Sample records for unstable high-dimensional biochemical
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Patterns of Stochastic Behavior in Dynamically Unstable High-Dimensional Biochemical Networks
Rosenfeld, Simon
2009-01-01
The question of dynamical stability and stochastic behavior of large biochemical networks is discussed. It is argued that stringent conditions of asymptotic stability have very little chance to materialize in a multidimensional system described by the differential equations of chemical kinetics. The reason is that the criteria of asymptotic stability (Routh-Hurwitz, Lyapunov criteria, Feinberg’s Deficiency Zero theorem) would impose the limitations of very high algebraic order on the kinetic rates and stoichiometric coefficients, and there are no natural laws that would guarantee their unconditional validity. Highly nonlinear, dynamically unstable systems, however, are not necessarily doomed to collapse, as a simple Jacobian analysis would suggest. It is possible that their dynamics may assume the form of pseudo-random fluctuations quite similar to a shot noise, and, therefore, their behavior may be described in terms of Langevin and Fokker-Plank equations. We have shown by simulation that the resulting pseudo-stochastic processes obey the heavy-tailed Generalized Pareto Distribution with temporal sequence of pulses forming the set of constituent-specific Poisson processes. Being applied to intracellular dynamics, these properties are naturally associated with burstiness, a well documented phenomenon in the biology of gene expression. PMID:19838330
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Modeling unstable alcohol flooding of DNAPL-contaminated columns
NASA Astrophysics Data System (ADS)
Roeder, Eberhard; Falta, Ronald W.
Alcohol flooding, consisting of injection of a mixture of alcohol and water, is one source removal technology for dense non-aqueous phase liquids (DNAPLs) currently under investigation. An existing compositional multiphase flow simulator (UTCHEM) was adapted to accurately represent the equilibrium phase behavior of ternary and quaternary alcohol/DNAPL systems. Simulator predictions were compared to laboratory column experiments and the results are presented here. It was found that several experiments involved unstable displacements of the NAPL bank by the alcohol flood or of the alcohol flood by the following water flood. Unstable displacement led to additional mixing compared to ideal displacement. This mixing was approximated by a large dispersion in one-dimensional simulations and or by including permeability heterogeneities on a very small scale in three-dimensional simulations. Three-dimensional simulations provided the best match. Simulations of unstable displacements require either high-resolution grids, or need to consider the mixing of fluids in a different manner to capture the resulting effects on NAPL recovery.
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Cairoli, Andrea; Piovani, Duccio; Jensen, Henrik Jeldtoft
2014-12-31
We propose a new procedure to monitor and forecast the onset of transitions in high-dimensional complex systems. We describe our procedure by an application to the tangled nature model of evolutionary ecology. The quasistable configurations of the full stochastic dynamics are taken as input for a stability analysis by means of the deterministic mean-field equations. Numerical analysis of the high-dimensional stability matrix allows us to identify unstable directions associated with eigenvalues with a positive real part. The overlap of the instantaneous configuration vector of the full stochastic system with the eigenvectors of the unstable directions of the deterministic mean-field approximation is found to be a good early warning of the transitions occurring intermittently.
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Time Harmonic Two-Dimensional Cavity Scar Statistics: Convex Mirrors and Bowtie
Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Kotulski, Joseph Daniel; ...
2011-02-10
Here, this article examines the localization of time harmonic high-frequency modal fields in two-dimensional cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This article examines the enhancements for these unstable orbits when the opposing mirrors are convex, constructing the high-frequency field in the scar region using elliptic cylinder coordinates in combination with a random reflection phase from the outer chaotic region. Finally, the enhancements when the cavity is symmetric as well as asymmetric about the orbit are examined.
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Alfvén Turbulence Driven by High-Dimensional Interior Crisis in the Solar Wind
NASA Astrophysics Data System (ADS)
Chian, A. C.-L.; Rempel, E. L.; Macau, E. E. N.; Rosa, R. R.; Christiansen, F.
2003-09-01
Alfvén intermittent turbulence has been observed in the solar wind. It has been previously shown that the interplanetary Alfvén intermittent turbulence can appear due to a low-dimensional temporal chaos [1]. In this paper, we study the nonlinear spatiotemporal dynamics of Alfvén waves governed by the Kuramoto-Sivashinsky equation which describes the phase evolution of a large-amplitude Alfvén wave. We investigate the Alfvén turbulence driven by a high-dimensional interior crisis, which is a global bifurcation caused by the collision of a chaotic attractor with an unstable periodic orbit. This nonlinear phenomenon is analyzed using the numerical solutions of the model equation. The identification of the unstable periodic orbits and their invariant manifolds is fundamental for understanding the instability, chaos and turbulence in complex systems such as the solar wind plasma. The high-dimensional dynamical system approach to space environment turbulence developed in this paper can improve our interpretation of the origin and the nature of Alfvén turbulence observed in the solar wind.
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NASA Astrophysics Data System (ADS)
Inovenkov, Igor; Echkina, Eugenia; Ponomarenko, Loubov
Magnetic reconnection is a fundamental process in astrophysical, space and laboratory plasma. In essence, it represents a change of topology of the magnetic field caused by readjustment of the structure of the magnetic field lines. This change leads to release of energy accumulated in the field. We consider transformation process of structurally unstable magnetic configurations into the structurally steady ones from the point of view of the Catastrophe theory. Special attention is paid to modeling of evolution of the structurally unstable three-dimensional magnetic fields.
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Three-dimensional instability of standing waves
NASA Astrophysics Data System (ADS)
Zhu, Qiang; Liu, Yuming; Yue, Dick K. P.
2003-12-01
We investigate the three-dimensional instability of finite-amplitude standing surface waves under the influence of gravity. The analysis employs the transition matrix (TM) approach and uses a new high-order spectral element (HOSE) method for computation of the nonlinear wave dynamics. HOSE is an extension of the original high-order spectral method (HOS) wherein nonlinear wave wave and wave body interactions are retained up to high order in wave steepness. Instead of global basis functions in HOS, however, HOSE employs spectral elements to allow for complex free-surface geometries and surface-piercing bodies. Exponential convergence of HOS with respect to the total number of spectral modes (for a fixed number of elements) and interaction order is retained in HOSE. In this study, we use TM-HOSE to obtain the stability of general three-dimensional perturbations (on a two-dimensional surface) on two classes of standing waves: plane standing waves in a rectangular tank; and radial/azimuthal standing waves in a circular basin. For plane standing waves, we confirm the known result of two-dimensional side-bandlike instability. In addition, we find a novel three-dimensional instability for base flow of any amplitude. The dominant component of the unstable disturbance is an oblique (standing) wave oriented at an arbitrary angle whose frequency is close to the (nonlinear) frequency of the original standing wave. This finding is confirmed by direct long-time simulations using HOSE which show that the nonlinear evolution leads to classical Fermi Pasta Ulam recurrence. For the circular basin, we find that, beyond a threshold wave steepness, a standing wave (of nonlinear frequency Omega) is unstable to three-dimensional perturbations. The unstable perturbation contains two dominant (standing-wave) components, the sum of whose frequencies is close to 2Omega. From the cases we consider, the critical wave steepness is found to generally decrease/increase with increasing radial/azimuthal mode number of the base standing wave. Finally, we show that the instability we find for both two- and three-dimensional standing waves is a result of third-order (quartet) resonance.
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NASA Astrophysics Data System (ADS)
Mirus, Kevin Andrew
In this thesis, the possibility of controlling low- and high-dimensional chaotic systems by periodically driving an accessible system parameter is examined. This method has been carried out on several numerical systems and the MST Reversed Field Pinch. The numerical systems investigated include the logistic equation, the Lorenz equations, the Rossler equations, a coupled lattice of logistic equations, a coupled lattice of Lorenz equations, the Yoshida equations, which model tearing mode fluctuations in a plasma, and a neural net model for magnetic fluctuations on MST. This method was tested on the MST by sinusoidally driving a magnetic flux through the toroidal gap of the device. Numerically, periodic drives were found to be most effective at producing limit cycle behavior or significantly reducing the dimension of the system when the perturbation frequency was near natural frequencies of unstable periodic orbits embedded in the attractor of the unperturbed system. Several different unstable periodic orbits have been stabilized in this way for the low-dimensional numerical systems, sometimes with perturbation amplitudes that were less than 5% of the nominal value of the parameter being perturbed. In high- dimensional systems, limit cycle behavior and significant decreases in the system dimension were also achieved using perturbations with frequencies near the natural unstable periodic orbit frequencies. Results for the MST were not this encouraging, most likely because of an insufficient drive amplitude, the extremely high dimension of the plasma behavior, large amounts of noise, and a lack of stationarity in the transient plasma pulses.
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Detecting unstable periodic orbits in chaotic time series using synchronization
NASA Astrophysics Data System (ADS)
Olyaei, Ali Azimi; Wu, Christine; Kinsner, Witold
2017-07-01
An alternative approach of detecting unstable periodic orbits in chaotic time series is proposed using synchronization techniques. A master-slave synchronization scheme is developed, in which the chaotic system drives a system of harmonic oscillators through a proper coupling condition. The proposed scheme is designed so that the power of the coupling signal exhibits notches that drop to zero once the system approaches an unstable orbit yielding an explicit indication of the presence of a periodic motion. The results shows that the proposed approach is particularly suitable in practical situations, where the time series is short and noisy, or it is obtained from high-dimensional chaotic systems.
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NASA Astrophysics Data System (ADS)
Yu, Geliang; Yang, Cao; Khestanova, Ekaterina; Mishchenko, Artem; Kretinin, Andy; Gorbachev, Roman; Novoselov, Konstantin; Andre, Geim; Manchester Group Team
Many layered materials can be cleaved down to individual atomic planes, similar to graphene, but only a small minority of them are stable under ambient conditions. The rest reacts and decomposes in air, which has severely hindered their investigation and possible uses. Here we introduce a remedial approach based on cleavage, transfer, alignment and encapsulation of airsensitive crystals, all inside a controlled inert atmosphere. To illustrate the technology, we choose two archetypal two-dimensional crystals unstable in air: black phosphorus and niobium diselenide. Our field-effect devices made from their monolayers are conductive and fully stable under ambient conditions, in contrast to the counterparts processed in air. NbSe2 remains superconducting down to the monolayer thickness. Starting with a trilayer, phosphorene devices reach sufficiently high mobilities to exhibit Landau quantization. The approach offers a venue to significantly expand the range of experimentally accessible two-dimensional crystals and their heterostructures.
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Crisis route to chaos in semiconductor lasers subjected to external optical feedback
NASA Astrophysics Data System (ADS)
Wishon, Michael J.; Locquet, Alexandre; Chang, C. Y.; Choi, D.; Citrin, D. S.
2018-03-01
Semiconductor lasers subjected to optical feedback have been intensively used as archetypical testbeds for high-speed (sub-ns) and high-dimensional nonlinear dynamics. By simultaneously extracting all the dynamical variables, we demonstrate that for larger current, the commonly named "quasiperiodic" route is in fact based on mixed external-cavity solutions that lock the oscillation frequency of the intensity, voltage, and separation in optical frequency through a mechanism involving successive rejections along the unstable manifold of an antimode. We show that chaos emerges from a crisis resulting from the inability to maintain locking as the unstable manifold becomes inaccessible.
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Investigation Into Radiation-Induced Compaction of Zerodur (trademark)
NASA Technical Reports Server (NTRS)
Edwards, D. L.; Herren, K.; Hayden, M.; McDonald, K.; Sims, J. A.; Semmel, C. L.
1996-01-01
Zerodur is a low coefficient of thermal expansion glass-ceramic material. This property makes Zerodur an excellent material for high precision optical substrates. Functioning as a high precision optical substrate, a material must be dimensionally stable in the system operating environment. Published data indicate that Zerodur is dimensionally unstable when exposed to large doses of ionizing radiation. The dimensional instability is discussed as an increase in Zerodur density. This increase in density is described as a compaction. Experimental data showing proton-induced compaction of Zerodur is presented. The dependence of compaction on proton dose was determined to be a power law relationship.
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Investigation Into Radiation-Induced Compaction of Zerodur (trademark)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Edwards, D.L.; Herren, K.; Hayden, M.
1996-03-01
Zerodur is a low coefficient of thermal expansion glass-ceramic material. This property makes Zerodur an excellent material for high precision optical substrates. Functioning as a high precision optical substrate, a material must be dimensionally stable in the system operating environment. Published data indicate that Zerodur is dimensionally unstable when exposed to large doses of ionizing radiation. The dimensional instability is discussed as an increase in Zerodur density. This increase in density is described as a compaction. Experimental data showing proton-induced compaction of Zerodur is presented. The dependence of compaction on proton dose was determined to be a power law relationship.
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Stability of Thin Liquid Sheet Flows
NASA Technical Reports Server (NTRS)
McConley, Marc W.; Chubb, Donald L.; McMaster, Matthew S.; Afjeh, Abdollah A.
1997-01-01
A two-dimensional, linear stability analysis of a thin nonplanar liquid sheet flow in vacuum is carried out. A sheet flow created by a narrow slit of W and tau attains a nonplanar cross section as a consequence of cylinders forming on the sheet edge under the influence of surface tension forces. The region where these edge cylinders join the sheet is one of high curvature, and this is found to be the location where instability is most likely to occur. The sheet flow is found to be unstable, but with low growth rates for symmetric wave disturbances and high growth rates for antisymmetric disturbances. By combining the symmetric and antisymmetric disturbance modes, a wide range of stability characteristics is obtained. The product of unstable growth rate and flow time is proportional to the width-to-thickness ratio of the sift generating the sheet Three-dimensional effects can alter these results, particularly when the sheet length-to-width ratio is not much greater than unity.
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CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
DOE Office of Scientific and Technical Information (OSTI.GOV)
Haraldsdóttir, Hulda S.; Cousins, Ben; Thiele, Ines
In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to their high dimensionality and inherent anisotropy. Here, we present an implementation of a new sampling algorithm, coordinate hit-and-run with rounding (CHRR). This algorithm is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. CHRR provably converges to a uniform stationary sampling distribution. Wemore » apply it to metabolic networks of increasing dimensionality. We show that it converges several times faster than a popular artificial centering hit-and-run algorithm, enabling reliable and tractable sampling of genome-scale biochemical networks.« less
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CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
Haraldsdóttir, Hulda S.; Cousins, Ben; Thiele, Ines; ...
2017-01-31
In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to their high dimensionality and inherent anisotropy. Here, we present an implementation of a new sampling algorithm, coordinate hit-and-run with rounding (CHRR). This algorithm is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. CHRR provably converges to a uniform stationary sampling distribution. Wemore » apply it to metabolic networks of increasing dimensionality. We show that it converges several times faster than a popular artificial centering hit-and-run algorithm, enabling reliable and tractable sampling of genome-scale biochemical networks.« less
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Three-dimensional skyrmions in spin-2 Bose–Einstein condensates
NASA Astrophysics Data System (ADS)
Tiurev, Konstantin; Ollikainen, Tuomas; Kuopanportti, Pekko; Nakahara, Mikio; Hall, David S.; Möttönen, Mikko
2018-05-01
We introduce topologically stable three-dimensional skyrmions in the cyclic and biaxial nematic phases of a spin-2 Bose–Einstein condensate. These skyrmions exhibit exceptionally high mapping degrees resulting from the versatile symmetries of the corresponding order parameters. We show how these structures can be created in existing experimental setups and study their temporal evolution and lifetime by numerically solving the three-dimensional Gross–Pitaevskii equations for realistic parameter values. Although the biaxial nematic and cyclic phases are observed to be unstable against transition towards the ferromagnetic phase, their lifetimes are long enough for the skyrmions to be imprinted and detected experimentally.
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Fu, Chunjiang; Suzuki, Yasuyuki; Kiyono, Ken; Morasso, Pietro; Nomura, Taishin
2014-01-01
Stability of human gait is the ability to maintain upright posture during walking against external perturbations. It is a complex process determined by a number of cross-related factors, including gait trajectory, joint impedance and neural control strategies. Here, we consider a control strategy that can achieve stable steady-state periodic gait while maintaining joint flexibility with the lowest possible joint impedance. To this end, we carried out a simulation study of a heel-toe footed biped model with hip, knee and ankle joints and a heavy head-arms-trunk element, working in the sagittal plane. For simplicity, the model assumes a periodic desired joint angle trajectory and joint torques generated by a set of feed-forward and proportional-derivative feedback controllers, whereby the joint impedance is parametrized by the feedback gains. We could show that a desired steady-state gait accompanied by the desired joint angle trajectory can be established as a stable limit cycle (LC) for the feedback controller with an appropriate set of large feedback gains. Moreover, as the feedback gains are decreased for lowering the joint stiffness, stability of the LC is lost only in a few dimensions, while leaving the remaining large number of dimensions quite stable: this means that the LC becomes saddle-type, with a low-dimensional unstable manifold and a high-dimensional stable manifold. Remarkably, the unstable manifold remains of low dimensionality even when the feedback gains are decreased far below the instability point. We then developed an intermittent neural feedback controller that is activated only for short periods of time at an optimal phase of each gait stride. We characterized the robustness of this design by showing that it can better stabilize the unstable LC with small feedback gains, leading to a flexible gait, and in particular we demonstrated that such an intermittent controller performs better if it drives the state point to the stable manifold, rather than directly to the LC. The proposed intermittent control strategy might have a high affinity for the inverted pendulum analogy of biped gait, providing a dynamic view of how the step-to-step transition from one pendular stance to the next can be achieved stably in a robust manner by a well-timed neural intervention that exploits the stable modes embedded in the unstable dynamics. PMID:25339687
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Fu, Chunjiang; Suzuki, Yasuyuki; Kiyono, Ken; Morasso, Pietro; Nomura, Taishin
2014-12-06
Stability of human gait is the ability to maintain upright posture during walking against external perturbations. It is a complex process determined by a number of cross-related factors, including gait trajectory, joint impedance and neural control strategies. Here, we consider a control strategy that can achieve stable steady-state periodic gait while maintaining joint flexibility with the lowest possible joint impedance. To this end, we carried out a simulation study of a heel-toe footed biped model with hip, knee and ankle joints and a heavy head-arms-trunk element, working in the sagittal plane. For simplicity, the model assumes a periodic desired joint angle trajectory and joint torques generated by a set of feed-forward and proportional-derivative feedback controllers, whereby the joint impedance is parametrized by the feedback gains. We could show that a desired steady-state gait accompanied by the desired joint angle trajectory can be established as a stable limit cycle (LC) for the feedback controller with an appropriate set of large feedback gains. Moreover, as the feedback gains are decreased for lowering the joint stiffness, stability of the LC is lost only in a few dimensions, while leaving the remaining large number of dimensions quite stable: this means that the LC becomes saddle-type, with a low-dimensional unstable manifold and a high-dimensional stable manifold. Remarkably, the unstable manifold remains of low dimensionality even when the feedback gains are decreased far below the instability point. We then developed an intermittent neural feedback controller that is activated only for short periods of time at an optimal phase of each gait stride. We characterized the robustness of this design by showing that it can better stabilize the unstable LC with small feedback gains, leading to a flexible gait, and in particular we demonstrated that such an intermittent controller performs better if it drives the state point to the stable manifold, rather than directly to the LC. The proposed intermittent control strategy might have a high affinity for the inverted pendulum analogy of biped gait, providing a dynamic view of how the step-to-step transition from one pendular stance to the next can be achieved stably in a robust manner by a well-timed neural intervention that exploits the stable modes embedded in the unstable dynamics.
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KP Equation in a Three-Dimensional Unmagnetized Warm Dusty Plasma with Variable Dust Charge
NASA Astrophysics Data System (ADS)
El-Shorbagy, Kh. H.; Mahassen, Hania; El-Bendary, Atef Ahmed
2017-12-01
In this work, we investigate the propagation of three-dimensional nonlinear dust-acoustic and dust-Coulomb waves in an unmagnetized warm dusty plasma consisting of electrons, ions, and charged dust particles. The grain charge fluctuation is incorporated through the current balance equation. Using the perturbation method, a Kadomtsev-Petviashvili (KP) equation is obtained. It has been shown that the charge fluctuation would modify the wave structures, and the waves in such systems are unstable due to high-order long wave perturbations.
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High-frequency electromagnetic scarring in three-dimensional axisymmetric convex cavities
Warne, Larry K.; Jorgenson, Roy E.
2016-04-13
Here, this article examines the localization of high-frequency electromagnetic fields in three-dimensional axisymmetric cavities along periodic paths between opposing sides of the cavity. When these orbits lead to unstable localized modes, they are known as scars. This article treats the case where the opposing sides, or mirrors, are convex. Particular attention is focused on the normalization through the electromagnetic energy theorem. Both projections of the field along the scarred orbit as well as field point statistics are examined. Statistical comparisons are made with a numerical calculation of the scars run with an axisymmetric simulation.
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Three-dimensional Simulations of Jets from Keplerian Disks: Self-regulatory Stability
NASA Astrophysics Data System (ADS)
Ouyed, Rachid; Clarke, David A.; Pudritz, Ralph E.
2003-01-01
We present the extension of previous two-dimensional simulations of the time-dependent evolution of nonrelativistic outflows from the surface of Keplerian accretion disks to three dimensions. As in the previous work, we investigate the outflow that arises from a magnetized accretion disk that is initially in hydrostatic balance with its surrounding cold corona. The accretion disk itself is taken to provide a set of fixed boundary conditions for the problem. We find that the mechanism of jet acceleration is identical to what was established from the previous two-dimensional simulations. The three-dimensional results are consistent with the theory of steady, axisymmetric, centrifugally driven disk winds up to the Alfvén surface of the outflow. Beyond the Alfvén surface, however, the jet in three dimensions becomes unstable to nonaxisymmetric, Kelvin-Helmholtz instabilities. The most important result of our work is that while the jet is unstable at super-Alfvénic speeds, it survives the onset of unstable modes that appear in this physical regime. We show that jets maintain their long-term stability through a self-limiting process wherein the average Alfvénic Mach number within the jet is maintained to the order of unity. This is accomplished in at least two ways. First, the poloidal magnetic field is concentrated along the central axis of the jet forming a ``backbone'' in which the Alfvén speed is sufficiently high to reduce the average jet Alfvénic Mach number to unity. Second, the onset of higher order Kelvin-Helmholtz ``flute'' modes (m>=2) reduces the efficiency with which the jet material is accelerated and transfers kinetic energy of the outflow into the stretched, poloidal field lines of the distorted jet. This too has the effect of increasing the Alfvén speed and thereby reducing the Alfvénic Mach number. The jet is able to survive the onset of the more destructive m=1 mode in this way. Our simulations also show that jets can acquire corkscrew or wobbling types of geometries in this relatively stable end state depending on the nature of the perturbations on them. Finally, we suggest that jets go into alternating periods of low and high activity since the disappearance of unstable modes in the sub-Alfvénic regime enables another cycle of acceleration to super-Alfvénic speeds.
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Self-aggregation of clouds in conditionally unstable moist convection
Pauluis, Olivier; Schumacher, Jörg
2011-01-01
The behavior of moist Rayleigh–Bénard convection is investigated using a Boussinesq model with a simplified thermodynamics for phase transitions. This idealized configuration makes the problem accessible to high-resolution three-dimensional direct numerical simulations without small-scale parameterizations of the turbulence for extended layers with aspect ratios up to 64. Our study is focused on the frequently observed conditionally unstable environment that is stably stratified for unsaturated air, but is unstable for cloudy air. We find that no sharp threshold for the transition to convective turbulence exists, a situation similar to wall-bounded shear flows. Rather, the transition depends on the amplitude of the initial perturbation of the quiescent equilibrium and on the aspect ratio of the convective domain. In contrast to the classical dry Rayleigh–Bénard case, convection is highly asymmetric with respect to the vertical direction. Moist upwelling air inside turbulent cloud aggregates is surrounded by ambient regions of slowly descending unsaturated air. It is also found that conditionally unstable moist convection is inefficient at transporting energy. Our study suggests that there is an upper bound on the Nusselt number in moist convection that is lower than that of the classical dry case. PMID:21768333
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Hüttlin, Petra; Grützner, Paul A.; Weilbacher, Frank; Matschke, Stefan; Popp, Erik
2018-01-01
Background Unstable conditions of the craniocervical junction such as atlanto-occipital dislocation (AOD) or atlanto-axial instability (AAI) are severe injuries with a high risk of tetraplegia or death. Immobilization by a cervical collar to protect the patient from secondary damage is a standard procedure in trauma patients. If the application of a cervical collar to a patient with an unstable craniocervical condition may cause segmental motion and secondary injury to the spinal cord is unknown. The aim of the current study is (i) to analyze compression on the dural sac and (ii) to determine relative motion of the cervical spine during the procedure of applying a cervical collar in case of ligamentous unstable craniocervical junction. Methods and findings Ligamentous AOD as well as AOD combined with ligamentous AAI was simulated in two newly developed cadaveric trauma models. Compression of the dural sac and segmental angulation in the upper cervical spine were measured on video fluoroscopy after myelography during the application of a cervical collar. Furthermore, overall three-dimensional motion of the cervical spine was measured by a motion tracking system. In six cadavers each, the two new trauma models on AOD and AOD combined with AAI could be implemented. Mean dural sac compression was significantly increased to -1.1 mm (-1.3 to -0.7 mm) in case of AOD and -1.2 mm (-1.6 to -0.6 mm) in the combined model of AOD and AAI. Furthermore, there is a significant increased angulation at the C0/C1 level in the AOD model. Immense three-dimensional movement up to 22.9° of cervical spine flexion was documented during the procedure. Conclusion The current study pointed out that applying a cervical collar in general will cause immense three-dimensional movement. In case of unstable craniocervical junction, this leads to a dural sac compression and thus to possible damage to the spinal cord. PMID:29624623
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Thutupalli, Shashi; Sun, Mingzhai; Bunyak, Filiz; Palaniappan, Kannappan; Shaevitz, Joshua W.
2015-01-01
The formation of a collectively moving group benefits individuals within a population in a variety of ways. The surface-dwelling bacterium Myxococcus xanthus forms dynamic collective groups both to feed on prey and to aggregate during times of starvation. The latter behaviour, termed fruiting-body formation, involves a complex, coordinated series of density changes that ultimately lead to three-dimensional aggregates comprising hundreds of thousands of cells and spores. How a loose, two-dimensional sheet of motile cells produces a fixed aggregate has remained a mystery as current models of aggregation are either inconsistent with experimental data or ultimately predict unstable structures that do not remain fixed in space. Here, we use high-resolution microscopy and computer vision software to spatio-temporally track the motion of thousands of individuals during the initial stages of fruiting-body formation. We find that cells undergo a phase transition from exploratory flocking, in which unstable cell groups move rapidly and coherently over long distances, to a reversal-mediated localization into one-dimensional growing streams that are inherently stable in space. These observations identify a new phase of active collective behaviour and answer a long-standing open question in Myxococcus development by describing how motile cell groups can remain statistically fixed in a spatial location. PMID:26246416
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Rajpathak, Bhooshan, E-mail: bhooshan@ee.iitb.ac.in; Pillai, Harish K., E-mail: hp@ee.iitb.ac.in; Bandyopadhyay, Santanu, E-mail: santanu@me.iitb.ac.in
2015-10-15
In this paper, we analytically examine the unstable periodic orbits and chaotic orbits of the 1-D linear piecewise-smooth discontinuous map. We explore the existence of unstable orbits and the effect of variation in parameters on the coexistence of unstable orbits. Further, we show that this structuring is different from the well known period adding cascade structure associated with the stable periodic orbits of the same map. Further, we analytically prove the existence of chaotic orbit for this map.
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Zeng, Canjun; Xiao, Jidong; Wu, Zhanglin; Huang, Wenhua
2015-01-01
The aim of this study is to evaluate the efficacy and feasibility of three-dimensional printing (3D printing) assisted internal fixation of unstable pelvic fracture from minimal invasive para-rectus abdominis approach. A total of 38 patients with unstable pelvic fractures were analyzed retrospectively from August 2012 to February 2014. All cases were treated operatively with internal fixation assisted by three-dimensional printing from minimal invasive para-rectus abdominis approach. Both preoperative CT and three-dimensional reconstruction were performed. Pelvic model was created by 3D printing. Data including the best entry points, plate position and direction and length of screw were obtained from simulated operation based on 3D printing pelvic model. The diaplasis and internal fixation were performed by minimal invasive para-rectus abdominis approach according to the optimized dada in real surgical procedure. Matta and Majeed score were used to evaluate currative effects after operation. According to the Matta standard, the outcome of the diaplasis achieved 97.37% with excellent and good. Majeed assessment showed 94.4% with excellent and good. The imageological examination showed consistency of internal fixation and simulated operation. The mean operation time was 110 minutes, mean intraoperative blood loss 320 ml, and mean incision length 6.5 cm. All patients have achieved clinical healing, with mean healing time of 8 weeks. Three-dimensional printing assisted internal fixation of unstable pelvic fracture from minimal invasive para-rectus abdominis approach is feasible and effective. This method has the advantages of trauma minimally, bleeding less, healing rapidly and satisfactory reduction, and worthwhile for spreading in clinical practice.
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Dynamical behavior of lean swirling premixed flame generated by change in gravitational orientation
NASA Astrophysics Data System (ADS)
Gotoda, Hiroshi; Miyano, Takaya; Shepherd, Ian
2010-11-01
The dynamic behavior of flame front instability in lean swirling premixed flame generated by the effect of gravitational orientation has been experimentally investigated in this work. When the gravitational direction is changed relative to the flame front, i.e., in inverted gravity, an unstably fluctuating flame (unstable flame) is formed in a limited domain of equivalence ratio and swirl number (Gotoda. H et al., Physical Review E, vol. 81, 026211, 2010). The time history of flame front fluctuations show that in the buoyancy-dominated region, chaotic irregular fluctuation with low frequencies is superimposed on the dominant periodic oscillation of the unstable flame. This periodic oscillation is produced by unstable large-scale vortex motion in combustion products generated by a change in the buoyancy/swirl interaction due to the inversion of gravitational orientation. As a result, the dynamic behavior of the unstable flame becomes low-dimensional deterministic chaos. Its dynamics maintains low-dimensional deterministic chaos even in the momentum-dominated region, in which vortex breakdown in the combustion products clearly occurs. These results were clearly demonstrated by the use of nonlinear time series analysis based on chaos theory, which has not been widely applied to the investigation of combustion phenomena.
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Numerical Investigation of Three-dimensional Instability of Standing Waves
NASA Astrophysics Data System (ADS)
Zhu, Qiang; Liu, Yuming; Yue, Dick K. P.
2002-11-01
We study the three-dimensional instability of finite-amplitude standing waves under the influence of gravity using the transition matrix method. For accurate calculation of the transition matrices, we apply an efficient high-order spectral element method for nonlinear wave dynamics in complex domain. We consider two types of standing waves: (a) plane standing waves; and (b) standing waves in a circular tank. For the former, in addition to the confirmation of the side-band-like instability, we find a new three-dimensional instability for arbitrary base standing waves. The dominant component of the unstable disturbance is an oblique standing wave, with an arbitrary angle relative to the base flow, whose frequency is approximately equal to that of the base standing wave. Based on direct simulations, we confirm such a three-dimensional instability and show the occurrence of the Fermi-Pasta-Ulam recurrence phenomenon during nonlinear evolution. For the latter, we find that beyond a threshold wave steepness, the standing wave with frequency Ω becomes unstable to a small three-dimensional disturbance, which contains two dominant standing-wave components with frequencies ω1 and ω_2, provided that 2Ω ω1 + ω_2. The threshold wave steepness is found to decrease/increase as the radial/azimuthal wavenumber of the base standing wave increases. We show that the instability of standing waves in rectangular and circular tanks is caused by third-order quartet resonances between base flow and disturbance.
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Hypothesis testing for band size detection of high-dimensional banded precision matrices.
An, Baiguo; Guo, Jianhua; Liu, Yufeng
2014-06-01
Many statistical analysis procedures require a good estimator for a high-dimensional covariance matrix or its inverse, the precision matrix. When the precision matrix is banded, the Cholesky-based method often yields a good estimator of the precision matrix. One important aspect of this method is determination of the band size of the precision matrix. In practice, crossvalidation is commonly used; however, we show that crossvalidation not only is computationally intensive but can be very unstable. In this paper, we propose a new hypothesis testing procedure to determine the band size in high dimensions. Our proposed test statistic is shown to be asymptotically normal under the null hypothesis, and its theoretical power is studied. Numerical examples demonstrate the effectiveness of our testing procedure.
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Boundary between stable and unstable regimes of accretion. Ordered and chaotic unstable regimes
NASA Astrophysics Data System (ADS)
Blinova, A. A.; Romanova, M. M.; Lovelace, R. V. E.
2016-07-01
We present a new study of the Rayleigh-Taylor unstable regime of accretion on to rotating magnetized stars in a set of high grid resolution three-dimensional magnetohydrodynamic simulations performed in low-viscosity discs. We find that the boundary between the stable and unstable regimes is determined almost entirely by the fastness parameter ωs = Ω⋆/ΩK(rm), where Ω⋆ is the angular velocity of the star and ΩK(rm) is the angular velocity of the Keplerian disc at the disc-magnetosphere boundary r = rm. We found that accretion is unstable if ωs ≲ 0.6. Accretion through instabilities is present in stars with different magnetospheric sizes. However, only in stars with relatively small magnetospheres, rm/R⋆ ≲ 7, do the unstable tongues produce chaotic hotspots on the stellar surface and irregular light curves. At even smaller values of the fastness parameter, ωs ≲ 0.45, multiple irregular tongues merge, forming one or two ordered unstable tongues that rotate with the angular frequency of the inner disc. This transition occurs in stars with even smaller magnetospheres, rm/R⋆ ≲ 4.2. Most of our simulations were performed at a small tilt of the dipole magnetosphere, Θ = 5°, and a small viscosity parameter α = 0.02. Test simulations at higher α values show that many more cases become unstable, and the light curves become even more irregular. Test simulations at larger tilts of the dipole Θ show that instability is present, however, accretion in two funnel streams dominates if Θ ≳ 15°. The results of these simulations can be applied to accreting magnetized stars with relatively small magnetospheres: Classical T Tauri stars, accreting millisecond X-ray pulsars, and cataclysmic variables.
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Welsch, Goetz H; Mamisch, Tallal C; Hughes, Timothy; Domayer, Stephan; Marlovits, Stefan; Trattnig, Siegfried
2008-09-01
Morphological and biochemical magnetic resonance imaging (MRI) is due to high field MR systems, advanced coil technology, and sophisticated sequence protocols capable of visualizing articular cartilage in vivo with high resolution in clinical applicable scan time. Several conventional two-dimensional (2D) and three-dimensional (3D) approaches show changes in cartilage structure. Furthermore newer isotropic 3D sequences show great promise in improving cartilage imaging and additionally in diagnosing surrounding pathologies within the knee joint. Functional MR approaches are additionally able to provide a specific measure of the composition of cartilage. Cartilage physiology and ultra-structure can be determined, changes in cartilage macromolecules can be detected, and cartilage repair tissue can thus be assessed and potentially differentiated. In cartilage defects and following nonsurgical and surgical cartilage repair, morphological MRI provides the basis for diagnosis and follow-up evaluation, whereas biochemical MRI provides a deeper insight into the composition of cartilage and cartilage repair tissue. A combination of both, together with clinical evaluation, may represent a desirable multimodal approach in the future, also available in routine clinical use.
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CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.
Haraldsdóttir, Hulda S; Cousins, Ben; Thiele, Ines; Fleming, Ronan M T; Vempala, Santosh
2017-06-01
In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to their high dimensionality and inherent anisotropy. Here, we present an implementation of a new sampling algorithm, coordinate hit-and-run with rounding (CHRR). This algorithm is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. CHRR provably converges to a uniform stationary sampling distribution. We apply it to metabolic networks of increasing dimensionality. We show that it converges several times faster than a popular artificial centering hit-and-run algorithm, enabling reliable and tractable sampling of genome-scale biochemical networks. https://github.com/opencobra/cobratoolbox . ronan.mt.fleming@gmail.com or vempala@cc.gatech.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.
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Evolution of long-term coloration trends with biochemically unstable ingredients
Davis, Sarah N.; Andrews, John E.; Badyaev, Alexander V.
2016-01-01
The evolutionarily persistent and widespread use of carotenoid pigments in animal coloration contrasts with their biochemical instability. Consequently, evolution of carotenoid-based displays should include mechanisms to accommodate or limit pigment degradation. In birds, this could involve two strategies: (i) evolution of a moult immediately prior to the mating season, enabling the use of particularly fast-degrading carotenoids and (ii) evolution of the ability to stabilize dietary carotenoids through metabolic modification or association with feather keratins. Here, we examine evolutionary lability and transitions between the two strategies across 126 species of birds. We report that species that express mostly unmodified, fast-degrading, carotenoids have pre-breeding moults, and a particularly short time between carotenoid deposition and the subsequent breeding season. Species that expressed mostly slow-degrading carotenoids in their plumage accomplished this through increased metabolic modification of dietary carotenoids, and the selective expression of these slow-degrading compounds. In these species, the timing of moult was not associated with carotenoid composition of plumage displays. Using repeated samples from individuals of one species, we found that metabolic modification of dietary carotenoids significantly slowed their degradation between moult and breeding season. Thus, the most complex and colourful ornamentation is likely the most biochemically stable in birds, and depends less on ecological factors, such as moult timing and migration tendency. We suggest that coevolution of metabolic modification, selective expression and biochemical stability of plumage carotenoids enables the use of unstable pigments in long-term evolutionary trends in plumage coloration. PMID:27194697
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On the Transition from Two-Dimensional to Three-Dimensional MHD Turbulence
NASA Technical Reports Server (NTRS)
Thess, A.; Zikanov, Oleg
2004-01-01
We report a theoretical investigation of the robustness of two-dimensional inviscid MHD flows at low magnetic Reynolds numbers with respect to three-dimensional perturbations. We analyze three model problems, namely flow in the interior of a triaxial ellipsoid, an unbounded vortex with elliptical streamlines, and a vortex sheet parallel to the magnetic field. We demonstrate that motion perpendicular to the magnetic field with elliptical streamlines becomes unstable with respect to the elliptical instability once the velocity has reached a critical magnitude whose value tends to zero as the eccentricity of the streamlines becomes large. Furthermore, vortex sheets parallel to the magnetic field, which are unstable for any velocity and any magnetic field, are found to emit eddies with vorticity perpendicular to the magnetic field and with an aspect ratio proportional to N(sup 1/2). The results suggest that purely two-dimensional motion without Joule energy dissipation is a singular type of flow which does not represent the asymptotic behaviour of three-dimensional MHD turbulence in the limit of infinitely strong magnetic fields.
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Two-dimensional heteroclinic attractor in the generalized Lotka-Volterra system
NASA Astrophysics Data System (ADS)
Afraimovich, Valentin S.; Moses, Gregory; Young, Todd
2016-05-01
We study a simple dynamical model exhibiting sequential dynamics. We show that in this model there exist sets of parameter values for which a cyclic chain of saddle equilibria, O k , k=1,\\ldots,p , have two-dimensional unstable manifolds that contain orbits connecting each O k to the next two equilibrium points O k+1 and O k+2 in the chain ({{O}p+1}={{O}1} ). We show that the union of these equilibria and their unstable manifolds form a two-dimensional surface with a boundary that is homeomorphic to a cylinder if p is even and a Möbius strip if p is odd. If, further, each equilibrium in the chain satisfies a condition called ‘dissipativity’, then this surface is asymptotically stable.
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On the secondary instability of the most dangerous Goertler vortex
NASA Technical Reports Server (NTRS)
Otto, S. R.; Denier, James P.
1993-01-01
Recent studies have demonstrated the most unstable Goertler vortex mode is found in flows, both two and three-dimensional, with regions of (moderately) large body curvature and these modes reside within a thin layer situated at the base of the conventional boundary layer. Further work concerning the nonlinear development of the most dangerous mode demonstrates that the flow results in a self induced flow reversal. However, prior to the point at which flow reversal is encountered, the total streamwise velocity profile is found to be highly inflectional in nature. Previous work then suggests that the nonlinear vortex state will become unstable to secondary, inviscid, Rayleigh wave instabilities prior to the point of flow reversal. Our concern is with the secondary instability of the nonlinear vortex states, which result from the streamwise evolution of the most unstable Goertler vortex mode, with the aim of determining whether such modes can induce a transition to a fully turbulent state before separation is encountered.
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Experimental Control of Thermocapillary Convection in a Liquid Bridge
NASA Technical Reports Server (NTRS)
Petrov, Valery; Schatz, Michael F.; Muehlner, Kurt A.; VanHook, Stephen J.; McCormick, W. D.; Swift, Jack B.; Swinney, Harry L.
1996-01-01
We demonstrate the stabilization of an isolated unstable periodic orbit in a liquid bridge convection experiment. A model independent, nonlinear control algorithm uses temperature measurements near the liquid interface to compute control perturbations which are applied by a thermoelectric element. The algorithm employs a time series reconstruction of a nonlinear control surface in a high dimensional phase space to alter the system dynamics.
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The Goertler vortex instability mechanism in three-dimensional boundary layers
NASA Technical Reports Server (NTRS)
Hall, P.
1984-01-01
The two dimensional boundary layer on a concave wall is centrifugally unstable with respect to vortices aligned with the basic flow for sufficiently high values of the Goertler number. However, in most situations of practical interest the basic flow is three dimensional and previous theoretical investigations do not apply. The linear stability of the flow over an infinitely long swept wall of variable curvature is considered. If there is no pressure gradient in the boundary layer the instability problem can always be related to an equivalent two dimensional calculation. However, in general, this is not the case and even for small values of the crossflow velocity field dramatic differences between the two and three dimensional problems emerge. When the size of the crossflow is further increased, the vortices in the neutral location have their axes locally perpendicular to the vortex lines of the basic flow.
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NASA Astrophysics Data System (ADS)
Fruman, Mark D.; Remmler, Sebastian; Achatz, Ulrich; Hickel, Stefan
2014-10-01
A systematic approach to the direct numerical simulation (DNS) of breaking upper mesospheric inertia-gravity waves of amplitude close to or above the threshold for static instability is presented. Normal mode or singular vector analysis applied in a frame of reference moving with the phase velocity of the wave (in which the wave is a steady solution) is used to determine the most likely scale and structure of the primary instability and to initialize nonlinear "2.5-D" simulations (with three-dimensional velocity and vorticity fields but depending only on two spatial coordinates). Singular vector analysis is then applied to the time-dependent 2.5-D solution to predict the transition of the breaking event to three-dimensional turbulence and to initialize three-dimensional DNS. The careful choice of the computational domain and the relatively low Reynolds numbers, on the order of 25,000, relevant to breaking waves in the upper mesosphere, makes the three-dimensional DNS tractable with present-day computing clusters. Three test cases are presented: a statically unstable low-frequency inertia-gravity wave, a statically and dynamically stable inertia-gravity wave, and a statically unstable high-frequency gravity wave. The three-dimensional DNS are compared to ensembles of 2.5-D simulations. In general, the decay of the wave and generation of turbulence is faster in three dimensions, but the results are otherwise qualitatively and quantitatively similar, suggesting that results of 2.5-D simulations are meaningful if the domain and initial condition are chosen properly.
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Control of extreme events in the bubbling onset of wave turbulence.
Galuzio, P P; Viana, R L; Lopes, S R
2014-04-01
We show the existence of an intermittent transition from temporal chaos to turbulence in a spatially extended dynamical system, namely, the forced and damped one-dimensional nonlinear Schrödinger equation. For some values of the forcing parameter, the system dynamics intermittently switches between ordered states and turbulent states, which may be seen as extreme events in some contexts. In a Fourier phase space, the intermittency takes place due to the loss of transversal stability of unstable periodic orbits embedded in a low-dimensional subspace. We mapped these transversely unstable regions and perturbed the system in order to significantly reduce the occurrence of extreme events of turbulence.
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NASA Astrophysics Data System (ADS)
Rincón, Ángel; Panotopoulos, Grigoris
2018-01-01
We study for the first time the stability against scalar perturbations, and we compute the spectrum of quasinormal modes of three-dimensional charged black holes in Einstein-power-Maxwell nonlinear electrodynamics assuming running couplings. Adopting the sixth order Wentzel-Kramers-Brillouin (WKB) approximation we investigate how the running of the couplings change the spectrum of the classical theory. Our results show that all modes corresponding to nonvanishing angular momentum are unstable both in the classical theory and with the running of the couplings, while the fundamental mode can be stable or unstable depending on the running parameter and the electric charge.
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The Multi-dimensional Character of Core-collapse Supernovae
Hix, W. R.; Lentz, E. J.; Bruenn, S. W.; ...
2016-03-01
Core-collapse supernovae, the culmination of massive stellar evolution, are spectacular astronomical events and the principle actors in the story of our elemental origins. Our understanding of these events, while still incomplete, centers around a neutrino-driven central engine that is highly hydrodynamically unstable. Increasingly sophisticated simulations reveal a shock that stalls for hundreds of milliseconds before reviving. Though brought back to life by neutrino heating, the development of the supernova explosion is inextricably linked to multi-dimensional fluid flows. In this paper, the outcomes of three-dimensional simulations that include sophisticated nuclear physics and spectral neutrino transport are juxtaposed to learn about themore » nature of the three-dimensional fluid flow that shapes the explosion. Comparison is also made between the results of simulations in spherical symmetry from several groups, to give ourselves confidence in the understanding derived from this juxtaposition.« less
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Jiménez-Aquino, J I; Romero-Bastida, M
2011-07-01
The detection of weak signals through nonlinear relaxation times for a Brownian particle in an electromagnetic field is studied in the dynamical relaxation of the unstable state, characterized by a two-dimensional bistable potential. The detection process depends on a dimensionless quantity referred to as the receiver output, calculated as a function of the nonlinear relaxation time and being a characteristic time scale of our system. The latter characterizes the complete dynamical relaxation of the Brownian particle as it relaxes from the initial unstable state of the bistable potential to its corresponding steady state. The one-dimensional problem is also studied to complement the description.
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Three-dimensional Numerical Simulations of Rayleigh-Taylor Unstable Flames in Type Ia Supernovae
NASA Astrophysics Data System (ADS)
Zingale, M.; Woosley, S. E.; Rendleman, C. A.; Day, M. S.; Bell, J. B.
2005-10-01
Flame instabilities play a dominant role in accelerating the burning front to a large fraction of the speed of sound in a Type Ia supernova. We present a three-dimensional numerical simulation of a Rayleigh-Taylor unstable carbon flame, following its evolution through the transition to turbulence. A low-Mach number hydrodynamics method is used, freeing us from the harsh time step restrictions imposed by sound waves. We fully resolve the thermal structure of the flame and its reaction zone, eliminating the need for a flame model. A single density is considered, 1.5×107 g cm-3, and half-carbon, half-oxygen fuel: conditions under which the flame propagated in the flamelet regime in our related two-dimensional study. We compare to a corresponding two-dimensional simulation and show that while fire polishing keeps the small features suppressed in two dimensions, turbulence wrinkles the flame on far smaller scales in the three-dimensional case, suggesting that the transition to the distributed burning regime occurs at higher densities in three dimensions. Detailed turbulence diagnostics are provided. We show that the turbulence follows a Kolmogorov spectrum and is highly anisotropic on the large scales, with a much larger integral scale in the direction of gravity. Furthermore, we demonstrate that it becomes more isotropic as it cascades down to small scales. On the basis of the turbulent statistics and the flame properties of our simulation, we compute the Gibson scale. We show the progress of the turbulent flame through a classic combustion regime diagram, indicating that the flame just enters the distributed burning regime near the end of our simulation.
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Deterministic annealing for density estimation by multivariate normal mixtures
NASA Astrophysics Data System (ADS)
Kloppenburg, Martin; Tavan, Paul
1997-03-01
An approach to maximum-likelihood density estimation by mixtures of multivariate normal distributions for large high-dimensional data sets is presented. Conventionally that problem is tackled by notoriously unstable expectation-maximization (EM) algorithms. We remove these instabilities by the introduction of soft constraints, enabling deterministic annealing. Our developments are motivated by the proof that algorithmically stable fuzzy clustering methods that are derived from statistical physics analogs are special cases of EM procedures.
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Mechanistic insights into energy conservation by flavin-based electron bifurcation.
Lubner, Carolyn E; Jennings, David P; Mulder, David W; Schut, Gerrit J; Zadvornyy, Oleg A; Hoben, John P; Tokmina-Lukaszewska, Monika; Berry, Luke; Nguyen, Diep M; Lipscomb, Gina L; Bothner, Brian; Jones, Anne K; Miller, Anne-Frances; King, Paul W; Adams, Michael W W; Peters, John W
2017-06-01
The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. The unprecedented range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.
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NASA Technical Reports Server (NTRS)
Otto, S. R.; Bassom, Andrew P.
1992-01-01
The nonlinear development is studied of the most unstable Gortler mode within a general 3-D boundary layer upon a suitably concave surface. The structure of this mode was first identified by Denier, Hall and Seddougui (1991) who demonstrated that the growth rate of this instability is O(G sup 3/5) where G is the Gortler number (taken to be large here), which is effectively a measure of the curvature of the surface. Previous researchers have described the fate of the most unstable mode within a 2-D boundary layer. Denier and Hall (1992) discussed the fully nonlinear development of the vortex in this case and showed that the nonlinearity causes a breakdown of the flow structure. The effect of crossflow and unsteadiness upon an infinitesimal unstable mode was elucidated by Bassom and Hall (1991). They demonstrated that crossflow tends to stabilize the most unstable Gortler mode, and for certain crossflow/frequency combinations the Gortler mode may be made neutrally stable. These vortex configurations naturally lend themselves to a weakly nonlinear stability analysis; work which is described in a previous article by the present author. Here we extend the ideas of Denier and Hall (1992) to the three-dimensional boundary layer problem. It is found that the numerical solution of the fully nonlinear equations is best conducted using a method which is essentially an adaption of that utilized by Denier and Hall (1992). The influence of crossflow and unsteadiness upon the breakdown of the flow is described.
