as where the heat source is the exhaust of an automobile, or any other heat source with dynamic temperature and heat flux conditions.

Thermoelectric power generator with intermediate loop

DOEpatents

Bel,; Lon, E [Altadena, CA; Crane, Douglas Todd [Pasadena, CA

2009-10-27

A thermoelectric power generator is disclosed for use to generate electrical power from heat, typically waste heat. An intermediate heat transfer loop forms a part of the system to permit added control and adjustability in the system. This allows the thermoelectric power generator to more effectively and efficiently generate power in the face of dynamically varying temperatures and heat flux conditions, such as where the heat source is the exhaust of an automobile, or any other heat source with dynamic temperature and heat flux conditions.

Paraxial Stage of the Spatiotemporal Dynamics of Loop Solitons

NASA Astrophysics Data System (ADS)

Sazonov, Sergey V.

2018-03-01

Using the averaged Lagrangian method, an analytic study of the spatiotemporal dynamics of extremely short loop solitons of the generalized Vakhnenko-Schäfer-Wayne equation is carried out. The conditions under which soliton propagation occurs in the modes of defocusing and self-focusing are determined. It is shown that transverse defocusing is accompanied by a temporal compression of the soliton and a decrease in its amplitude. At the same time, with transverse self-focusing, its temporal broadening and peak amplification occur.

Mobile application MDDCS for modeling the expansion dynamics of a dislocation loop in FCC metals

NASA Astrophysics Data System (ADS)

Kirilyuk, Vasiliy; Petelin, Alexander; Eliseev, Andrey

2017-11-01

A mobile version of the software package Dynamic Dislocation of Crystallographic Slip (MDDCS) designed for modeling the expansion dynamics of dislocation loops and formation of a crystallographic slip zone in FCC-metals is examined. The paper describes the possibilities for using MDDCS, the application interface, and the database scheme. The software has a simple and intuitive interface and does not require special training. The user can set the initial parameters of the experiment, carry out computational experiments, export parameters and results of the experiment into separate text files, and display the experiment results on the device screen.

Linearizing feedforward/feedback attitude control

NASA Technical Reports Server (NTRS)

Paielli, Russell A.; Bach, Ralph E.

1991-01-01

An approach to attitude control theory is introduced in which a linear form is postulated for the closed-loop rotation error dynamics, then the exact control law required to realize it is derived. The nonminimal (four-component) quaternion form is used to attitude because it is globally nonsingular, but the minimal (three-component) quaternion form is used for attitude error because it has no nonlinear constraints to prevent the rotational error dynamics from being linearized, and the definition of the attitude error is based on quaternion algebra. This approach produces an attitude control law that linearizes the closed-loop rotational error dynamics exactly, without any attitude singularities, even if the control errors become large.

Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein

PubMed Central

Kumar, Ritesh; Qi, Yifei; Matsumura, Hirotoshi; Lovell, Scott; Yao, Huili; Battaile, Kevin P.; Im, Wonpil; Moënne-Loccoz, Pierre; Rivera, Mario

2017-01-01

Previous characterization of hemophores from Serratia marcescens (HasAs), Pseudomonas aeruginosa (HasAp) and Yersinia pestis (HasAyp) showed that hemin binds between two loops, where it is axially coordinated by H32 and Y75. The Y75 loop is structurally conserved in all three hemophores and harbors conserved ligand Y75. The other loop contains H32 in HasAs and HasAp, but a noncoordinating Q32 in HasAyp. The H32 loop in apo-HasAs and apo-HasAp is in an open conformation, which places H32 about 30 Å from the hemin-binding site. Hence, hemin binding onto the Y75 loop of HasAs or HasAp triggers a large relocation of the H32 loop from an open- to a closed-loop conformation and enables coordination of the hemin-iron by H32. In comparison, the Q32 loop in apo-HasAyp is in the closed conformation and hemin binding occurs with minimal reorganization and without coordinative interactions with the Q32 loop. Studies in crystallo and in solution have established that the open H32 loop in apo-HasAp and apo-HasAs is well structured and minimally affected by conformational dynamics. In this study we address the intriguing issue of the stability of the H32 loop in apo-HasAp and how hemin binding triggers its relocation. We address this question with a combination of NMR spectroscopy, X-ray crystallography, and molecular dynamics simulations and find that R33 is critical to the stability of the open H32 loop. Replacing R33 with A causes the H32 loop in R33A apo-HasAp to adopt a conformation similar to that of holo-HasAp. Finally, stopped-flow absorption and resonance Raman analyses of hemin binding to apo-R33A HasAp indicates that the closed H32 loop slows down the insertion of the heme inside the binding pocket, presumably as it obstructs access to the hydrophobic platform on the Y75 loop, but accelerate the completion of the heme iron coordination. PMID:27074415

Sitnikov problem in the cyclic kite configuration

NASA Astrophysics Data System (ADS)

Shahbaz Ullah, M.; Bhatnagar, K. B.; Hassan, M. R.

2014-12-01

This manuscript deals with the development of the series solutions of the Sitnikov kite configuration by the methods given of Lindstedt-Poincarė, using Green's function and MacMillan. Next we have developed averaged equation of motion by applying the Van der Pol transformation and averaging technique of Guckenheimer and Holmes (Nonlinear oscillations, dynamical system bifurcations of vector fields. Springer, Berlin, 1983). In addition to the resonance criterion at the 3/2 commensurability we have chosen ω=2 n/3, n=2, ω is the angular velocity of the coordinate system. Lastly the periodicity of the solutions has been examined by the Poincarė section.

An inexpensive, multipurpose physical pendulum

NASA Astrophysics Data System (ADS)

Schultz, David

2012-10-01

The pendulum is a highly versatile tool for teaching physics. Many special purpose pendula for student experiments have been described.1-4 In this paper, I describe an inexpensive, multipurpose physical pendulum that can function as both a variable gravity and ballistic pendulum. I designed the apparatus for use in a rotational dynamics unit of the AP Physics C mechanics course. The use of a bike wheel hub pivot allows for low-friction, rugged operation that yields results commensurate with those obtained with much more expensive pendula available on the market (typically 500 per unit5), placing these types of experiments within reach of the teacher on a restricted budget.

Hippocampal closed-loop modeling and implications for seizure stimulation design

NASA Astrophysics Data System (ADS)

Sandler, Roman A.; Song, Dong; Hampson, Robert E.; Deadwyler, Sam A.; Berger, Theodore W.; Marmarelis, Vasilis Z.

2015-10-01

Objective. Traditional hippocampal modeling has focused on the series of feedforward synapses known as the trisynaptic pathway. However, feedback connections from CA1 back to the hippocampus through the entorhinal cortex (EC) actually make the hippocampus a closed-loop system. By constructing a functional closed-loop model of the hippocampus, one may learn how both physiological and epileptic oscillations emerge and design efficient neurostimulation patterns to abate such oscillations. Approach. Point process input-output models where estimated from recorded rodent hippocampal data to describe the nonlinear dynamical transformation from CA3 → CA1, via the schaffer-collateral synapse, and CA1 → CA3 via the EC. Each Volterra-like subsystem was composed of linear dynamics (principal dynamic modes) followed by static nonlinearities. The two subsystems were then wired together to produce the full closed-loop model of the hippocampus. Main results. Closed-loop connectivity was found to be necessary for the emergence of theta resonances as seen in recorded data, thus validating the model. The model was then used to identify frequency parameters for the design of neurostimulation patterns to abate seizures. Significance. Deep-brain stimulation (DBS) is a new and promising therapy for intractable seizures. Currently, there is no efficient way to determine optimal frequency parameters for DBS, or even whether periodic or broadband stimuli are optimal. Data-based computational models have the potential to be used as a testbed for designing optimal DBS patterns for individual patients. However, in order for these models to be successful they must incorporate the complex closed-loop structure of the seizure focus. This study serves as a proof-of-concept of using such models to design efficient personalized DBS patterns for epilepsy.

Hippocampal closed-loop modeling and implications for seizure stimulation design.

PubMed

Sandler, Roman A; Song, Dong; Hampson, Robert E; Deadwyler, Sam A; Berger, Theodore W; Marmarelis, Vasilis Z

2015-10-01

Traditional hippocampal modeling has focused on the series of feedforward synapses known as the trisynaptic pathway. However, feedback connections from CA1 back to the hippocampus through the entorhinal cortex (EC) actually make the hippocampus a closed-loop system. By constructing a functional closed-loop model of the hippocampus, one may learn how both physiological and epileptic oscillations emerge and design efficient neurostimulation patterns to abate such oscillations. Point process input-output models where estimated from recorded rodent hippocampal data to describe the nonlinear dynamical transformation from CA3 → CA1, via the schaffer-collateral synapse, and CA1 → CA3 via the EC. Each Volterra-like subsystem was composed of linear dynamics (principal dynamic modes) followed by static nonlinearities. The two subsystems were then wired together to produce the full closed-loop model of the hippocampus. Closed-loop connectivity was found to be necessary for the emergence of theta resonances as seen in recorded data, thus validating the model. The model was then used to identify frequency parameters for the design of neurostimulation patterns to abate seizures. Deep-brain stimulation (DBS) is a new and promising therapy for intractable seizures. Currently, there is no efficient way to determine optimal frequency parameters for DBS, or even whether periodic or broadband stimuli are optimal. Data-based computational models have the potential to be used as a testbed for designing optimal DBS patterns for individual patients. However, in order for these models to be successful they must incorporate the complex closed-loop structure of the seizure focus. This study serves as a proof-of-concept of using such models to design efficient personalized DBS patterns for epilepsy.

Hippocampal Closed-Loop Modeling and Implications for Seizure Stimulation Design

PubMed Central

Sandler, Roman A.; Song, Dong; Hampson, Robert E.; Deadwyler, Sam A.; Berger, Theodore W.; Marmarelis, Vasilis Z.

2016-01-01

Objective Traditional hippocampal modeling has focused on the series of feedforward synapses known as the trisynaptic pathway. However, feedback connections from CA1 back to the hippocampus through the Entorhinal Cortex (EC) actually make the hippocampus a closed-loop system. By constructing a functional closed-loop model of the hippocampus, one may learn how both physiological and epileptic oscillations emerge and design efficient neurostimulation patterns to abate such oscillations. Approach Point process input-output models where estimated from recorded rodent hippocampal data to describe the nonlinear dynamical transformation from CA3→CA1, via the Schaffer-Collateral synapse, and CA1→CA3 via the EC. Each Volterra-like subsystem was composed of linear dynamics (Principal Dynamic Modes) followed by static nonlinearities. The two subsystems were then wired together to produce the full closed-loop model of the hippocampus. Main Results Closed-loop connectivity was found to be necessary for the emergence of theta resonances as seen in recorded data, thus validating the model. The model was then used to identify frequency parameters for the design of neurostimulation patterns to abate seizures. Significance DBS is a new and promising therapy for intractable seizures. Currently, there is no efficient way to determine optimal frequency parameters for DBS, or even whether periodic or broadband stimuli are optimal. Data-based computational models have the potential to be used as a testbed for designing optimal DBS patterns for individual patients. However, in order for these models to be successful they must incorporate the complex closed-loop structure of the seizure focus. This study serves as a proof-of-concept of using such models to design efficient personalized DBS patterns for epilepsy. PMID:26355815

Actin Hydrophobic Loop (262-274) and Filament Nucleation and Elongation

PubMed Central

Shvetsov, Alexander; Galkin, Vitold E.; Orlova, Albina; Phillips, Martin; Bergeron, Sarah E.; Rubenstein, Peter A.; Egelman, Edward H.; Reisler, Emil

2014-01-01

Summary The importance of actin hydrophobic loop 262-274 dynamics to actin polymerization and filament stability has been shown recently using a yeast actin mutant, L180C/L269C/C374A, in which the hydrophobic loop could be locked in a “parked” conformation by a disulfide bond between C180 and C269. Such a cross-linked G-actin does not form filaments, suggesting nucleation and/or elongation inhibition. To determine the role of loop dynamics in filament nucleation and/or elongation, we studied the polymerization of the cross-linked actin in the presence of cofilin - to assist with actin nucleation - and with phalloidin, to stabilize the elongating filament segments. We demonstrate here that together, but not alone, phalloidin and cofilin co-rescue the polymerization of cross-linked actin. The polymerization was also rescued by filament seeds added together with phalloidin but not with cofilin. Thus, loop immobilization via cross-linking inhibits both filament nucleation and elongation. Nevertheless, the conformational changes needed to catalyze ATP hydrolysis by actin occur in the cross-linked actin. When actin filaments are fully decorated by cofilin the helical twist of F-actin changes by ~ 5° per subunit. Electron microscopic analysis of filaments rescued by cofilin and phalloidin revealed a dense contact between opposite strands in F-actin, and a change of twist by ~ 1° per subunit, indicating either partial or disordered attachment of cofilin to F-actin and/or a competition between cofilin and phalloidin to alter F-actin symmetry. Our findings show an importance of the hydrophobic loop conformational dynamics to both actin nucleation and elongation and reveal that the inhibition of these two steps in the cross-linked actin can be relieved by appropriate factors. PMID:18037437

Control-structure interaction in precision pointing servo loops

NASA Technical Reports Server (NTRS)

Spanos, John T.

1989-01-01

The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

Towards the use of Structural Loop Analysis to Study System Behaviour of Socio-Ecological Systems.

NASA Astrophysics Data System (ADS)

Abram, Joseph; Dyke, James

2016-04-01

Maintaining socio-ecological systems in desirable states is key to developing a growing economy, alleviating poverty and achieving a sustainable future. While the driving forces of an environmental system are often well known, the dynamics impacting these drivers can be hidden within a tangled structure of causal chains and feedback loops. A lack of understanding of a system's dynamic structure and its influence on a system's behaviour can cause unforeseen side-effects during model scenario testing and policy implementation. Structural Loop analysis of socio-ecological system models identifies dominant feedback structures during times of behavioural shift, allowing the user to monitor key influential drivers during model simulation. This work carries out Loop Eigenvalue Elasticity Analysis (LEEA) on three system dynamic models, exploring tipping points in lake systems undergoing eutrophication. The purpose is to explore the potential benefits and limitations of the technique in the field of socio-ecology. The LEEA technique shows promise for socio-ecological systems which undergo regime shifts or express oscillatory trends, but shows limited usefulness with large models. The results of this work highlight changes in feedback loop dominance, years prior to eutrophic tipping events in lake systems. LEEA could be used as an early warning signal to impending system changes, complementary to other known early warning signals. This approach could improve our understanding during critical times of a system's behaviour, changing how we approach model analysis and the way scenario testing and policy implementation are addressed in socio-ecological system models.

The insertion of human dynamics models in the flight control loops of V/STOL research aircraft. Appendix 2: The optimal control model of a pilot in V/STOL aircraft control loops

NASA Technical Reports Server (NTRS)

Zipf, Mark E.

1989-01-01

An overview is presented of research work focussed on the design and insertion of classical models of human pilot dynamics within the flight control loops of V/STOL aircraft. The pilots were designed and configured for use in integrated control system research and design. The models of human behavior that were considered are: McRuer-Krendel (a single variable transfer function model); and Optimal Control Model (a multi-variable approach based on optimal control and stochastic estimation theory). These models attempt to predict human control response characteristics when confronted with compensatory tracking and state regulation tasks. An overview, mathematical description, and discussion of predictive limitations of the pilot models is presented. Design strategies and closed loop insertion configurations are introduced and considered for various flight control scenarios. Models of aircraft dynamics (both transfer function and state space based) are developed and discussed for their use in pilot design and application. Pilot design and insertion are illustrated for various flight control objectives. Results of pilot insertion within the control loops of two V/STOL research aricraft (Sikorski Black Hawk UH-60A, McDonnell Douglas Harrier II AV-8B) are presented and compared against actual pilot flight data. Conclusions are reached on the ability of the pilot models to adequately predict human behavior when confronted with similar control objectives.

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

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

Le Trong, Isolde; University of Washington, Box 357742, Seattle, WA 98195-7742; Chu, Vano

2013-06-01

The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop. Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing themore » biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide–biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin–biotin complex.« less

Kalman Orbit Optimized Loop Tracking

NASA Technical Reports Server (NTRS)

Young, Lawrence E.; Meehan, Thomas K.

2011-01-01

Under certain conditions of low signal power and/or high noise, there is insufficient signal to noise ratio (SNR) to close tracking loops with individual signals on orbiting Global Navigation Satellite System (GNSS) receivers. In addition, the processing power available from flight computers is not great enough to implement a conventional ultra-tight coupling tracking loop. This work provides a method to track GNSS signals at very low SNR without the penalty of requiring very high processor throughput to calculate the loop parameters. The Kalman Orbit-Optimized Loop (KOOL) tracking approach constitutes a filter with a dynamic model and using the aggregate of information from all tracked GNSS signals to close the tracking loop for each signal. For applications where there is not a good dynamic model, such as very low orbits where atmospheric drag models may not be adequate to achieve the required accuracy, aiding from an IMU (inertial measurement unit) or other sensor will be added. The KOOL approach is based on research JPL has done to allow signal recovery from weak and scintillating signals observed during the use of GPS signals for limb sounding of the Earth s atmosphere. That approach uses the onboard PVT (position, velocity, time) solution to generate predictions for the range, range rate, and acceleration of the low-SNR signal. The low- SNR signal data are captured by a directed open loop. KOOL builds on the previous open loop tracking by including feedback and observable generation from the weak-signal channels so that the MSR receiver will continue to track and provide PVT, range, and Doppler data, even when all channels have low SNR.

OBSERVATIONAL SIGNATURES OF CORONAL LOOP HEATING AND COOLING DRIVEN BY FOOTPOINT SHUFFLING

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

Dahlburg, R. B.; Taylor, B. D.; Einaudi, G.

The evolution of a coronal loop is studied by means of numerical simulations of the fully compressible three-dimensional magnetohydrodynamic equations using the HYPERION code. The footpoints of the loop magnetic field are advected by random motions. As a consequence, the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is nonuniformly distributed so that only a fraction of the coronal mass and volume gets heated at any time. Temperature and density are highly structured at scalesmore » that, in the solar corona, remain observationally unresolved: the plasma of our simulated loop is multithermal, where highly dynamical hotter and cooler plasma strands are scattered throughout the loop at sub-observational scales. Numerical simulations of coronal loops of 50,000 km length and axial magnetic field intensities ranging from 0.01 to 0.04 T are presented. To connect these simulations to observations, we use the computed number densities and temperatures to synthesize the intensities expected in emission lines typically observed with the Extreme Ultraviolet Imaging Spectrometer on Hinode. These intensities are used to compute differential emission measure distributions using the Monte Carlo Markov Chain code, which are very similar to those derived from observations of solar active regions. We conclude that coronal heating is found to be strongly intermittent in space and time, with only small portions of the coronal loop being heated: in fact, at any given time, most of the corona is cooling down.« less

Three parameters optimizing closed-loop control in sequential segmental neuromuscular stimulation.

PubMed

Zonnevijlle, E D; Somia, N N; Perez Abadia, G; Stremel, R W; Maldonado, C J; Werker, P M; Kon, M; Barker, J H

1999-05-01

In conventional dynamic myoplasties, the force generation is poorly controlled. This causes unnecessary fatigue of the transposed/transplanted electrically stimulated muscles and causes damage to the involved tissues. We introduced sequential segmental neuromuscular stimulation (SSNS) to reduce muscle fatigue by allowing part of the muscle to rest periodically while the other parts work. Despite this improvement, we hypothesize that fatigue could be further reduced in some applications of dynamic myoplasty if the muscles were made to contract according to need. The first necessary step is to gain appropriate control over the contractile activity of the dynamic myoplasty. Therefore, closed-loop control was tested on a sequentially stimulated neosphincter to strive for the best possible control over the amount of generated pressure. A selection of parameters was validated for optimizing control. We concluded that the frequency of corrections, the threshold for corrections, and the transition time are meaningful parameters in the controlling algorithm of the closed-loop control in a sequentially stimulated myoplasty.

Understanding social forces involved in diabetes outcomes: a systems science approach to quality-of-life research.

PubMed

Lounsbury, David W; Hirsch, Gary B; Vega, Chawntel; Schwartz, Carolyn E

2014-04-01

The field of quality-of-life (QOL) research would benefit from learning about and integrating systems science approaches that model how social forces interact dynamically with health and affect the course of chronic illnesses. Our purpose is to describe the systems science mindset and to illustrate the utility of a system dynamics approach to promoting QOL research in chronic disease, using diabetes as an example. We build a series of causal loop diagrams incrementally, introducing new variables and their dynamic relationships at each stage. These causal loop diagrams demonstrate how a common set of relationships among these variables can generate different disease and QOL trajectories for people with diabetes and also lead to a consideration of non-clinical (psychosocial and behavioral) factors that can have implications for program design and policy formulation. The policy implications of the causal loop diagrams are discussed, and empirical next steps to validate the diagrams and quantify the relationships are described.

System identification of dynamic closed-loop control of total peripheral resistance by arterial and cardiopulmonary baroreceptors

NASA Technical Reports Server (NTRS)

Aljuri, A. N.; Bursac, N.; Marini, R.; Cohen, R. J.

2001-01-01

Prolonged exposure to microgravity in space flight missions (days) impairs the mechanisms responsible for defense of arterial blood pressure (ABP) and cardiac output (CO) against orthostatic stress in the post-flight period. The mechanisms responsible for the observed orthostatic intolerance are not yet completely understood. Additionally, effective counter measures to attenuate this pathophysiological response are not available. The aim of this study was to investigate the ability of our proposed system identification method to predict closed-loop dynamic changes in TPR induced by changes in mean arterial pressure (MAP) and right atrial pressure (RAP). For this purpose we designed and employed a novel experimental animal model for the examination of arterial and cardiopulmonary baroreceptors in the dynamic closed-loop control of total peripheral resistance (TPR), and applied system identification to the analysis of beat-to-beat fluctuations in the measured signals. Grant numbers: NAG5-4989. c 2001. Elsevier Science Ltd. All rights reserved.

Tight Loops Close-Up [video

NASA Image and Video Library

2014-05-19

NASA's Solar Dynamics Observatory (SDO) zoomed in almost to its maximum level to watch tight, bright loops and much longer, softer loops shift and sway above an active region on the sun, while a darker blob of plasma in their midst was pulled about every which way (May 13-14, 2014). The video clip covers just over a day beginning at 14:19 UT on May 13. The frames were taken in the 171-angstroms wavelength of extreme ultraviolet light, but colorized red, instead of its usual bronze tone. This type of dynamic activity continues almost non-stop on the sun as opposing magnetic forces tangle with each other. Credit: NASA/Solar Dynamics Observatory NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

A nonlinear dynamical analogue model of geomagnetic activity

NASA Technical Reports Server (NTRS)

Klimas, A. J.; Baker, D. N.; Roberts, D. A.; Fairfield, D. H.; Buechner, J.

1992-01-01

Consideration is given to the solar wind-magnetosphere interaction within the framework of deterministic nonlinear dynamics. An earlier dripping faucet analog model of the low-dimensional solar wind-magnetosphere system is reviewed, and a plasma physical counterpart to that model is constructed. A Faraday loop in the magnetotail is considered, and the relationship of electric potentials on the loop to changes in the magnetic flux threading the loop is developed. This approach leads to a model of geomagnetic activity which is similar to the earlier mechanical model but described in terms of the geometry and plasma contents of the magnetotail. The model is characterized as an elementary time-dependent global convection model. The convection evolves within a magnetotail shape that varies in a prescribed manner in response to the dynamical evolution of the convection. The result is a nonlinear model capable of exhibiting a transition from regular to chaotic loading and unloading. The model's behavior under steady loading and also some elementary forms of time-dependent loading is discussed.

A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase

PubMed Central

Bae, Sung-Hun; Duggan, Brendan M.; Benkovic, Stephen J.; Dyson, H. Jane; Wright, Peter E

2013-01-01

Correlated networks of amino acids have been proposed to play a fundamental role in allostery and enzyme catalysis. These networks of amino acids can be traced from surface-exposed residues all the way into the active site, and disruption of these networks can decrease enzyme activity. Substitution of the distal Gly121 residue in E.coli dihydrofolate reductase results in up to a 200-fold decrease in the hydride transfer rate despite the fact that the residue is located 15 Å from the active-site center. In the present study, NMR relaxation experiments are used to demonstrate that dynamics on the ps-ns and μs-ms timescales are changed significantly in the G121V mutant of dihydrofolate reductase. In particular, ps-ns timescale dynamics are decreased in the FG loop (containing the mutated residue 121) and the neighboring active-site loop (the Met20 loop) in the mutant compared to wild-type enzyme, suggesting that these loops are dynamically coupled. Changes in methyl order parameters reveal a pathway by which dynamic perturbations can be propagated more than 25 Å across the protein from the site of mutation. All of the enzyme complexes, including the model Michaelis complex with folate and NADP+ bound, assume an occluded ground state conformation, and we do not observe sampling of a higher energy closed conformation by 15N R2 relaxation dispersion. This is highly significant, since it is only in the closed conformation that the cofactor and substrate reactive centers are positioned for reaction. The mutation also impairs μs - ms timescale fluctuations that have been implicated in product release from the wild type enzyme. Our results are consistent with an important role for Gly121 in controlling protein dynamics critical for enzyme function and further validate the dynamic energy landscape hypothesis of enzyme catalysis. PMID:23758161

A closed-loop photon beam control study for the Advanced Light Source

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

Portmann, G.; Bengtsson, J.

1993-05-01

The third generation Advanced Light Source (ALS) will produce extremely bright photon beams using undulators and wigglers. In order to position the photon beams accurate to the micron level, a closed-loop feedback system is being developed. Using photon position monitors and dipole corrector magnets, a closed-loop system can automatically compensate for modeling uncertainties and exogenous disturbances. The following paper will present a dynamics model for the perturbations of the closed orbit of the electron beam in the ALS storage ring including the vacuum chamber magnetic field penetration effects. Using this reference model, two closed-loop feedback algorithms will be compared --more » a classical PI controller and a two degree-of-freedom approach. The two degree-of-freedom method provides superior disturbance rejection while maintaining the desired performance goals. Both methods will address the need to gain schedule the controller due to the time varying dynamics introduced by changing field strengths when scanning the insertion devices.« less

OT2_wlanger_7: Dynamics of Giant Magnetic Gas Loops and Their Connection to the CMZ in the Galactic Center

NASA Astrophysics Data System (ADS)

Langer, W.

2011-09-01

Understanding the mass transfer and dynamics among the Galactic Center, the disk, and the halo of the Milky Way is fundamental to the study of the evolution of galaxies and star formation. Recently several giant loops of molecular gas (GML) have been found in the Galactic Center from CO maps, which are likely the result of the magnetic Parker instability. There is new evidence of a possible connection between these loops and the Central Molecular Zone as shown in a sparse [CII] sampling made by the Herschel Key Project GOT C+. Here we propose to map various features of the GMLs and the interface region in [CII] with HIFI. We will also map the foot points of the loop, which are thought to be highly shocked regions, in the ortho 110-101 line of water, which is a known shock tracer. With this data we will characterize different ISM components and their flow among these Galactic Center features.

Fabrication of YBa2Cu3O7 twin-boundary-junction dc SQUID by using a focused-ion-beam pattern technique

NASA Astrophysics Data System (ADS)

Lee, Sung Hoon; Lee, Soon-Gul

2017-09-01

We have fabricated YBa2Cu3O7 (YBCO) dc SQUIDs containing nanobridges across twin boundaries of LaAlO3 (LAO) substrates as Josephson elements by using a focused ion beam (FIB) etching method and measured their transport properties. The beam energy was 30 keV and the current was 1.5 pA for the nanobridge pattern. Each bridge with a nominal width of 200 nm crossed a twin boundary in the (100) direction. The SQUID loop had a 10 μm × 10 μm hole with a 5.7 μm average linewidth. The SQUID voltage showed modulations in response to the external flux with a maximum modulation depth of 350 μV at 77.0 K. HR-XRD spectra showed that the epitaxially grown YBCO film was twinned in commensurate with the twinning of the LAO substrate. Tilting of the c-axis of YBCO across the twin boundary is believed to play a role as a tunnel barrier.

Spatial-pattern-induced evolution of a self-replicating loop network.

PubMed

Suzuki, Keisuke; Ikegami, Takashi

2006-01-01

We study a system of self-replicating loops in which interaction rules between individuals allow competition that leads to the formation of a hypercycle-like network. The main feature of the model is the multiple layers of interaction between loops, which lead to both global spatial patterns and local replication. The network of loops manifests itself as a spiral structure from which new kinds of self-replicating loops emerge at the boundaries between different species. In these regions, larger and more complex self-replicating loops live for longer periods of time, managing to self-replicate in spite of their slower replication. Of particular interest is how micro-scale interactions between replicators lead to macro-scale spatial pattern formation, and how these macro-scale patterns in turn perturb the micro-scale replication dynamics.

An estimator-predictor approach to PLL loop filter design

NASA Technical Reports Server (NTRS)

Statman, J. I.; Hurd, W. J.

1986-01-01

An approach to the design of digital phase locked loops (DPLLs), using estimation theory concepts in the selection of a loop filter, is presented. The key concept is that the DPLL closed-loop transfer function is decomposed into an estimator and a predictor. The estimator provides recursive estimates of phase, frequency, and higher order derivatives, while the predictor compensates for the transport lag inherent in the loop. This decomposition results in a straightforward loop filter design procedure, enabling use of techniques from optimal and sub-optimal estimation theory. A design example for a particular choice of estimator is presented, followed by analysis of the associated bandwidth, gain margin, and steady state errors caused by unmodeled dynamics. This approach is under consideration for the design of the Deep Space Network (DSN) Advanced Receiver Carrier DPLL.

Closed-loop analysis and control of a non-inverting buck-boost converter

NASA Astrophysics Data System (ADS)

Chen, Zengshi; Hu, Jiangang; Gao, Wenzhong

2010-11-01

In this article, a cascade controller is designed and analysed for a non-inverting buck-boost converter. The fast inner current loop uses sliding mode control. The slow outer voltage loop uses the proportional-integral (PI) control. Stability analysis and selection of PI gains are based on the nonlinear closed-loop error dynamics incorporating both the inner and outer loop controllers. The closed-loop system is proven to have a nonminimum phase structure. The voltage transient due to step changes of input voltage or resistance is predictable. The operating range of the reference voltage is discussed. The controller is validated by a simulation circuit. The simulation results show that the reference output voltage is well-tracked under system uncertainties or disturbances, confirming the validity of the proposed controller.

Positive And Negative Feedback Loops Coupled By Common Transcription Activator And Repressor

NASA Astrophysics Data System (ADS)

Sielewiesiuk, Jan; Łopaciuk, Agata

2015-03-01

Dynamical systems consisting of two interlocked loops with negative and positive feedback have been studied using the linear analysis of stability and numerical solutions. Conditions for saddle-node bifurcation were formulated in a general form. Conditions for Hopf bifurcations were found in a few symmetrical cases. Auto-oscillations, when they exist, are generated by the negative feedback repressive loop. This loop determines the frequency and amplitude of oscillations. The positive feedback loop of activation slightly modifies the oscillations. Oscillations are possible when the difference between Hilll's coefficients of the repression and activation is sufficiently high. The highly cooperative activation loop with a fast turnover slows down or even makes the oscillations impossible. The system under consideration can constitute a component of epigenetic or enzymatic regulation network.

Osmotic mechanism of the loop extrusion process

NASA Astrophysics Data System (ADS)

Yamamoto, Tetsuya; Schiessel, Helmut

2017-09-01

The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

Numerical Simulation of DC Coronal Heating

NASA Astrophysics Data System (ADS)

Dahlburg, Russell B.; Einaudi, G.; Taylor, Brian D.; Ugarte-Urra, Ignacio; Warren, Harry; Rappazzo, A. F.; Velli, Marco

2016-05-01

Recent research on observational signatures of turbulent heating of a coronal loop will be discussed. The evolution of the loop is is studied by means of numerical simulations of the fully compressible three-dimensional magnetohydrodynamic equations using the HYPERION code. HYPERION calculates the full energy cycle involving footpoint convection, magnetic reconnection, nonlinear thermal conduction and optically thin radiation. The footpoints of the loop magnetic field are convected by random photospheric motions. As a consequence the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is non-uniformly distributed so that only a fraction of thecoronal mass and volume gets heated at any time. Temperature and density are highly structured at scales which, in the solar corona, remain observationally unresolved: the plasma of the simulated loop is multi thermal, where highly dynamical hotter and cooler plasma strands are scattered throughout the loop at sub-observational scales. Typical simulated coronal loops are 50000 km length and have axial magnetic field intensities ranging from 0.01 to 0.04 Tesla. To connect these simulations to observations the computed number densities and temperatures are used to synthesize the intensities expected in emission lines typically observed with the Extreme ultraviolet Imaging Spectrometer (EIS) on Hinode. These intensities are then employed to compute differential emission measure distributions, which are found to be very similar to those derived from observations of solar active regions.

Observational Signatures of Coronal Heating

NASA Astrophysics Data System (ADS)

Dahlburg, R. B.; Einaudi, G.; Ugarte-Urra, I.; Warren, H. P.; Rappazzo, A. F.; Velli, M.; Taylor, B.

2016-12-01

Recent research on observational signatures of turbulent heating of a coronal loop will be discussed. The evolution of the loop is is studied by means of numericalsimulations of the fully compressible three-dimensionalmagnetohydrodynamic equations using the HYPERION code. HYPERION calculates the full energy cycle involving footpoint convection, magnetic reconnection,nonlinear thermal conduction and optically thin radiation.The footpoints of the loop magnetic field are convected by random photospheric motions. As a consequence the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is non-uniformly distributed so that only a fraction of thecoronal mass and volume gets heated at any time. Temperature and density are highly structured at scales which, in the solar corona, remain observationally unresolved: the plasma of the simulated loop is multi-thermal, where highly dynamical hotter and cooler plasma strands arescattered throughout the loop at sub-observational scales. Typical simulated coronal loops are 50000 km length and have axial magnetic field intensities ranging from 0.01 to 0.04 Tesla.To connect these simulations to observations the computed numberdensities and temperatures are used to synthesize the intensities expected inemission lines typically observed with the Extreme ultraviolet Imaging Spectrometer(EIS) on Hinode. These intensities are then employed to compute differentialemission measure distributions, which are found to be very similar to those derivedfrom observations of solar active regions.

A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop

DOE PAGES

Simakov, Nikolay; Leonard, David A.; Smith, Jeremy C.; ...

2016-09-26

Widespread antibiotic resistance, particularly when mediated by broad-spectrum β-lactamases, has major implications for public health. Substitutions in the active site often allow broad-spectrum enzymes to accommodate diverse types of β-lactams. Substitutions observed outside the active site are thought to compensate for the loss of thermal stability. The OXA-1 clade of class D β-lactamases contains a pair of conserved cysteines located outside the active site that forms a disulfide bond in the periplasm. In this paper, the effect of the distal disulfide bond on the structure and dynamics of OXA-1 was investigated via 4 μs molecular dynamics simulations. The results revealmore » that the disulfide promotes the preorganized orientation of the catalytic residues and affects the conformation of the functionally important Ω loop. Furthermore, principal component analysis reveals differences in the global dynamics between the oxidized and reduced forms, especially in the motions involving the Ω loop. A dynamical network analysis indicates that, in the oxidized form, in addition to its role in ligand binding, the KTG family motif is a central hub of the global dynamics. Finally, as activity of OXA-1 has been measured only in the reduced form, we suggest that accurate assessment of its functional profile would require oxidative conditions mimicking periplasm.« less

De Haas van Alphen effect of PrB6 in commensurate and incommensurate phases

NASA Astrophysics Data System (ADS)

Endo, M.; Isshiki, T.; Kimura, N.; Aoki, H.; Kunii, S.

2006-05-01

We have studied the de Haas-van Alphen effect in the commensurate (C) and incommensurate (IC) phases of PrB6. It is found that the amplitudes and effective masses of the two oscillations α1 and α2 from the main Fermi surface are approximately the same in the C phase while they are considerably different in the IC phase.

Higher-Order Adaptive Finite-Element Methods for Kohn-Sham Density Functional Theory

DTIC Science & Technology

2012-07-03

systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemi- cal accuracy...calculations. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of materials systems contain- ing a...benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance.

PubMed

Carstens, Heiko; Renner, Christian; Milbradt, Alexander G; Moroder, Luis; Tavan, Paul

2005-03-29

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.

Sweeping Arches and Loops [video

NASA Image and Video Library

2014-07-10

Two active regions with their intense magnetic fields produced towering arches and spiraling coils of solar loops above them (June 29 - July 1, 2014) as they rotated into view. When viewed in extreme ultraviolet light, magnetic field lines are revealed by charged particles that travel along them. These active regions appear as dark sunspots when viewed in filtered light. Note the small blast in the upper of the two major active regions, followed by more coils of loops as the region reorganizes itself. The still was taken on June 30 at 10:33 UT. Credit: NASA/Solar Dynamics Observatory Two active regions with their intense magnetic fields produced towering arches and spiraling coils of solar loops above them (June 29 - July 1, 2014) as they rotated into view. When viewed in extreme ultraviolet light, magnetic field lines are revealed by charged particles that travel along them. These active regions appear as dark sunspots when viewed in filtered light. Note the small blast in the upper of the two major active regions, followed by more coils of loops as the region reorganizes itself. The still was taken on June 30 at 10:33 UT. Credit: Solar Dynamics Observatory/NASA.

Dynamic Droop–Based Inertial Control of a Doubly-Fed Induction Generator

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

Hwang, Min; Muljadi, Eduard; Park, Jung-Wook

2016-07-01

If a large disturbance occurs in a power grid, two auxiliary loops for the inertial control of a wind turbine generator have been used: droop loop and rate of change of frequency (ROCOF) loop. Because their gains are fixed, difficulties arise in determining them suitable for all grid and wind conditions. This paper proposes a dynamic droop-based inertial control scheme of a doubly-fed induction generator (DFIG). The scheme aims to improve the frequency nadir (FN) and ensure stable operation of a DFIG. To achieve the first goal, the scheme uses a droop loop, but it dynamically changes its gain basedmore » on the ROCOF to release a large amount of kinetic energy during the initial stage of a disturbance. To do this, a shaping function that relates the droop to the ROCOF is used. To achieve the second goal, different shaping functions, which depend on rotor speeds, are used to give a large contribution in high wind conditions and prevent over-deceleration in low wind conditions during inertial control. The performance of the proposed scheme was investigated under various wind conditions using an EMTP-RV simulator. The results indicate that the scheme improves the FN and ensures stable operation of a DFIG.« less

Spin-wave dynamics and exchange interactions in multiferroic NdFe3(BO3)4 explored by inelastic neutron scattering

NASA Astrophysics Data System (ADS)

Golosovsky, I. V.; Ovsyanikov, A. K.; Aristov, D. N.; Matveeva, P. G.; Mukhin, A. A.; Boehm, M.; Regnault, L.-P.; Bezmaternykh, L. N.

2018-04-01

Magnetic excitations and exchange interactions in multiferroic NdFe3(BO3)4 were studied by inelastic neutron scattering in the phase with commensurate antiferromagnetic structure. The observed spectra were analyzed in the frame of the linear spin-wave theory. It was shown that only the model, which includes the exchange interactions within eight coordination spheres, describes satisfactorily all observed dispersion curves. The calculation showed that the spin-wave dynamics is governed by the strongest antiferromagnetic intra-chain interaction and three almost the same inter-chain interactions. Other interactions, including ferromagnetic exchange, appeared to be insignificant. The overall energy balance of the antiferromagnetic inter-chain exchange interactions, which couple the moments from the adjacent ferromagnetic layers as well as within a layer, stabilizes ferromagnetic arrangement in the latter. It demonstrates that the pathway geometry plays a crucial role in forming of the magnetic structure.

Large-Scale Fluorescence Calcium-Imaging Methods for Studies of Long-Term Memory in Behaving Mammals

PubMed Central

Jercog, Pablo; Rogerson, Thomas; Schnitzer, Mark J.

2016-01-01

During long-term memory formation, cellular and molecular processes reshape how individual neurons respond to specific patterns of synaptic input. It remains poorly understood how such changes impact information processing across networks of mammalian neurons. To observe how networks encode, store, and retrieve information, neuroscientists must track the dynamics of large ensembles of individual cells in behaving animals, over timescales commensurate with long-term memory. Fluorescence Ca2+-imaging techniques can monitor hundreds of neurons in behaving mice, opening exciting avenues for studies of learning and memory at the network level. Genetically encoded Ca2+ indicators allow neurons to be targeted by genetic type or connectivity. Chronic animal preparations permit repeated imaging of neural Ca2+ dynamics over multiple weeks. Together, these capabilities should enable unprecedented analyses of how ensemble neural codes evolve throughout memory processing and provide new insights into how memories are organized in the brain. PMID:27048190

Robust Flutter Analysis for Aeroservoelastic Systems

NASA Astrophysics Data System (ADS)

Kotikalpudi, Aditya

The dynamics of a flexible air vehicle are typically described using an aeroservoelastic model which accounts for interaction between aerodynamics, structural dynamics, rigid body dynamics and control laws. These subsystems can be individually modeled using a theoretical approach and experimental data from various ground tests can be combined into them. For instance, a combination of linear finite element modeling and data from ground vibration tests may be used to obtain a validated structural model. Similarly, an aerodynamic model can be obtained using computational fluid dynamics or simple panel methods and partially updated using limited data from wind tunnel tests. In all cases, the models obtained for these subsystems have a degree of uncertainty owing to inherent assumptions in the theory and errors in experimental data. Suitable uncertain models that account for these uncertainties can be built to study the impact of these modeling errors on the ability to predict dynamic instabilities known as flutter. This thesis addresses the methods used for modeling rigid body dynamics, structural dynamics and unsteady aerodynamics of a blended wing design called the Body Freedom Flutter vehicle. It discusses the procedure used to incorporate data from a wide range of ground based experiments in the form of model uncertainties within these subsystems. Finally, it provides the mathematical tools for carrying out flutter analysis and sensitivity analysis which account for these model uncertainties. These analyses are carried out for both open loop and controller in the loop (closed loop) cases.

Fiber-bragg grating-loop ringdown method and apparatus

DOEpatents

Wang, Chuji [Starkville, MS

2008-01-29

A device comprising a fiber grating loop ringdown (FGLRD) system of analysis is disclosed. A fiber Bragg grating (FBG) or Long-Period grating (LPG) written in a section of single mode fused silica fiber is incorporated into a fiber loop. By utilizing the wing areas of the gratings' bandwidth as a wavelength dependent attenuator of the light transmission, a fiber grating loop ringdown concept is formed. One aspect of the present invention is temperature sensing, which has been demonstrated using the disclosed device. Temperature measurements in the areas of accuracy, stability, high temperature, and dynamic range are also described.

Atomistic modeling of shock-induced void collapse in copper

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

Davila, L P; Erhart, P; Bringa, E M

2005-03-09

Nonequilibrium molecular dynamics (MD) simulations show that shock-induced void collapse in copper occurs by emission of shear loops. These loops carry away the vacancies which comprise the void. The growth of the loops continues even after they collide and form sessile junctions, creating a hardened region around the collapsing void. The scenario seen in our simulations differs from current models that assume that prismatic loop emission is responsible for void collapse. We propose a new dislocation-based model that gives excellent agreement with the stress threshold found in the MD simulations for void collapse as a function of void radius.

Does the brain use sliding variables for the control of movements?

PubMed

Hanneton, S; Berthoz, A; Droulez, J; Slotine, J J

1997-12-01

Delays in the transmission of sensory and motor information prevent errors from being instantaneously available to the central nervous system (CNS) and can reduce the stability of a closed-loop control strategy. On the other hand, the use of a pure feedforward control (inverse dynamics) requires a perfect knowledge of the dynamic behavior of the body and of manipulated objects. Sensory feedback is essential both to accommodate unexpected errors and events and to compensate for uncertainties about the dynamics of the body. Experimental observations concerning the control of posture, gaze and limbs have shown that the CNS certainly uses a combination of closed-loop and open-loop control. Feedforward components of movement, such as eye saccades, occur intermittently and present a stereotyped kinematic profile. In visuo-manual tracking tasks, hand movements exhibit velocity peaks that occur intermittently. When a delay or a slow dynamics are inserted in the visuo-manual control loop, intermittent step-and-hold movements appear clearly in the hand trajectory. In this study, we investigated strategies used by human subjects involved in the control of a particular dynamic system. We found strong evidence for substantial nonlinearities in the commands produced. The presence of step-and-hold movements seemed to be the major source of nonlinearities in the control loop. Furthermore, the stereotyped ballistic-like kinematics of these rapid and corrective movements suggests that they were produced in an open-loop way by the CNS. We analyzed the generation of ballistic movements in the light of sliding control theory assuming that they occurred when a sliding variable exceeded a constant threshold. In this framework, a sliding variable is defined as a composite variable (a combination of the instantaneous tracking error and its temporal derivatives) that fulfills a specific stability criterion. Based on this hypothesis and on the assumption of a constant reaction time, the tracking error and its derivatives should be correlated at a particular time lag before movement onset. A peak of correlation was found for a physiologically plausible reaction time, corresponding to a stable composite variable. The direction and amplitude of the ongoing stereotyped movements seemed also be adjusted in order to minimize this variable. These findings suggest that, during visually guided movements, human subjects attempt to minimize such a composite variable and not the instantaneous error. This minimization seems to be obtained by the execution of stereotyped corrective movements.

X-56A MUTT: Aeroservoelastic Modeling

NASA Technical Reports Server (NTRS)

Ouellette, Jeffrey A.

2015-01-01

For the NASA X-56a Program, Armstrong Flight Research Center has been developing a set of linear states space models that integrate the flight dynamics and structural dynamics. These high order models are needed for the control design, control evaluation, and test input design. The current focus has been on developing stiff wing models to validate the current modeling approach. The extension of the modeling approach to the flexible wings requires only a change in the structural model. Individual subsystems models (actuators, inertial properties, etc.) have been validated by component level ground tests. Closed loop simulation of maneuvers designed to validate the flight dynamics of these models correlates very well flight test data. The open loop structural dynamics are also shown to correlate well to the flight test data.

Real-time dynamics simulation of the Cassini spacecraft using DARTS. Part 1: Functional capabilities and the spatial algebra algorithm

NASA Technical Reports Server (NTRS)

Jain, A.; Man, G. K.

1993-01-01

This paper describes the Dynamics Algorithms for Real-Time Simulation (DARTS) real-time hardware-in-the-loop dynamics simulator for the National Aeronautics and Space Administration's Cassini spacecraft. The spacecraft model consists of a central flexible body with a number of articulated rigid-body appendages. The demanding performance requirements from the spacecraft control system require the use of a high fidelity simulator for control system design and testing. The DARTS algorithm provides a new algorithmic and hardware approach to the solution of this hardware-in-the-loop simulation problem. It is based upon the efficient spatial algebra dynamics for flexible multibody systems. A parallel and vectorized version of this algorithm is implemented on a low-cost, multiprocessor computer to meet the simulation timing requirements.

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

Sakaguchi, Hidetsugu; Malomed, Boris A.

We study ordinary solitons and gap solitons (GS's) in the framework of the one-dimensional Gross-Pitaevskii equation (GPE) with a combination of both linear and nonlinear lattice potentials. The main points of the analysis are the effects of (in)commensurability between the lattices, the development of analytical methods, viz., the variational approximation (VA) for narrow ordinary solitons and various forms of the averaging method for broad solitons of both types, and also the study of the mobility of the solitons. Under the direct commensurability (equal periods of the lattices, L{sub lin}=L{sub nonlin}), the family of ordinary solitons is similar to its counterpartmore » in the GPE without external potentials. In the case of the subharmonic commensurability with L{sub lin}=(1/2)L{sub nonlin}, or incommensurability, there is an existence threshold for the ordinary solitons and the scaling relation between their amplitude and width is different from that in the absence of the potentials. GS families demonstrate a bistability unless the direct commensurability takes place. Specific scaling relations are found for them as well. Ordinary solitons can be readily set in motion by kicking. GS's are also mobile and feature inelastic collisions. The analytical approximations are shown to be quite accurate, predicting correct scaling relations for the soliton families in different cases. The stability of the ordinary solitons is fully determined by the Vakhitov-Kolokolov (VK) criterion (i.e., a negative slope in the dependence between the solitons's chemical potential mu and norm N). The stability of GS families obeys an inverted ('anti-VK') criterion dmu/dN>0, which is explained by the approximation based on the averaging method. The present system provides for the unique possibility to check the anti-VK criterion, as mu(N) dependencies for GS's feature turning points except in the case of direct commensurability.« less

Weak and Dynamic GNSS Signal Tracking Strategies for Flight Missions in the Space Service Volume

PubMed Central

Jing, Shuai; Zhan, Xingqun; Liu, Baoyu; Chen, Maolin

2016-01-01

Weak-signal and high-dynamics are of two primary concerns of space navigation using GNSS (Global Navigation Satellite System) in the space service volume (SSV). The paper firstly defines a reference assumption third-order phase-locked loop (PLL) as the baseline of an onboard GNSS receiver, and proves the incompetence of this conventional architecture. Then an adaptive four-state Kalman filter (KF)-based algorithm is introduced to realize the optimization of loop noise bandwidth, which can adaptively regulate its filter gain according to the received signal power and line-of-sight (LOS) dynamics. To overcome the matter of losing lock in weak-signal and high-dynamic environments, an open loop tracking strategy aided by an inertial navigation system (INS) is recommended, and the traditional maximum likelihood estimation (MLE) method is modified in a non-coherent way by reconstructing the likelihood cost function. Furthermore, a typical mission with combined orbital maneuvering and non-maneuvering arcs is taken as a destination object to test the two proposed strategies. Finally, the experiment based on computer simulation identifies the effectiveness of an adaptive four-state KF-based strategy under non-maneuvering conditions and the virtue of INS-assisted methods under maneuvering conditions. PMID:27598164

Weak and Dynamic GNSS Signal Tracking Strategies for Flight Missions in the Space Service Volume.

PubMed

Jing, Shuai; Zhan, Xingqun; Liu, Baoyu; Chen, Maolin

2016-09-02

Weak-signal and high-dynamics are of two primary concerns of space navigation using GNSS (Global Navigation Satellite System) in the space service volume (SSV). The paper firstly defines a reference assumption third-order phase-locked loop (PLL) as the baseline of an onboard GNSS receiver, and proves the incompetence of this conventional architecture. Then an adaptive four-state Kalman filter (KF)-based algorithm is introduced to realize the optimization of loop noise bandwidth, which can adaptively regulate its filter gain according to the received signal power and line-of-sight (LOS) dynamics. To overcome the matter of losing lock in weak-signal and high-dynamic environments, an open loop tracking strategy aided by an inertial navigation system (INS) is recommended, and the traditional maximum likelihood estimation (MLE) method is modified in a non-coherent way by reconstructing the likelihood cost function. Furthermore, a typical mission with combined orbital maneuvering and non-maneuvering arcs is taken as a destination object to test the two proposed strategies. Finally, the experiment based on computer simulation identifies the effectiveness of an adaptive four-state KF-based strategy under non-maneuvering conditions and the virtue of INS-assisted methods under maneuvering conditions.

Periodic vortex pinning by regular structures in Nb thin films: magnetic vs. structural effects

NASA Astrophysics Data System (ADS)

Montero, Maria Isabel; Jonsson-Akerman, B. Johan; Schuller, Ivan K.

2001-03-01

The defects present in a superconducting material can lead to a great variety of static and dynamic vortex phases. In particular, the interaction of the vortex lattice with regular arrays of pinning centers such as holes or magnetic dots gives rise to commensurability effects. These commensurability effects can be observed in the magnetoresistance and in the critical current dependence with the applied field. In recent years, experimental results have shown that there is a dependence of the periodic pinning effect on the properties of the vortex lattice (i.e. vortex-vortex interactions, elastic energy and vortex velocity) and also on the dots characteristics (i.e. dot size, distance between dots, magnetic character of the dot material, etc). However, there is not still a good understanding of the nature of the main pinning mechanisms by the magnetic dots. To clarify this important issue, we have studied and compared the periodic pinning effects in Nb films with rectangular arrays of Ni, Co and Fe dots, as well as the pinning effects in a Nb film deposited on a hole patterned substrate without any magnetic material. We will discuss the differences on pinning energies arising from magnetic effects as compared to structural effects of the superconducting film. This work was supported by NSF and DOE. M.I. Montero acknowledges postdoctoral fellowship by the Secretaria de Estado de Educacion y Universidades (Spain).

Phononic Origins of Friction in Carbon Nanotube Oscillators.

PubMed

Prasad, Matukumilli V D; Bhattacharya, Baidurya

2017-04-12

Phononic coupling can have a significant role in friction between nanoscale surfaces. We find frictional dissipation per atom in carbon nanotube (CNT) oscillators to depend significantly on interface features such as contact area, commensurability, and by end-capping of the inner core. We perform large-scale phonon wavepacket MD simulations to study phonon coupling between a 250 nm long (10,10) outer tube and inner cores of four different geometries. Five different phonon polarizations known to have dominant roles in thermal transport are selected, and transmission coefficient plots for a range of phonon energies along with phonon scattering dynamics at specific energies are obtained. We find that the length of interface affects friction only through LA phonon scattering and has a significant nonlinear effect on total frictional force. Incommensurate contact does not always give rise to superlubricity: the net effect of two competing interaction mechanisms shown by longitudinal and transverse phonons decides the role of commensurability. Capping of the core has no effect on acoustic phonons but destroys the coherence of transverse optical phonons and creates diffusive scattering. In contrast, the twisting and radial breathing phonon modes have perfect transmission at all energies and can be deemed as the enablers of ultralow friction in CNT oscillators. Our work suggests that tuning of interface geometries can give rise to desirable friction properties in nanoscale devices.

A continuum model for dynamic analysis of the Space Station

NASA Technical Reports Server (NTRS)

Thomas, Segun

1989-01-01

Dynamic analysis of the International Space Station using MSC/NASTRAN had 1312 rod elements, 62 beam elements, 489 nodes and 1473 dynamic degrees of freedom. A realtime, man-in-the-loop simulation of such a model is impractical. This paper discusses the mathematical model for realtime dynamic simulation of the Space Station. Several key questions in structures and structural dynamics are addressed. First, to achieve a significant reduction in the number of dynamic degrees of freedom, a continuum equivalent representation of the Space Station truss structure which accounted for the unsymmetry of the basic configuration and resulted in the coupling of extensional and transverse deformation, is developed. Next, dynamic equations for the continuum equivalent of the Space Station truss structure are formulated using a matrix version of Kane's dynamical equations. Flexibility is accounted for by using a theory that accommodates extension, bending in two principal planes and shear displacement. Finally, constraint equations suitable for dynamic analysis of flexible bodies with closed loop configuration are developed and solution of the resulting system of equations is based on the zero eigenvalue theorem.

Design and evaluation of a robust dynamic neurocontroller for a multivariable aircraft control problem

NASA Technical Reports Server (NTRS)

Troudet, T.; Garg, S.; Merrill, W.

1992-01-01

The design of a dynamic neurocontroller with good robustness properties is presented for a multivariable aircraft control problem. The internal dynamics of the neurocontroller are synthesized by a state estimator feedback loop. The neurocontrol is generated by a multilayer feedforward neural network which is trained through backpropagation to minimize an objective function that is a weighted sum of tracking errors, and control input commands and rates. The neurocontroller exhibits good robustness through stability margins in phase and vehicle output gains. By maintaining performance and stability in the presence of sensor failures in the error loops, the structure of the neurocontroller is also consistent with the classical approach of flight control design.

AGARD (Advisory Group for Aerospace Research & Development) Index of Publications, 1986-1988

DTIC Science & Technology

1989-08-01

measurements are used in forming the navigation and the baro-inertial loop as well The system communicates with equations to solve for the user position...processing techniques in the tracking ROBERT P. DENARO and G JEFFREY GEIER In AGARD, The loops . and later in the navigation processing ot the Kalman...avionics investigations to predict the dynamic structural response of flexible assessment. The current status of real time, pilot-in-the- loop flight

Extension of loop quantum gravity to f(R) theories.

PubMed

Zhang, Xiangdong; Ma, Yongge

2011-04-29

The four-dimensional metric f(R) theories of gravity are cast into connection-dynamical formalism with real su(2) connections as configuration variables. Through this formalism, the classical metric f(R) theories are quantized by extending the loop quantization scheme of general relativity. Our results imply that the nonperturbative quantization procedure of loop quantum gravity is valid not only for general relativity but also for a rather general class of four-dimensional metric theories of gravity.

Microbial Community Dynamics of a Simulated Chloraminated Drinking Water Distribution System Subjected to Episodes of Nitrification

EPA Science Inventory

Bacterial populations were examined in a simulated chloraminated drinking water distribution system (i.e. loop). The loop (BW-AB-I) received chlorinated municipal water (BW-C) amended with ammonia (2mg/L monochloramine). After six years of continuous operation, the operational ...

Long range dynamic effects of point-mutations trap a response regulator in an active conformation

PubMed Central

Bobay, Benjamin G.; Thompson, Richele J.; Hoch, James A.; Cavanagh, John

2010-01-01

When a point-mutation in a protein elicits a functional change, it is most common to assign this change to local structural perturbations. Here we show that point-mutations, distant from an essential highly dynamic kinase recognition loop in the response regulator Spo0F, lock this loop in an active conformation. This ‘conformational trapping’ results in functionally hyperactive Spo0F. Consequently, point-mutations are seen to affect functionally critical motions both close to and far from the mutational site. PMID:20828564

Diagram reduction in problem of critical dynamics of ferromagnets: 4-loop approximation

NASA Astrophysics Data System (ADS)

Adzhemyan, L. Ts; Ivanova, E. V.; Kompaniets, M. V.; Vorobyeva, S. Ye

2018-04-01

Within the framework of the renormalization group approach to the models of critical dynamics, we propose a method for a considerable reduction of the number of integrals needed to calculate the critical exponents. With this method we perform a calculation of the critical exponent z of model A at 4-loop level, where our method allows one to reduce the number of integrals from 66 to 17. The way of constructing the integrand in a Feynman representation of such diagrams is discussed. Integrals were estimated numerically with a sector decomposition technique.

Multiloop Manual Control of Dynamic Systems

NASA Technical Reports Server (NTRS)

Hess, R. A.; Mcnally, B. D.

1984-01-01

Human interaction with a simple, multiloop dynamic system in which the human's activity was systematically varied by changing the levels of automation was studied. The control loop structure resulting from the task definition parallels that for any multiloop manual control system, is considered a sterotype. Simple models of the human in the task, and upon extending a technique for describing the manner in which the human subjectively quantifies his opinion of task difficulty were developed. A man in the loop simulation which provides data to support and direct the analytical effort is presented.

Geometrical criteria for characterizing open and closed states of WPD-loop in PTP1B

NASA Astrophysics Data System (ADS)

Shinde, Ranajit Nivrutti; Elizabeth Sobhia, M.

2012-06-01

Distinctive movement of WPD-loop occurs during the catalysis of phosphotyrosine by protein tyrosine phosphatase 1B (PTP1B). This loop is in the "open" state in apo-form whereas it is catalytically competent in the "closed" state. During the closure of this loop, unique hydrogen bond interactions are formed between different residues of the PTP1B. Present study examines such interactions from the available 118 crystal structures of PTP1B. It gives insights into the five novel hydrogen bonds essentially formed in the "closed" loop structures. Additionally, the study provides distance ranges between the atoms involved in the hydrogen bonds. This information can be used as a geometrical criterion in the characterization of conformational state of the WPD-loop especially in the molecular dynamics simulations.

REVIEWS OF TOPICAL PROBLEMS: Coronal magnetic loops

NASA Astrophysics Data System (ADS)

Zaitsev, Valerii V.; Stepanov, Alexander V.

2008-11-01

The goal of this review is to outline some new ideas in the physics of coronal magnetic loops, the fundamental structural elements of the atmospheres of the Sun and flaring stars, which are involved in phenomena such as stellar coronal heating, flare energy release, charged particle acceleration, and the modulation of optical, radio, and X-ray emissions. The Alfvén-Carlqvist view of a coronal loop as an equivalent electric circuit allows a good physical understanding of loop processes. Describing coronal loops as MHD-resonators explains various ways in which flaring emissions from the Sun and stars are modulated, whereas modeling them by magnetic mirror traps allows one to describe the dynamics and emission of high-energy particles. Based on these approaches, loop plasma and fast particle parameters are obtained and models for flare energy release and stellar corona heating are developed.

Closed-Loop Control of Complex Networks: A Trade-Off between Time and Energy

NASA Astrophysics Data System (ADS)

Sun, Yong-Zheng; Leng, Si-Yang; Lai, Ying-Cheng; Grebogi, Celso; Lin, Wei

2017-11-01

Controlling complex nonlinear networks is largely an unsolved problem at the present. Existing works focus either on open-loop control strategies and their energy consumptions or on closed-loop control schemes with an infinite-time duration. We articulate a finite-time, closed-loop controller with an eye toward the physical and mathematical underpinnings of the trade-off between the control time and energy as well as their dependence on the network parameters and structure. The closed-loop controller is tested on a large number of real systems including stem cell differentiation, food webs, random ecosystems, and spiking neuronal networks. Our results represent a step forward in developing a rigorous and general framework to control nonlinear dynamical networks with a complex topology.

Closed Brayton cycle power conversion systems for nuclear reactors :

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

Wright, Steven A.; Lipinski, Ronald J.; Vernon, Milton E.

2006-04-01

This report describes the results of a Sandia National Laboratories internally funded research program to study the coupling of nuclear reactors to gas dynamic Brayton power conversion systems. The research focused on developing integrated dynamic system models, fabricating a 10-30 kWe closed loop Brayton cycle, and validating these models by operating the Brayton test-loop. The work tasks were performed in three major areas. First, the system equations and dynamic models for reactors and Closed Brayton Cycle (CBC) systems were developed and implemented in SIMULINKTM. Within this effort, both steady state and dynamic system models for all the components (turbines, compressors,more » reactors, ducting, alternators, heat exchangers, and space based radiators) were developed and assembled into complete systems for gas cooled reactors, liquid metal reactors, and electrically heated simulators. Various control modules that use proportional-integral-differential (PID) feedback loops for the reactor and the power-conversion shaft speed were also developed and implemented. The simulation code is called RPCSIM (Reactor Power and Control Simulator). In the second task an open cycle commercially available Capstone C30 micro-turbine power generator was modified to provide a small inexpensive closed Brayton cycle test loop called the Sandia Brayton test-Loop (SBL-30). The Capstone gas-turbine unit housing was modified to permit the attachment of an electrical heater and a water cooled chiller to form a closed loop. The Capstone turbine, compressor, and alternator were used without modification. The Capstone systems nominal operating point is 1150 K turbine inlet temperature at 96,000 rpm. The annular recuperator and portions of the Capstone control system (inverter) and starter system also were reused. The rotational speed of the turbo-machinery is controlled by adjusting the alternator load by using the electrical grid as the load bank. The SBL-30 test loop was operated at the manufacturers site (Barber-Nichols Inc.) and installed and operated at Sandia. A sufficiently detailed description of the loop is provided in this report along with the design characteristics of the turbo-alternator-compressor set to allow other researchers to compare their results with those measured in the Sandia test-loop. The third task consisted of a validation effort. In this task the test loop was operated and compared with the modeled results to develop a more complete understanding of this electrically heated closed power generation system and to validate the model. The measured and predicted system temperatures and pressures are in good agreement, indicating that the model is a reasonable representation of the test loop. Typical deviations between the model and the hardware results are less than 10%. Additional tests were performed to assess the capability of the Brayton engine to continue to remove decay heat after the reactor/heater is shutdown, to develop safe and effective control strategies, and to access the effectiveness of gas inventory control as an alternative means to provide load following. In one test the heater power was turned off to simulate a rapid reactor shutdown, and the turbomachinery was driven solely by the sensible heat stored in the heater for over 71 minutes without external power input. This is an important safety feature for CBC systems as it means that the closed Brayton loop will keep cooling the reactor without the need for auxiliary power (other than that needed to circulate the waste heat rejection coolant) provided the heat sink is available.« less

A linear quadratic Gaussian with loop transfer recovery proximity operations autopilot for spacecraft. M.S. Thesis - MIT

NASA Technical Reports Server (NTRS)

Chen, George T.

1987-01-01

An automatic control scheme for spacecraft proximity operations is presented. The controller is capable of holding the vehicle at a prescribed location relative to a target, or maneuvering it to a different relative position using straight line-of-sight translations. The autopilot uses a feedforward loop to initiate and terminate maneuvers, and for operations at nonequilibrium set-points. A multivariate feedback loop facilitates precise position and velocity control in the presence of sensor noise. The feedback loop is formulated using the Linear Quadratic Gaussian (LQG) with Loop Transfer Recovery (LTR) design procedure. Linear models of spacecraft dynamics, adapted from Clohessey-Wiltshire Equations, are augmented and loop shaping techniques are applied to design a target feedback loop. The loop transfer recovery procedure is used to recover the frequency domain properties of the target feedback loop. The resulting compensator is integrated into an autopilot which is tested in a high fidelity Space Shuttle Simulator. The autopilot performance is evaluated for a variety of proximity operations tasks envisioned for future Shuttle flights.

Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: a model from molecular simulations.