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NASA Astrophysics Data System (ADS)
Schuh, Terance; Li, Yutong; Elghossain, Geena; Wiita, Paul J.
2018-06-01
We have computed a suite of simulations of propagating three-dimensional relativistic jets, involving substantial ranges of initial jet Lorentz factors and ratios of jet density to external medium density. These allow us to categorize the respective AGN into Fanaroff-Riley class I (jet dominated) and FR class II (lobe-dominated) based upon the stability and morphology of the simulations. We used the Athena code to produce a substantial collection of large 3D variations of jets, many of which propagate stably and quickly for over 100 jet radii, but others of which eventually go unstable and fill up slowing advancing lobes. Most of these simulations have jet-to-ambient medium densities between 0.005 and 0.5 and velocities between 0.90c and 0.995c. Comparing the times when some jets go unstable to these initial parameters allow us to find a threshold where radio-loud AGNs transition from class II to class I. With these high resolution fully 3D relativistic simulations we can represent the jets more accurately and thus improve upon and refine earlier results that were based on 2D simulations.
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NASA Astrophysics Data System (ADS)
Korovinskiy, D. B.; Erkaev, N. V.; Semenov, V. S.; Ivanov, I. B.; Kiehas, S. A.; Ryzhkov, I. I.
2018-02-01
The stability of the Fadeev-like current sheet with respect to transversally propagating kink-like perturbations (flapping mode) is considered in terms of two-dimensional linear magnetohydrodynamic numerical simulations. It is found that the current sheet is stable when the total pressure minimum is located in the sheet center and unstable when the maximum value is reached there. It is shown that an unstable spot of any size enforces the whole sheet to be unstable, though the increment of instability decreases with the reduction of the unstable domain. In unstable sheets, the dispersion curve of instability shows a good match with the double-gradient (DG) model prediction. Here, the typical growth rate (short-wavelength limit) is close to the DG estimate averaged over the unstable region. In stable configurations, the typical frequency matches the maximum DG estimate. The dispersion curve of oscillations demonstrates a local maximum at wavelength ˜0.7 sheet half-width, which is a new feature that is absent in simplified analytical solutions.
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Computational hydrodynamics and optical performance of inductively-coupled plasma adaptive lenses
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mortazavi, M.; Urzay, J., E-mail: jurzay@stanford.edu; Mani, A.
2015-06-15
This study addresses the optical performance of a plasma adaptive lens for aero-optical applications by using both axisymmetric and three-dimensional numerical simulations. Plasma adaptive lenses are based on the effects of free electrons on the phase velocity of incident light, which, in theory, can be used as a phase-conjugation mechanism. A closed cylindrical chamber filled with Argon plasma is used as a model lens into which a beam of light is launched. The plasma is sustained by applying a radio-frequency electric current through a coil that envelops the chamber. Four different operating conditions, ranging from low to high powers andmore » induction frequencies, are employed in the simulations. The numerical simulations reveal complex hydrodynamic phenomena related to buoyant and electromagnetic laminar transport, which generate, respectively, large recirculating cells and wall-normal compression stresses in the form of local stagnation-point flows. In the axisymmetric simulations, the plasma motion is coupled with near-wall axial striations in the electron-density field, some of which propagate in the form of low-frequency traveling disturbances adjacent to vortical quadrupoles that are reminiscent of Taylor-Görtler flow structures in centrifugally unstable flows. Although the refractive-index fields obtained from axisymmetric simulations lead to smooth beam wavefronts, they are found to be unstable to azimuthal disturbances in three of the four three-dimensional cases considered. The azimuthal striations are optically detrimental, since they produce high-order angular aberrations that account for most of the beam wavefront error. A fourth case is computed at high input power and high induction frequency, which displays the best optical properties among all the three-dimensional simulations considered. In particular, the increase in induction frequency prevents local thermalization and leads to an axisymmetric distribution of electrons even after introduction of spatial disturbances. The results highlight the importance of accounting for spatial effects in the numerical computations when optical analyses of plasma lenses are pursued in this range of operating conditions.« less
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Nonlinear Thermal Instability in Compressible Viscous Flows Without Heat Conductivity
NASA Astrophysics Data System (ADS)
Jiang, Fei
2018-04-01
We investigate the thermal instability of a smooth equilibrium state, in which the density function satisfies Schwarzschild's (instability) condition, to a compressible heat-conducting viscous flow without heat conductivity in the presence of a uniform gravitational field in a three-dimensional bounded domain. We show that the equilibrium state is linearly unstable by a modified variational method. Then, based on the constructed linearly unstable solutions and a local well-posedness result of classical solutions to the original nonlinear problem, we further construct the initial data of linearly unstable solutions to be the one of the original nonlinear problem, and establish an appropriate energy estimate of Gronwall-type. With the help of the established energy estimate, we finally show that the equilibrium state is nonlinearly unstable in the sense of Hadamard by a careful bootstrap instability argument.
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Origin of Slope Failure in the Ursa Region, Northern Gulf of Mexico
NASA Astrophysics Data System (ADS)
Stigall, J.; Dugan, B.
2008-12-01
We use one-dimensional fluid flow and stability models to predict the evolution of overpressure and stability conditions of IODP Expedition Sites U1322 and U1324 in the Ursa region, northern Gulf of Mexico. Simulations of homogenous mud deposited at 3 and 12 mm/yr for Sites U1322 and U1324, with permeability (k) on the order of 10-17m2 and bulk compressibility of .4 /MPa, predict overpressures up to .45MPa and 1MPa in shallow sediments (<200m below sea floor). With limit equilibrium calculations for an infinite slope, these overpressures equate to a factor of safety (FS) greater than 10 and 4.5 for a internal friction angle of 26° and a seafloor slope of 2°. This implies stability throughout the last 50,000 years. Seismic and core observations, however, document major slope failures that span the entire Ursa region. Permeability in this region is well constrained by laboratory experiments, so we investigate how pulsed (high-to-low) sedimentation rates could have created unstable conditions, FS <1. Models with periods of high sedimentation generate overpressure that create unstable conditions while maintaining the time-averaged sedimentation rates. Other factors which are not possible to simulate in one dimension, such as a complex basin geometry, also influence the conditions that caused the past failures. A two-dimensional model linking lateral flow between the sites with the interpreted geometry from seismic stratigraphy gives a better picture of the flow field and instability within the basin. Asymmetrical loading of permeable sediments could have created a lateral difference in pore pressures which would have driven lateral flow from Site U1324 to Site U1322 where overpressures are higher than our one-dimensional models suggest. We anticipate that two-dimensional models with transient sedimentation patterns will enhance our understanding of flow in marginally stable environments and triggers of slope failures in passive margin systems.
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Mechanistic insights into energy conservation by flavin-based electron bifurcation
Lubner, Carolyn E.; Jennings, David P.; Mulder, David W.; ...
2017-04-10
The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. As a result, the unprecedentedmore » range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.« less
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Mechanistic insights into energy conservation by flavin-based electron bifurcation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lubner, Carolyn E.; Jennings, David P.; Mulder, David W.
The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. As a result, the unprecedentedmore » range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.« less
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Voss, Clifford I.; Simmons, Craig T.; Robinson, Neville I.
2010-01-01
This benchmark for three-dimensional (3D) numerical simulators of variable-density groundwater flow and solute or energy transport consists of matching simulation results with the semi-analytical solution for the transition from one steady-state convective mode to another in a porous box. Previous experimental and analytical studies of natural convective flow in an inclined porous layer have shown that there are a variety of convective modes possible depending on system parameters, geometry and inclination. In particular, there is a well-defined transition from the helicoidal mode consisting of downslope longitudinal rolls superimposed upon an upslope unicellular roll to a mode consisting of purely an upslope unicellular roll. Three-dimensional benchmarks for variable-density simulators are currently (2009) lacking and comparison of simulation results with this transition locus provides an unambiguous means to test the ability of such simulators to represent steady-state unstable 3D variable-density physics.
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Flutter, Postflutter, and Control of a Supersonic Wing Section
NASA Technical Reports Server (NTRS)
Marzocca, Piergiovanni; Librescu, Liviu; Silva, Walter A.
2002-01-01
A number of issues related to the flutter and postflutter of two-dimensional supersonic lifting surfaces are addressed. Among them there are the 1) investigation of the implications of the nonlinear unsteady aerodynamics and structural nonlinearities on the stable/unstable character of the limit cycle and 2) study of the implications of the incorporation of a control capability on both the flutter boundary and the postflutter behavior. To this end, a powerful methodology based on the Lyapunov first quantity is implemented. Such a treatment of the problem enables one to get a better understanding of the various factors involved in the nonlinear aeroelastic problem, including the stable and unstable limit cycle. In addition, it constitutes a first step toward a more general investigation of nonlinear aeroelastic phenomena of three-dimensional lifting surfaces.
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NASA Astrophysics Data System (ADS)
Chen, Gui-Qiang; Wang, Ya-Guang
2008-03-01
Compressible vortex sheets are fundamental waves, along with shocks and rarefaction waves, in entropy solutions to multidimensional hyperbolic systems of conservation laws. Understanding the behavior of compressible vortex sheets is an important step towards our full understanding of fluid motions and the behavior of entropy solutions. For the Euler equations in two-dimensional gas dynamics, the classical linearized stability analysis on compressible vortex sheets predicts stability when the Mach number M > sqrt{2} and instability when M < sqrt{2} ; and Artola and Majda’s analysis reveals that the nonlinear instability may occur if planar vortex sheets are perturbed by highly oscillatory waves even when M > sqrt{2} . For the Euler equations in three dimensions, every compressible vortex sheet is violently unstable and this instability is the analogue of the Kelvin Helmholtz instability for incompressible fluids. The purpose of this paper is to understand whether compressible vortex sheets in three dimensions, which are unstable in the regime of pure gas dynamics, become stable under the magnetic effect in three-dimensional magnetohydrodynamics (MHD). One of the main features is that the stability problem is equivalent to a free-boundary problem whose free boundary is a characteristic surface, which is more delicate than noncharacteristic free-boundary problems. Another feature is that the linearized problem for current-vortex sheets in MHD does not meet the uniform Kreiss Lopatinskii condition. These features cause additional analytical difficulties and especially prevent a direct use of the standard Picard iteration to the nonlinear problem. In this paper, we develop a nonlinear approach to deal with these difficulties in three-dimensional MHD. We first carefully formulate the linearized problem for the current-vortex sheets to show rigorously that the magnetic effect makes the problem weakly stable and establish energy estimates, especially high-order energy estimates, in terms of the nonhomogeneous terms and variable coefficients. Then we exploit these results to develop a suitable iteration scheme of the Nash Moser Hörmander type to deal with the loss of the order of derivative in the nonlinear level and establish its convergence, which leads to the existence and stability of compressible current-vortex sheets, locally in time, in three-dimensional MHD.
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NASA Astrophysics Data System (ADS)
González, P. A.; Övgün, Ali; Saavedra, Joel; Vásquez, Yerko
2018-06-01
In this paper we consider the three-dimensional Gödel black hole as a background and we study the vector particle tunneling from this background in order to obtain the Hawking temperature. Then, we study the propagation of a massive charged scalar field and we find the quasinormal modes analytically, which turns out be unstable as a consequence of the existence of closed time-like curves. Also, we consider the flux at the horizon and at infinity, and we compute the reflection and transmission coefficients as well as the absorption cross section. Mainly, we show that massive charged scalar waves can be superradiantly amplified by the three-dimensional Gödel black hole and that the coefficients have an oscillatory behavior. Moreover, the absorption cross section is null at the high frequency limit and for certain values of the frequency.
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NASA Astrophysics Data System (ADS)
Guo, Jia; Xu, Yanhong; Jin, Shangbin; Chen, Long; Kaji, Toshihiko; Honsho, Yoshihito; Addicoat, Matthew A.; Kim, Jangbae; Saeki, Akinori; Ihee, Hyotcherl; Seki, Shu; Irle, Stephan; Hiramoto, Masahiro; Gao, Jia; Jiang, Donglin
2013-11-01
Covalent organic frameworks are a class of crystalline organic porous materials that can utilize π-π-stacking interactions as a driving force for the crystallization of polygonal sheets to form layered frameworks and ordered pores. However, typical examples are chemically unstable and lack intrasheet π-conjugation, thereby significantly limiting their applications. Here we report a chemically stable, electronically conjugated organic framework with topologically designed wire frameworks and open nanochannels, in which the π conjugation-spans the two-dimensional sheets. Our framework permits inborn periodic ordering of conjugated chains in all three dimensions and exhibits a striking combination of properties: chemical stability, extended π-delocalization, ability to host guest molecules and hole mobility. We show that the π-conjugated organic framework is useful for high on-off ratio photoswitches and photovoltaic cells. Therefore, this strategy may constitute a step towards realizing ordered semiconducting porous materials for innovations based on two-dimensionally extended π systems.
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Flare particle acceleration in the interaction of twisted coronal flux ropes
NASA Astrophysics Data System (ADS)
Threlfall, J.; Hood, A. W.; Browning, P. K.
2018-03-01
Aim. The aim of this work is to investigate and characterise non-thermal particle behaviour in a three-dimensional (3D) magnetohydrodynamical (MHD) model of unstable multi-threaded flaring coronal loops. Methods: We have used a numerical scheme which solves the relativistic guiding centre approximation to study the motion of electrons and protons. The scheme uses snapshots from high resolution numerical MHD simulations of coronal loops containing two threads, where a single thread becomes unstable and (in one case) destabilises and merges with an additional thread. Results: The particle responses to the reconnection and fragmentation in MHD simulations of two loop threads are examined in detail. We illustrate the role played by uniform background resistivity and distinguish this from the role of anomalous resistivity using orbits in an MHD simulation where only one thread becomes unstable without destabilising further loop threads. We examine the (scalable) orbit energy gains and final positions recovered at different stages of a second MHD simulation wherein a secondary loop thread is destabilised by (and merges with) the first thread. We compare these results with other theoretical particle acceleration models in the context of observed energetic particle populations during solar flares.
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Maximizing the Biochemical Resolving Power of Fluorescence Microscopy
Esposito, Alessandro; Popleteeva, Marina; Venkitaraman, Ashok R.
2013-01-01
Most recent advances in fluorescence microscopy have focused on achieving spatial resolutions below the diffraction limit. However, the inherent capability of fluorescence microscopy to non-invasively resolve different biochemical or physical environments in biological samples has not yet been formally described, because an adequate and general theoretical framework is lacking. Here, we develop a mathematical characterization of the biochemical resolution in fluorescence detection with Fisher information analysis. To improve the precision and the resolution of quantitative imaging methods, we demonstrate strategies for the optimization of fluorescence lifetime, fluorescence anisotropy and hyperspectral detection, as well as different multi-dimensional techniques. We describe optimized imaging protocols, provide optimization algorithms and describe precision and resolving power in biochemical imaging thanks to the analysis of the general properties of Fisher information in fluorescence detection. These strategies enable the optimal use of the information content available within the limited photon-budget typically available in fluorescence microscopy. This theoretical foundation leads to a generalized strategy for the optimization of multi-dimensional optical detection, and demonstrates how the parallel detection of all properties of fluorescence can maximize the biochemical resolving power of fluorescence microscopy, an approach we term Hyper Dimensional Imaging Microscopy (HDIM). Our work provides a theoretical framework for the description of the biochemical resolution in fluorescence microscopy, irrespective of spatial resolution, and for the development of a new class of microscopes that exploit multi-parametric detection systems. PMID:24204821
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Petri net modeling of high-order genetic systems using grammatical evolution.
Moore, Jason H; Hahn, Lance W
2003-11-01
Understanding how DNA sequence variations impact human health through a hierarchy of biochemical and physiological systems is expected to improve the diagnosis, prevention, and treatment of common, complex human diseases. We have previously developed a hierarchical dynamic systems approach based on Petri nets for generating biochemical network models that are consistent with genetic models of disease susceptibility. This modeling approach uses an evolutionary computation approach called grammatical evolution as a search strategy for optimal Petri net models. We have previously demonstrated that this approach routinely identifies biochemical network models that are consistent with a variety of genetic models in which disease susceptibility is determined by nonlinear interactions between two DNA sequence variations. In the present study, we evaluate whether the Petri net approach is capable of identifying biochemical networks that are consistent with disease susceptibility due to higher order nonlinear interactions between three DNA sequence variations. The results indicate that our model-building approach is capable of routinely identifying good, but not perfect, Petri net models. Ideas for improving the algorithm for this high-dimensional problem are presented.
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Numerical Simulations of Dynamical Mass Transfer in Binaries
NASA Astrophysics Data System (ADS)
Motl, P. M.; Frank, J.; Tohline, J. E.
1999-05-01
We will present results from our ongoing research project to simulate dynamically unstable mass transfer in near contact binaries with mass ratios different from one. We employ a fully three-dimensional self-consistent field technique to generate synchronously rotating polytropic binaries. With our self-consistent field code we can create equilibrium binaries where one component is, by radius, within about 99 of filling its Roche lobe for example. These initial configurations are evolved using a three-dimensional, Eulerian hydrodynamics code. We make no assumptions about the symmetry of the subsequent flow and the entire binary system is evolved self-consistently under the influence of its own gravitational potential. For a given mass ratio and polytropic index for the binary components, mass transfer via Roche lobe overflow can be predicted to be stable or unstable through simple theoretical arguments. The validity of the approximations made in the stability calculations are tested against our numerical simulations. We acknowledge support from the U.S. National Science Foundation through grants AST-9720771, AST-9528424, and DGE-9355007. This research has been supported, in part, by grants of high-performance computing time on NPACI facilities at the San Diego Supercomputer Center, the Texas Advanced Computing Center and through the PET program of the NAVOCEANO DoD Major Shared Resource Center in Stennis, MS.
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Three-Dimensional Electromagnetic High Frequency Axisymmetric Cavity Scars.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Warne, Larry Kevin; Jorgenson, Roy Eberhardt
This report examines the localization of high frequency electromagnetic fi elds in three-dimensional axisymmetric cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This report treats both the case where the opposing sides, or mirrors, are convex, where there are no interior foci, and the case where they are concave, leading to interior foci. The scalar problem is treated fi rst but the approximations required to treat the vector fi eld components are also examined. Particular att ention is focused on the normalization through themore » electromagnetic energy theorem. Both projections of the fi eld along the scarred orbit as well as point statistics are examined. Statistical comparisons are m ade with a numerical calculation of the scars run with an axisymmetric simulation. This axisymmetric cas eformstheoppositeextreme(wherethetwomirror radii at each end of the ray orbit are equal) from the two -dimensional solution examined previously (where one mirror radius is vastly di ff erent from the other). The enhancement of the fi eldontheorbitaxiscanbe larger here than in the two-dimensional case. Intentionally Left Blank« less
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Numerical modeling of consolidation processes in hydraulically deposited soils
NASA Astrophysics Data System (ADS)
Brink, Nicholas Robert
Hydraulically deposited soils are encountered in many common engineering applications including mine tailing and geotextile tube fills, though the consolidation process for such soils is highly nonlinear and requires the use of advanced numerical techniques to provide accurate predictions. Several commercially available finite element codes poses the ability to model soil consolidation, and it was the goal of this research to assess the ability of two of these codes, ABAQUS and PLAXIS, to model the large-strain, two-dimensional consolidation processes which occur in hydraulically deposited soils. A series of one- and two-dimensionally drained rectangular models were first created to assess the limitations of ABAQUS and PLAXIS when modeling consolidation of highly compressible soils. Then, geotextile tube and TSF models were created to represent actual scenarios which might be encountered in engineering practice. Several limitations were discovered, including the existence of a minimum preconsolidation stress below which numerical solutions become unstable.
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NASA Astrophysics Data System (ADS)
Balasuriya, Sanjeeva
2016-12-01
State-dependent time-impulsive perturbations to a two-dimensional autonomous flow with stable and unstable manifolds are analysed by posing in terms of an integral equation which is valid in both forwards- and backwards-time. The impulses destroy the smooth invariant manifolds, necessitating new definitions for stable and unstable pseudo-manifolds. Their time-evolution is characterised by solving a Volterra integral equation of the second kind with discontinuous inhomogeniety. A criteria for heteroclinic trajectory persistence in this impulsive context is developed, as is a quantification of an instantaneous flux across broken heteroclinic manifolds. Several examples, including a kicked Duffing oscillator and an underwater explosion in the vicinity of an eddy, are used to illustrate the theory.
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Robust vortex lines, vortex rings, and hopfions in three-dimensional Bose-Einstein condensates
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bisset, R. N.; Wang, Wenlong; Ticknor, Christopher
Performing a systematic Bogoliubov–de Gennes spectral analysis, we illustrate that stationary vortex lines, vortex rings, and more exotic states, such as hopfions, are robust in three-dimensional atomic Bose-Einstein condensates, for large parameter intervals. Importantly, we find that the hopfion can be stabilized in a simple parabolic trap, without the need for trap rotation or inhomogeneous interactions. We supplement our spectral analysis by studying the dynamics of such stationary states; we find them to be robust against significant perturbations of the initial state. In the unstable regimes, we not only identify the unstable mode, such as a quadrupolar or hexapolar mode,more » but we also observe the corresponding instability dynamics. Moreover, deep in the Thomas-Fermi regime, we investigate the particlelike behavior of vortex rings and hopfions.« less
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Robust vortex lines, vortex rings, and hopfions in three-dimensional Bose-Einstein condensates
Bisset, R. N.; Wang, Wenlong; Ticknor, Christopher; ...
2015-12-07
Performing a systematic Bogoliubov–de Gennes spectral analysis, we illustrate that stationary vortex lines, vortex rings, and more exotic states, such as hopfions, are robust in three-dimensional atomic Bose-Einstein condensates, for large parameter intervals. Importantly, we find that the hopfion can be stabilized in a simple parabolic trap, without the need for trap rotation or inhomogeneous interactions. We supplement our spectral analysis by studying the dynamics of such stationary states; we find them to be robust against significant perturbations of the initial state. In the unstable regimes, we not only identify the unstable mode, such as a quadrupolar or hexapolar mode,more » but we also observe the corresponding instability dynamics. Moreover, deep in the Thomas-Fermi regime, we investigate the particlelike behavior of vortex rings and hopfions.« less
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NASA Astrophysics Data System (ADS)
González, P. A.; Papantonopoulos, Eleftherios; Saavedra, Joel; Vásquez, Yerko
2017-03-01
We study the instability of near extremal and extremal four-dimensional anti-de Sitter charged hairy black holes to radial neutral massive and charged massless scalar field perturbations. We solve the scalar field equation by using the improved asymptotic iteration method and the time domain analysis, and we find the quasinormal frequencies. For the charged scalar perturbations, we find the superradiance condition by computing the reflection coefficient in the low-frequency limit, and we show that in the superradiance regime, which depends on the scalar hair charge, all modes of radial charged massless perturbations are unstable, indicating that the charged hairy black hole is superradiantly unstable. On the other hand, calculating the quasinormal frequencies of radial neutral scalar perturbations in this background, we find stability of the charged hairy black hole.
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Perturbation Effects on a Supercritical C7H16/N2 Mixing Layer
NASA Technical Reports Server (NTRS)
Okongo'o, Nora; Bellan, Josette
2008-01-01
A computational-simulation study has been presented of effects of perturbation wavelengths and initial Reynolds numbers on the transition to turbulence of a heptane/nitrogen mixing layer at supercritical pressure. The governing equations for the simulations were the same as those of related prior studies reported in NASA Tech Briefs. Two-dimensional (2D) simulations were performed with initially im posed span wise perturbations whereas three-dimensional (3D) simulations had both streamwise and spanwise initial perturbations. The 2D simulations were undertaken to ascertain whether perturbations having the shortest unstable wavelength obtained from a linear stability analysis for inviscid flow are unstable in viscous nonlinear flows. The goal of the 3D simulations was to ascertain whether perturbing the mixing layer at different wavelengths affects the transition to turbulence. It was found that transitions to turbulence can be obtained at different perturbation wavelengths, provided that they are longer than the shortest unstable wavelength as determined by 2D linear stability analysis for the inviscid case and that the initial Reynolds number is proportionally increased as the wavelength is decreased. The transitional states thus obtained display different dynamic and mixture characteristics, departing strongly from the behaviors of perfect gases and ideal mixtures.
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NASA Astrophysics Data System (ADS)
Wang, Qiqi; Rigas, Georgios; Esclapez, Lucas; Magri, Luca; Blonigan, Patrick
2016-11-01
Bluff body flows are of fundamental importance to many engineering applications involving massive flow separation and in particular the transport industry. Coherent flow structures emanating in the wake of three-dimensional bluff bodies, such as cars, trucks and lorries, are directly linked to increased aerodynamic drag, noise and structural fatigue. For low Reynolds laminar and transitional regimes, hydrodynamic stability theory has aided the understanding and prediction of the unstable dynamics. In the same framework, sensitivity analysis provides the means for efficient and optimal control, provided the unstable modes can be accurately predicted. However, these methodologies are limited to laminar regimes where only a few unstable modes manifest. Here we extend the stability analysis to low-dimensional chaotic regimes by computing the Lyapunov covariant vectors and their associated Lyapunov exponents. We compare them to eigenvectors and eigenvalues computed in traditional hydrodynamic stability analysis. Computing Lyapunov covariant vectors and Lyapunov exponents also enables the extension of sensitivity analysis to chaotic flows via the shadowing method. We compare the computed shadowing sensitivities to traditional sensitivity analysis. These Lyapunov based methodologies do not rely on mean flow assumptions, and are mathematically rigorous for calculating sensitivities of fully unsteady flow simulations.
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Shi, Chengdi; Cai, Leyi; Hu, Wei; Sun, Junying
2017-09-19
ABSTRACTS Objective: To study the method of X-ray diagnosis of unstable pelvic fractures displaced in three-dimensional (3D) space and its clinical application in closed reduction. Five models of hemipelvic displacement were made in an adult pelvic specimen. Anteroposterior radiographs of the pelvis were analyzed in PACS. The method of X-ray diagnosis was applied in closed reductions. From February 2012 to June 2016, 23 patients (15 men, 8 women; mean age, 43.4 years) with unstable pelvic fractures were included. All patients were treated by closed reduction and percutaneous cannulate screw fixation of the pelvic ring. According to Tile's classification, the patients were classified into type B1 in 7 cases, B2 in 3, B3 in 3, C1 in 5, C2 in 3, and C3 in 2. The operation time and intraoperative blood loss were recorded. Postoperative images were evaluated by Matta radiographic standards. Five models of displacement were made successfully. The X-ray features of the models were analyzed. For clinical patients, the average operation time was 44.8 min (range, 20-90 min) and the average intraoperative blood loss was 35.7 (range, 20-100) mL. According to the Matta standards, 7 cases were excellent, 12 cases were good, and 4 were fair. The displacements in 3D space of unstable pelvic fractures can be diagnosed rapidly by X-ray analysis to guide closed reduction, with a satisfactory clinical outcome.
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Exploration of graphene oxide as an intelligent platform for cancer vaccines
NASA Astrophysics Data System (ADS)
Yue, Hua; Wei, Wei; Gu, Zonglin; Ni, Dezhi; Luo, Nana; Yang, Zaixing; Zhao, Lin; Garate, Jose Antonio; Zhou, Ruhong; Su, Zhiguo; Ma, Guanghui
2015-11-01
We explored an intelligent vaccine system via facile approaches using both experimental and theoretical techniques based on the two-dimensional graphene oxide (GO). Without extra addition of bio/chemical stimulators, the microsized GO imparted various immune activation tactics to improve the antigen immunogenicity. A high antigen adsorption was acquired, and the mechanism was revealed to be a combination of electrostatic, hydrophobic, and π-π stacking interactions. The ``folding GO'' acted as a cytokine self-producer and antigen reservoir and showed a particular autophagy, which efficiently promoted the activation of antigen presenting cells (APCs) and subsequent antigen cross-presentation. Such a ``One but All'' modality thus induced a high level of anti-tumor responses in a programmable way and resulted in efficient tumor regression in vivo. This work may shed light on the potential use of a new dimensional nano-platform in the development of high-performance cancer vaccines.We explored an intelligent vaccine system via facile approaches using both experimental and theoretical techniques based on the two-dimensional graphene oxide (GO). Without extra addition of bio/chemical stimulators, the microsized GO imparted various immune activation tactics to improve the antigen immunogenicity. A high antigen adsorption was acquired, and the mechanism was revealed to be a combination of electrostatic, hydrophobic, and π-π stacking interactions. The ``folding GO'' acted as a cytokine self-producer and antigen reservoir and showed a particular autophagy, which efficiently promoted the activation of antigen presenting cells (APCs) and subsequent antigen cross-presentation. Such a ``One but All'' modality thus induced a high level of anti-tumor responses in a programmable way and resulted in efficient tumor regression in vivo. This work may shed light on the potential use of a new dimensional nano-platform in the development of high-performance cancer vaccines. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04986e
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A collaborative visual analytics suite for protein folding research.
Harvey, William; Park, In-Hee; Rübel, Oliver; Pascucci, Valerio; Bremer, Peer-Timo; Li, Chenglong; Wang, Yusu
2014-09-01
Molecular dynamics (MD) simulation is a crucial tool for understanding principles behind important biochemical processes such as protein folding and molecular interaction. With the rapidly increasing power of modern computers, large-scale MD simulation experiments can be performed regularly, generating huge amounts of MD data. An important question is how to analyze and interpret such massive and complex data. One of the (many) challenges involved in analyzing MD simulation data computationally is the high-dimensionality of such data. Given a massive collection of molecular conformations, researchers typically need to rely on their expertise and prior domain knowledge in order to retrieve certain conformations of interest. It is not easy to make and test hypotheses as the data set as a whole is somewhat "invisible" due to its high dimensionality. In other words, it is hard to directly access and examine individual conformations from a sea of molecular structures, and to further explore the entire data set. There is also no easy and convenient way to obtain a global view of the data or its various modalities of biochemical information. To this end, we present an interactive, collaborative visual analytics tool for exploring massive, high-dimensional molecular dynamics simulation data sets. The most important utility of our tool is to provide a platform where researchers can easily and effectively navigate through the otherwise "invisible" simulation data sets, exploring and examining molecular conformations both as a whole and at individual levels. The visualization is based on the concept of a topological landscape, which is a 2D terrain metaphor preserving certain topological and geometric properties of the high dimensional protein energy landscape. In addition to facilitating easy exploration of conformations, this 2D terrain metaphor also provides a platform where researchers can visualize and analyze various properties (such as contact density) overlayed on the top of the 2D terrain. Finally, the software provides a collaborative environment where multiple researchers can assemble observations and biochemical events into storyboards and share them in real time over the Internet via a client-server architecture. The software is written in Scala and runs on the cross-platform Java Virtual Machine. Binaries and source code are available at http://www.aylasoftware.org and have been released under the GNU General Public License. Copyright © 2014 Elsevier Inc. All rights reserved.
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Development of Turbulent Magnetic Reconnection in a Magnetic Island
DOE Office of Scientific and Technical Information (OSTI.GOV)
Huang, Can; Lu, Quanming; Wang, Rongsheng
In this paper, with two-dimensional particle-in-cell simulations, we report that the electron Kelvin–Helmholtz instability is unstable in the current layer associated with a large-scale magnetic island, which is formed in multiple X-line guide field reconnections. The current sheet is fragmented into many small current sheets with widths down to the order of the electron inertial length. Secondary magnetic reconnection then occurs in these fragmented current sheets, which leads to a turbulent state. The electrons are highly energized in such a process.
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Chiu, E; Lamoreux, M L; Orlow, S J
1993-09-01
Ocular pigmentation in the mouse occurs primarily postnatally as a result of the melanization of neural crest-derived melanocytes. Using immunologic and biochemical techniques, we demonstrate that in normal mice the expression of tyrosinase and the related proteins TRP-1 and TRP-2, rises during the first week of life, remains elevated for a week, and then steadily declines to low levels by adulthood. Sucrose gradient density centrifugation demonstrates that tyrosinase, TRP-1 and TRP-2 are present in high molecular weight forms in the eyes of wild-type mice. The normal time course is disrupted in mice carrying the pink-eyed unstable (p(un)) mutation at the P-locus, a model for tyrosinase-positive albinism in man. Tyrosinase and TRP-2 are present at wild-type levels in the eyes of p(un)/p(un) mice at birth, but, rather than rising, their levels rapidly decline over the first week of life. TRP-1 is almost undetectable, even at birth. High molecular weight complexes could not be detected in eyes of p(un)/p(un) mice. Our results suggest that postnatal ocular melanogenesis in the mouse presents an attractive model for the study of the orderly expression and action of the proteins involved in eumelanin synthesis, and that the p(un) mutation disrupts this temporally controlled process.
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Trapping virtual pores by crystal retro-engineering
NASA Astrophysics Data System (ADS)
Little, Marc A.; Briggs, Michael E.; Jones, James T. A.; Schmidtmann, Marc; Hasell, Tom; Chong, Samantha Y.; Jelfs, Kim E.; Chen, Linjiang; Cooper, Andrew I.
2015-02-01
Stable guest-free porous molecular crystals are uncommon. By contrast, organic molecular crystals with guest-occupied cavities are frequently observed, but these cavities tend to be unstable and collapse on removal of the guests—this feature has been referred to as ‘virtual porosity’. Here, we show how we have trapped the virtual porosity in an unstable low-density organic molecular crystal by introducing a second molecule that matches the size and shape of the unstable voids. We call this strategy ‘retro-engineering’ because it parallels organic retrosynthetic analysis, and it allows the metastable two-dimensional hexagonal pore structure in an organic solvate to be trapped in a binary cocrystal. Unlike the crystal with virtual porosity, the cocrystal material remains single crystalline and porous after removal of guests by heating.
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On the analysis of the double Hopf bifurcation in machining processes via centre manifold reduction
NASA Astrophysics Data System (ADS)
Molnar, T. G.; Dombovari, Z.; Insperger, T.; Stepan, G.
2017-11-01
The single-degree-of-freedom model of orthogonal cutting is investigated to study machine tool vibrations in the vicinity of a double Hopf bifurcation point. Centre manifold reduction and normal form calculations are performed to investigate the long-term dynamics of the cutting process. The normal form of the four-dimensional centre subsystem is derived analytically, and the possible topologies in the infinite-dimensional phase space of the system are revealed. It is shown that bistable parameter regions exist where unstable periodic and, in certain cases, unstable quasi-periodic motions coexist with the equilibrium. Taking into account the non-smoothness caused by loss of contact between the tool and the workpiece, the boundary of the bistable region is also derived analytically. The results are verified by numerical continuation. The possibility of (transient) chaotic motions in the global non-smooth dynamics is shown.
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Canards and black swans in a model of a 3-D autocatalator
NASA Astrophysics Data System (ADS)
Shchepakina, E.
2005-01-01
The mathematical model of a 3-D autocatalator is studied using the geometric theory of singular perturbations, namely, the black swan and canard techniques. Critical regimes are modeled by canards (one-dimensional stable-unstable slow integral manifolds). The meaning of criticality here is as follows. The critical regime corresponds to a chemical reaction which separates the domain of self-accelerating reactions from the domain of slow reactions. A two-dimensional stable-unstable slow integral manifold (black swan) consisting entirely of canards, which simulate the critical phenomena for different initial data of the dynamical system, is constructed. It is shown that this procedure leads to the phenomenon of auto-oscillations in the chemical system. The geometric approach combined with asymptotic and numerical methods permits us to explain the strong parametric sensitivity and to obtain asymptotic representations of the critical behavior of the chemical system.
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Computation in Dynamically Bounded Asymmetric Systems
Rutishauser, Ueli; Slotine, Jean-Jacques; Douglas, Rodney
2015-01-01
Previous explanations of computations performed by recurrent networks have focused on symmetrically connected saturating neurons and their convergence toward attractors. Here we analyze the behavior of asymmetrical connected networks of linear threshold neurons, whose positive response is unbounded. We show that, for a wide range of parameters, this asymmetry brings interesting and computationally useful dynamical properties. When driven by input, the network explores potential solutions through highly unstable ‘expansion’ dynamics. This expansion is steered and constrained by negative divergence of the dynamics, which ensures that the dimensionality of the solution space continues to reduce until an acceptable solution manifold is reached. Then the system contracts stably on this manifold towards its final solution trajectory. The unstable positive feedback and cross inhibition that underlie expansion and divergence are common motifs in molecular and neuronal networks. Therefore we propose that very simple organizational constraints that combine these motifs can lead to spontaneous computation and so to the spontaneous modification of entropy that is characteristic of living systems. PMID:25617645
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NASA Astrophysics Data System (ADS)
Sheng, Shaoxiang; Li, Wenbin; Gou, Jian; Cheng, Peng; Chen, Lan; Wu, Kehui
2018-05-01
Tip-enhanced Raman spectroscopy (TERS), which combines scanning probe microscopy with the Raman spectroscopy, is capable to access the local structure and chemical information simultaneously. However, the application of ambient TERS is limited by the unstable and poorly controllable experimental conditions. Here, we designed a high performance TERS system based on a low-temperature ultrahigh-vacuum scanning tunneling microscope (LT-UHV-STM) and combined with a molecular beam epitaxy (MBE) system. It can be used for growing two-dimensional (2D) materials and for in situ STM and TERS characterization. Using a 2D silicene sheet on the Ag(111) surface as a model system, we achieved an unprecedented 109 Raman single enhancement factor in combination with a TERS spatial resolution down to 0.5 nm. The results show that TERS combined with a MBE system can be a powerful tool to study low dimensional materials and surface science.
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Guo, Jia; Xu, Yanhong; Jin, Shangbin; Chen, Long; Kaji, Toshihiko; Honsho, Yoshihito; Addicoat, Matthew A.; Kim, Jangbae; Saeki, Akinori; Ihee, Hyotcherl; Seki, Shu; Irle, Stephan; Hiramoto, Masahiro; Gao, Jia; Jiang, Donglin
2013-01-01
Covalent organic frameworks are a class of crystalline organic porous materials that can utilize π–π-stacking interactions as a driving force for the crystallization of polygonal sheets to form layered frameworks and ordered pores. However, typical examples are chemically unstable and lack intrasheet π-conjugation, thereby significantly limiting their applications. Here we report a chemically stable, electronically conjugated organic framework with topologically designed wire frameworks and open nanochannels, in which the π conjugation-spans the two-dimensional sheets. Our framework permits inborn periodic ordering of conjugated chains in all three dimensions and exhibits a striking combination of properties: chemical stability, extended π-delocalization, ability to host guest molecules and hole mobility. We show that the π-conjugated organic framework is useful for high on-off ratio photoswitches and photovoltaic cells. Therefore, this strategy may constitute a step towards realizing ordered semiconducting porous materials for innovations based on two-dimensionally extended π systems. PMID:24220603
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Stability in chemical and biological systems: Multistage polyenzymatic reactions
NASA Astrophysics Data System (ADS)
Varfolomeev, S. D.; Lukovenkov, A. V.
2010-08-01
General principles of the theory of stability of solutions to differential equations are considered. The stability of equations describing the dynamics of changes in reagent concentrations in polyenzymatic biochemical chains is analyzed. Various mechanisms of formation of stable and unstable stationary states are considered, and unbalanced regimes and collapse are analyzed. The influence of systems of toxins and drugs on stability is studied. An interpretation of pathological processes based on stability theory is given.
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Weatherill, D.; Simmons, C.T.; Voss, C.I.; Robinson, N.I.
2004-01-01
This study proposes the use of several problems of unstable steady state convection with variable fluid density in a porous layer of infinite horizontal extent as two-dimensional (2-D) test cases for density-dependent groundwater flow and solute transport simulators. Unlike existing density-dependent model benchmarks, these problems have well-defined stability criteria that are determined analytically. These analytical stability indicators can be compared with numerical model results to test the ability of a code to accurately simulate buoyancy driven flow and diffusion. The basic analytical solution is for a horizontally infinite fluid-filled porous layer in which fluid density decreases with depth. The proposed test problems include unstable convection in an infinite horizontal box, in a finite horizontal box, and in an infinite inclined box. A dimensionless Rayleigh number incorporating properties of the fluid and the porous media determines the stability of the layer in each case. Testing the ability of numerical codes to match both the critical Rayleigh number at which convection occurs and the wavelength of convection cells is an addition to the benchmark problems currently in use. The proposed test problems are modelled in 2-D using the SUTRA [SUTRA-A model for saturated-unsaturated variable-density ground-water flow with solute or energy transport. US Geological Survey Water-Resources Investigations Report, 02-4231, 2002. 250 p] density-dependent groundwater flow and solute transport code. For the case of an infinite horizontal box, SUTRA results show a distinct change from stable to unstable behaviour around the theoretical critical Rayleigh number of 4??2 and the simulated wavelength of unstable convection agrees with that predicted by the analytical solution. The effects of finite layer aspect ratio and inclination on stability indicators are also tested and numerical results are in excellent agreement with theoretical stability criteria and with numerical results previously reported in traditional fluid mechanics literature. ?? 2004 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Malek, N. A.; Hasini, H.; Yusoff, M. Z.
2013-06-01
Unsteadiness in supersonic flow in nozzles can be generated by the release of heat due to spontaneous condensation. The heat released is termed "supercritical" and may be responsible for turbine blades failure in turbine cascade as it causes a supersonic flow to decelerate. When the Mach number is reduced to unity, the flow can no longer sustain the additional heat and becomes unstable. This paper aims to numerically investigate the unsteadiness caused by supercritical heat addition in one-dimensional condensing flows. The governing equations for mass, momentum and energy, coupled with the equations describing the wetness fraction and droplet growth are integrated and solved iteratively to reveal the final solution. Comparison is made with well-established experimental and numerical solution done by previous researchers that shows similar phenomena.
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Crisis of the chaotic attractor of a climate model: a transfer operator approach
NASA Astrophysics Data System (ADS)
Tantet, Alexis; Lucarini, Valerio; Lunkeit, Frank; Dijkstra, Henk A.
2018-05-01
The destruction of a chaotic attractor leading to rough changes in the dynamics of a dynamical system is studied. Local bifurcations are known to be characterised by a single or a pair of characteristic exponents crossing the imaginary axis. As a result, the approach of such bifurcations in the presence of noise can be inferred from the slowing down of the decay of correlations (Held and Kleinen 2004 Geophys. Res. Lett. 31 1–4). On the other hand, little is known about global bifurcations involving high-dimensional attractors with several positive Lyapunov exponents. It is known that the global stability of chaotic attractors may be characterised by the spectral properties of the Koopman (Mauroy and Mezić 2016 IEEE Trans. Autom. Control 61 3356–69) or the transfer operators governing the evolution of statistical ensembles. Accordingly, it has recently been shown (Tantet 2017 J. Stat. Phys. 1–33) that a boundary crisis in the Lorenz flow coincides with the approach to the unit circle of the eigenvalues of these operators associated with motions about the attractor, the stable resonances. A second class of resonances, the unstable resonances, are responsible for the decay of correlations and mixing on the attractor. In the deterministic case, these cannot be expected to be affected by general boundary crises. Here, however, we give an example of a chaotic system in which slowing down of the decay of correlations of some observables does occur at the approach of a boundary crisis. The system considered is a high-dimensional, chaotic climate model of physical relevance. Moreover, coarse-grained approximations of the transfer operators on a reduced space, constructed from a long time series of the system, give evidence that this behaviour is due to the approach of unstable resonances to the unit circle. That the unstable resonances are affected by the crisis can be physically understood from the fact that the process responsible for the instability, the ice-albedo feedback, is also active on the attractor. Finally, we discuss implications regarding response theory and the design of early-warning signals.
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On the interaction of Tollmien-Schlichting waves in axisymmetric supersonic flows
NASA Technical Reports Server (NTRS)
Duck, P. W.; Hall, P.
1988-01-01
Two-dimensional lower branch Tollmien-Schlichting waves described by triple-deck theory are always stable for planar supersonic flows. The possible occurrence of axisymmetric unstable modes in the supersonic flow around an axisymmetric body is investigated. In particular flows around bodies with typical radii comparable with the thickness of the upper deck are considered. It is shown that such unstable modes exist below a critical nondimensional radius of the body a sub 0. At values of the radius above a sub 0 all the modes are stable while if unstable modes exist they are found to occur in pairs. The interaction of these modes in the nonlinear regime is investigated using a weakly nonlinear approach and it is found that, dependent on the frequencies of the imposed Tollmien-Schlichting waves, either of the modes can be set up.
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On the interaction of Tollmien-Schlichting waves in axisymmetric supersonic flows
NASA Technical Reports Server (NTRS)
Duck, P. W.; Hall, P.
1989-01-01
Two-dimensional lower branch Tollmien-Schlichting waves described by triple-deck theory are always stable for planar supersonic flows. The possible occurrence of axisymmetric unstable modes in the supersonic flow around an axisymmetric body is investigated. In particular flows around bodies with typical radii comparable with the thickness of the upper deck are considered. It is shown that such unstable modes exist below a critical nondimensional radius of the body a sub O. At values of the radius above a sub O all the modes are stable while if unstable modes exist they are found to occur in pairs. The interaction of these modes in the nonlinear regime is investigated using a weakly nonlinear approach and it is found that, dependent on the frequencies of the imposed Tollmien-Schlichting waves, either of the modes can be set up.
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Vibration-Resistant Support for Halide Lamps
NASA Technical Reports Server (NTRS)
Kiss, J.
1987-01-01
Lamp envelope protected against breakage. Old and new mounts for halide arc lamp sealed in housing with parabolic refector and quartz window. New version supports lamp with compliant garters instead of rigid brazed joint at top and dimensionally unstable finger stock at bottom.
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Adiabatic coarse-graining and simulations of stochastic biochemical networks
Sinitsyn, N. A.; Hengartner, Nicolas; Nemenman, Ilya
2009-01-01
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach is similar to the Born–Oppenheimer approximation in quantum mechanics and follows from the stochastic path integral representation of the cumulant generating function of reaction events. In applications with a small number of chemical reactions, it produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, interpretable representation and can be used for high-accuracy, low-complexity coarse-grained numerical simulations. As an example, we derive the coarse-grained description for a chain of biochemical reactions and show that the coarse-grained and the microscopic simulations agree, but the former is 3 orders of magnitude faster. PMID:19525397
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Spearhead Nanometric Field-Effect Transistor Sensors for Single-Cell Analysis.
Zhang, Yanjun; Clausmeyer, Jan; Babakinejad, Babak; Córdoba, Ainara López; Ali, Tayyibah; Shevchuk, Andrew; Takahashi, Yasufumi; Novak, Pavel; Edwards, Christopher; Lab, Max; Gopal, Sahana; Chiappini, Ciro; Anand, Uma; Magnani, Luca; Coombes, R Charles; Gorelik, Julia; Matsue, Tomokazu; Schuhmann, Wolfgang; Klenerman, David; Sviderskaya, Elena V; Korchev, Yuri
2016-03-22
Nanometric field-effect-transistor (FET) sensors are made on the tip of spear-shaped dual carbon nanoelectrodes derived from carbon deposition inside double-barrel nanopipettes. The easy fabrication route allows deposition of semiconductors or conducting polymers to comprise the transistor channel. A channel from electrodeposited poly pyrrole (PPy) exhibits high sensitivity toward pH changes. This property is exploited by immobilizing hexokinase on PPy nano-FETs to give rise to a selective ATP biosensor. Extracellular pH and ATP gradients are key biochemical constituents in the microenvironment of living cells; we monitor their real-time changes in relation to cancer cells and cardiomyocytes. The highly localized detection is possible because of the high aspect ratio and the spear-like design of the nano-FET probes. The accurately positioned nano-FET sensors can detect concentration gradients in three-dimensional space, identify biochemical properties of a single living cell, and after cell membrane penetration perform intracellular measurements.
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Spearhead Nanometric Field-Effect Transistor Sensors for Single-Cell Analysis
Córdoba, Ainara López; Ali, Tayyibah; Shevchuk, Andrew; Takahashi, Yasufumi; Novak, Pavel; Edwards, Christopher; Lab, Max; Gopal, Sahana; Chiappini, Ciro; Anand, Uma; Magnani, Luca; Coombes, R. Charles; Gorelik, Julia; Matsue, Tomokazu; Schuhmann, Wolfgang; Klenerman, David; Sviderskaya, Elena V.; Korchev, Yuri
2016-01-01
Nanometric field-effect-transistor (FET) sensors are made on the tip of spear-shaped dual carbon nanoelectrodes derived from carbon deposition inside double-barrel nanopipettes. The easy fabrication route allows deposition of semiconductors or conducting polymers to comprise the transistor channel. A channel from electrodeposited poly pyrrole (PPy) exhibits high sensitivity toward pH changes. This property is exploited by immobilizing hexokinase on PPy nano-FETs to give rise to a selective ATP biosensor. Extracellular pH and ATP gradients are key biochemical constituents in the microenvironment of living cells; we monitor their real-time changes in relation to cancer cells and cardiomyocytes. The highly localized detection is possible because of the high aspect ratio and the spear-like design of the nano-FET probes. The accurately positioned nano-FET sensors can detect concentration gradients in three-dimensional space, identify biochemical properties of a single living cell, and after cell membrane penetration perform intracellular measurements. PMID:26816294
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Study on color difference estimation method of medicine biochemical analysis
NASA Astrophysics Data System (ADS)
Wang, Chunhong; Zhou, Yue; Zhao, Hongxia; Sun, Jiashi; Zhou, Fengkun
2006-01-01
The biochemical analysis in medicine is an important inspection and diagnosis method in hospital clinic. The biochemical analysis of urine is one important item. The Urine test paper shows corresponding color with different detection project or different illness degree. The color difference between the standard threshold and the test paper color of urine can be used to judge the illness degree, so that further analysis and diagnosis to urine is gotten. The color is a three-dimensional physical variable concerning psychology, while reflectance is one-dimensional variable; therefore, the estimation method of color difference in urine test can have better precision and facility than the conventional test method with one-dimensional reflectance, it can make an accurate diagnose. The digital camera is easy to take an image of urine test paper and is used to carry out the urine biochemical analysis conveniently. On the experiment, the color image of urine test paper is taken by popular color digital camera and saved in the computer which installs a simple color space conversion (RGB -> XYZ -> L *a *b *)and the calculation software. Test sample is graded according to intelligent detection of quantitative color. The images taken every time were saved in computer, and the whole illness process will be monitored. This method can also use in other medicine biochemical analyses that have relation with color. Experiment result shows that this test method is quick and accurate; it can be used in hospital, calibrating organization and family, so its application prospect is extensive.