PubMed

Lai, Yen-Ting; Cheng, Chao-Sheng; Liu, Yu-Nan; Liu, Yaw-Jen; Lyu, Ping-Chiang

2008-09-01

Plant nonspecific lipid transfer proteins (nsLTPs) are small, basic proteins constituted mainly of alpha-helices and stabilized by four conserved disulfide bridges. They are characterized by the presence of a tunnel-like hydrophobic cavity, capable of transferring various lipid molecules between lipid bilayers in vitro. In this study, molecular dynamics (MD) simulations were performed at room temperature to investigate the effects of lipid binding on the dynamic properties of rice nsLTP1. Rice nsLTP1, either in the free form or complexed with one or two lipids was subjected to MD simulations. The C-terminal loop was very flexible both before and after lipid binding, as revealed by calculating the root-mean-square fluctuation. After lipid binding, the flexibility of some residues that were not in direct contact with lipid molecules increased significantly, indicating an increase of entropy in the region distal from the binding site. Essential dynamics analysis revealed clear differences in motion between unliganded and liganded rice nsLTP1s. In the free form of rice nsLTP1, loop1 exhibited the largest directional motion. This specific essential motion mode diminished after binding one or two lipid molecules. To verify the origin of the essential motion observed in the free form of rice nsLTP1, we performed multiple sequence alignments to probe the intrinsic motion encoded in the primary sequence. We found that the amino acid sequence of loop1 is highly conserved among plant nsLTP1s, thus revealing its functional importance during evolution. Furthermore, the sequence of loop1 is composed mainly of amino acids with short side chains. In this study, we show that MD simulations, together with essential dynamics analysis, can be used to determine structural and dynamic differences of rice nsLTP1 upon lipid binding. 2008 Wiley-Liss, Inc.

Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching.

PubMed

Harrison, Rane A; Lu, Jia; Carrasco, Martin; Hunter, John; Manandhar, Anuj; Gondi, Sudershan; Westover, Kenneth D; Engen, John R

2016-11-20

Structural dynamics of Ras proteins contributes to their activity in signal transduction cascades. Directly targeting Ras proteins with small molecules may rely on the movement of a conserved structural motif, switch II. To understand Ras signaling and advance Ras-targeting strategies, experimental methods to measure Ras dynamics are required. Here, we demonstrate the utility of hydrogen-deuterium exchange (HDX) mass spectrometry (MS) to measure Ras dynamics by studying representatives from two branches of the Ras superfamily, Ras and Rho. A comparison of differential deuterium exchange between active (GMPPNP-bound) and inactive (GDP-bound) proteins revealed differences between the families, with the most notable differences occurring in the phosphate-binding loop and switch II. The P-loop exchange signature correlated with switch II dynamics observed in molecular dynamics simulations focused on measuring main-chain movement. HDX provides a means of evaluating Ras protein dynamics, which may be useful for understanding the mechanisms of Ras signaling, including activated signaling of pathologic mutants, and for targeting strategies that rely on protein dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Closed loop performance of a brushless dc motor powered electromechanical actuator for flight control applications. [computerized simulation for Shuttle Orbiter applications

NASA Technical Reports Server (NTRS)

Demerdash, N. A.; Nehl, T. W.

1980-01-01

A comprehensive digital model for the analysis and possible optimization of the closed loop dynamic (instantaneous) performance of a power conditioner fed, brushless dc motor powered, electromechanical actuator system (EMA) is presented. This model was developed for the simulation of the dynamic performance of an actual prototype EMA built for NASA-JSC as a possible alternative to hydraulic actuators for consideration in Space Shuttle Orbiter applications. Excellent correlation was achieved between numerical model simulation and experimental test results obtained from the actual hardware. These results include: various current and voltage waveforms in the machine-power conditioner (MPC) unit, flap position as well as other control loop variables in response to step commands of change of flap position. These results with consequent conclusions are detailed in the paper.

Assessing Command and Control System Vulnerabilities in Underdeveloped, Degraded and Denied Operational Environments

DTIC Science & Technology

2013-06-01

simulation of complex systems (Sterman 2000, Meadows 2008): a) Causal Loop Diagrams. A Causal Loop Diagram ( CLD ) is used to represent the feedback...structure of the dynamic system. CLDs consist of variables in the system being connected by arrows to show their causal influences and relationships. It is...distribution of orders will be included in the model. 6.4.2 Causal Loop Diagrams The CLD , as seen in Figure 5, is derived from the WDA constructs for the

Ballet of Loops

NASA Image and Video Library

2018-06-11

Giant, bright coronal loops trace out the magnetic field lines above an active region from June 4-6, 2018. The wavelength of extreme ultraviolet light shown here is emitted by ionized iron travelling along the field lines, super-heated to approximately 1 million degrees K. Coronal loops were not seen in this level of detail until the Solar Dynamics Observatory was launched in 2010 and came online, giving solar scientists new data with which to study the Sun and its processes. https://photojournal.jpl.nasa.gov/catalog/PIA22508

Active load control during rolling maneuvers. [performed in the Langley Transonic Dynamics Tunnel

NASA Technical Reports Server (NTRS)

Woods-Vedeler, Jessica A.; Pototzky, Anthony S.; Hoadley, Sherwood T.

1994-01-01

A rolling maneuver load alleviation (RMLA) system has been demonstrated on the active flexible wing (AFW) wind tunnel model in the Langley Transonic Dynamics Tunnel (TDT). The objective was to develop a systematic approach for designing active control laws to alleviate wing loads during rolling maneuvers. Two RMLA control laws were developed that utilized outboard control-surface pairs (leading and trailing edge) to counteract the loads and that used inboard trailing-edge control-surface pairs to maintain roll performance. Rolling maneuver load tests were performed in the TDT at several dynamic pressures that included two below and one 11 percent above open-loop flutter dynamic pressure. The RMLA system was operated simultaneously with an active flutter suppression system above open-loop flutter dynamic pressure. At all dynamic pressures for which baseline results were obtained, torsion-moment loads were reduced for both RMLA control laws. Results for bending-moment load reductions were mixed; however, design equations developed in this study provided conservative estimates of load reduction in all cases.

Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.

PubMed

Chen, Jonathan L; VanEtten, Damian M; Fountain, Matthew A; Yildirim, Ilyas; Disney, Matthew D

2017-07-11

RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

Commensurability and transformations of adsorbed phases on a heterogeneous solid with periodic distribution of surface energy

NASA Astrophysics Data System (ADS)

Cortés, Joaquin; Valencia, Eliana

1997-07-01

Monte Carlo experiments are used to investigate the adsorption of argon on a heterogeneous solid with a periodic distribution of surface energy. A study is made of the relation between the adsorbate molecule's diameter and the distance between the sites of maximum surface energy on the critical temperature, the observed phase changes, and the commensurability of the surface phase structure determined in the simulation.

An analysis of potassium iodide (KI) prophylaxis for the general public in the event of a nuclear accident

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

Behling, H.; Behling, K.; Amarasooriya, H.

1995-02-01

A generic difficulty encountered in cost-benefit analyses is the quantification of major elements that define the costs and the benefits in commensurate units. In this study, the costs of making KI available for public use, and the avoidance of thyroidal health effects predicted to be realized from the availability of that KI (i.e., the benefits), are defined in the commensurate units of dollars.

Non-Fermi surface nesting driven commensurate magnetic ordering in Fe-doped S r 2 Ru O 4

DOE PAGES

Zhu, M.; Shanavas, K. V.; Wang, Y.; ...

2017-02-10

Sr 2RuO 4, an unconventional superconductor, is known to possess an incommensurate spin-density wave instability driven by Fermi surface nesting. Here we report a static spin-density wave ordering with a commensurate propagation vector q c = (0.250.250) in Fe-doped Sr 2RuO 4, despite the magnetic fluctuations persisting at the incommensurate wave vectors q ic = (0.30.3L) as in the parent compound. The latter feature is corroborated by the first-principles calculations, which show that Fe substitution barely changes the nesting vector of the Fermi surface. Finally, these results suggest that in addition to the known incommensurate magnetic instability, Sr 2RuO 4more » is also in proximity to a commensurate magnetic tendency that can be stabilized via Fe doping.« less

Dynamics of the GB3 loop regions from MD simulation: how much of it is real?

PubMed

Li, Tong; Jing, Qingqing; Yao, Lishan

2011-04-07

A total of 1.1 μs of molecular dynamics (MD) simulations were performed to study the structure and dynamics of protein GB3. The simulation motional amplitude of the loop regions is generally overestimated in comparison with the experimental backbone N-H order parameters S(2). Two-state behavior is observed for several residues in these regions, with the minor state population in the range of 3-13%. Further inspection suggests that the (φ, ψ) dihedral angles of the minor states deviate from the GB3 experimental values, implying the existence of nonnative states. After fitting the MD trajectories of these residues to the NMR RDCs, the minor state populations are significantly reduced by at least 80%, suggesting that MD simulations are strongly biased toward the minor states, thus overestimating the dynamics of the loop regions. The optimized trajectories produce intra, sequential H(N)-H(α) RDCs and intra (3)J(HNHα) that are not included in the trajectories fitting for these residues that are closer to the experimental data. Unlike GB3, 0.55 μs MD simulations of protein ubiquitin do not show distinctive minor states, and the derived NMR order parameters are better converged. Our findings indicate that the artifacts of the simulations depend on the specific system studied and that one should be cautious interpreting the enhanced dihedral dynamics from long MD simulations.

Cross Slip of Dislocation Loops in GaN Under Shear

DTIC Science & Technology

2014-03-01

methodology 2.1 Discrete dislocation dynamic ( DDD ) simula- tions In this work, we employ a modified version of the ParaDiS code [15, 16]. First a...plane. 4 Conclusions The cross slip mechanisms of different dislocation loops have been studied via DDD simulations using the type <a> active

Efficient dynamic modeling of manipulators containing closed kinematic loops

NASA Astrophysics Data System (ADS)

Ferretti, Gianni; Rocco, Paolo

An approach to efficiently solve the forward dynamics problem for manipulators containing closed chains is proposed. The two main distinctive features of this approach are: the dynamics of the equivalent open loop tree structures (any closed loop can be in general modeled by imposing some additional kinematic constraints to a suitable tree structure) is computed through an efficient Newton Euler formulation; the constraint equations relative to the most commonly adopted closed chains in industrial manipulators are explicitly solved, thus, overcoming the redundancy of Lagrange's multipliers method while avoiding the inefficiency due to a numerical solution of the implicit constraint equations. The constraint equations considered for an explicit solution are those imposed by articulated gear mechanisms and planar closed chains (pantograph type structures). Articulated gear mechanisms are actually used in all industrial robots to transmit motion from actuators to links, while planar closed chains are usefully employed to increase the stiffness of the manipulators and their load capacity, as well to reduce the kinematic coupling of joint axes. The accuracy and the efficiency of the proposed approach are shown through a simulation test.

Towards cosmological dynamics from loop quantum gravity

NASA Astrophysics Data System (ADS)

Li, Bao-Fei; Singh, Parampreet; Wang, Anzhong

2018-04-01

We present a systematic study of the cosmological dynamics resulting from an effective Hamiltonian, recently derived in loop quantum gravity using Thiemann's regularization and earlier obtained in loop quantum cosmology (LQC) by keeping the Lorentzian term explicit in the Hamiltonian constraint. We show that quantum geometric effects result in higher than quadratic corrections in energy density in comparison to LQC, causing a nonsingular bounce. Dynamics can be described by the Hamilton or Friedmann-Raychaudhuri equations, but the map between the two descriptions is not one to one. A careful analysis resolves the tension on symmetric versus asymmetric bounce in this model, showing that the bounce must be asymmetric and symmetric bounce is physically inconsistent, in contrast to the standard LQC. In addition, the current observations only allow a scenario where the prebounce branch is asymptotically de Sitter, similar to a quantization of the Schwarzschild interior in LQC, and the postbounce branch yields the classical general relativity. For a quadratic potential, we find that a slow-roll inflation generically happens after the bounce, which is quite similar to what happens in LQC.

Design and development of a novel viscoelastic ankle-foot prosthesis based on the human ankle biomechanics.

PubMed

Safaeepour, Zahra; Esteki, Ali; Tabatabai Ghomshe, Farhad; Mousavai, Mohammad E

2014-10-01

In the present study, a new approach was applied to design and develop a viscoelastic ankle-foot prosthesis. The aim was to replicate the intact ankle moment-angle loop in the normal walking speed. The moment-angle loop of intact ankle was divided into four parts, and the appropriate models including two viscoelastic units of spring-damper mechanism were considered to replicate the passive ankle dynamics. The developed prototype was then tested on a healthy subject with the amputee gait simulator. The result showed that prosthetic ankle moment-angle loop was similar to that of intact ankle with the distinct four periods. The findings suggest that the prototype successfully provided the human ankle passive dynamics. Therefore, the viscoelastic units could imitate the four periods of a normal gait. The novel viscoelastic foot prosthesis could provide natural ankle dynamics in a gait cycle. Applying simple but biomechanical approach is suggested in conception of new designs for prosthetic ankle-foot mechanisms. © The International Society for Prosthetics and Orthotics 2014.

Spatiotemporal dynamics in excitable homogeneous random networks composed of periodically self-sustained oscillation.

PubMed

Qian, Yu; Liu, Fei; Yang, Keli; Zhang, Ge; Yao, Chenggui; Ma, Jun

2017-09-19

The collective behaviors of networks are often dependent on the network connections and bifurcation parameters, also the local kinetics plays an important role in contributing the consensus of coupled oscillators. In this paper, we systematically investigate the influence of network structures and system parameters on the spatiotemporal dynamics in excitable homogeneous random networks (EHRNs) composed of periodically self-sustained oscillation (PSO). By using the dominant phase-advanced driving (DPAD) method, the one-dimensional (1D) Winfree loop is exposed as the oscillation source supporting the PSO, and the accurate wave propagation pathways from the oscillation source to the whole network are uncovered. Then, an order parameter is introduced to quantitatively study the influence of network structures and system parameters on the spatiotemporal dynamics of PSO in EHRNs. Distinct results induced by the network structures and the system parameters are observed. Importantly, the corresponding mechanisms are revealed. PSO influenced by the network structures are induced not only by the change of average path length (APL) of network, but also by the invasion of 1D Winfree loop from the outside linking nodes. Moreover, PSO influenced by the system parameters are determined by the excitation threshold and the minimum 1D Winfree loop. Finally, we confirmed that the excitation threshold and the minimum 1D Winfree loop determined PSO will degenerate as the system size is expanded.

Application of system dynamics for developing financially self-sustaining management policies for water and wastewater systems.

PubMed

Rehan, R; Knight, M A; Haas, C T; Unger, A J A

2011-10-15

Recently enacted regulations in Canada and elsewhere require water utilities to be financially self-sustaining over the long-term. This implies full cost recovery for providing water and wastewater services to users. This study proposes a new approach to help water utilities plan to meet the requirements of the new regulations. A causal loop diagram is developed for a financially self-sustaining water utility which frames water and wastewater network management as a complex system with multiple interconnections and feedback loops. The novel System Dynamics approach is used to develop a demonstration model for water and wastewater network management. This is the first known application of System Dynamics to water and wastewater network management. The network simulated is that of a typical Canadian water utility that has under invested in maintenance. Model results show that with no proactive rehabilitation strategy the utility will need to substantially increase its user fees to achieve financial sustainability. This increase is further exacerbated when price elasticity of water demand is considered. When the utility pursues proactive rehabilitation, financial sustainability is achieved with lower user fees. Having demonstrated the significance of feedback loops for financial management of water and wastewater networks, the paper makes the case for a more complete utility model that considers the complexity of the system by incorporating all feedback loops. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Double closed-loop control of integrated optical resonance gyroscope with mean-square exponential stability.

PubMed

Li, Hui; Liu, Liying; Lin, Zhili; Wang, Qiwei; Wang, Xiao; Feng, Lishuang

2018-01-22

A new double closed-loop control system with mean-square exponential stability is firstly proposed to optimize the detection accuracy and dynamic response characteristic of the integrated optical resonance gyroscope (IORG). The influence mechanism of optical nonlinear effects on system detection sensitivity is investigated to optimize the demodulation gain, the maximum sensitivity and the linear work region of a gyro system. Especially, we analyze the effect of optical parameter fluctuation on the parameter uncertainty of system, and investigate the influence principle of laser locking-frequency noise on the closed-loop detection accuracy of angular velocity. The stochastic disturbance model of double closed-loop IORG is established that takes the unfavorable factors such as optical effect nonlinearity, disturbed disturbance, optical parameter fluctuation and unavoidable system noise into consideration. A robust control algorithm is also designed to guarantee the mean-square exponential stability of system with a prescribed H ∞ performance in order to improve the detection accuracy and dynamic performance of IORG. The conducted experiment results demonstrate that the IORG has a dynamic response time less than 76us, a long-term bias stability 7.04°/h with an integration time of 10s over one-hour test, and the corresponding bias stability 1.841°/h based on Allan deviation, which validate the effectiveness and usefulness of the proposed detection scheme.

Feedback control laws for highly maneuverable aircraft

NASA Technical Reports Server (NTRS)

Garrard, William L.; Balas, Gary J.

1995-01-01

During this year, we concentrated our efforts on the design of controllers for lateral/directional control using mu synthesis. This proved to be a more difficult task than we anticipated and we are still working on the designs. In the lateral-directional control problem, the inputs are pilot lateral stick and pedal commands and the outputs are roll rate about the velocity vector and side slip angle. The control effectors are ailerons, rudder deflection, and directional thrust vectoring vane deflection which produces a yawing moment about the body axis. Our math model does not contain any provision for thrust vectoring of rolling moment. This has resulted in limitations of performance at high angles of attack. During 1994-95, the following tasks for the lateral-directional controllers were accomplished: (1) Designed both inner and outer loop dynamic inversion controllers. These controllers are implemented using accelerometer outputs rather than an a priori model of the vehicle aerodynamics; (2) Used classical techniques to design controllers for the system linearized by dynamics inversion. These controllers acted to control roll rate and Dutch roll response; (3) Implemented the inner loop dynamic inversion and classical controllers on the six DOF simulation; (4) Developed a lateral-directional control allocation scheme based on minimizing required control effort among the ailerons, rudder, and directional thrust vectoring; and (5) Developed mu outer loop controllers combined with classical inner loop controllers.

OSCILLATION OF NEWLY FORMED LOOPS AFTER MAGNETIC RECONNECTION IN THE SOLAR CHROMOSPHERE

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

Yang, Shuhong; Xiang, Yongyuan, E-mail: shuhongyang@nao.cas.cn

With the high spatial and temporal resolution Hα images from the New Vacuum Solar Telescope, we focus on two groups of loops with an X-shaped configuration in the dynamic chromosphere. We find that the anti-directed loops approach each other and reconnect continually. The connectivity of the loops is changed and new loops are formed and stack together. The stacked loops are sharply bent, implying that they are greatly impacted by the magnetic tension force. When another reconnection process takes place, one new loop is formed and stacks with the previously formed ones. Meanwhile, the stacked loops retract suddenly and movemore » toward the balance position, performing an overshoot movement, which led to an oscillation with an average period of about 45 s. The oscillation of newly formed loops after magnetic reconnection in the chromosphere is observed for the first time. We suggest that the stability of the stacked loops is destroyed due to the attachment of the last new loop and then suddenly retract under the effect of magnetic tension. Because of the retraction, another lower loop is pushed outward and performs an oscillation with a period of about 25 s. The different oscillation periods may be due to their difference in three parameters, i.e., loop length, plasma density, and magnetic field strength.« less

Dynamic coal mine model. [Generic feedback-loop model

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

Hamilton, M.S.

1978-01-01

This study examines the determinants of the productive life cycle of a single hypothetical coal mine. The article addresses the questions of how long the mine will operate, what its annual production will be, and what percentage of the resource base will be recovered. As greatly expanded production requires capital investment, the investment decision is singled out as the principal determinant of the mine's dynamic behavior. A simple dynamic feedback loop model was constructed, the performance of which is compared with actual data to see how well the model can reproduce known behavior. Exogenous variables, such as the price ofmore » coal, the wage rate, operating costs, and the tax structure, are then changed to see how these changes affect the mine's performance.« less

Cycle-averaged dynamics of a periodically driven, closed-loop circulation model

NASA Technical Reports Server (NTRS)

Heldt, T.; Chang, J. L.; Chen, J. J. S.; Verghese, G. C.; Mark, R. G.

2005-01-01

Time-varying elastance models have been used extensively in the past to simulate the pulsatile nature of cardiovascular waveforms. Frequently, however, one is interested in dynamics that occur over longer time scales, in which case a detailed simulation of each cardiac contraction becomes computationally burdensome. In this paper, we apply circuit-averaging techniques to a periodically driven, closed-loop, three-compartment recirculation model. The resultant cycle-averaged model is linear and time invariant, and greatly reduces the computational burden. It is also amenable to systematic order reduction methods that lead to further efficiencies. Despite its simplicity, the averaged model captures the dynamics relevant to the representation of a range of cardiovascular reflex mechanisms. c2004 Elsevier Ltd. All rights reserved.

Perception as a closed-loop convergence process.

PubMed

Ahissar, Ehud; Assa, Eldad

2016-05-09

Perception of external objects involves sensory acquisition via the relevant sensory organs. A widely-accepted assumption is that the sensory organ is the first station in a serial chain of processing circuits leading to an internal circuit in which a percept emerges. This open-loop scheme, in which the interaction between the sensory organ and the environment is not affected by its concurrent downstream neuronal processing, is strongly challenged by behavioral and anatomical data. We present here a hypothesis in which the perception of external objects is a closed-loop dynamical process encompassing loops that integrate the organism and its environment and converging towards organism-environment steady-states. We discuss the consistency of closed-loop perception (CLP) with empirical data and show that it can be synthesized in a robotic setup. Testable predictions are proposed for empirical distinction between open and closed loop schemes of perception.

Perception as a closed-loop convergence process

PubMed Central

Ahissar, Ehud; Assa, Eldad

2016-01-01

Perception of external objects involves sensory acquisition via the relevant sensory organs. A widely-accepted assumption is that the sensory organ is the first station in a serial chain of processing circuits leading to an internal circuit in which a percept emerges. This open-loop scheme, in which the interaction between the sensory organ and the environment is not affected by its concurrent downstream neuronal processing, is strongly challenged by behavioral and anatomical data. We present here a hypothesis in which the perception of external objects is a closed-loop dynamical process encompassing loops that integrate the organism and its environment and converging towards organism-environment steady-states. We discuss the consistency of closed-loop perception (CLP) with empirical data and show that it can be synthesized in a robotic setup. Testable predictions are proposed for empirical distinction between open and closed loop schemes of perception. DOI: http://dx.doi.org/10.7554/eLife.12830.001 PMID:27159238

Open-Loop HIRF Experiments Performed on a Fault Tolerant Flight Control Computer

NASA Technical Reports Server (NTRS)

Koppen, Daniel M.

1997-01-01

During the third quarter of 1996, the Closed-Loop Systems Laboratory was established at the NASA Langley Research Center (LaRC) to study the effects of High Intensity Radiated Fields on complex avionic systems and control system components. This new facility provided a link and expanded upon the existing capabilities of the High Intensity Radiated Fields Laboratory at LaRC that were constructed and certified during 1995-96. The scope of the Closed-Loop Systems Laboratory is to place highly integrated avionics instrumentation into a high intensity radiated field environment, interface the avionics to a real-time flight simulation that incorporates aircraft dynamics, engines, sensors, actuators and atmospheric turbulence, and collect, analyze, and model aircraft performance. This paper describes the layout and functionality of the Closed-Loop Systems Laboratory, and the open-loop calibration experiments that led up to the commencement of closed-loop real-time flight experiments.

Competition and quality in health care markets: a differential-game approach.

PubMed

Brekke, Kurt R; Cellini, Roberto; Siciliani, Luigi; Straume, Odd Rune

2010-07-01

We investigate the effect of competition on quality in health care markets with regulated prices taking a differential game approach, in which quality is a stock variable. Using a Hotelling framework, we derive the open-loop solution (health care providers set the optimal investment plan at the initial period) and the feedback closed-loop solution (providers move investments in response to the dynamics of the states). Under the closed-loop solution competition is more intense in the sense that providers observe quality in each period and base their investment on this information. If the marginal provision cost is constant, the open-loop and closed-loop solutions coincide, and the results are similar to the ones obtained by static models. If the marginal provision cost is increasing, investment and quality are lower in the closed-loop solution (when competition is more intense). In this case, static models tend to exaggerate the positive effect of competition on quality.

General relativistic dynamics of an extreme mass-ratio binary interacting with an external body

NASA Astrophysics Data System (ADS)

Yang, Huan; Casals, Marc

2017-10-01

We study the dynamics of a hierarchical three-body system in the general relativistic regime: an extreme mass-ratio inner binary under the tidal influence of an external body. The inner binary consists of a central Schwarzschild black hole and a test body moving around it. We discuss three types of tidal effects on the orbit of the test body. First, the angular momentum of the inner binary precesses around the angular momentum of the outer binary. Second, the tidal field drives a "transient resonance" when the radial and azimuthal frequencies are commensurable. In contrast with resonances driven by the gravitational self-force, this tidal-driven resonance may boost the orbital angular momentum and eccentricity (a relativistic version of the Kozai-Lidov effect). Finally, for an orbit-dynamical effect during the nonresonant phase, we calculate the correction to the innermost stable circular (mean) orbit due to the tidal interaction. Hierarchical three-body systems are potential sources for future space-based gravitational wave missions, and the tidal effects that we find could contribute significantly to their waveform.

Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop

PubMed Central

Meng, Yilin; Roux, Benoît

2013-01-01

Molecular dynamics umbrella sampling simulations are used to compare the relative stability of the active conformation of the catalytic domain of c-Src kinase while the tyrosine 416 in the activation loop (A-loop) is either unphosphorylated or phosphorylated. When the A-loop is unphosphorylated, there is considerable flexiblity of the kinase. While the active conformation of the kinase is not forbidden and can be visited transiently, it is not the predominant state. This is consistent with the view that c-Src displays some catalytic activity even when the A-loop is unphosphorylated. In contrast, phosphorylation of the A-loop contributes to stabilize several structural features that are critical for catalysis, such as the hydrophobic regulatory spine, the HRD motif, and the electrostatic switch. In summary, the free energy landscape calculations demonstrate that phosphorylation of tyrosine 416 in the A-loop essentially “locks” the kinase into its catalytically competent conformation. PMID:24103328

Molecular principles underlying dual RNA specificity in the Drosophila SNF protein.

PubMed

Weber, Gert; DeKoster, Gregory T; Holton, Nicole; Hall, Kathleen B; Wahl, Markus C

2018-06-07

The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the auxiliary U2A' protein. Here we investigate its functions by crystal structures of SNF alone and bound to U1 stem-loop II, U2A' or U2 stem-loop IV and U2A', SNF dynamics from NMR spectroscopy, and structure-guided mutagenesis in binding studies. We find that different loop-closing base pairs and a nucleotide exchange at the tips of the loops contribute to differential SNF affinity for the RNAs. U2A' immobilizes SNF and RNA residues to restore U2 stem-loop IV binding affinity, while U1 stem-loop II binding does not require such adjustments. Our findings show how U2A' can modulate RNA specificity of SNF without changing SNF conformation or relying on direct RNA contacts.

Nonequilibrium Chromosome Looping via Molecular Slip Links

NASA Astrophysics Data System (ADS)

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2017-09-01

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

PubMed Central

Huang, Xuhui; Wang, Dong; Weiss, Dahlia R.; Bushnell, David A.; Kornberg, Roger D.; Levitt, Michael

2010-01-01

A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis of RNA polymerase II (pol II) transcription elongation. Recently resolved X-ray structures showed that the trigger loop forms direct interactions with the β-phosphate and base of the matched nucleotide triphosphate (NTP) through residues His1085 and Leu1081, respectively. In order to understand the role of these two critical residues in stabilizing active site conformation in the dynamic complex, we performed all-atom molecular dynamics simulations of the wild-type pol II elongation complex and its mutants in explicit solvent. In the wild-type complex, we found that the trigger loop is stabilized in the “closed” conformation, and His1085 forms a stable interaction with the NTP. Simulations of point mutations of His1085 are shown to affect this interaction; simulations of alternative protonation states, which are inaccessible through experiment, indicate that only the protonated form is able to stabilize the His1085-NTP interaction. Another trigger loop residue, Leu1081, stabilizes the incoming nucleotide position through interaction with the nucleotide base. Our simulations of this Leu mutant suggest a three-component mechanism for correctly positioning the incoming NTP in which (i) hydrophobic contact through Leu1081, (ii) base stacking, and (iii) base pairing work together to minimize the motion of the incoming NTP base. These results complement experimental observations and provide insight into the role of the trigger loop on transcription fidelity. PMID:20798057

Dynamic parameter identification of robot arms with servo-controlled electrical motors

NASA Astrophysics Data System (ADS)

Jiang, Zhao-Hui; Senda, Hiroshi

2005-12-01

This paper addresses the issue of dynamic parameter identification of the robot manipulator with servo-controlled electrical motors. An assumption is made that all kinematical parameters, such as link lengths, are known, and only dynamic parameters containing mass, moment of inertia, and their functions need to be identified. First, we derive dynamics of the robot arm with a linear form of the unknown dynamic parameters by taking dynamic characteristics of the motor and servo unit into consideration. Then, we implement the parameter identification approach to identify the unknown parameters with respect to individual link separately. A pseudo-inverse matrix is used for formulation of the parameter identification. The optimal solution is guaranteed in a sense of least-squares of the mean errors. A Direct Drive (DD) SCARA type industrial robot arm AdeptOne is used as an application example of the parameter identification. Simulations and experiments for both open loop and close loop controls are carried out. Comparison of the results confirms the correctness and usefulness of the parameter identification and the derived dynamic model.

Dynamic stability and handling qualities tests on a highly augmented, statically unstable airplane

NASA Technical Reports Server (NTRS)

Gera, Joseph; Bosworth, John T.

1987-01-01

Novel flight test and analysis techniques in the flight dynamics and handling qualities area are described. These techniques were utilized at NASA Ames-Dryden during the initial flight envelope clearance of the X-29A aircraft. It is shown that the open-loop frequency response of an aircraft with highly relaxed static stability can be successfully computed on the ground from telemetry data. Postflight closed-loop frequency response data were obtained from pilot-generated frequency sweeps and it is found that the current handling quality requirements for high-maneuverability aircraft are generally applicable to the X-29A.

3D MHD Models of Active Region Loops

NASA Technical Reports Server (NTRS)

Ofman, Leon

2004-01-01

Present imaging and spectroscopic observations of active region loops allow to determine many physical parameters of the coronal loops, such as the density, temperature, velocity of flows in loops, and the magnetic field. However, due to projection effects many of these parameters remain ambiguous. Three dimensional imaging in EUV by the STEREO spacecraft will help to resolve the projection ambiguities, and the observations could be used to setup 3D MHD models of active region loops to study the dynamics and stability of active regions. Here the results of 3D MHD models of active region loops are presented, and the progress towards more realistic 3D MHD models of active regions. In particular the effects of impulsive events on the excitation of active region loop oscillations, and the generation, propagations and reflection of EIT waves are shown. It is shown how 3D MHD models together with 3D EUV observations can be used as a diagnostic tool for active region loop physical parameters, and to advance the science of the sources of solar coronal activity.

Predicting Flow Reversals in a Computational Fluid Dynamics Simulated Thermosyphon Using Data Assimilation.

PubMed

Reagan, Andrew J; Dubief, Yves; Dodds, Peter Sheridan; Danforth, Christopher M

2016-01-01

A thermal convection loop is a annular chamber filled with water, heated on the bottom half and cooled on the top half. With sufficiently large forcing of heat, the direction of fluid flow in the loop oscillates chaotically, dynamics analogous to the Earth's weather. As is the case for state-of-the-art weather models, we only observe the statistics over a small region of state space, making prediction difficult. To overcome this challenge, data assimilation (DA) methods, and specifically ensemble methods, use the computational model itself to estimate the uncertainty of the model to optimally combine these observations into an initial condition for predicting the future state. Here, we build and verify four distinct DA methods, and then, we perform a twin model experiment with the computational fluid dynamics simulation of the loop using the Ensemble Transform Kalman Filter (ETKF) to assimilate observations and predict flow reversals. We show that using adaptively shaped localized covariance outperforms static localized covariance with the ETKF, and allows for the use of less observations in predicting flow reversals. We also show that a Dynamic Mode Decomposition (DMD) of the temperature and velocity fields recovers the low dimensional system underlying reversals, finding specific modes which together are predictive of reversal direction.

Predicting Flow Reversals in a Computational Fluid Dynamics Simulated Thermosyphon Using Data Assimilation

PubMed Central

Reagan, Andrew J.; Dubief, Yves; Dodds, Peter Sheridan; Danforth, Christopher M.

2016-01-01

A thermal convection loop is a annular chamber filled with water, heated on the bottom half and cooled on the top half. With sufficiently large forcing of heat, the direction of fluid flow in the loop oscillates chaotically, dynamics analogous to the Earth’s weather. As is the case for state-of-the-art weather models, we only observe the statistics over a small region of state space, making prediction difficult. To overcome this challenge, data assimilation (DA) methods, and specifically ensemble methods, use the computational model itself to estimate the uncertainty of the model to optimally combine these observations into an initial condition for predicting the future state. Here, we build and verify four distinct DA methods, and then, we perform a twin model experiment with the computational fluid dynamics simulation of the loop using the Ensemble Transform Kalman Filter (ETKF) to assimilate observations and predict flow reversals. We show that using adaptively shaped localized covariance outperforms static localized covariance with the ETKF, and allows for the use of less observations in predicting flow reversals. We also show that a Dynamic Mode Decomposition (DMD) of the temperature and velocity fields recovers the low dimensional system underlying reversals, finding specific modes which together are predictive of reversal direction. PMID:26849061

Flow rate and temperature characteristics in steady state condition on FASSIP-01 loop during commissioning

NASA Astrophysics Data System (ADS)

Juarsa, M.; Giarno; Rohman, A. N.; Heru K., G. B.; Witoko, J. P.; Sony Tjahyani, D. T.

2018-02-01

The need for large-scale experimental facilities to investigate the phenomenon of natural circulation flow rate becomes a necessity in the development of nuclear reactor safety management. The FASSIP-01 loop has been built to determine the natural circulation flow rate performance in the large-scale media and aimed to reduce errors in the results for its application in the design of new generation reactors. The commissioning needs to be done to define the capability of the FASSIP-01 loop and to prescribe the experiment limitations. On this commissioning, two scenarios experimental method has been used. The first scenario is a static condition test which was conducted to verify measurement system response during 24 hours without electrical load in heater and cooler, there is water and no water inside the rectangular loop. Second scenario is a dynamics condition that aims to understand the flow rate, a dynamic test was conducted using heater power of 5627 watts and coolant flow rate in the HSS loop of 9.35 LPM. The result of this test shows that the temperature characterization on static test provide a recommendation, that the experiments should be done at night because has a better environmental temperature stability compared to afternoon, with stable temperature around 1°C - 3°C. While on the dynamic test, the water temperature difference between the inlet-outlets in the heater area is quite large, about 7 times the temperature difference in the cooler area. The magnitude of the natural circulation flow rate calculated is much larger at about 300 times compared to the measured flow rate with different flow rate profiles.

Closed-Loop System Identification Experience for Flight Control Law and Flying Qualities Evaluation of a High Performance Fighter Aircraft

NASA Technical Reports Server (NTRS)

Murphy, Patrick C.

1996-01-01

This paper highlights some of the results and issues associated with estimating models to evaluate control law design methods and design criteria for advanced high performance aircraft. Experimental fighter aircraft such as the NASA-High Alpha Research Vehicle (HARV) have the capability to maneuver at very high angles of attack where nonlinear aerodynamics often predominate. HARV is an experimental F/A-18, configured with thrust vectoring and conformal actuated nose strakes. Identifying closed-loop models for this type of aircraft can be made difficult by nonlinearities and high order characteristics of the system. In this paper, only lateral-directional axes are considered since the lateral-directional control law was specifically designed to produce classical airplane responses normally expected with low-order, rigid-body systems. Evaluation of the control design methodology was made using low-order equivalent systems determined from flight and simulation. This allowed comparison of the closed-loop rigid-body dynamics achieved in flight with that designed in simulation. In flight, the On Board Excitation System was used to apply optimal inputs to lateral stick and pedals at five angles at attack : 5, 20, 30, 45, and 60 degrees. Data analysis and closed-loop model identification were done using frequency domain maximum likelihood. The structure of identified models was a linear state-space model reflecting classical 4th-order airplane dynamics. Input time delays associated with the high-order controller and aircraft system were accounted for in data preprocessing. A comparison of flight estimated models with small perturbation linear design models highlighted nonlinearities in the system and indicated that the closed-loop rigid-body dynamics were sensitive to input amplitudes at 20 and 30 degrees angle of attack.

Closed-Loop System Identification Experience for Flight Control Law and Flying Qualities Evaluation of a High Performance Fighter Aircraft

NASA Technical Reports Server (NTRS)

Murphy, Patrick C.

1999-01-01

This paper highlights some of the results and issues associated with estimating models to evaluate control law design methods and design criteria for advanced high performance aircraft. Experimental fighter aircraft such as the NASA High Alpha Research Vehicle (HARV) have the capability to maneuver at very high angles of attack where nonlinear aerodynamics often predominate. HARV is an experimental F/A-18, configured with thrust vectoring and conformal actuated nose strakes. Identifying closed-loop models for this type of aircraft can be made difficult by nonlinearities and high-order characteristics of the system. In this paper only lateral-directional axes are considered since the lateral-directional control law was specifically designed to produce classical airplane responses normally expected with low-order, rigid-body systems. Evaluation of the control design methodology was made using low-order equivalent systems determined from flight and simulation. This allowed comparison of the closed-loop rigid-body dynamics achieved in flight with that designed in simulation. In flight, the On Board Excitation System was used to apply optimal inputs to lateral stick and pedals at five angles of attack: 5, 20, 30, 45, and 60 degrees. Data analysis and closed-loop model identification were done using frequency domain maximum likelihood. The structure of the identified models was a linear state-space model reflecting classical 4th-order airplane dynamics. Input time delays associated with the high-order controller and aircraft system were accounted for in data preprocessing. A comparison of flight estimated models with small perturbation linear design models highlighted nonlinearities in the system and indicated that the estimated closed-loop rigid-body dynamics were sensitive to input amplitudes at 20 and 30 degrees angle of attack.

Active vibration control using a modal-domain fiber optic sensor

NASA Technical Reports Server (NTRS)

Cox, David E.

1992-01-01

A closed-loop control experiment is described in which vibrations of a cantilevered beam are suppressed using measurements from a modal-domain fiber optic sensor. Modal-domain sensors are interference between the modes of a few-mode optical waveguide to detect strain. The fiber is bonded along the length of the beam and provides a measurement related to the strain distribution on the surface of the beam. A model for the fiber optic sensor is derived, and this model is integrated with the dynamic model of the beam. A piezoelectric actuator is also bonded to the beam and used to provide control forces. Control forces are obtained through dynamic compensation of the signal from the fiber optic sensor. The compensator is implemented with a real-time digital controller. Analytical models are verified by comparing simulations to experimental results for both open-loop and closed-loop configurations.

Solar Coronal Loop Dynamics Near the Null Point Above Active Region NOAA 2666

NASA Astrophysics Data System (ADS)

Filippov, B.

2018-06-01

We analyse observations of a saddle-like structure in the corona above the western limb of the Sun on 2017 July 18. The structure was clearly outlined by coronal loops with typical coronal temperature no more than 1 MK. The dynamics of loops showed convergence towards the centre of the saddle in the vertical direction and divergence in the horizontal direction. The event is a clear example of smooth coronal magnetic field reconnection. No heating manifestations in the reconnection region or magnetically connected areas were observed. Potential magnetic field calculations, which use as the boundary condition the SDO/HMI magnetogram taken on July 14, showed the presence of a null point at the height of 122 arcsec above the photosphere just at the centre of the saddle structure. The shape of field lines fits the fan-spine magnetic configuration above NOAA 2666.

A new RISE-based adaptive control of PKMs: design, stability analysis and experiments

NASA Astrophysics Data System (ADS)

Bennehar, M.; Chemori, A.; Bouri, M.; Jenni, L. F.; Pierrot, F.

2018-03-01

This paper deals with the development of a new adaptive control scheme for parallel kinematic manipulators (PKMs) based on Rrbust integral of the sign of the error (RISE) control theory. Original RISE control law is only based on state feedback and does not take advantage of the modelled dynamics of the manipulator. Consequently, the overall performance of the resulting closed-loop system may be poor compared to modern advanced model-based control strategies. We propose in this work to extend RISE by including the nonlinear dynamics of the PKM in the control loop to improve its overall performance. More precisely, we augment original RISE control scheme with a model-based adaptive control term to account for the inherent nonlinearities in the closed-loop system. To demonstrate the relevance of the proposed controller, real-time experiments are conducted on the Delta robot, a three-degree-of-freedom (3-DOF) PKM.

Decay-less kink oscillations in coronal loops

NASA Astrophysics Data System (ADS)

Anfinogentov, S.; Nisticò, G.; Nakariakov, V. M.

2013-12-01

Context. Kink oscillations of coronal loops in an off-limb active region are detected with the Imaging Assembly Array (AIA) instruments of the Solar Dynamics Observatory (SDO) at 171 Å. Aims: We aim to measure periods and amplitudes of kink oscillations of different loops and to determinate the evolution of the oscillation phase along the oscillating loop. Methods: Oscillating coronal loops were visually identified in the field of view of SDO/AIA and STEREO/EUVI-A: the loop length was derived by three-dimensional analysis. Several slits were taken along the loops to assemble time-distance maps. We identified oscillatory patterns and retrieved periods and amplitudes of the oscillations. We applied the cross-correlation technique to estimate the phase shift between oscillations at different segments of oscillating loops. Results: We found that all analysed loops show low-amplitude undamped transverse oscillations. Oscillation periods of loops in the same active region range from 2.5 to 11 min, and are different for different loops. The displacement amplitude is lower than 1 Mm. The oscillation phase is constant along each analysed loop. The spatial structure of the phase of the oscillations corresponds to the fundamental standing kink mode. We conclude that the observed behaviour is consistent with the empirical model in terms of a damped harmonic resonator affected by a non-resonant continuously operating external force. A movie is available in electronic form at http://www.aanda.org

Protein Loop Structure Prediction Using Conformational Space Annealing.

PubMed

Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

2017-05-22

We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

PubMed Central

Sloma, Michael F.; Mathews, David H.

2016-01-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

Mass and energy supply of a cool coronal loop near its apex

NASA Astrophysics Data System (ADS)

Yan, Limei; Peter, Hardi; He, Jiansen; Xia, Lidong; Wang, Linghua

2018-03-01

Context. Different models for the heating of solar corona assume or predict different locations of the energy input: concentrated at the footpoints, at the apex, or uniformly distributed. The brightening of a loop could be due to the increase in electron density ne, the temperature T, or a mixture of both. Aim. We investigate possible reasons for the brightening of a cool loop at transition region temperatures through imaging and spectral observation. Methods: We observed a loop with the Interface Region Imaging Spectrograph (IRIS) and used the slit-jaw images together with spectra taken at a fixed slit position to study the evolution of plasma properties in and below the loop. We used spectra of Si IV, which forms at around 80 000 K in equilibrium, to identify plasma motions and derive electron densities from the ratio of inter-combination lines of O IV. Additional observations from the Solar Dynamics Observatory (SDO) were employed to study the response at coronal temperatures (Atmospheric Imaging Assembly, AIA) and to investigate the surface magnetic field below the loop (Helioseismic and Magnetic Imager, HMI). Results: The loop first appears at transition region temperatures and later also at coronal temperatures, indicating a heating of the plasma in the loop. The appearance of hot plasma in the loop coincides with a possible accelerating upflow seen in Si IV, with the Doppler velocity shifting continuously from -70 km s-1 to -265 km s-1. The 3D magnetic field lines extrapolated from the HMI magnetogram indicate possible magnetic reconnection between small-scale magnetic flux tubes below or near the loop apex. At the same time, an additional intensity enhancement near the loop apex is visible in the IRIS slit-jaw images at 1400 Å. These observations suggest that the loop is probably heated by the interaction between the loop and the upflows, which are accelerated by the magnetic reconnection between small-scale magnetic flux tubes at lower altitudes. Before and after the possible heating phase, the intensity changes in the optically thin (Si IV) and optical thick line (C II) are mainly contributed by the density variation without significant heating. Conclusions: We therefore provide evidence for the heating of an envelope loop that is affected by accelerating upflows, which are probably launched by magnetic reconnection between small-scale magnetic flux tubes underneath the envelope loop. This study emphasizes that in the complex upper atmosphere of the Sun, the dynamics of the 3D coupled magnetic field and flow field plays a key role in thermalizing 1D structures such as coronal loops. An animation associated to Fig. 1 is available at http://https://www.aanda.org

Alterations in aerobic energy expenditure and neuromuscular function during a simulated cross-country skiathlon with the skating technique.

PubMed

Fabre, Nicolas; Mourot, Laurent; Zoppirolli, Chiara; Andersson, Erik; Willis, Sarah J; Holmberg, Hans-Christer

2015-04-01

Here, we tested the hypothesis that aerobic energy expenditure (AEE) is higher during a simulated 6-km (2 loops of 3-km each) "skiathlon" than during skating only on a treadmill and attempted to link any such increase to biomechanical and neuromuscular responses. Six elite male cross-country skiers performed two pre-testing time-trials (TT) to determine their best performances and to choose an appropriate submaximal speed for collection of physiological, biomechanical and neuromuscular data during two experimental sessions (exp). Each skier used, in randomized order, either the classical (CL) or skating technique (SK) for the first 3-km loop, followed by transition to the skating technique for the second 3-km loop. Respiratory parameters were recorded continuously. The EMG activity of the triceps brachii (TBr) and vastus lateralis (VLa) muscles during isometric contractions performed when the skiers were stationary (i.e., just before the first loop, during the transition, and after the second loop); their corresponding activity during dynamic contractions; and pole and plantar forces during the second loop were recorded. During the second 3-km of the TT, skating speed was significantly higher for the SK-SK than CL-SK. During this second loop, AEE was also higher (+1.5%) for CL-SKexp than SK-SKexp, in association with higher VLa EMG activity during both isometric and dynamic contractions, despite no differences in plantar or pole forces, poling times or cycle rates. Although the underlying mechanism remains unclear, during a skiathlon, the transition between the sections of classical skiing and skating alters skating performance (i.e., skiing speed), AEE and neuromuscular function. Copyright © 2015 Elsevier B.V. All rights reserved.

Simulations of Solar Jets Confined by Coronal Loops

NASA Technical Reports Server (NTRS)

Wyper, P. F.; De Vore, C. R.

2016-01-01

Coronal jets are collimated, dynamic events that occur over a broad range of spatial scales in the solar corona. In the open magnetic field of coronal holes, jets form quasi-radial spires that can extend far out into the heliosphere, while in closed-field regions the jet outflows are confined to the corona. We explore the application of the embedded-bipole model to jets occurring in closed coronal loops. In this model, magnetic free energy is injected slowly by footpoint motions that introduce twist within the closed dome of the jet source region, and is released rapidly by the onset of an ideal kink-like instability. Two length scales characterize the system: the width (N) of the jet source region and the footpoint separation (L) of the coronal loop that envelops the jet source. We find that both the conditions for initiation and the subsequent dynamics are highly sensitive to the ratio L/N. The longest-lasting and most energetic jets occur along long coronal loops with large L/N ratios, and share many of the features of open-field jets, while smaller L/N ratios produce shorter-duration, less energetic jets that are affected by reflections from the far-loop footpoint. We quantify the transition between these behaviors and show that our model replicates key qualitative and quantitative aspects of both quiet Sun and active-region loop jets. We also find that there connection between the closed dome and surrounding coronal loop is very extensive: the cumulative reconnected flux at least matches the total flux beneath the dome for small L/N, and is more than double that value for large L/N.

SIMULATIONS OF SOLAR JETS CONFINED BY CORONAL LOOPS

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

Wyper, P. F.; DeVore, C. R., E-mail: peter.f.wyper@nasa.gov, E-mail: c.richard.devore@nasa.gov

Coronal jets are collimated, dynamic events that occur over a broad range of spatial scales in the solar corona. In the open magnetic field of coronal holes, jets form quasi-radial spires that can extend far out into the heliosphere, while in closed-field regions the jet outflows are confined to the corona. We explore the application of the embedded-bipole model to jets occurring in closed coronal loops. In this model, magnetic free energy is injected slowly by footpoint motions that introduce twist within the closed dome of the jet source region, and is released rapidly by the onset of an idealmore » kink-like instability. Two length scales characterize the system: the width (N) of the jet source region and the footpoint separation (L) of the coronal loop that envelops the jet source. We find that both the conditions for initiation and the subsequent dynamics are highly sensitive to the ratio L/N. The longest-lasting and most energetic jets occur along long coronal loops with large L/N ratios, and share many of the features of open-field jets, while smaller L/N ratios produce shorter-duration, less energetic jets that are affected by reflections from the far-loop footpoint. We quantify the transition between these behaviors and show that our model replicates key qualitative and quantitative aspects of both quiet Sun and active-region loop jets. We also find that the reconnection between the closed dome and surrounding coronal loop is very extensive: the cumulative reconnected flux at least matches the total flux beneath the dome for small L/N, and is more than double that value for large L/N.« less

Slipping magnetic reconnection during an X-class solar flare observed by SDO/AIA

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

Dudík, J.; Del Zanna, G.; Mason, H. E.

2014-04-01

We present SDO/AIA observations of an eruptive X-class flare of 2012 July 12, and compare its evolution with the predictions of a three-dimensional (3D) numerical simulation. We focus on the dynamics of flare loops that are seen to undergo slipping reconnection during the flare. In the Atmospheric Imaging Assembly (AIA) 131 Å observations, lower parts of 10 MK flare loops exhibit an apparent motion with velocities of several tens of km s{sup –1} along the developing flare ribbons. In the early stages of the flare, flare ribbons consist of compact, localized bright transition-region emission from the footpoints of the flaremore » loops. A differential emission measure analysis shows that the flare loops have temperatures up to the formation of Fe XXIV. A series of very long, S-shaped loops erupt, leading to a coronal mass ejection observed by STEREO. The observed dynamics are compared with the evolution of magnetic structures in the 'standard solar flare model in 3D.' This model matches the observations well, reproducing the apparently slipping flare loops, S-shaped erupting loops, and the evolution of flare ribbons. All of these processes are explained via 3D reconnection mechanisms resulting from the expansion of a torus-unstable flux rope. The AIA observations and the numerical model are complemented by radio observations showing a noise storm in the metric range. Dm-drifting pulsation structures occurring during the eruption indicate plasmoid ejection and enhancement of the reconnection rate. The bursty nature of radio emission shows that the slipping reconnection is still intermittent, although it is observed to persist for more than an hour.« less

Understanding the molecular mechanism of the broad and potent neutralization of HIV-1 by antibody VRC01 from the perspective of molecular dynamics simulation and binding free energy calculations.

PubMed

Zhang, Yan; Pan, Dabo; Shen, Yulin; Jin, Nengzhi; Liu, Huanxiang; Yao, Xiaojun

2012-09-01

VRC01 is one of the most broadly and potently neutralizing HIV-1 antibodies known-it has been shown to neutralize 91 % of the tested primary isolate Env pseudoviruses by recognizing the viral envelope glycoprotein gp120. To explore the mechanism of HIV-1 neutralization by VRC01 and thus obtain valuable information for vaccine design, we performed molecular dynamics simulations and binding free energy calculations for apo-VRC01, apo-gp120, and the gp120-VRC01 complex. For gp120, residue energy decomposition analysis showed that the hotspot residues Asn280, Lys282, Asp368, Ile371, and Asp457 are located in three primary loops, including the CD4-binding loop, loop D, and loop V5. For VRC01, the hotspot residues Trp47, Trp50, Asn58, Arg61, Gln64, Trp100, and Tyr91 mainly come from CDR2 of the heavy chain. By decomposing the binding free energy into different components, intermolecular van der Waals interactions and nonpolar solvation were found to dominate the binding process. Principal component analysis of loops D and V5, which are related to neutralization resistance, indicated that these two areas have a larger conformational space in apo-gp120 compared to bound gp120. A comparison of three representative structures from the cluster analysis of loops D and V5 indicated that changes primarily occur at the tip of loop V5, and are caused by fluctuations in the terminal Glu1 residue of the antibody. This information can be used to guide the design of vaccines and small molecule inhibitors.

Scalable boson sampling with time-bin encoding using a loop-based architecture.

PubMed

Motes, Keith R; Gilchrist, Alexei; Dowling, Jonathan P; Rohde, Peter P

2014-09-19

We present an architecture for arbitrarily scalable boson sampling using two nested fiber loops. The architecture has fixed experimental complexity, irrespective of the size of the desired interferometer, whose scale is limited only by fiber and switch loss rates. The architecture employs time-bin encoding, whereby the incident photons form a pulse train, which enters the loops. Dynamically controlled loop coupling ratios allow the construction of the arbitrary linear optics interferometers required for boson sampling. The architecture employs only a single point of interference and may thus be easier to stabilize than other approaches. The scheme has polynomial complexity and could be realized using demonstrated present-day technologies.

Structural Effect of the Asp345a Insertion in Penicillin-Binding Protein 2 from Penicillin-Resistant Strains of Neisseria gonorrhoeae

PubMed Central

2015-01-01

A hallmark of penicillin-binding protein 2 (PBP2) from penicillin-resistant strains of Neisseria gonorrhoeae is insertion of an aspartate after position 345. The insertion resides on a loop near the active site and is immediately adjacent to an existing aspartate (Asp346) that forms a functionally important hydrogen bond with Ser363 of the SxN conserved motif. Insertion of other amino acids, including Glu and Asn, can also lower the rate of acylation by penicillin, but these insertions abolish transpeptidase function. Although the kinetic consequences of the Asp insertion are well-established, how it impacts the structure of PBP2 is unknown. Here, we report the 2.2 Å resolution crystal structure of a truncated construct of PBP2 containing all five mutations present in PBP2 from the penicillin-resistant strain 6140, including the Asp insertion. Commensurate with the strict specificity for the Asp insertion over similar amino acids, the insertion does not cause disordering of the structure, but rather induces localized flexibility in the β2c−β2d loop. The crystal structure resolves the ambiguity of whether the insertion is Asp345a or Asp346a (due to the adjacent Asp) because the hydrogen bond between Asp346 and Ser362 is preserved and the insertion is therefore Asp346a. The side chain of Asp346a projects directly toward the β-lactam-binding site near Asn364 of the SxN motif. The Asp insertion may lower the rate of acylation by sterically impeding binding of the antibiotic or by hindering breakage of the β-lactam ring during acylation because of the negative charge of its side chain. PMID:25403720

Structural effect of the Asp345a insertion in penicillin-binding protein 2 from penicillin-resistant strains of Neisseria gonorrhoeae.

PubMed

Fedarovich, Alena; Cook, Edward; Tomberg, Joshua; Nicholas, Robert A; Davies, Christopher

2014-12-09

A hallmark of penicillin-binding protein 2 (PBP2) from penicillin-resistant strains of Neisseria gonorrhoeae is insertion of an aspartate after position 345. The insertion resides on a loop near the active site and is immediately adjacent to an existing aspartate (Asp346) that forms a functionally important hydrogen bond with Ser363 of the SxN conserved motif. Insertion of other amino acids, including Glu and Asn, can also lower the rate of acylation by penicillin, but these insertions abolish transpeptidase function. Although the kinetic consequences of the Asp insertion are well-established, how it impacts the structure of PBP2 is unknown. Here, we report the 2.2 Å resolution crystal structure of a truncated construct of PBP2 containing all five mutations present in PBP2 from the penicillin-resistant strain 6140, including the Asp insertion. Commensurate with the strict specificity for the Asp insertion over similar amino acids, the insertion does not cause disordering of the structure, but rather induces localized flexibility in the β2c-β2d loop. The crystal structure resolves the ambiguity of whether the insertion is Asp345a or Asp346a (due to the adjacent Asp) because the hydrogen bond between Asp346 and Ser362 is preserved and the insertion is therefore Asp346a. The side chain of Asp346a projects directly toward the β-lactam-binding site near Asn364 of the SxN motif. The Asp insertion may lower the rate of acylation by sterically impeding binding of the antibiotic or by hindering breakage of the β-lactam ring during acylation because of the negative charge of its side chain.

NON-POTENTIAL FIELDS IN THE QUIET SUN NETWORK: EXTREME-ULTRAVIOLET AND MAGNETIC FOOTPOINT OBSERVATIONS

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

Chesny, D. L.; Oluseyi, H. M.; Orange, N. B.

The quiet Sun (QS) magnetic network is known to contain dynamics which are indicative of non-potential fields. Non-potential magnetic fields forming ''S-shaped'' loop arcades can lead to the breakdown of static activity and have only been observed in high temperature X-ray coronal structures—some of which show eruptive behavior. Thus, analysis of this type of atmospheric structuring has been restricted to large-scale coronal fields. Here we provide the first identification of non-potential loop arcades exclusive to the QS supergranulation network. High-resolution Atmospheric Imaging Assembly data from the Solar Dynamics Observatory have allowed for the first observations of fine-scale ''S-shaped'' loop arcadesmore » spanning the network. We have investigated the magnetic footpoint flux evolution of these arcades from Heliospheric and Magnetic Imager data and find evidence of evolving footpoint flux imbalances accompanying the formation of these non-potential fields. The existence of such non-potentiality confirms that magnetic field dynamics leading to the build up of helicity exist at small scales. QS non-potentiality also suggests a self-similar formation process between the QS network and high temperature corona and the existence of self-organized criticality (SOC) in the form of loop-pair reconnection and helicity dissipation. We argue that this type of behavior could lead to eruptive forms of SOC as seen in active region (AR) and X-ray sigmoids if sufficient free magnetic energy is available. QS magnetic network dynamics may be considered as a coronal proxy at supergranular scales, and events confined to the network can even mimic those in coronal ARs.« less

Accumulation of dislocation loops in the α phase of Zr Excel alloy under heavy ion irradiation

NASA Astrophysics Data System (ADS)

Yu, Hongbing; Yao, Zhongwen; Idrees, Yasir; Zhang, He K.; Kirk, Mark A.; Daymond, Mark R.

2017-08-01

In-situ heavy ion irradiations were performed on the high Sn content Zr alloy 'Excel', measuring type dislocation loop accumulation up to irradiation damage doses of 10 dpa at a range of temperatures. The high content of Sn, which diffuses slowly, and the thin foil geometry of the sample provide a unique opportunity to study an extreme case where displacement cascades dominate the loop formation and evolution. The dynamic observation of dislocation loop evolution under irradiation at 200 °C reveals that type dislocation loops can form at very low dose (0.0025 dpa). The size of the dislocation loops increases slightly with irradiation damage dose. The mechanism controlling loop growth in this study is different from that in neutron irradiation; in this study, larger dislocation loops can condense directly from the interaction of displacement cascades and the high concentration of point defects in the matrix. The size of the dislocation loop is dependent on the point defect concentration in the matrix. A negative correlation between the irradiation temperature and the dislocation loop size was observed. A comparison between cascade dominated loop evolution (this study), diffusion dominated loop evolution (electron irradiation) and neutron irradiation suggests that heavy ion irradiation alone may not be enough to accurately reproduce neutron irradiation induced loop structures. An alternative method is proposed in this paper. The effects of Sn on the displacement cascades, defect yield, and the diffusion behavior of point defects are established.

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

PubMed

Salmon, Loïc; Giambaşu, George M; Nikolova, Evgenia N; Petzold, Katja; Bhattacharya, Akash; Case, David A; Al-Hashimi, Hashim M

2015-10-14

Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.

Neurodynamics in the Sensorimotor Loop: Representing Behavior Relevant External Situations

PubMed Central

Pasemann, Frank

2017-01-01

In the context of the dynamical system approach to cognition and supposing that brains or brain-like systems controlling the behavior of autonomous systems are permanently driven by their sensor signals, the paper approaches the question of neurodynamics in the sensorimotor loop in a purely formal way. This is carefully done by addressing the problem in three steps, using the time-discrete dynamics of standard neural networks and a fiber space representation for better clearness. Furthermore, concepts like meta-transients, parametric stability and dynamical forms are introduced, where meta-transients describe the effect of realistic sensor inputs, parametric stability refers to a class of sensor inputs all generating the “same type” of dynamic behavior, and a dynamical form comprises the corresponding class of parametrized dynamical systems. It is argued that dynamical forms are the essential internal representatives of behavior relevant external situations. Consequently, it is suggested that dynamical forms are the basis for a memory of these situations. Finally, based on the observation that not all brain process have a direct effect on the motor activity, a natural splitting of neurodynamics into vertical (internal) and horizontal (effective) parts is introduced. PMID:28217092

The ground state of the Frenkel-Kontorova model

NASA Astrophysics Data System (ADS)

Babushkin, A. Yu.; Abkaryan, A. K.; Dobronets, B. S.; Krasikov, V. S.; Filonov, A. N.

2016-09-01

The continual approximation of the ground state of the discrete Frenkel-Kontorova model is tested using a symmetric algorithm of numerical simulation. A "kaleidoscope effect" is found, which means that the curves representing the dependences of the relative extension of an N-atom chain vary periodically with increasing N. Stairs of structural transitions for N ≫ 1 are analyzed by the channel selection method with the approximation N = ∞. Images of commensurable and incommensurable structures are constructed. The commensurable-incommensurable phase transitions are stepwise.

A unified perspective on robot control - The energy Lyapunov function approach

NASA Technical Reports Server (NTRS)

Wen, John T.

1990-01-01

A unified framework for the stability analysis of robot tracking control is presented. By using an energy-motivated Lyapunov function candidate, the closed-loop stability is shown for a large family of control laws sharing a common structure of proportional and derivative feedback and a model-based feedforward. The feedforward can be zero, partial or complete linearized dynamics, partial or complete nonlinear dynamics, or linearized or nonlinear dynamics with parameter adaptation. As result, the dichotomous approaches to the robot control problem based on the open-loop linearization and nonlinear Lyapunov analysis are both included in this treatment. Furthermore, quantitative estimates of the trade-offs between different schemes in terms of the tracking performance, steady state error, domain of convergence, realtime computation load and required a prior model information are derived.

The TRAPPIST-1 system: orbital evolution, tidal dissipation, formation and habitability

NASA Astrophysics Data System (ADS)

Papaloizou, J. C. B.; Szuszkiewicz, Ewa; Terquem, Caroline

2018-06-01

We study the dynamical evolution of the TRAPPIST-1 system under the influence of orbital circularization through tidal interaction with the central star. We find that systems with parameters close to the observed one evolve into a state where consecutive planets are linked by first-order resonances and consecutive triples, apart from planets c, d and e, by connected three-body Laplace resonances. The system expands with period ratios increasing and mean eccentricities decreasing with time. This evolution is largely driven by tides acting on the innermost planets, which then influence the outer ones. In order that deviations from commensurability become significant only on Gyr time-scales or longer, we require that the tidal parameter associated with the planets has to be such that Q΄ > ˜102 - 3. At the same time, if we start with two subsystems, with the inner three planets comprising the inner one, Q΄ associated with the planets has to be on the order (and not significantly exceeding) 102 - 3 for the two subsystems to interact and end up in the observed configuration. This scenario is also supported by modelling of the evolution through disc migration which indicates that the whole system cannot have migrated inwards together. Also, in order to avoid large departures from commensurabilities, the system cannot have stalled at a disc inner edge for significant time periods. We discuss the habitability consequences of the tidal dissipation implied by our modelling, concluding that planets d, e and f are potentially in habitable zones.

Fulde-Ferrell-Larkin-Ovchinnikov superconductivity in the layered organic superconductor β "-(BEDT-TTF ) 4[(H3O ) Ga (C2O4)3] C6H5NO2

NASA Astrophysics Data System (ADS)

Uji, S.; Iida, Y.; Sugiura, S.; Isono, T.; Sugii, K.; Kikugawa, N.; Terashima, T.; Yasuzuka, S.; Akutsu, H.; Nakazawa, Y.; Graf, D.; Day, P.

2018-04-01

Resistance and magnetic torque measurements are reported in a layered organic superconductor, β "-(BEDT-TTF ) 4[(H3O ) Ga (C2O4)3] C6H5NO2 with Tc=4.8 K, where BEDT-TTF stands for bis(ethylenedithio)tetrathiafulvalene. Because of the large anion between the BEDT-TTF conducting layers, the superconductivity of this salt is highly anisotropic. In magnetic fields parallel to the conducting layers for T =0.4 K, the magnetic torque shows a large diamagnetic signal associated with hysteresis up to ˜21 T, suggesting the upper critical field Hc 2≳21 T at 0.4 K. The large reduction of the diamagnetic signal is observed above 16 T, which shows a Fulde and Ferrell and Larkin and Ovchinnikov (FFLO) phase transition. For T =0.5 K, the interlayer resistance has nonzero value in a wide field region up to Hc 2, arising from the Josephson vortex dynamics. Successive dips in the second derivative curves of the resistance are observed between 16 T and Hc 2, which are ascribed to the commensurability effect between the Josephson vortex lattice and the order parameter oscillation of the FFLO phase. The commensurability effect is observed only in nearly parallel fields, showing that the FFLO phase is stable in a very limited field angle region. The temperature-field phase diagram is determined.