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NASA Astrophysics Data System (ADS)
Wan, Yuanxin; Sha, Ye; Luo, Shaochuan; Deng, Weijia; Wang, Xiaoliang; Xue, Gi; Zhou, Dongshan
2015-11-01
Tin dioxide (SnO2) is an attractive material for anodes in energy storage devices, because it has four times the theoretical capacity of the prevalent anode material (graphite). The main obstacle hampers SnO2 from practical application is the pulverization problem caused by drastic volume change (∼300%) during lithium-ion insertion or extraction, which would lead to the loss of electrical conductivity, unstable solid-electrolyte interphase (SEI) formation and consequently severe capacity fading in the cycling. Here, we anchored the SnO2 nanocrystals into three dimensional graphene gel network to tackle this problem. As a result of the three dimensional (3-D) architecture, the huge volume change during cycling was tolerated by the large free space in this 3-D construction, resulting in a high capacity of 1090 mAh g-1 even after 200 cycles. What's more, at a higher current density 5 A g-1, a reversible capacity of about 491 mAh g-1 was achieved with this electrode.
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A transition in the viscous fingering instability in miscible fluids
NASA Astrophysics Data System (ADS)
Videbaek, Thomas; Nagel, Sidney R.
2017-11-01
The viscous fingering instability in a quasi-two dimensional Hele-Shaw cell is an example of complex structure formation from benign initial conditions. When the invading fluid has the lesser viscosity, the interface between the two fluids is unstable to finger formation. Here, we study the instability between pairs of miscible fluids in a circular cell with fluid injected at its center. As the injection rate is decreased, diffusion will smooth out the discontinuity in the gap-averaged viscosity at the interface between the fluids. At high injection rates (i.e., high Péclet number, Pe), fingering is associated with three-dimensional structure within the gap between the confining plates. On lowering Pe, we find a sharp transition in the finger morphology at a critical value, Pec (ηi /ηo) 1 / 2 , with ηi (ηo) being the viscosity of the inner (outer) fluid; at this point, the width of the fingers jumps, the length of the fingers shrinks towards zero and the three-dimensional structure goes from half filling to fully filling the gap. Thus, by controlling the viscosity contrast at the interface, one can alter and even completely suppress the instability.
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NASA Astrophysics Data System (ADS)
Karasso, P. S.; Mungal, M. G.
1991-05-01
This study investigates the structure and mixing of the two-dimensional turbulent mixing layer when subjected to longitudinal streamwise curvature. The straight layer is now well known to be dominated by the primary Kelvin-Helmholtz (KH) instability as well as the secondary Taylor-Goertler (TG) instability. For equal density fluids, placing the high-speed fluid on the inside of a streamwise bend causes the TG instability to be enhanced (unstable case), while placing the low-speed fluid on the inside of the same bend leads to the suppression of the TG instability (stable case). The location of the mixing transition is correspondingly altered. Our goal is to study the changes to the mixing field and growth rate resulting from the competition between instabilities. Our studies are performed in a newly constructed blow-down water facility capable of high Reynolds numbers and excellent optical access. Maximum flow speeds are 2 and 0.25 m/sec for the high- and low-speed sides, respectively, leading to maximum Reynolds numbers of 80 000 based on velocity difference and the width of the layer. We are able to dye one stream with a fluorescent dye, thus providing several planar views of the flow under laser sheet illumination. These views are superior to conventional approaches as they are free of wall effects and are not spatially integrating. However, our most useful diagnostic of the structure of the flow is the ability to record high-speed images of the end view of the flow that are then reconstructed by computer using the volume rendering technique of Jiménez et al.1 This approach is especially useful as it allows us to compare the structural changes to the flow resulting from the competition between the KH and TG instabilities. Another advantage is the fact that several hundred frames, covering many characteristic times, are incorporated into the rendered image and thus capture considerably more flow physics than do still images. We currently have our rendering techniques fully operational,2 and are presently acquiring high quality high-speed movies of the various flow cases. Our findings to date, based on planar time-averaged and instantaneous views, show the following: (1) a 50% increase in growth rate from the stable to the unstable case resulting from mild curvature; (2) an enhancement of the TG vortices in the unstable case, but without major disruption of the KH instability which remains relatively intact; and (3) the occurrence of the KH instability at angles tilted with respect to the splitter plate tip, in agreement with the predictions of linear stability theory. This final observation has not been reported to date, primarily because sheet techniques have not been used at Reynolds numbers as high as the present study. The presentation will provide detailed views of the changes between the stable, straight, and unstable cases using our volume rendering approach, and will provide statistical measures such as changes to vortex spacing and size, to quantify such changes.
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Stability of surface plastic flow in large strain deformation of metals
NASA Astrophysics Data System (ADS)
Viswanathan, Koushik; Udapa, Anirduh; Sagapuram, Dinakar; Mann, James; Chandrasekar, Srinivasan
We examine large-strain unconstrained simple shear deformation in metals using a model two-dimensional cutting system and high-speed in situ imaging. The nature of the deformation mode is shown to be a function of the initial microstructure state of the metal and the deformation geometry. For annealed metals, which exhibit large ductility and strain hardening capacity, the commonly assumed laminar flow mode is inherently unstable. Instead, the imposed shear is accommodated by a highly rotational flow-sinuous flow-with vortex-like components and large-amplitude folding on the mesoscale. Sinuous flow is triggered by a plastic instability on the material surface ahead of the primary region of shear. On the other hand, when the material is extensively strain-hardened prior to shear, laminar flow again becomes unstable giving way to shear banding. The existence of these flow modes is established by stability analysis of laminar flow. The role of the initial microstructure state in determining the change in stability from laminar to sinuous / shear-banded flows in metals is elucidated. The implications for cutting, forming and wear processes for metals, and to surface plasticity phenomena such as mechanochemical Rehbinder effects are discussed.
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NASA Astrophysics Data System (ADS)
Nan, Lijun; Li, Yashan; Cui, Changwei; Ning, Na; Huang, Jing; Xu, Chengdong; Zhang, Xiaofang; Yang, Ruiqun; Zhong, Yingxue
2018-04-01
The stability of wine is an important feature during the wine aging, which is mainly reflected in the balance of color, taste and aroma during the wine aging. During the wine fermentation, the role of microbes and enzymes including the interaction between them caused the mutual penetration, combination, decomposition and transformation among the substances in connection with color, aroma and taste in wine, which led to the instability of wine. After the fermentation of wine, the long aging period could just stabilize the wine. Still, the quality of wine had changed a lot. Based on the indicative changes in wine, such as microbiological interactions, biochemical reactions as well as interactions between the microorganism and biochemical reactions, the impact of changes of the basic biochemical and physicochemical indices on the stability of red wine were reviewed, and developmental suggestions in the future were also put forward in this paper, in order to reveal the mechanism of instability through the effect of dynamic change on the stability of red wine and analyze the unstable root of the red wine, which could lay a foundation for further research, and provide help for actual production.
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Kostev, I V; Teryoshin, V A; Sotckaya, Ya A; Homutyanskay, N I; Dolgopolova, E V; Salamech, K A
2015-01-01
At the patients with nonalcoholic steatohepatitis on a background of diabetes mellitus type 11, after completion of the generally accepted medical treatment there was no normalization of indexes of the glutation system (the level of recovered glutation and activity of enzymes the glutation redox--system was saved decreased), that in a clinical plan was represented in a presence unstable clinical and biochemical remission of disease.
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Sotskaya, Ya A; Homutyanskaya, N I; Dolgopolova, E V; Salamekh, K A
2015-01-01
At the patients with nonalcoholic steatohepatitis on a background of diabetes mellitus type II, after completion of the generally accepted medical treatment there was no normalization of indexes of the glutation system (the level of recovered glutation and activity of enzymes the glutation redox-system was saved decreased), that in a clinical plan was represented in.a presence unstable clinical and biochemical remission of disease.
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Universal dynamical properties preclude standard clustering in a large class of biochemical data.
Gomez, Florian; Stoop, Ralph L; Stoop, Ruedi
2014-09-01
Clustering of chemical and biochemical data based on observed features is a central cognitive step in the analysis of chemical substances, in particular in combinatorial chemistry, or of complex biochemical reaction networks. Often, for reasons unknown to the researcher, this step produces disappointing results. Once the sources of the problem are known, improved clustering methods might revitalize the statistical approach of compound and reaction search and analysis. Here, we present a generic mechanism that may be at the origin of many clustering difficulties. The variety of dynamical behaviors that can be exhibited by complex biochemical reactions on variation of the system parameters are fundamental system fingerprints. In parameter space, shrimp-like or swallow-tail structures separate parameter sets that lead to stable periodic dynamical behavior from those leading to irregular behavior. We work out the genericity of this phenomenon and demonstrate novel examples for their occurrence in realistic models of biophysics. Although we elucidate the phenomenon by considering the emergence of periodicity in dependence on system parameters in a low-dimensional parameter space, the conclusions from our simple setting are shown to continue to be valid for features in a higher-dimensional feature space, as long as the feature-generating mechanism is not too extreme and the dimension of this space is not too high compared with the amount of available data. For online versions of super-paramagnetic clustering see http://stoop.ini.uzh.ch/research/clustering. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Chaos in driven Alfvén systems: unstable periodic orbits and chaotic saddles
NASA Astrophysics Data System (ADS)
Chian, A. C.-L.; Santana, W. M.; Rempel, E. L.; Borotto, F. A.; Hada, T.; Kamide, Y.
2007-01-01
The chaotic dynamics of Alfvén waves in space plasmas governed by the derivative nonlinear Schrödinger equation, in the low-dimensional limit described by stationary spatial solutions, is studied. A bifurcation diagram is constructed, by varying the driver amplitude, to identify a number of nonlinear dynamical processes including saddle-node bifurcation, boundary crisis, and interior crisis. The roles played by unstable periodic orbits and chaotic saddles in these transitions are analyzed, and the conversion from a chaotic saddle to a chaotic attractor in these dynamical processes is demonstrated. In particular, the phenomenon of gap-filling in the chaotic transition from weak chaos to strong chaos via an interior crisis is investigated. A coupling unstable periodic orbit created by an explosion, within the gaps of the chaotic saddles embedded in a chaotic attractor following an interior crisis, is found numerically. The gap-filling unstable periodic orbits are responsible for coupling the banded chaotic saddle (BCS) to the surrounding chaotic saddle (SCS), leading to crisis-induced intermittency. The physical relevance of chaos for Alfvén intermittent turbulence observed in the solar wind is discussed.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Goto, R.; Hatori, T.; Miura, H., E-mail: miura.hideaki@nifs.ac.jp
Two-fluid and the finite Larmor effects on linear and nonlinear growth of the Rayleigh-Taylor instability in a two-dimensional slab are studied numerically with special attention to high-wave-number dynamics and nonlinear structure formation at a low β-value. The two effects stabilize the unstable high wave number modes for a certain range of the β-value. In nonlinear simulations, the absence of the high wave number modes in the linear stage leads to the formation of the density field structure much larger than that in the single-fluid magnetohydrodynamic simulation, together with a sharp density gradient as well as a large velocity difference. Themore » formation of the sharp velocity difference leads to a subsequent Kelvin-Helmholtz-type instability only when both the two-fluid and finite Larmor radius terms are incorporated, whereas it is not observed otherwise. It is shown that the emergence of the secondary instability can modify the outline of the turbulent structures associated with the primary Rayleigh-Taylor instability.« less
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Study on the SPR responses of various DNA probe concentrations by parallel scan spectral SPR imaging
NASA Astrophysics Data System (ADS)
Ma, Suihua; Liu, Le; Lu, Weiping; Zhang, Yaou; He, Yonghong; Guo, Jihua
2008-12-01
SPR sensors have become a high sensitive and label free method for characterizing and quantifying chemical and biochemical interactions. However, the relations between the SPR refractive index response and the property (such as concentrations) of biochemical probes are still lacking. In this paper, an experimental study on the SPR responses of varies concentrations of Legionella pneumophila mip DNA probes is presented. We developed a novel two-dimensional SPR sensing technique-parallel scan spectral SPR imaging-to detect an array of mip gene probes. This technique offers quantitative refractive index information with a high sensing throughput. By detecting mip DNA probes with different concentrations, we obtained the relations between the SPR refractive index response and the concentrations of mip DNA probes. These results are valuable for design and developing SPR based mip gene biochips.
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NASA Astrophysics Data System (ADS)
Ghil, M.; Zaliapin, I.; Thompson, S.
2008-05-01
We consider a delay differential equation (DDE) model for El-Niño Southern Oscillation (ENSO) variability. The model combines two key mechanisms that participate in ENSO dynamics: delayed negative feedback and seasonal forcing. We perform stability analyses of the model in the three-dimensional space of its physically relevant parameters. Our results illustrate the role of these three parameters: strength of seasonal forcing b, atmosphere-ocean coupling κ, and propagation period τ of oceanic waves across the Tropical Pacific. Two regimes of variability, stable and unstable, are separated by a sharp neutral curve in the (b, τ) plane at constant κ. The detailed structure of the neutral curve becomes very irregular and possibly fractal, while individual trajectories within the unstable region become highly complex and possibly chaotic, as the atmosphere-ocean coupling κ increases. In the unstable regime, spontaneous transitions occur in the mean "temperature" (i.e., thermocline depth), period, and extreme annual values, for purely periodic, seasonal forcing. The model reproduces the Devil's bleachers characterizing other ENSO models, such as nonlinear, coupled systems of partial differential equations; some of the features of this behavior have been documented in general circulation models, as well as in observations. We expect, therefore, similar behavior in much more detailed and realistic models, where it is harder to describe its causes as completely.
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Instabilities in Englert-type supergravity solutions
NASA Astrophysics Data System (ADS)
Page, Don N.; Pope, C. N.
1984-09-01
We show that all eleven-dimensional Englert-type supergravity solutions (in which the four-index field has internal components) constructed from internal spaces M7 having two or more Killing spinors, are unstable. Permanent address: Blackett Laboratory, Imperial College, London SW7 2BZ, United Kingdom.
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Elliptical Instability of Rotating Von Karman Street
NASA Astrophysics Data System (ADS)
Stegner, A.; Pichon, T.; Beunier, M.
Clouds often reveal a meso-scale vortex shedding in the wake of mountainous islands. Unlike the classical bi-dimensional Von-Karman street, these observed vortex street are affected by the earth rot ation and vertical stratification. Theses effects could induce a selective destabilization of anticyclonic vortices. It is well known that inertial instability (also called centrifugal instability) induce a three- dimensional destabilization of anticyclonic structures when the absolute vorticity is larger than the local Coriolis parameter. However, we have shown, by the mean of laboratory experiments, that it is a different type of instability which is mainly responsible for asymmetric rotating Von-Karman street. A serie of experiments were performed to study the wake of a cylinder in a rotating fluid, at medium Reynolds number and order one Rossby number. We have shown that the vertical structure of unstable anticyclonic vortices is characteristic of an elliptical instability. Besides, unlike the inertial instability, the vertical unstable wavelength depends on the Rossby number.
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A Dynamical Systems Approach to the Design of the Science Orbit Around Europa
NASA Technical Reports Server (NTRS)
Gomez, Gerard; Lara, Martin; Russell, Ryan P.
2006-01-01
The science orbit for a future mission to Europa requires low eccentricity, low altitude, and high inclination. However, high inclination orbits around planetary satellites are unstable due to third-body perturbations. Without control, the orbiter impacts Europa after few weeks. To minimize control, a tour over the stable-unstable, averaged manifolds of unstable frozen orbits has been suggested. We proceed with the unaveraged equations and study the manifolds of unstable orbits that are periodic in a rotating frame attached to Europa. Massive numerical computation helps in understanding the unstable dynamics close to Europa, and, thus, in selecting long lifetime high inclination orbits. A final test of a selected set of initial conditions on a high fidelity, ephemeris model, validate the results.
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NASA Astrophysics Data System (ADS)
Heizler, Shay I.; Kessler, David A.
2017-06-01
Mode-I fracture exhibits microbranching in the high velocity regime where the simple straight crack is unstable. For velocities below the instability, classic modeling using linear elasticity is valid. However, showing the existence of the instability and calculating the dynamics postinstability within the linear elastic framework is difficult and controversial. The experimental results give several indications that the microbranching phenomenon is basically a three-dimensional (3D) phenomenon. Nevertheless, the theoretical effort has been focused mostly on two-dimensional (2D) modeling. In this paper we study the microbranching instability using three-dimensional atomistic simulations, exploring the difference between the 2D and the 3D models. We find that the basic 3D fracture pattern shares similar behavior with the 2D case. Nevertheless, we exhibit a clear 3D-2D transition as the crack velocity increases, whereas as long as the microbranches are sufficiently small, the behavior is pure 3D behavior, whereas at large driving, as the size of the microbranches increases, more 2D-like behavior is exhibited. In addition, in 3D simulations, the quantitative features of the microbranches, separating the regimes of steady-state cracks (mirror) and postinstability (mist-hackle) are reproduced clearly, consistent with the experimental findings.
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Three-dimensional envelope instability in periodic focusing channels
NASA Astrophysics Data System (ADS)
Qiang, Ji
2018-03-01
The space-charge driven envelope instability can be of great danger in high intensity accelerators and was studied using a two-dimensional (2D) envelope model and three-dimensional (3D) macroparticle simulations before. In this paper, we study the instability for a bunched beam using a three-dimensional envelope model in a periodic solenoid and radio-frequency (rf) focusing channel and a periodic quadrupole and rf focusing channel. This study shows that when the transverse zero current phase advance is below 90 ° , the beam envelope can still become unstable if the longitudinal zero current phase advance is beyond 90 ° . For the transverse zero current phase advance beyond 90 ° , the instability stopband width becomes larger with the increase of the longitudinal focusing strength and even shows different structure from the 2D case when the longitudinal zero current phase advance is beyond 90 ° . Breaking the symmetry of two longitudinal focusing rf cavities and the symmetry between the horizontal focusing and the vertical focusing in the transverse plane in the periodic quadrupole and rf channel makes the instability stopband broader. This suggests that a more symmetric accelerator lattice design might help reduce the range of the envelope instability in parameter space.
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Hu, Liyan; Pandey, Amit V; Eggimann, Sandra; Rüfenacht, Véronique; Möslinger, Dorothea; Nuoffer, Jean-Marc; Häberle, Johannes
2013-11-29
Argininosuccinic aciduria (ASA) is an autosomal recessive urea cycle disorder caused by deficiency of argininosuccinate lyase (ASL) with a wide clinical spectrum from asymptomatic to severe hyperammonemic neonatal onset life-threatening courses. We investigated the role of ASL transcript variants in the clinical and biochemical variability of ASA. Recombinant proteins for ASL wild type, mutant p.E189G, and the frequently occurring transcript variants with exon 2 or 7 deletions were (co-)expressed in human embryonic kidney 293T cells. We found that exon 2-deleted ASL forms a stable truncated protein with no relevant activity but a dose-dependent dominant negative effect on enzymatic activity after co-expression with wild type or mutant ASL, whereas exon 7-deleted ASL is unstable but seems to have, nevertheless, a dominant negative effect on mutant ASL. These findings were supported by structural modeling predictions for ASL heterotetramer/homotetramer formation. Illustrating the physiological relevance, the predominant occurrence of exon 7-deleted ASL was found in two patients who were both heterozygous for the ASL mutant p.E189G. Our results suggest that ASL transcripts can contribute to the highly variable phenotype in ASA patients if expressed at high levels. Especially, the exon 2-deleted ASL variant may form a heterotetramer with wild type or mutant ASL, causing markedly reduced ASL activity.
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Subbarao, Udumula; Sarkar, Sumanta; Jana, Rajkumar; Bera, Sourav S; Peter, Sebastian C
2016-06-06
We conceptually selected the compounds REPb3 (RE = Eu, Yb), which are unstable in air, and converted them to the stable materials in ambient conditions by the chemical processes of "nanoparticle formation" and "dimensional reduction". The nanoparticles and the bulk counterparts were synthesized by the solvothermal and high-frequency induction furnace heating methods, respectively. The reduction of the particle size led to the valence transition of the rare earth atom, which was monitored through magnetic susceptibility and X-ray absorption near edge spectroscopy (XANES) measurements. The stability was checked by X-ray diffraction and thermogravimetric analysis over a period of seven months in oxygen and argon atmospheres and confirmed by XANES. The nanoparticles showed outstanding stability toward aerial oxidation over a period of seven months compared to the bulk counterpart, as the latter one is more prone to the oxidation within a few days.
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A note on chaotic unimodal maps and applications.
Zhou, C T; He, X T; Yu, M Y; Chew, L Y; Wang, X G
2006-09-01
Based on the word-lift technique of symbolic dynamics of one-dimensional unimodal maps, we investigate the relation between chaotic kneading sequences and linear maximum-length shift-register sequences. Theoretical and numerical evidence that the set of the maximum-length shift-register sequences is a subset of the set of the universal sequence of one-dimensional chaotic unimodal maps is given. By stabilizing unstable periodic orbits on superstable periodic orbits, we also develop techniques to control the generation of long binary sequences.
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Cross Flow Effects on Glaze Ice Roughness Formation
NASA Technical Reports Server (NTRS)
Tsao, Jen-Ching
2004-01-01
The present study examines the impact of large-scale cross flow on the creation of ice roughness elements on the leading edge of a swept wing under glaze icing conditions. A three-dimensional triple-deck structure is developed to describe the local interaction of a 3 D air boundary layer with ice sheets and liquid films. A linear stability analysis is presented here. It is found that, as the sweep angle increases, the local icing instabilities enhance and the most linearly unstable modes are strictly three dimensional.
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Act-and-wait time-delayed feedback control of autonomous systems
NASA Astrophysics Data System (ADS)
Pyragas, Viktoras; Pyragas, Kestutis
2018-02-01
Recently an act-and-wait modification of time-delayed feedback control has been proposed for the stabilization of unstable periodic orbits in nonautonomous dynamical systems (Pyragas and Pyragas, 2016 [30]). The modification implies a periodic switching of the feedback gain and makes the closed-loop system finite-dimensional. Here we extend this modification to autonomous systems. In order to keep constant the phase difference between the controlled orbit and the act-and-wait switching function an additional small-amplitude periodic perturbation is introduced. The algorithm can stabilize periodic orbits with an odd number of real unstable Floquet exponents using a simple single-input single-output constraint control.
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A new illusion of projected three-dimensional space
NASA Technical Reports Server (NTRS)
Ellis, Stephen R.; Grunwald, Arthur
1987-01-01
When perspective projections of orbital trajectories plotted in local-vertical local-horizontal coordinates are viewed with certain viewing angles, their appearance becomes perceptually unstable. They often lose their trochoidal appearance and reorganize as helices. This reorganization may be due to the viewer's familiarity with coiled springs.
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Davies, Sarah K; Fearn, Sarah; Allsopp, Luke P; Harrison, Freya; Ware, Ecaterina; Diggle, Stephen P; Filloux, Alain; McPhail, David S; Bundy, Jacob G
2017-01-01
Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight-secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection. IMPORTANCE Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples-both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium-derived metabolites in complex biological samples could be very important in the future for helping to understand how sample matrices impact the survival of bacteria under antibiotic challenge. We have shown that an imaging mass spectrometric technique, TOF-SIMS, will be potentially extremely valuable for this kind of research in the future.
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Microscale electrokinetic transport and stability
NASA Astrophysics Data System (ADS)
Chen, Chuan-Hua
Electrokinetics is a leading mechanism for transport and separation of biochemical samples in microdevices due to its favorable scaling at small scales. However, electrokinetic systems can become highly unstable, and this instability adversely affects key processes such as sample stacking and electrophoretic separation. This dissertation deals with two major topics: a novel planar micropump exploiting the favorable scaling of electroosmosis at the microscale, and a fundamental study of electrokinetic flow instabilities induced by electrical conductivity gradients. Electroosmotic micropumps use field-induced ion drag to drive liquids and achieve high pressures in a compact design with no moving parts. An analytical model applicable to planar, etched-structure micropumps was developed to guide the geometrical design and working fluid selection. Standard microlithography and wet etching techniques were used to fabricate a pump 1 mm long along the flow direction and 0.9 mum by 38 mm in cross section. The pump produced a maximum pressure of 0.33 atm and a maximum flow rate of 15 mul/min at 1 kV applied potential with deionized water as working fluid. The pump performance agreed well with the theoretical model. Electrokinetic flow instabilities occur under high electric field in the presence of electrical conductivity gradients. In a microfluidic T-junction 11 mum by 155 mum in cross section, aqueous electrolytes of 10:1 conductivity ratio were electrokinetically driven into a common mixing channel. Convectively unstable waves were observed at 0.5 kV/cm, and upstream propagating waves at 1.5 kV/cm. A physical model for this instability has been developed. A linear stability analysis of the governing equations in the thin-layer limit predicts both qualitative trends and quantitative features that agree well with experimental data. Briggs-Bers criteria were applied to select physically unstable modes and determine the nature of instability. Conductivity gradients and bulk charge accumulation are a crucial factor in the instability. The role of electroosmotic flow is mainly as a convecting medium. The instability is governed by two key controlling parameters: the ratio of dynamic to dissipative forces which determines the onset of instability, and the ratio of electroviscous to electroosmotic velocities which governs the convective versus absolute nature of instability.
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Exact coherent structures and chaotic dynamics in a model of cardiac tissue
DOE Office of Scientific and Technical Information (OSTI.GOV)
Byrne, Greg; Marcotte, Christopher D.; Grigoriev, Roman O., E-mail: roman.grigoriev@physics.gatech.edu
Unstable nonchaotic solutions embedded in the chaotic attractor can provide significant new insight into chaotic dynamics of both low- and high-dimensional systems. In particular, in turbulent fluid flows, such unstable solutions are referred to as exact coherent structures (ECS) and play an important role in both initiating and sustaining turbulence. The nature of ECS and their role in organizing spatiotemporally chaotic dynamics, however, is reasonably well understood only for systems on relatively small spatial domains lacking continuous Euclidean symmetries. Construction of ECS on large domains and in the presence of continuous translational and/or rotational symmetries remains a challenge. This ismore » especially true for models of excitable media which display spiral turbulence and for which the standard approach to computing ECS completely breaks down. This paper uses the Karma model of cardiac tissue to illustrate a potential approach that could allow computing a new class of ECS on large domains of arbitrary shape by decomposing them into a patchwork of solutions on smaller domains, or tiles, which retain Euclidean symmetries locally.« less
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NASA Technical Reports Server (NTRS)
Hall, Philip; Bennett, James
1986-01-01
The Taylor-Goertler vortex instability equations are formulated for steady and unsteady interacting boundary-layer flows. The effective Goertler number is shown to be a function of the wall shape in the boundary layer and the possibility of both steady and unsteady Taylor-Goertler modes exists. As an example the steady flow in a symmetrically constricted channel is considered and it is shown that unstable Goertler vortices exist before the boundary layers at the wall develop the Goldstein singularity discussed by Smith and Daniels (1981). As an example of an unsteady spatially varying basic state, it is considered the instability of high-frequency large-amplitude two- and three-dimensional Tollmien-Schlichting waves in a curved channel. It is shown that they are unstable in the first 'Stokes-layer stage' of the hierarchy of nonlinear states discussed by Smith and Burggraf (1985). This instability of Tollmien-Schlichting waves in an internal flow can occur in the presence of either convex or concave curvature. Some discussion of this instability in external flows is given.
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Two-dimensional antimonene single crystals grown by van der Waals epitaxy.
Ji, Jianping; Song, Xiufeng; Liu, Jizi; Yan, Zhong; Huo, Chengxue; Zhang, Shengli; Su, Meng; Liao, Lei; Wang, Wenhui; Ni, Zhenhua; Hao, Yufeng; Zeng, Haibo
2016-11-15
Unlike the unstable black phosphorous, another two-dimensional group-VA material, antimonene, was recently predicted to exhibit good stability and remarkable physical properties. However, the synthesis of high-quality monolayer or few-layer antimonenes, sparsely reported, has greatly hindered the development of this new field. Here, we report the van der Waals epitaxy growth of few-layer antimonene monocrystalline polygons, their atomical microstructure and stability in ambient condition. The high-quality, few-layer antimonene monocrystalline polygons can be synthesized on various substrates, including flexible ones, via van der Waals epitaxy growth. Raman spectroscopy and transmission electron microscopy reveal that the obtained antimonene polygons have buckled rhombohedral atomic structure, consistent with the theoretically predicted most stable β-phase allotrope. The very high stability of antimonenes was observed after aging in air for 30 days. First-principle and molecular dynamics simulation results confirmed that compared with phosphorene, antimonene is less likely to be oxidized and possesses higher thermodynamic stability in oxygen atmosphere at room temperature. Moreover, antimonene polygons show high electrical conductivity up to 10 4 S m -1 and good optical transparency in the visible light range, promising in transparent conductive electrode applications.
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Two-dimensional antimonene single crystals grown by van der Waals epitaxy
Ji, Jianping; Song, Xiufeng; Liu, Jizi; Yan, Zhong; Huo, Chengxue; Zhang, Shengli; Su, Meng; Liao, Lei; Wang, Wenhui; Ni, Zhenhua; Hao, Yufeng; Zeng, Haibo
2016-01-01
Unlike the unstable black phosphorous, another two-dimensional group-VA material, antimonene, was recently predicted to exhibit good stability and remarkable physical properties. However, the synthesis of high-quality monolayer or few-layer antimonenes, sparsely reported, has greatly hindered the development of this new field. Here, we report the van der Waals epitaxy growth of few-layer antimonene monocrystalline polygons, their atomical microstructure and stability in ambient condition. The high-quality, few-layer antimonene monocrystalline polygons can be synthesized on various substrates, including flexible ones, via van der Waals epitaxy growth. Raman spectroscopy and transmission electron microscopy reveal that the obtained antimonene polygons have buckled rhombohedral atomic structure, consistent with the theoretically predicted most stable β-phase allotrope. The very high stability of antimonenes was observed after aging in air for 30 days. First-principle and molecular dynamics simulation results confirmed that compared with phosphorene, antimonene is less likely to be oxidized and possesses higher thermodynamic stability in oxygen atmosphere at room temperature. Moreover, antimonene polygons show high electrical conductivity up to 104 S m−1 and good optical transparency in the visible light range, promising in transparent conductive electrode applications. PMID:27845327
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Penalized gaussian process regression and classification for high-dimensional nonlinear data.
Yi, G; Shi, J Q; Choi, T
2011-12-01
The model based on Gaussian process (GP) prior and a kernel covariance function can be used to fit nonlinear data with multidimensional covariates. It has been used as a flexible nonparametric approach for curve fitting, classification, clustering, and other statistical problems, and has been widely applied to deal with complex nonlinear systems in many different areas particularly in machine learning. However, it is a challenging problem when the model is used for the large-scale data sets and high-dimensional data, for example, for the meat data discussed in this article that have 100 highly correlated covariates. For such data, it suffers from large variance of parameter estimation and high predictive errors, and numerically, it suffers from unstable computation. In this article, penalized likelihood framework will be applied to the model based on GPs. Different penalties will be investigated, and their ability in application given to suit the characteristics of GP models will be discussed. The asymptotic properties will also be discussed with the relevant proofs. Several applications to real biomechanical and bioinformatics data sets will be reported. © 2011, The International Biometric Society No claim to original US government works.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Espinal, Laura; Wong-Ng, Winnie; Kaduk, James A.
2014-09-24
The development of sorbents for next-generation CO{sub 2} mitigation technologies will require better understanding of CO{sub 2}/sorbent interactions. Among the sorbents under consideration are shape-selective microporous molecular sieves with hierarchical pore morphologies of reduced dimensionality. We have characterized the non-equilibrium CO{sub 2} sorption of OMS-2, a well-known one-dimensional microporous octahedral molecular sieve with manganese oxide framework. Remarkably, we find that the degree of CO{sub 2} sorption hysteresis increases when the gas/sorbent system is allowed to equilibrate for longer times at each pressure step. Density functional theory calculations indicate a 'gate-keeping' role of the cation in the tunnel, only allowing CO{submore » 2} molecules to enter fully into the tunnel via a highly unstable transient state when CO{sub 2} loadings exceed 0.75 mmol/g. The energy barrier associated with the gate-keeping effect suggests an adsorption mechanism in which kinetic trapping of CO{sub 2} is responsible for the observed hysteretic behavior.« less
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A numerical study of transition control by periodic suction-blowing
NASA Technical Reports Server (NTRS)
Biringen, Sedat
1987-01-01
The applicability of active control of transition by periodic suction-blowing is investigated via direct numerical simulations of the Navier-Stokes equations. The time-evolution of finite-amplitude disturbances in plane channel flow is compared in detail with and without control. The analysis indicates that, for relatively small three dimensional amplitudes, a two dimensional control effectively reduces disturbance growth rates even for linearly unstable Reynolds numbers. After the flow goes through secondary instability, three dimensional control seems necessary to stabilize the flow. An investigation of the temperature field suggests that passive temperature contamination is operative to reflect the flow dynamics during transition.
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A mechanism for hot-spot generation in a reactive two-dimensional sheared viscous layer
NASA Astrophysics Data System (ADS)
Timms, Robert; Purvis, Richard; Curtis, John P.
2018-05-01
A two-dimensional model for the non-uniform melting of a thin sheared viscous layer is developed. An asymptotic solution is presented for both a non-reactive and a reactive material. It is shown that the melt front is linearly stable to small perturbations in the non-reactive case, but becomes linearly unstable upon introduction of an Arrhenius source term to model the chemical reaction. Results demonstrate that non-uniform melting acts as a mechanism to generate hot spots that are found to be sufficient to reduce the time to ignition when compared with the corresponding one-dimensional model of melting.
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High-resolution mapping of bifurcations in nonlinear biochemical circuits
NASA Astrophysics Data System (ADS)
Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.
2016-08-01
Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.
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Cartilage magnetic resonance imaging techniques at 3 T: current status and future directions.
Thakkar, Rashmi S; Subhawong, Ty; Carrino, John A; Chhabra, Avneesh
2011-04-01
Magnetic resonance imaging (MRI) remains the imaging modality of choice for morphological and compositional evaluation of the articular cartilage. Accurate detection and characterization of cartilage lesions are necessary to guide the medical and surgical therapy and are also critical for longitudinal studies of the cartilage. Recent work using 3.0-T MRI systems shows promise in improving detection and characterization of the cartilage lesions, particularly with increasing use of high-resolution and high-contrast 3-dimensional sequences, which allow detailed morphological assessment of cartilage in arbitrary imaging planes. In addition, implementation of biochemical sequences in clinically feasible scan times has a potential in the early detection of cartilage lesions before they become morphologically apparent. This article discusses relative advantages and disadvantages of various commonly used as well as experimental MRI techniques to directly assess the morphology and indirectly evaluate the biochemical composition of the articular cartilage.
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One-dimensional Turbulence Models of Type I X-ray Bursts
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hou, Chen
Type I X-ray bursts are caused by thermonuclear explosions occurring on the surface of an accreting neutron star in a binary star system. Observations and simulations of these phenomena are of great importance for understanding the fundamental properties of neutron stars and dense matter because the equation of state for cold dense matter can be constrained by the mass-radius relationship of neutron stars. During the bursts, turbulence plays a key role in mixing the fuels and driving the unstable nuclear burning process. This dissertation presents one-dimensional models of photospheric radius expansion bursts with a new approach to simulate turbulent advection.more » Compared with the traditional mixing length theory, the one-dimensional turbulence (ODT) model represents turbulent motions by a sequence of maps that are generated according to a stochastic process. The light curves I obtained with the ODT models are in good agreement with those of the KEPLER model in which the mixing length theory and various diffusive processes are applied. The abundance comparison, however, indicates that the differences in turbulent regions and turbulent diffusivities result in more 12C survival during the bursts in the ODT models, which can make a difference in the superbursts phenomena triggered by unstable carbon burning.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Garaud, Pascale; Brummell, Nicholas
2015-12-10
Fingering convection (otherwise known as thermohaline convection) is an instability that occurs in stellar radiative interiors in the presence of unstable compositional gradients. Numerical simulations have been used in order to estimate the efficiency of mixing induced by this instability. However, fully three-dimensional (3D) computations in the parameter regime appropriate for stellar astrophysics (i.e., low Prandtl number) are prohibitively expensive. This raises the question of whether two-dimensional (2D) simulations could be used instead to achieve the same goals. In this work, we address this issue by comparing the outcome of 2D and 3D simulations of fingering convection at low Prandtlmore » number. We find that 2D simulations are never appropriate. However, we also find that the required 3D computational domain does not have to be very wide: the third dimension only needs to contain a minimum of two wavelengths of the fastest-growing linearly unstable mode to capture the essentially 3D dynamics of small-scale fingering. Narrow domains, however, should still be used with caution since they could limit the subsequent development of any large-scale dynamics typically associated with fingering convection.« less
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On the precision of quasi steady state assumptions in stochastic dynamics
NASA Astrophysics Data System (ADS)
Agarwal, Animesh; Adams, Rhys; Castellani, Gastone C.; Shouval, Harel Z.
2012-07-01
Many biochemical networks have complex multidimensional dynamics and there is a long history of methods that have been used for dimensionality reduction for such reaction networks. Usually a deterministic mass action approach is used; however, in small volumes, there are significant fluctuations from the mean which the mass action approach cannot capture. In such cases stochastic simulation methods should be used. In this paper, we evaluate the applicability of one such dimensionality reduction method, the quasi-steady state approximation (QSSA) [L. Menten and M. Michaelis, "Die kinetik der invertinwirkung," Biochem. Z 49, 333369 (1913)] for dimensionality reduction in case of stochastic dynamics. First, the applicability of QSSA approach is evaluated for a canonical system of enzyme reactions. Application of QSSA to such a reaction system in a deterministic setting leads to Michaelis-Menten reduced kinetics which can be used to derive the equilibrium concentrations of the reaction species. In the case of stochastic simulations, however, the steady state is characterized by fluctuations around the mean equilibrium concentration. Our analysis shows that a QSSA based approach for dimensionality reduction captures well the mean of the distribution as obtained from a full dimensional simulation but fails to accurately capture the distribution around that mean. Moreover, the QSSA approximation is not unique. We have then extended the analysis to a simple bistable biochemical network model proposed to account for the stability of synaptic efficacies; the substrate of learning and memory [J. E. Lisman, "A mechanism of memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase," Proc. Natl. Acad. Sci. U.S.A. 82, 3055-3057 (1985)], 10.1073/pnas.82.9.3055. Our analysis shows that a QSSA based dimensionality reduction method results in errors as big as two orders of magnitude in predicting the residence times in the two stable states.
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NASA Astrophysics Data System (ADS)
Calini, A.; Schober, C. M.
2013-09-01
In this article we present the results of a broad numerical investigation on the stability of breather-type solutions of the nonlinear Schrödinger (NLS) equation, specifically the one- and two-mode breathers for an unstable plane wave, which are frequently used to model rogue waves. The numerical experiments involve large ensembles of perturbed initial data for six typical random perturbations. Ensemble estimates of the "closeness", A(t), of the perturbed solution to an element of the respective unperturbed family indicate that the only neutrally stable breathers are the ones of maximal dimension, that is: given an unstable background with N unstable modes, the only neutrally stable breathers are the N-dimensional ones (obtained as a superimposition of N simple breathers via iterated Backlund transformations). Conversely, breathers which are not fully saturated are sensitive to noisy environments and are unstable. Interestingly, A(t) is smallest for the coalesced two-mode breather indicating the coalesced case may be the most robust two-mode breather in a laboratory setting. The numerical simulations confirm and provide a realistic realization of the stability behavior established analytically by the authors.
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Structure and Stability of One-Dimensional Detonations in Ethylene-Air Mixtures
NASA Technical Reports Server (NTRS)
Yungster, S.; Radhakrishnan, K.; Perkins, High D. (Technical Monitor)
2003-01-01
The propagation of one-dimensional detonations in ethylene-air mixtures is investigated numerically by solving the one-dimensional Euler equations with detailed finite-rate chemistry. The numerical method is based on a second-order spatially accurate total-variation-diminishing scheme and a point implicit, first-order-accurate, time marching algorithm. The ethylene-air combustion is modeled with a 20-species, 36-step reaction mechanism. A multi-level, dynamically adaptive grid is utilized, in order to resolve the structure of the detonation. Parametric studies over an equivalence ratio range of 0.5 less than phi less than 3 for different initial pressures and degrees of detonation overdrive demonstrate that the detonation is unstable for low degrees of overdrive, but the dynamics of wave propagation varies with fuel-air equivalence ratio. For equivalence ratios less than approximately 1.2 the detonation exhibits a short-period oscillatory mode, characterized by high-frequency, low-amplitude waves. Richer mixtures (phi greater than 1.2) exhibit a low-frequency mode that includes large fluctuations in the detonation wave speed; that is, a galloping propagation mode is established. At high degrees of overdrive, stable detonation wave propagation is obtained. A modified McVey-Toong short-period wave-interaction theory is in excellent agreement with the numerical simulations.
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An Interview with Matthew P. Greving, PhD. Interview by Vicki Glaser.
Greving, Matthew P
2011-10-01
Matthew P. Greving is Chief Scientific Officer at Nextval Inc., a company founded in early 2010 that has developed a discovery platform called MassInsight™.. He received his PhD in Biochemistry from Arizona State University, and prior to that he spent nearly 7 years working as a software engineer. This experience in solving complex computational problems fueled his interest in developing technologies and algorithms related to acquisition and analysis of high-dimensional biochemical data. To address the existing problems associated with label-based microarray readouts, he beganwork on a technique for label-free mass spectrometry (MS) microarray readout compatible with both matrix-assisted laser/desorption ionization (MALDI) and matrix-free nanostructure initiator mass spectrometry (NIMS). This is the core of Nextval’s MassInsight technology, which utilizes picoliter noncontact deposition of high-density arrays on mass-readout substrates along with computational algorithms for high-dimensional data processingand reduction.
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Meng, X Flora; Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M
2017-05-01
Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. © 2017 The Author(s).
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Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M.
2017-01-01
Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. PMID:28566513
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Growth rates of the buoyancy-driven instability of an autocatalytic reaction front in a narrow cell
Bockmann; Muller
2000-09-18
Experimental studies were performed on the buoyancy-driven instability of an autocatalytic reaction front in a quasi-2D cell. The unstable density stratification at an ascending front leads to convection that results in a fingerlike front deformation. The growth rates of the spatial modes of the instability are determined at the initial stage. A stabilization is found at higher wave numbers, while the system is unstable against low wave number perturbations. Whereas comparison with a reported model governed by Hele-Shaw flow fails, a two-dimensional Navier-Stokes model yields more satisfactory results. Still, present deviations suggest the presence of an additional mechanism that suppresses the growth.
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Thermodynamics of higher dimensional black holes with higher order thermal fluctuations
NASA Astrophysics Data System (ADS)
Pourhassan, B.; Kokabi, K.; Rangyan, S.
2017-12-01
In this paper, we consider higher order corrections of the entropy, which coming from thermal fluctuations, and find their effect on the thermodynamics of higher dimensional charged black holes. Leading order thermal fluctuation is logarithmic term in the entropy while higher order correction is proportional to the inverse of original entropy. We calculate some thermodynamics quantities and obtain the effect of logarithmic and higher order corrections of entropy on them. Validity of the first law of thermodynamics investigated and Van der Waals equation of state of dual picture studied. We find that five-dimensional black hole behaves as Van der Waals, but higher dimensional case have not such behavior. We find that thermal fluctuations are important in stability of black hole hence affect unstable/stable black hole phase transition.
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Mechanism of Rifampicin Inactivation in Nocardia farcinica
Abdelwahab, Heba; Martin Del Campo, Julia S.; Dai, Yumin; Adly, Camelia; El-Sohaimy, Sohby; Sobrado, Pablo
2016-01-01
A novel mechanism of rifampicin (Rif) resistance has recently been reported in Nocardia farcinica. This new mechanism involves the activity of rifampicin monooxygenase (RifMO), a flavin-dependent monooxygenase that catalyzes the hydroxylation of Rif, which is the first step in the degradation pathway. Recombinant RifMO was overexpressed and purified for biochemical analysis. Kinetic characterization revealed that Rif binding is necessary for effective FAD reduction. RifMO exhibits only a 3-fold coenzyme preference for NADPH over NADH. RifMO catalyzes the incorporation of a single oxygen atom forming an unstable intermediate that eventually is converted to 2′-N-hydroxy-4-oxo-Rif. Stable C4a-hydroperoxyflavin was not detected by rapid kinetics methods, which is consistent with only 30% of the activated oxygen leading to product formation. These findings represent the first reported detailed biochemical characterization of a flavin-monooxygenase involved in antibiotic resistance. PMID:27706151
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Simulation of Supersonic Base Flows: Numerical Investigations Using DNS, LES, and URANS
2006-10-01
global instabilities were found for a two-dimensional bluff body with a blunt base by Hannemann & Oertel (1989). Oertel (1990) found that the... Hannemann , K. & Oertel, H. 1989 Numerical simulation of the absolutely and convectively unstable wake. J. Fluid Mech. 199, 55–88. Harris, P. J. 1997
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Appleton, P L; Quyn, A J; Swift, S; Näthke, I
2009-05-01
Visualizing overall tissue architecture in three dimensions is fundamental for validating and integrating biochemical, cell biological and visual data from less complex systems such as cultured cells. Here, we describe a method to generate high-resolution three-dimensional image data of intact mouse gut tissue. Regions of highest interest lie between 50 and 200 mum within this tissue. The quality and usefulness of three-dimensional image data of tissue with such depth is limited owing to problems associated with scattered light, photobleaching and spherical aberration. Furthermore, the highest-quality oil-immersion lenses are designed to work at a maximum distance of
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Nanodisc-Tm: Rapid functional assessment of nanodisc reconstituted membrane proteins by CPM assay.
Ashok, Yashwanth; Jaakola, Veli-Pekka
2016-01-01
Membrane proteins are generally unstable in detergents. Therefore, biochemical and biophysical studies of membrane proteins in lipidic environments provides a near native-like environment suitable for membrane proteins. However, manipulation of proteins embedded in lipid bilayer has remained difficult. Methods such as nanodiscs and lipid cubic phase have been developed for easy manipulation of membrane proteins and have yielded significant insights into membrane proteins. Traditionally functional reconstitution of receptors in nanodiscs has been studied with radioligands. We present a simple and faster method for studying the functionality of reconstituted membrane proteins for routine characterization of protein batches after initial optimization of suitable conditions using radioligands. The benefits of the method are •Faster and generic method to assess functional reconstitution of membrane proteins.•Adaptable in high throughput format (≥96 well format).•Stability measurement in near-native lipid environment and lipid dependent melting temperatures.
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NASA Astrophysics Data System (ADS)
Huck, Thierry; Vallis, Geoffrey K.
2001-08-01
What can we learn from performing a linear stability analysis of the large-scale ocean circulation? Can we predict from the basic state the occurrence of interdecadal oscillations, such as might be found in a forward integration of the full equations of motion? If so, do the structure and period of the linearly unstable modes resemble those found in a forward integration? We pursue here a preliminary study of these questions for a case in idealized geometry, in which the full nonlinear behavior can also be explored through forward integrations. Specifically, we perform a three-dimensional linear stability analysis of the thermally-driven circulation of the planetary geostrophic equations. We examine the resulting eigenvalues and eigenfunctions, comparing them with the structure of the interdecadal oscillations found in the fully nonlinear model in various parameter regimes. We obtain a steady state by running the time-dependent, nonlinear model to equilibrium using restoring boundary conditions on surface temperature. If the surface heat fluxes are then diagnosed, and these values applied as constant flux boundary conditions, the nonlinear model switches into a state of perpetual, finite amplitude, interdecadal oscillations. We construct a linearized version of the model by empirically evaluating the tangent linear matrix at the steady state, under both restoring and constant-flux boundary conditions. An eigen-analysis shows there are no unstable eigenmodes of the linearized model with restoring conditions. In contrast, under constant flux conditions, we find a single unstable eigenmode that shows a striking resemblance to the fully-developed oscillations in terms of three-dimensional structure, period and growth rate. The mode may be damped through either surface restoring boundary conditions or sufficiently large horizontal tracer diffusion. The success of this simple numerical method in idealized geometry suggests applications in the study of the stability of the ocean circulation in more realistic configurations, and the possibility of predicting potential oceanic modes, even weakly damped, that might be excited by stochastic atmospheric forcing or mesoscale ocean eddies.
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Getmanskii, Iliya V.; Steglenko, Dmitrii V.; Koval, Vitaliy V.; Zaitsev, Stanislav A.
2017-01-01
Abstract With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two‐ and three‐dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two‐ and three‐layer systems resulted in the construction of a three‐dimensional supertetrahedral borane crystal structure. The two‐dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three‐dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm−3) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. PMID:28402596
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NASA Astrophysics Data System (ADS)
Takamoto, M.
2018-05-01
In this paper, the temporal evolution of three-dimensional relativistic current sheets in Poynting-dominated plasma is studied for the first time. Over the past few decades, a lot of efforts have been conducted on studying the evolution of current sheets in two-dimensional space, and concluded that sufficiently long current sheets always evolve into the so-called plasmoid chain, which provides a fast reconnection rate independent of its resistivity. However, it is suspected that plasmoid chain can exist only in the case of two-dimensional approximation, and would show transition to turbulence in three-dimensional space. We performed three-dimensional numerical simulation of relativistic current sheet using resistive relativistic magnetohydrodynamic approximation. The results showed that the three-dimensional current sheets evolve not into plasmoid chain but turbulence. The resulting reconnection rate is 0.004, which is much smaller than that of plasmoid chain. The energy conversion from magnetic field to kinetic energy of turbulence is just 0.01 per cent, which is much smaller than typical non-relativistic cases. Using the energy principle, we also showed that the plasmoid is always unstable for a displacement in the opposite direction to its acceleration, probably interchange-type instability, and this always results in seeds of turbulence behind the plasmoids. Finally, the temperature distribution along the sheet is discussed, and it is found that the sheet is less active than plasmoid chain. Our finding can be applied for many high-energy astrophysical phenomena, and can provide a basic model of the general current sheet in Poynting-dominated plasma.
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The effect of unstable sandals on instability in gait in healthy female subjects.
Price, Carina; Smith, Laura; Graham-Smith, Philip; Jones, Richard
2013-07-01
Unstable footwear generally lacks thorough peer-review published research to support concepts and marketing claims. The purpose of this study was to investigate the instability induced by four (FitFlop, Masai Barefoot Technology, Reebok Easy-Tone and Skechers Tone-Ups) commercially available unstable sandals and one stable control sandal (Earth) in walking in 15 females (mean±SD age was 29±6.7 years, mass 62.6±6.9kg and height 167.1±4.2cm). Three-dimensional motion with synchronised electromyography and kinetic data were collected. Walking speed and step length remained consistent between conditions, however double support time decreased in Masai Barefoot Technology. Centre of pressure data identified no consistent difference between the stable control and the unstable sandals, however Masai Barefoot Technology reduced the anterior-posterior range of centre of pressure. Muscle activity differed significantly at the ankle in the unstable footwear. FitFlop, Reebok and Skechers increased peroneal activity during pre-swing, whereas Masai Barefoot Technology increased medial gastrocnemius and decreased tibialis anterior activity in loading response and mid-stance. The larger rocker sole of the Masai Barefoot Technology altered gait and muscle activation with regard to braking and progression in the sagittal plane. Reebok, Skechers and FitFlop, with softer, less stable foreparts increased evertor action at toe-off, having their effect in the coronal plane. The study highlighted that any instability induced by the shoes is design-specific. Copyright © 2013 Elsevier B.V. All rights reserved.
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Evolution of a magnetic flux tube in two-dimensional penetrative convection
NASA Technical Reports Server (NTRS)
Jennings, R. L.; Brandenburg, A.; Nordlund, A.; Stein, R. F.
1992-01-01
Highly supercritical compressible convection is simulated in a two-dimensional domain in which the upper half is unstable to convection while the lower half is stably stratified. This configuration is an idealization of the layers near the base of the solar convection zone. Once the turbulent flow is well developed, a toroidal magnetic field B sub tor is introduced to the stable layer. The field's evolution is governed by an advection-diffusion-type equation, and the Lorentz force does not significantly affect the flow. After many turnover times the field is stratified such that the absolute value of B sub tor/rho is approximately constant in the convective layer, where rho is density, while in the stable layer this ratio decreases linearly with depth. Consequently most of the magnetic flux is stored in the overshoot layer. The inclusion of rotation leads to travelling waves which transport magnetic flux latitudinally in a manner reminiscent of the migrations seen during the solar cycle.
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Superconductivity in Hydrides Doped with Main Group Elements Under Pressure
NASA Astrophysics Data System (ADS)
Shamp, Andrew; Zurek, Eva
2017-01-01
A priori crystal structure prediction techniques have been used to explore the phase diagrams of hydrides of main group elements under pressure. A number of novel phases with the chemical formulas MHn, n > 1 and M = Li, Na, K, Rb, Cs; MHn, n > 2 and M= Mg, Ca, Sr, Ba; HnI with n > 1 and PH, PH2, PH3 have been predicted to be stable at pressures achievable in diamond anvil cells. The hydrogenic lattices within these phases display a number of structural motifs including H2δ- , H-, H-3 , as well as one-dimensional and three-dimensional extended structures. A wide range of superconducting critical temperatures, Tcs, are predicted for these hydrides. The mechanism of metallization and the propensity for superconductivity are dependent upon the structural motifs present in these phases, and in particular on their hydrogenic sublattices. Phases that are thermodynamically unstable, but dynamically stable, are accessible experimentally. The observed trends provide insight on how to design hydrides that are superconducting at high temperatures.
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Bomphrey, Richard J.; Henningsson, Per; Michaelis, Dirk; Hollis, David
2012-01-01
Aerodynamic structures generated by animals in flight are unstable and complex. Recent progress in quantitative flow visualization has advanced our understanding of animal aerodynamics, but measurements have hitherto been limited to flow velocities at a plane through the wake. We applied an emergent, high-speed, volumetric fluid imaging technique (tomographic particle image velocimetry) to examine segments of the wake of desert locusts, capturing fully three-dimensional instantaneous flow fields. We used those flow fields to characterize the aerodynamic footprint in unprecedented detail and revealed previously unseen wake elements that would have gone undetected by two-dimensional or stereo-imaging technology. Vortex iso-surface topographies show the spatio-temporal signature of aerodynamic force generation manifest in the wake of locusts, and expose the extent to which animal wakes can deform, potentially leading to unreliable calculations of lift and thrust when using conventional diagnostic methods. We discuss implications for experimental design and analysis as volumetric flow imaging becomes more widespread. PMID:22977102
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Mode calculations in unstable resonators with flowing saturable gain. 1:hermite-gaussian expansion.
Siegman, A E; Sziklas, E A
1974-12-01
We present a procedure for calculating the three-dimensional mode pattern, the output beam characteristics, and the power output of an oscillating high-power laser taking into account a nonuniform, transversely flowing, saturable gain medium; index inhomogeneities inside the laser resonator; and arbitrary mirror distortion and misalignment. The laser is divided into a number of axial segments. The saturated gain-and-index variation. across each short segment is lumped into a complex gain profile across the midplane of that segment. The circulating optical wave within the resonator is propagated from midplane to midplane in free-space fashion and is multiplied by the lumped complex gain profile upon passing through each midplane. After each complete round trip of the optical wave inside the resonator, the saturated gain profiles are recalculated based upon the circulating fields in the cavity. The procedure when applied to typical unstable-resonator flowing-gain lasers shows convergence to a single distorted steady-state mode of oscillation. Typical near-field and far-field results are presented. Several empirical rules of thumb for finite truncated Hermite-Gaussian expansions, including an approximate sampling theorem, have been developed as part of the calculations.
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Lifecycle of miscible viscous fingering: onset to shutdown
NASA Astrophysics Data System (ADS)
Nijjer, Japinder S.; Hewitt, Duncan R.; Neufeld, Jerome A.
2017-11-01
When a viscous fluid is injected into a porous medium or Hele-Shaw cell that is initially saturated with a more viscous fluid, the flow can be unstable to viscous fingering. We investigate the long-time dynamics of miscible viscous fingering in a homogeneous, planar, two-dimensional porous medium using high-resolution numerical simulations. At late times, we identify a new flow regime which consists of a pair of counter-propagating fingers that diffuse and slow, leaving a linearly well-mixed interior. We derive an analytic solution for this regime, and show that, in contrast to previous suggestions, the flow always evolves to this regime irrespective of the viscosity ratio and Peclet number. As a consequence, we find the instability can only ever generate a finite amount of advective mixing. We also describe the full life-cycle of miscible viscous fingering, which can be partitioned into three regimes: an early-time linearly unstable regime, an intermediate-time non-linear regime, and a late-time exchange-flow regime. We identify, using linear stability theory, a critical Peclet number below which the flow is always stable, and derive a model for the evolution of the transversely averaged concentration in the intermediate-time regime, which extends previous empirical models.
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ERIC Educational Resources Information Center
Beltramini, Leila Maria; Araujo, Ana Paula Ulian; de Oliveira, Tales Henrique Goncalves; dos Santos Abel, Luciano Douglas; da Silva, Aparecido Rodrigues; dos Santos, Neusa Fernandes
2006-01-01
International specialized literature focused on research in biology education is sadly scarce, especially regarding biochemical and molecular aspects. In this light, researchers from this Centre for Structural Molecular Biotechnology developed and evaluated a three-dimensional educational model named "Building Life Molecules DNA and RNA." The…
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Yasui, Yutaka; McLerran, Dale; Adam, Bao-Ling; Winget, Marcy; Thornquist, Mark; Feng, Ziding
2003-01-01
Discovery of "signature" protein profiles that distinguish disease states (eg, malignant, benign, and normal) is a key step towards translating recent advancements in proteomic technologies into clinical utilities. Protein data generated from mass spectrometers are, however, large in size and have complex features due to complexities in both biological specimens and interfering biochemical/physical processes of the measurement procedure. Making sense out of such high-dimensional complex data is challenging and necessitates the use of a systematic data analytic strategy. We propose here a data processing strategy for two major issues in the analysis of such mass-spectrometry-generated proteomic data: (1) separation of protein "signals" from background "noise" in protein intensity measurements and (2) calibration of protein mass/charge measurements across samples. We illustrate the two issues and the utility of the proposed strategy using data from a prostate cancer biomarker discovery project as an example.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fu, G.Y.; Cooper, W.A.; Gruber, R.
1992-06-01
The TERPSICHORE three-dimensional linear ideal magnetohydrodynamic (MHD) stability code ({ital Theory} {ital of} {ital Fusion} {ital Plasmas}, Proceedings of the Joint Varenna--Lausanne International Workshop, Chexbres, Switzerland, 1988 (Editrice Compositori, Bologna, Italy, 1989), p. 93; {ital Controlled} {ital Fusion} {ital and} {ital Plasma} {ital Heating}, Proceedings of the 17th European Conference, Amsterdam, The Netherlands (European Physical Society, Petit-Lancy, Switzerland, 1990), Vol. 14B, Part II, p. 931; {ital Theory} {ital of} {ital Fusion} {ital Plasmas}, Proceedings of the Joint Varenna--Lausanne International Workshop, Valla Monastero, Varenna, Italy, 1990 (Editrice Compositori, Bologna, Italy, 1990), p. 655) has been extended to the full MHD equations.more » The new code is used to calculate the physical growth rates of nonlocal low-{ital n} modes for {ital l}=2 torsatron configurations. A comprehensive investigation of the relation between the Mercier modes and the low-{ital n} modes has been performed. The unstable localized low-{ital n} modes are found to be correlated with the Mercier criterion. Finite growth rates of the low-{ital n} modes correspond to finite values of the Mercier criterion parameter. Near the Mercier marginal stability boundary, the low-{ital n} modes tend to be weakly unstable with very small growth rates. However, the stability of global-type low-{ital n} modes is found to be decorrelated from that of Mercier modes. The low-{ital n} modes with global radial structures can be more stable or more unstable than Mercier modes.« less
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Experimental studies on the stability and transition of 3-dimensional boundary layers
NASA Technical Reports Server (NTRS)
Nitschke-Kowsky, P.
1987-01-01
Three-dimensional unstable boundary layers were investigated as to their characteristic instabilities, leading to turbulence. Standing cross-flow instabilities and traveling waves preceding the transition were visualized with the hydrogen bubble technique in the boundary layer above the wall of a swept cylinder. With the sublimation method and hot film technique, a model consisting of a swept flat plate with a pressure-inducing displacement body in the 1 m wind tunnel was studied. Standing waves and traveling waves in a broad frequency are observed. The boundary layer of this model is close to the assumptions of the theory.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Copeland, Edmund J.; Tsumagari, Mitsuo I.
2009-07-15
We study the classical and absolute stability of Q-balls in scalar field theories with flat potentials arising in both gravity-mediated and gauge-mediated models. We show that the associated Q-matter formed in gravity-mediated potentials can be stable against decay into their own free particles as long as the coupling constant of the nonrenormalizable term is small, and that all of the possible three-dimensional Q-ball configurations are classically stable against linear fluctuations. Three-dimensional gauge-mediated Q-balls can be absolutely stable in the thin-wall limit, but are completely unstable in the thick-wall limit.
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Preliminary study of the three-dimensional deformation of the vortex in Karman vortex street
NASA Astrophysics Data System (ADS)
Ling, Guocan; Guo, Liang; Wu, Zuobin; Ma, Huiyang
1992-03-01
The mechanism for 3D evolution of the isolated Karman vortex and the thin-vortex filament in a circular cylinder wake is studied numerically using the LIA method. The results show that the vortex motion is unstable for small 3D disturbances in the separated wake of a circular cylinder. Karman vortex in the time-averaged wake flowfield wolves into a horseshoe-spoon-like 3D structure. The thin vortex filament deforms three-dimensionally in the braid and generates streamwise vortex structures which incline to the region maximum-deformation direction of the flowfield.
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Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach
2006-02-01
Anthony J Williams, X-C May Lu, Renwu Chen, Zhilin Liao, Rebeca Connors, Kevin K Wang, Ron L Hayes, Frank C Tortella, Jitendra R Dave. High throughput... YANG , A., et al. (2002). Evalu- ation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell...apoptosis. J. Biol. Chem. 279, 1030–1039. Kuida K., Zheng T. S., Na S., Kuan C., Yang D., Karasuyama H., Rakic P. and Flavell R. A. (1996) Decreased apoptosis
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Kinetic Simulations of the Lowest-order Unstable Mode of Relativistic Magnetostatic Equilibria
NASA Astrophysics Data System (ADS)
Nalewajko, Krzysztof; Zrake, Jonathan; Yuan, Yajie; East, William E.; Blandford, Roger D.
2016-08-01
We present the results of particle-in-cell numerical pair plasma simulations of relativistic two-dimensional magnetostatic equilibria known as the “Arnold-Beltrami-Childress” fields. In particular, we focus on the lowest-order unstable configuration consisting of two minima and two maxima of the magnetic vector potential. Breaking of the initial symmetry leads to exponential growth of the electric energy and to the formation of two current layers, which is consistent with the picture of “X-point collapse” first described by Syrovatskii. Magnetic reconnection within the layers heats a fraction of particles to very high energies. After the saturation of the linear instability, the current layers are disrupted and the system evolves chaotically, diffusing the particle energies in a stochastic second-order Fermi process, leading to the formation of power-law energy distributions. The power-law slopes harden with the increasing mean magnetization, but they are significantly softer than those produced in simulations initiated from Harris-type layers. The maximum particle energy is proportional to the mean magnetization, which is attributed partly to the increase of the effective electric field and partly to the increase of the acceleration timescale. We describe in detail the evolving structure of the dynamical current layers and report on the conservation of magnetic helicity. These results can be applied to highly magnetized astrophysical environments, where ideal plasma instabilities trigger rapid magnetic dissipation with efficient particle acceleration and flares of high-energy radiation.
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KINETIC SIMULATIONS OF THE LOWEST-ORDER UNSTABLE MODE OF RELATIVISTIC MAGNETOSTATIC EQUILIBRIA
DOE Office of Scientific and Technical Information (OSTI.GOV)
Nalewajko, Krzysztof; Zrake, Jonathan; Yuan, Yajie
2016-08-01
We present the results of particle-in-cell numerical pair plasma simulations of relativistic two-dimensional magnetostatic equilibria known as the “Arnold–Beltrami–Childress” fields. In particular, we focus on the lowest-order unstable configuration consisting of two minima and two maxima of the magnetic vector potential. Breaking of the initial symmetry leads to exponential growth of the electric energy and to the formation of two current layers, which is consistent with the picture of “X-point collapse” first described by Syrovatskii. Magnetic reconnection within the layers heats a fraction of particles to very high energies. After the saturation of the linear instability, the current layers aremore » disrupted and the system evolves chaotically, diffusing the particle energies in a stochastic second-order Fermi process, leading to the formation of power-law energy distributions. The power-law slopes harden with the increasing mean magnetization, but they are significantly softer than those produced in simulations initiated from Harris-type layers. The maximum particle energy is proportional to the mean magnetization, which is attributed partly to the increase of the effective electric field and partly to the increase of the acceleration timescale. We describe in detail the evolving structure of the dynamical current layers and report on the conservation of magnetic helicity. These results can be applied to highly magnetized astrophysical environments, where ideal plasma instabilities trigger rapid magnetic dissipation with efficient particle acceleration and flares of high-energy radiation.« less
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Buhrke, Thorsten; Brecht, Marc; Lubitz, Wolfgang; Friedrich, Bärbel
2002-09-01
[NiFe] hydrogenases contain a highly conserved histidine residue close to the [NiFe] active site which is altered by a glutamine residue in the H(2)-sensing [NiFe] hydrogenases. In this study, we exchanged the respective glutamine residue of the H(2) sensor (RH) of Ralstonia eutropha, Q67 of the RH large subunit HoxC, by histidine, asparagine and glutamate. The replacement by histidine and asparagine resulted in slightly unstable RH proteins which were hardly affected in their regulatory and enzymatic properties. The exchange to glutamate led to a completely unstable RH protein. The purified wild-type RH and the mutant protein with the Gln/His exchange were analysed by continuous-wave and pulsed electron paramagnetic resonance (EPR) techniques. We observed a coupling of a nitrogen nucleus with the [NiFe] active site for the mutant protein which was absent in the spectrum of the wild-type RH. A combination of theoretical calculations with the experimental data provided an explanation for the observed coupling. It is shown that the coupling is due to the formation of a weak hydrogen bond between the protonated N(epsilon) nucleus of the histidine with the sulfur of a conserved cysteine residue which coordinates the metal atoms of the [NiFe] active site as a bridging ligand. The effect of this hydrogen bond on the local structure of the [NiFe] active site is discussed.
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Scaffolding for Three-Dimensional Embryonic Vasculogenesis
NASA Astrophysics Data System (ADS)
Kraehenbuehl, Thomas P.; Aday, Sezin; Ferreira, Lino S.
Biomaterial scaffolds have great potential to support efficient vascular differentiation of embryonic stem cells. Vascular cell fate-specific biochemical and biophysical cues have been identified and incorporated into three-dimensional (3D) biomaterials to efficiently direct embryonic vasculogenesis. The resulting vascular-like tissue can be used for regenerative medicine applications, further elucidation of biophysical and biochemical cues governing vasculogenesis, and drug discovery. In this chapter, we give an overview on the following: (1) developmental cues for directed differentiation of human embryonic stem cells (hESCs) into vascular cells, (2) 3D vascular differentiation in embryoid bodies (EBs), (3) preparation of 3D scaffolds for the vascular differentiation of hESCs, and (4) the most significant studies combining scaffolding and hESCs for development of vascular-like tissue.
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Lattice black branes: sphere packing in general relativity
NASA Astrophysics Data System (ADS)
Dias, Óscar J. C.; Santos, Jorge E.; Way, Benson
2018-05-01
We perturbatively construct asymptotically R^{1,3}× T^2 black branes with multiple inhomogeneous directions and show that some of them are thermodynamically preferred over uniform branes in both the microcanonical and canonical ensembles. This demonstrates that, unlike five-dimensional black strings, the instability of some unstable black branes has a plausible endpoint that does not require a violation of cosmic censorship.
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Materials processing in a centrifuge - Numerical modeling of macrogravity effects
NASA Technical Reports Server (NTRS)
Ramachandran, N.; Downey, J. P.; Jones, J. C.; Curreri, P. A.
1992-01-01
The fluid mechanics associated with crystal growth processes on a centrifuge is investigated. A simple scaling analysis is used to examine the relative magnitudes of the forces acting on the system and good agreement is obtained with previous studies. A two-dimensional model of crystal growth on a centrifuge is proposed and calculations are undertaken to help in understanding the fundamental transport processes within the crystal growth cell. Results from three-dimensional calculations of actual centrifuge-based crystal growth systems are presented both for the thermodynamically stable and unstable configurations. The calculations show the existence of flow bifurcations in certain configurations but not in all instances. The numerical simulations also show that the centrifugal force is the dominant stabilizing force on fluid convection in the stable configuration. The stabilizing influence of the Coriolis force is found to be only secondary in nature. No significant impact of gravity gradient is found in the calculations. Simulations of unstable configurations show that the Coriolis force has a stabilizing influence on fluid motion by delaying the onset of unsteady convection. Detailed flow and thermal field characteristics are presented for all the different cases that are simulated.
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NASA Astrophysics Data System (ADS)
Kumar, Avanish; Narayanam, Chaitanya; Khanna, Rajesh; Puri, Sanjay
2017-12-01
We address in detail the problem of true morphological phase separation (MPS) in three-dimensional or (2 +1 )-dimensional unstable thin liquid films (>100 nm) under the influence of gravity. The free-energy functionals of these films are asymmetric and show two points of common tangency, which facilitates the formation of two equilibrium phases. Three distinct patterns formed by relative preponderance of these phases are clearly identified in "true MPS". Asymmetricity induces two different pathways of pattern formation, viz., defect and direct pathway for true MPS. The pattern formation and phase-ordering dynamics have been studied using statistical measures such as structure factor, correlation function, and growth laws. In the late stage of coarsening, the system reaches into a scaling regime for both pathways, and the characteristic domain size follows the Lifshitz-Slyozov growth law [L (t ) ˜t1 /3] . However, for the defect pathway, there is a crossover of domain growth behavior from L (t ) ˜t1 /4→t1 /3 in the dynamical scaling regime. We also underline the analogies and differences behind the mechanisms of MPS and true MPS in thin liquid films and generic spinodal phase separation in binary mixtures.
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Comparison of Laminar and Linear Eddy Model Closures for Combustion Instability Simulations
2015-07-01
14. ABSTRACT Unstable liquid rocket engines can produce highly complex dynamic flowfields with features such as rapid changes in temperature and...applicability. In the present study, the linear eddy model (LEM) is applied to an unstable single element liquid rocket engine to assess its performance and to...Sankaran‡ Air Force Research Laboratory, Edwards AFB, CA, 93524 Unstable liquid rocket engines can produce highly complex dynamic flowfields with features
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NASA Astrophysics Data System (ADS)
Egorov, I. V.; Novikov, A. V.; Fedorov, A. V.
2017-08-01
A method for direct numerical simulation of three-dimensional unsteady disturbances leading to a laminar-turbulent transition at hypersonic flow speeds is proposed. The simulation relies on solving the full three-dimensional unsteady Navier-Stokes equations. The computational technique is intended for multiprocessor supercomputers and is based on a fully implicit monotone approximation scheme and the Newton-Raphson method for solving systems of nonlinear difference equations. This approach is used to study the development of three-dimensional unstable disturbances in a flat-plate and compression-corner boundary layers in early laminar-turbulent transition stages at the free-stream Mach number M = 5.37. The three-dimensional disturbance field is visualized in order to reveal and discuss features of the instability development at the linear and nonlinear stages. The distribution of the skin friction coefficient is used to detect laminar and transient flow regimes and determine the onset of the laminar-turbulent transition.
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Major and Modified Nucleosides, RNA, and DNA
NASA Astrophysics Data System (ADS)
Gehrke, Charles W.; Kuo, Kenneth C.
Most analytical chemists are well aware of the rapid rate of development of high-performance liquid chromatography (HPLC) over the past 5 years. A number of articles have been published in Analytical Chemistry on different topics in HPLC and many papers appear in the chromatographic journals. Some books also have been published covering this subject. HPLC has proved to be a very effective, broadly applicable chromatographic method for the separation and analysis of complex molecules in fields as diverse as biochemistry and environmental, pharmaceutical, medical, and polymer chemistry. HPLC is now having a major impact on the clinical and research aspects of medical biochemistry. Although the contributions of HPLC to other disciplines generally complements gas-liquid chromatography, this method is destined to play a much greater role in medical and biochemical research. This is because many of the biomolecules, owing to their molecular complexity and size, are thermally unstable or nonvolatile, preventing or complicating an analysis by GC. A major factor contributing to the powerful advances in biomedical liquid chromatography is the development of reversed-phase high-performance liquid chromatography (RP-HPLC) using n-alkyl and phenyl chemically bonded substrates.
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Unstable spiral waves and local Euclidean symmetry in a model of cardiac tissue.
Marcotte, Christopher D; Grigoriev, Roman O
2015-06-01
This paper investigates the properties of unstable single-spiral wave solutions arising in the Karma model of two-dimensional cardiac tissue. In particular, we discuss how such solutions can be computed numerically on domains of arbitrary shape and study how their stability, rotational frequency, and spatial drift depend on the size of the domain as well as the position of the spiral core with respect to the boundaries. We also discuss how the breaking of local Euclidean symmetry due to finite size effects as well as the spatial discretization of the model is reflected in the structure and dynamics of spiral waves. This analysis allows identification of a self-sustaining process responsible for maintaining the state of spiral chaos featuring multiple interacting spirals.
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NASA Astrophysics Data System (ADS)
Montague, James A.; Pinder, George F.; Gonyea, Jay V.; Hipko, Scott; Watts, Richard
2018-05-01
Magnetic resonance imaging is used to observe solute transport in a 40 cm long, 26 cm diameter sand column that contained a central core of low permeability silica surrounded by higher permeability well-sorted sand. Low concentrations (2.9 g/L) of Magnevist, a gadolinium based contrast agent, produce density driven convection within the column when it starts in an unstable state. The unstable state, for this experiment, exists when higher density contrast agent is present above the lower density water. We implement a numerical model in OpenFOAM to reproduce the observed fluid flow and transport from a density difference of 0.3%. The experimental results demonstrate the usefulness of magnetic resonance imaging in observing three-dimensional gravity-driven convective-dispersive transport behaviors in medium scale experiments.
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Nonsingular solutions and instabilities in Einstein-scalar-Gauss-Bonnet cosmology
NASA Astrophysics Data System (ADS)
Sberna, Laura; Pani, Paolo
2017-12-01
It is generically believed that higher-order curvature corrections to the Einstein-Hilbert action might cure the curvature singularities that plague general relativity. Here we consider Einstein-scalar-Gauss-Bonnet gravity, the only four-dimensional, ghost-free theory with quadratic curvature terms. For any choice of the coupling function and of the scalar potential, we show that the theory does not allow for bouncing solutions in the flat and open Friedmann universe. For the case of a closed universe, using a reverse-engineering method, we explicitly provide a bouncing solution which is nevertheless linearly unstable in the scalar gravitational sector. Moreover, we show that the expanding, singularity-free, early-time cosmologies allowed in the theory are unstable. These results rely only on analyticity and finiteness of cosmological variables at early times.
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On the phenomenon of mixed dynamics in Pikovsky-Topaj system of coupled rotators
NASA Astrophysics Data System (ADS)
Gonchenko, A. S.; Gonchenko, S. V.; Kazakov, A. O.; Turaev, D. V.
2017-07-01
A one-parameter family of time-reversible systems on three-dimensional torus is considered. It is shown that the dynamics is not conservative, namely the attractor and repeller intersect but not coincide. We explain this as the manifestation of the so-called mixed dynamics phenomenon which corresponds to a persistent intersection of the closure of the stable periodic orbits and the closure of the completely unstable periodic orbits. We search for the stable and unstable periodic orbits indirectly, by finding non-conservative saddle periodic orbits and heteroclinic connections between them. In this way, we are able to claim the existence of mixed dynamics for a large range of parameter values. We investigate local and global bifurcations that can be used for the detection of mixed dynamics.
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NASA Astrophysics Data System (ADS)
Santos, D.; Duarte, B.; Caçador, I.
2015-12-01
The increasing metal pollution in salt marshes and its influence on the plants that inhabit these ecosystems, has become a major concern with serious implications on the species establishment. Juncus acutus is a highly common halophyte specie in Portuguese marshes. Seeds from his specie were exposed to a range of different Cd concentrations (0.05, 0.1, 0.5 and 1 μM) in order to evaluate the effects of acute Cd stress on seed germination and growth as well as on seedling pigment composition, photosynthetic apparatus and oxidative stress biomarkers. Seedling length was higher than in control in every Cd treatment, however biomass showed a decrease. It was also observed that increasing Cd treatments, lead to a proportional increase in the Cd tissue concentration. Also the Cd-substituted chlorophylls showed an increase with increasing Cd doses that were applied. This substitution results in a non-functional chlorophyll molecule, highly unstable under moderate light intensities which inevitably reduces the efficiency of the LHC II. As consequence, there was a decrease in the use-efficiency of the harvested energy, leading to a decay in the photosynthetic capacity and energy accumulation, which was dissipated as heat. As for the antioxidant enzymes, SOD and APX presented higher activity, responding to increasing cadmium concentrations. Thus, becomes evident that Cd affects negatively, both biochemically and photochemically, the establishment by seed process of J. acutus highlighting the potential of the use of this specie seed as potential sentinel and ecotoxicity test in extreme conditions.
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In-line digital holography with phase-shifting Greek-ladder sieves
NASA Astrophysics Data System (ADS)
Xie, Jing; Zhang, Junyong; Zhang, Yanli; Zhou, Shenlei; Zhu, Jianqiang
2018-04-01
Phase shifting is the key technique in in-line digital holography, but traditional phase shifters have their own limitations in short wavelength regions. Here, phase-shifting Greek-ladder sieves with amplitude-only modulation are introduced into in-line digital holography, which are essentially a kind of diffraction lens with three-dimensional array diffraction-limited foci. In the in-line digital holographic experiment, we design two kinds of sieves by lithography and verify the validity of their phase-shifting function by measuring a 1951 U.S. Air Force resolution test target and three-dimensional array foci. With advantages of high resolving power, low cost, and no limitations at shorter wavelengths, phase-shifting Greek-ladder sieves have great potential in X-ray holography or biochemical microscopy for the next generation of synchrotron light sources.
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Fully three-dimensional direct numerical simulation of a plunging breaker
NASA Astrophysics Data System (ADS)
Lubin, Pierre; Vincent, Stéphane; Caltagirone, Jean-Paul; Abadie, Stéphane
2003-07-01
The scope of this paper is to show the results obtained for simulating three-dimensional breaking waves by solving the Navier-Stokes equations in air and water. The interface tracking is achieved by a Lax-Wendroff TVD scheme (Total Variation Diminishing), which is able to handle interface reconnections. We first present the equations and the numerical methods used in this work. We then proceed to the study of a three-dimensional plunging breaking wave, using initial conditions corresponding to unstable periodic sinusoidal waves of large amplitudes. We compare the results obtained for two simulations, a longshore depth perturbation has been introduced in the solution of the flow equations in order to see the transition from a two-dimensional velocity field to a fully three-dimensional one after plunging. Breaking processes including overturning, splash-up and breaking induced vortex-like motion beneath the surface are presented and discussed. To cite this article: P. Lubin et al., C. R. Mecanique 331 (2003).
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Getmanskii, Iliya V; Minyaev, Ruslan M; Steglenko, Dmitrii V; Koval, Vitaliy V; Zaitsev, Stanislav A; Minkin, Vladimir I
2017-08-14
With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two- and three-dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two- and three-layer systems resulted in the construction of a three-dimensional supertetrahedral borane crystal structure. The two-dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three-dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm -3 ) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
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Goggin, Danica E.; Powles, Stephen B.; Steadman, Kathryn J.
2011-01-01
Seed dormancy in wild Lolium rigidum Gaud (annual ryegrass) populations is highly variable and not well characterized at the biochemical level. To identify some of the determinants of dormancy level in these seeds, the proteomes of subpopulations selected for low and high levels of primary dormancy were compared by two-dimensional polyacrylamide gel electrophoresis of extracts from mature, dry seeds. High-dormancy seeds showed higher expression of small heat shock proteins, enolase, and glyoxalase I than the low-dormancy seeds. The functional relevance of these differences in protein expression was confirmed by the fact that high-dormancy seeds were more tolerant to high temperatures imposed at imbibition and had consistently higher glyoxalase I activity over 0–42 d dark stratification. Higher expression of a putative glutathione peroxidase in low-dormancy seeds was not accompanied by higher activity, but these seeds had a slightly more oxidized glutathione pool and higher total peroxidase activity. Overall, these biochemical and physiological differences suggest that L. rigidum seeds selected for low dormancy are more prepared for rapid germination via peroxidase-mediated cell wall weakening, whilst seeds selected for high dormancy are constitutively prepared to survive environmental stresses, even in the absence of stress during seed development. PMID:20974739
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NASA Astrophysics Data System (ADS)
Zhang, Wen-shuai; Cai, Hong-bo; Zhu, Shao-ping
2018-05-01
The role of ion–ion acoustic instabilities in the formation and dissipation of collisionless electrostatic shock waves driven by counter-streaming supersonic plasma flows has been investigated via two-dimensional particle-in-cell simulations. The nonlinear evolution of unstable waves and ion velocity distributions has been analyzed in detail. It is found that for electrostatic shocks driven by moderate-velocity flows, longitudinal and oblique ion–ion acoustic instabilities can be excited in the downstream and upstream regions, which lead to thermalization of the transmitted and reflected ions, respectively. For high-velocity flows, oblique ion–ion acoustic instabilities can develop in the overlap layer during the shock formation process and impede the shock formation.
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Fluid-acoustic interactions in a low area ratio supersonic jet ejector
NASA Technical Reports Server (NTRS)
Krothapalli, Anjaneyulu; Ross, Christopher; Yamomoto, K.; Joshi, M. C.
1994-01-01
An experimental investigation carried out to determine aerodynamic and acoustic characteristics of a low area ratio rectangular jet ejector is reported. A supersonic primary jet issuing from a rectangular convergent-divergent nozzle of aspect ratio 4, into a rectangular duct of area ratio 3, was used. Improved performance was found when the ejector screech tone is most intense and appears to match the most unstable Strouhal number of the free rectangular jet. When the primary jet was operating at over and ideally expanded conditions, significant noise reduction was obtained with the ejector as compared to a corresponding free jet. Application of particle image velocimetry to high speed ejector flows was demonstrated through the measurement of instantaneous two dimensional velocity fields.
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Parametric decay of oblique Alfvén waves in two-dimensional hybrid simulations.
Verscharen, D; Marsch, E; Motschmann, U; Müller, J
2012-08-01
Certain types of plasma waves are known to become parametrically unstable under specific plasma conditions, in which the pump wave will decay into several daughter waves with different wavenumbers and frequencies. In the past, the related plasma instabilities have been treated analytically for various parameter regimes and by use of various numerical methods, yet the oblique propagation with respect to the background magnetic field has rarely been dealt with in two dimensions, mainly because of the high computational demand. Here we present a hybrid-simulation study of the parametric decay of a moderately oblique Alfvén wave having elliptical polarization. It is found that such a compressive wave can decay into waves with higher and lower wavenumbers than the pump.
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Bootstrapping Least Squares Estimates in Biochemical Reaction Networks
Linder, Daniel F.
2015-01-01
The paper proposes new computational methods of computing confidence bounds for the least squares estimates (LSEs) of rate constants in mass-action biochemical reaction network and stochastic epidemic models. Such LSEs are obtained by fitting the set of deterministic ordinary differential equations (ODEs), corresponding to the large volume limit of a reaction network, to network’s partially observed trajectory treated as a continuous-time, pure jump Markov process. In the large volume limit the LSEs are asymptotically Gaussian, but their limiting covariance structure is complicated since it is described by a set of nonlinear ODEs which are often ill-conditioned and numerically unstable. The current paper considers two bootstrap Monte-Carlo procedures, based on the diffusion and linear noise approximations for pure jump processes, which allow one to avoid solving the limiting covariance ODEs. The results are illustrated with both in-silico and real data examples from the LINE 1 gene retrotranscription model and compared with those obtained using other methods. PMID:25898769
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NASA Astrophysics Data System (ADS)
Gradzki, Marek J.; Mizerski, Krzysztof A.
2018-03-01
Magnetic buoyancy instability in weakly resistive and thermally conductive plasma is an important mechanism of magnetic field expulsion in astrophysical systems. It is often invoked, e.g., in the context of the solar interior. Here, we revisit a problem introduc`ed by Gilman: the short-wavelength linear stability of a plane layer of compressible isothermal and weakly diffusive fluid permeated by a horizontal magnetic field of strength decreasing with height. In this physical setting, we investigate the effect of weak resistivity and weak thermal conductivity on the short-wavelength perturbations, localized in the vertical direction, and show that the presence of diffusion allows to establish the wavelength of the most unstable mode, undetermined in an ideal fluid. When diffusive effects are neglected, the perturbations are amplified at a rate that monotonically increases as the wavelength tends to zero. We demonstrate that, when the resistivity and thermal conduction are introduced, the wavelength of the most unstable perturbation is established and its scaling law with the diffusion parameters depends on gradients of the mean magnetic field, temperature, and density. Three main dynamical regimes are identified, with the wavelength of the most unstable mode scaling as either λ /d∼ {{ \\mathcal U }}κ 3/5 or λ /d∼ {{ \\mathcal U }}κ 3/4 or λ /d∼ {{ \\mathcal U }}κ 1/3, where d is the layer thickness and {{ \\mathcal U }}κ is the ratio of the characteristic thermal diffusion velocity scale to the free-fall velocity. Our analytic results are backed up by a series of numerical solutions. The two-dimensional interchange modes are shown to dominate over three-dimensional ones when the magnetic field and/or temperature gradients are strong enough.
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Three-dimensional label-free imaging and quantification of lipid droplets in live hepatocytes
NASA Astrophysics Data System (ADS)
Kim, Kyoohyun; Lee, Seoeun; Yoon, Jonghee; Heo, Jihan; Choi, Chulhee; Park, Yongkeun
2016-11-01
Lipid droplets (LDs) are subcellular organelles with important roles in lipid storage and metabolism and involved in various diseases including cancer, obesity, and diabetes. Conventional methods, however, have limited ability to provide quantitative information on individual LDs and have limited capability for three-dimensional (3-D) imaging of LDs in live cells especially for fast acquisition of 3-D dynamics. Here, we present an optical method based on 3-D quantitative phase imaging to measure the 3-D structural distribution and biochemical parameters (concentration and dry mass) of individual LDs in live cells without using exogenous labelling agents. The biochemical change of LDs under oleic acid treatment was quantitatively investigated, and 4-D tracking of the fast dynamics of LDs revealed the intracellular transport of LDs in live cells.
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Preferential flow systems amended with biogeochemical components: imaging of a two-dimensional study
NASA Astrophysics Data System (ADS)
Pales, Ashley R.; Li, Biting; Clifford, Heather M.; Kupis, Shyla; Edayilam, Nimisha; Montgomery, Dawn; Liang, Wei-zhen; Dogan, Mine; Tharayil, Nishanth; Martinez, Nicole; Moysey, Stephen; Powell, Brian; Darnault, Christophe J. G.
2018-04-01
The vadose zone is a highly interactive heterogeneous system through which water enters the subsurface system by infiltration. This paper details the effects of simulated plant exudate and soil component solutions upon unstable flow patterns in a porous medium (ASTM silica sand; US Silica, Ottawa, IL, USA) through the use of two-dimensional tank light transmission method (LTM). The contact angle (θ) and surface tension (γ) of two simulated plant exudate solutions (i.e., oxalate and citrate) and two soil component solutions (i.e., tannic acid and Suwannee River natural organic matter, SRNOM) were analyzed to determine the liquid-gas and liquid-solid interface characteristics of each. To determine if the unstable flow formations were dependent on the type and concentration of the simulated plant exudates and soil components, the analysis of the effects of the simulated plant exudate and soil component solutions were compared to a control solution (Hoagland nutrient solution with 0.01 M NaCl). Fingering flow patterns, vertical and horizontal water saturation profiles, water saturation at the fingertips, finger dimensions and velocity, and number of fingers were obtained using the light transmission method. Significant differences in the interface properties indicated a decrease between the control and the plant exudate and soil component solutions tested; specifically, the control (θ = 64.5° and γ = 75.75 mN m-1) samples exhibited a higher contact angle and surface tension than the low concentration of citrate (θ = 52.6° and γ = 70.8 mN m-1). Wetting front instability and fingering flow phenomena were reported in all infiltration experiments. The results showed that the plant exudates and soil components influenced the soil infiltration as differences in finger geometries, velocities, and water saturation profiles were detected when compared to the control. Among the tested solutions and concentrations of soil components, the largest finger width (10.19 cm) was generated by the lowest tannic acid solution concentration (0.1 mg L-1), and the lowest finger width (6.00 cm) was induced by the highest SRNOM concentration (10 mg L-1). Similarly, for the plant exudate solutions, the largest finger width (8.36 cm) was generated by the lowest oxalate solution concentration (0.1 mg L-1), and the lowest finger width (6.63 cm) was induced by the lowest citrate concentration (0.1 mg L-1). The control solution produced fingers with average width of 8.30 cm. Additionally, the wettability of the medium for the citrate, oxalate, and SRNOM solutions increased with an increase in concentration. Our research demonstrates that the plant exudates and soil components which are biochemical compounds produced and released in soil are capable of influencing the process of infiltration in soils. The results of this research also indicate that soil wettability, expressed as
cosθ 1/2, should be included in the scaling of the finger dimension, i.e., finger width, when using the Miller and Miller (1956) scaling theory for the scaling of flow in porous media. -
A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions.
Samal, Satya Swarup; Grigoriev, Dima; Fröhlich, Holger; Weber, Andreas; Radulescu, Ovidiu
2015-12-01
Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The gist of the method is the notion of tropical equilibration that provides approximate descriptions of slow invariant manifolds. Compared to extant numerical algorithms such as the intrinsic low-dimensional manifold method, our approach is symbolic and utilizes orders of magnitude instead of precise values of the model parameters. Application of this method to a large collection of biochemical network models supports the idea that the number of dynamical variables in minimal models of cell physiology can be small, in spite of the large number of molecular regulatory actors.
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Supersonic shear flows in laser driven high-energy-density plasmas created by the Nike laser
NASA Astrophysics Data System (ADS)
Harding, E. C.; Drake, R. P.; Gillespie, R. S.; Grosskopf, M. J.; Ditmar, J. R.; Aglitskiy, Y.; Weaver, J. L.; Velikovich, A. L.; Plewa, T.
2008-11-01
In high-energy-density (HED) plasmas the Kelvin-Helmholtz (KH) instability plays an important role in the evolution of Rayleigh-Taylor (RT) and Richtmyer-Meshkov (RM) unstable interfaces, as well as material interfaces that experience the passage one or multiple oblique shocks. Despite the potentially important role of the KH instability few experiments have been carried out to explore its behavior in the high-energy-density regime. We report on the evolution of a supersonic shear flow that is generated by the release of a high velocity (>100 km/s) aluminum plasma onto a CRF foam (ρ = 0.1 g/cc) surface. In order to seed the Kelvin-Helmholtz (KH) instability various two-dimensional sinusoidal perturbations (λ = 100, 200, and 300 μm with peak-to-valley amplitudes of 10, 20, and 30 μm respectively) have been machined into the foam surface. This experiment was performed using the Nike laser at the Naval Research Laboratory.
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NASA Astrophysics Data System (ADS)
Henri, Christopher; Fernàndez-Garcia, Daniel
2015-04-01
Modeling multi-species reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterwards. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.
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NASA Astrophysics Data System (ADS)
Henri, Christopher V.; Fernàndez-Garcia, Daniel
2014-09-01
Modeling multispecies reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterward. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.
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Efficient ASK-assisted system for expression and purification of plant F-box proteins.
Li, Haiou; Yao, Ruifeng; Ma, Sui; Hu, Shuai; Li, Suhua; Wang, Yupei; Yan, Chun; Xie, Daoxin; Yan, Jianbin
2017-11-01
Ubiquitin-mediated protein degradation plays an essential role in plant growth and development as well as responses to environmental and endogenous signals. F-box protein is one of the key components of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which recruit specific substrate proteins for subsequent ubiquitination and 26S proteasome-mediated degradation to regulate developmental processes and signaling networks. However, it is not easy to obtain purified F-box proteins with high activity due to their unstable protein structures. Here, we found that Arabidopsis SKP-like proteins (ASKs) can significantly improve soluble expression of F-box proteins and maintain their bioactivity. We established an efficient ASK-assisted method to express and purify plant F-box proteins. The method meets a broad range of criteria required for the biochemical analysis or protein crystallization of plant F-box proteins. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.
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Brooks, Mark A; Gewartowski, Kamil; Mitsiki, Eirini; Létoquart, Juliette; Pache, Roland A; Billier, Ysaline; Bertero, Michela; Corréa, Margot; Czarnocki-Cieciura, Mariusz; Dadlez, Michal; Henriot, Véronique; Lazar, Noureddine; Delbos, Lila; Lebert, Dorothée; Piwowarski, Jan; Rochaix, Pascal; Böttcher, Bettina; Serrano, Luis; Séraphin, Bertrand; van Tilbeurgh, Herman; Aloy, Patrick; Perrakis, Anastassis; Dziembowski, Andrzej
2010-09-08
For high-throughput structural studies of protein complexes of composition inferred from proteomics data, it is crucial that candidate complexes are selected accurately. Herein, we exemplify a procedure that combines a bioinformatics tool for complex selection with in vivo validation, to deliver structural results in a medium-throughout manner. We have selected a set of 20 yeast complexes, which were predicted to be feasible by either an automated bioinformatics algorithm, by manual inspection of primary data, or by literature searches. These complexes were validated with two straightforward and efficient biochemical assays, and heterologous expression technologies of complex components were then used to produce the complexes to assess their feasibility experimentally. Approximately one-half of the selected complexes were useful for structural studies, and we detail one particular success story. Our results underscore the importance of accurate target selection and validation in avoiding transient, unstable, or simply nonexistent complexes from the outset. Copyright © 2010 Elsevier Ltd. All rights reserved.
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Time-delayed feedback technique for suppressing instabilities in time-periodic flow
NASA Astrophysics Data System (ADS)
Shaabani-Ardali, Léopold; Sipp, Denis; Lesshafft, Lutz
2017-11-01
A numerical method is presented that allows to compute time-periodic flow states, even in the presence of hydrodynamic instabilities. The method is based on filtering nonharmonic components by way of delayed feedback control, as introduced by Pyragas [Phys. Lett. A 170, 421 (1992), 10.1016/0375-9601(92)90745-8]. Its use in flow problems is demonstrated here for the case of a periodically forced laminar jet, subject to a subharmonic instability that gives rise to vortex pairing. The optimal choice of the filter gain, which is a free parameter in the stabilization procedure, is investigated in the context of a low-dimensional model problem, and it is shown that this model predicts well the filter performance in the high-dimensional flow system. Vortex pairing in the jet is efficiently suppressed, so that the unstable periodic flow state in response to harmonic forcing is accurately retrieved. The procedure is straightforward to implement inside any standard flow solver. Memory requirements for the delayed feedback control can be significantly reduced by means of time interpolation between checkpoints. Finally, the method is extended for the treatment of periodic problems where the frequency is not known a priori. This procedure is demonstrated for a three-dimensional cubic lid-driven cavity in supercritical conditions.
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Reentrant Phase Coherence in Superconducting Nanowire Composites.
Ansermet, Diane; Petrović, Alexander P; He, Shikun; Chernyshov, Dmitri; Hoesch, Moritz; Salloum, Diala; Gougeon, Patrick; Potel, Michel; Boeri, Lilia; Andersen, Ole Krogh; Panagopoulos, Christos
2016-01-26
The short coherence lengths characteristic of low-dimensional superconductors are associated with usefully high critical fields or temperatures. Unfortunately, such materials are often sensitive to disorder and suffer from phase fluctuations in the superconducting order parameter which diverge with temperature T, magnetic field H, or current I. We propose an approach to overcome synthesis and fluctuation problems: building superconductors from inhomogeneous composites of nanofilaments. Macroscopic crystals of quasi-one-dimensional Na2-δMo6Se6 featuring Na vacancy disorder (δ ≈ 0.2) are shown to behave as percolative networks of superconducting nanowires. Long-range order is established via transverse coupling between individual one-dimensional filaments, yet phase coherence remains unstable to fluctuations and localization in the zero (T,H,I) limit. However, a region of reentrant phase coherence develops upon raising (T,H,I). We attribute this phenomenon to an enhancement of the transverse coupling due to electron delocalization. Our observations of reentrant phase coherence coincide with a peak in the Josephson energy EJ at nonzero (T,H,I), which we estimate using a simple analytical model for a disordered anisotropic superconductor. Na2-δMo6Se6 is therefore a blueprint for a future generation of nanofilamentary superconductors with inbuilt resilience to phase fluctuations at elevated (T,H,I).
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Study of Active Micromixer Driven by Electrothermal Force
NASA Astrophysics Data System (ADS)
Huang, Kuan-Rong; Chang, Jeng-Shian; Chao, Sheng D.; Wung, Tzong-Shyan; Wu, Kuang-Chong
2012-04-01
Biochemical applications of microchips often require a rapid mixing of different fluid samples. At the microscale level, fluid flow is usually a highly ordered laminar flow and diffusion is the primary mechanism for mixing owing to the lack of disturbances, yielding inefficiency for practical biochemical analysis. In this work, we design a prototype active micromixer by employing the electrothermal effect. We apply to the flow microchannel a non-uniform AC electric field, which can generate an electrothermal force on the fluid flow and induce vortex pairs for enhancing mixing efficiency. The performance of this active micromixer is studied and compared, under the same mixing quality, with that of a conventional passive micromixer of the same size with obstacles in the flow channel by three-dimensional finite element simulations. The numerical results show that the pressure drop between the inlet and the outlet for the active micromixer is much less than (only 3000th) that for the passive micro-mixer with the same mixing quality. To obtain an optimal mixing quality, we have systematically studied the mixing quality by varying the geometrical arrangements of the electrodes. An almost complete mixing can be obtained using a specific design. Moreover, the temperature increases around the electrodes are lower than 3 K, which does not adversely affect the biochemical analysis. It is suggested that the prototype active micromixer designed is promising and effective and useful for biochemical analysis.