MASM: a market architecture for sensor management in distributed sensor networks

NASA Astrophysics Data System (ADS)

Viswanath, Avasarala; Mullen, Tracy; Hall, David; Garga, Amulya

2005-03-01

Rapid developments in sensor technology and its applications have energized research efforts towards devising a firm theoretical foundation for sensor management. Ubiquitous sensing, wide bandwidth communications and distributed processing provide both opportunities and challenges for sensor and process control and optimization. Traditional optimization techniques do not have the ability to simultaneously consider the wildly non-commensurate measures involved in sensor management in a single optimization routine. Market-oriented programming provides a valuable and principled paradigm to designing systems to solve this dynamic and distributed resource allocation problem. We have modeled the sensor management scenario as a competitive market, wherein the sensor manager holds a combinatorial auction to sell the various items produced by the sensors and the communication channels. However, standard auction mechanisms have been found not to be directly applicable to the sensor management domain. For this purpose, we have developed a specialized market architecture MASM (Market architecture for Sensor Management). In MASM, the mission manager is responsible for deciding task allocations to the consumers and their corresponding budgets and the sensor manager is responsible for resource allocation to the various consumers. In addition to having a modified combinatorial winner determination algorithm, MASM has specialized sensor network modules that address commensurability issues between consumers and producers in the sensor network domain. A preliminary multi-sensor, multi-target simulation environment has been implemented to test the performance of the proposed system. MASM outperformed the information theoretic sensor manager in meeting the mission objectives in the simulation experiments.

Robust Synchronization Schemes for Dynamic Channel Environments

NASA Technical Reports Server (NTRS)

Xiong, Fugin

2003-01-01

Professor Xiong will investigate robust synchronization schemes for dynamic channel environment. A sliding window will be investigated for symbol timing synchronizer and an open loop carrier estimator for carrier synchronization. Matlab/Simulink will be used for modeling and simulations.

Application of the Tool for Turbine Engine Closed-Loop Transient Analysis (TTECTrA) for Dynamic Systems Analysis

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Zinnecker, Alicia M.

2014-01-01

The aircraft engine design process seeks to achieve the best overall system-level performance, weight, and cost for a given engine design. This is achieved by a complex process known as systems analysis, where steady-state simulations are used to identify trade-offs that should be balanced to optimize the system. The steady-state simulations and data on which systems analysis relies may not adequately capture the true performance trade-offs that exist during transient operation. Dynamic Systems Analysis provides the capability for assessing these trade-offs at an earlier stage of the engine design process. The concept of dynamic systems analysis and the type of information available from this analysis are presented in this paper. To provide this capability, the Tool for Turbine Engine Closed-loop Transient Analysis (TTECTrA) was developed. This tool aids a user in the design of a power management controller to regulate thrust, and a transient limiter to protect the engine model from surge at a single flight condition (defined by an altitude and Mach number). Results from simulation of the closed-loop system may be used to estimate the dynamic performance of the model. This enables evaluation of the trade-off between performance and operability, or safety, in the engine, which could not be done with steady-state data alone. A design study is presented to compare the dynamic performance of two different engine models integrated with the TTECTrA software.

Dynamical Consequences of Bandpass Feedback Loops in a Bacterial Phosphorelay

PubMed Central

Sen, Shaunak; Garcia-Ojalvo, Jordi; Elowitz, Michael B.

2011-01-01

Under conditions of nutrient limitation, Bacillus subtilis cells terminally differentiate into a dormant spore state. Progression to sporulation is controlled by a genetic circuit consisting of a phosphorelay embedded in multiple transcriptional feedback loops, which is used to activate the master regulator Spo0A by phosphorylation. These transcriptional regulatory interactions are “bandpass”-like, in the sense that activation occurs within a limited band of Spo0A∼P concentrations. Additionally, recent results show that the phosphorelay activation occurs in pulses, in a cell-cycle dependent fashion. However, the impact of these pulsed bandpass interactions on the circuit dynamics preceding sporulation remains unclear. In order to address this question, we measured key features of the bandpass interactions at the single-cell level and analyzed them in the context of a simple mathematical model. The model predicted the emergence of a delayed phase shift between the pulsing activity of the different sporulation genes, as well as the existence of a stable state, with elevated Spo0A activity but no sporulation, embedded within the dynamical structure of the system. To test the model, we used time-lapse fluorescence microscopy to measure dynamics of single cells initiating sporulation. We observed the delayed phase shift emerging during the progression to sporulation, while a re-engineering of the sporulation circuit revealed behavior resembling the predicted additional state. These results show that periodically-driven bandpass feedback loops can give rise to complex dynamics in the progression towards sporulation. PMID:21980382

Stability Assessment and Tuning of an Adaptively Augmented Classical Controller for Launch Vehicle Flight Control

NASA Technical Reports Server (NTRS)

VanZwieten, Tannen; Zhu, J. Jim; Adami, Tony; Berry, Kyle; Grammar, Alex; Orr, Jeb S.; Best, Eric A.

2014-01-01

Recently, a robust and practical adaptive control scheme for launch vehicles [ [1] has been introduced. It augments a classical controller with a real-time loop-gain adaptation, and it is therefore called Adaptive Augmentation Control (AAC). The loop-gain will be increased from the nominal design when the tracking error between the (filtered) output and the (filtered) command trajectory is large; whereas it will be decreased when excitation of flex or sloshing modes are detected. There is a need to determine the range and rate of the loop-gain adaptation in order to retain (exponential) stability, which is critical in vehicle operation, and to develop some theoretically based heuristic tuning methods for the adaptive law gain parameters. The classical launch vehicle flight controller design technics are based on gain-scheduling, whereby the launch vehicle dynamics model is linearized at selected operating points along the nominal tracking command trajectory, and Linear Time-Invariant (LTI) controller design techniques are employed to ensure asymptotic stability of the tracking error dynamics, typically by meeting some prescribed Gain Margin (GM) and Phase Margin (PM) specifications. The controller gains at the design points are then scheduled, tuned and sometimes interpolated to achieve good performance and stability robustness under external disturbances (e.g. winds) and structural perturbations (e.g. vehicle modeling errors). While the GM does give a bound for loop-gain variation without losing stability, it is for constant dispersions of the loop-gain because the GM is based on frequency-domain analysis, which is applicable only for LTI systems. The real-time adaptive loop-gain variation of the AAC effectively renders the closed-loop system a time-varying system, for which it is well-known that the LTI system stability criterion is neither necessary nor sufficient when applying to a Linear Time-Varying (LTV) system in a frozen-time fashion. Therefore, a generalized stability metric for time-varying loop=gain perturbations is needed for the AAC.

Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.

PubMed

Spasic, Aleksandar; Kennedy, Scott D; Needham, Laura; Manoharan, Muthiah; Kierzek, Ryszard; Turner, Douglas H; Mathews, David H

2018-05-01

The RNA "GAGU" duplex, (5'GAC GAGU GUCA) 2 , contains the internal loop (5'-GAGU-3') 2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans -Watson-Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2'- endo conformation. This differs markedly from the internal loops, (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-UAGG-3') 2 , which all have cis -Watson-Crick/Watson-Crick AG "imino" pairs flanked by cis -Watson-Crick/Watson-Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-U AG G-3') 2 internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5'-UAGG-3') 2 , equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5'-GAGU-3') 2 loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5'-GAGU-3') 2 internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed. © 2018 Spasic et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Tunable Fermi Contour Anisotropy in GaAs Electron and Hole Systems

NASA Astrophysics Data System (ADS)

Kamburov, Dobromir G.

This Thesis explores the ballistic transport of quasi two-dimensional (2D) electron and hole systems confined to GaAs quantum wells and subjected to a periodic, strain-induced density modulation. In the presence of an applied perpendicular magnetic field, whenever the diameter of the charged carriers' cyclotron orbit becomes commensurate with the period of the density modulation, the sample's resistance exhibits commensurability features. We use the commensurability effects to directly probe the size of the cyclotron orbit, the Fermi contour, and the spin-polarization of particles at low magnetic field and of composite fermions near even-denominator Landau level filling factors (nu). We establish how the commensurability signatures depend on the sample parameters, including the carrier density, the modulation period, and the width of the confining quantum well. In the presence of a small perpendicular magnetic field (B⊥ ), both 2D electrons and holes are essentially spin-unpolarized and their Fermi contours are nearly circular. When an additional parallel component B∥ is introduced, it couples to the carriers' out-of-plane motion and leads to a severe distortion of the energy bands and the Fermi contours. The degree of anisotropy is typically stronger in the wider quantum wells but it also depends on the carrier type. For a given QW width, holes become anisotropic more readily than electrons. The application of B ∥ also affects the spin-polarization of the carriers. Hole samples, for example, become more spin-polarized compared to electrons. We can semi-quantitatively explain the shape and size of the electron and hole Fermi contours with a theoretical calculation with no adjustable parameters based on an 8 x 8 Kane Hamiltonian. In addition to the electron and hole data at low perpendicular magnetic fields, we observe commensurability features for composite fermions near Landau level filling factors nu = 3=2, 1/2, and 1/4. Our data reveal an asymmetry of the composite fermion commensurability features on the two sides of filling factors nu = 1=2 and 3=2. The asymmetry is a fascinating manifestation of a subtle breaking of the particle-hole equivalence in the ballistic transport of composite fermions. It is consistent with a transport picture in which the minority carriers capture flux quanta to form composite fermions. We also employ commensurability oscillations as a tool to probe and quantify the effect of B∥ on the composite fermion Fermi contours. Our measurements reveal that, thanks to the finite layer thickness of the carriers and the coupling of their out-of-plane motion to B∥, the Fermi contours of nu = 1=2 and 3/2 composite fermions are significantly distorted. Furthermore, depending on the width of the quantum well and the sample density, in the vicinity of nu = 3=2 the spin-polarization of the composite fermions varies while near nu = 1=2 they remain fully spin-polarized.

Dynamic nucleoplasmic and nucleolar localization of mammalian RNase H1 in response to RNAP I transcriptional R-loops

PubMed Central

Sun, Hong; De Hoyos, Cheryl L.; Bailey, Jeffrey K.; Liang, Xue-hai; Crooke, Stanley T.

2017-01-01

Abstract An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migration of RNase H1 and R-loops from nucleoli to perinucleolar ring structures was observed upon inhibition of RNAP I transcription. Treatment with camptothecin which transiently stabilized nucleolar R-loops recruited RNase H1 to the nucleoli. It has been reported that the absence of Topoisomerase and RNase H activity in Escherichia coli or Saccharomyces cerevisiae caused R-loop accumulation along rDNA. We found that the distribution of RNase H1 and Top1 along rDNA coincided at sites where R-loops accumulated in mammalian cells. Loss of either RNase H1 or Top1 caused R-loop accumulation, and the accumulation of R-loops was exacerbated when both proteins were depleted. Importantly, we observed that protein levels of Top1 were negatively correlated with the abundance of RNase H1. We conclude that Top1 and RNase H1 are partially functionally redundant in mammalian cells to suppress RNAP I transcription-associate R-loops. PMID:28977560

Quantitative implementation of the endogenous molecular-cellular network hypothesis in hepatocellular carcinoma.

PubMed

Wang, Gaowei; Zhu, Xiaomei; Gu, Jianren; Ao, Ping

2014-06-06

A quantitative hypothesis for cancer genesis and progression-the endogenous molecular-cellular network hypothesis, intended to include both genetic and epigenetic causes of cancer-has been proposed recently. Using this hypothesis, here we address the molecular basis for maintaining normal liver and hepatocellular carcinoma (HCC), and the potential strategy to cure or relieve HCC. First, we elaborate the basic assumptions of the hypothesis and establish a core working network of HCC according to the hypothesis. Second, we quantify the working network by a nonlinear dynamical system. We show that the working network reproduces the main known features of normal liver and HCC at both the modular and molecular levels. Lastly, the validated working network reveals that (i) specific positive feedback loops are responsible for the maintenance of normal liver and HCC; (ii) inhibiting proliferation and inflammation-related positive feedback loops and simultaneously inducing a liver-specific positive feedback loop is predicated as a potential strategy to cure or relieve HCC; and (iii) the genesis and regression of HCC are asymmetric. In light of the characteristic properties of the nonlinear dynamical system, we demonstrate that positive feedback loops must exist as a simple and general molecular basis for the maintenance of heritable phenotypes, such as normal liver and HCC, and regulating the positive feedback loops directly or indirectly provides potential strategies to cure or relieve HCC.

An adaptive human response mechanism controlling the V/STOL aircraft. Appendix 3: The adaptive control model of a pilot in V/STOL aircraft control loops. M.S. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Kucuk, Senol

1988-01-01

Importance of the role of human operator in control systems has led to the particular area of manual control theory. Human describing functions were developed to model human behavior for manual control studies to take advantage of the successful and safe human operations. A single variable approach is presented that can be extended for multi-variable tasks where a low order human response model is used together with its rules, to adapt the model on-line, being capable of responding to the changes in the controlled element dynamics. Basic control theory concepts are used to combine the model, constrained with the physical observations, particularly, for the case of aircraft control. Pilot experience is represented as the initial model parameters. An adaptive root-locus method is presented as the adaptation law of the model where the closed loop bandwidth of the system is to be preserved in a stable manner with the adjustments of the pilot handling qualities which relate the latter to the closed loop bandwidth and damping of the closed loop pilot aircraft combination. A Kalman filter parameter estimator is presented as the controlled element identifier of the adaptive model where any discrepancies of the open loop dynamics from the presented one, are sensed to be compensated.

A closed-loop multi-level model of glucose homeostasis

PubMed Central

Uluseker, Cansu; Simoni, Giulia; Dauriz, Marco; Matone, Alice

2018-01-01

Background The pathophysiologic processes underlying the regulation of glucose homeostasis are considerably complex at both cellular and systemic level. A comprehensive and structured specification for the several layers of abstraction of glucose metabolism is often elusive, an issue currently solvable with the hierarchical description provided by multi-level models. In this study we propose a multi-level closed-loop model of whole-body glucose homeostasis, coupled with the molecular specifications of the insulin signaling cascade in adipocytes, under the experimental conditions of normal glucose regulation and type 2 diabetes. Methodology/Principal findings The ordinary differential equations of the model, describing the dynamics of glucose and key regulatory hormones and their reciprocal interactions among gut, liver, muscle and adipose tissue, were designed for being embedded in a modular, hierarchical structure. The closed-loop model structure allowed self-sustained simulations to represent an ideal in silico subject that adjusts its own metabolism to the fasting and feeding states, depending on the hormonal context and invariant to circadian fluctuations. The cellular level of the model provided a seamless dynamic description of the molecular mechanisms downstream the insulin receptor in the adipocytes by accounting for variations in the surrounding metabolic context. Conclusions/Significance The combination of a multi-level and closed-loop modeling approach provided a fair dynamic description of the core determinants of glucose homeostasis at both cellular and systemic scales. This model architecture is intrinsically open to incorporate supplementary layers of specifications describing further individual components influencing glucose metabolism. PMID:29420588

The use of real-time, hardware-in-the-loop simulation in the design and development of the new Hughes HS601 spacecraft attitude control system

NASA Technical Reports Server (NTRS)

Slafer, Loren I.

1989-01-01

Realtime simulation and hardware-in-the-loop testing is being used extensively in all phases of the design, development, and testing of the attitude control system (ACS) for the new Hughes HS601 satellite bus. Realtime, hardware-in-the-loop simulation, integrated with traditional analysis and pure simulation activities is shown to provide a highly efficient and productive overall development program. Implementation of high fidelity simulations of the satellite dynamics and control system algorithms, capable of real-time execution (using applied Dynamics International's System 100), provides a tool which is capable of being integrated with the critical flight microprocessor to create a mixed simulation test (MST). The MST creates a highly accurate, detailed simulated on-orbit test environment, capable of open and closed loop ACS testing, in which the ACS design can be validated. The MST is shown to provide a valuable extension of traditional test methods. A description of the MST configuration is presented, including the spacecraft dynamics simulation model, sensor and actuator emulators, and the test support system. Overall system performance parameters are presented. MST applications are discussed; supporting ACS design, developing on-orbit system performance predictions, flight software development and qualification testing (augmenting the traditional software-based testing), mission planning, and a cost-effective subsystem-level acceptance test. The MST is shown to provide an ideal tool in which the ACS designer can fly the spacecraft on the ground.

REFLECTION OF PROPAGATING SLOW MAGNETO-ACOUSTIC WAVES IN HOT CORONAL LOOPS: MULTI-INSTRUMENT OBSERVATIONS AND NUMERICAL MODELING

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

Mandal, Sudip; Banerjee, Dipankar; Pant, Vaibhav

Slow MHD waves are important tools for understanding coronal structures and dynamics. In this paper, we report a number of observations from the X-Ray Telescope (XRT) on board HINODE and Solar Dynamic Observatory /Atmospheric Imaging Assembly (AIA) of reflecting longitudinal waves in hot coronal loops. To our knowledge, this is the first report of this kind as seen from the XRT and simultaneously with the AIA. The wave appears after a micro-flare occurs at one of the footpoints. We estimate the density and temperature of the loop plasma by performing differential emission measure (DEM) analysis on the AIA image sequence.more » The estimated speed of propagation is comparable to or lower than the local sound speed, suggesting it to be a propagating slow wave. The intensity perturbation amplitude, in every case, falls very rapidly as the perturbation moves along the loop and eventually vanishes after one or more reflections. To check the consistency of such reflection signatures with the obtained loop parameters, we perform a 2.5D MHD simulation, which uses the parameters obtained from our observation as inputs, and perform forward modeling to synthesize AIA 94 Å images. Analyzing the synthesized images, we obtain the same properties of the observables as for the real observation. From the analysis we conclude that a footpoint heating can generate a slow wave which then reflects back and forth in the coronal loop before fading. Our analysis of the simulated data shows that the main agent for this damping is anisotropic thermal conduction.« less

The application of the analog signal to discrete time interval converter to the signal conditioner power supplies

NASA Technical Reports Server (NTRS)

Schoenfeld, A. D.; Yu, Y.

1973-01-01

The Analog Signal to Discrete Time Interval Converter microminiaturized module was utilized to control the signal conditioner power supplies. The multi-loop control provides outstanding static and dynamic performance characteristics, exceeding those generally associated with single-loop regulators. Eight converter boards, each containing three independent dc to dc converter, were built, tested, and delivered.

Commensurate Priors for Incorporating Historical Information in Clinical Trials Using General and Generalized Linear Models

PubMed Central

Hobbs, Brian P.; Sargent, Daniel J.; Carlin, Bradley P.

2014-01-01

Assessing between-study variability in the context of conventional random-effects meta-analysis is notoriously difficult when incorporating data from only a small number of historical studies. In order to borrow strength, historical and current data are often assumed to be fully homogeneous, but this can have drastic consequences for power and Type I error if the historical information is biased. In this paper, we propose empirical and fully Bayesian modifications of the commensurate prior model (Hobbs et al., 2011) extending Pocock (1976), and evaluate their frequentist and Bayesian properties for incorporating patient-level historical data using general and generalized linear mixed regression models. Our proposed commensurate prior models lead to preposterior admissible estimators that facilitate alternative bias-variance trade-offs than those offered by pre-existing methodologies for incorporating historical data from a small number of historical studies. We also provide a sample analysis of a colon cancer trial comparing time-to-disease progression using a Weibull regression model. PMID:24795786

Electronic self-organization in the single-layer manganite $$\\rm Pr_{1-x}Ca_{1+x}MnO4$$

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

Ye, Feng; Chi, Songxue; Fernandez-Baca, Jaime A

We use neutron scattering to investigate the doping evolution of the magnetic correlations in the single-layer manganitemore » $$\\rm Pr_{\\it 1-x}Ca_{\\it 1+x}MnO_4$$, away from the $x=0.5$ composition where the CE-type commensurate antiferromagnetic (AF) structure is stable. We find that short-range incommensurate spin correlations develop as the system is electron doped ($x<0.5$), which coexist with the CE-type AF order. This suggests that electron doping in this system induces an inhomogeneous electronic self-organization, where commensurate AF patches with $x=0.5$ are separated by electron-rich domain walls with short range magnetic correlations. This behavior is strikingly different than for the three-dimensional $$\\rm Pr_{\\it 1-x}Ca_{\\it x}MnO_3$$, where the long-range CE-type commensurate AF structure is stable over a wide range of electron or hole doping around $x=0.5$.« less

Crossover from Commensurate to Incommensurate Antiferromagnetism in Stoichiometric NaFeAs Revealed by Single-Crystal 23Na,75As-NMR Experiments

NASA Astrophysics Data System (ADS)

Kitagawa, Kentaro; Mezaki, Yuji; Matsubayashi, Kazuyuki; Uwatoko, Yoshiya; Takigawa, Masashi

2011-03-01

We report the results of 23Na and 75As nuclear magnetic resonance (NMR) experiments on a self-flux grown high-quality single crystal of stoichiometric NaFeAs. The NMR spectra reveal a tetragonal to twinned-orthorhombic structural phase transition at TO = 57 K and an antiferromagnetic (AF) transition at TAF = 45 K. The divergent behavior of nuclear relaxation rate near TAF shows significant anisotropy, indicating that the critical slowing down of stripe-type AF fluctuations are strongly anisotropic in spin space. The NMR spectra at sufficiently low temperatures consist of sharp peaks showing a commensurate stripe AF order with a small moment of ˜0.3 μB. However, the spectra just below TAF exhibit a highly asymmetric broadening pointing to an incommensurate modulation. The commensurate-incommensurate crossover in NaFeAs shows a certain similarity to the behavior of SrFe2As2 under high pressure.

Stability of vacancy-type defect clusters in Ni based on first-principles and molecular dynamics simulations

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-10-17

Using first-principles calculations based on density-functional theory, the energetics of different vacancy-type defects, including voids, stacking fault tetrahedra (SFT) and vacancy loops, in Ni are investigated. It is found that voids are more stable than SFT at 0 K, which is also the case after taking into account the volumetric strains. By carrying out ab initio molecular dynamics simulations at temperatures up to 1000 K, direct transformations from vacancy loops and voids into SFT are observed. Our results suggest the importance of temperature effects in determining thermodynamic stability of vacancy clusters in face-centered cubic metals.

Nonlinear cellular dynamics of keratinocytes in normal and psoriatic epidermis under action of UV radiation

NASA Astrophysics Data System (ADS)

Stolnitz, Mikhail M.; Medvedev, Boris A.; Gribko, Tatyana V.

2004-05-01

The semi-phenomenological model of epidermal cell dynamics is submitted. The model takes into account three types of basal layer keratinocytes (stem, transient amplifying, terminally differentiated), distribution of first two types cells on mitotic cycle stages and resting states, keratinocytes-lymphocytes interactions that provide a positive feedback loop, influence of more differentiated cells on their progenitors that provide a negative feedback loop. Simplified model are developed and its stationary solutions are received. The opportunity of interpretation of some received modes as corresponding to various stages of psoriasis is discussed. Influence of UV-radiation on transitions between various modes of epidermis functioning is qualitatively analyzed.

Dynamic magnetic hysteresis and nonlinear susceptibility of antiferromagnetic nanoparticles

NASA Astrophysics Data System (ADS)

Kalmykov, Yuri P.; Ouari, Bachir; Titov, Serguey V.

2016-08-01

The nonlinear ac stationary response of antiferromagnetic nanoparticles subjected to both external ac and dc fields of arbitrary strength and orientation is investigated using Brown's continuous diffusion model. The nonlinear complex susceptibility and dynamic magnetic hysteresis (DMH) loops of an individual antiferromagnetic nanoparticle are evaluated and compared with the linear regime for extensive ranges of the anisotropy, the ac and dc magnetic fields, damping, and the specific antiferromagnetic parameter. It is shown that the shape and area of the DMH loops of antiferromagnetic particles are substantially altered by applying a dc field that permits tuning of the specific magnetic power loss in the nanoparticles.

Robust Adaptive Dynamic Programming of Two-Player Zero-Sum Games for Continuous-Time Linear Systems.

PubMed

Fu, Yue; Fu, Jun; Chai, Tianyou

2015-12-01

In this brief, an online robust adaptive dynamic programming algorithm is proposed for two-player zero-sum games of continuous-time unknown linear systems with matched uncertainties, which are functions of system outputs and states of a completely unknown exosystem. The online algorithm is developed using the policy iteration (PI) scheme with only one iteration loop. A new analytical method is proposed for convergence proof of the PI scheme. The sufficient conditions are given to guarantee globally asymptotic stability and suboptimal property of the closed-loop system. Simulation studies are conducted to illustrate the effectiveness of the proposed method.

Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy

NASA Technical Reports Server (NTRS)

Blumberg, Seth; Gajraj, Arivalagan; Pennington, Matthew W.; Meiners, Jens-Christian

2005-01-01

Tethered particle microscopy is a powerful tool to study the dynamics of DNA molecules and DNA-protein complexes in single-molecule experiments. We demonstrate that stroboscopic total internal reflection microscopy can be used to characterize the three-dimensional spatiotemporal motion of DNA-tethered particles. By calculating characteristic measures such as symmetry and time constants of the motion, well-formed tethers can be distinguished from defective ones for which the motion is dominated by aberrant surface effects. This improves the reliability of measurements on tether dynamics. For instance, in observations of protein-mediated DNA looping, loop formation is distinguished from adsorption and other nonspecific events.

Loop quantum cosmology of Bianchi IX: effective dynamics

NASA Astrophysics Data System (ADS)

Corichi, Alejandro; Montoya, Edison

2017-03-01

We study solutions to the effective equations for the Bianchi IX class of spacetimes within loop quantum cosmology (LQC). We consider Bianchi IX models whose matter content is a massless scalar field, by numerically solving the loop quantum cosmology effective equations, with and without inverse triad corrections. The solutions are classified using certain geometrically motivated classical observables. We show that both effective theories—with lapse N  =  V and N  =  1—resolve the big bang singularity and reproduce the classical dynamics far from the bounce. Moreover, due to the positive spatial curvature, there is an infinite number of bounces and recollapses. We study the limit of large field momentum and show that both effective theories reproduce the same dynamics, thus recovering general relativity. We implement a procedure to identify amongst the Bianchi IX solutions, those that behave like k  =  0,1 FLRW as well as Bianchi I, II, and VII0 models. The effective solutions exhibit Bianchi I phases with Bianchi II transitions and also Bianchi VII0 phases, which had not been studied before. We comment on the possible implications of these results for a quantum modification to the classical BKL behaviour.

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions

PubMed Central

2015-01-01

The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5′-rUGACU loop of the isolated SLV has been shown to adopt a Mg2+-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg2+ ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg2+-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg2+-bound loop structure. We propose this structure is a “gatekeeper” or precursor to Mg2+ binding when those ions are present. PMID:26328924

Estimation of joint stiffness with a compliant load.

PubMed

Ludvig, Daniel; Kearney, Robert E

2009-01-01

Joint stiffness defines the dynamic relationship between the position of the joint and the torque acting about it. It consists of two components: intrinsic and reflex stiffness. Many previous studies have investigated joint stiffness in an open-loop environment, because the current algorithm in use is an open-loop algorithm. This paper explores issues related to the estimation of joint stiffness when subjects interact with compliant loads. First, we show analytically how the bias in closed-loop estimates of joint stiffness depends on the properties of the load, the noise power, and length of the estimated impulse response functions (IRF). We then demonstrate with simulations that the open-loop analysis will fail completely for an elastic load but may succeed for an inertial load. We further show that the open-loop analysis can yield unbiased results with an inertial load and document IRF length, signal-to-noise ratio needed, and minimum inertia needed for the analysis to succeed. Thus, by using a load with a properly selected inertia, open-loop analysis can be used under closed-loop conditions.

Mini-filament Eruption as the Initiation of a Jet along Coronal Loops

NASA Astrophysics Data System (ADS)

Hong, Junchao; Jiang, Yunchun; Yang, Jiayan; Yang, Bo; Xu, Zhe; Xiang, Yongyuan

2016-10-01

Minifilament eruptions (MFEs) and coronal jets are different types of solar small-scale explosive events. We report an MFE observed at the New Vacuum Solar Telescope (NVST). As seen in the NVST Hα images, during the rising phase, the minifilament erupts outward orthogonally to its length, accompanied with a flare-like brightening at the bottom. Afterward, dark materials are found to possibly extend along the axis of the expanded filament body. The MFE is analogous to large filament eruptions. However, a simultaneous observation of the Solar Dynamics Observatory shows that a jet is initiated and flows out along nearby coronal loops during the rising phase of the MFE. Meanwhile, small hot loops, which connect the original eruptive site of the minifilament to the footpoints of the coronal loops, are formed successively. A differential emission measure analysis demonstrates that, on the top of the new small loops, a hot cusp structure exists. We conjecture that the magnetic fields of the MFE interact with magnetic fields of the coronal loops. This interaction is interpreted as magnetic reconnection that produces the jet and the small hot loops.

Stacking order dynamics in the quasi-two-dimensional dichalcogenide 1 T-TaS 2 probed with MeV ultrafast electron diffraction

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

Le Guyader, L.; Chase, T.; Reid, A. H.

Transitions between different charge density wave (CDW) states in quasi-two-dimensional materials may be accompanied also by changes in the inter-layer stacking of the CDW. Using MeV ultrafast electron diffraction, the out-of-plane stacking order dynamics in the quasi-two-dimensional dichalcogenide 1 T-TaS 2 is investigated for the first time. From the intensity of the CDW satellites aligned around the commensurate l = 1/6 characteristic stacking order, it is found out that this phase disappears with a 0.3 ps time constant. Simultaneously, in the same experiment, the emergence of the incommensurate phase, with a slightly slower 2.0 ps time constant, is determined frommore » the intensity of the CDW satellites aligned around the incommensurate l = 1/3 characteristic stacking order. Finally, these results might be of relevance in understanding the metallic character of the laser-induced metastable “hidden” state recently discovered in this compound.« less

Spreading of Electrolyte Drops on Charged Surfaces: Electric Double Layer Effects on Drop Dynamics

NASA Astrophysics Data System (ADS)

Bae, Kyeong; Sinha, Shayandev; Chen, Guang; Das, Siddhartha

2015-11-01

Drop spreading is one of the most fundamental topics of wetting. Here we study the spreading of electrolyte drops on charged surfaces. The electrolyte solution in contact with the charged solid triggers the formation of an electric double layer (EDL). We develop a theory to analyze how the EDL affects the drop spreading. The drop dynamics is studied by probing the EDL effects on the temporal evolution of the contact angle and the base radius (r). The EDL effects are found to hasten the spreading behaviour - this is commensurate to the EDL effects causing a ``philic'' tendency in the drops (i.e., drops attaining a contact angle smaller than its equilibrium value), as revealed by some of our recent papers. We also develop scaling laws to illustrate the manner in which the EDL effects make the r versus time (t) variation deviate from the well known r ~tn variation, thereby pinpointing the attainment of different EDL-mediated spreading regimes.

Decoupling of ion conductivity from segmental dynamics in oligomeric ethylene oxide functionalized oxanorbornene dicarboximide homopolymers

DOE PAGES

Adams, Marisa; Richmond, Victoria; Smith, Douglas; ...

2017-03-24

Here, in order to design more effective solid polymer electrolytes, it is important to decouple ion conductivityfrom polymer segmental motion. To that end, novel polymers based on oxanorbornene dicarboximidemonomers with varying lengths of oligomeric ethylene oxide side chains have been synthesized usingring opening metathesis polymerization. These unique polymers have a fairly rigid and bulky backboneand were used to investigate the decoupling of ion motion from polymer segmental dynamics. Ionconductivity was measured using broadband dielectric spectroscopy for varying levels of added lithiumsalt. The conductivity data demonstrate six to seven orders of separation in timescale of ion conductivityfrom polymer segmental motion formore » polymers with shorter ethylene oxide side chains. However,commensurate changes in the glass transition temperatures T g reduce the effect of decoupling in ionconductivity and lead to lower conductivity at ambient conditions. These results suggest that both anincrease in decoupling and a reduction in T g might be required to develop solid polymer electrolytes withhigh ion conductivity at room temperature.« less

Magnetic structure and excitation spectrum of the hyperhoneycomb Kitaev magnet β -Li2IrO3

NASA Astrophysics Data System (ADS)

Ducatman, Samuel; Rousochatzakis, Ioannis; Perkins, Natalia B.

2018-03-01

We present a theoretical study of the static and dynamical properties of the three-dimensional, hyperhoneycomb Kitaev magnet β -Li2IrO3 . We argue that the observed incommensurate order can be understood in terms of a long-wavelength twisting of a nearby commensurate period-3 state, with the same key qualitatively features. The period-3 state shows very different structure when either the Kitaev interaction K or the off-diagonal exchange anisotropy Γ is dominant. A comparison of the associated static spin structure factors with reported scattering experiments in zero and finite fields gives strong evidence that β -Li2IrO3 lies in the regime of dominant Kitaev coupling, and that the Heisenberg exchange J is much weaker than both K and Γ . Our predictions for the magnon excitation spectra, the dynamical spin structure factors, and their polarization dependence provide additional distinctive fingerprints that can be checked experimentally.

Stacking order dynamics in the quasi-two-dimensional dichalcogenide 1T-TaS2 probed with MeV ultrafast electron diffraction.

PubMed

Le Guyader, L; Chase, T; Reid, A H; Li, R K; Svetin, D; Shen, X; Vecchione, T; Wang, X J; Mihailovic, D; Dürr, H A

2017-07-01

Transitions between different charge density wave (CDW) states in quasi-two-dimensional materials may be accompanied also by changes in the inter-layer stacking of the CDW. Using MeV ultrafast electron diffraction, the out-of-plane stacking order dynamics in the quasi-two-dimensional dichalcogenide 1 T -TaS 2 is investigated for the first time. From the intensity of the CDW satellites aligned around the commensurate l  = 1/6 characteristic stacking order, it is found out that this phase disappears with a 0.3 ps time constant. Simultaneously, in the same experiment, the emergence of the incommensurate phase, with a slightly slower 2.0 ps time constant, is determined from the intensity of the CDW satellites aligned around the incommensurate l  = 1/3 characteristic stacking order. These results might be of relevance in understanding the metallic character of the laser-induced metastable "hidden" state recently discovered in this compound.

Stacking order dynamics in the quasi-two-dimensional dichalcogenide 1 T-TaS 2 probed with MeV ultrafast electron diffraction

DOE PAGES

Le Guyader, L.; Chase, T.; Reid, A. H.; ...

2017-05-03

Transitions between different charge density wave (CDW) states in quasi-two-dimensional materials may be accompanied also by changes in the inter-layer stacking of the CDW. Using MeV ultrafast electron diffraction, the out-of-plane stacking order dynamics in the quasi-two-dimensional dichalcogenide 1 T-TaS 2 is investigated for the first time. From the intensity of the CDW satellites aligned around the commensurate l = 1/6 characteristic stacking order, it is found out that this phase disappears with a 0.3 ps time constant. Simultaneously, in the same experiment, the emergence of the incommensurate phase, with a slightly slower 2.0 ps time constant, is determined frommore » the intensity of the CDW satellites aligned around the incommensurate l = 1/3 characteristic stacking order. Finally, these results might be of relevance in understanding the metallic character of the laser-induced metastable “hidden” state recently discovered in this compound.« less

Evaluation of driver reactions for effective use of dynamic message signs in Richmond, Virginia.

DOT National Transportation Integrated Search

2010-02-01

Dynamic message signs (DMS) are used in conjunction with other media to communicate traffic conditions, general information, and recommended diversion strategies to motorists. Previous studies using loop detector data to estimate diversion rates attr...

Cavitation in Amorphous Solids

NASA Astrophysics Data System (ADS)

Guan, Pengfei; Lu, Shuo; Spector, Michael J. B.; Valavala, Pavan K.; Falk, Michael L.

2013-05-01

Molecular dynamics simulations of cavitation in a Zr50Cu50 metallic glass exhibit a waiting time dependent cavitation rate. On short time scales nucleation rates and critical cavity sizes are commensurate with a classical theory of nucleation that accounts for both the plastic dissipation during cavitation and the cavity size dependence of the surface energy. All but one parameter, the Tolman length, can be extracted directly from independent calculations or estimated from physical principles. On longer time scales strain aging in the form of shear relaxations results in a systematic decrease of cavitation rate. The high cavitation rates that arise due to the suppression of the surface energy in small cavities provide a possible explanation for the quasibrittle fracture observed in metallic glasses.

Dynamic testing of a single-degree-of-freedom strapdown gyroscope

NASA Technical Reports Server (NTRS)

Lory, C. B.; Feldman, J.; Sinkiewicz, J. S., Jr.

1971-01-01

Test methods and results are presented for the equivalent average input rate of a single-degree-of-freedom gyroscope operated both open loop and with a ternary-logic pulse-torque-to-balance loop during multiaxis angular oscillation. For the open-loop tests, good agreement was obtained with theoretical results. Two-axis testing was performed for oscillations about the Input-Output axes, the Input-Spin axes, and the Spin-Output axes. These tests run in the torque-to-balance mode revealed significant departures from open-loop results in the induced drift rate. An analysis is developed explaining much of the closed-loop data presented. Test data for the gryoscope in a ternary torque-to-balance loop with constant input rates is presented. The tests demonstrate that the instrument rate linearity does not change with interrogation frequency from 3,600 to 14,400 Hz if the torque coil is tuned to offer a resistive load to the current switch. Analysis cited shows that gyroscope lag compensation eliminates multiple pulsing and other equivalent forms of degraded resolution in a wide variety of quantizing loops. This result is test verified for the ternary delta-modulator loop.

Enhanced Performance Controller Design for Stochastic Systems by Adding Extra State Estimation onto the Existing Closed Loop Control

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

Zhou, Yuyang; Zhang, Qichun; Wang, Hong

To enhance the performance of the tracking property , this paper presents a novel control algorithm for a class of linear dynamic stochastic systems with unmeasurable states, where the performance enhancement loop is established based on Kalman filter. Without changing the existing closed loop with the PI controller, the compensative controller is designed to minimize the variances of the tracking errors using the estimated states and the propagation of state variances. Moreover, the stability of the closed-loop systems has been analyzed in the mean-square sense. A simulated example is included to show the effectiveness of the presented control algorithm, wheremore » encouraging results have been obtained.« less

Engineering challenges of BioNEMS: the integration of microfluidics, micro- and nanodevices, models and external control for systems biology.

PubMed

Wikswo, J P; Prokop, A; Baudenbacher, F; Cliffel, D; Csukas, B; Velkovsky, M

2006-08-01

Systems biology, i.e. quantitative, postgenomic, postproteomic, dynamic, multiscale physiology, addresses in an integrative, quantitative manner the shockwave of genetic and proteomic information using computer models that may eventually have 10(6) dynamic variables with non-linear interactions. Historically, single biological measurements are made over minutes, suggesting the challenge of specifying 10(6) model parameters. Except for fluorescence and micro-electrode recordings, most cellular measurements have inadequate bandwidth to discern the time course of critical intracellular biochemical events. Micro-array expression profiles of thousands of genes cannot determine quantitative dynamic cellular signalling and metabolic variables. Major gaps must be bridged between the computational vision and experimental reality. The analysis of cellular signalling dynamics and control requires, first, micro- and nano-instruments that measure simultaneously multiple extracellular and intracellular variables with sufficient bandwidth; secondly, the ability to open existing internal control and signalling loops; thirdly, external BioMEMS micro-actuators that provide high bandwidth feedback and externally addressable intracellular nano-actuators; and, fourthly, real-time, closed-loop, single-cell control algorithms. The unravelling of the nested and coupled nature of cellular control loops requires simultaneous recording of multiple single-cell signatures. Externally controlled nano-actuators, needed to effect changes in the biochemical, mechanical and electrical environment both outside and inside the cell, will provide a major impetus for nanoscience.

Nanoflares, Spicules, and Other Small-Scale Dynamic Phenomena on the Sun

NASA Technical Reports Server (NTRS)

Klimchuk, James

2010-01-01

There is abundant evidence of highly dynamic phenomena occurring on very small scales in the solar atmosphere. For example, the observed pr operties of many coronal loops can only be explained if the loops are bundles of unresolved strands that are heated impulsively by nanoflares. Type II spicules recently discovered by Hinode are an example of small-scale impulsive events occurring in the chromosphere. The exist ence of these and other small-scale phenomena is not surprising given the highly structured nature of the magnetic field that is revealed by photospheric observations. Dynamic phenomena also occur on much lar ger scales, including coronal jets, flares, and CMEs. It is tempting to suggest that these different phenomena are all closely related and represent a continuous distribution of sizes and energies. However, this is a dangerous over simplification in my opinion. While it is tru e that the phenomena all involve "magnetic reconnection" (the changin g of field line connectivity) in some form, how this occurs depends s trongly on the magnetic geometry. A nanoflare resulting from the interaction of tangled magnetic strands within a confined coronal loop is much different from a major flare occurring at the current sheet form ed when a CME rips open an active region. I will review the evidence for ubiquitous small-scale dynamic phenomena on the Sun and discuss wh y different phenomena are not all fundamentally the same.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.

PubMed

Sloma, Michael F; Mathews, David H

2016-12-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. © 2016 Sloma and Mathews; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

On the Origin of Tremor in Parkinson’s Disease

PubMed Central

Dovzhenok, Andrey; Rubchinsky, Leonid L.

2012-01-01

The exact origin of tremor in Parkinson’s disease remains unknown. We explain why the existing data converge on the basal ganglia-thalamo-cortical loop as a tremor generator and consider a conductance-based model of subthalamo-pallidal circuits embedded into a simplified representation of the basal ganglia-thalamo-cortical circuit to investigate the dynamics of this loop. We show how variation of the strength of dopamine-modulated connections in the basal ganglia-thalamo-cortical loop (representing the decreasing dopamine level in Parkinson’s disease) leads to the occurrence of tremor-like burst firing. These tremor-like oscillations are suppressed when the connections are modulated back to represent a higher dopamine level (as it would be the case in dopaminergic therapy), as well as when the basal ganglia-thalamo-cortical loop is broken (as would be the case for ablative anti-parkinsonian surgeries). Thus, the proposed model provides an explanation for the basal ganglia-thalamo-cortical loop mechanism of tremor generation. The strengthening of the loop leads to tremor oscillations, while the weakening or disconnection of the loop suppresses them. The loop origin of parkinsonian tremor also suggests that new tremor-suppression therapies may have anatomical targets in different cortical and subcortical areas as long as they are within the basal ganglia-thalamo-cortical loop. PMID:22848541

Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

DOE PAGES

Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; ...

2015-06-11

Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z),more » mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[n i(t,z)•n i(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.« less

High-pressure ultrasonic study of the commensurate-incommensurate spin-density-wave transition in an antiferromagnetic Cr-0.3 at. % Ru alloy single crystal

NASA Astrophysics Data System (ADS)

Cankurtaran, M.; Saunders, G. A.; Wang, Q.; Ford, P. J.; Alberts, H. L.

1992-12-01

A comprehensive experimental study has been made of the elastic and nonlinear acoustic behavior of a dilute Cr alloy as it undergoes a commensurate (C)-incommensurate (I) spin-density-wave transition. Simultaneous measurements of the temperature dependence of ultrasonic wave velocity and attenuation of longitudinal and shear 10-MHz ultrasonic waves propagated along both the [100] and the [110] direction of Cr-0.3 at. % Ru alloy single crystal have been made in the temperature range 200-300 K. The temperature dependence of ultrasonic attenuation for each mode is characterized by a spikelike peak centered at TCI (=238.6 K) (on cooling) and at TIC (=255.6 K) (on warming). The velocities of both longitudinal and shear ultrasonic waves exhibit a large and steep increase at TCI on cooling and a similar drop at TIC on warming with a pronounced hysteresis between TIC and TCI. These observations show that the transition between the commensurate and incommensurate phases is first order. Measurements of the effects of hydrostatic pressure (up to 0.15 GPa) on the velocities of ultrasonic waves, which were made at several fixed temperatures between 248 and 297 K, show similar features: a steep increase at PCI (increasing pressure) and a similar drop at PIC (decreasing pressure) with a well-defined hysteresis. Both TCI and TIC increase strongly and approximately linearly with pressure, the mean values of dTCI/dP and dTIC/dP being (333+/-3) K/GPa and (277+/-5) K/GPa, respectively. The pressure and temperature dependencies of the anomalies in the ultrasonic wave velocity have been used to locate both the C-I and I-C boundaries on the magnetic P-T phase diagram. There is a triple point (at about 315 K and 0.22 GPa) where the paramagnetic, commensurate, and incommensurate spin-density-wave phases coexist. Results for the complete sets of the elastic stiffness tensor components and their hydrostatic pressure derivatives have been used to evaluate the acoustic-mode Grüneisen parameters in both the commensurate and incommensurate phases. These quantify the vibrational anharmonicity of each acoustic phonon mode in the long-wavelength limit and establish which acoustic modes interact strongly with the spin-density waves. Pronounced longitudinal acoustic-mode softening under pressure results in negative Grüneisen parameters, a particularly marked feature of the commensurate phase.

Numerical simulations of loops heated to solar flare temperatures. III - Asymmetrical heating

NASA Technical Reports Server (NTRS)

Cheng, C.-C.; Doschek, G. A.; Karpen, J. T.

1984-01-01

A numerical model is defined for asymmetric full solar flare loop heating and comparisons are made with observational data. The Dynamic Flux Tube Model is used to describe the heating process in terms of one-dimensional, two fluid conservation equations of mass, energy and momentum. An adaptive grid allows for the downward movement of the transition region caused by an advancing conduction front. A loop 20,000 km long is considered, along with a flare heating system and the hydrodynamic evolution of the loop. The model was applied to generating line profiles and spatial X-ray and UV line distributions, which were compared with SMM, P78-1 and Hintori data for Fe, Ca and Mg spectra. Little agreement was obtained, and it is suggested that flares be treated as multi-loop phenomena. Finally, it is concluded that chromospheric evaporation is not an effective mechanism for generating the soft X-ray bursts associated with flares.

A novel double loop control model design for chemical unstable processes.

PubMed

Cong, Er-Ding; Hu, Ming-Hui; Tu, Shan-Tung; Xuan, Fu-Zhen; Shao, Hui-He

2014-03-01

In this manuscript, based on Smith predictor control scheme for unstable process in industry, an improved double loop control model is proposed for chemical unstable processes. Inner loop is to stabilize integrating the unstable process and transform the original process to first-order plus pure dead-time dynamic stable process. Outer loop is to enhance the performance of set point response. Disturbance controller is designed to enhance the performance of disturbance response. The improved control system is simple with exact physical meaning. The characteristic equation is easy to realize stabilization. Three controllers are separately design in the improved scheme. It is easy to design each controller and good control performance for the respective closed-loop transfer function separately. The robust stability of the proposed control scheme is analyzed. Finally, case studies illustrate that the improved method can give better system performance than existing design methods. © 2013 ISA Published by ISA All rights reserved.

Dynamics of a multi-thermal loop in the solar corona

NASA Astrophysics Data System (ADS)

Nisticò, G.; Anfinogentov, S.; Nakariakov, V. M.

2014-10-01

Context. We present an observation of a long-living multi-thermal coronal loop, visible in different extreme ultra-violet wavebands of SDO/AIA in a quiet-Sun region close to the western solar limb. Aims: Analysis of persistent kink displacements of the loop seen in different bandpasses that correspond to different temperatures of the plasma allows sub-resolution structuring of the loop to be revealed. Methods: A vertically oriented slit is taken at the loop top, and time-distance maps are made from it. Loop displacements in time-distance maps are automatically tracked with the Gaussian fitting technique and fitted with a sinusoidal function that is "guessed". Wavelet transforms are further used in order to quantify the periodicity variation in time of the kink oscillations. Results: The loop strands are found to oscillate with the periods ranging between 3 and 15 min. The oscillations are observed in intermittent regime with temporal changes in the period and amplitude. The oscillations are different at three analysed wavelengths. Conclusions: This finding suggests that the loop-like threads seen at different wavelengths are not co-spatial, hence that the loop consists of several multi-thermal strands. The detected irregularity of the oscillations can be associated with a stochastic driver acting at the footpoints of the loop. A movie associated to Fig. 1 is available in electronic form at http://www.aanda.org

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Closed-loop, pilot/vehicle analysis of the approach and landing task

NASA Technical Reports Server (NTRS)

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

1985-01-01

Optimal-control-theoretic modeling and frequency-domain analysis is the methodology proposed to evaluate analytically the handling qualities of higher-order manually controlled dynamic systems. Fundamental to the methodology is evaluating the interplay between pilot workload and closed-loop pilot/vehicle performance and stability robustness. The model-based metric for pilot workload is the required pilot phase compensation. Pilot/vehicle performance and loop stability is then evaluated using frequency-domain techniques. When these techniques were applied to the flight-test data for thirty-two highly-augmented fighter configurations, strong correlation was obtained between the analytical and experimental results.

Effect of GNSS receiver carrier phase tracking loops on earthquake monitoring performance

NASA Astrophysics Data System (ADS)

Clare, Adam; Lin, Tao; Lachapelle, Gérard

2017-06-01

This research focuses on the performance of GNSS receiver carrier phase tracking loops for early earthquake monitoring systems. An earthquake was simulated using a hardware simulator and position, velocity and acceleration displacements were obtained to recreate the dynamics of the 2011 Tohoku earthquake. Using a software defined receiver, GSNRx, tracking bandwidths of 5, 10, 15, 20, 30, 40 and 50 Hz along with integration times of 1, 5 and 10 ms were tested. Using the phase lock indicator, an adaptive tracking loop was designed and tested to maximize performance for this application.

MIMO model of an interacting series process for Robust MPC via System Identification.

PubMed

Wibowo, Tri Chandra S; Saad, Nordin

2010-07-01

This paper discusses the empirical modeling using system identification technique with a focus on an interacting series process. The study is carried out experimentally using a gaseous pilot plant as the process, in which the dynamic of such a plant exhibits the typical dynamic of an interacting series process. Three practical approaches are investigated and their performances are evaluated. The models developed are also examined in real-time implementation of a linear model predictive control. The selected model is able to reproduce the main dynamic characteristics of the plant in open-loop and produces zero steady-state errors in closed-loop control system. Several issues concerning the identification process and the construction of a MIMO state space model for a series interacting process are deliberated. 2010 ISA. Published by Elsevier Ltd. All rights reserved.

Experimental and theoretical investigation of the magnetization dynamics of an artificial square spin ice cluster

NASA Astrophysics Data System (ADS)

Pohlit, Merlin; Stockem, Irina; Porrati, Fabrizio; Huth, Michael; Schröder, Christian; Müller, Jens

2016-10-01

We study the magnetization dynamics of a spin ice cluster which is a building block of an artificial square spin ice fabricated by focused electron-beam-induced deposition both experimentally and theoretically. The spin ice cluster is composed of twelve interacting Co nanoislands grown directly on top of a high-resolution micro-Hall sensor. By employing micromagnetic simulations and a macrospin model, we calculate the magnetization and the experimentally investigated stray field emanating from a single nanoisland. The parameters determined from a comparison with the experimental hysteresis loop are used to derive an effective single-dipole macrospin model that allows us to investigate the dynamics of the spin ice cluster. Our model reproduces the experimentally observed non-deterministic sequences in the magnetization curves as well as the distinct temperature dependence of the hysteresis loop.

The Nosé–Hoover looped chain thermostat for low temperature thawed Gaussian wave-packet dynamics

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

Coughtrie, David J.; Tew, David P.

2014-05-21

We have used a generalised coherent state resolution of the identity to map the quantum canonical statistical average for a general system onto a phase-space average over the centre and width parameters of a thawed Gaussian wave packet. We also propose an artificial phase-space density that has the same behaviour as the canonical phase-space density in the low-temperature limit, and have constructed a novel Nosé–Hoover looped chain thermostat that generates this density in conjunction with variational thawed Gaussian wave-packet dynamics. This forms a new platform for evaluating statistical properties of quantum condensed-phase systems that has an explicit connection to themore » time-dependent Schrödinger equation, whilst retaining many of the appealing features of path-integral molecular dynamics.« less

Mathematical multi-scale model of the cardiovascular system including mitral valve dynamics. Application to ischemic mitral insufficiency

PubMed Central

2011-01-01

Background Valve dysfunction is a common cardiovascular pathology. Despite significant clinical research, there is little formal study of how valve dysfunction affects overall circulatory dynamics. Validated models would offer the ability to better understand these dynamics and thus optimize diagnosis, as well as surgical and other interventions. Methods A cardiovascular and circulatory system (CVS) model has already been validated in silico, and in several animal model studies. It accounts for valve dynamics using Heaviside functions to simulate a physiologically accurate "open on pressure, close on flow" law. However, it does not consider real-time valve opening dynamics and therefore does not fully capture valve dysfunction, particularly where the dysfunction involves partial closure. This research describes an updated version of this previous closed-loop CVS model that includes the progressive opening of the mitral valve, and is defined over the full cardiac cycle. Results Simulations of the cardiovascular system with healthy mitral valve are performed, and, the global hemodynamic behaviour is studied compared with previously validated results. The error between resulting pressure-volume (PV) loops of already validated CVS model and the new CVS model that includes the progressive opening of the mitral valve is assessed and remains within typical measurement error and variability. Simulations of ischemic mitral insufficiency are also performed. Pressure-Volume loops, transmitral flow evolution and mitral valve aperture area evolution follow reported measurements in shape, amplitude and trends. Conclusions The resulting cardiovascular system model including mitral valve dynamics provides a foundation for clinical validation and the study of valvular dysfunction in vivo. The overall models and results could readily be generalised to other cardiac valves. PMID:21942971

Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line.

PubMed

Siciliano, Velia; Menolascina, Filippo; Marucci, Lucia; Fracassi, Chiara; Garzilli, Immacolata; Moretti, Maria Nicoletta; di Bernardo, Diego

2011-06-01

Understanding the relationship between topology and dynamics of transcriptional regulatory networks in mammalian cells is essential to elucidate the biology of complex regulatory and signaling pathways. Here, we characterised, via a synthetic biology approach, a transcriptional positive feedback loop (PFL) by generating a clonal population of mammalian cells (CHO) carrying a stable integration of the construct. The PFL network consists of the Tetracycline-controlled transactivator (tTA), whose expression is regulated by a tTA responsive promoter (CMV-TET), thus giving rise to a positive feedback. The same CMV-TET promoter drives also the expression of a destabilised yellow fluorescent protein (d2EYFP), thus the dynamic behaviour can be followed by time-lapse microscopy. The PFL network was compared to an engineered version of the network lacking the positive feedback loop (NOPFL), by expressing the tTA mRNA from a constitutive promoter. Doxycycline was used to repress tTA activation (switch off), and the resulting changes in fluorescence intensity for both the PFL and NOPFL networks were followed for up to 43 h. We observed a striking difference in the dynamics of the PFL and NOPFL networks. Using non-linear dynamical models, able to recapitulate experimental observations, we demonstrated a link between network topology and network dynamics. Namely, transcriptional positive autoregulation can significantly slow down the "switch off" times, as compared to the non-autoregulated system. Doxycycline concentration can modulate the response times of the PFL, whereas the NOPFL always switches off with the same dynamics. Moreover, the PFL can exhibit bistability for a range of Doxycycline concentrations. Since the PFL motif is often found in naturally occurring transcriptional and signaling pathways, we believe our work can be instrumental to characterise their behaviour.

Dynamics of the CMZ - Giant Magnetic Loops Connection in the Galactic Center

NASA Astrophysics Data System (ADS)

Langer, William

2012-10-01

Understanding the mass transfer and dynamics among the Galactic Center, the disk, and the halo of the Milky Way is fundamental to the study of the evolution of galaxies and star formation. Several giant molecular loops (GML), detected in CO maps of the Galactic Center, are likely the result of the magnetic Parker instability. We have new evidence of a possible dynamical connection between these loops and the Central Molecular Zone (CMZ) from a sparse [CII] sampling from our Herschel Open Time Key Project GOT C+. The CMZ-GML region is dynamically active and is likely to have a significant ionized component. However, we have no information on the distribution and dynamics of the ionized gas. The fine-structure lines of [NII] are key probes of the warm ionized medium (WIM) and along with the [CII] can isolate the different ionization components. We have a Herschel OT2 Priority 1 program to map the GML and the CMZ-GML connection in [CII] in more detail. However, we did not propose needed [NII] observations due to an incomplete analysis of our limited GOT C+ data at the time. Here we propose to observe with the SOFIA/GREAT instrument, [NII] in the CMZ-GML interface region using the L1b band, and serendipitously CO (16-15) using band L2. With this data, combined with our Herschel HIFI [CII], Mopra 12CO (1-0) and 13CO (1-0), and HI, we will characterize these important ISM components and their motions in these Galactic Center features. These observations of the nearest such regions of galactic center activity, also have bearing on the dynamics of other galactic nuclei.

Tracing Water Vapor and Ice During Dust Growth

NASA Astrophysics Data System (ADS)

Krijt, Sebastiaan; Ciesla, Fred J.; Bergin, Edwin A.

2016-12-01

The processes that govern the evolution of dust and water (in the form of vapor or ice) in protoplanetary disks are intimately connected. We have developed a model that simulates dust coagulation, dust dynamics (settling, turbulent mixing), vapor diffusion, and condensation/sublimation of volatiles onto grains in a vertical column of a protoplanetary disk. We employ the model to study how dust growth and dynamics influence the vertical distribution of water vapor and water ice in the region just outside the radial snowline. Our main finding is that coagulation (boosted by the enhanced stickiness of icy grains) and the ensuing vertical settling of solids results in water vapor being depleted, but not totally removed, from the region above the snowline on a timescale commensurate with the vertical turbulent mixing timescale. Depending on the strength of the turbulence and the temperature, the depletion can reach factors of up to ˜50 in the disk atmosphere. In our isothermal column, this vapor depletion results in the vertical snowline moving closer to the midplane (by up to 2 gas scale heights) and the gas-phase {{C}}/{{O}} ratio above the vertical snowline increasing. Our findings illustrate the importance of dynamical effects and the need for understanding coevolutionary dynamics of gas and solids in planet-forming environments.

PREDICT: Privacy and Security Enhancing Dynamic Information Monitoring

DTIC Science & Technology

2015-08-03

consisting of global server-side probabilistic assignment by an untrusted server using cloaked locations, followed by feedback-loop guided local...12], consisting of global server-side probabilistic assignment by an untrusted server using cloaked locations, followed by feedback-loop guided...these methods achieve high sensing coverage with low cost using cloaked locations [3]. In follow-on work, the issue of mobility is addressed. Task

Robust Control Design for Flight Control

DTIC Science & Technology

1989-07-01

controller may be designed to produce desired responses to pilot commands, responses to external (atmospheric) disturbances may be unusual and...suggested for stabilizing open loop unstable aircraft result in nonminimum phase zeros in the dynamics as seen by the pilot . This issue has not been...stability test it does retain several essential features of the popular single loop test developed by Nyquist. In particular, it identifies a Nyquist

Unbiased, scalable sampling of protein loop conformations from probabilistic priors.

PubMed

Zhang, Yajia; Hauser, Kris

2013-01-01

Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors

PubMed Central

2013-01-01

Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175

Application of the principal fractional meta-trigonometric functions for the solution of linear commensurate-order time-invariant fractional differential equations.

PubMed

Lorenzo, C F; Hartley, T T; Malti, R

2013-05-13

A new and simplified method for the solution of linear constant coefficient fractional differential equations of any commensurate order is presented. The solutions are based on the R-function and on specialized Laplace transform pairs derived from the principal fractional meta-trigonometric functions. The new method simplifies the solution of such fractional differential equations and presents the solutions in the form of real functions as opposed to fractional complex exponential functions, and thus is directly applicable to real-world physics.

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

PubMed Central

2012-01-01

Background During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile “trigger loop” of the catalytic subunit closes on the nucleoside triphosphate (NTP) substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the “bridge helix” that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing. Results All atom molecular dynamics simulations of Thermus thermophilus (Tt) RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as “switch” residues) trade atomic contacts (ion pairs or hydrogen bonds) in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc) RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a closed trigger loop. Conclusions Switching between catalytic and translocating RNAP forms involves closing and opening of the trigger loop and long-range conformational changes in the atomic contacts of amino acid side chains, some located at a considerable distance from the trigger loop and active site. Trigger loop closing appears to support chemistry and the fidelity of RNA synthesis. Trigger loop opening and limited bridge helix bending appears to promote forward nucleic acid translocation. PMID:22676913

Androgynous, Reconfigurable Closed Loop Feedback Controlled Low Impact Docking System With Load Sensing Electromagnetic Capture Ring

NASA Technical Reports Server (NTRS)

Lewis, James L. (Inventor); Carroll, Monty B. (Inventor); Morales, Ray H. (Inventor); Le, Thang D. (Inventor)

2002-01-01

The present invention relates to a fully androgynous, reconfigurable closed loop feedback controlled low impact docking system with load sensing electromagnetic capture ring. The docking system of the present invention preferably comprises two Docking- assemblies, each docking assembly comprising a load sensing ring having an outer face, one of more electromagnets, one or more load cells coupled to said load sensing ring. The docking assembly further comprises a plurality of actuator arms coupled to said load sensing ring and capable of dynamically adjusting the orientation of said load sensing ring and a reconfigurable closed loop control system capable of analyzing signals originating from said plurality of load cells and of outputting real time control for each of the actuators. The docking assembly of the present invention incorporates an active load sensing system to automatically dynamically adjust the load sensing ring during capture instead of requiring significant force to push and realign the ring.

Understanding a successful obesity prevention initiative in children under 5 from a systems perspective.

PubMed

Owen, Brynle; Brown, Andrew D; Kuhlberg, Jill; Millar, Lynne; Nichols, Melanie; Economos, Christina; Allender, Steven

2018-01-01

Systems thinking represents an innovative and logical approach to understanding complexity in community-based obesity prevention interventions. We report on an approach to apply systems thinking to understand the complexity of a successful obesity prevention intervention in early childhood (children aged up to 5 years) conducted in a regional city in Victoria, Australia. A causal loop diagram (CLD) was developed to represent system elements related to a successful childhood obesity prevention intervention in early childhood. Key stakeholder interviews (n = 16) were examined retrospectively to generate purposive text data, create microstructures, and form a CLD. A CLD representing key stakeholder perceptions of a successful intervention comprised six key feedback loops explaining changes in project implementation over time. The loops described the dynamics of collaboration, network formation, community awareness, human resources, project clarity, and innovation. The CLD developed provides a replicable means to capture, evaluate and disseminate a description of the dynamic elements of a successful obesity prevention intervention in early childhood.

A reconfigurable visual-programming library for real-time closed-loop cellular electrophysiology

PubMed Central

Biró, István; Giugliano, Michele

2015-01-01

Most of the software platforms for cellular electrophysiology are limited in terms of flexibility, hardware support, ease of use, or re-configuration and adaptation for non-expert users. Moreover, advanced experimental protocols requiring real-time closed-loop operation to investigate excitability, plasticity, dynamics, are largely inaccessible to users without moderate to substantial computer proficiency. Here we present an approach based on MATLAB/Simulink, exploiting the benefits of LEGO-like visual programming and configuration, combined to a small, but easily extendible library of functional software components. We provide and validate several examples, implementing conventional and more sophisticated experimental protocols such as dynamic-clamp or the combined use of intracellular and extracellular methods, involving closed-loop real-time control. The functionality of each of these examples is demonstrated with relevant experiments. These can be used as a starting point to create and support a larger variety of electrophysiological tools and methods, hopefully extending the range of default techniques and protocols currently employed in experimental labs across the world. PMID:26157385

Study of toluene stability for an Organic Rankine Cycle (ORC) space-based power system

NASA Technical Reports Server (NTRS)

Havens, Vance; Ragaller, Dana

1988-01-01

The design, fabrication, assembly, and endurance operation of a dynamic test loop, built to evaluate the thermal stability of a proposed Organic Rankine Cycle (ORC) working fluid, is discussed. The test fluid, toluene, was circulated through a heater, simulated turbine, regenerator, condenser and pump to duplicate an actual ORC system. The maximum nominal fluid temperature, 750 F, was at the turbine simulator inlet. Samples of noncondensible gases and liquid toluene were taken periodically during the test. The samples were analyzed to identify the degradation products formed and the quantity of these products. From these data it was possible to determine the degradation rate of the working fluid and the generation rate of noncondensible gases. A further goal of this work was to relate the degradation observed in the dynamic operating loop to degradation obtained in isothermal capsule tests. This relationship was the basis for estimating the power loop degradation in the Space Station Organic Rankine Cycle system.

Space Station on-orbit solar array loads during assembly

NASA Astrophysics Data System (ADS)

Ghofranian, S.; Fujii, E.; Larson, C. R.

This paper is concerned with the closed-loop dynamic analysis of on-orbit maneuvers when the Space Shuttle is fully mated to the Space Station Freedom. A flexible model of the Space Station in the form of component modes is attached to a rigid orbiter and on-orbit maneuvers are performed using the Shuttle Primary Reaction Control System jets. The traditional approach for this type of problems is to perform an open-loop analysis to determine the attitude control system jet profiles based on rigid vehicles and apply the resulting profile to a flexible Space Station. In this study a closed-loop Structure/Control model was developed in the Dynamic Analysis and Design System (DADS) program and the solar array loads were determined for single axis maneuvers with various delay times between jet firings. It is shown that the Digital Auto Pilot jet selection is affected by Space Station flexibility. It is also shown that for obtaining solar array loads the effect of high frequency modes cannot be ignored.