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Intermittent gravity-driven flow of grains through narrow pipes
NASA Astrophysics Data System (ADS)
Alvarez, Carlos A.; de Moraes Franklin, Erick
2017-01-01
Grain flows through pipes are frequently found in various settings, such as in pharmaceutical, chemical, petroleum, mining and food industries. In the case of size-constrained gravitational flows, density waves consisting of alternating high- and low-compactness regions may appear. This study investigates experimentally the dynamics of density waves that appear in gravitational flows of fine grains through vertical and slightly inclined pipes. The experimental device consisted of a transparent glass pipe through which different populations of glass spheres flowed driven by gravity. Our experiments were performed under controlled ambient temperature and relative humidity, and the granular flow was filmed with a high-speed camera. Experimental results concerning the length scales and celerities of density waves are presented, together with a one-dimensional model and a linear stability analysis. The analysis exhibits the presence of a long-wavelength instability, with the most unstable mode and a cut-off wavenumber whose values are in agreement with the experimental results.
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Sign phase transition in the problem of interfering directed paths
NASA Astrophysics Data System (ADS)
Baldwin, C. L.; Laumann, C. R.; Spivak, B.
2018-01-01
We investigate the statistical properties of interfering directed paths in disordered media. At long distance, the average sign of the sum over paths may tend to zero (sign disordered) or remain finite (sign ordered) depending on dimensionality and the concentration of negative scattering sites x . We show that in two dimensions the sign-ordered phase is unstable even for arbitrarily small x by identifying rare destabilizing events. In three dimensions, we present strong evidence that there is a sign phase transition at a finite xc>0 . These results have consequences for several different physical systems. In two-dimensional insulators at low temperature, the variable-range-hopping magnetoresistance is always negative, while in three dimensions, it changes sign at the point of the sign phase transition. We also show that in the sign-disordered regime a small magnetic field may enhance superconductivity in a random system of D -wave superconducting grains embedded in a metallic matrix. Finally, the existence of the sign phase transition in three dimensions implies new features in the spin-glass phase diagram at high temperature.
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Modelling and analysis of the sugar cataract development process using stochastic hybrid systems.
Riley, D; Koutsoukos, X; Riley, K
2009-05-01
Modelling and analysis of biochemical systems such as sugar cataract development (SCD) are critical because they can provide new insights into systems, which cannot be easily tested with experiments; however, they are challenging problems due to the highly coupled chemical reactions that are involved. The authors present a stochastic hybrid system (SHS) framework for modelling biochemical systems and demonstrate the approach for the SCD process. A novel feature of the framework is that it allows modelling the effect of drug treatment on the system dynamics. The authors validate the three sugar cataract models by comparing trajectories computed by two simulation algorithms. Further, the authors present a probabilistic verification method for computing the probability of sugar cataract formation for different chemical concentrations using safety and reachability analysis methods for SHSs. The verification method employs dynamic programming based on a discretisation of the state space and therefore suffers from the curse of dimensionality. To analyse the SCD process, a parallel dynamic programming implementation that can handle large, realistic systems was developed. Although scalability is a limiting factor, this work demonstrates that the proposed method is feasible for realistic biochemical systems.
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NASA Astrophysics Data System (ADS)
Huang, Lijun; Tian, Huiping; Yang, Daquan; Zhou, Jian; Liu, Qi; Zhang, Pan; Ji, Yuefeng
2014-12-01
We propose a high figure of merit (FOM) biochemical sensor by designing a ring defect coupled resonator (RDCR) based on photonic crystal (PhC) slab. The design consists of ring resonant cavity which is coupled in and out with ring and line defect PhC structure. By a three dimensional finite-different time-domain (3D-FDTD) method, we demonstrate that the quality (Q) factor is greatly enhanced by altering the radius of air holes inner the ring resonant cavity and adjusting the width of line defect waveguide. In this paper, we obtain a highest Q up to 107 through numerical calculations. Even though water absorption at telecom wavelength range and random roughness of fabrication is considered, a Q of ~33,517 can be achieved. Simultaneously the proposed sensor possesses sensitivity (S) of 330 nm/RIU (refractive index unit), resulting in FOM of ~8000. Moreover, a minimal detection limit (DL) is obtained as good as 1.24×10-5. Therefore, these suggest that this design is a promising candidate for label-free biochemical sensing in medical diagnosis, life science and environmental monitoring.
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Time-dependent Tonks-Langmuir model is unstable
NASA Astrophysics Data System (ADS)
Sheridan, T. E.; Baalrud, S. D.
2017-11-01
We investigate a time-dependent extension of the Tonks-Langmuir model for a one-dimensional plasma discharge with collisionless kinetic ions and Boltzmann electrons. Ions are created uniformly throughout the volume and flow from the center of the discharge to the boundary wall due to a self-consistent, zero-order electric field. Solving this model using a particle-in-cell simulation, we observe coherent low-frequency, long-wavelength unstable ion waves which move toward the boundary with a speed below both the ion acoustic speed and the average ion velocity. The maximum amplitude of the wave potential fluctuations peaks at ≈0.09 Te near the wall, where Te is the electron temperature in electron volts. Using linear kinetic theory, we identify this instability as slow ion-acoustic wave modes which are destabilized by the zero-order electric field.
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Montague, James A; Pinder, George F; Gonyea, Jay V; Hipko, Scott; Watts, Richard
2018-05-01
Magnetic resonance imaging is used to observe solute transport in a 40cm long, 26cm diameter sand column that contained a central core of low permeability silica surrounded by higher permeability well-sorted sand. Low concentrations (2.9g/L) of Magnevist, a gadolinium based contrast agent, produce density driven convection within the column when it starts in an unstable state. The unstable state, for this experiment, exists when higher density contrast agent is present above the lower density water. We implement a numerical model in OpenFOAM to reproduce the observed fluid flow and transport from a density difference of 0.3%. The experimental results demonstrate the usefulness of magnetic resonance imaging in observing three-dimensional gravity-driven convective-dispersive transport behaviors in medium scale experiments. Copyright © 2017 Elsevier B.V. All rights reserved.
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Probing Neutron-Skin Thickness of Unstable Nuclei with Total Reaction Cross Sections
NASA Astrophysics Data System (ADS)
Horiuchi, Wataru; Suzuki, Yasuyuki; Inakura, Tsunenori
We present our recent analysis of the total reaction cross sections, σR, of unstable nuclei and discuss their sensitivity to the neutron-skin thickness. The σR is calculated with the Glauber model using projectile densities obtained with the Skyrme-Hartree-Fock method on the three-dimensional coordinate space. We cover 91 nuclei of O, Ne, Mg, Si, S, Ca, and Ni isotopes. Defining a reaction radius, aR = √{σ R/π } , to characterize the nuclear size and target (proton or 12C) dependence, we see the 12C target probes the matter radius while the proton target is sensitive to the skin-thickness. We find an empirical formula for expressing aR with the point matter radius and the skin thickness, which can be used to determine the skin thickness.
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Retention of the Native Epigenome in Purified Mammalian Chromatin
Ehrensberger, Andreas H.; Franchini, Don-Marc; East, Philip; George, Roger; Matthews, Nik; Maslen, Sarah L.; Svejstrup, Jesper Q.
2015-01-01
A protocol is presented for the isolation of native mammalian chromatin as fibers of 25–250 nucleosomes under conditions that preserve the natural epigenetic signature. The material is composed almost exclusively of histones and DNA and conforms to the structure expected by electron microscopy. All sequences probed for were retained, indicating that the material is representative of the majority of the genome. DNA methylation marks and histone marks resembled the patterns observed in vivo. Importantly, nucleosome positions also remained largely unchanged, except on CpG islands, where nucleosomes were found to be unstable. The technical challenges of reconstituting biochemical reactions with native mammalian chromatin are discussed. PMID:26248330
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Biochemical heterogeneity in glutathione synthetase deficiency.
Spielberg, S P; Garrick, M D; Corash, L M; Butler, J D; Tietze, F; Rogers, L; Schulman, J D
1978-01-01
Two different clinical syndromes are associated with glutathione synthetase deficiency, one presenting with hemolytic anemia and 5-oxoprolinuria, the other with isolated hemolysis. We have differentiated these disorders on an enzymatic basis. In 5-oxoprolinuria, all cell types examined have grossly deficient enzyme activity and glutathione content. In contrast, in the nonoxoprolinuric variant, erythrocytes have decreased enzyme activity and glutathione content, whereas nucleated cells maintain substantial levels of both. The enzyme in this disorder is unstable in vitro and has shortened survival in intact erythrocytes. Nucleated cells appear able to maintain sufficient enzyme activity and concentrations of glutathione to suppress overproduction of 5-oxoproline. PMID:659603
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α,ω-dihexyl-sexithiophene thin films for solution-gated organic field-effect transistors
NASA Astrophysics Data System (ADS)
Schamoni, Hannah; Noever, Simon; Nickel, Bert; Stutzmann, Martin; Garrido, Jose A.
2016-02-01
While organic semiconductors are being widely investigated for chemical and biochemical sensing applications, major drawbacks such as the poor device stability and low charge carrier mobility in aqueous electrolytes have not yet been solved to complete satisfaction. In this work, solution-gated organic field-effect transistors (SGOFETs) based on the molecule α,ω-dihexyl-sexithiophene (DH6T) are presented as promising platforms for in-electrolyte sensing. Thin films of DH6T were investigated with regard to the influence of the substrate temperature during deposition on the grain size and structural order. The performance of SGOFETs can be improved by choosing suitable growth parameters that lead to a two-dimensional film morphology and a high degree of structural order. Furthermore, the capability of the SGOFETs to detect changes in the pH or ionic strength of the gate electrolyte is demonstrated and simulated. Finally, excellent transistor stability is confirmed by continuously operating the device over a period of several days, which is a consequence of the low threshold voltage of DH6T-based SGOFETs. Altogether, our results demonstrate the feasibility of high performance and highly stable organic semiconductor devices for chemical or biochemical applications.
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Rational Protein Engineering Guided by Deep Mutational Scanning
Shin, HyeonSeok; Cho, Byung-Kwan
2015-01-01
Sequence–function relationship in a protein is commonly determined by the three-dimensional protein structure followed by various biochemical experiments. However, with the explosive increase in the number of genome sequences, facilitated by recent advances in sequencing technology, the gap between protein sequences available and three-dimensional structures is rapidly widening. A recently developed method termed deep mutational scanning explores the functional phenotype of thousands of mutants via massive sequencing. Coupled with a highly efficient screening system, this approach assesses the phenotypic changes made by the substitution of each amino acid sequence that constitutes a protein. Such an informational resource provides the functional role of each amino acid sequence, thereby providing sufficient rationale for selecting target residues for protein engineering. Here, we discuss the current applications of deep mutational scanning and consider experimental design. PMID:26404267
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Observation of Two-Dimensional Localized Jones-Roberts Solitons in Bose-Einstein Condensates
NASA Astrophysics Data System (ADS)
Meyer, Nadine; Proud, Harry; Perea-Ortiz, Marisa; O'Neale, Charlotte; Baumert, Mathis; Holynski, Michael; Kronjäger, Jochen; Barontini, Giovanni; Bongs, Kai
2017-10-01
Jones-Roberts solitons are the only known class of stable dark solitonic solutions of the nonlinear Schrödinger equation in two and three dimensions. They feature a distinctive elongated elliptical shape that allows them to travel without change of form. By imprinting a triangular phase pattern, we experimentally generate two-dimensional Jones-Roberts solitons in a three-dimensional atomic Bose-Einstein condensate. We monitor their dynamics, observing that this kind of soliton is indeed not affected by dynamic (snaking) or thermodynamic instabilities, that instead make other classes of dark solitons unstable in dimensions higher than one. Our results confirm the prediction that Jones-Roberts solitons are stable solutions of the nonlinear Schrödinger equation and promote them for applications beyond matter wave physics, like energy and information transport in noisy and inhomogeneous environments.
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Extension of modified power method to two-dimensional problems
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Peng; Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919; Lee, Hyunsuk
2016-09-01
In this study, the generalized modified power method was extended to two-dimensional problems. A direct application of the method to two-dimensional problems was shown to be unstable when the number of requested eigenmodes is larger than a certain problem dependent number. The root cause of this instability has been identified as the degeneracy of the transfer matrix. In order to resolve this instability, the number of sub-regions for the transfer matrix was increased to be larger than the number of requested eigenmodes; and a new transfer matrix was introduced accordingly which can be calculated by the least square method. Themore » stability of the new method has been successfully demonstrated with a neutron diffusion eigenvalue problem and the 2D C5G7 benchmark problem. - Graphical abstract:.« less
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Li, Xiaodong; Zhang, Jianxiang; Hu, Qiaoling; Li, Xiaohui
2011-11-01
Polystyrene-poly(acrylic acid)/poly(allylamine hydrochloride) polyelectrolyte multilayer was found to be instable and apt to reconstruct in the pure water. By depositing polystyrene-poly(acrylic acid)/poly(allylamine hydrochloride) multilayer on the polystyrene-poly(acrylic acid) hybrid CaCO(3) templates, novel polyelectrolyte capsules could be prepared after the removal of the templates. The resultant capsules could keep their three-dimensional (3D) spherical shape after being dried at room temperature, dramatically different from the conventional polyelectrolyte capsules based on nonhybrid templates by layer-by-layer procedure. The instable polyelectrolyte multilayer, hybrid templates, and assembly cycles were demonstrated to be three indispensable factors responsible for the formation of this type of 3D stable capsules. The formation mechanism was also discussed in this study. Copyright © 2011 Elsevier Inc. All rights reserved.
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Periodic orbits around areostationary points in the Martian gravity field
NASA Astrophysics Data System (ADS)
Liu, Xiao-Dong; Baoyin, Hexi; Ma, Xing-Rui
2012-05-01
This study investigates the problem of areostationary orbits around Mars in three-dimensional space. Areostationary orbits are expected to be used to establish a future telecommunication network for the exploration of Mars. However, no artificial satellites have been placed in these orbits thus far. The characteristics of the Martian gravity field are presented, and areostationary points and their linear stability are calculated. By taking linearized solutions in the planar case as the initial guesses and utilizing the Levenberg-Marquardt method, families of periodic orbits around areostationary points are shown to exist. Short-period orbits and long-period orbits are found around linearly stable areostationary points, but only short-period orbits are found around unstable areostationary points. Vertical periodic orbits around both linearly stable and unstable areostationary points are also examined. Satellites in these periodic orbits could depart from areostationary points by a few degrees in longitude, which would facilitate observation of the Martian topography. Based on the eigenvalues of the monodromy matrix, the evolution of the stability index of periodic orbits is determined. Finally, heteroclinic orbits connecting the two unstable areostationary points are found, providing the possibility for orbital transfer with minimal energy consumption.
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The Green's function in a channel with a sound-absorbing cover in the case of a uniform flow
NASA Astrophysics Data System (ADS)
Sobolev, A. F.
2012-07-01
We study the modal structure of an acoustic field of a point source as function of channel wall admittance in the case of a two-dimensional channel. The characteristic equation for determining the eigen-values corresponding to the boundary problem is studied in the form of this equation's dependence on the admittance, which varies in the entire complex plane. All modes, without exception, existing in the channel and forming the source field are classified based on the obtained topography of the characteristic equation. The expressions that describe the amplitudes and spatial distribution of the hydrodynamic modes, attenuation rate (for stable modes), or increment (for unstable modes) were obtained as functions of the wall admittance and flow velocity. It is shown that in addition to the hydrodynamic unstable modes existing downstream from the source, hydrodynamic unstable modes exist upstream from the source at any admittance. They appear only when the admittance has an elastic character. It is shown that hydrodynamic modes are induced only in the case when the source is located close to the wall or on the wall. The amplitude of these modes decreases exponentially with distance from the wall.
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Capillary instability of elliptic liquid jets
NASA Astrophysics Data System (ADS)
Amini, Ghobad; Dolatabadi, Ali
2011-08-01
Instability of a liquid jet issuing from an elliptic nozzle in Rayleigh mode is investigated and its behavior is compared with a circular jet. Mathematical solution of viscous free-surface flow for asymmetric geometry is complicated if 3-D analytical solutions are to be obtained. Hence, one-dimensional Cosserat (directed curve) equations are used which can be assumed as a low order form of Navier-Stokes equations for slender jets. Linear solution is performed using perturbation method. Temporal dispersion equation is derived to find the most unstable wavelength responsible for the jet breakup. The obtained results for a circular jet (i.e., an ellipse with an aspect ratio of one) are compared with the classical results of Rayleigh and Weber for inviscid and viscous cases, respectively. It is shown that in the Rayleigh regime, which is the subject of this research, symmetric perturbations are unstable while asymmetric perturbations are stable. Consequently, spatial analysis is performed and the variation of growth rate under the effect of perturbation frequencies for various jet velocities is demonstrated. Results reveal that in comparison with a circular jet, the elliptic jet is more unstable. Furthermore, among liquid jets with elliptical cross sections, those with larger ellipticities have a larger instability growth rate.
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Stability analysis of unsteady ablation fronts
DOE Office of Scientific and Technical Information (OSTI.GOV)
Betti, R.; McCrory, R.L.; Verdon, C.P.
1993-08-01
The linear stability analysis of unsteady ablation fronts, is carried out for a semi-infinite uniform medium. For a laser accelerated target, it is shown that a properly selected modulation of the laser intensity can lead to the dynamic stabilization or growth-rate reduction of a large portion of the unstable spectrum. The theory is in qualitative agreement with the numerical results obtained by using the two-dimensional hydrodynamic code ORCHID.
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Stability analysis of unsteady ablation fronts
DOE Office of Scientific and Technical Information (OSTI.GOV)
Betti, R.; McCrory, R.L.; Verdon, C.P.
1993-11-08
The linear stability analysis of unsteady ablation fronts is carried out for a semi-infinite uniform medium. For a laser accelerated target, it is shown that a properly selected modulation of the laser intensity can lead to the dynamic stabilization or growth-rate reduction of a large portion of the unstable spectrum. The theory is in qualitative agreement with the numerical results obtained by using the two-dimensional hydrodynamic code ORCHID.
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Multistability and hidden attractors in a relay system with hysteresis
NASA Astrophysics Data System (ADS)
Zhusubaliyev, Zhanybai T.; Mosekilde, Erik; Rubanov, Vasily G.; Nabokov, Roman A.
2015-06-01
For nonlinear dynamic systems with switching control, the concept of a "hidden attractor" naturally applies to a stable dynamic state that either (1) coexists with the stable switching cycle or (2), if the switching cycle is unstable, has a basin of attraction that does not intersect with the neighborhood of that cycle. We show how the equilibrium point of a relay system disappears in a boundary-equilibrium bifurcation as the system enters the region of autonomous switching dynamics and demonstrate experimentally how a relay system can exhibit large amplitude chaotic oscillations at high values of the supply voltage. By investigating a four-dimensional model of the experimental relay system we finally show how a variety of hidden periodic, quasiperiodic and chaotic attractors arise, transform and disappear through different bifurcations.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Khor, Richard; Duchesne, Gillian; Monash University, Melbourne
Purpose: To evaluate the outcomes of patients treated for intermediate- and high-risk prostate cancer with a single schedule of either external beam radiation therapy (EBRT) and high-dose-rate brachytherapy (HDRB) boost or EBRT alone. Methods and Materials: From 2001-2006, 344 patients received EBRT with HDRB boost for definitive treatment of intermediate- or high-risk prostate cancer. The prescribed EBRT dose was 46 Gy in 23 fractions, with a HDR boost of 19.5 Gy in 3 fractions. This cohort was compared to a contemporaneously treated cohort who received EBRT to 74 Gy in 37 fractions, using a matched pair analysis. Three-dimensional conformal EBRTmore » was used. Matching was performed using a propensity score matching technique. High-risk patients constituted 41% of the matched cohorts. Five-year clinical and biochemical outcomes were analyzed. Results: Initial significant differences in prognostic indicators between the unmatched treatment cohorts were rendered negligible after matching, providing a total of 688 patients. Median biochemical follow-up was 60.5 months. The 5-year freedom from biochemical failure was 79.8% (95% confidence interval [CI], 74.3%-85.0%) and 70.9% (95% CI, 65.4%-76.0%) for the HDRB and EBRT groups, respectively, equating to a hazard ratio of 0.59 (95% CI, 0.43-0.81, P=.0011). Interaction analyses showed no alteration in HDR efficacy when planned androgen deprivation therapy was administered (P=.95), but a strong trend toward reduced efficacy was shown compared to EBRT in high-risk cases (P=.06). Rates of grade 3 urethral stricture were 0.3% (95% CI, 0%-0.9%) and 11.8% (95% CI, 8.1%-16.5%) for EBRT and HDRB, respectively (P<.0001). No differences in clinical outcomes were observed. Conclusions: This comparison of 2 individual contemporaneously treated HDRB and EBRT approaches showed improved freedom from biochemical progression with the HDR approach. The benefit was more pronounced in intermediate- risk patients but needs to be weighed against an increased risk of urethral toxicity.« less
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Analysis of the high-dimensional naming game with committed minorities
NASA Astrophysics Data System (ADS)
Pickering, William; Szymanski, Boleslaw K.; Lim, Chjan
2016-05-01
The naming game has become an archetype for linguistic evolution and mathematical social behavioral analysis. In the model presented here, there are N individuals and K words. Our contribution is developing a robust method that handles the case when K =O (N ) . The initial condition plays a crucial role in the ordering of the system. We find that the system with high Shannon entropy has a higher consensus time and a lower critical fraction of zealots compared to low-entropy states. We also show that the critical number of committed agents decreases with the number of opinions and grows with the community size for each word. These results complement earlier conclusions that diversity of opinion is essential for evolution; without it, the system stagnates in the status quo [S. A. Marvel et al., Phys. Rev. Lett. 109, 118702 (2012), 10.1103/PhysRevLett.109.118702]. In contrast, our results suggest that committed minorities can more easily conquer highly diverse systems, showing them to be inherently unstable.
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The phase diagram of high-pressure superionic ice
Sun, Jiming; Clark, Bryan K.; Torquato, Salvatore; ...
2015-08-28
Superionic ice is a special group of ice phases at high temperature and pressure, which may exist in ice-rich planets and exoplanets. In superionic ice liquid hydrogen coexists with a crystalline oxygen sublattice. At high pressures, the properties of superionic ice are largely unknown. Here we report evidence that from 280 GPa to 1.3 TPa, there are several competing phases within the close-packed oxygen sublattice. At even higher pressure, the close-packed structure of the oxygen sublattice becomes unstable to a new unusual superionic phase in which the oxygen sublattice takes the P2 1/c symmetry. We also discover that higher pressuremore » phases have lower transition temperatures. The diffusive hydrogen in the P2 1/c superionic phase shows strong anisotropic behaviour and forms a quasi-two-dimensional liquid. The ionic conductivity changes abruptly in the solid to close-packed superionic phase transition, but continuously in the solid to P2 1/c superionic phase transition.« less
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Godlewska, Marlena; Krasuska, Wanda
2018-01-01
Thyroid peroxidase (TPO) is an enzyme and autoantigen expressed in thyroid and breast tissues. Thyroid TPO undergoes a complex maturation process however, nothing is known about post-translational modifications of breast-expressed TPO. In this study, we have investigated the biochemical properties of TPO expressed in normal and cancerous human breast tissues, and the maturation process and antigenicity of TPO present in a panel of human breast tissue-derived cell lines. We found that the molecular weight of breast TPO was slightly lower than that of thyroid TPO due to decreased glycosylation and as suggest results of Western blot also shorter amino acid chain. Breast TPO exhibit enzymatic activity and isoelectric point comparable to that of thyroid TPO. The biochemical properties of TPO expressed in mammary cell lines and normal thyrocytes are similar regarding glycan content, molecular weight and isoelectric point. However, no peroxidase activity and dimer formation was detected in any of these cell lines since the majority of TPO protein was localized in the cytoplasmic compartment, and the TPO expression at the cell surface was too low to detect its enzymatic activity. Lactoperoxidase, a protein highly homologous to TPO expressed also in breast tissues, does not influence the obtained data. TPO expressed in the cell lines was recognized by a broad panel of TPO-specific antibodies. Although some differences in biochemical properties between thyroid and breast TPO were observed, they do not seem to be critical for the overall three-dimensional structure. This conclusion is supported by the fact that TPO expressed in breast tissues and cell lines reacts well with conformation-sensitive antibodies. Taking into account a close resemblance between both proteins, especially high antigenicity, future studies should investigate the potential immunotherapies directed against breast-expressed TPO and its specific epitopes. PMID:29513734
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Godlewska, Marlena; Krasuska, Wanda; Czarnocka, Barbara
2018-01-01
Thyroid peroxidase (TPO) is an enzyme and autoantigen expressed in thyroid and breast tissues. Thyroid TPO undergoes a complex maturation process however, nothing is known about post-translational modifications of breast-expressed TPO. In this study, we have investigated the biochemical properties of TPO expressed in normal and cancerous human breast tissues, and the maturation process and antigenicity of TPO present in a panel of human breast tissue-derived cell lines. We found that the molecular weight of breast TPO was slightly lower than that of thyroid TPO due to decreased glycosylation and as suggest results of Western blot also shorter amino acid chain. Breast TPO exhibit enzymatic activity and isoelectric point comparable to that of thyroid TPO. The biochemical properties of TPO expressed in mammary cell lines and normal thyrocytes are similar regarding glycan content, molecular weight and isoelectric point. However, no peroxidase activity and dimer formation was detected in any of these cell lines since the majority of TPO protein was localized in the cytoplasmic compartment, and the TPO expression at the cell surface was too low to detect its enzymatic activity. Lactoperoxidase, a protein highly homologous to TPO expressed also in breast tissues, does not influence the obtained data. TPO expressed in the cell lines was recognized by a broad panel of TPO-specific antibodies. Although some differences in biochemical properties between thyroid and breast TPO were observed, they do not seem to be critical for the overall three-dimensional structure. This conclusion is supported by the fact that TPO expressed in breast tissues and cell lines reacts well with conformation-sensitive antibodies. Taking into account a close resemblance between both proteins, especially high antigenicity, future studies should investigate the potential immunotherapies directed against breast-expressed TPO and its specific epitopes.
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NASA Astrophysics Data System (ADS)
Barelko, V. V.; Pomogailo, A. D.; Dzhardimalieva, G. I.; Evstratova, S. I.; Rozenberg, A. S.; Uflyand, I. E.
1999-06-01
The phenomenon of autowave (frontal) solid phase polymerization of metal-containing monomers based on metal-acrylamide complexes is considered. The comparison of the features of autowave processes realized in both the single-component matrices of the monomer and the matrices filled by the fiberglass materials is performed. The unstable regimes of the polymerization wave as well as the conditions for the stabilization of the flat front in the filled matrices are described. The peculiarities of the frontal regimes in the three- and two-dimensional media are studied. Some possibilities for using of autowave polymerization in the fabrication of the polymer-fiberglass composites and composition prepregs are discussed.
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DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia
DOE Office of Scientific and Technical Information (OSTI.GOV)
Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.
Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less
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DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia
Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.
2017-01-16
Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less
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NASA Astrophysics Data System (ADS)
Zhang, Chun-Sen; Zhang, Meng-Meng; Zhang, Wei-Xing
2017-01-01
This paper outlines a low-cost, user-friendly photogrammetric technique with nonmetric cameras to obtain excavation site digital sequence images, based on photogrammetry and computer vision. Digital camera calibration, automatic aerial triangulation, image feature extraction, image sequence matching, and dense digital differential rectification are used, combined with a certain number of global control points of the excavation site, to reconstruct the high precision of measured three-dimensional (3-D) models. Using the acrobatic figurines in the Qin Shi Huang mausoleum excavation as an example, our method solves the problems of little base-to-height ratio, high inclination, unstable altitudes, and significant ground elevation changes affecting image matching. Compared to 3-D laser scanning, the 3-D color point cloud obtained by this method can maintain the same visual result and has advantages of low project cost, simple data processing, and high accuracy. Structure-from-motion (SfM) is often used to reconstruct 3-D models of large scenes and has lower accuracy if it is a reconstructed 3-D model of a small scene at close range. Results indicate that this method quickly achieves 3-D reconstruction of large archaeological sites and produces heritage site distribution of orthophotos providing a scientific basis for accurate location of cultural relics, archaeological excavations, investigation, and site protection planning. This proposed method has a comprehensive application value.
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Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V
2015-02-01
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.
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Bouzidi, Nadia; Betbout, Fethi; Maatouk, Faouzi; Gamra, Habib; Miled, Abdelhedi; Ferchichi, Salima
2017-12-01
We aimed to evaluate the relationship of serum activin A levels with risk factors, clinical presentation, biochemical marker levels, extent, and severity of atherosclerotic coronary artery disease (CAD). In total, 310 CAD patients [92 with ST-segment elevation myocardial infarction (STEMI), 111 with non-STEMI (NSTEMI), and 107 with unstable angina (UA)] and 207 healthy subjects (controls) were enrolled. Activin A levels in all participants were measured using ELISA. Angiographic measurements were performed in patients and not in the healthy subjects. Activin A levels were higher in all patient groups than in controls (patients vs. controls, p=0.041; NSTEMI vs. UA, p=0.744; STEMI vs. UA, p=0.172; NSTEMI vs. STEMI, p=0.104). According to the cut-off value of activin A level, patients with high and low activin A levels had a similar distribution of clinical and biochemical variables but the prevalence of severe stenosis was observed in groups with high activin A levels. Our results revealed that activin A levels did not decrease as thrombolysis in myocardial infarction (risk score increased (p=0.590). The area under the ROC curve for activin A levels in patients was 0.590±0.047 (95% CI: 0.439-0.591, p=0.193). In multiple analysis of the overall population, male gender (ß=-0.260; 95% CI: -617.39 to -110.04; p=0.005) was an independent predictor of activin A levels. This study indicated that activin A can not be a predictive marker in CAD and is not associated with extensive and severe CAD. In contrast, the increase in activin A levels in patients, especially in patients with different clinical groups of acute coronary syndromes, suggested its involvement in atherosclerosis.
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Sakellarios, Antonis I; Siogkas, Panagiotis K; Athanasiou, Lambros S; Exarchos, Themis P; Papafaklis, Michail I; Bourantas, Christos V; Naka, Katerina K; Michalis, Lampros K; Filipovic, Nenad; Parodi, Oberdan; Fotiadis, Dimitrios I
2013-01-01
Low density lipoprotein (LDL) has a significant role on the atherosclerotic plaque development, while the concentration of high density lipoproteins (HDL) is considered to play an atheroprotective role according to several biochemical mechanisms. In this work, it is the first time that both LDL and HDL concentrations are taken into account in order to predict the regions prone for plaque development. Our modeling approach is based on the use of a realistic three-dimensional reconstructed pig coronary artery in two time points. Biochemical data measured in the pig were also included in order to develop a more customized model. We modeled coronary blood flow by solving the Navier-Stokes equations in the arterial lumen and plasma filtration in the arterial wall using Darcy's Law. HDL transport was modeled only in the arterial lumen using the convection-diffusion equation, while LDL transport was modeled both in the lumen and the arterial wall. An additional novelty of this work is that we model the oxidation of LDL taking into account the atheroprotective role of HDL. The results of our model were in good agreement with histological findings demonstrating that increased oxidized LDL is found near regions of advanced plaques, while non-oxidized LDL is found in regions of early plaque types.
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[INVITED] Tilted fiber grating mechanical and biochemical sensors
NASA Astrophysics Data System (ADS)
Guo, Tuan; Liu, Fu; Guan, Bai-Ou; Albert, Jacques
2016-04-01
The tilted fiber Bragg grating (TFBG) is a new kind of fiber-optic sensor that possesses all the advantages of well-established Bragg grating technology in addition to being able to excite cladding modes resonantly. This device opens up a multitude of opportunities for single-point sensing in hard-to-reach spaces with very controllable cross-sensitivities, absolute and relative measurements of various parameters, and an extreme sensitivity to materials external to the fiber without requiring the fiber to be etched or tapered. Over the past five years, our research group has been developing multimodal fiber-optic sensors based on TFBG in various shapes and forms, always keeping the device itself simple to fabricate and compatible with low-cost manufacturing. This paper presents a brief review of the principle, fabrication, characterization, and implementation of TFBGs, followed by our progress in TFBG sensors for mechanical and biochemical applications, including one-dimensional TFBG vibroscopes, accelerometers and micro-displacement sensors; two-dimensional TFBG vector vibroscopes and vector rotation sensors; reflective TFBG refractometers with in-fiber and fiber-to-fiber configurations; polarimetric and plasmonic TFBG biochemical sensors for in-situ detection of cell, protein and glucose.
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An ischemia-guided approach for risk stratification in patients with acute coronary syndromes.
Pepine, C J
2000-12-28
The optimal management approach for patients with non-ST-segment elevation acute coronary syndromes continues to be an issue of debate. An ischemia-guided strategy appears to be effective as an alternative to either a very conservative "wait-and-see" approach or a very aggressive routine revascularization approach. The need for another approach is supported by the lack of conclusive evidence-based results favoring an early routine invasive treatment strategy. In the Thrombolysis in Myocardial Infarction (TIMI) IIIB trial, there were no differences in the incidence of death or myocardial infarction (MI) between patients treated with an early invasive approach and those treated with a conservative approach to treatment. Significantly worse outcomes were shown in patients assigned to an early invasive strategy in the Veterans Affairs Non-Q-Wave Infarction Strategies in Hospital (VANQWISH) trial at 1-year follow-up (111 clinical events in the invasive group vs 85 in the conservative group; p = 0.05). Registry information, including that from the Organization to Assess Strategies for Ischemic Syndromes (OASIS), which included approximately 8,000 patients with unstable angina or suspected MI, has even suggested an excess hazard with a routine invasive approach. Patients with non-ST-segment elevation MI observed in the Global Use of Strategies to Open Occluded Coronary Arteries in Acute Coronary Syndromes (GUSTO)-IIB and Platelet IIb/IIIa in Unstable Angina: Receptor Suppression Using Integrilin Therapy (PURSUIT) trials also fared better with an ischemia-guided strategy. Even the recent FRagmin and Fast Revascularization during InStability in Coronary artery disease (FRISC II) trial investigators had to be very selective relative to eliminating high-risk patients in the first week and treating with intense anti-ischemic therapy and 5-7 days of low-molecular-weight heparin therapy to show an advantage for assigned revascularization. A careful clinical evaluation with attention to early risk stratification is essential in the ischemia-guided approach. The Braunwald classification for unstable angina helps identify independent clinical predictors of a poor outcome; high risk is clearly associated with Braunwald class III and type C. Electrocardiographic and biochemical markers for myocardial necrosis (cardiac troponin T or I) are important tools for assessing the presence and degree of ischemia and associated risk for adverse outcome. Noninvasive evaluation of left ventricular ejection fraction is essential for identifying those at high risk due to impaired contractile function. When these conventional markers do not provide conclusive information, noninvasive stress testing is most helpful to further identify those at highest risk for revascularization.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zou, Ling; Zhao, Haihua; Kim, Seung Jun
In this study, the classical Welander’s oscillatory natural circulation problem is investigated using high-order numerical methods. As originally studied by Welander, the fluid motion in a differentially heated fluid loop can exhibit stable, weakly instable, and strongly instable modes. A theoretical stability map has also been originally derived from the stability analysis. Numerical results obtained in this paper show very good agreement with Welander’s theoretical derivations. For stable cases, numerical results from both the high-order and low-order numerical methods agree well with the non-dimensional flow rate analytically derived. The high-order numerical methods give much less numerical errors compared to themore » low-order methods. For stability analysis, the high-order numerical methods could perfectly predict the stability map, while the low-order numerical methods failed to do so. For all theoretically unstable cases, the low-order methods predicted them to be stable. The result obtained in this paper is a strong evidence to show the benefits of using high-order numerical methods over the low-order ones, when they are applied to simulate natural circulation phenomenon that has already gain increasing interests in many future nuclear reactor designs.« less
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Superconcentrated electrolytes for a high-voltage lithium-ion battery
Wang, Jianhui; Yamada, Yuki; Sodeyama, Keitaro; Chiang, Ching Hua; Tateyama, Yoshitaka; Yamada, Atsuo
2016-01-01
Finding a viable electrolyte for next-generation 5 V-class lithium-ion batteries is of primary importance. A long-standing obstacle has been metal-ion dissolution at high voltages. The LiPF6 salt in conventional electrolytes is chemically unstable, which accelerates transition metal dissolution of the electrode material, yet beneficially suppresses oxidative dissolution of the aluminium current collector; replacing LiPF6 with more stable lithium salts may diminish transition metal dissolution but unfortunately encounters severe aluminium oxidation. Here we report an electrolyte design that can solve this dilemma. By mixing a stable lithium salt LiN(SO2F)2 with dimethyl carbonate solvent at extremely high concentrations, we obtain an unusual liquid showing a three-dimensional network of anions and solvent molecules that coordinate strongly to Li+ ions. This simple formulation of superconcentrated LiN(SO2F)2/dimethyl carbonate electrolyte inhibits the dissolution of both aluminium and transition metal at around 5 V, and realizes a high-voltage LiNi0.5Mn1.5O4/graphite battery that exhibits excellent cycling durability, high rate capability and enhanced safety. PMID:27354162
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Turbulence and wave particle interactions in solar-terrestrial plasmas
NASA Technical Reports Server (NTRS)
Dulk, G. A.
1982-01-01
Theoretical modelling of two dimensional compressible convection in the Sun shows that convective flows can extend over many pressure scale heights without the nonlinear motions becoming supersonic, and that compressional work arising from pressure fluctuations can be comparable to that by buoyancy forces. These results are contrary to what was supposed in prevailing mixing length models for solar convection, and they imply a much greater degree of organized flow extending over the full depth of the convection zone. The nonlinear penetration of motions into the stable region below the convection zone was emphasized. These compressible flows are dominated by downward directed plumes in the unstable zone. Their strong penetration into the region of stable stratification below excites a broad spectrum of internal gravity waves there, and these in turn feed back upon the convection in the unstable zone to produce a rich time dependence.
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Magnetohydrodynamic Simulations of the Wiggle Instability in Spiral Galaxies
NASA Astrophysics Data System (ADS)
Tanaka, Minoru; Wada, Keiichi; Machida, Mami; Matsumoto, Ryoji; Miyaji, Shigeki
2005-09-01
We studied the stability of galactic spiral shocks through two dimensional global magnetohydrodynamic simulations. Recently, Wada & Koda (2003) showed, using global hydrodynamic simulations, that galactic gas flows behind a spiral shock becomes unstable against a perturbation parallel to the shock front and form spur-like density structures. They attributed the origin of this wiggle instability to the Kelvin-Helmholtz (K-H) instability triggered by the acceleration of the gas behind the shock. We carried out global simulations including galactic magnetic fields. The initial magnetic field is assumed to be either uniform or purely toroidal. We found that although the magnetic field reduces the growth rate of the K-H instability, wiggle instability develops even in galaxies with μG magnetic fields. We also present the results of local simulations to demonstrate the dependence of the growth rate of the instability with the wavelength. The interval of spurs is determined by the most unstable wavelength of the wiggle instability.
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Tachyon cosmology with non-vanishing minimum potential: a unified model
DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, Huiquan, E-mail: hqli@ustc.edu.cn
2012-07-01
We investigate the tachyon condensation process in the effective theory with non-vanishing minimum potential and its implications to cosmology. It is shown that the tachyon condensation on an unstable three-brane described by this modified tachyon field theory leads to lower-dimensional branes (defects) forming within a stable three-brane. Thus, in the cosmological background, we can get well-behaved tachyon matter after tachyon inflation, (partially) avoiding difficulties encountered in the original tachyon cosmological models. This feature also implies that the tachyon inflated and reheated universe is followed by a Chaplygin gas dark matter and dark energy universe. Hence, such an unstable three-brane behavesmore » quite like our universe, reproducing the key features of the whole evolutionary history of the universe and providing a unified description of inflaton, dark matter and dark energy in a very simple single-scalar field model.« less
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Phase separation and long-wavelength charge instabilities in spin-orbit coupled systems
NASA Astrophysics Data System (ADS)
Seibold, G.; Bucheli, D.; Caprara, S.; Grilli, M.
2015-01-01
We investigate a two-dimensional electron model with Rashba spin-orbit interaction where the coupling constant g=g(n) depends on the electronic density. It is shown that this dependence may drive the system unstable towards a long-wavelength charge density wave (CDW) where the associated second-order instability occurs in close vicinity to global phase separation. For very low electron densities the CDW instability is nesting-induced and the modulation follows the Fermi momentum kF. At higher density the instability criterion becomes independent of kF and the system may become unstable in a broad momentum range. Finally, upon filling the upper spin-orbit split band, finite momentum instabilities disappear in favor of phase separation alone. We discuss our results with regard to the inhomogeneous phases observed at the LaAlO3/SrTiO3 or LaTiO3/SrTiO3 interfaces.
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Preferential flow in the vadose zone and interface dynamics: Impact of microbial exudates
NASA Astrophysics Data System (ADS)
Li, Biting; Pales, Ashley R.; Clifford, Heather M.; Kupis, Shyla; Hennessy, Sarah; Liang, Wei-Zhen; Moysey, Stephen; Powell, Brian; Finneran, Kevin T.; Darnault, Christophe J. G.
2018-03-01
In the hydrological cycle, the infiltration process is a critical component in the distribution of water into the soil and in the groundwater system. The nonlinear dynamics of the soil infiltration process yield preferential flow which affects the water distribution in soil. Preferential flow is influenced by the interactions between water, soil, plants, and microorganisms. Although the relationship among the plant roots, their rhizodeposits and water transport in soil has been the subject of extensive study, the effect of microbial exudates has been studied in only a few cases. Here the authors investigated the influence of two artificial microbial exudates-catechol and riboflavin-on the infiltration process, particularly unstable fingered flow, one form of preferential flow. Flow experiments investigating the effects of types and concentrations of microbial exudates on unstable fingered flow were conducted in a two-dimensional tank that was filled with ASTM
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Predicting electromagnetic ion cyclotron wave amplitude from unstable ring current plasma conditions
Fu, Xiangrong; Cowee, Misa M.; Jordanova, Vania K.; ...
2016-11-01
Electromagnetic ion cyclotron (EMIC) waves in the Earth's inner magnetosphere are enhanced fluctuations driven unstable by ring current ion temperature anisotropy. EMIC waves can resonate with relativistic electrons and play an important role in precipitation of MeV radiation belt electrons. In this study, we investigate the excitation and saturation of EMIC instability in a homogeneous plasma using both linear theory and nonlinear hybrid simulations. We have explored a four-dimensional parameter space, carried out a large number of simulations, and derived a scaling formula that relates the saturation EMIC wave amplitude to initial plasma conditions. Finally, such scaling can be usedmore » in conjunction with ring current models like ring current-atmosphere interactions model with self-consistent magnetic field to provide global dynamic EMIC wave maps that will be more accurate inputs for radiation belt modeling than statistical models.« less
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Heating, Cooling, and Gravitational Instabilities in Protostellar and Protoplanetary Disks
NASA Astrophysics Data System (ADS)
Pickett, B. K.; Mejia, A. C.; Durisen, R. H.
2001-12-01
We present three-dimensional hydrodynamic simulations of protostellar disk models, in order to explore how the interplay between heating and cooling regulates significant gravitational instabilities. Artificial viscosity is used to treat irreversible heating, such as would occur in shocks; volumetric cooling at several different rates is also applied throughout a broad radial region of the disk. We study the evolution of a disk that is already unstable (due to the low value of the Toomre Q parameter), and a marginally unstable disk that is cooled towards instability. The evolutions have implications for the transport of mass and angular momentum in protostellar disks, the effects of gravitational instabilities on the vertical structure of the disks, and the formation of stellar and substellar companions on dynamic time scales due to disk instabilties. This work is supported by grants from the NASA Planetary Geology and Geophysics and Origins of Solar Systems Programs.
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NASA Astrophysics Data System (ADS)
Cholemari, Murali R.; Arakeri, Jaywant H.
2005-08-01
We study the stability of surface waves on the radial film flow created by a vertical cylindrical water jet striking a horizontal plate. In such flows, surface waves have been found to be unstable and can cause transition to turbulence. This surface-wave-induced transition is different from the well-known Tollmien-Schlichting wave-induced transition. The present study aims at understanding the instability and the transition process. We do a temporal stability analysis by assuming the flow to be locally two-dimensional but including spatial variations to first order in the basic flow. The waves are found to be dispersive, mostly unstable, and faster than the mean flow. Spatial variation is the major destabilizing factor. Experiments are done to test the results of the linear stability analysis and to document the wave breakup and transition. Comparison between theory and experiments is fairly good and indicates the adequacy of the model.
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Exploring Stability of General Relativistic Accretion Disks
NASA Astrophysics Data System (ADS)
Korobkin, Oleg; Abdikamalov, Ernazar; Schnetter, Erik; Stergioulas, Nikolaos; Zink, Burkhard
2011-04-01
Self-gravitating relativistic disks around black holes can form as transient structures in a number of astrophysical scenarios, involving core collapse of massive stars and mergers of compact ob jects. I will present results on our recent study of the stability of such disks against runaway and non-axisymmetric instabilities, which we explore using three-dimensional hydrodynamics simulations in full general relativity. All of our models develop unstable non-axisymmetric modes on a dynamical timescale. We observe two distinct types of instabilities: the Papaloizou-Pringle and the so-called intermediate type instabilities. The development of the non-axisymmetric mode with azimuthal number m=1 is accompanied by an outspiraling motion of the black hole, which significantly amplifies the growth rate of the m=1 mode in some cases. We will discuss the types, growth rates and pattern speeds of the unstable modes, as well as the detectability of the gravitational waves from such objects.
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Convective instabilities in SN 1987A
NASA Technical Reports Server (NTRS)
Benz, Willy; Thielemann, Friedrich-Karl
1990-01-01
Following Bandiera (1984), it is shown that the relevant criterion to determine the stability of a blast wave, propagating through the layers of a massive star in a supernova explosion, is the Schwarzschild (or Ledoux) criterion rather than the Rayleigh-Taylor criterion. Both criteria coincide only in the incompressible limit. Results of a linear stability analysis are presented for a one-dimensional (spherical) explosion in a realistic model for the progenitor of SN 1987A. When applying the Schwarzschild criterion, unstable regions get extended considerably. Convection is found to develop behind the shock, with a characteristic growth rate corresponding to a time scale much smaller than the shock traversal time. This ensures that efficient mixing will take place. Since the entire ejected mass is found to be convectively unstable, Ni can be transported outward, even into the hydrogen envelope, while hydrogen can be mixed deep into the helium core.
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Unstable Memories Create a High-Level Representation that Enables Learning Transfer.
Mosha, Neechi; Robertson, Edwin M
2016-01-11
A memory is unstable, making it susceptible to interference and disruption, after its acquisition [1-4]. The function or possible benefit of a memory being unstable at its acquisition is not well understood. Potentially, instability may be critical for the communication between recently acquired memories, which would allow learning in one task to be transferred to the other subsequent task [1, 5]. Learning may be transferred between any memories that are unstable, even between different types of memory. Here, we test the link between a memory being unstable and the transfer of learning to a different type of memory task. We measured how learning in one task transferred to and thus improved learning in a subsequent task. There was transfer from a motor skill to a word list task and, vice versa, from a word list to a motor skill task. What was transferred was a high-level relationship between elements, rather than knowledge of the individual elements themselves. Memory instability was correlated with subsequent transfer, suggesting that transfer was related to the instability of the memory. Using different methods, we stabilized the initial memory, preventing it from being susceptible to interference, and found that these methods consistently prevented transfer to the subsequent memory task. This suggests that the transfer of learning across diverse tasks is due to a high-level representation that can only be formed when a memory is unstable. Our work has identified an important function of memory instability. Copyright © 2016 Elsevier Ltd. All rights reserved.
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A photoreversible protein-patterning approach for guiding stem cell fate in three-dimensional gels
NASA Astrophysics Data System (ADS)
Deforest, Cole A.; Tirrell, David A.
2015-05-01
Although biochemically patterned hydrogels are capable of recapitulating many critical aspects of the heterogeneous cellular niche, exercising spatial and temporal control of the presentation and removal of biomolecular signalling cues in such systems has proved difficult. Here, we demonstrate a synthetic strategy that exploits two bioorthogonal photochemistries to achieve reversible immobilization of bioactive full-length proteins with good spatial and temporal control within synthetic, cell-laden biomimetic scaffolds. A photodeprotection-oxime-ligation sequence permits user-defined quantities of proteins to be anchored within distinct subvolumes of a three-dimensional matrix, and an ortho-nitrobenzyl ester photoscission reaction facilitates subsequent protein removal. By using this approach to pattern the presentation of the extracellular matrix protein vitronectin, we accomplished reversible differentiation of human mesenchymal stem cells to osteoblasts in a spatially defined manner. Our protein-patterning approach should provide further avenues to probe and direct changes in cell physiology in response to dynamic biochemical signalling.
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Gajendran, Varun K; Szabo, Robert M; Myo, George K; Curtiss, Shane B
2009-12-01
Open or unstable metacarpal fractures frequently require open reduction and internal fixation. Locking plate technology has improved fixation of unstable fractures in certain settings. In this study, we hypothesized that there would be a difference in strength of fixation using double-row locking plates compared with single- and double-row non-locking plates in comminuted metacarpal fractures. We tested our hypothesis in a gap metacarpal fracture model simulating comminution using fourth-generation, biomechanical testing-grade composite sawbones. The metacarpals were divided into 6 groups of 15 bones each. Groups 1 and 4 were plated with a standard 6-hole, 2.3-mm plate in AO fashion. Groups 2 and 5 were plated with a 6-hole double-row 3-dimensional non-locking plate with bicortical screws aimed for convergence. Groups 3 and 6 were plated with a 6-hole double-row 3-dimensional locking plate with unicortical screws. The plated metacarpals were then tested to failure against cantilever apex dorsal bending (groups 1-3) and torsion (groups 4-6). The loads to failure in groups 1 to 3 were 198 +/- 18, 223 +/- 29, and 203 +/- 19 N, respectively. The torques to failure in groups 4 to 6 were 2,033 +/- 155, 3,190 +/- 235, and 3,161 +/- 268 N mm, respectively. Group 2 had the highest load to failure, whereas groups 5 and 6 shared the highest torques to failure (p < .05). Locking and non-locking double-row plates had equivalent bending and torsional stiffness, significantly higher than observed for the single-row non-locking plate. No other statistical differences were noted between groups. When subjected to the physiologically relevant forces of apex dorsal bending and torsion in a comminuted metacarpal fracture model, double-row 3-dimensional non-locking plates provided superior stability in bending and equivalent stability in torsion compared with double-row 3-dimensional locking plates, whereas single-row non-locking plates provided the least stability.
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Lucy, J. A.; Lichti, F. Ulrike
1969-01-01
1. The reactions of retinol and retinoic acid with iodine were investigated since knowledge of the chemical reactions of vitamin A with acceptors of electrons may shed light on its biochemical mode of action. 2. Colloidal retinol, but not retinoic acid, reacts with iodine to yield a blue–green complex that rapidly decomposes, giving iodide and an unknown species with λmax. at 870mμ. 3. In addition, both retinol and retinoic acid reduce iodine to iodide by a reaction that does not involve an intermediate coloured complex; this reaction appears to yield unstable carbonium ion derivatives of the vitamin. 4. The presence of water greatly facilitates the production of iodide from vitamin A and iodine. 5. Possible chemical pathways involved in these reactions are discussed. 6. It is suggested that the chemical properties of retinol and retinoic acid that underlie their biochemical behaviour might be apparent only when the molecules are at a lipid–water interface, and that vitamin A might be expected to react with a number of different electron acceptors in vivo. PMID:5801297
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Biomimetic strategies for the glioblastoma microenvironment
NASA Astrophysics Data System (ADS)
Cha, Junghwa; Kim, Pilnam
2017-12-01
Glioblastoma multiforme (GBM) is a devastating type of tumor with high mortality, caused by extensive infiltration into adjacent tissue and rapid recurrence. Most therapies for GBM have focused on the cytotoxicity, and have not targeted GBM spread. However, there have been numerous attempts to improve therapy by addressing GBM invasion, through understanding and mimicking its behavior using three-dimensional (3D) experimental models. Compared with two-dimensional models and in vivo animal models, 3D GBM models can capture the invasive motility of glioma cells within a 3D environment comprising many cellular and non-cellular components. Based on tissue engineering techniques, GBM invasion has been investigated within a biologically relevant environment, from biophysical and biochemical perspectives, to clarify the pro-invasive factors of GBM. This review discusses the recent progress in techniques for modeling the microenvironments of GBM tissue and suggests future directions with respect to recreating the GBM microenvironment and preclinical applications.
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NASA Astrophysics Data System (ADS)
Böhme, Martina; Hermanns, Reginald L.; Oppikofer, Thierry; Penna, Ivanna
2016-04-01
Unstable rock slopes that can cause large failures of the rock-avalanche type have been mapped in Norway for almost two decades. Four sites have earlier been characterized as high-risk objects based on expertise of few researchers. This resulted in installing continuous monitoring systems and set-up of an early-warning system for those four sites. Other unstable rock slopes have not been ranked related to their hazard or risk. There are ca. 300 other sites known of which 70 sites were installed for periodic deformation measurements using multiple techniques (Global Navigation Satellite Systems, extensometers, measurement bolts, and others). In 2012 a systematic hazard and risk classification system for unstable rock slopes was established in Norway and the mapping approach adapted to that in 2013. Now, the first 22 sites were classified for hazard, consequences and risk using this classification system. The selection of the first group of sites to be classified was based on an assumed high hazard or risk and importance given to the sites by Norwegian media and the public. Nine of the classified 22 unstable rock slopes are large sites that deform inhomogeneously or are strongly broken up in individual blocks. This suggests that different failure scenarios are possible that need to be analyzed individually. A total of 35 failure scenarios for those nine unstable rock slopes were considered. The hazard analyses were based on 9 geological parameters defined in the classification system. The classification system will be presented based on the Gamanjunni unstable rock slope. This slope has a well developed back scarp that exposes 150 m preceding displacement. The lateral limits of the unstable slope are clearly visible in the morphology and InSAR displacement data. There have been no single structures observed that allow sliding kinematically. The lower extend of the displacing rock mass is clearly defined in InSAR data and by a zone of higher rock fall activity. Yearly average displacement rates of up to 6 cm are measured with differential GNSS and InSAR. Cosmogenic nuclide dating suggests an acceleration of the present displacement compared to the average displacement since the initiation of the gravitational movement approximately 7000 years ago. Furthermore, there exists a pre-historic rock avalanche 3 km north along the same slope. These characteristics result in a very high hazard for the Gamanjunni unstable rock slope. The consequence analyses focus on the possibility of life loss only. For this the number of persons in the area that can be affected by either the rock slope failure itself and/or its secondary consequence of a displacement wave in case that a rock slope failure would hit a water body is estimated. For Gamanjunni the direct consequences are approximately 40 casualties, representing medium consequences. A total of 48 scenarios were finally analyzed for hazard, consequences and risk. The results are plotted in a risk matrix with 5 hazard and 5 consequence classes, leading to 4 risk classes. One unstable rock slope was classified as very high hazard, 9 scenarios as high hazard, 25 as medium hazard and 13 as low hazard, while none were classified as very low hazard. The consequence analyses for those scenarios resulted in 5 scenarios with very high consequences (>1000 potential casualties), 13 scenarios with high consequences (100-1000 casualties), 9 scenarios with medium consequences (10-100 casualties), 6 scenarios with low consequences (1-10 casualties) and 15 scenarios with very low consequences (0-1 casualties). This resulted in a high risk for 6 scenarios, medium to high risk for 16 scenarios, medium risk for 7 scenarios and low risk for 19 scenarios. These results allow determining which unstable rock slopes do not require further follow-up and on which further investigations and/or mitigation measures should be considered.
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NASA Astrophysics Data System (ADS)
Wedin, Håkan; Cherubini, Stefania
2016-12-01
The asymptotic suction boundary layer (ASBL) is used for studying two permeability models, namely the Darcy and the Forchheimer model, the latter being more physically correct according to the literature. The term that defines the two apart is a function of the non-Darcian wall permeability {\\hat{K}}2 and of the wall suction {\\hat{V}}0, whereas the Darcian wall permeability {\\hat{K}}1 is common to the two models. The underlying interest of the study lies in the field of transition to turbulence where focus is put on two-dimensional nonlinear traveling waves (TWs) and their three-dimensional linear stability. Following a previous study by Wedin et al (2015 Phys. Rev. E 92 013022), where only the Darcy model was considered, the present work aims at comparing the two models, assessing where in the parameter space they cease to produce the same results. For low values of {\\hat{K}}1 both models produce almost identical TW solutions. However, when both increasing the suction {\\hat{V}}0 to sufficiently high amplitudes (i.e. lowering the Reynolds number Re, based on the displacement thickness) and using large values of the wall porosity, differences are observed. In terms of the non-dimensional Darcian wall permeability parameter, a, strong differences in the overall shape of the bifurcation curves are observed for a≳ 0.70, with the emergence of a new family of solutions at Re lower than 100. For these large values of a, a Forchheimer number {{Fo}}\\max ≳ 0.5 is found, where Fo expresses the ratio between the kinetic and viscous forces acting on the porous wall. Moreover, the minimum Reynolds number, {{Re}}g, for which the Navier-Stokes equations allow for nonlinear solutions, decreases for increasing values of a. Fixing the streamwise wavenumber to α = 0.154, as used in the study by Wedin et al referenced above, we find that {{Re}}g is lowered from Re ≈ 3000 for zero permeability, to below 50 for a = 0.80 for both permeability models. Finally, the stability of the TW solutions is assessed using a three-dimensional linearized direct numerical simulation (DNS). Low-frequency unstable modes are found for both permeability models; however, the Darcy model is found to overpredict the growth rate, and underpredict the streamwise extension of the most unstable mode. These results indicate that a careful choice of the underlying permeability model is crucial for accurately studying the transition to turbulence of boundary-layer flows over porous walls.
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Dey, Snigdhadip; Joshi, Amitabh
2013-01-01
Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546
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Evolution of a localized Langmuir packet in the solar wind and on auroral field lines
NASA Technical Reports Server (NTRS)
Roth, I.; Muschietti, L.; Brown, E. F.; Gray, P. C.
1994-01-01
Langmuir emissions in space are reported to be clumpy and intermittent. The high-frequency wave power appears concentrated in spatial packets, whether amidst the solar wind or on auroral field lines. Due to the plasma motion relative to the spacecraft, determining the source for the wave free energy in the three-dimensional electron distribution function has always been difficult, since the unstable features pass by the detector in presumably too short time to be measured. The range of unstable phase velocities and growth rates have generally been estimated rather than determined by unequivocal measurements. The analysis of wave-particle interactions in a space environment has taken recently a new turn with the development of wave correlators on board rockets and satellites. Such instruments seek to identify correlations between the phase of the wave-field and the fluxes of energetic particles. The data interpretation is complex, however, it must be backed by a detailed theoretical understanding of the wave-particle interaction, including the phase relation for inhomogeneous packets. To this end Langmuir packets interacting with fast electrons can be studied in the appropriate regime by means of particle-in-cell simulations, provided that one succeeds in reducing the level of the fluctuations, enhancing the signal-to-noise ratio, and incorporating the appropriate boundary conditions. The first results of such simulations are presented here as a test and expansion of previous analysis.
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Instability of Non-uniform Toroidal Magnetic Fields in Accretion Disks
NASA Astrophysics Data System (ADS)
Hirabayashi, Kota; Hoshino, Masahiro
2016-05-01
We present a new type of instability that is expected to drive magnetohydrodynamic (MHD) turbulence from a purely toroidal magnetic field in an accretion disk. It is already known that in a differentially rotating system, the uniform toroidal magnetic field is unstable due to magnetorotational instability (MRI) under a non-axisymmetric and vertical perturbation, while it is stable under a purely vertical perturbation. Contrary to the previous study, this paper proposes an unstable mode completely confined to the equatorial plane, driven by the expansive nature of the magnetic pressure gradient force under a non-uniform toroidal field. The basic nature of this growing eigenmode, which we name “magneto-gradient driven instability,” is studied using linear analysis, and the corresponding nonlinear evolution is then investigated using two-dimensional ideal MHD simulations. Although a single localized magnetic field channel alone cannot provide sufficient Maxwell stress to contribute significantly to the angular momentum transport, we find that the mode coupling between neighboring toroidal fields under multiple localized magnetic field channels drastically generates a highly turbulent state and leads to the enhanced transport of angular momentum, which is comparable to the efficiency seen in previous studies on MRIs. This horizontally confined mode may play an important role in the saturation of an MRI through complementray growth with the toroidal MRIs and coupling with magnetic reconnection.
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INSTABILITY OF NON-UNIFORM TOROIDAL MAGNETIC FIELDS IN ACCRETION DISKS
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hirabayashi, Kota; Hoshino, Masahiro, E-mail: hirabayashi-k@eps.s.u-tokyo.ac.jp
We present a new type of instability that is expected to drive magnetohydrodynamic (MHD) turbulence from a purely toroidal magnetic field in an accretion disk. It is already known that in a differentially rotating system, the uniform toroidal magnetic field is unstable due to magnetorotational instability (MRI) under a non-axisymmetric and vertical perturbation, while it is stable under a purely vertical perturbation. Contrary to the previous study, this paper proposes an unstable mode completely confined to the equatorial plane, driven by the expansive nature of the magnetic pressure gradient force under a non-uniform toroidal field. The basic nature of thismore » growing eigenmode, which we name “magneto-gradient driven instability,” is studied using linear analysis, and the corresponding nonlinear evolution is then investigated using two-dimensional ideal MHD simulations. Although a single localized magnetic field channel alone cannot provide sufficient Maxwell stress to contribute significantly to the angular momentum transport, we find that the mode coupling between neighboring toroidal fields under multiple localized magnetic field channels drastically generates a highly turbulent state and leads to the enhanced transport of angular momentum, which is comparable to the efficiency seen in previous studies on MRIs. This horizontally confined mode may play an important role in the saturation of an MRI through complementray growth with the toroidal MRIs and coupling with magnetic reconnection.« less
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Characteristics of atmospheric Ar/NH3 DBD and its comparison with He/N2 DBD
NASA Astrophysics Data System (ADS)
Yao, Congwei; Chen, Sile; Wang, Shuai; Chang, Zhengshi; Sun, Anbang; Mu, Haibao; Zhang, Guan-Jun
2018-06-01
The discharge mode and photoelectric characteristics of Ar/NH3 DBD (dielectric barrier discharge) are studied to discuss the stability of the discharge under the influence of Penning ionization and attachment reaction. There are three discharge modes, including stable uniform glow discharge, unstable glow discharge and unstable columnar discharge. Discharge instability, including nonuniform discharge and discharge channel split, occurs under low (<0.10%) or high (>0.35%) volume fractions of NH3, which are understood to be caused by an insufficiently strong Penning effect or a strong attachment reaction, respectively. The attachment reaction of NH3 can also lead to a weaker emission intensity for Ar/NH3 DBD, in particular regarding the emission of OH(A2Σ+). Ar/NH3 and He/N2 DBDs are also compared. In He/N2 DBD, the emission intensity of OH(A2Σ+) changes less with increasing N2 volume fraction, which may be attributed to the lack of attachment reaction. Compared with Ar/NH3 DBD, the single discharge channel in He/N2 DBD is narrower, but the discharge area is wider, which should be induced by the higher Townsend ionization coefficient nonlinearity of He/N2 and the absence of attachment reaction in He/N2, respectively. In the end, a one-dimensional fluid model of Ar/NH3 DBD is built to verify the explanation of experimental results.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Múnera, Héctor A., E-mail: hmunera@hotmail.com; Retired professor, Department of Physics, Universidad Nacional de Colombia, Bogotá, Colombia, South America
2016-07-07
It is postulated that there exists a fundamental energy-like fluid, which occupies the flat three-dimensional Euclidean space that contains our universe, and obeys the two basic laws of classical physics: conservation of linear momentum, and conservation of total energy; the fluid is described by the classical wave equation (CWE), which was Schrödinger’s first candidate to develop his quantum theory. Novel solutions for the CWE discovered twenty years ago are nonharmonic, inherently quantized, and universal in the sense of scale invariance, thus leading to quantization at all scales of the universe, from galactic clusters to the sub-quark world, and yielding amore » unified Lorentz-invariant quantum theory ab initio. Quingal solutions are isomorphic under both neo-Galilean and Lorentz transformations, and exhibit nother remarkable property: intrinsic unstability for large values of ℓ (a quantum number), thus limiting the size of each system at a given scale. Unstability and scale-invariance together lead to nested structures observed in our solar system; unstability may explain the small number of rows in the chemical periodic table, and nuclear unstability of nuclides beyond lead and bismuth. Quingal functions lend mathematical basis for Boscovich’s unified force (which is compatible with many pieces of evidence collected over the past century), and also yield a simple geometrical solution for the classical three-body problem, which is a useful model for electronic orbits in simple diatomic molecules. A testable prediction for the helicoidal-type force is suggested.« less
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NASA Astrophysics Data System (ADS)
Milledge, David; Bellugi, Dino; McKean, Jim; Dietrich, William E.
2013-04-01
Current practice in regional-scale shallow landslide hazard assessment is to adopt a one-dimensional slope stability representation. Such a representation cannot produce discrete landslides and thus cannot make predictions on landslide size. Furthermore, one-dimensional approaches cannot include lateral effects, which are known to be important in defining instability. Here we derive an alternative model that accounts for lateral resistance by representing the forces acting on each margin of an unstable block of soil. We model boundary frictional resistances using 'at rest' earth pressure on the lateral sides, and 'active' and 'passive' pressure, using the log-spiral method, on the upslope and downslope margins. We represent root reinforcement on each margin assuming that root cohesion declines exponentially with soil depth. We test our model's ability to predict failure of an observed landslide where the relevant parameters are relatively well constrained and find that our model predicts failure at the observed location and predicts that larger or smaller failures conformal to the observed shape are indeed more stable. We use a sensitivity analysis of the model to show that lateral reinforcement sets a minimum landslide size, and that the additional strength at the downslope boundary results in optimal shapes that are longer in the downslope direction. However, reinforcement effects alone cannot fully explain the size or shape distributions of observed landslides, highlighting the importance of the spatial pattern of key parameters (e.g. pore water pressure and soil depth) at the watershed scale. The application of the model at this scale requires an efficient method to find unstable shapes among an exponential number of candidates. In this context, the model allows a more extensive examination of the controls on landslide size, shape and location.
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Application of parameter estimation to highly unstable aircraft
NASA Technical Reports Server (NTRS)
Maine, R. E.; Murray, J. E.
1986-01-01
This paper discusses the application of parameter estimation to highly unstable aircraft. It includes a discussion of the problems in applying the output error method to such aircraft and demonstrates that the filter error method eliminates these problems. The paper shows that the maximum likelihood estimator with no process noise does not reduce to the output error method when the system is unstable. It also proposes and demonstrates an ad hoc method that is similar in form to the filter error method, but applicable to nonlinear problems. Flight data from the X-29 forward-swept-wing demonstrator is used to illustrate the problems and methods discussed.
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Application of parameter estimation to highly unstable aircraft
NASA Technical Reports Server (NTRS)
Maine, R. E.; Murray, J. E.
1986-01-01
The application of parameter estimation to highly unstable aircraft is discussed. Included are a discussion of the problems in applying the output error method to such aircraft and demonstrates that the filter error method eliminates these problems. The paper shows that the maximum likelihood estimator with no process noise does not reduce to the output error method when the system is unstable. It also proposes and demonstrates an ad hoc method that is similar in form to the filter error method, but applicable to nonlinear problems. Flight data from the X-29 forward-swept-wing demonstrator is used to illustrate the problems and methods discussed.
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NASA Astrophysics Data System (ADS)
Guzzo, Massimiliano; Lega, Elena
2018-06-01
The circular restricted three-body problem has five relative equilibria L1 ,L2, . . . ,L5. The invariant stable-unstable manifolds of the center manifolds originating at the partially hyperbolic equilibria L1 ,L2 have been identified as the separatrices for the motions which transit between the regions of the phase-space which are internal or external with respect to the two massive bodies. While the stable and unstable manifolds of the planar problem have been extensively studied both theoretically and numerically, the spatial case has not been as deeply investigated. This paper is devoted to the global computation of these manifolds in the spatial case with a suitable finite time chaos indicator. The definition of the chaos indicator is not trivial, since the mandatory use of the regularizing Kustaanheimo-Stiefel variables may introduce discontinuities in the finite time chaos indicators. From the study of such discontinuities, we define geometric chaos indicators which are globally defined and smooth, and whose ridges sharply approximate the stable and unstable manifolds of the center manifolds of L1 ,L2. We illustrate the method for the Sun-Jupiter mass ratio, and represent the topology of the asymptotic manifolds using sections and three-dimensional representations.
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Dynamic topology and flux rope evolution during non-linear tearing of 3D null point current sheets
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wyper, P. F., E-mail: peterw@maths.dundee.ac.uk; Pontin, D. I., E-mail: dpontin@maths.dundee.ac.uk
2014-10-15
In this work, the dynamic magnetic field within a tearing-unstable three-dimensional current sheet about a magnetic null point is described in detail. We focus on the evolution of the magnetic null points and flux ropes that are formed during the tearing process. Generally, we find that both magnetic structures are created prolifically within the layer and are non-trivially related. We examine how nulls are created and annihilated during bifurcation processes, and describe how they evolve within the current layer. The type of null bifurcation first observed is associated with the formation of pairs of flux ropes within the current layer.more » We also find that new nulls form within these flux ropes, both following internal reconnection and as adjacent flux ropes interact. The flux ropes exhibit a complex evolution, driven by a combination of ideal kinking and their interaction with the outflow jets from the main layer. The finite size of the unstable layer also allows us to consider the wider effects of flux rope generation. We find that the unstable current layer acts as a source of torsional magnetohydrodynamic waves and dynamic braiding of magnetic fields. The implications of these results to several areas of heliophysics are discussed.« less
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Quasi-static MHD processes in earth's magnetosphere
NASA Technical Reports Server (NTRS)
Voigt, Gerd-Hannes
1988-01-01
An attempt is made to use the MHD equilibrium theory to describe the global magnetic field configuration of earth's magnetosphere and its time evolution under the influence of magnetospheric convection. To circumvent the difficulties inherent in today's MHD codes, use is made of a restriction to slowly time-dependent convection processes with convective velocities well below the typical Alfven speed. This restriction leads to a quasi-static MHD theory. The two-dimensional theory is outlined, and it is shown how sequences of two-dimensional equilibria evolve into a steady state configuration that is likely to become tearing mode unstable. It is then concluded that magnetospheric substorms occur periodically in earth's magnetosphere, thus being an integral part of the entire convection cycle.
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Plasma crystal dynamics measured with a three-dimensional plenoptic camera
NASA Astrophysics Data System (ADS)
Jambor, M.; Nosenko, V.; Zhdanov, S. K.; Thomas, H. M.
2016-03-01
Three-dimensional (3D) imaging of a single-layer plasma crystal was performed using a commercial plenoptic camera. To enhance the out-of-plane oscillations of particles in the crystal, the mode-coupling instability (MCI) was triggered in it by lowering the discharge power below a threshold. 3D coordinates of all particles in the crystal were extracted from the recorded videos. All three fundamental wave modes of the plasma crystal were calculated from these data. In the out-of-plane spectrum, only the MCI-induced hot spots (corresponding to the unstable hybrid mode) were resolved. The results are in agreement with theory and show that plenoptic cameras can be used to measure the 3D dynamics of plasma crystals.
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Plasma crystal dynamics measured with a three-dimensional plenoptic camera.
Jambor, M; Nosenko, V; Zhdanov, S K; Thomas, H M
2016-03-01
Three-dimensional (3D) imaging of a single-layer plasma crystal was performed using a commercial plenoptic camera. To enhance the out-of-plane oscillations of particles in the crystal, the mode-coupling instability (MCI) was triggered in it by lowering the discharge power below a threshold. 3D coordinates of all particles in the crystal were extracted from the recorded videos. All three fundamental wave modes of the plasma crystal were calculated from these data. In the out-of-plane spectrum, only the MCI-induced hot spots (corresponding to the unstable hybrid mode) were resolved. The results are in agreement with theory and show that plenoptic cameras can be used to measure the 3D dynamics of plasma crystals.
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Three-dimensional analysis of tokamaks and stellarators
Garabedian, Paul R.
2008-01-01
The NSTAB equilibrium and stability code and the TRAN Monte Carlo transport code furnish a simple but effective numerical simulation of essential features of present tokamak and stellarator experiments. When the mesh size is comparable to the island width, an accurate radial difference scheme in conservation form captures magnetic islands successfully despite a nested surface hypothesis imposed by the mathematics. Three-dimensional asymmetries in bifurcated numerical solutions of the axially symmetric tokamak problem are relevant to the observation of unstable neoclassical tearing modes and edge localized modes in experiments. Islands in compact stellarators with quasiaxial symmetry are easier to control, so these configurations will become good candidates for magnetic fusion if difficulties with safety and stability are encountered in the International Thermonuclear Experimental Reactor (ITER) project. PMID:18768807
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Study of chaos in chaotic satellite systems
NASA Astrophysics Data System (ADS)
Khan, Ayub; Kumar, Sanjay
2018-01-01
In this paper, we study the qualitative behaviour of satellite systems using bifurcation diagrams, Poincaré section, Lyapunov exponents, dissipation, equilibrium points, Kaplan-Yorke dimension etc. Bifurcation diagrams with respect to the known parameters of satellite systems are analysed. Poincaré sections with different sowing axes of the satellite are drawn. Eigenvalues of Jacobian matrices for the satellite system at different equilibrium points are calculated to justify the unstable regions. Lyapunov exponents are estimated. From these studies, chaos in satellite system has been established. Solution of equations of motion of the satellite system are drawn in the form of three-dimensional, two-dimensional and time series phase portraits. Phase portraits and time series display the chaotic nature of the considered system.
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Barelko, V. V.; Pomogailo, A. D.; Dzhardimalieva, G. I.; Evstratova, S. I.; Rozenberg, A. S.; Uflyand, I. E.
1999-06-01
The phenomenon of autowave (frontal) solid phase polymerization of metal-containing monomers based on metal-acrylamide complexes is considered. The comparison of the features of autowave processes realized in both the single-component matrices of the monomer and the matrices filled by the fiberglass materials is performed. The unstable regimes of the polymerization wave as well as the conditions for the stabilization of the flat front in the filled matrices are described. The peculiarities of the frontal regimes in the three- and two-dimensional media are studied. Some possibilities for using of autowave polymerization in the fabrication of the polymer-fiberglass composites and composition prepregs are discussed. (c) 1999 American Institute of Physics.
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Experimental investigation of two-phase heat transfer in a porous matrix.
NASA Technical Reports Server (NTRS)
Von Reth, R.; Frost, W.
1972-01-01
One-dimensional two-phase flow transpiration cooling through porous metal is studied experimentally. The experimental data is compared with a previous one-dimensional analysis. Good agreement with calculated temperature distribution is obtained as long as the basic assumptions of the analytical model are satisfied. Deviations from the basic assumptions are caused by nonhomogeneous and oscillating flow conditions. Preliminary derivation of nondimensional parameters which characterize the stable and unstable flow conditions is given. Superheated liquid droplets observed sputtering from the heated surface indicated incomplete evaporation at heat fluxes well in access of the latent energy transport. A parameter is developed to account for the nonequilibrium thermodynamic effects. Measured and calculated pressure drops show contradicting trends which are attributed to capillary forces.
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Biparametric equilibria bifurcations of the Pierce diode: A one-dimensional plasma-filled device
DOE Office of Scientific and Technical Information (OSTI.GOV)
Terra, Maisa O.
2011-03-15
The equilibria bifurcations of the biparametric version of the classical Pierce diode, a one-dimensional plasma-filled device, are analyzed in detail. Our investigation reveals that this spatiotemporal model is not structurally stable in relation to a second control parameter, the ratio of the plasma ion density to the injected electron beam density. For the first time, we relate the existence of one-fluid chaotic regions with specific biparametric equilibria bifurcations, identifying the restricted regions in the parametric plane where they occur. We show that the system presents several biparametric scenarios involving codimension-two transcritical bifurcations. Finally, we provide the spatial profile of themore » stable and unstable one-fluid equilibria in order to describe their metamorphoses.« less
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NASA Astrophysics Data System (ADS)
Citro, V.; Luchini, P.; Giannetti, F.; Auteri, F.
2017-09-01
The study of the stability of a dynamical system described by a set of partial differential equations (PDEs) requires the computation of unstable states as the control parameter exceeds its critical threshold. Unfortunately, the discretization of the governing equations, especially for fluid dynamic applications, often leads to very large discrete systems. As a consequence, matrix based methods, like for example the Newton-Raphson algorithm coupled with a direct inversion of the Jacobian matrix, lead to computational costs too large in terms of both memory and execution time. We present a novel iterative algorithm, inspired by Krylov-subspace methods, which is able to compute unstable steady states and/or accelerate the convergence to stable configurations. Our new algorithm is based on the minimization of the residual norm at each iteration step with a projection basis updated at each iteration rather than at periodic restarts like in the classical GMRES method. The algorithm is able to stabilize any dynamical system without increasing the computational time of the original numerical procedure used to solve the governing equations. Moreover, it can be easily inserted into a pre-existing relaxation (integration) procedure with a call to a single black-box subroutine. The procedure is discussed for problems of different sizes, ranging from a small two-dimensional system to a large three-dimensional problem involving the Navier-Stokes equations. We show that the proposed algorithm is able to improve the convergence of existing iterative schemes. In particular, the procedure is applied to the subcritical flow inside a lid-driven cavity. We also discuss the application of Boostconv to compute the unstable steady flow past a fixed circular cylinder (2D) and boundary-layer flow over a hemispherical roughness element (3D) for supercritical values of the Reynolds number. We show that Boostconv can be used effectively with any spatial discretization, be it a finite-difference, finite-volume, finite-element or spectral method.
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Bakshi, Neil K; Jameel, Omar F; Merrill, Zachary F; Debski, Richard E; Sekiya, Jon K
2016-08-01
This study compared the amount of glenohumeral abduction during arm abduction in the affected and unaffected shoulders of 3 groups of patients with shoulder instability: failed surgical stabilization, successful surgical stabilization, and unstable shoulder with no prior surgical intervention. All patients underwent bilateral shoulder computed tomography scans in 3 positions: 0° of abduction and 0° of external rotation (0-0 position), 30° of abduction and 30° of external rotation (30-30 position), and arms maximally abducted (overhead position). Three-dimensional computed tomography reconstruction was performed for both shoulders in all 3 positions. A specialized coordinate system marked specific points and directions on the humerus and glenoid of each model. These coordinates were used to calculate the glenohumeral abduction for the normal and affected sides in the 0-0, 30-30, and overhead positions. Thirty-nine patients with shoulder instability were included, of whom 14 had failed surgical repairs, 10 had successful surgical repairs, and 15 had unstable shoulders with no prior surgical intervention. In the overhead position, patients with failed surgical intervention had significantly less glenohumeral abduction in the failed shoulder (95.6° ± 12.7°) compared with the normal shoulder (101.5° ± 12.4°, P = .02). Patients with successfully stabilized shoulders had significantly less glenohumeral abduction in the successfully stabilized shoulder (93.6° ± 10.8°) compared with the normal shoulder (102.1° ± 12.5°, P = .03). Unstable shoulders with no prior surgical intervention (102.1° ± 10.3°) did not differ when compared with the normal shoulders (101.9° ± 10.9°, P = .95). Surgical intervention, regardless of its success, limits the amount of abduction at the glenohumeral joint. Level III, retrospective comparative study. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.
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Transient growth analysis of the flow past a circular cylinder
NASA Astrophysics Data System (ADS)
Abdessemed, N.; Sharma, A. S.; Sherwin, S. J.; Theofilis, V.
2009-04-01
We apply direct transient growth analysis in complex geometries to investigate its role in the primary and secondary bifurcation/transition process of the flow past a circular cylinder. The methodology is based on the singular value decomposition of the Navier-Stokes evolution operator linearized about a two-dimensional steady or periodic state which leads to the optimal growth modes. Linearly stable and unstable steady flow at Re=45 and 50 is considered first, where the analysis demonstrates that strong two-dimensional transient growth is observed with energy amplifications of order of 103 at U∞τ/D≈30. Transient growth at Re=50 promotes the linear instability which ultimately saturates into the well known von-Kármán street. Subsequently we consider the transient growth upon the time-periodic base state corresponding to the von-Kármán street at Re=200 and 300. Depending upon the spanwise wavenumber the flow at these Reynolds numbers are linearly unstable due to the so-called mode A and B instabilities. Once again energy amplifications of order of 103 are observed over a time interval of τ /T=2, where T is the time period of the base flow shedding. In all cases the maximum energy of the optimal initial conditions are located within a diameter of the cylinder in contrast to the spatial distribution of the unstable eigenmodes which extend far into the downstream wake. It is therefore reasonable to consider the analysis as presenting an accelerator to the existing modal mechanism. The rapid amplification of the optimal growth modes highlights their importance in the transition process for flow past circular cylinder, particularly when comparing with experimental results where these types of convective instability mechanisms are likely to be activated. The spatial localization, close to the cylinder, of the optimal initial condition may be significant when considering strategies to promote or control shedding.
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Evolution and End Point of the Black String Instability: Large D Solution.
Emparan, Roberto; Suzuki, Ryotaku; Tanabe, Kentaro
2015-08-28
We derive a simple set of nonlinear, (1+1)-dimensional partial differential equations that describe the dynamical evolution of black strings and branes to leading order in the expansion in the inverse of the number of dimensions D. These equations are easily solved numerically. Their solution shows that thin enough black strings are unstable to developing inhomogeneities along their length, and at late times they asymptote to stable nonuniform black strings. This proves an earlier conjecture about the end point of the instability of black strings in a large enough number of dimensions. If the initial black string is very thin, the final configuration is highly nonuniform and resembles a periodic array of localized black holes joined by short necks. We also present the equations that describe the nonlinear dynamics of anti-de Sitter black branes at large D.
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Modelling maximum river flow by using Bayesian Markov Chain Monte Carlo
NASA Astrophysics Data System (ADS)
Cheong, R. Y.; Gabda, D.
2017-09-01
Analysis of flood trends is vital since flooding threatens human living in terms of financial, environment and security. The data of annual maximum river flows in Sabah were fitted into generalized extreme value (GEV) distribution. Maximum likelihood estimator (MLE) raised naturally when working with GEV distribution. However, previous researches showed that MLE provide unstable results especially in small sample size. In this study, we used different Bayesian Markov Chain Monte Carlo (MCMC) based on Metropolis-Hastings algorithm to estimate GEV parameters. Bayesian MCMC method is a statistical inference which studies the parameter estimation by using posterior distribution based on Bayes’ theorem. Metropolis-Hastings algorithm is used to overcome the high dimensional state space faced in Monte Carlo method. This approach also considers more uncertainty in parameter estimation which then presents a better prediction on maximum river flow in Sabah.
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Strong quantum scarring by local impurities
Luukko, Perttu J. J.; Drury, Byron; Klales, Anna; Kaplan, Lev; Heller, Eric J.; Räsänen, Esa
2016-01-01
We discover and characterise strong quantum scars, or quantum eigenstates resembling classical periodic orbits, in two-dimensional quantum wells perturbed by local impurities. These scars are not explained by ordinary scar theory, which would require the existence of short, moderately unstable periodic orbits in the perturbed system. Instead, they are supported by classical resonances in the unperturbed system and the resulting quantum near-degeneracy. Even in the case of a large number of randomly scattered impurities, the scars prefer distinct orientations that extremise the overlap with the impurities. We demonstrate that these preferred orientations can be used for highly efficient transport of quantum wave packets across the perturbed potential landscape. Assisted by the scars, wave-packet recurrences are significantly stronger than in the unperturbed system. Together with the controllability of the preferred orientations, this property may be very useful for quantum transport applications. PMID:27892510
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Strong quantum scarring by local impurities
NASA Astrophysics Data System (ADS)
Luukko, Perttu J. J.; Drury, Byron; Klales, Anna; Kaplan, Lev; Heller, Eric J.; Räsänen, Esa
2016-11-01
We discover and characterise strong quantum scars, or quantum eigenstates resembling classical periodic orbits, in two-dimensional quantum wells perturbed by local impurities. These scars are not explained by ordinary scar theory, which would require the existence of short, moderately unstable periodic orbits in the perturbed system. Instead, they are supported by classical resonances in the unperturbed system and the resulting quantum near-degeneracy. Even in the case of a large number of randomly scattered impurities, the scars prefer distinct orientations that extremise the overlap with the impurities. We demonstrate that these preferred orientations can be used for highly efficient transport of quantum wave packets across the perturbed potential landscape. Assisted by the scars, wave-packet recurrences are significantly stronger than in the unperturbed system. Together with the controllability of the preferred orientations, this property may be very useful for quantum transport applications.
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Strong quantum scarring by local impurities.
Luukko, Perttu J J; Drury, Byron; Klales, Anna; Kaplan, Lev; Heller, Eric J; Räsänen, Esa
2016-11-28
We discover and characterise strong quantum scars, or quantum eigenstates resembling classical periodic orbits, in two-dimensional quantum wells perturbed by local impurities. These scars are not explained by ordinary scar theory, which would require the existence of short, moderately unstable periodic orbits in the perturbed system. Instead, they are supported by classical resonances in the unperturbed system and the resulting quantum near-degeneracy. Even in the case of a large number of randomly scattered impurities, the scars prefer distinct orientations that extremise the overlap with the impurities. We demonstrate that these preferred orientations can be used for highly efficient transport of quantum wave packets across the perturbed potential landscape. Assisted by the scars, wave-packet recurrences are significantly stronger than in the unperturbed system. Together with the controllability of the preferred orientations, this property may be very useful for quantum transport applications.
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Bio-inspired routes for synthesizing efficient nanoscale platinum electrocatalysts
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cha, Jennifer N.; Wang, Joseph
2014-08-31
The overall objective of the proposed research is to use fundamental advances in bionanotechnology to design powerful platinum nanocrystal electrocatalysts for fuel cell applications. The new economically-viable, environmentally-friendly, bottom-up biochemical synthetic strategy will produce platinum nanocrystals with tailored size, shape and crystal orientation, hence leading to a maximum electrochemical reactivity. There are five specific aims to the proposed bio-inspired strategy for synthesizing efficient electrocatalytic platinum nanocrystals: (1) isolate peptides that both selectively bind particular crystal faces of platinum and promote the nucleation and growth of particular nanocrystal morphologies, (2) pattern nanoscale 2-dimensional arrays of platinum nucleating peptides from DNA scaffolds,more » (3) investigate the combined use of substrate patterned peptides and soluble peptides on nanocrystal morphology and growth (4) synthesize platinum crystals on planar and large-area carbon electrode supports, and (5) perform detailed characterization of the electrocatalytic behavior as a function of catalyst size, shape and morphology. Project Description and Impact: This bio-inspired collaborative research effort will address key challenges in designing powerful electrocatalysts for fuel cell applications by employing nucleic acid scaffolds in combination with peptides to perform specific, environmentally-friendly, simultaneous bottom-up biochemical synthesis and patterned assembly of highly uniform and efficient platinum nanocrystal catalysts. Bulk synthesis of nanoparticles usually produces a range of sizes, accessible catalytic sites, crystal morphologies, and orientations, all of which lead to inconsistent catalytic activities. In contrast, biological systems routinely demonstrate exquisite control over inorganic syntheses at neutral pH and ambient temperature and pressures. Because the orientation and arrangement of the templating biomolecules can be precisely controlled, the nanocrystals boast a defined shape, morphology, orientation and size and are synthesized at benign reaction conditions. Adapting the methods of biomineralization towards the synthesis of platinum nanocrystals will allow effective control at a molecular level of the synthesis of highly active metal electrocatalysts, with readily tailored properties, through tuning of the biochemical inputs. The proposed research will incorporate many facets of biomineralization by: (1) isolating peptides that selectively bind particular crystal faces of platinum (2) isolating peptides that promote the nucleation and growth of particular nanocrystal morphologies (3) using two-dimensional DNA scaffolds to control the spatial orientation and density of the platinum nucleating peptides, and (4) combining bio-templating and soluble peptides to control crystal nucleation, orientation, and morphology. The resulting platinum nanocrystals will be evaluated for their electrocatalytic behavior (on common carbon supports) to determine their optimal size, morphology and crystal structure. We expect that such rational biochemical design will lead to highly uniform and efficient platinum nanocrystal catalysts for fuel cell applications.« less
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Koopman, Heather N; Zahorodny, Zoey P
2008-01-01
The vertebrate head has undergone enormous modification from the features borne by early ancestors. The growth of skull bones has been well studied in many species, yet little is known about corresponding soft tissue development. Among mammals, some of the most unusual examples of cranial evolution exist in the toothed whales (odontocetes). Specialized fat bodies in toothed whale heads play important roles in sound transmission and reception. These fat bodies contain unique endogenous lipids, with favourable acoustic properties, arranged in highly organized, three-dimensional patterns. We link variation in developmental rates of acoustic fats with life-history strategy, using bottlenose dolphins and harbour porpoises. Porpoise acoustic fats attain adult configurations earlier (less than 1 year) and at a faster pace than dolphins. The accelerated lipid accumulation in porpoises reflects the earlier need for fully functional echolocation systems. Dolphins enjoy 3–6 years of maternal care; porpoises must achieve total independence by approximately nine months. Further, a stereotypic ‘blueprint’ for the spatial distribution of lipids is established prior to birth, demonstrating the highly conserved nature of the intricate biochemical arrangement in acoustic tissues. This system illustrates an unusual case of soft tissue development being constrained by life history, rather than the more commonly observed mechanistic or phyletic constraints. PMID:18611851
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Linear and nonlinear instability in vertical counter-current laminar gas-liquid flows
NASA Astrophysics Data System (ADS)
Schmidt, Patrick; Ó Náraigh, Lennon; Lucquiaud, Mathieu; Valluri, Prashant
2016-04-01
We consider the genesis and dynamics of interfacial instability in vertical gas-liquid flows, using as a model the two-dimensional channel flow of a thin falling film sheared by counter-current gas. The methodology is linear stability theory (Orr-Sommerfeld analysis) together with direct numerical simulation of the two-phase flow in the case of nonlinear disturbances. We investigate the influence of two main flow parameters on the interfacial dynamics, namely the film thickness and pressure drop applied to drive the gas stream. To make contact with existing studies in the literature, the effect of various density contrasts is also examined. Energy budget analyses based on the Orr-Sommerfeld theory reveal various coexisting unstable modes (interfacial, shear, internal) in the case of high density contrasts, which results in mode coalescence and mode competition, but only one dynamically relevant unstable interfacial mode for low density contrast. A study of absolute and convective instability for low density contrast shows that the system is absolutely unstable for all but two narrow regions of the investigated parameter space. Direct numerical simulations of the same system (low density contrast) show that linear theory holds up remarkably well upon the onset of large-amplitude waves as well as the existence of weakly nonlinear waves. For high density contrasts, corresponding more closely to an air-water-type system, linear stability theory is also successful at determining the most-dominant features in the interfacial wave dynamics at early-to-intermediate times. Nevertheless, the short waves selected by the linear theory undergo secondary instability and the wave train is no longer regular but rather exhibits chaotic motion. The same linear stability theory predicts when the direction of travel of the waves changes — from downwards to upwards. We outline the practical implications of this change in terms of loading and flooding. The change in direction of the wave propagation is represented graphically in terms of a flow map based on the liquid and gas flow rates and the prediction carries over to the nonlinear regime with only a small deviation.
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Linear and nonlinear instability in vertical counter-current laminar gas-liquid flows
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schmidt, Patrick; Lucquiaud, Mathieu; Valluri, Prashant, E-mail: prashant.valluri@ed.ac.uk
We consider the genesis and dynamics of interfacial instability in vertical gas-liquid flows, using as a model the two-dimensional channel flow of a thin falling film sheared by counter-current gas. The methodology is linear stability theory (Orr-Sommerfeld analysis) together with direct numerical simulation of the two-phase flow in the case of nonlinear disturbances. We investigate the influence of two main flow parameters on the interfacial dynamics, namely the film thickness and pressure drop applied to drive the gas stream. To make contact with existing studies in the literature, the effect of various density contrasts is also examined. Energy budget analysesmore » based on the Orr-Sommerfeld theory reveal various coexisting unstable modes (interfacial, shear, internal) in the case of high density contrasts, which results in mode coalescence and mode competition, but only one dynamically relevant unstable interfacial mode for low density contrast. A study of absolute and convective instability for low density contrast shows that the system is absolutely unstable for all but two narrow regions of the investigated parameter space. Direct numerical simulations of the same system (low density contrast) show that linear theory holds up remarkably well upon the onset of large-amplitude waves as well as the existence of weakly nonlinear waves. For high density contrasts, corresponding more closely to an air-water-type system, linear stability theory is also successful at determining the most-dominant features in the interfacial wave dynamics at early-to-intermediate times. Nevertheless, the short waves selected by the linear theory undergo secondary instability and the wave train is no longer regular but rather exhibits chaotic motion. The same linear stability theory predicts when the direction of travel of the waves changes — from downwards to upwards. We outline the practical implications of this change in terms of loading and flooding. The change in direction of the wave propagation is represented graphically in terms of a flow map based on the liquid and gas flow rates and the prediction carries over to the nonlinear regime with only a small deviation.« less
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Linear instability of supersonic plane wakes
NASA Technical Reports Server (NTRS)
Papageorgiou, D. T.
1989-01-01
In this paper we present a theoretical and numerical study of the growth of linear disturbances in the high-Reynolds-number and laminar compressible wake behind a flat plate which is aligned with a uniform stream. No ad hoc assumptions are made as to the nature of the undisturbed flow (in contrast to previous investigations) but instead the theory is developed rationally by use of proper wake-profiles which satisfy the steady equations of motion. The initial growth of near wake perturbation is governed by the compressible Rayleigh equation which is studied analytically for long- and short-waves. These solutions emphasize the asymptotic structures involved and provide a rational basis for a nonlinear development. The evolution of arbitrary wavelength perturbations is addressed numerically and spatial stability solutions are presented that account for the relative importance of the different physical mechanisms present, such as three-dimensionality, increasing Mach numbers enough (subsonic) Mach numbers, there exists a region of absolute instability very close to the trailing-edge with the majority of the wake being convectively unstable. At higher Mach numbers (but still not large-hypersonic) the absolute instability region seems to disappear and the maximum available growth-rates decrease considerably. Three-dimensional perturbations provide the highest spatial growth-rates.
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Kanayama, Mieko; Suzuki, Machiko; Yuma, Yoshikazu
2016-01-01
The present study aimed to identify and characterize potential burnout types and the relationship between burnout and collaboration over time. Latent class growth analysis and the growth mixture model were used to identify and characterize heterogeneous patterns of longitudinal stability and change in burnout, and the relationship between burnout and collaboration. We collected longitudinal data at three time points based on Japanese academic terms. The 396 study participants included academic teachers, yogo teachers, and registered nurses in Japanese special needs schools. The best model included four types of both burnout and collaboration in latent class growth analysis with intercept, slope, and quadratic terms. The four types of burnout were as follows: low stable, moderate unstable, high unstable, and high decreasing. They were identified as involving inverse collaboration function. The results indicated that there could be dynamic burnout types, namely moderate unstable, high unstable, and high decreasing, when focusing on growth trajectories in latent class analyses. The finding that collaboration was dynamic for dynamic burnout types and stable for stable burnout types is of great interest. This was probably related to the inverse relationship between the two constructs. PMID:27366107
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Exploring information transmission in gene networks using stochastic simulation and machine learning
NASA Astrophysics Data System (ADS)
Park, Kyemyung; Prüstel, Thorsten; Lu, Yong; Narayanan, Manikandan; Martins, Andrew; Tsang, John
How gene regulatory networks operate robustly despite environmental fluctuations and biochemical noise is a fundamental question in biology. Mathematically the stochastic dynamics of a gene regulatory network can be modeled using chemical master equation (CME), but nonlinearity and other challenges render analytical solutions of CMEs difficult to attain. While approaches of approximation and stochastic simulation have been devised for simple models, obtaining a more global picture of a system's behaviors in high-dimensional parameter space without simplifying the system substantially remains a major challenge. Here we present a new framework for understanding and predicting the behaviors of gene regulatory networks in the context of information transmission among genes. Our approach uses stochastic simulation of the network followed by machine learning of the mapping between model parameters and network phenotypes such as information transmission behavior. We also devised ways to visualize high-dimensional phase spaces in intuitive and informative manners. We applied our approach to several gene regulatory circuit motifs, including both feedback and feedforward loops, to reveal underexplored aspects of their operational behaviors. This work is supported by the Intramural Program of NIAID/NIH.
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NASA Astrophysics Data System (ADS)
Theresia, Martha; Priadi, Cindy Rianti
2017-03-01
The anaerobic digestion (AD) process from organic waste is often unstable due to the high concentration of Volatile Fatty Acids (VFAs). The purpose of this research was to determine/evaluate the production of methane using biochemical methane potential (BMP) test with two substrate combinations, consisted of organic waste and cow manure as buffer. BMP test conducted for 35 days at a temperature of ± 35°C by measuring the volume and concentration of biogas every week and testing the sample characteristics before and after the test. The result of the sample variation showed there was no significantly difference of methane volume in the 5th week except the variation of organic waste/cow manure: 12/1 to 3/1, but the sample with a ratio of 3/1 yielded the highest methane potential of 0,58 ± 0.015 (n = 3) LCH4/gr Volatile Solid. The addition of cow manure stabilized the condition of all variations during BMP test with VFAs/alkalinity <0.3 although Carbon/Nitogen ratio of each variation is <20.
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Pair aligning improved motility of Quincke rollers.
Lu, Shi Qing; Zhang, Bing Yue; Zhang, Zhi Chao; Shi, Yan; Zhang, Tian Hui
2018-06-06
Density-dependent speed is studied in a two-dimensional active colloid in which the colloidal particles are propelled by an external electric field via a Quincke rotation. Above the critcal electric field, dense dynamic clusters form spotaneously, in which the particles are highly aligned in velocity and move much faster than isolated units. Detailed observations on pair collision reveal that the alignment of velocity is induced by the long-ranged hydrodynamic interactions and the improvement of speed in the clusters arises from pair aligning in which two particles are closely paired and rotate synchronically. In the aligning state, the short-range in-plane dipole-dipole attraction enhances the rotation torque and gives rises to a larger rolling speed. The pair aligning becomes difficult and unstable at high electric field where the normal dipole-dipole repulsion becomes dominant. As a consequence, the dependence of speed on density becomes weak increasingly upon the increase of the electric field. This result offers an interpretation for the discrepancy between our and previous observations on Quincke rollers.