An adaptive molecular timer in p53-meidated cell fate decision

NASA Astrophysics Data System (ADS)

Zhang, Xiao-Peng; Wang, Ping; Liu, Feng; Wang, Wei

The tumor suppressor p53 decides cellular outcomes in the DNA damage response. It is intriguing to explore the link between p53 dynamics and cell fates. We developed a theoretical model of p53 signaling network to clarify the mechanism of cell fate decision mediated by its dynamics. We found that the interplay between p53-Mdm2 negative feedback loop and p53-PTEN-Mdm2 positive feedback loop shapes p53 dynamics. Depending on the intensity of DNA damage, p53 shows three modes of dynamics: persistent pulses, two-phase dynamics with pulses followed by sustained high levels and straightforward high levels. Especially, p53 shows two-phase dynamics upon moderated damage and the required number of p53 pulses before apoptosis induction decreases with increasing DNA damage. Our results suggested there exists an adaptive molecular timer that determines whether and when the apoptosis switch should be triggered. We clarified the mechanism behind the switching of p53 dynamical modes by bifurcation analysis. Moreover, we reproduced the experimental results that drug additions alter p53 pulses to sustained p53 activation and leads to senescence. Our work may advance the understanding the significance of p53 dynamics in tumor suppression. This work was supported by National Natural Science Foundation of China (Nos. 11175084, 11204126 and 31361163003).

Long-Term Pavement Performance Materials Characterization Program: Verification of Dynamic Test Systems with an Emphasis on Resilient Modulus

DOT National Transportation Integrated Search

2005-09-01

This document describes a procedure for verifying a dynamic testing system (closed-loop servohydraulic). The procedure is divided into three general phases: (1) electronic system performance verification, (2) calibration check and overall system perf...

Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Hung, Shih-Wei; Hsiao, Pai-Yi; Chieng, Ching-Chang

2011-05-01

Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single cardiotoxin (CTX) protein from a methyl-terminated self-assembled monolayer (SAM) surface was investigated by means of steered molecular dynamics (SMD) simulations. The simulation results indicated that Loop I is the first loop to depart from the SAM surface, which is in good agreement with the results of the nuclear magnetic resonance spectroscopy experiment. The free energy landscape and the thermodynamic force of the CTX desorption process was represented by the PMF and by the derivative of PMF with respect to distance, respectively. By applying Jarzynski's equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski's equality, were compared with the conventional umbrella sampling method. The best estimation was obtained by using the fluctuation-dissipation estimator with a pulling velocity of v = 0.25 nm/ns for the present study.

Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and

History-Based Response Threshold Model for Division of Labor in Multi-Agent Systems

PubMed Central

Lee, Wonki; Kim, DaeEun

2017-01-01

Dynamic task allocation is a necessity in a group of robots. Each member should decide its own task such that it is most commensurate with its current state in the overall system. In this work, the response threshold model is applied to a dynamic foraging task. Each robot employs a task switching function based on the local task demand obtained from the surrounding environment, and no communication occurs between the robots. Each individual member has a constant-sized task demand history that reflects the global demand. In addition, it has response threshold values for all of the tasks and manages the task switching process depending on the stimuli of the task demands. The robot then determines the task to be executed to regulate the overall division of labor. This task selection induces a specialized tendency for performing a specific task and regulates the division of labor. In particular, maintaining a history of the task demands is very effective for the dynamic foraging task. Various experiments are performed using a simulation with multiple robots, and the results show that the proposed algorithm is more effective as compared to the conventional model. PMID:28555031

Conformational Control of Ultrafast Molecular Rotor Property: Tuning Viscosity Sensing Efficiency by Twist Angle Variation.

PubMed

Ghosh, Rajib; Kushwaha, Archana; Das, Dipanwita

2017-09-21

Fluorescent molecular rotors find widespread application in sensing and imaging of microscopic viscosity in complex chemical and biological media. Development of viscosity-sensitive ultrafast molecular rotor (UMR) relies upon the understanding of the excited-state dynamics and their implications for viscosity-dependent fluorescence signaling. Unraveling the structure-property relationship of UMR behavior is of significance toward development of an ultrasensitive fluorescence microviscosity sensor. Herein we show that the ground-state equilibrium conformation has an important role in the ultrafast twisting dynamics of UMRs and consequent viscosity sensing efficiency. Synthesis, photophysics, and ultrafast spectroscopic experiments in conjunction with quantum chemical calculation of a series of UMRs based on dimethylaniline donor and benzimidazolium acceptor with predefined ground-state torsion angle led us to unravel that the ultrafast torsional dynamics around the bond connecting donor and acceptor groups profoundly influences the molecular rotor efficiency. This is the first experimental demonstration of conformational control of small-molecule-based UMR efficiencies which can have wider implication toward development of fluorescence sensors based on the UMR principle. Conformation-controlled UMR efficiency has been shown to exhibit commensurate fluorescence enhancement upon DNA binding.

Tribology of the lubricant quantized sliding state.

PubMed

Castelli, Ivano Eligio; Capozza, Rosario; Vanossi, Andrea; Santoro, Giuseppe E; Manini, Nicola; Tosatti, Erio

2009-11-07

In the framework of Langevin dynamics, we demonstrate clear evidence of the peculiar quantized sliding state, previously found in a simple one-dimensional boundary lubricated model [A. Vanossi et al., Phys. Rev. Lett. 97, 056101 (2006)], for a substantially less idealized two-dimensional description of a confined multilayer solid lubricant under shear. This dynamical state, marked by a nontrivial "quantized" ratio of the averaged lubricant center-of-mass velocity to the externally imposed sliding speed, is recovered, and shown to be robust against the effects of thermal fluctuations, quenched disorder in the confining substrates, and over a wide range of loading forces. The lubricant softness, setting the width of the propagating solitonic structures, is found to play a major role in promoting in-registry commensurate regions beneficial to this quantized sliding. By evaluating the force instantaneously exerted on the top plate, we find that this quantized sliding represents a dynamical "pinned" state, characterized by significantly low values of the kinetic friction. While the quantized sliding occurs due to solitons being driven gently, the transition to ordinary unpinned sliding regimes can involve lubricant melting due to large shear-induced Joule heating, for example at large speed.

Dynamics of temporal variations in phonatory flow.

PubMed

Krane, Michael H; Barry, Michael; Wei, Timothy

2010-07-01

This paper addresses the dynamic relevance of time variations of phonatory airflow, commonly neglected under the quasisteady phonatory flow assumption. In contrast to previous efforts, which relied on direct measurement of glottal impedance, this work uses spatially and temporally resolved measurements of the velocity field to estimate the unsteady and convective acceleration terms in the unsteady Bernoulli equation. Theoretical considerations suggest that phonatory flow is inherently unsteady when two related conditions apply: (1) that the unsteady and convective accelerations are commensurate, and (2) that the inertia of the glottal jet is non-negligible. Acceleration waveforms, computed from experimental data, show that unsteady and convective accelerations to be the same order of magnitude, throughout the cycle, and that the jet flow contributes significantly to the unsteady acceleration. In the middle of the cycle, however, jet inertia is negligible because the convective and unsteady accelerations nearly offset one another in the jet region. These results, consistent with previous findings treating quasisteady phonatory flow, emphasize that unsteady acceleration cannot be neglected during the final stages of the phonation cycle, during which voice sound power and spectral content are largely determined. Furthermore, glottal jet dynamics must be included in any model of phonatory airflow.

Dynamics of temporal variations in phonatory flow1

PubMed Central

Krane, Michael H.; Barry, Michael; Wei, Timothy

2010-01-01

This paper addresses the dynamic relevance of time variations of phonatory airflow, commonly neglected under the quasisteady phonatory flow assumption. In contrast to previous efforts, which relied on direct measurement of glottal impedance, this work uses spatially and temporally resolved measurements of the velocity field to estimate the unsteady and convective acceleration terms in the unsteady Bernoulli equation. Theoretical considerations suggest that phonatory flow is inherently unsteady when two related conditions apply: (1) that the unsteady and convective accelerations are commensurate, and (2) that the inertia of the glottal jet is non-negligible. Acceleration waveforms, computed from experimental data, show that unsteady and convective accelerations to be the same order of magnitude, throughout the cycle, and that the jet flow contributes significantly to the unsteady acceleration. In the middle of the cycle, however, jet inertia is negligible because the convective and unsteady accelerations nearly offset one another in the jet region. These results, consistent with previous findings treating quasisteady phonatory flow, emphasize that unsteady acceleration cannot be neglected during the final stages of the phonation cycle, during which voice sound power and spectral content are largely determined. Furthermore, glottal jet dynamics must be included in any model of phonatory airflow. PMID:20649231

Cooperativity of self-organized Brownian motors pulling on soft cargoes.

PubMed

Orlandi, Javier G; Blanch-Mercader, Carles; Brugués, Jan; Casademunt, Jaume

2010-12-01

We study the cooperative dynamics of Brownian motors moving along a one-dimensional track when an external load is applied to the leading motor, mimicking molecular motors pulling on membrane-bound cargoes in intracellular traffic. Due to the asymmetric loading, self-organized motor clusters form spontaneously. We model the motors with a two-state noise-driven ratchet formulation and study analytically and numerically the collective velocity-force and efficiency-force curves resulting from mutual interactions, mostly hard-core repulsion and weak (nonbinding) attraction. We analyze different parameter regimes including the limits of weak noise, mean-field behavior, rigid coupling, and large numbers of motors, for the different interactions. We present a general framework to classify and quantify cooperativity. We show that asymmetric loading leads generically to enhanced cooperativity beyond the simple superposition of the effects of individual motors. For weakly attracting interactions, the cooperativity is mostly enhanced, including highly coordinated motion of motors and complex nonmonotonic velocity-force curves, leading to self-regulated clusters. The dynamical scenario is enriched by resonances associated to commensurability of different length scales. Large clusters exhibit synchronized dynamics and bidirectional motion. Biological implications are discussed.

Cooperativity of self-organized Brownian motors pulling on soft cargoes

NASA Astrophysics Data System (ADS)

Orlandi, Javier G.; Blanch-Mercader, Carles; Brugués, Jan; Casademunt, Jaume

2010-12-01

We study the cooperative dynamics of Brownian motors moving along a one-dimensional track when an external load is applied to the leading motor, mimicking molecular motors pulling on membrane-bound cargoes in intracellular traffic. Due to the asymmetric loading, self-organized motor clusters form spontaneously. We model the motors with a two-state noise-driven ratchet formulation and study analytically and numerically the collective velocity-force and efficiency-force curves resulting from mutual interactions, mostly hard-core repulsion and weak (nonbinding) attraction. We analyze different parameter regimes including the limits of weak noise, mean-field behavior, rigid coupling, and large numbers of motors, for the different interactions. We present a general framework to classify and quantify cooperativity. We show that asymmetric loading leads generically to enhanced cooperativity beyond the simple superposition of the effects of individual motors. For weakly attracting interactions, the cooperativity is mostly enhanced, including highly coordinated motion of motors and complex nonmonotonic velocity-force curves, leading to self-regulated clusters. The dynamical scenario is enriched by resonances associated to commensurability of different length scales. Large clusters exhibit synchronized dynamics and bidirectional motion. Biological implications are discussed.

Optimal spacecraft formation establishment and reconfiguration propelled by the geomagnetic Lorentz force

NASA Astrophysics Data System (ADS)

Huang, Xu; Yan, Ye; Zhou, Yang

2014-12-01

The Lorentz force acting on an electrostatically charged spacecraft as it moves through the planetary magnetic field could be utilized as propellantless electromagnetic propulsion for orbital maneuvering, such as spacecraft formation establishment and formation reconfiguration. By assuming that the Earth's magnetic field could be modeled as a tilted dipole located at the center of Earth that corotates with Earth, a dynamical model that describes the relative orbital motion of Lorentz spacecraft is developed. Based on the proposed dynamical model, the energy-optimal open-loop trajectories of control inputs, namely, the required specific charges of Lorentz spacecraft, for Lorentz-propelled spacecraft formation establishment or reconfiguration problems with both fixed and free final conditions constraints are derived via Gauss pseudospectral method. The effect of the magnetic dipole tilt angle on the optimal control inputs and the relative transfer trajectories for formation establishment or reconfiguration is also investigated by comparisons with the results derived from a nontilted dipole model. Furthermore, a closed-loop integral sliding mode controller is designed to guarantee the trajectory tracking in the presence of external disturbances and modeling errors. The stability of the closed-loop system is proved by a Lyapunov-based approach. Numerical simulations are presented to verify the validity of the proposed open-loop control methods and demonstrate the performance of the closed-loop controller. Also, the results indicate the dipole tilt angle should be considered when designing control strategies for Lorentz-propelled spacecraft formation establishment or reconfiguration.

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

Antolin, P.; Vissers, G.; Shibata, K., E-mail: antolin@astro.uio.n, E-mail: g.j.m.vissers@astro.uio.n, E-mail: shibata@kwasan.kyoto-u.ac.j

Reported observations in H{alpha}, Ca II H, and K or other chromospheric lines of coronal rain trace back to the days of the Skylab mission. Corresponding to cool and dense plasma, coronal rain is often observed falling down along coronal loops in active regions. A physical explanation for this spectacular phenomenon has been put forward thanks to numerical simulations of loops with footpoint-concentrated heating, a heating scenario in which cool condensations naturally form in the corona. This effect has been termed 'catastrophic cooling' and is the predominant explanation for coronal rain. In this work, we further investigate the link betweenmore » this phenomenon and the heating mechanisms acting in the corona. We start by analyzing observations of coronal rain at the limb in the Ca II H line performed by the Hinode satellite, and derive interesting statistical properties concerning the dynamics. We then compare the observations with 1.5-dimensional MHD simulations of loops being heated by small-scale discrete events concentrated toward the footpoints (that could come, for instance, from magnetic reconnection events), and by Alfven waves generated at the photospheric level. Both our observation and simulation results suggest that coronal rain is a far more common phenomenon than previously thought. Also, we show that the structure and dynamics of condensations are far more sensitive to the internal pressure changes in loops than to gravity. Furthermore, it is found that if a loop is predominantly heated from Alfven waves, coronal rain is inhibited due to the characteristic uniform heating they produce. Hence, coronal rain may not only point to the spatial distribution of the heating in coronal loops but also to the agent of the heating itself. We thus propose coronal rain as a marker for coronal heating mechanisms.« less

Assessing the effect of D59P mutation in the DE loop region in amyloid aggregation propensity of β2-microglobulin: A molecular dynamics simulation study.

PubMed

Narang, Simranjeet S; Shuaib, Suniba; Goyal, Deepti; Goyal, Bhupesh

2018-01-01

Dialysis-related amyloidosis (DRA) is a severe condition characterized by the accumulation of amyloidogenic β2-microglobulin (β2m) protein around skeletal joints and bones. The recent studies highlighted a critical role of the DE loop region for β2m stability and amyloid aggregation propensity. Despite significant efforts, the molecular mechanism of enhanced aggregation due to D59P mutation in the DE loop region remain elusive. In the present study, explicit-solvent molecular dynamics (MD) simulations were performed to examine the key changes in the structural and dynamic properties of wild type (wt) β2m upon D59P mutation. MD simulations reveal a decrease in the average number of hydrogen bonds in the loop regions on D59P mutation that enhances conformational flexibility, which lead to higher aggregation propensity of D59P as compare to wt β2m. The principal component analysis (PCA) highlight that D59P covers a larger region of phase space and display a higher trace value than wt β2m, which suggest an overall enhancement in the conformational flexibility. D59P display two minimum energy basins in the free energy landscape (FEL) that are associated with thermodynamically less stable conformational states as compare to single minimum energy basin in wt β2m. The present study provides theoretical insights into the molecular mechanism behind the higher aggregation propensity of D59P as compare to wt β2m. © 2017 Wiley Periodicals, Inc.

Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations.

PubMed

Guan, Shanshan; Zhao, Li; Jin, Hanyong; Shan, Ning; Han, Weiwei; Wang, Song; Shan, Yaming

2017-02-01

Phosphotriesterase-like lactonases (PLLs) have received much attention because of their physical and chemical properties. They may have widespread applications in various fields. For example, they show potential for quorum-sensing signaling pathways and organophosphorus (OP) detoxification in agricultural science. However, the mechanism by which PLLs hydrolyze, which involves OP compounds and lactones and a variety of distinct catalytic efficiencies, has only rarely been explored. In the present study, molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of DrPLL, a member of the PLL superfamily in Deinococcus radiodurans, bound to two substrates, δ-nonanoic lactone and paraoxon. It has been observed that there is a 16-fold increase in the catalytic efficiency of the two mutant strains of DrPLL (F26G/C72I) vs. the wild-type enzyme toward the hydrolysis of paraoxon, but an explanation for this behavior is currently lacking. The analysis of the molecular trajectories of DrPLL bound to δ-nonanoic lactone indicated that lactone-induced conformational changes take place in loop 8, which is near the active site. Binding to paraoxon may lead to conformational displacement of loop 1 residues, which could lead to the deformation of the active site and so trigger the entry of the paraoxon into the active site. The efficiency of the F26G/C72I mutant was increased by decreasing the displacement of loop 1 residues and increasing the flexibility of loop 8 residues. These results provide a molecular-level explanation for the experimental behavior.

Thermal responses in a coronal loop maintained by wave heating mechanisms

NASA Astrophysics Data System (ADS)

Matsumoto, Takuma

2018-05-01

A full 3-dimensional compressible magnetohydrodynamic (MHD) simulation is conducted to investigate the thermal responses of a coronal loop to the dynamic dissipation processes of MHD waves. When the foot points of the loop are randomly and continuously forced, the MHD waves become excited and propagate upward. Then, 1-MK temperature corona is produced naturally as the wave energy dissipates. The excited wave packets become non-linear just above the magnetic canopy, and the wave energy cascades into smaller spatial scales. Moreover, collisions between counter-propagating Alfvén wave packets increase the heating rate, resulting in impulsive temperature increases. Our model demonstrates that the heating events in the wave-heated loops can be nanoflare-like in the sense that they are spatially localized and temporally intermittent.

Compensated control loops for a 30-cm ion thruster

NASA Technical Reports Server (NTRS)

Robson, R. R.

1976-01-01

The vaporizer dynamic control characteristics of a 30-cm diameter mercury ion thruster were determined by operating the thruster in an open loop steady state mode and then introducing a small sinusoidal signal on the main, cathode, or neutralizer vaporizer current and observing the response of the beam current, discharge voltage, and neutralizer keeper voltage, respectively. This was done over a range of frequencies and operating conditions. From these data, Bode plots for gain and phase were made and mathematical models were obtained. The Bode plots and mathematical models were analyzed for stability and appropriate compensation networks determined. The compensated control loops were incorporated into a power processor and operated with a thruster. The time responses of the compensated loops to changes in set points and recovery from arc conditions are presented.

Experimental Study of Flexible Plate Vibration Control by Using Two-Loop Sliding Mode Control Strategy

NASA Astrophysics Data System (ADS)

Yang, Jingyu; Lin, Jiahui; Liu, Yuejun; Yang, Kang; Zhou, Lanwei; Chen, Guoping

2017-08-01

It is well known that intelligent control theory has been used in many research fields, novel modeling method (DROMM) is used for flexible rectangular active vibration control, and then the validity of new model is confirmed by comparing finite element model with new model. In this paper, taking advantage of the dynamics of flexible rectangular plate, a two-loop sliding mode (TSM) MIMO approach is introduced for designing multiple-input multiple-output continuous vibration control system, which can overcome uncertainties, disturbances or unstable dynamics. An illustrative example is given in order to show the feasibility of the method. Numerical simulations and experiment confirm the effectiveness of the proposed TSM MIMO controller.

Nonlinear susceptibility and dynamic hysteresis loops of magnetic nanoparticles with biaxial anisotropy

NASA Astrophysics Data System (ADS)

Ouari, Bachir; Titov, Serguey V.; El Mrabti, Halim; Kalmykov, Yuri P.

2013-02-01

The nonlinear ac susceptibility and dynamic magnetic hysteresis (DMH) of a single domain ferromagnetic particle with biaxial anisotropy subjected to both external ac and dc fields of arbitrary strength and orientation are treated via Brown's continuous diffusions model [W. F. Brown, Jr., Phys. Rev. 130, 1677 (1963)] of magnetization orientations. The DMH loops and nonlinear ac susceptibility strongly depend on the dc and ac field strengths, the polar angle between the easy axis of the particle, the external field vectors, temperature, and damping. In contrast to uniaxial particles, the nonlinear ac stationary response and DMH strongly depend on the azimuthal direction of the ac field and the biaxiality parameter Δ.

Fundamental Structure of Loop Quantum Gravity

NASA Astrophysics Data System (ADS)

Han, Muxin; Ma, Yongge; Huang, Weiming

In the recent twenty years, loop quantum gravity, a background independent approach to unify general relativity and quantum mechanics, has been widely investigated. The aim of loop quantum gravity is to construct a mathematically rigorous, background independent, non-perturbative quantum theory for a Lorentzian gravitational field on a four-dimensional manifold. In the approach, the principles of quantum mechanics are combined with those of general relativity naturally. Such a combination provides us a picture of, so-called, quantum Riemannian geometry, which is discrete on the fundamental scale. Imposing the quantum constraints in analogy from the classical ones, the quantum dynamics of gravity is being studied as one of the most important issues in loop quantum gravity. On the other hand, the semi-classical analysis is being carried out to test the classical limit of the quantum theory. In this review, the fundamental structure of loop quantum gravity is presented pedagogically. Our main aim is to help non-experts to understand the motivations, basic structures, as well as general results. It may also be beneficial to practitioners to gain insights from different perspectives on the theory. We will focus on the theoretical framework itself, rather than its applications, and do our best to write it in modern and precise langauge while keeping the presentation accessible for beginners. After reviewing the classical connection dynamical formalism of general relativity, as a foundation, the construction of the kinematical Ashtekar-Isham-Lewandowski representation is introduced in the content of quantum kinematics. The algebraic structure of quantum kinematics is also discussed. In the content of quantum dynamics, we mainly introduce the construction of a Hamiltonian constraint operator and the master constraint project. At last, some applications and recent advances are outlined. It should be noted that this strategy of quantizing gravity can also be extended to obtain other background-independent quantum gauge theories. There is no divergence within this background-independent and diffeomorphism-invariant quantization program of matter coupled to gravity.

Functional roles of H98 and W99 and β2α2 loop dynamics in the α-l-arabinofuranosidase from Thermobacillus xylanilyticus.

PubMed

Arab-Jaziri, Faten; Bissaro, Bastien; Barbe, Sophie; Saurel, Olivier; Débat, Hélène; Dumon, Claire; Gervais, Virginie; Milon, Alain; André, Isabelle; Fauré, Régis; O'Donohue, Michael J

2012-10-01

This study is focused on the elucidation of the functional role of the mobile β2α2 loop in the α-L-arabinofuranosidase from Thermobacillus xylanilyticus, and particularly on the roles of loop residues H98 and W99. Using site-directed mutagenesis, coupled to characterization methods including isothermal titration calorimetry (ITC) and saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, and molecular dynamics simulations, it has been possible to provide a molecular level view of interactions and the consequences of mutations. Binding of para-nitrophenyl α-L-arabinofuranoside (pNP-α-l-Araf) to the wild-type arabinofuranosidase was characterized by K(d) values (0.32 and 0.16 mm, from ITC and STD-NMR respectively) that highly resembled that of the arabinoxylo-oligosaccharide XA(3)XX (0.21 mm), and determination of the thermodynamic parameters of enzyme : pNP-α-L-Araf binding revealed that this process is driven by favourable entropy, which is linked to the movement of the β2α2 loop. Loop closure relocates the solvent-exposed W99 into a buried location, allowing its involvement in substrate binding and in the formation of a functional active site. Similarly, the data underline the role of H98 in the ‘dynamic’ formation and definition of a catalytically operational active site, which may be a specific feature of a subset of GH51 arabinofuranosidases. Substitution of H98 and W99 by alanine or phenylalanine revealed that mutations affected K(M) and/or k(cat). Molecular dynamics performed on W99A implied that this mutation causes the loss of a hydrogen bond and leads to an alternative binding mode that is detrimental for catalysis. STD-NMR experiments revealed altered binding of the aglycon motif in the active site, combined with reduced STD intensities of the α-L-arabinofuranosyl moiety for W99 substitutions. © 2012 The Authors Journal compilation © 2012 FEBS.

Characterizing system dynamics with a weighted and directed network constructed from time series data

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

Sun, Xiaoran, E-mail: sxr0806@gmail.com; School of Mathematics and Statistics, The University of Western Australia, Crawley WA 6009; Small, Michael, E-mail: michael.small@uwa.edu.au

In this work, we propose a novel method to transform a time series into a weighted and directed network. For a given time series, we first generate a set of segments via a sliding window, and then use a doubly symbolic scheme to characterize every windowed segment by combining absolute amplitude information with an ordinal pattern characterization. Based on this construction, a network can be directly constructed from the given time series: segments corresponding to different symbol-pairs are mapped to network nodes and the temporal succession between nodes is represented by directed links. With this conversion, dynamics underlying the timemore » series has been encoded into the network structure. We illustrate the potential of our networks with a well-studied dynamical model as a benchmark example. Results show that network measures for characterizing global properties can detect the dynamical transitions in the underlying system. Moreover, we employ a random walk algorithm to sample loops in our networks, and find that time series with different dynamics exhibits distinct cycle structure. That is, the relative prevalence of loops with different lengths can be used to identify the underlying dynamics.« less

Mitotic chromosome compaction via active loop extrusion

NASA Astrophysics Data System (ADS)

Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

Formation of chromosomal domains in interphase by loop extrusion

NASA Astrophysics Data System (ADS)

Fudenberg, Geoffrey

While genomes are often considered as one-dimensional sequences, interphase chromosomes are organized in three dimensions with an essential role for regulating gene expression. Recent studies have shown that Topologically Associating Domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes. Despite observations that architectural proteins, including CTCF, demarcate and maintain the borders of TADs, the mechanisms underlying TAD formation remain unknown. Here we propose that loop extrusion underlies the formation TADs. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops, but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. This process dynamically forms loops of various sizes within but not between TADs. Using polymer simulations, we find that loop extrusion can produce TADs as determined by our analyses of the highest-resolution experimental data. Moreover, we find that loop extrusion can explain many diverse experimental observations, including: the preferential orientation of CTCF motifs and enrichments of architectural proteins at TAD boundaries; TAD boundary deletion experiments; and experiments with knockdown or depletion of CTCF, cohesin, and cohesin-loading factors. Together, the emerging picture from our work is that TADs are formed by rapidly associating, growing, and dissociating loops, presenting a clear framework for understanding interphase chromosomal organization.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

NASA Astrophysics Data System (ADS)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

Determination of Fermi contour and spin polarization of ν = 3 2 composite fermions via ballistic commensurability measurements

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

Kamburov, D.; Mueed, M. A.; Jo, I.

2014-12-01

We report ballistic transport commensurability minima in the magnetoresistance of nu = 3/2 composite fermions (CFs). The CFs are formed in high-quality two-dimensional electron systems confined to wide GaAs quantum wells and subjected to an in-plane, unidirectional periodic potential modulation. We observe a slight asymmetry of the CF commensurability positions with respect to nu = 3/2, which we explain quantitatively by comparing three CF density models and concluding that the nu = 3/2 CFs are likely formed by the minority carriers in the upper energy spin state of the lowest Landau level. Our data also allow us to probe themore » shape and size of the CF Fermi contour. At a fixed electron density of similar or equal to 1.8x10(11) cm(-2), as the quantum well width increases from 30 to 60 nm, the CFs show increasing spin polarization. We attribute this to the enhancement of the Zeeman energy relative to the Coulomb energy in wider wells where the latter is softened because of the larger electron layer thickness. The application of an additional parallel magnetic field (B-parallel to) leads to a significant distortion of the CF Fermi contour as B-parallel to couples to the CFs' out-of-plane orbital motion. The distortion is much more severe compared to the nu = 1/2 CF case at comparable B-parallel to. Moreover, the applied B-parallel to further spin-polarizes the nu = 3/2 CFs as deduced from the positions of the commensurability minima.« less

Investigation of the commensurate magnetic structure in the heavy-fermion compound CePt 2 In 7 using magnetic resonant x-ray diffraction

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

Gauthier, Nicolas; Wermeille, Didier; Casati, Nicola

In this paper, we investigated the magnetic structure of the heavy-fermion compound CePt 2In 7 below T N = 5.34 (2) K using magnetic resonant x-ray diffraction at ambient pressure. The magnetic order is characterized by a commensurate propagation vector k 1/2 = (1/2, 1/2, 1/2) with spins lying in the basal plane. Our measurements did not reveal the presence of an incommensurate order propagating along the high-symmetry directions in reciprocal space but cannot exclude other incommensurate modulations or weak scattering intensities. The observed commensurate order can be described equivalently by either a single-k structure or by a multi-k structure.more » Furthermore we explain how a commensurate-only ordering may explain the broad distribution of internal fields observed in nuclear quadrupolar resonance experiments [Sakai et al., Phys. Rev. B 83, 140408 (2011)] that was previously attributed to an incommensurate order. We also report powder x-ray diffraction showing that the crystallographic structure of CePt 2In 7 changes monotonically with pressure up to P = 7.3 GPa at room temperature. The determined bulk modulus B 0 = 81.1 (3) GPa is similar to those of the Ce-115 family. Broad diffraction peaks confirm the presence of pronounced strain in polycrystalline samples of CePt 2In 7. Lastly, we discuss how strain effects can lead to different electronic and magnetic properties between polycrystalline and single crystal samples.« less

Investigation of the commensurate magnetic structure in the heavy-fermion compound CePt 2 In 7 using magnetic resonant x-ray diffraction

DOE PAGES

Gauthier, Nicolas; Wermeille, Didier; Casati, Nicola; ...

2017-08-10

In this paper, we investigated the magnetic structure of the heavy-fermion compound CePt 2In 7 below T N = 5.34 (2) K using magnetic resonant x-ray diffraction at ambient pressure. The magnetic order is characterized by a commensurate propagation vector k 1/2 = (1/2, 1/2, 1/2) with spins lying in the basal plane. Our measurements did not reveal the presence of an incommensurate order propagating along the high-symmetry directions in reciprocal space but cannot exclude other incommensurate modulations or weak scattering intensities. The observed commensurate order can be described equivalently by either a single-k structure or by a multi-k structure.more » Furthermore we explain how a commensurate-only ordering may explain the broad distribution of internal fields observed in nuclear quadrupolar resonance experiments [Sakai et al., Phys. Rev. B 83, 140408 (2011)] that was previously attributed to an incommensurate order. We also report powder x-ray diffraction showing that the crystallographic structure of CePt 2In 7 changes monotonically with pressure up to P = 7.3 GPa at room temperature. The determined bulk modulus B 0 = 81.1 (3) GPa is similar to those of the Ce-115 family. Broad diffraction peaks confirm the presence of pronounced strain in polycrystalline samples of CePt 2In 7. Lastly, we discuss how strain effects can lead to different electronic and magnetic properties between polycrystalline and single crystal samples.« less

Virtual grasping: closed-loop force control using electrotactile feedback.

PubMed

Jorgovanovic, Nikola; Dosen, Strahinja; Djozic, Damir J; Krajoski, Goran; Farina, Dario

2014-01-01

Closing the control loop by providing somatosensory feedback to the user of a prosthesis is a well-known, long standing challenge in the field of prosthetics. Various approaches have been investigated for feedback restoration, ranging from direct neural stimulation to noninvasive sensory substitution methods. Although there are many studies presenting closed-loop systems, only a few of them objectively evaluated the closed-loop performance, mostly using vibrotactile stimulation. Importantly, the conclusions about the utility of the feedback were partly contradictory. The goal of the current study was to systematically investigate the capability of human subjects to control grasping force in closed loop using electrotactile feedback. We have developed a realistic experimental setup for virtual grasping, which operated in real time, included a set of real life objects, as well as a graphical and dynamical model of the prosthesis. We have used the setup to test 10 healthy, able bodied subjects to investigate the role of training, feedback and feedforward control, robustness of the closed loop, and the ability of the human subjects to generalize the control to previously "unseen" objects. Overall, the outcomes of this study are very optimistic with regard to the benefits of feedback and reveal various, practically relevant, aspects of closed-loop control.

Partial Reflection and Trapping of a Fast-mode Wave in Solar Coronal Arcade Loops

NASA Astrophysics Data System (ADS)

Kumar, Pankaj; Innes, D. E.

2015-04-01

We report on the first direct observation of a fast-mode wave propagating along and perpendicular to cool (171 Å) arcade loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly (AIA). The wave was associated with an impulsive/compact flare near the edge of a sunspot. The EUV wavefront expanded radially outward from the flare center and decelerated in the corona from 1060 to 760 km s-1 within ˜3-4 minutes. Part of the EUV wave propagated along a large-scale arcade of cool loops and was partially reflected back to the flare site. The phase speed of the wave was about 1450 km s-1, which is interpreted as a fast-mode wave. A second overlying loop arcade, orientated perpendicular to the cool arcade, is heated and becomes visible in the AIA hot channels. These hot loops sway in time with the EUV wave, as it propagated to and fro along the lower loop arcade. We suggest that an impulsive energy release at one of the footpoints of the arcade loops causes the onset of an EUV shock wave that propagates along and perpendicular to the magnetic field.