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Formation and evolution of bubbly screens in confined oscillating bubbly liquids.
Shklyaev, Sergey; Straube, Arthur V
2010-01-01
We consider the dynamics of dilute monodisperse bubbly liquid confined by two plane solid walls and subject to small-amplitude high-frequency oscillations normal to the walls. The initial state corresponds to the uniform distribution of bubbles and motionless liquid. The period of external driving is assumed much smaller than typical relaxation times for a single bubble but larger than the period of volume eigenoscillations. The time-averaged description accounting for the two-way coupling between the liquid and the bubbles is applied. We show that the model predicts accumulation of bubbles in thin sheets parallel to the walls. These singular structures, which are formally characterized by infinitely thin width and infinitely high concentration, are referred to as bubbly screens. The formation of a bubbly screen is described analytically in terms of a self-similar solution, which is in agreement with numerical simulations. We study the evolution of bubbly screens and detect a one-dimensional stationary state, which is shown to be unconditionally unstable.
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Formation and evolution of bubbly screens in confined oscillating bubbly liquids
NASA Astrophysics Data System (ADS)
Shklyaev, Sergey; Straube, Arthur V.
2010-01-01
We consider the dynamics of dilute monodisperse bubbly liquid confined by two plane solid walls and subject to small-amplitude high-frequency oscillations normal to the walls. The initial state corresponds to the uniform distribution of bubbles and motionless liquid. The period of external driving is assumed much smaller than typical relaxation times for a single bubble but larger than the period of volume eigenoscillations. The time-averaged description accounting for the two-way coupling between the liquid and the bubbles is applied. We show that the model predicts accumulation of bubbles in thin sheets parallel to the walls. These singular structures, which are formally characterized by infinitely thin width and infinitely high concentration, are referred to as bubbly screens. The formation of a bubbly screen is described analytically in terms of a self-similar solution, which is in agreement with numerical simulations. We study the evolution of bubbly screens and detect a one-dimensional stationary state, which is shown to be unconditionally unstable.
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A common-path phase-shift interferometry surface plasmon imaging system
NASA Astrophysics Data System (ADS)
Su, Y.-T.; Chen, Shean-Jen; Yeh, T.-L.
2005-03-01
A biosensing imaging system is proposed based on the integration of surface plasmon resonance (SPR) and common-path phase-shift interferometry (PSI) techniques to measure the two-dimensional spatial phase variation caused by biomolecular interactions upon a sensing chip. The SPR phase imaging system can offer high resolution and high-throughout screening capabilities to analyze microarray biomolecular interaction without the need for additional labeling. With the long-term stability advantage of the common-path PSI technique even with external disturbances such as mechanical vibration, buffer flow noise, and laser unstable issue, the system can match the demand of real-time kinetic study for biomolecular interaction analysis (BIA). The SPR-PSI imaging system has achieved a detection limit of 2×10-7 refraction index change, a long-term phase stability of 2.5x10-4π rms over four hours, and a spatial phase resolution of 10-3 π with a lateral resolution of 100μm.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chianese, Marco; Merle, Alexander, E-mail: chianese@na.infn.it, E-mail: amerle@mpp.mpg.de
The high energy events observed at the IceCube Neutrino Observatory have triggered many investigations interpreting the highly energetic neutrinos detected as decay products of heavy unstable Dark Matter particles. However, while very detailed treatments of the IceCube phenomenology exist, only a few references focus on the (non-trivial) Dark Matter production part—and all of those rely on relatively complicated new models which are not always testable directly. We instead investigate two of the most minimal scenarios possible, where the operator responsible for the IceCube events is directly involved in Dark Matter production. We show that the simplest (four-dimensional) operator is notmore » powerful enough to accommodate all constraints. A more non-minimal setting (at mass dimension six), however, can do both fitting all the data and also allowing for a comparatively small parameter space only, parts of which can be in reach of future observations. We conclude that minimalistic approaches can be enough to explain all data required, while complicated new physics seems not to be required by IceCube.« less
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Large-eddy and unsteady RANS simulations of a shock-accelerated heavy gas cylinder
Morgan, B. E.; Greenough, J. A.
2015-04-08
Two-dimensional numerical simulations of the Richtmyer–Meshkov unstable “shock-jet” problem are conducted using both large-eddy simulation (LES) and unsteady Reynolds-averaged Navier–Stokes (URANS) approaches in an arbitrary Lagrangian–Eulerian hydrodynamics code. Turbulence statistics are extracted from LES by running an ensemble of simulations with multimode perturbations to the initial conditions. Detailed grid convergence studies are conducted, and LES results are found to agree well with both experiment and high-order simulations conducted by Shankar et al. (Phys Fluids 23, 024102, 2011). URANS results using a k–L approach are found to be highly sensitive to initialization of the turbulence lengthscale L and to the timemore » at which L becomes resolved on the computational mesh. As a result, it is observed that a gradient diffusion closure for turbulent species flux is a poor approximation at early times, and a new closure based on the mass-flux velocity is proposed for low-Reynolds-number mixing.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Patel, Nita; Faria, Sergio, E-mail: sergio.faria@muhc.mcgill.ca; Cury, Fabio
2013-07-01
Purpose: To report long-term outcomes of low- and intermediate-risk prostate cancer patients treated with high-dose hypofractionated radiation therapy (HypoRT). Methods and Materials: Patients with low- and intermediate-risk prostate cancer were treated using 3-dimensional conformal radiation therapy to a dose of 66 Gy in 22 daily fractions of 3 Gy without hormonal therapy. A uniform 7-mm margin was created around the prostate for the planning target volume, and treatment was prescribed to the isocenter. Treatment was delivered using daily ultrasound image-guided radiation therapy. Common Terminology Criteria for Adverse Events, version 3.0, was used to prospectively score toxicity. Biochemical failure was definedmore » as the nadir prostate-specific antigen level plus 2 ng/mL. Results: A total of 129 patients were treated between November 2002 and December 2005. With a median follow-up of 90 months, the 5- and 8-year actuarial biochemical control rates were 97% and 92%, respectively. The 5- and 8-year actuarial overall survival rates were 92% and 88%, respectively. Only 1 patient died from prostate cancer at 92 months after treatment, giving an 8-year actuarial cancer-specific survival of 98%. Radiation therapy was well tolerated, with 57% of patients not experiencing any acute gastrointestinal (GI) or genitourinary (GU) toxicity. For late toxicity, the worst grade ≥2 rate for GI and GU toxicity was 27% and 33%, respectively. There was no grade >3 toxicity. At last follow-up, the rate of grade ≥2 for both GI and GU toxicity was only 1.5%. Conclusions: Hypofractionation with 66 Gy in 22 fractions prescribed to the isocenter using 3-dimensional conformal radiation therapy produces excellent biochemical control rates, with moderate toxicity. However, this regimen cannot be extrapolated to the intensity modulated radiation therapy technique.« less
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Moore, Stephen R; Ritter, Linda E; Gibbons, Catherine F; Grosovsky, Andrew J
2005-10-01
Structural chromosomal rearrangements are commonly observed in tumor karyotypes and in radiation-induced genomic instability. Here we report the effects of TP53 deficiency on karyotypic stability before and after irradiation using related cells and clones differing in cellular TP53 status. The parental cell line, TK6, is a TP53 wild-type human B-lymphoblastoid line with a highly stable karyotype. In the two TK6 derivatives used here, TP53 has been inactivated by biochemical means (expression of HPV16 E6; TK6-5E) or genetic means (allelic inactivation; NH32). Biochemical inactivation of TP53 (TK6-5E) had little effect on the spontaneous karyotype, whereas allelic inactivation of TP53 (NH32) resulted in a modest increase in spontaneous karyotypic instability. After 2 Gy gamma irradiation, the number of unstable clones derived from TP53-deficient cells was significantly elevated compared to the TP53 wild-type counterpart. Extensively destabilized clones were common after irradiation in the set of clones derived from NH32 cells, and one was observed in the set of TK6-5E clones; however, they were never observed in TK6-derived clones. In two of the irradiated NH32 clones, whole chromosomes or chromosome bands were preferentially involved in alterations. These results suggest that genomic instability may differ both quantitatively and qualitatively as a consequence of altered TP53 expression. Some of the results showing repeated and preferential chromosome involvement in aberrations support a model in which instability may be driven by cis mechanisms.
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Wear Behavior of an Unstable Knee: Stabilization via Implant Design?
Reinders, Jörn; Kretzer, Jan Philippe
2014-01-01
Background. Wear-related failures and instabilities are frequent failure mechanisms of total knee replacements. High-conforming designs may provide additional stability for the joint. This study analyzes the effects of a ligamentous insufficiency on the stability and the wear behavior of a high-conforming knee design. Methods. Two simulator wear tests were performed on a high-conforming total knee replacement design. In the first, a ligamentous-stable knee replacement with a sacrificed anterior cruciate ligament was simulated. In the second, a ligamentous-unstable knee with additionally insufficient posterior cruciate ligament and medial collateral ligament was simulated. Wear was determined gravimetrically and wear particles were analyzed. Implant kinematics was recorded during simulation. Results. Significantly higher wear rates (P ≤ 0.001) were observed for the unstable knee (14.58 ± 0.56 mg/106 cycles) compared to the stable knee (7.97 ± 0.87 mg/106 cycles). A higher number of wear particles with only small differences in wear particle characteristics were observed. Under unstable knee conditions, kinematics increased significantly for translations and rotations (P ≤ 0.01). This increase was mainly attributed to higher tibial posterior translation and internal rotations. Conclusion. Higher kinematics under unstable test conditions is a result of insufficient stabilization via implant design. Due to the higher kinematics, increased wear was observed in this study. PMID:25276820
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On the evolution of the Universe
NASA Astrophysics Data System (ADS)
Kondratenko, P. O.
2014-12-01
In this paper a model of creation and evolution of the universe in which the laws of physics are performed. The model implies that our Universe is a part of a Super-Universe as a separate layer in the fiber space, and the information communication exists between adjacent layers through the single point. During the formation of Super-Universe it was filled first a one-dimensional World of Field-time, then a two-dimensional (1+1) World was filled with energy and Planck's particles which carry the electric and magnetic charges. Completion of two-dimensional world filling leads to a "transfusion" of energy into the neighboring three-dimensional World which presents a world of known quarks which have the fractional electric charges, color charges, and spins. The next step is a "transfusion" of energy into the four-dimensional (3+1) World and the birth of the particles of this World. Evolution of this World has a completion by the brane creation of five-dimensional World. This evolution is accompanying by the birth of the entire set of stable and unstable heavy nuclei and atoms. A filling of each new layer at the fiber space does not bring the entropy into this space (i.e. cold and completely deterministic start of evolution). The proposed model supports the anthropic principle in the Universe.
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1982-01-01
We have examined the secretogogue responsiveness and the pattern of secretory proteins produced by a transplantable rat pancreatic acinar cell tumor. Dispersed tumor cells were found to discharge secretory proteins in vitro when incubated with hormones that act on four different classes of receptors: carbamylcholine, caerulein, secretin- vasoactive intestinal peptide, and bombesin. With all hormones tested, maximal discharge from tumor cells was only about one-half that of control pancreatic lobules, but occurred at the same dose optima except for secretin, whose dose optimum was 10-fold higher. Biochemical analysis of secretory proteins discharged by the tumor cells was carried out by crossed immunoelectrophoresis and by two-dimensional isoelectric focusing-SDS polyacrylamide gel electrophoresis. To establish a baseline for comparison, secretory proteins from normal rat pancreas were identified according to enzymatic activity and correlated with migration position on two-dimensional gels. Our results indicate that a group of basic polypeptides including proelastase, basic trypsinogen, basic chymotrypsinogen, and ribonuclease, two out of three forms of procarboxypeptidase B, and the major lipase species were greatly reduced or absent in tumor cell secretion. In contrast, the amount of acidic chymotrypsinogen was notably increased compared with normal acinar cells. Although the acinar tumor cells are highly differentiated cytologically and express functional receptors for several classes of pancreatic secretagogues, they show quantitative and qualitative differences when compared with normal pancreas with regard to their production of secretory proteins. PMID:6185502
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Asynchronous vibration problem of centrifugal compressor
NASA Technical Reports Server (NTRS)
Fujikawa, T.; Ishiguro, N.; Ito, M.
1980-01-01
An unstable asynchronous vibration problem in a high pressure centrifugal compressor and the remedial actions against it are described. Asynchronous vibration of the compressor took place when the discharge pressure (Pd) was increased, after the rotor was already at full speed. The typical spectral data of the shaft vibration indicate that as the pressure Pd increases, pre-unstable vibration appears and becomes larger, and large unstable asynchronous vibration occurs suddenly (Pd = 5.49MPa). A computer program was used which calculated the logarithmic decrement and the damped natural frequency of the rotor bearing systems. The analysis of the log-decrement is concluded to be effective in preventing unstable vibration in both the design stage and remedial actions.
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Zou, Ling; Zhao, Haihua; Kim, Seung Jun
2016-11-16
In this study, the classical Welander’s oscillatory natural circulation problem is investigated using high-order numerical methods. As originally studied by Welander, the fluid motion in a differentially heated fluid loop can exhibit stable, weakly instable, and strongly instable modes. A theoretical stability map has also been originally derived from the stability analysis. Numerical results obtained in this paper show very good agreement with Welander’s theoretical derivations. For stable cases, numerical results from both the high-order and low-order numerical methods agree well with the non-dimensional flow rate analytically derived. The high-order numerical methods give much less numerical errors compared to themore » low-order methods. For stability analysis, the high-order numerical methods could perfectly predict the stability map, while the low-order numerical methods failed to do so. For all theoretically unstable cases, the low-order methods predicted them to be stable. The result obtained in this paper is a strong evidence to show the benefits of using high-order numerical methods over the low-order ones, when they are applied to simulate natural circulation phenomenon that has already gain increasing interests in many future nuclear reactor designs.« less
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Escape rates over potential barriers: variational principles and the Hamilton-Jacobi equation
NASA Astrophysics Data System (ADS)
Cortés, Emilio; Espinosa, Francisco
We describe a rigorous formalism to study some extrema statistics problems, like maximum probability events or escape rate processes, by taking into account that the Hamilton-Jacobi equation completes, in a natural way, the required set of boundary conditions of the Euler-Lagrange equation, for this kind of variational problem. We apply this approach to a one-dimensional stochastic process, driven by colored noise, for a double-parabola potential, where we have one stable and one unstable steady states.
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Transverse instability of periodic and generalized solitary waves for a fifth-order KP model
NASA Astrophysics Data System (ADS)
Haragus, Mariana; Wahlén, Erik
2017-02-01
We consider a fifth-order Kadomtsev-Petviashvili equation which arises as a two-dimensional model in the classical water-wave problem. This equation possesses a family of generalized line solitary waves which decay exponentially to periodic waves at infinity. We prove that these solitary waves are transversely spectrally unstable and that this instability is induced by the transverse instability of the periodic tails. We rely upon a detailed spectral analysis of some suitably chosen linear operators.
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Identification of species- and tissue-specific proteins using proteomic strategy
NASA Astrophysics Data System (ADS)
Chernukha, I. M.; Vostrikova, N. L.; Kovalev, L. I.; Shishkin, S. S.; Kovaleva, M. A.; Manukhin, Y. S.
2017-09-01
Proteomic technologies have proven to be very effective for detecting biochemical changes in meat products, such as changes in tissue- and species-specific proteins. In the tissues of cattle, pig, horse and camel M. longissimus dorsi both tissue- and species specific proteins were detected using two dimensional electrophoresis. Species-specific isoforms of several muscle proteins were also identified. The identified and described proteins of cattle, pig, horse and camel skeletal muscles (including mass spectra of the tryptic peptides) were added to the national free access database “Muscle organ proteomics”. This research has enabled the development of new highly sensitive technologies for meat product quality control against food fraud.
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Robust Optimization Design Algorithm for High-Frequency TWTs
NASA Technical Reports Server (NTRS)
Wilson, Jeffrey D.; Chevalier, Christine T.
2010-01-01
Traveling-wave tubes (TWTs), such as the Ka-band (26-GHz) model recently developed for the Lunar Reconnaissance Orbiter, are essential as communication amplifiers in spacecraft for virtually all near- and deep-space missions. This innovation is a computational design algorithm that, for the first time, optimizes the efficiency and output power of a TWT while taking into account the effects of dimensional tolerance variations. Because they are primary power consumers and power generation is very expensive in space, much effort has been exerted over the last 30 years to increase the power efficiency of TWTs. However, at frequencies higher than about 60 GHz, efficiencies of TWTs are still quite low. A major reason is that at higher frequencies, dimensional tolerance variations from conventional micromachining techniques become relatively large with respect to the circuit dimensions. When this is the case, conventional design- optimization procedures, which ignore dimensional variations, provide inaccurate designs for which the actual amplifier performance substantially under-performs that of the design. Thus, this new, robust TWT optimization design algorithm was created to take account of and ameliorate the deleterious effects of dimensional variations and to increase efficiency, power, and yield of high-frequency TWTs. This design algorithm can help extend the use of TWTs into the terahertz frequency regime of 300-3000 GHz. Currently, these frequencies are under-utilized because of the lack of efficient amplifiers, thus this regime is known as the "terahertz gap." The development of an efficient terahertz TWT amplifier could enable breakthrough applications in space science molecular spectroscopy, remote sensing, nondestructive testing, high-resolution "through-the-wall" imaging, biomedical imaging, and detection of explosives and toxic biochemical agents.
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Ultra High Mode Mix in NIF NIC Implosions
NASA Astrophysics Data System (ADS)
Scott, Robbie; Garbett, Warren
2017-10-01
This work re-examines a sub-set of the low adiabat implosions from the National Ignition Campaign in an effort to better understand potential phenomenological sources of `excess' mix observed experimentally. An extensive effort has been made to match both shock-timing and backlit radiography (Con-A) implosion data in an effort to reproduce the experimental conditions as accurately as possible. Notably a 30% reduction in ablation pressure at peak drive is required to match the experimental data. The reduced ablation pressure required to match the experimental data allows the ablator to decompress, in turn causing the DT ice-ablator interface to go Rayleigh-Taylor unstable early in the implosion acceleration phase. Post-processing the runs with various mix models indicates high-mode mix from the DT ice-ablator interface may penetrate deep into the hotspot. This work offers a potential explanation of why these low-adiabat implosions exhibited significantly higher levels of mix than expected from high-fidelity multi-dimensional simulations. Through this new understanding, a possible route forward for low-adiabat implosions on NIF is suggested.
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Hurricane, O A; Smalyuk, V A; Raman, K; Schilling, O; Hansen, J F; Langstaff, G; Martinez, D; Park, H-S; Remington, B A; Robey, H F; Greenough, J A; Wallace, R; Di Stefano, C A; Drake, R P; Marion, D; Krauland, C M; Kuranz, C C
2012-10-12
Following the successful demonstration of an OMEGA laser-driven platform for generating and studying nearly two-dimensional unstable plasma shear layers [Hurricane et al., Phys. Plasmas 16, 056305 (2009); Harding et al., Phys. Rev. Lett. 103, 045005 (2009)], this Letter reports on the first quantitative measurement of turbulent mixing in a high-energy-density plasma. As a blast wave moves parallel to an unperturbed interface between a low-density foam and a high-density plastic, baroclinic vorticity is deposited at the interface and a Kelvin-Helmholtz instability-driven turbulent mixing layer is created in the postshock flow due to surface roughness. The spatial scale and density profile of the turbulent layer are diagnosed using x-ray radiography with sufficiently small uncertainty so that the data can be used to ~0.17 μm) in the postshock plasma flow are consistent with an "inertial subrange," within which a Kolmogorov turbulent energy cascade can be active. An illustration of comparing the data set with the predictions of a two-equation turbulence model in the ares radiation hydrodynamics code is also presented.
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Three-dimensional femtosecond laser processing for lab-on-a-chip applications
NASA Astrophysics Data System (ADS)
Sima, Felix; Sugioka, Koji; Vázquez, Rebeca Martínez; Osellame, Roberto; Kelemen, Lóránd; Ormos, Pal
2018-02-01
The extremely high peak intensity associated with ultrashort pulse width of femtosecond laser allows us to induce nonlinear interaction such as multiphoton absorption and tunneling ionization with materials that are transparent to the laser wavelength. More importantly, focusing the femtosecond laser beam inside the transparent materials confines the nonlinear interaction only within the focal volume, enabling three-dimensional (3D) micro- and nanofabrication. This 3D capability offers three different schemes, which involve undeformative, subtractive, and additive processing. The undeformative processing preforms internal refractive index modification to construct optical microcomponents including optical waveguides. Subtractive processing can realize the direct fabrication of 3D microfluidics, micromechanics, microelectronics, and photonic microcomponents in glass. Additive processing represented by two-photon polymerization enables the fabrication of 3D polymer micro- and nanostructures for photonic and microfluidic devices. These different schemes can be integrated to realize more functional microdevices including lab-on-a-chip devices, which are miniaturized laboratories that can perform reaction, detection, analysis, separation, and synthesis of biochemical materials with high efficiency, high speed, high sensitivity, low reagent consumption, and low waste production. This review paper describes the principles and applications of femtosecond laser 3D micro- and nanofabrication for lab-on-a-chip applications. A hybrid technique that promises to enhance functionality of lab-on-a-chip devices is also introduced.
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Reduction and relative equilibria for the two-body problem on spaces of constant curvature
NASA Astrophysics Data System (ADS)
Borisov, A. V.; García-Naranjo, L. C.; Mamaev, I. S.; Montaldi, J.
2018-06-01
We consider the two-body problem on surfaces of constant nonzero curvature and classify the relative equilibria and their stability. On the hyperbolic plane, for each q>0 we show there are two relative equilibria where the masses are separated by a distance q. One of these is geometrically of elliptic type and the other of hyperbolic type. The hyperbolic ones are always unstable, while the elliptic ones are stable when sufficiently close, but unstable when far apart. On the sphere of positive curvature, if the masses are different, there is a unique relative equilibrium (RE) for every angular separation except π /2. When the angle is acute, the RE is elliptic, and when it is obtuse the RE can be either elliptic or linearly unstable. We show using a KAM argument that the acute ones are almost always nonlinearly stable. If the masses are equal, there are two families of relative equilibria: one where the masses are at equal angles with the axis of rotation (`isosceles RE') and the other when the two masses subtend a right angle at the centre of the sphere. The isosceles RE are elliptic if the angle subtended by the particles is acute and is unstable if it is obtuse. At π /2, the two families meet and a pitchfork bifurcation takes place. Right-angled RE are elliptic away from the bifurcation point. In each of the two geometric settings, we use a global reduction to eliminate the group of symmetries and analyse the resulting reduced equations which live on a five-dimensional phase space and possess one Casimir function.
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Formation of a Chern-Simons cylindrical wormhole during evolution of manifolds
NASA Astrophysics Data System (ADS)
Sepehri, Alireza; Ghaffary, Tooraj; Naimi, Yaghoob; Ghaforyan, Hossein; Ebrahimzadeh, Majid
In this paper, the formation of cylindrical wormhole during evolution of manifolds is studied. It is shown that this type of wormholes may be produced at two stages and then disappeared very fast at the third stage. First, one N-dimensional is formed by joining point-like manifolds. Then, this manifold is torn and two child manifolds plus one Chern-Simons manifold appeared. Our universe is born on one of the child manifolds and connected to the other one by Chern-Simons manifold. At the third stage, this Chern-Simons manifold-which plays the role of cylindrical wormhole, dissolves into universes and gives its energy to them and causes inflation. Thus, the Chern-Simons cylindrical wormhole is unstable and dissolves in our four-dimensional universes and another universe very fast.
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NASA Technical Reports Server (NTRS)
Tripp, John S.; Patek, Stephen D.
1988-01-01
Measurement of planar skin friction forces in aerodynamic testing currently requires installation of two perpendicularly mounted, single-axis balances; consequently, force components must be sensed at two distinct locations. A two-axis instrument developed at the Langley Research Center to overcome this disadvantage allows measurement of a two-dimensional force at one location. This paper describes a feedback-controlled nulling circuit developed for the NASA two-axis balance which, without external compensation, is inherently unstable because of its low friction mechanical design. Linear multivariable control theory is applied to an experimentally validated mathematical model of the balance to synthesize a state-variable feedback control law. Pole placement techniques and computer simulation studies are employed to select eigenvalues which provide ideal transient response with decoupled sensing dynamics.
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Magic tilt angle for stabilizing two-dimensional solitons by dipole-dipole interactions
NASA Astrophysics Data System (ADS)
Chen, Xing-You; Chuang, You-Lin; Lin, Chun-Yan; Wu, Chien-Ming; Li, Yongyao; Malomed, Boris A.; Lee, Ray-Kuang
2017-10-01
In the framework of the Gross-Pitaevskii equation, we study the formation and stability of effectively two-dimensional solitons in dipolar Bose-Einstein condensates (BECs), with dipole moments polarized at an arbitrary angle θ relative to the direction normal to the system's plane. Using numerical methods and the variational approximation, we demonstrate that unstable Townes solitons, created by the contact attractive interaction, may be completely stabilized (with an anisotropic shape) by the dipole-dipole interaction (DDI), in the interval θcr<θ ≤π /2 . The stability boundary θcr weakly depends on the relative strength of the DDI, remaining close to the magic angle θm=arccos(1 /√{3 }) . The results suggest that DDIs provide a generic mechanism for the creation of stable BEC solitons in higher dimensions.
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A role for myelin-associated peroxisomes in maintaining paranodal loops and axonal integrity.
Kassmann, Celia M; Quintes, Susanne; Rietdorf, Jens; Möbius, Wiebke; Sereda, Michael Werner; Nientiedt, Tobias; Saher, Gesine; Baes, Myriam; Nave, Klaus-Armin
2011-07-21
Demyelinating diseases of the nervous system cause axon loss but the underlying mechanisms are not well understood. Here we show by confocal and electron microscopy that in myelin-forming glia peroxisomes are associated with myelin membranes. When peroxisome biogenesis is experimentally perturbed in Pex5 conditional mouse mutants, myelination by Schwann cells appears initially normal. However, in nerves of older mice paranodal loops become physically unstable and develop swellings filled with vesicles and electron-dense material. This novel model of a demyelinating neuropathy demonstrates that peroxisomes serve an important function in the peripheral myelin compartment, required for long-term axonal integrity. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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Stamper, David M.; Walch, Marianne; Jacobs, Rachel N.
2003-01-01
The bacterial population of a graywater treatment system was monitored over the course of 100 days, along with several wastewater biochemical parameters. The graywater treatment system employed an 1,800-liter membrane bioreactor (MBR) to process the waste, with essentially 100% recycling of the biomass. Graywater feed consisting of 10% galley water and 90% laundry water, selected to approximate the graywater composition on board U.S. Navy ships, was collected offsite. Five-day biological oxygen demand (BOD5), oils and greases (O/G), nitrogen, and phosphorus were monitored in the feed and were found to vary greatly day to day. Changes in the bacterial population were monitored by PCR amplification of region 332 to 518 (Escherichia coli numbering) of the 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE) analysis of the resultant PCR products. DGGE analysis indicated a diverse and unstable bacterial population throughout the 100-day period, with spikes in feed strength causing significant changes in community structure. Long-term similarity between the communities was 0 to 25%, depending on the method of analysis. In spite of the unstable bacterial population, the MBR system was able to meet effluent quality parameters approximately 90% of the time. PMID:12571004
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Stamper, David M; Walch, Marianne; Jacobs, Rachel N
2003-02-01
The bacterial population of a graywater treatment system was monitored over the course of 100 days, along with several wastewater biochemical parameters. The graywater treatment system employed an 1,800-liter membrane bioreactor (MBR) to process the waste, with essentially 100% recycling of the biomass. Graywater feed consisting of 10% galley water and 90% laundry water, selected to approximate the graywater composition on board U.S. Navy ships, was collected offsite. Five-day biological oxygen demand (BOD(5)), oils and greases (O/G), nitrogen, and phosphorus were monitored in the feed and were found to vary greatly day to day. Changes in the bacterial population were monitored by PCR amplification of region 332 to 518 (Escherichia coli numbering) of the 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE) analysis of the resultant PCR products. DGGE analysis indicated a diverse and unstable bacterial population throughout the 100-day period, with spikes in feed strength causing significant changes in community structure. Long-term similarity between the communities was 0 to 25%, depending on the method of analysis. In spite of the unstable bacterial population, the MBR system was able to meet effluent quality parameters approximately 90% of the time.
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Liu, Chang-Jun; Dixon, Richard A.
2001-01-01
The bioactive isoflavonoids of the Leguminosae often are methylated on the 4′-position of their B-rings. Paradoxically, reverse genetic evidence implicates alfalfa isoflavone O-methyltransferase (IOMT) in the biosynthesis of 4′-O-methylated isoflavonoids such as the phytoalexin medicarpin in vivo, whereas biochemical studies indicate that IOMT has strict specificity for methylation of the A-ring 7-hydroxyl of daidzein, the presumed substrate for O-methylation, in vitro. Radiolabeling and isotope dilution studies now confirm that daidzein is not an intermediate in isoflavonoid phytoalexin biosynthesis in alfalfa. Furthermore, protein gel blot analysis and confocal microscopy of a transiently expressed IOMT–green fluorescent protein fusion in alfalfa leaves show that the operationally soluble IOMT localizes to endomembranes after elicitation of the isoflavonoid pathway. We propose that IOMT colocalizes with the endoplasmic reticulum–associated isoflavone synthase cytochrome P450 to ensure rapid B-ring methylation of the unstable 2,4′,7-trihydroxyisoflavanone product of isoflavone synthase, thereby preventing its dehydration to daidzein and subsequent A-ring methylation by free IOMT. In this way, metabolic channeling at the entry point into isoflavonoid phytoalexin biosynthesis protects an unstable intermediate from an unproductive metabolic conversion. PMID:11752378
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Complexity of the laminar-turbulent boundary in pipe flow
NASA Astrophysics Data System (ADS)
Budanur, Nazmi Burak; Hof, Björn
2018-05-01
Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions.
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Convection induced by thermal gradients on thin reaction fronts
NASA Astrophysics Data System (ADS)
Ruelas Paredes, David R. A.; Vasquez, Desiderio A.
2017-09-01
We present a thin front model for the propagation of chemical reaction fronts in liquids inside a Hele-Shaw cell or porous media. In this model we take into account density gradients due to thermal and compositional changes across a thin interface. The front separating reacted from unreacted fluids evolves following an eikonal relation between the normal speed and the curvature. We carry out a linear stability analysis of convectionless flat fronts confined in a two-dimensional rectangular domain. We find that all fronts are stable to perturbations of short wavelength, but they become unstable for some wavelengths depending on the values of compositional and thermal gradients. If the effects of these gradients oppose each other, we observe a range of wavelengths that make the flat front unstable. Numerical solutions of the nonlinear model show curved fronts of steady shape with convection propagating faster than flat fronts. Exothermic fronts increase the temperature of the fluid as they propagate through the domain. This increment in temperature decreases with increasing speed.
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Four-state rock-paper-scissors games in constrained Newman-Watts networks.
Zhang, Guo-Yong; Chen, Yong; Qi, Wei-Kai; Qing, Shao-Meng
2009-06-01
We study the cyclic dominance of three species in two-dimensional constrained Newman-Watts networks with a four-state variant of the rock-paper-scissors game. By limiting the maximal connection distance Rmax in Newman-Watts networks with the long-range connection probability p , we depict more realistically the stochastic interactions among species within ecosystems. When we fix mobility and vary the value of p or Rmax, the Monte Carlo simulations show that the spiral waves grow in size, and the system becomes unstable and biodiversity is lost with increasing p or Rmax. These results are similar to recent results of Reichenbach et al. [Nature (London) 448, 1046 (2007)], in which they increase the mobility only without including long-range interactions. We compared extinctions with or without long-range connections and computed spatial correlation functions and correlation length. We conclude that long-range connections could improve the mobility of species, drastically changing their crossover to extinction and making the system more unstable.
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Origin of chaos near three-dimensional quantum vortices: A general Bohmian theory
NASA Astrophysics Data System (ADS)
Tzemos, Athanasios C.; Efthymiopoulos, Christos; Contopoulos, George
2018-04-01
We provide a general theory for the structure of the quantum flow near three-dimensional (3D) nodal lines, i.e., one-dimensional loci where the 3D wave function becomes equal to zero. In suitably defined coordinates (comoving with the nodal line) the generic structure of the flow implies the formation of 3D quantum vortices. We show that such vortices are accompanied by nearby invariant lines of the comoving quantum flow, called X lines, which are normally hyperbolic. Furthermore, the stable and unstable manifolds of the X lines produce chaotic scatterings of nearby quantum (Bohmian) trajectories, thus inducing an intricate form of the quantum current in the neighborhood of each 3D quantum vortex. Generic formulas describing the structure around 3D quantum vortices are provided, applicable to an arbitrary choice of 3D wave function. We also give specific numerical examples as well as a discussion of the physical consequences of chaos near 3D quantum vortices.
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Origin of chaos near three-dimensional quantum vortices: A general Bohmian theory.
Tzemos, Athanasios C; Efthymiopoulos, Christos; Contopoulos, George
2018-04-01
We provide a general theory for the structure of the quantum flow near three-dimensional (3D) nodal lines, i.e., one-dimensional loci where the 3D wave function becomes equal to zero. In suitably defined coordinates (comoving with the nodal line) the generic structure of the flow implies the formation of 3D quantum vortices. We show that such vortices are accompanied by nearby invariant lines of the comoving quantum flow, called X lines, which are normally hyperbolic. Furthermore, the stable and unstable manifolds of the X lines produce chaotic scatterings of nearby quantum (Bohmian) trajectories, thus inducing an intricate form of the quantum current in the neighborhood of each 3D quantum vortex. Generic formulas describing the structure around 3D quantum vortices are provided, applicable to an arbitrary choice of 3D wave function. We also give specific numerical examples as well as a discussion of the physical consequences of chaos near 3D quantum vortices.
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NASA Technical Reports Server (NTRS)
Zhang, D.; Anthes, R. A.
1982-01-01
A one-dimensional, planetary boundary layer (PBL) model is presented and verified using April 10, 1979 SESAME data. The model contains two modules to account for two different regimes of turbulent mixing. Separate parameterizations are made for stable and unstable conditions, with a predictive slab model for surface temperature. Atmospheric variables in the surface layer are calculated with a prognostic model, with moisture included in the coupled surface/PBL modeling. Sensitivity tests are performed for factors such as moisture availability, albedo, surface roughness, and thermal capacity, and a 24 hr simulation is summarized for day and night conditions. The comparison with the SESAME data comprises three hour intervals, using a time-dependent geostrophic wind. Close correlations were found with daytime conditions, but not in nighttime thermal structure, while the turbulence was faithfully predicted. Both geostrophic flow and surface characteristics were shown to have significant effects on the model predictions
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A Computational Study of Shear Layer Receptivity
NASA Astrophysics Data System (ADS)
Barone, Matthew; Lele, Sanjiva
2002-11-01
The receptivity of two-dimensional, compressible shear layers to local and external excitation sources is examined using a computational approach. The family of base flows considered consists of a laminar supersonic stream separated from nearly quiescent fluid by a thin, rigid splitter plate with a rounded trailing edge. The linearized Euler and linearized Navier-Stokes equations are solved numerically in the frequency domain. The flow solver is based on a high order finite difference scheme, coupled with an overset mesh technique developed for computational aeroacoustics applications. Solutions are obtained for acoustic plane wave forcing near the most unstable shear layer frequency, and are compared to the existing low frequency theory. An adjoint formulation to the present problem is developed, and adjoint equation calculations are performed using the same numerical methods as for the regular equation sets. Solutions to the adjoint equations are used to shed light on the mechanisms which control the receptivity of finite-width compressible shear layers.
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Metastable structure of Li13Si4
NASA Astrophysics Data System (ADS)
Gruber, Thomas; Bahmann, Silvia; Kortus, Jens
2016-04-01
The Li13Si4 phase is one out of several crystalline lithium silicide phases, which is a potential electrode material for lithium ion batteries and contains a high theoretical specific capacity. By means of ab initio methods like density functional theory (DFT) many properties such as heat capacity or heat of formation can be calculated. These properties are based on the calculation of phonon frequencies, which contain information about the thermodynamical stability. The current unit cell of "Li13Si4" given in the ICSD database is unstable with respect to DFT calculations. We propose a modified unit cell that is stable in the calculations. The evolutionary algorithm EVO found a structure very similar to the ICSD one with both of them containing metastable lithium positions. Molecular dynamic simulations show a phase transition between both structures where these metastable lithium atoms move. This phase transition is achieved by a very fast one-dimensional lithium diffusion and stabilizes this phase.
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Elastic Differential Cross Sections
NASA Technical Reports Server (NTRS)
Werneth, Charles M.; Maung, Khin M.; Ford, William P.; Norbury, John W.; Vera, Michael D.
2014-01-01
The eikonal, partial wave (PW) Lippmann-Schwinger, and three-dimensional Lippmann-Schwinger (LS3D) methods are compared for nuclear reactions that are relevant for space radiation applications. Numerical convergence of the eikonal method is readily achieved when exact formulas of the optical potential are used for light nuclei (A less than or equal to 16) and the momentum-space optical potential is used for heavier nuclei. The PW solution method is known to be numerically unstable for systems that require a large number of partial waves, and, as a result, the LS3D method is employed. The effect of relativistic kinematics is studied with the PW and LS3D methods and is compared to eikonal results. It is recommended that the LS3D method be used for high energy nucleon- nucleus reactions and nucleus-nucleus reactions at all energies because of its rapid numerical convergence and stability.
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Nuclear Cross Sections for Space Radiation Applications
NASA Technical Reports Server (NTRS)
Werneth, C. M.; Maung, K. M.; Ford, W. P.; Norbury, J. W.; Vera, M. D.
2015-01-01
The eikonal, partial wave (PW) Lippmann-Schwinger, and three-dimensional Lippmann-Schwinger (LS3D) methods are compared for nuclear reactions that are relevant for space radiation applications. Numerical convergence of the eikonal method is readily achieved when exact formulas of the optical potential are used for light nuclei (A = 16) and the momentum-space optical potential is used for heavier nuclei. The PW solution method is known to be numerically unstable for systems that require a large number of partial waves, and, as a result, the LS3D method is employed. The effect of relativistic kinematics is studied with the PW and LS3D methods and is compared to eikonal results. It is recommended that the LS3D method be used for high energy nucleon-nucleus reactions and nucleus-nucleus reactions at all energies because of its rapid numerical convergence and stability for both non-relativistic and relativistic kinematics.
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Evolving Gravitationally Unstable Disks over Cosmic Time: Implications for Thick Disk Formation
NASA Astrophysics Data System (ADS)
Forbes, John; Krumholz, Mark; Burkert, Andreas
2012-07-01
Observations of disk galaxies at z ~ 2 have demonstrated that turbulence driven by gravitational instability can dominate the energetics of the disk. We present a one-dimensional simulation code, which we have made publicly available, that economically evolves these galaxies from z ~ 2 to z ~ 0 on a single CPU in a matter of minutes, tracking column density, metallicity, and velocity dispersions of gaseous and multiple stellar components. We include an H2-regulated star formation law and the effects of stellar heating by transient spiral structure. We use this code to demonstrate a possible explanation for the existence of a thin and thick disk stellar population and the age-velocity-dispersion correlation of stars in the solar neighborhood: the high velocity dispersion of gas in disks at z ~ 2 decreases along with the cosmological accretion rate, while at lower redshift the dynamically colder gas forms the low velocity dispersion stars of the thin disk.
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Surrogate-Based Optimization of Biogeochemical Transport Models
NASA Astrophysics Data System (ADS)
Prieß, Malte; Slawig, Thomas
2010-09-01
First approaches towards a surrogate-based optimization method for a one-dimensional marine biogeochemical model of NPZD type are presented. The model, developed by Oschlies and Garcon [1], simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column and is driven by ocean circulation data. A key issue is to minimize the misfit between the model output and given observational data. Our aim is to reduce the overall optimization cost avoiding expensive function and derivative evaluations by using a surrogate model replacing the high-fidelity model in focus. This in particular becomes important for more complex three-dimensional models. We analyse a coarsening in the discretization of the model equations as one way to create such a surrogate. Here the numerical stability crucially depends upon the discrete stepsize in time and space and the biochemical terms. We show that for given model parameters the level of grid coarsening can be choosen accordingly yielding a stable and satisfactory surrogate. As one example of a surrogate-based optimization method we present results of the Aggressive Space Mapping technique (developed by John W. Bandler [2, 3]) applied to the optimization of this one-dimensional biogeochemical transport model.
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Two-dimensional electrophoretic analysis of nuclear matrix proteins in human colon adenocarcinoma.
Toumpanaki, A; Baltatzis, G E; Gaitanarou, E; Seretis, E; Toumpanakis, C; Aroni, K; Kittas, Christos; Voloudakis-Baltatzis, I E
2009-01-01
The aim of the present study was to observe possible qualitative and quantitative expression differences between nuclear matrix proteins (NMPs) of human colon adenocarcinoma and their mirror biopsies, using the technique of two-dimensional gel electrophoresis, in order to identify the existence of specific NMP fingerprints for colon cancer. Colon tissues were examined ultrastructurally and NMPs were isolated biochemically, by serial extraction of lipids, soluble proteins, DNA, RNA, and intermediate filaments and were separated according to their isoelectric point (pI) and their molecular weight (MW) by high-resolution two-dimensional electrophoresis (2D). By comparing the 2D electropherograms of colon cancer tissues and mirror biopsy tissues we observed qualitative and quantitative expression differences between their NMPs but also a differentiation of NMP composition between the stages of malignancy. Moreover, despite the similarities between mirror biopsy samples, a highlight percentage of exception was observed. Electrophoretic results provided in this study demonstrated that the examined NMPs could be further investigated as potential markers for detection of colorectal cancer in an early stage, for the assessment of the disease progression, as well as useful tools for individual therapy and for preventing a possible recurrence of cancer and metastasis.
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Biotechnology of oil palm: strategies towards manipulation of lipid content and composition.
Parveez, Ghulam Kadir Ahmad; Rasid, Omar Abdul; Masani, Mat Yunus Abdul; Sambanthamurthi, Ravigadevi
2015-04-01
Oil palm is a major economic crop for Malaysia. The major challenges faced by the industry are labor shortage, availability of arable land and unstable commodity price. This has caused the industry to diversify its applications into higher value products besides increasing its yield. While conventional breeding has its limitations, biotechnology was identified as one of the tools for overcoming the above challenges. Research on biotechnology of oil palm began more than two decades ago leveraging a multidisciplinary approach involving biochemical studies, gene and promoter isolation, transformation vector construction and finally genetic transformation to produce the targeted products. The main target of oil palm biotechnology research is to increase oleic acid in the mesocarp. Other targets are stearic acid, palmitoleic acid, ricinoleic acid, lycopene (carotenoid) and biodegradable plastics. Significant achievements were reported for the biochemical studies, isolation of useful oil palm genes and characterization of important promoters. A large number of transformation constructs for various targeted products were successfully produced using the isolated oil palm genes and promoters. Finally transformation of these constructs into oil palm embryogenic calli was carried out while the regeneration of transgenic oil palm harboring the useful genes is in progress.
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DYNAMICAL INSTABILITIES IN HIGH-OBLIQUITY SYSTEMS
DOE Office of Scientific and Technical Information (OSTI.GOV)
Tamayo, D.; Nicholson, P. D.; Burns, J. A.
2013-03-01
High-inclination circumplanetary orbits that are gravitationally perturbed by the central star can undergo Kozai oscillations-large-amplitude, coupled variations in the orbital eccentricity and inclination. We first study how this effect is modified by incorporating perturbations from the planetary oblateness. Tremaine et al. found that, for planets with obliquities >68. Degree-Sign 875, orbits in the equilibrium local Laplace plane are unstable to eccentricity perturbations over a finite radial range and execute large-amplitude chaotic oscillations in eccentricity and inclination. In the hope of making that treatment more easily understandable, we analyze the problem using orbital elements, confirming this threshold obliquity. Furthermore, we findmore » that orbits inclined to the Laplace plane will be unstable over a broader radial range, and that such orbits can go unstable for obliquities less than 68. Degree-Sign 875. Finally, we analyze the added effects of radiation pressure, which are important for dust grains and provide a natural mechanism for particle semimajor axes to sweep via Poynting-Robertson drag through any unstable range. For low-eccentricity orbits in the equilibrium Laplace plane, we find that generally the effect persists; however, the unstable radial range is shifted and small retrograde particles can avoid the instability altogether. We argue that this occurs because radiation pressure modifies the equilibrium Laplace plane.« less
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Fibrous Hydrogels for Cell Encapsulation: A Modular and Supramolecular Approach.
Włodarczyk-Biegun, Małgorzata K; Farbod, Kambiz; Werten, Marc W T; Slingerland, Cornelis J; de Wolf, Frits A; van den Beucken, Jeroen J J P; Leeuwenburgh, Sander C G; Cohen Stuart, Martien A; Kamperman, Marleen
2016-01-01
Artificial 3-dimensional (3D) cell culture systems, which mimic the extracellular matrix (ECM), hold great potential as models to study cellular processes under controlled conditions. The natural ECM is a 3D structure composed of a fibrous hydrogel that provides both mechanical and biochemical cues to instruct cell behavior. Here we present an ECM-mimicking genetically engineered protein-based hydrogel as a 3D cell culture system that combines several key features: (1) Mild and straightforward encapsulation meters (1) ease of ut I am not so sure.encapsulation of the cells, without the need of an external crosslinker. (2) Supramolecular assembly resulting in a fibrous architecture that recapitulates some of the unique mechanical characteristics of the ECM, i.e. strain-stiffening and self-healing behavior. (3) A modular approach allowing controlled incorporation of the biochemical cue density (integrin binding RGD domains). We tested the gels by encapsulating MG-63 osteoblastic cells and found that encapsulated cells not only respond to higher RGD density, but also to overall gel concentration. Cells in 1% and 2% (weight fraction) protein gels showed spreading and proliferation, provided a relative RGD density of at least 50%. In contrast, in 4% gels very little spreading and proliferation occurred, even for a relative RGD density of 100%. The independent control over both mechanical and biochemical cues obtained in this modular approach renders our hydrogels suitable to study cellular responses under highly defined conditions.
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Hess, Ricarda; Jaeschke, Anna; Neubert, Holger; Hintze, Vera; Moeller, Stephanie; Schnabelrauch, Matthias; Wiesmann, Hans-Peter; Hart, David A; Scharnweber, Dieter
2012-12-01
In vivo, bone formation is a complex, tightly regulated process, influenced by multiple biochemical and physical factors. To develop a vital bone tissue engineering construct, all of these individual components have to be considered and integrated to gain an in vivo-like stimulation of target cells. The purpose of the present studies was to investigate the synergistic role of defined biochemical and physical microenvironments with respect to osteogenic differentiation of human mesenchymal stem cells (MSCs). Biochemical microenvironments have been designed using artificial extracellular matrices (aECMs), containing collagen I (coll) and glycosaminoglycans (GAGs) like chondroitin sulfate (CS), or a high-sulfated hyaluronan derivative (sHya), formulated as coatings on three-dimensional poly(caprolactone-co-lactide) (PCL) scaffolds. As part of the physical microenvironment, cells were exposed to pulsed electric fields via transformer-like coupling (TC). Results showed that aECM containing sHya enhanced osteogenic differentiation represented by increases in ALP activity and gene-expression (RT-qPCR) of several bone-related proteins (RUNX-2, ALP, OPN). Electric field stimulation alone did not influence cell proliferation, but osteogenic differentiation was enhanced if osteogenic supplements were provided, showing synergistic effects by the combination of sHya and electric fields. These results will improve the understanding of bone regeneration processes and support the development of effective tissue engineered bone constructs. Copyright © 2012 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Li, Sen; Zhong, Zhong
2014-02-01
An improved flux-gradient relationship between momentum φm(ζ) and sensible heat φh(ζ) is obtained by the use of the observational data over an alpine meadow in the eastern Tibet Plateau, in Maqu of China during the period June to August, 2010. The empirical coefficients of Businger—Dyer type function for the cases of unstable and stable stratification are modified. Non-dimensional vertical gradients of wind and potential temperature are calculated by three fitting functions; that is, the log—linear, log—square, and log—cubic functions, respectively. It is found that the von Karman constant approaches 0.4025 and the Prandtl number is about 1.10 based on the measurements in near-neutral conditions, which are within reasonable range proposed in previous studies. The revised flux-gradient profile functions of -1/5 power law for momentum and -1/3 power law for sensible heat are best fitted in unstable stratification conditions. Meanwhile, 2/5 power law, instead of linear functions, is more appropriate in stable stratification cases for momentum and sensible heat. Compared with results from previous studies in which traditional functions are used, the momentum and sensible heat fluxes estimated by the revised profile functions in the current study are much closer to the observations for the unstable and stable stratification conditions.
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Brachytherapy of prostate cancer after colectomy for colorectal cancer: pilot experience.