FINE STRUCTURES AND OVERLYING LOOPS OF CONFINED SOLAR FLARES

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

Yang, Shuhong; Zhang, Jun; Xiang, Yongyuan, E-mail: shuhongyang@nao.cas.cn

2014-10-01

Using the Hα observations from the New Vacuum Solar Telescope at the Fuxian Solar Observatory, we focus on the fine structures of three confined flares and the issue why all the three flares are confined instead of eruptive. All the three confined flares take place successively at the same location and have similar morphologies, so can be termed homologous confined flares. In the simultaneous images obtained by the Solar Dynamics Observatory, many large-scale coronal loops above the confined flares are clearly observed in multi-wavelengths. At the pre-flare stage, two dipoles emerge near the negative sunspot, and the dipolar patches aremore » connected by small loops appearing as arch-shaped Hα fibrils. There exists a reconnection between the small loops, and thus the Hα fibrils change their configuration. The reconnection also occurs between a set of emerging Hα fibrils and a set of pre-existing large loops, which are rooted in the negative sunspot, a nearby positive patch, and some remote positive faculae, forming a typical three-legged structure. During the flare processes, the overlying loops, some of which are tracked by activated dark materials, do not break out. These direct observations may illustrate the physical mechanism of confined flares, i.e., magnetic reconnection between the emerging loops and the pre-existing loops triggers flares and the overlying loops prevent the flares from being eruptive.« less

Pilot-in-the-Loop CFD Method Development

DTIC Science & Technology

2016-02-01

Contract # N00014-14-C-0020 Pilot-in-the-Loop CFD Method Development Progress Report (CDRL A001) Progress Report for Period: October 21...of the aircraft from the rest of its external environment. For example, ship airwake are calculated using CFD solutions without the presence of the...approaches with the goal of real time, fully coupled CFD for virtual dynamic interface modeling & simulation. Penn State is supporting the project

Pilot-in-the Loop CFD Method Development

DTIC Science & Technology

2016-04-27

Contract # N00014-14-C-0020 Pilot-in-the-Loop CFD Method Development Progress Report (CDRL A001) Progress Report for Period: January 21...aerodynamics of the aircraft from the rest of its external environment. For example, ship airwake are calculated using CFD solutions without the presence of...hardware approaches with the goal of real time, fully coupled CFD for virtual dynamic interface modeling & simulation. Penn State is supporting the project

Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution

PubMed Central

Tu, Chao; Tan, Yu-Hong; Shaw, Gary; Zhou, Zheng; Bai, Yawen; Luo, Ray; Ji, Xinhua

2008-01-01

Tumor suppressor p53 is a sequence-specific DNA-binding protein and its central DNA-binding domain (DBD) harbors six hotspots (Arg175, Gly245, Arg248, Arg249, Arg273 and Arg282) for human cancers. Here, the crystal structure of a low-frequency hotspot mutant, p53DBD(R282Q), is reported at 1.54 Å resolution together with the results of molecular-dynamics simulations on the basis of the structure. In addition to eliminating a salt bridge, the R282Q mutation has a significant impact on the properties of two DNA-binding loops (L1 and L3). The L1 loop is flexible in the wild type, but it is not flexible in the mutant. The L3 loop of the wild type is not flexible, whereas it assumes two conformations in the mutant. Molecular-dynamics simulations indicated that both conformations of the L3 loop are accessible under biological conditions. It is predicted that the elimination of the salt bridge and the inversion of the flexibility of L1 and L3 are directly or indirectly responsible for deactivating the tumor suppressor p53. PMID:18453682

Closed-Loop, Multichannel Experimentation Using the Open-Source NeuroRighter Electrophysiology Platform

PubMed Central

Newman, Jonathan P.; Zeller-Townson, Riley; Fong, Ming-Fai; Arcot Desai, Sharanya; Gross, Robert E.; Potter, Steve M.

2013-01-01

Single neuron feedback control techniques, such as voltage clamp and dynamic clamp, have enabled numerous advances in our understanding of ion channels, electrochemical signaling, and neural dynamics. Although commercially available multichannel recording and stimulation systems are commonly used for studying neural processing at the network level, they provide little native support for real-time feedback. We developed the open-source NeuroRighter multichannel electrophysiology hardware and software platform for closed-loop multichannel control with a focus on accessibility and low cost. NeuroRighter allows 64 channels of stimulation and recording for around US $10,000, along with the ability to integrate with other software and hardware. Here, we present substantial enhancements to the NeuroRighter platform, including a redesigned desktop application, a new stimulation subsystem allowing arbitrary stimulation patterns, low-latency data servers for accessing data streams, and a new application programming interface (API) for creating closed-loop protocols that can be inserted into NeuroRighter as plugin programs. This greatly simplifies the design of sophisticated real-time experiments without sacrificing the power and speed of a compiled programming language. Here we present a detailed description of NeuroRighter as a stand-alone application, its plugin API, and an extensive set of case studies that highlight the system’s abilities for conducting closed-loop, multichannel interfacing experiments. PMID:23346047

Test-area surface tension calculation of the graphene-methane interface: Fluctuations and commensurability

NASA Astrophysics Data System (ADS)

d'Oliveira, H. D.; Davoy, X.; Arche, E.; Malfreyt, P.; Ghoufi, A.

2017-06-01

The surface tension (γ) of methane on a graphene monolayer is calculated by using the test-area approach. By using a united atom model to describe methane molecules, strong fluctuations of surface tension as a function of the surface area of the graphene are evidenced. In contrast with the liquid-vapor interfaces, the use of a larger cutoff does not fully erase the fluctuations in the surface tension. Counterintuitively, the description of methane and graphene from the Optimized Potentials for Liquid Simulations all-atom model and a flexible model, respectively, led to a lessening in the surface tension fluctuations. This result suggests that the origin of fluctuations in γ is due to a model-effect rather than size-effects. We show that the molecular origin of these fluctuations is the result of a commensurable organization between both graphene and methane. This commensurable structure can be avoided by describing methane and graphene from a flexible force field. Although differences in γ with respect to the model have been often reported, it is the first time that the model drastically affects the physics of a system.

Robust spin-valley polarization in commensurate Mo S2 /graphene heterostructures

NASA Astrophysics Data System (ADS)

Du, Luojun; Zhang, Qian; Gong, Benchao; Liao, Mengzhou; Zhu, Jianqi; Yu, Hua; He, Rui; Liu, Kai; Yang, Rong; Shi, Dongxia; Gu, Lin; Yan, Feng; Zhang, Guangyu; Zhang, Qingming

2018-03-01

The investigation and control of quantum degrees of freedom (DoFs) of carriers lie at the heart of condensed-matter physics and next-generation electronics/optoelectronics. van der Waals heterostructures stacked from distinct two-dimensional (2D) crystals offer an unprecedented platform for combining the superior properties of individual 2D materials and manipulating spin, layer, and valley DoFs. Mo S2 /graphene heterostructures, harboring prominent spin-transport properties of graphene, giant spin-orbit coupling, and spin-valley polarization of Mo S2 , are predicted as a perfect venue for optospintronics. Here, we report the epitaxial growth of commensurate Mo S2 on graphene with high quality by chemical vapor deposition, and demonstrate robust temperature-independent spin-valley polarization at off-resonant excitation. We further show that the helicity of B exciton is larger than that of A exciton, allowing the manipulation of spin bits in the commensurate heterostructures by both optical helicity and wavelength. Our results open a window for controlling spin DoF by light and pave a way for taking spin qubits as information carriers in the next-generation valley-controlled optospintronics.

Singularity-free backstepping controller for model helicopters.

PubMed

Zou, Yao; Huo, Wei

2016-11-01

This paper develops a backstepping controller for model helicopters to achieve trajectory tracking without singularity, which occurs in the attitude representation when the roll or pitch reaches ±π2. Based on a simplified model with unmodeled dynamics, backstepping technique is introduced to exploit the controller and hyperbolic tangent functions are utilized to compensate the unmodeled dynamics. Firstly, a position loop controller is designed for the position tracking, where an auxiliary dynamic system with suitable parameters is introduced to warrant the singularity-free requirement for the extracted command attitude. Then, a novel attitude loop controller is proposed to obviate singularity. It is demonstrated that, based on the established criteria for selecting controller parameters and desired trajectories, the proposed controller realizes the singularity-free trajectory tracking of the model helicopter. Simulations confirm the theoretical results. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

A Parametric Computational Model of the Action Potential of Pacemaker Cells.

PubMed

Ai, Weiwei; Patel, Nitish D; Roop, Partha S; Malik, Avinash; Andalam, Sidharta; Yip, Eugene; Allen, Nathan; Trew, Mark L

2018-01-01

A flexible, efficient, and verifiable pacemaker cell model is essential to the design of real-time virtual hearts that can be used for closed-loop validation of cardiac devices. A new parametric model of pacemaker action potential is developed to address this need. The action potential phases are modeled using hybrid automaton with one piecewise-linear continuous variable. The model can capture rate-dependent dynamics, such as action potential duration restitution, conduction velocity restitution, and overdrive suppression by incorporating nonlinear update functions. Simulated dynamics of the model compared well with previous models and clinical data. The results show that the parametric model can reproduce the electrophysiological dynamics of a variety of pacemaker cells, such as sinoatrial node, atrioventricular node, and the His-Purkinje system, under varying cardiac conditions. This is an important contribution toward closed-loop validation of cardiac devices using real-time heart models.

Divergence compensation for hardware-in-the-loop simulation of stiffness-varying discrete contact in space

NASA Astrophysics Data System (ADS)

Qi, Chenkun; Zhao, Xianchao; Gao, Feng; Ren, Anye; Hu, Yan

2016-11-01

The hardware-in-the-loop (HIL) contact simulation for flying objects in space is challenging due to the divergence caused by the time delay. In this study, a divergence compensation approach is proposed for the stiffness-varying discrete contact. The dynamic response delay of the motion simulator and the force measurement delay are considered. For the force measurement delay, a phase lead based force compensation approach is used. For the dynamic response delay of the motion simulator, a response error based force compensation approach is used, where the compensation force is obtained from the real-time identified contact stiffness and real-time measured position response error. The dynamic response model of the motion simulator is not required. The simulations and experiments show that the simulation divergence can be compensated effectively and satisfactorily by using the proposed approach.

Close-loop Dynamic Stall Control on a Pitching Airfoil

NASA Astrophysics Data System (ADS)

Giles, Ian; Corke, Thomas

2017-11-01

A closed-loop control scheme utilizing a plasma actuator to control dynamic stall is presented. The plasma actuator is located at the leading-edge of a pitching airfoil. It initially pulses at an unsteady frequency that perturbs the boundary layer flow over the suction surface of the airfoil. As the airfoil approaches and enters stall, the amplification of the unsteady disturbance is detected by an onboard pressure sensor also located near the leading edge. Once detected, the actuator is switched to a higher voltage control state that in static airfoil experiments would reattach the flow. The threshold level of the detection is a parameter in the control scheme. Three stall regimes were examined: light, medium, and deep stall, that were defined by their stall penetration angles. The results showed that in general, the closed-loop control scheme was effective at controlling dynamic stall. The cycle-integrated lift improved in all cases, and increased by as much as 15% at the lowest stall penetration angle. As important, the cycle-integrated aerodynamic damping coefficient also increased in all cases, and was made to be positive at the light stall regime where it traditionally is negative. The latter is important in applications where negative damping can lead to stall flutter.

Group theoretical quantization of isotropic loop cosmology

NASA Astrophysics Data System (ADS)

Livine, Etera R.; Martín-Benito, Mercedes

2012-06-01

We achieve a group theoretical quantization of the flat Friedmann-Robertson-Walker model coupled to a massless scalar field adopting the improved dynamics of loop quantum cosmology. Deparemetrizing the system using the scalar field as internal time, we first identify a complete set of phase space observables whose Poisson algebra is isomorphic to the su(1,1) Lie algebra. It is generated by the volume observable and the Hamiltonian. These observables describe faithfully the regularized phase space underlying the loop quantization: they account for the polymerization of the variable conjugate to the volume and for the existence of a kinematical nonvanishing minimum volume. Since the Hamiltonian is an element in the su(1,1) Lie algebra, the dynamics is now implemented as SU(1, 1) transformations. At the quantum level, the system is quantized as a timelike irreducible representation of the group SU(1, 1). These representations are labeled by a half-integer spin, which gives the minimal volume. They provide superselection sectors without quantization anomalies and no factor ordering ambiguity arises when representing the Hamiltonian. We then explicitly construct SU(1, 1) coherent states to study the quantum evolution. They not only provide semiclassical states but truly dynamical coherent states. Their use further clarifies the nature of the bounce that resolves the big bang singularity.

Steering and positioning targets for HWIL IR testing at cryogenic conditions

NASA Astrophysics Data System (ADS)

Perkes, D. W.; Jensen, G. L.; Higham, D. L.; Lowry, H. S.; Simpson, W. R.

2006-05-01

In order to increase the fidelity of hardware-in-the-loop ground-truth testing, it is desirable to create a dynamic scene of multiple, independently controlled IR point sources. ATK-Mission Research has developed and supplied the steering mirror systems for the 7V and 10V Space Simulation Test Chambers at the Arnold Engineering Development Center (AEDC), Air Force Materiel Command (AFMC). A portion of the 10V system incorporates multiple target sources beam-combined at the focal point of a 20K cryogenic collimator. Each IR source consists of a precision blackbody with cryogenic aperture and filter wheels mounted on a cryogenic two-axis translation stage. This point source target scene is steered by a high-speed steering mirror to produce further complex motion. The scene changes dynamically in order to simulate an actual operational scene as viewed by the System Under Test (SUT) as it executes various dynamic look-direction changes during its flight to a target. Synchronization and real-time hardware-in-the-loop control is accomplished using reflective memory for each subsystem control and feedback loop. This paper focuses on the steering mirror system and the required tradeoffs of optical performance, precision, repeatability and high-speed motion as well as the complications of encoder feedback calibration and operation at 20K.

A nonlinear optimal control approach for chaotic finance dynamics

NASA Astrophysics Data System (ADS)

Rigatos, G.; Siano, P.; Loia, V.; Tommasetti, A.; Troisi, O.

2017-11-01

A new nonlinear optimal control approach is proposed for stabilization of the dynamics of a chaotic finance model. The dynamic model of the financial system, which expresses interaction between the interest rate, the investment demand, the price exponent and the profit margin, undergoes approximate linearization round local operating points. These local equilibria are defined at each iteration of the control algorithm and consist of the present value of the systems state vector and the last value of the control inputs vector that was exerted on it. The approximate linearization makes use of Taylor series expansion and of the computation of the associated Jacobian matrices. The truncation of higher order terms in the Taylor series expansion is considered to be a modelling error that is compensated by the robustness of the control loop. As the control algorithm runs, the temporary equilibrium is shifted towards the reference trajectory and finally converges to it. The control method needs to compute an H-infinity feedback control law at each iteration, and requires the repetitive solution of an algebraic Riccati equation. Through Lyapunov stability analysis it is shown that an H-infinity tracking performance criterion holds for the control loop. This implies elevated robustness against model approximations and external perturbations. Moreover, under moderate conditions the global asymptotic stability of the control loop is proven.

Design and hardware-in-loop implementation of collision avoidance algorithms for heavy commercial road vehicles

NASA Astrophysics Data System (ADS)

Rajaram, Vignesh; Subramanian, Shankar C.

2016-07-01

An important aspect from the perspective of operational safety of heavy road vehicles is the detection and avoidance of collisions, particularly at high speeds. The development of a collision avoidance system is the overall focus of the research presented in this paper. The collision avoidance algorithm was developed using a sliding mode controller (SMC) and compared to one developed using linear full state feedback in terms of performance and controller effort. Important dynamic characteristics such as load transfer during braking, tyre-road interaction, dynamic brake force distribution and pneumatic brake system response were considered. The effect of aerodynamic drag on the controller performance was also studied. The developed control algorithms have been implemented on a Hardware-in-Loop experimental set-up equipped with the vehicle dynamic simulation software, IPG/TruckMaker®. The evaluation has been performed for realistic traffic scenarios with different loading and road conditions. The Hardware-in-Loop experimental results showed that the SMC and full state feedback controller were able to prevent the collision. However, when the discrepancies in the form of parametric variations were included, the SMC provided better results in terms of reduced stopping distance and lower controller effort compared to the full state feedback controller.

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web

USGS Publications Warehouse

Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.

2004-01-01

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

Development of a hardware-in-loop attitude control simulator for a CubeSat satellite

NASA Astrophysics Data System (ADS)

Tapsawat, Wittawat; Sangpet, Teerawat; Kuntanapreeda, Suwat

2018-01-01

Attitude control is an important part in satellite on-orbit operation. It greatly affects the performance of satellites. Testing of an attitude determination and control subsystem (ADCS) is very challenging since it might require attitude dynamics and space environment in the orbit. This paper develops a low-cost hardware-in-loop (HIL) simulator for testing an ADCS of a CubeSat satellite. The simulator consists of a numerical simulation part, a hardware part, and a HIL interface hardware unit. The numerical simulation part includes orbital dynamics, attitude dynamics and Earth’s magnetic field. The hardware part is the real ADCS board of the satellite. The simulation part outputs satellite’s angular velocity and geomagnetic field information to the HIL interface hardware. Then, based on this information, the HIL interface hardware generates I2C signals mimicking the signals of the on-board rate-gyros and magnetometers and consequently outputs the signals to the ADCS board. The ADCS board reads the rate-gyro and magnetometer signals, calculates control signals, and drives the attitude actuators which are three magnetic torquers (MTQs). The responses of the MTQs sensed by a separated magnetometer are feedback to the numerical simulation part completing the HIL simulation loop. Experimental studies are conducted to demonstrate the feasibility and effectiveness of the simulator.

Chromospheric counterparts of solar transition region unresolved fine structure loops

NASA Astrophysics Data System (ADS)

Pereira, Tiago M. D.; Rouppe van der Voort, Luc; Hansteen, Viggo H.; De Pontieu, Bart

2018-04-01

Low-lying loops have been discovered at the solar limb in transition region temperatures by the Interface Region Imaging Spectrograph (IRIS). They do not appear to reach coronal temperatures, and it has been suggested that they are the long-predicted unresolved fine structures (UFS). These loops are dynamic and believed to be visible during both heating and cooling phases. Making use of coordinated observations between IRIS and the Swedish 1-m Solar Telescope, we study how these loops impact the solar chromosphere. We show for the first time that there is indeed a chromospheric signal of these loops, seen mostly in the form of strong Doppler shifts and a conspicuous lack of chromospheric heating. In addition, we find that several instances have a inverse Y-shaped jet just above the loop, suggesting that magnetic reconnection is driving these events. Our observations add several puzzling details to the current knowledge of these newly discovered structures; this new information must be considered in theoretical models. Two movies associated to Fig. 1 are available at http://https://www.aanda.org

The magnetosphere as system

NASA Astrophysics Data System (ADS)

Siscoe, G. L.

2012-12-01

What is a system? A group of elements interacting with each other so as to create feedback loops. A system gets complex as the number of feedback loops increases and as the feedback loops exhibit time delays. Positive and negative feedback loops with time delays can give a system intrinsic time dependence and emergent properties. A system generally has input and output flows of something (matter, energy, money), which, if time variable, add an extrinsic component to its behavior. The magnetosphere is a group of elements interacting through feedback loops, some with time delays, driven by energy and mass inflow from a variable solar wind and outflow into the atmosphere and solar wind. The magnetosphere is a complex system. With no solar wind, there is no behavior. With solar wind, there is behavior from intrinsic and extrinsic causes. As a contribution to taking a macroscopic view of magnetospheric dynamics, to treating the magnetosphere as a globally integrated, complex entity, I will discus the magnetosphere as a system, its feedback loops, time delays, emergent behavior, and intrinsic and extrinsic behavior modes.

Evolution of dislocation loops in austenitic stainless steels implanted with high concentration of hydrogen

NASA Astrophysics Data System (ADS)

Zheng, Zhongcheng; Gao, Ning; Tang, Rui; Yu, Yanxia; Zhang, Weiping; Shen, Zhenyu; Long, Yunxiang; Wei, Yaxia; Guo, Liping

2017-10-01

It has been found that under certain conditions, hydrogen retention would be strongly enhanced in irradiated austenitic stainless steels. To investigate the effect of the retained hydrogen on the defect microstructure, AL-6XN stainless steel specimens were irradiated with low energy (100 keV) H2+ so that high concentration of hydrogen was injected into the specimens while considerable displacement damage dose (up to 7 dpa) was also achieved. Irradiation induced dislocation loops and voids were characterised by transmission electron microscopy. For specimens irradiated to 7 dpa at 290 °C, dislocation loops with high number density were found and the void swelling was observed. At 380 °C, most of dislocation loops were unfaulted and tangled at 7 dpa, and the void swellings were observed at 5 dpa and above. Combining the data from low dose in previous work to high dose, four stages of dislocation loops evolution with hydrogen retention were suggested. Finally, molecular dynamics simulation was made to elucidate the division of large dislocation loops under irradiation.

Thermally induced all-optical inverter and dynamic hysteresis loops in graphene oxide dispersions.

PubMed

Melle, Sonia; Calderón, Oscar G; Egatz-Gómez, Ana; Cabrera-Granado, E; Carreño, F; Antón, M A

2015-11-01

We experimentally study the temporal dynamics of amplitude-modulated laser beams propagating through a water dispersion of graphene oxide sheets in a fiber-to-fiber U-bench. Nonlinear refraction induced in the sample by thermal effects leads to both phase reversing of the transmitted signals and dynamic hysteresis in the input-output power curves. A theoretical model including beam propagation and thermal lensing dynamics reproduces the experimental findings.

Flatness-based adaptive fuzzy control of chaotic finance dynamics

NASA Astrophysics Data System (ADS)

Rigatos, G.; Siano, P.; Loia, V.; Tommasetti, A.; Troisi, O.

2017-11-01

A flatness-based adaptive fuzzy control is applied to the problem of stabilization of the dynamics of a chaotic finance system, describing interaction between the interest rate, the investment demand and the price exponent. By proving that the system is differentially flat and by applying differential flatness diffeomorphisms, its transformation to the linear canonical (Brunovsky) is performed. For the latter description of the system, the design of a stabilizing state feedback controller becomes possible. A first problem in the design of such a controller is that the dynamic model of the finance system is unknown and thus it has to be identified with the use neurofuzzy approximators. The estimated dynamics provided by the approximators is used in the computation of the control input, thus establishing an indirect adaptive control scheme. The learning rate of the approximators is chosen from the requirement the system's Lyapunov function to have always a negative first-order derivative. Another problem that has to be dealt with is that the control loop is implemented only with the use of output feedback. To estimate the non-measurable state vector elements of the finance system, a state observer is implemented in the control loop. The computation of the feedback control signal requires the solution of two algebraic Riccati equations at each iteration of the control algorithm. Lyapunov stability analysis demonstrates first that an H-infinity tracking performance criterion is satisfied. This signifies elevated robustness against modelling errors and external perturbations. Moreover, the global asymptotic stability is proven for the control loop.

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.

PubMed

Ahnert, S E; Fink, T M A

2016-07-01

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. © 2016 The Authors.

Defect-induced change of temperature-dependent elastic constants in BCC iron

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

Gao, N.; Setyawan, W.; Zhang, S. H.

2017-07-01

The effects of radiation-induced defects (randomly distributed vacancies, voids, and interstitial dislocation loops) on temperature-dependent elastic constants, C11, C12, and C44 in BCC iron, are studied with molecular dynamics method. The elastic constants are found to decrease with increasing temperatures for all cases containing different defects. The presence of vacancies, voids, or interstitial loops further decreases the elastic constants. For a given number of point defects, the randomly distributed vacancies show the strongest effect compared to voids or interstitial loops. All these results are expected to provide useful information to combine with experimental results for further understanding of radiation damage.

Multivariable control of the Space Shuttle Remote Manipulator System using linearization by state feedback. M.S. Thesis

NASA Technical Reports Server (NTRS)

Gettman, Chang-Ching LO

1993-01-01

This thesis develops and demonstrates an approach to nonlinear control system design using linearization by state feedback. The design provides improved transient response behavior allowing faster maneuvering of payloads by the SRMS. Modeling uncertainty is accounted for by using a second feedback loop designed around the feedback linearized dynamics. A classical feedback loop is developed to provide the easy implementation required for the relatively small on board computers. Feedback linearization also allows the use of higher bandwidth model based compensation in the outer loop, since it helps maintain stability in the presence of the nonlinearities typically neglected in model based designs.

Design of PI Controlled Non Isolated Bidirectional DC to DC Converter for Electric Vehicle Application

NASA Astrophysics Data System (ADS)

Geetha, A.; Subramani, C.; Thamizh Thentral, T. M.; Krithika, V.; Usha, S.

2018-04-01

Non isolated Bidirectional DC-DC Converter (NIBDDC) is a good interface between DC source and inverter Fed induction motor drive. This paper deals with comparison between open loop and PI controlled Bidirectional DC to DC Converter Inverter System (BDDCIS). The modelling and control of BDDC is becomes an important issue. Open loop BDDCIS and closed loop PI controlled BDDCIS are designed, modelled and simulated using Matlab- simulink and their results are presented. The investigations indicate superior performance of PI controlled BDDCIS. The proposed BDDCIS has advantages like bidirectional power transfer ability, reduced hardware count and improved dynamic response.

STEREOSCOPIC OBSERVATION OF SLIPPING RECONNECTION IN A DOUBLE CANDLE-FLAME-SHAPED SOLAR FLARE

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

Gou, Tingyu; Liu, Rui; Wang, Yuming

2016-04-20

The 2011 January 28 M1.4 flare exhibits two side-by-side candle-flame-shaped flare loop systems underneath a larger cusp-shaped structure during the decay phase, as observed at the northwestern solar limb by the Solar Dynamics Observatory . The northern loop system brightens following the initiation of the flare within the southern loop system, but all three cusp-shaped structures are characterized by ∼10 MK temperatures, hotter than the arch-shaped loops underneath. The “Ahead” satellite of the Solar Terrestrial Relations Observatory provides a top view, in which the post-flare loops brighten sequentially, with one end fixed while the other apparently slipping eastward. By performingmore » stereoscopic reconstruction of the post-flare loops in EUV and mapping out magnetic connectivities, we found that the footpoints of the post-flare loops are slipping along the footprint of a hyperbolic flux tube (HFT) separating the two loop systems and that the reconstructed loops share similarity with the magnetic field lines that are traced starting from the same HFT footprint, where the field lines are relatively flexible. These results argue strongly in favor of slipping magnetic reconnection at the HFT. The slipping reconnection was likely triggered by the flare and manifested as propagative dimmings before the loop slippage is observed. It may contribute to the late-phase peak in Fe xvi 33.5 nm, which is even higher than its main-phase counterpart, and may also play a role in the density and temperature asymmetry observed in the northern loop system through heat conduction.« less

Unresolved fine-scale structure in solar coronal loop-tops

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

Scullion, E.; Van der Voort, L. Rouppe; Wedemeyer, S.

2014-12-10

New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certainmore » circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.« less

NMR studies of the dynamics of high-spin nitrophorins: comparative studies of NP4 and NP2 at close to physiological pH.

PubMed

Berry, Robert E; Muthu, Dhanasekaran; Yang, Fei; Walker, F Ann

2015-01-20

The β-barrel nitrophorin (NP) heme proteins are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands. NO is bound to iron of the NPs and is released by dilution and an increase in pH when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect, there are four nitrophorins, NP1-NP4, which have sequence similarities in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical). The available crystal structures of NP4 have been used to propose that pH-dependent changes in the conformation of two loops between adjacent β-strands at the front opening of the protein, the A-B and G-H loops, determine the rate of NO release. At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this work, the aqua complexes of NP4 and NP2 have been investigated by nuclear magnetic resonance (NMR) relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics at pH 6.5; at pH 7.3, much more dynamics of the loops and most of the β-strands are observed while the α-helices remain fairly rigid. In comparison, NP2-OH2 shows much less dynamics, albeit somewhat more than that of the previously reported NP2-NO complex [Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910-7925]. The reasons for this major difference between NP4 and NP2 are discussed.

NMR Studies of the Dynamics of High-Spin Nitrophorins: Comparative Studies of NP4 and NP2 at Close to Physiological pH

PubMed Central

2015-01-01

The β-barrel nitrophorin (NP) heme proteins are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands. NO is bound to iron of the NPs and is released by dilution and an increase in pH when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect, there are four nitrophorins, NP1–NP4, which have sequence similarities in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical). The available crystal structures of NP4 have been used to propose that pH-dependent changes in the conformation of two loops between adjacent β-strands at the front opening of the protein, the A–B and G–H loops, determine the rate of NO release. At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this work, the aqua complexes of NP4 and NP2 have been investigated by nuclear magnetic resonance (NMR) relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics at pH 6.5; at pH 7.3, much more dynamics of the loops and most of the β-strands are observed while the α-helices remain fairly rigid. In comparison, NP2-OH2 shows much less dynamics, albeit somewhat more than that of the previously reported NP2-NO complex [Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910–7925]. The reasons for this major difference between NP4 and NP2 are discussed. PMID:25486224

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

Lott, P. Aaron; Woodward, Carol S.; Evans, Katherine J.

Performing accurate and efficient numerical simulation of global atmospheric climate models is challenging due to the disparate length and time scales over which physical processes interact. Implicit solvers enable the physical system to be integrated with a time step commensurate with processes being studied. The dominant cost of an implicit time step is the ancillary linear system solves, so we have developed a preconditioner aimed at improving the efficiency of these linear system solves. Our preconditioner is based on an approximate block factorization of the linearized shallow-water equations and has been implemented within the spectral element dynamical core within themore » Community Atmospheric Model (CAM-SE). Furthermore, in this paper we discuss the development and scalability of the preconditioner for a suite of test cases with the implicit shallow-water solver within CAM-SE.« less

Strong Selective Adsorption of Polymers.

PubMed

Ge, Ting; Rubinstein, Michael

2015-06-09

A scaling theory is developed for selective adsorption of polymers induced by the strong binding between specific monomers and complementary surface adsorption sites. By "selective" we mean specific attraction between a subset of all monomers, called "sticky", and a subset of surface sites, called "adsorption sites". We demonstrate that, in addition to the expected dependence on the polymer volume fraction ϕ bulk in the bulk solution, selective adsorption strongly depends on the ratio between two characteristic length scales, the root-mean-square distance l between neighboring sticky monomers along the polymer, and the average distance d between neighboring surface adsorption sites. The role of the ratio l / d arises from the fact that a polymer needs to deform to enable the spatial commensurability between its sticky monomers and the surface adsorption sites for selective adsorption. We study strong selective adsorption of both telechelic polymers with two end monomers being sticky and multisticker polymers with many sticky monomers between sticky ends. For telechelic polymers, we identify four adsorption regimes at l / d < 1 that are characterized by the fraction of occupied adsorption sites and whether the dominant conformation of adsorbed chains is a single-end-adsorbed "mushroom" or double-end-adsorbed loop. For l / d > 1, we expect that the adsorption layer at exponentially low ϕ bulk consists of separated unstretched loops, while as ϕ bulk increases the layer crosses over to a brush of extended loops with a second layer of weakly overlapping tails. For multisticker chains, in the limit of exponentially low ϕ bulk , adsorbed polymers are well separated from each other. As l / d increases, the conformation of an individual polymer changes from a single-end-adsorbed "mushroom" to a random walk of loops. For high ϕ bulk , adsorbed polymers at small l / d are mushrooms that cover all the adsorption sites. At sufficiently large l / d , adsorbed multisticker polymers strongly overlap. We anticipate the formation of a self-similar carpet and with increasing l / d a two-layer structure with a brush of loops covered by a self-similar carpet. As l / d exceeds the threshold determined by the adsorption energy, the brush of loops under the carpet reaches a saturated state, resulting in a l / d -independent brush-under-carpet structure, which can also be applied to describe adsorbed multisticker polymers in nonselective adsorption where a sticker can strongly bind to any place on the adsorption surface. We examine the adsorbed amount Γ of multisticker polymers in different regimes for selective adsorption. If the adsorbed multisticker polymers are nonoverlapping mushrooms, the adsorbed amount Γ increases linearly with the surface density of adsorption sites Σ ≈ 1/ d 2 . In the self-similar carpet regime, Γ increases sublinearly as Σ 0.15 in a good solvent, while only logarithmically in a theta solvent. Formation of a brush layer under the carpet contributes an additional adsorbed amount. This additional amount increases linearly with Σ and eventually dominates the overall adsorbed amount Γ before saturating at a plateau value controlled by the adsorption energy.

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2017-06-02

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.