Koutrouvelis, Panos G; Theodorescu, Dan; Katz, Stuart; Lailas, Niko; Hendricks, Fred
2005-01-01
We present a method of brachytherapy for prostate cancer using a 3-dimensional stereotactic system and computerized tomography guidance in patients without a rectum due to previous treatment for colorectal cancer. From June 1994 to November 2003 a cohort of 800 patients were treated with brachytherapy for prostate cancer. Four patients had previously been treated for colorectal cancer with 4,500 cGy external beam radiation therapy, abdominoperineal resection and chemotherapy, while 1 underwent abdominoperineal resection alone for ulcerative colitis. Because of previous radiation therapy, these patients were not candidates for salvage external beam radiation therapy or radical prostatectomy and they had no rectum for transrectal ultrasound guided transperineal brachytherapy or cryotherapy. A previously described, 3-dimensional stereotactic system was used for brachytherapy in these patients. The prescribed radiation dose was 120 to 144 Gy with iodine seeds in rapid strand format. Patient followup included clinical examination and serum prostate specific antigen measurement. Average followup was 18.6 months. Four patients had excellent biochemical control, while 1 had biochemical failure. Patients did not experience any gastrointestinal morbidity. One patient had a stricture of the distal ureter, requiring a stent. Three-dimensional computerized tomography guided brachytherapy for prostate cancer in patients with a history of colorectal cancer who have no rectum is a feasible method of treatment.
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Lee, Bi-Shen; Lin, Pi-Chen; Lin, Ding-Zheng; Yen, Ta-Jen
2018-01-11
We present a three-dimensional patterned (3DP) multifunctional substrate with the functions of ultra-thin layer chromatography (UTLC) and surface enhanced Raman scattering (SERS), which simultaneously enables mixture separation, target localization and label-free detection. This multifunctional substrate is comprised of a 3DP silicon nanowires array (3DP-SiNWA), decorated with silver nano-dendrites (AgNDs) atop. The 3DP-SiNWA is fabricated by a facile photolithographic process and low-cost metal assisted chemical etching (MaCE) process. Then, the AgNDs are decorated onto 3DP-SiNWA by a wet chemical reduction process, obtaining 3DP-AgNDs@SiNWA multifunctional substrates. With various patterns designed on the substrates, the signal intensity could be maximized by the excellent confinement and concentrated effects of patterns. By using this 3DP-AgNDs@SiNWA substrate to scrutinize the mixture of two visible dyes, the individual target could be recognized and further boosted the Raman signal of target 15.42 times comparing to the un-patterned AgNDs@SiNWA substrate. Therefore, such a three-dimensional patterned multifunctional substrate empowers rapid mixture screening, and can be readily employed in practical applications for biochemical assays, food safety and other fields.
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Kundu, Subrata; Chakraborty, Dipjyoti; Kundu, Anirban; Pal, Amita
2013-01-01
Vigna mungo, a tropical leguminous plant, highly susceptible to yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus (MYMIV) resulting in high yield penalty. The molecular events occurring during compatible and incompatible interactions between V. mungo and MYMIV pathosystem are yet to be explored. In this study biochemical analyses in conjunction with proteomics of MYMIV-susceptible and -resistant V. mungo genotypes were executed to get an insight in the molecular events during compatible and incompatible plant-virus interactions. Biochemical analysis revealed an increase in phenolics, hydrogen peroxide and carbohydrate contents in both compatible and incompatible interactions; but the magnitudes were higher during incompatible interaction. In the resistant genotype the activities of superoxide dismutase and ascorbate peroxidase increased significantly, while catalase activity decreased. Comparative proteome analyses using two-dimensional gel electrophoresis coupled with mass spectrometry identified 109 differentially abundant proteins at 3, 7 and 14 days post MYMIV-inoculation. Proteins of several functional categories were differentially changed in abundance during both compatible and incompatible interactions. Among these, photosynthesis related proteins were mostly affected in the susceptible genotype resulting in reduced photosynthesis rate under MYMIV-stress. Differential intensities of chlorophyll fluorescence and chlorophyll contents are in congruence with proteomics data. It was revealed that Photosystem II electron transports are the primary targets of MYMIV during pathogenesis. Quantitative real time PCR analyses of selected genes corroborates with respective protein abundance during incompatible interaction. The network of various cellular pathways that are involved in inducing defense response contains several conglomerated cores of nodal proteins, of which ascorbate peroxidase, rubisco activase and serine/glycine hydroxymethyl transferase are the three major hubs with high connectivity. These nodal proteins play the crucial role of key regulators in bringing about a coordinated defense response in highly orchestrated manner. Biochemical and proteomic analyses revealed early accumulation of the defense/stress related proteins involved in ROS metabolism during incompatible interaction. The robustness in induction of defense/stress and signal transduction related proteins is the key factor in inducing resistance. The mechanism of MYMIV-resistance in V. mungo involves redirection of carbohydrate flux towards pentose phosphate pathway. Some of these identified, differentially regulated proteins are also conferring abiotic stress responses illustrating harmony amongst different stress responses. To the best of our knowledge, this is the lone study deciphering differential regulations of V. mungo leaf proteome upon MYMIV infection elucidating the mode of resistance response at the biochemical level.
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Allosteric Models for Cooperative Polymerization of Linear Polymers
Miraldi, Emily R.; Thomas, Peter J.; Romberg, Laura
2008-01-01
In the cytoskeleton, unfavorable nucleation steps allow cells to regulate where, when, and how many polymers assemble. Nucleated polymerization is traditionally explained by a model in which multistranded polymers assemble cooperatively, whereas linear, single-stranded polymers do not. Recent data on the assembly of FtsZ, the bacterial homolog of tubulin, do not fit either category. FtsZ can polymerize into single-stranded protofilaments that are stable in the absence of lateral interactions, but that assemble cooperatively. We developed a model for cooperative polymerization that does not require polymers to be multistranded. Instead, a conformational change allows subunits in oligomers to associate with high affinity, whereas a lower-affinity conformation is favored in monomers. We derive equations for calculating polymer concentrations, subunit conformations, and the apparent affinity of subunits for polymer ends. Certain combinations of equilibrium constants produce the sharp critical concentrations characteristic of cooperative polymerization. In these cases, the low-affinity conformation predominates in monomers, whereas virtually all polymers are composed of high-affinity subunits. Our model predicts that the three routes to forming HH dimers all involve unstable intermediates, limiting nucleation. The mathematical framework developed here can represent allosteric assembly systems with a variety of biochemical interpretations, some of which can show cooperativity, and others of which cannot. PMID:18502809
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Unstable solitary-wave solutions of the generalized Benjamin-Bona-Mahony equation
DOE Office of Scientific and Technical Information (OSTI.GOV)
McKinney, W.R.; Restrepo, J.M.; Bona, J.L.
1994-06-01
The evolution of solitary waves of the gBBM equation is investigated computationally. The experiments confirm previously derived theoretical stability estimates and, more importantly, yield insights into their behavior. For example, highly energetic unstable solitary waves when perturbed are shown to evolve into several stable solitary waves.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Moll, Ryan; Garaud, Pascale; Stellmach, Stephan, E-mail: rmoll@soe.ucsc.edu
2016-05-20
Oscillatory double-diffusive convection (ODDC; also known as semi-convection) refers to a type of double-diffusive instability that occurs in regions of planetary and stellar interiors that have a destabilizing thermal stratification and a stabilizing mean molecular weight stratification. In this series of papers, we use an extensive suite of three-dimensional (3D) numerical simulations to quantify the transport of heat and chemical species by ODDC. Rosenblum et al. first showed that ODDC can either spontaneously form layers that significantly enhance the transport of heat and chemical species compared to microscopic transport or remain in a state dominated by large-scale gravity waves, inmore » which there is a more modest enhancement of the turbulent transport rates. Subsequent studies in this series focused on identifying under what conditions layers form and quantifying transport through layered systems. Here we proceed to characterize transport through systems that are unstable to ODDC, but do not undergo spontaneous layer formation. We measure the thermal and compositional fluxes in non-layered ODDC from both two-dimensional (2D) and 3D numerical simulations, and show that 3D simulations are well approximated by similar simulations in a 2D domain. We find that the turbulent mixing rate in this regime is weak and can, to a first-level approximation, be neglected. We conclude by summarizing the findings of papers I through III into a single prescription for transport systems unstable to ODDC.« less
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Passive control of a falling sphere by elliptic-shaped appendages
NASA Astrophysics Data System (ADS)
Lācis, Uǧis; Olivieri, Stefano; Mazzino, Andrea; Bagheri, Shervin
2017-03-01
The majority of investigations characterizing the motion of single or multiple particles in fluid flows consider canonical body shapes, such as spheres, cylinders, discs, etc. However, protrusions on bodies—either surface imperfections or appendages that serve a function—are ubiquitous in both nature and applications. In this work, we characterize how the dynamics of a sphere with an axis-symmetric wake is modified in the presence of thin three-dimensional elliptic-shaped protrusions. By investigating a wide range of three-dimensional appendages with different aspect ratios and lengths, we clearly show that the sphere with an appendage may robustly undergo an inverted-pendulum-like (IPL) instability. This means that the position of the appendage placed behind the sphere and aligned with the free-stream direction is unstable, similar to how an inverted pendulum is unstable under gravity. Due to this instability, nontrivial forces are generated on the body, leading to turn and drift, if the body is free to fall under gravity. Moreover, we identify the aspect ratio and length of the appendage that induces the largest side force on the sphere, and therefore also the largest drift for a freely falling body. Finally, we explain the physical mechanisms behind these observations in the context of the IPL instability, i.e., the balance between surface area of the appendage exposed to reversed flow in the wake and the surface area of the appendage exposed to fast free-stream flow.
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NASA Astrophysics Data System (ADS)
Kourdis, Panayotis D.; Steuer, Ralf; Goussis, Dimitris A.
2010-09-01
Large-scale models of cellular reaction networks are usually highly complex and characterized by a wide spectrum of time scales, making a direct interpretation and understanding of the relevant mechanisms almost impossible. We address this issue by demonstrating the benefits provided by model reduction techniques. We employ the Computational Singular Perturbation (CSP) algorithm to analyze the glycolytic pathway of intact yeast cells in the oscillatory regime. As a primary object of research for many decades, glycolytic oscillations represent a paradigmatic candidate for studying biochemical function and mechanisms. Using a previously published full-scale model of glycolysis, we show that, due to fast dissipative time scales, the solution is asymptotically attracted on a low dimensional manifold. Without any further input from the investigator, CSP clarifies several long-standing questions in the analysis of glycolytic oscillations, such as the origin of the oscillations in the upper part of glycolysis, the importance of energy and redox status, as well as the fact that neither the oscillations nor cell-cell synchronization can be understood in terms of glycolysis as a simple linear chain of sequentially coupled reactions.
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Peters, James G.; Wilber, W.G.; Crawford, Charles G.; Girardi, F.P.
1979-01-01
A digital computer model calibrated to observe stream conditions was used to evaluate water quality in West Fork Blue River, Washington County, IN. Instream dissolved-oxygen concentration averaged 96.5% of saturation at selected sites on West Fork Blue River during two 24-hour summer surveys. This high dissolved-oxygen concentration reflects small carbonaceous and nitrogenous waste loads; adequate dilution of waste by the stream; and natural reaeration. Nonpoint source waste loads accounted for an average of 53.2% of the total carbonaceous biochemical-oxygen demand and 90.2% of the nitrogenous biochemical-oxygen demand. Waste-load assimilation was studiedfor critical summer and winter low flows. Natural streamflow for these conditions was zero, so no benefit from dilution was provided. The projected stream reaeration capacity was not sufficient to maintain the minimum daily dissolved-oxygen concentration (5 milligrams per liter) in the stream with current waste-discharge restrictions. During winter low flow, ammonia toxicity, rather than dissolved-oxygen concentration, was the limiting water-quality criterion downstream from the Salem wastewater-treatment facility. (USGS)
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Hydrogel Based Biosensors for In Vitro Diagnostics of Biochemicals, Proteins, and Genes.
Jung, Il Young; Kim, Ji Su; Choi, Bo Ram; Lee, Kyuri; Lee, Hyukjin
2017-06-01
Hydrogel-based biosensors have drawn considerable attention due to their various advantages over conventional detection systems. Recent studies have shown that hydrogel biosensors can be excellent alternative systems to detect a wide range of biomolecules, including small biochemicals, pathogenic proteins, and disease specific genes. Due to the excellent physical properties of hydrogels such as the high water content and stimuli-responsive behavior of cross-linked network structures, this system can offer substantial improvement for the design of novel detection systems for various diagnostic applications. The other main advantage of hydrogels is the role of biomimetic three-dimensional (3D) matrix immobilizing enzymes and aptamers within the detection systems, which enhances their stability. This provides ideal reaction conditions for enzymes and aptamers to interact with substrates within the aqueous environment of the hydrogel. In this review, we have highlighted various novel detection approaches utilizing the outstanding properties of the hydrogel. This review summarizes the recent progress of hydrogel-based biosensors and discusses their future perspectives and clinical limitations to overcome. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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TURBULENT MAGNETOHYDRODYNAMIC RECONNECTION MEDIATED BY THE PLASMOID INSTABILITY
DOE Office of Scientific and Technical Information (OSTI.GOV)
Huang, Yi-Min; Bhattacharjee, A., E-mail: yiminh@princeton.edu
2016-02-10
It has been established that the Sweet–Parker current layer in high Lundquist number reconnection is unstable to the super-Alfvénic plasmoid instability. Past two-dimensional magnetohydrodynamic simulations have demonstrated that the plasmoid instability leads to a new regime where the Sweet–Parker current layer changes into a chain of plasmoids connected by secondary current sheets, and the averaged reconnection rate becomes nearly independent of the Lundquist number. In this work, a three-dimensional simulation with a guide field shows that the additional degree of freedom allows plasmoid instabilities to grow at oblique angles, which interact and lead to self-generated turbulent reconnection. The averaged reconnectionmore » rate in the self-generated turbulent state is of the order of a hundredth of the characteristic Alfvén speed, which is similar to the two-dimensional result but is an order of magnitude lower than the fastest reconnection rate reported in recent studies of externally driven three-dimensional turbulent reconnection. Kinematic and magnetic energy fluctuations both form elongated eddies along the direction of the local magnetic field, which is a signature of anisotropic magnetohydrodynamic turbulence. Both energy fluctuations satisfy power-law spectra in the inertial range, where the magnetic energy spectral index is in the range from −2.3 to −2.1, while the kinetic energy spectral index is slightly steeper, in the range from −2.5 to −2.3. The anisotropy of turbulence eddies is found to be nearly scale-independent, in contrast with the prediction of the Goldreich–Sridhar theory for anisotropic turbulence in a homogeneous plasma permeated by a uniform magnetic field.« less
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Towards a General Theory of Extremes for Observables of Chaotic Dynamical Systems.
Lucarini, Valerio; Faranda, Davide; Wouters, Jeroen; Kuna, Tobias
2014-01-01
In this paper we provide a connection between the geometrical properties of the attractor of a chaotic dynamical system and the distribution of extreme values. We show that the extremes of so-called physical observables are distributed according to the classical generalised Pareto distribution and derive explicit expressions for the scaling and the shape parameter. In particular, we derive that the shape parameter does not depend on the chosen observables, but only on the partial dimensions of the invariant measure on the stable, unstable, and neutral manifolds. The shape parameter is negative and is close to zero when high-dimensional systems are considered. This result agrees with what was derived recently using the generalized extreme value approach. Combining the results obtained using such physical observables and the properties of the extremes of distance observables, it is possible to derive estimates of the partial dimensions of the attractor along the stable and the unstable directions of the flow. Moreover, by writing the shape parameter in terms of moments of the extremes of the considered observable and by using linear response theory, we relate the sensitivity to perturbations of the shape parameter to the sensitivity of the moments, of the partial dimensions, and of the Kaplan-Yorke dimension of the attractor. Preliminary numerical investigations provide encouraging results on the applicability of the theory presented here. The results presented here do not apply for all combinations of Axiom A systems and observables, but the breakdown seems to be related to very special geometrical configurations.
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Towards a General Theory of Extremes for Observables of Chaotic Dynamical Systems
NASA Astrophysics Data System (ADS)
Lucarini, Valerio; Faranda, Davide; Wouters, Jeroen; Kuna, Tobias
2014-02-01
In this paper we provide a connection between the geometrical properties of the attractor of a chaotic dynamical system and the distribution of extreme values. We show that the extremes of so-called physical observables are distributed according to the classical generalised Pareto distribution and derive explicit expressions for the scaling and the shape parameter. In particular, we derive that the shape parameter does not depend on the chosen observables, but only on the partial dimensions of the invariant measure on the stable, unstable, and neutral manifolds. The shape parameter is negative and is close to zero when high-dimensional systems are considered. This result agrees with what was derived recently using the generalized extreme value approach. Combining the results obtained using such physical observables and the properties of the extremes of distance observables, it is possible to derive estimates of the partial dimensions of the attractor along the stable and the unstable directions of the flow. Moreover, by writing the shape parameter in terms of moments of the extremes of the considered observable and by using linear response theory, we relate the sensitivity to perturbations of the shape parameter to the sensitivity of the moments, of the partial dimensions, and of the Kaplan-Yorke dimension of the attractor. Preliminary numerical investigations provide encouraging results on the applicability of the theory presented here. The results presented here do not apply for all combinations of Axiom A systems and observables, but the breakdown seems to be related to very special geometrical configurations.
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Fabrication of 3D SiO x structures using patterned PMMA sacrificial layer
NASA Astrophysics Data System (ADS)
Li, Zhiqin; Xiang, Quan; Zheng, Mengjie; Bi, Kaixi; Chen, Yiqin; Chen, Keqiu; Duan, Huigao
2018-02-01
Three-dimensional (3D) nanofabrication based on electron-beam lithography (EBL) has drawn wide attention for various applications with its high patterning resolution and design flexibility. In this work, we present a bilayer EBL process to obtain 3D freestanding SiO x structures via the release of the bottom sacrificial layer. This new kind of bilayer process enables us to define various 3D freestanding SiO x structures with high resolution and low edge roughness. As a proof of concept for applications, metal-coated freestanding SiO x microplates with an underlying air gap were fabricated to form asymmetric Fabry-Perot resonators, which can be utilized for colorimetric refractive index sensing and thus also have application potential for biochemical detection, anti-counterfeiting and smart active nano-optical devices.
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New Frontiers in Optical Science: Terahertz Spectroscopy ot Two Dimensional Systems
NASA Astrophysics Data System (ADS)
Lee, Yun-Shik
2011-10-01
Terahertz (THz) radiation is electromagnetic radiation whose frequency lies between the microwave and infrared regions of the spectrum. Naturally occurring THz radiation fills up the space of everyday life providing warmth, yet this part of the spectrum remains the least explored region mainly due to the technical difficulties. The technological gap, however, has been rapidly diminishing for the last two decades. The new and exciting frontier of the THz science and technology has encroached on many different disciplines producing a broad range of applications such as medical imaging, sensing of biochemical agents, and ultra-high speed communication. Furthermore, the unique and advanced techniques of the THz spectroscopy have been proved to be a powerful tool to investigate the material properties inaccessible until recently. For example, THz waves strongly interact with electrons and holes in two dimensional systems, in which their dynamics are governed mainly by many-body Coulomb interactions. I will present our experimental studies demonstrating remarkable quantum effects in semiconductor nanostructures and exotic charge carrier dynamics in graphene.
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Combination of biochemical and mechanical cues for tendon tissue engineering.
Testa, Stefano; Costantini, Marco; Fornetti, Ersilia; Bernardini, Sergio; Trombetta, Marcella; Seliktar, Dror; Cannata, Stefano; Rainer, Alberto; Gargioli, Cesare
2017-11-01
Tendinopathies negatively affect the life quality of millions of people in occupational and athletic settings, as well as the general population. Tendon healing is a slow process, often with insufficient results to restore complete endurance and functionality of the tissue. Tissue engineering, using tendon progenitors, artificial matrices and bioreactors for mechanical stimulation, could be an important approach for treating rips, fraying and tissue rupture. In our work, C3H10T1/2 murine fibroblast cell line was exposed to a combination of stimuli: a biochemical stimulus provided by Transforming Growth Factor Beta (TGF-β) and Ascorbic Acid (AA); a three-dimensional environment represented by PEGylated-Fibrinogen (PEG-Fibrinogen) biomimetic matrix; and a mechanical induction exploiting a custom bioreactor applying uniaxial stretching. In vitro analyses by immunofluorescence and mechanical testing revealed that the proposed combined approach favours the organization of a three-dimensional tissue-like structure promoting a remarkable arrangement of the cells and the neo-extracellular matrix, reflecting into enhanced mechanical strength. The proposed method represents a novel approach for tendon tissue engineering, demonstrating how the combined effect of biochemical and mechanical stimuli ameliorates biological and mechanical properties of the artificial tissue compared to those obtained with single inducement. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.
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Erickson, Isaac E; van Veen, Steven C; Sengupta, Swarnali; Kestle, Sydney R; Mauck, Robert L
2011-10-01
Cartilage degeneration is common in the aged, and aged chondrocytes are inferior to juvenile chondrocytes in producing cartilage-specific extracellular matrix. Mesenchymal stem cells (MSCs) are an alternative cell type that can differentiate toward the chondrocyte phenotype. Aging may influence MSC chondrogenesis but remains less well studied, particularly in the bovine system. The objectives of this study were (1) to confirm age-related changes in bovine articular cartilage, establish how age affects chondrogenesis in cultured pellets for (2) chondrocytes and (3) MSCs, and (4) determine age-related changes in the biochemical and biomechanical development of clinically relevant MSC-seeded hydrogels. Native bovine articular cartilage from fetal (n = 3 donors), juvenile (n = 3 donors), and adult (n = 3 donors) animals was analyzed for mechanical and biochemical properties (n = 3-5 per donor). Chondrocyte and MSC pellets (n = 3 donors per age) were cultured for 6 weeks before analysis of biochemical content (n = 3 per donor). Bone marrow-derived MSCs of each age were also cultured within hyaluronic acid hydrogels for 3 weeks and analyzed for matrix deposition and mechanical properties (n = 4 per age). Articular cartilage mechanical properties and collagen content increased with age. We observed robust matrix accumulation in three-dimensional pellet culture by fetal chondrocytes with diminished collagen-forming capacity in adult chondrocytes. Chondrogenic induction of MSCs was greater in fetal and juvenile cell pellets. Likewise, fetal and juvenile MSCs in hydrogels imparted greater matrix and mechanical properties. Donor age and biochemical microenvironment were major determinants of both bovine chondrocyte and MSC functional capacity. In vitro model systems should be evaluated in the context of age-related changes and should be benchmarked against human MSC data.
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Purification and characterization of peroxidase from avocado (Persea americana Mill, cv. Hass).
Rojas-Reyes, José O; Robles-Olvera, Victor; Carvajal-Zarrabal, Octavio; Castro Matinez, Claudia; Waliszewski, Krzysztof N; Aguilar-Uscanga, María Guadalupe
2014-07-01
Avocado (Persea americana Mill, cv. Hass) fruit ranks tenth in terms of the most important products for Mexico. Avocado products are quite unstable due to the presence of oxidative enzymes such as polyphenol oxidase and peroxidase. The present study is to characterize the activity of purified avocado peroxidase from avocado in order to ascertain the biochemical and kinetic properties and their inhibition conditions. Purification was performed by Sephacryl S 200 HR gel filtration chromatography and its estimated molecular weight was 40 kDa. The zymogram showed an isoelectric point of 4.7. Six substrates were tested in order to ascertain the affinity of the enzyme for these substrates. The purified peroxidase was found to have low Km (0.296 mM) and high catalytic efficiency (2688 mM(-1) s(-1)) using 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid), optimum activity being reached at 51°C, pH 3.8. The addition of dithiothreitol, β-mercaptoethanol, ascorbic acid, sodium azide, L-cysteine and Tween-20 had high inhibitory effects, while metals ions such as Cu(+), Fe(2+) and Mn(2+) had weak inhibitory activity on purified avocado peroxidase. The purified avocado peroxidase exhibits high inhibition (Ki = 0.37 µM) with 1.97 µM n-propyl gallate using ABTS as substrate at 51°C, pH 3.8 for 10 min. © 2013 Society of Chemical Industry.
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Super-resolution links vinculin localization to function in focal adhesions.
Giannone, Grégory
2015-07-01
Integrin-based focal adhesions integrate biochemical and biomechanical signals from the extracellular matrix and the actin cytoskeleton. The combination of three-dimensional super-resolution imaging and loss- or gain-of-function protein mutants now links the nanoscale dynamic localization of proteins to their activation and function within focal adhesions.
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Cong, Guangzhi; Yan, Ru; Huang, Hui; Wang, Kai; Yan, Ning; Jin, Ping; Zhang, Na; Hou, Jianjun; Chen, Dapeng; Jia, Shaobin
2017-03-15
Hyperhomocysteinemia (Hhcy) is an independent risk factor of atherosclerosis and promotes unstable plaque formation. Epigenetic mechanisms play an important role in the pathogenesis of atherosclerosis induced by Hhcy. However, the exact mechanism is still undefined. Lesional apoptotic cells and necrotic core formation contribute greatly to the progression of plaque. The present study sought to determine whether modification of histone methylation is involved in macrophage apoptosis and unstable plaque formation in the condition of Hhcy. The unstable plaque formation, lesional apoptotic cells and status of histone methylation were monitored in the aortas of Hhcy ApoE -/- mice induced by a high-methionine (HM) diet for 20weeks. Involvement of histone methylation in macrophage apoptosis and foam cell formation were assessed in macrophage Raw 264.7 cells after being challenged with homocysteine alone or in combination with the histone methylation inhibitor BIX 01294. The unstable plaque formation and lesion apoptotic cells are increased in ApoE -/ - mice supplemented with high-methionine (HM), accompanied with a decreased expression of histone H3 lysine 9 dimethylation. Hhcy increases the apoptosis of macrophages and inhibits the histone H3 lysine 9 dimethylation, as well as the expression of histone methyltransferase G9a in vitro. Inhibition of histone methylation by BIX01294 enhances macrophage apoptosis and foam cell formation in vitro. Our data suggest that Hhcy promotes the progression of atherosclerosis via macrophage apoptosis. Histone methylation might be involved in macrophage apoptosis and unstable plaque formation in methionine induced hyperhomocysteinemic ApoE -/- mice. Copyright © 2017 Elsevier Inc. All rights reserved.
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Relativistic thermal electron scale instabilities in sheared flow plasma
NASA Astrophysics Data System (ADS)
Miller, Evan D.; Rogers, Barrett N.
2016-04-01
> The linear dispersion relation obeyed by finite-temperature, non-magnetized, relativistic two-fluid plasmas is presented, in the special case of a discontinuous bulk velocity profile and parallel wave vectors. It is found that such flows become universally unstable at the collisionless electron skin-depth scale. Further analyses are performed in the limits of either free-streaming ions or ultra-hot plasmas. In these limits, the system is highly unstable in the parameter regimes associated with either the electron scale Kelvin-Helmholtz instability (ESKHI) or the relativistic electron scale sheared flow instability (RESI) recently highlighted by Gruzinov. Coupling between these modes provides further instability throughout the remaining parameter space, provided both shear flow and temperature are finite. An explicit parameter space bound on the highly unstable region is found.
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Chemical functionalization of surfaces for building three-dimensional engineered biosensors
NASA Astrophysics Data System (ADS)
Marques, Marco E.; Mansur, Alexandra A. P.; Mansur, Herman S.
2013-06-01
This study presents a new approach for developing biosensors based on enzymatic systems with designed three-dimensional structures. Silica glass slides were chemically functionalized at surfaces by reacting with organosilanes, 3-mercaptopropyltriethoxysilane (MPTES), and 3-aminopropyltriethoxysilane (APTES), using sol-gel process at room temperature. The functionalization of the supports was characterized by contact angle measurements and FTIR spectroscopy. The first enzyme layer was covalently immobilized to the support by a bi-functional linker (glutaraldehyde). The second enzyme layer was deposited using the protein conjugation method based on the high affinity "avidin-biotin" interactions. Each enzyme was biotinylated before being added to the nanostructured system and avidin was used as the binder between consecutive enzyme layers. The biochemical response was assayed at all stages to certify that the enzymatic bioactivity was retained throughout the entire layer-by-layer (LBL) process. The model of building 3D-enzymatic systems was evaluated using the enzymatic structure with glucose oxidase (GOx) and horseradish peroxidase (HRP). It was verified that the amino-modified support presented the highest bioactivity response compared to the other chemical functionalities. Moreover, the bienzyme nanostructure demonstrated relevant biochemical activity upon injecting the glucose substrate into the system. Finally, as a proof of concept, the bienzyme systems were assayed using real samples of regular and sugar-free soft drinks where they effectively behaved as structured biosensor for glucose with the built-in 3D hybrid architecture. Based on the results, it can be foreseen the development of promising new nanomaterials for several analytical applications such as monitoring the quality of food and beverages for nutrition purposes.
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Reactive transport in a partially molten system with binary solid solution
NASA Astrophysics Data System (ADS)
Jordan, J.; Hesse, M. A.
2017-12-01
Melt extraction from the Earth's mantle through high-porosity channels is required to explain the composition of the oceanic crust. Feedbacks from reactive melt transport are thought to localize melt into a network of high-porosity channels. Recent studies invoke lithological heterogeneities in the Earth's mantle to seed the localization of partial melts. Therefore, it is necessary to understand the reaction fronts that form as melt flows across the lithological interface of a heterogeneity and the background mantle. Simplified melting models of such systems aide in the interpretation and formulation of larger scale mantle models. Motivated by the aforementioned facts, we present a chromatographic analysis of reactive melt transport across lithological boundaries, using theory for hyperbolic conservation laws. This is an extension of well-known linear trace element chromatography to the coupling of major elements and energy transport. Our analysis allows the prediction of the feedbacks that arise in reactive melt transport due to melting, freezing, dissolution and precipitation for frontal reactions. This study considers the simplified case of a rigid, partially molten porous medium with binary solid solution. As melt traverses a lithological contact-modeled as a Riemann problem-a rich set of features arise, including a reacted zone between an advancing reaction front and partial chemical preservation of the initial contact. Reactive instabilities observed in this study originate at the lithological interface rather than along a chemical gradient as in most studies of mantle dynamics. We present a regime diagram that predicts where reaction fronts become unstable, thereby allowing melt localization into high-porosity channels through reactive instabilities. After constructing the regime diagram, we test the one-dimensional hyperbolic theory against two-dimensional numerical experiments. The one-dimensional hyperbolic theory is sufficient for predicting the qualitative behavior of reactive melt transport simulations conducted in two-dimensions. The theoretical framework presented can be extended to more complex and realistic phase behavior, and is therefore a useful tool for understanding nonlinear feedbacks in reactive melt transport problems relevant to mantle dynamics.
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Three-Dimensional Computational Model for Flow in an Over-Expanded Nozzle With Porous Surfaces
NASA Technical Reports Server (NTRS)
Abdol-Hamid, K. S.; Elmiligui, Alaa; Hunter, Craig A.; Massey, Steven J.
2006-01-01
A three-Dimensional computational model is used to simulate flow in a non-axisymmetric, convergent-divergent nozzle incorporating porous cavities for shock-boundary layer interaction control. The nozzle has an expansion ratio (exit area/throat area) of 1.797 and a design nozzle pressure ratio of 8.78. Flow fields for the baseline nozzle (no porosity) and for the nozzle with porous surfaces of 10% openness are computed for Nozzle Pressure Ratio (NPR) varying from 1.29 to 9.54. The three dimensional computational results indicate that baseline (no porosity) nozzle performance is dominated by unstable, shock-induced, boundary-layer separation at over-expanded conditions. For NPR less than or equal to 1.8, the separation is three dimensional, somewhat unsteady, and confined to a bubble (with partial reattachment over the nozzle flap). For NPR greater than or equal to 2.0, separation is steady and fully detached, and becomes more two dimensional as NPR increased. Numerical simulation of porous configurations indicates that a porous patch is capable of controlling off design separation in the nozzle by either alleviating separation or by encouraging stable separation of the exhaust flow. In the present paper, computational simulation results, wall centerline pressure, mach contours, and thrust efficiency ratio are presented, discussed and compared with experimental data. Results indicate that comparisons are in good agreement with experimental data. The three-dimensional simulation improves the comparisons for over-expanded flow conditions as compared with two-dimensional assumptions.
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Albright, B. J.; Yin, L.; Bowers, K. J.; ...
2016-03-04
Two- and three-dimensional particle-in-cell simulations of stimulated Brillouin scattering(SBS) in laser speckle geometry have been analyzed to evaluate the relative importance of competing nonlinear processes in the evolution and saturation of SBS. It is found that ion-trapping-induced wavefront bowing and breakup of ion acoustic waves(IAW) and the associated side-loss of trapped ions dominate electron-trapping-induced IAW wavefront bowing and breakup, as well as the two-ion-wave decay instability over a range of ZT e/T i conditions and incident laser intensities. In the simulations, the latter instability does not govern the nonlinear saturation of SBS; however, evidence of two-ion-wave decay is seen, appearingmore » as a modulation of the ion acoustic wavefronts. This modulation is periodic in the laser polarization plane, anti-symmetric across the speckle axis, and of a wavenumber matching that of the incident laser pulse. Furthermore, a simple analytic model is provided for how spatial “imprinting” from a high frequency inhomogeneity (in this case, the density modulation from the laser) in an unstable system with continuum eigenmodes can selectively amplify modes with wavenumbers that match that of the inhomogeneity.« less
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Simulations of Viscous Accretion Flow around Black Holes in a Two-dimensional Cylindrical Geometry
NASA Astrophysics Data System (ADS)
Lee, Seong-Jae; Chattopadhyay, Indranil; Kumar, Rajiv; Hyung, Siek; Ryu, Dongsu
2016-11-01
We simulate shock-free and shocked viscous accretion flows onto a black hole in a two-dimensional cylindrical geometry, where initial conditions were chosen from analytical solutions. The simulation code used the Lagrangian total variation diminishing plus remap routine, which enabled us to attain high accuracy in capturing shocks and to handle the angular momentum distribution correctly. The inviscid shock-free accretion disk solution produced a thick disk structure, while the viscous shock-free solution attained a Bondi-like structure, but in either case, no jet activity nor any quasi-periodic oscillation (QPO)-like activity developed. The steady-state shocked solution in the inviscid as well as in the viscous regime matched theoretical predictions well. However, increasing viscosity renders the accretion shock unstable. Large-amplitude shock oscillation is accompanied by intermittent, transient inner multiple shocks. This oscillation of the inner part of the disk is interpreted as the source of QPO in hard X-rays observed in micro-quasars. Strong shock oscillation induces strong episodic jet emission. The jets also show the existence of shocks, which are produced as one shell hits the preceding one. The periodicities of the jets and shock oscillation are similar; the jets for the higher viscosity parameter appear to be stronger and faster.
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SIMULATIONS OF VISCOUS ACCRETION FLOW AROUND BLACK HOLES IN A TWO-DIMENSIONAL CYLINDRICAL GEOMETRY
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lee, Seong-Jae; Hyung, Siek; Chattopadhyay, Indranil
2016-11-01
We simulate shock-free and shocked viscous accretion flows onto a black hole in a two-dimensional cylindrical geometry, where initial conditions were chosen from analytical solutions. The simulation code used the Lagrangian total variation diminishing plus remap routine, which enabled us to attain high accuracy in capturing shocks and to handle the angular momentum distribution correctly. The inviscid shock-free accretion disk solution produced a thick disk structure, while the viscous shock-free solution attained a Bondi-like structure, but in either case, no jet activity nor any quasi-periodic oscillation (QPO)-like activity developed. The steady-state shocked solution in the inviscid as well as inmore » the viscous regime matched theoretical predictions well. However, increasing viscosity renders the accretion shock unstable. Large-amplitude shock oscillation is accompanied by intermittent, transient inner multiple shocks. This oscillation of the inner part of the disk is interpreted as the source of QPO in hard X-rays observed in micro-quasars. Strong shock oscillation induces strong episodic jet emission. The jets also show the existence of shocks, which are produced as one shell hits the preceding one. The periodicities of the jets and shock oscillation are similar; the jets for the higher viscosity parameter appear to be stronger and faster.« less
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Numerical simulations of a reduced model for blood coagulation
NASA Astrophysics Data System (ADS)
Pavlova, Jevgenija; Fasano, Antonio; Sequeira, Adélia
2016-04-01
In this work, the three-dimensional numerical resolution of a complex mathematical model for the blood coagulation process is presented. The model was illustrated in Fasano et al. (Clin Hemorheol Microcirc 51:1-14, 2012), Pavlova et al. (Theor Biol 380:367-379, 2015). It incorporates the action of the biochemical and cellular components of blood as well as the effects of the flow. The model is characterized by a reduction in the biochemical network and considers the impact of the blood slip at the vessel wall. Numerical results showing the capacity of the model to predict different perturbations in the hemostatic system are discussed.
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Dynamics of Active Separation Control at High Reynolds Numbers
NASA Technical Reports Server (NTRS)
Pack, LaTunia G.; Seifert, Avi
2000-01-01
A series of active flow control experiments were recently conducted at high Reynolds numbers on a generic separated configuration. The model simulates the upper surface of a 20% thick Glauert-Goldschmied type airfoil at zero angle of attack. The flow is fully turbulent since the tunnel sidewall boundary layer flows over the model. The main motivation for the experiments is to generate a comprehensive data base for validation of unsteady numerical simulation as a first step in the development of a CFD design tool, without which it would not be possible to effectively utilize the great potential of unsteady flow control. This paper focuses on the dynamics of several key features of the baseline as well as the controlled flow. It was found that the thickness of the upstream boundary layer has a negligible effect on the flow dynamics. It is speculated that separation is caused mainly by the highly convex surface while viscous effects are less important. The two-dimensional separated flow contains unsteady waves centered on a reduced frequency of 0.9, while in the three dimensional separated flow, frequencies around a reduced frequency of 0.3 and 1 are active. Several scenarios of resonant wave interaction take place at the separated shear-layer and in the pressure recovery region. The unstable reduced frequency bands for periodic excitation are centered on 1.5 and 5, but these reduced frequencies are based on the length of the baseline bubble that shortens due to the excitation. The conventional works well for the coherent wave features. Reproduction of these dynamic effects by a numerical simulation would provide benchmark validation.
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Analysis of precision in chemical oscillators: implications for circadian clocks
NASA Astrophysics Data System (ADS)
d'Eysmond, Thomas; De Simone, Alessandro; Naef, Felix
2013-10-01
Biochemical reaction networks often exhibit spontaneous self-sustained oscillations. An example is the circadian oscillator that lies at the heart of daily rhythms in behavior and physiology in most organisms including humans. While the period of these oscillators evolved so that it resonates with the 24 h daily environmental cycles, the precision of the oscillator (quantified via the Q factor) is another relevant property of these cell-autonomous oscillators. Since this quantity can be measured in individual cells, it is of interest to better understand how this property behaves across mathematical models of these oscillators. Current theoretical schemes for computing the Q factors show limitations for both high-dimensional models and in the vicinity of Hopf bifurcations. Here, we derive low-noise approximations that lead to numerically stable schemes also in high-dimensional models. In addition, we generalize normal form reductions that are appropriate near Hopf bifurcations. Applying our approximations to two models of circadian clocks, we show that while the low-noise regime is faithfully recapitulated, increasing the level of noise leads to species-dependent precision. We emphasize that subcomponents of the oscillator gradually decouple from the core oscillator as noise increases, which allows us to identify the subnetworks responsible for robust rhythms.
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Formation of Spiral-Arm Spurs and Bound Clouds in Vertically Stratified Galactic Gas Disks
NASA Astrophysics Data System (ADS)
Kim, Woong-Tae; Ostriker, Eve C.
2006-07-01
We investigate the growth of spiral-arm substructure in vertically stratified, self-gravitating, galactic gas disks, using local numerical MHD simulations. Our new models extend our previous two-dimensional studies, which showed that a magnetized spiral shock in a thin disk can undergo magneto-Jeans instability (MJI), resulting in regularly spaced interarm spur structures and massive gravitationally bound fragments. Similar spur (or ``feather'') features have recently been seen in high-resolution observations of several galaxies. Here we consider two sets of numerical models: two-dimensional simulations that use a ``thick-disk'' gravitational kernel, and three-dimensional simulations with explicit vertical stratification. Both models adopt an isothermal equation of state with cs=7 km s-1. When disks are sufficiently magnetized and self-gravitating, the result in both sorts of models is the growth of spiral-arm substructure similar to that in our previous razor-thin models. Reduced self-gravity due to nonzero disk thickness increases the spur spacing to ~10 times the Jeans length at the arm peak. Bound clouds that form from spur fragmentation have masses ~(1-3)×107 Msolar each, similar to the largest observed GMCs. The mass-to-flux ratios and specific angular momenta of the bound condensations are lower than large-scale galactic values, as is true for observed GMCs. We find that unmagnetized or weakly magnetized two-dimensional models are unstable to the ``wiggle instability'' previously identified by Wada & Koda. However, our fully three-dimensional models do not show this effect. Nonsteady motions and strong vertical shear prevent coherent vortical structures from forming, evidently suppressing the wiggle instability. We also find no clear traces of Parker instability in the nonlinear spiral arm substructures that emerge, although conceivably Parker modes may help seed the MJI at early stages since azimuthal wavelengths are similar.
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NASA Technical Reports Server (NTRS)
Ruffert, Maximilian; Arnett, David
1994-01-01
We investigate the hydrodynamics of three-dimensional classical Bondi-Hoyle accretion. Totally absorbing spheres of varying sizes (from 10 down to 0.01 accretion radii) move at Mach 3 relative to a homogeneous and slightly perturbed medium, which is taken to be an ideal gas (gamma = 5/3). To accommodate the long-range gravitational forces, the extent of the computational volume is 32(exp 3) accretion radii. We examine the influence of numerical procedure on physical behavior. The hydrodynamics is modeled by the 'piecewise parabolic method.' No energy sources (nuclear burning) or sinks (radiation, conduction) are included. The resolution in the vicinity of the accretor is increased by multiply nesting several (5-10) grids around the sphere, each finer grid being a factor of 2 smaller in zone dimension that the next coarser grid. The largest dynamic range (ratio of size of the largest grid to size of the finest zone) is 16,384. This allows us to include a coarse model for the surface of the accretor (vacuum sphere) on the finest grid, while at the same time evolving the gas on the coarser grids. Initially (at time t = 0-10), a shock front is set up, a Mach cone develops, and the accretion column is observable. Eventually the flow becomes unstable, destroying axisymmetry. This happens approximately when the mass accretion rate reaches the values (+/- 10%) predicted by the Bondi-Hoyle accretion formula (factor of 2 included). However, our three-dimensional models do not show the highly dynamic flip-flop flow so prominent in two-dimensional calculations performed by other authors. The flow, and thus the accretion rate of all quantities, shows quasi-periodic (P approximately equals 5) cycles between quiescent and active states. The interpolation formula proposed in an accompanying paper is found to follow the collected numerical data to within approximately 30%. The specific angular momentum accreted is of the same order of magnitude as the values previously found for two-dimensional flows.
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Chevalier, Michael W.; El-Samad, Hana
2014-01-01
Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled. PMID:25481130
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NASA Astrophysics Data System (ADS)
Chevalier, Michael W.; El-Samad, Hana
2014-12-01
Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.
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High resolution IVEM tomography of biological specimens
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sedat, J.W.; Agard, D.A.
Electron tomography is a powerful tool for elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. The introduction of intermediate voltage electron microscopes further extended the technique by providing the means to examine very large and non-symmetrical subcellular organelles, at resolutions beyond what would be possible using light microscopy. Recent studies using electron tomography on a variety of cellular organelles and assemblies such as centrosomes, kinetochores, and chromatin have clearly demonstrated the power of this technique for obtaining 3D structural information on non-symmetric cell components. When combined with biochemical and molecular observations, these 3D reconstructions have provided significantmore » new insights into biological function.« less
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Expression and Purification of Rat Glucose Transporter 1 in Pichia pastoris.
Venskutonytė, Raminta; Elbing, Karin; Lindkvist-Petersson, Karin
2018-01-01
Large amounts of pure and homogenous protein are a prerequisite for several biochemical and biophysical analyses, and in particular if aiming at resolving the three-dimensional protein structure. Here we describe the production of the rat glucose transporter 1 (GLUT1), a membrane protein facilitating the transport of glucose in cells. The protein is recombinantly expressed in the yeast Pichia pastoris. It is easily maintained and large-scale protein production in shaker flasks, as commonly performed in academic research laboratories, results in relatively high yields of membrane protein. The purification protocol describes all steps needed to obtain a pure and homogenous GLUT1 protein solution, including cell growth, membrane isolation, and chromatographic purification methods.
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Stability of a Light Sail Riding on a Laser Beam
DOE Office of Scientific and Technical Information (OSTI.GOV)
Manchester, Zachary; Loeb, Abraham, E-mail: zmanchester@seas.harvard.edu
2017-03-10
The stability of a light sail riding on a laser beam is analyzed both analytically and numerically. Conical sails on Gaussian beams, which have been studied in the past, are shown to be unstable without active control or additional mechanical modifications. A new architecture for a passively stable sail-and-beam configuration is proposed. The novel spherical shell design for the sail is capable of “beam riding” without the need for active feedback control. Full three-dimensional ray-tracing simulations are performed to verify our analytical results.
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Application of satellite data in variational analysis for global cyclonic systems
NASA Technical Reports Server (NTRS)
Achtemeier, G. L.
1987-01-01
The research goal was a variational data assimilation method that incorporates as dynamical constraints, the primitive equations for a moist, convectively unstable atmosphere and the radiative transfer equation. Variables to be adjusted include the three-dimensional vector wind, height, temperature, and moisture from rawinsonde data, and cloud-wind vectors, moisture, and radiance from satellite data. This presents a formidable mathematical problem. In order to facilitate thorough analysis of each of the model components, four variational models that divide the problem naturally according to increasing complexity are defined. Each model is summarized.
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New Kaluza-Klein instantons and the decay of AdS vacua
Ooguri, Hirosi; Spodyneiko, Lev
2017-07-19
We construct a generalization of Witten’s Kaluza-Klein instanton, where a higher-dimensional sphere (rather than a circle as in Witten’s instanton) collapses to zero size and the geometry terminates at a bubble of nothing, in a low energy effective theory of M theory. We then use the solution to exhibit the instability of nonsupersymmetric AdS 5 vacua in M theory compactified on positive Kähler-Einstein spaces, providing further evidence for the recent conjecture that any nonsupersymmetric anti–de Sitter vacuum supported by fluxes must be unstable.
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Simulations relevant to the beam instability in the foreshock
NASA Technical Reports Server (NTRS)
Cairns, I. H.; Nishikawa, K.-I.
1989-01-01
The results presently obtained from two-dimensional simulations of the reactive instability for Maxwellian beams and cutoff distributions are noted to be consistent with recent suggestions that electrons backstreaming into earth's foreshock have steep-sided cutoff distributions, which are initially unstable to the reactive instability, and that the back-reaction to the wave growth causes the instability to pass into its kinetic phase. It is demonstrated that the reactive instability is a bunching instability, and that the reactive instability saturates and passes over into the kinetic phase by particle trapping.
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Unstable matter and the 1-0 MeV gamma-ray background
NASA Technical Reports Server (NTRS)
Daly, Ruth A.
1988-01-01
The spectrum of photons produced by an unstable particle which decayed while the universe was young is calculated. This spectrum is compared to that of the 1-10 MeV shoulder, a feature of the high-energy, extragalactic gamma-ray background, whose origin has not yet been determined. The calculated spectrum contains two parameters which are adjusted to obtain a maximal fit to the observed spectrum; the fit thus obtained is accurate to the 99 percent confidence level. The implications for the mass, lifetime, initial abundance, and branching ratio of the unstable particle are discussed.
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NASA Astrophysics Data System (ADS)
Edelmann, P. V. F.; Röpke, F. K.; Hirschi, R.; Georgy, C.; Jones, S.
2017-07-01
Context. The treatment of mixing processes is still one of the major uncertainties in 1D stellar evolution models. This is mostly due to the need to parametrize and approximate aspects of hydrodynamics in hydrostatic codes. In particular, the effect of hydrodynamic instabilities in rotating stars, for example, dynamical shear instability, evades consistent description. Aims: We intend to study the accuracy of the diffusion approximation to dynamical shear in hydrostatic stellar evolution models by comparing 1D models to a first-principle hydrodynamics simulation starting from the same initial conditions. Methods: We chose an initial model calculated with the stellar evolution code GENEC that is just at the onset of a dynamical shear instability but does not show any other instabilities (e.g., convection). This was mapped to the hydrodynamics code SLH to perform a 2D simulation in the equatorial plane. We compare the resulting profiles in the two codes and compute an effective diffusion coefficient for the hydro simulation. Results: Shear instabilities develop in the 2D simulation in the regions predicted by linear theory to become unstable in the 1D stellar evolution model. Angular velocity and chemical composition is redistributed in the unstable region, thereby creating new unstable regions. After a period of time, the system settles in a symmetric, steady state, which is Richardson stable everywhere in the 2D simulation, whereas the instability remains for longer in the 1D model due to the limitations of the current implementation in the 1D code. A spatially resolved diffusion coefficient is extracted by comparing the initial and final profiles of mean atomic mass. Conclusions: The presented simulation gives a first insight on hydrodynamics of shear instabilities in a real stellar environment and even allows us to directly extract an effective diffusion coefficient. We see evidence for a critical Richardson number of 0.25 as regions above this threshold remain stable for the course of the simulation. The movie of the simulation is available at http://www.aanda.org
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Cai, Xianhua; Yu, Yang; Liu, Zhichao; Zhang, Meichao; Huang, Weibing
2014-08-01
Although there are many techniques for occipitocervical fixation, there have been no reports regarding occipitocervical fixation via the use of an anterior anatomical locking plate system. The biomechanics of this new system were analyzed by a three-dimensional finite element to provide a theoretical basis for clinical application. This was a modeling study. We studied a 27-year-old healthy male volunteer in whom cervical disease was excluded via X-ray examination. The states of stress and strain of these two internal fixation devices were analyzed. A three-dimensional finite element model of normal occiput-C2 was established based on the anatomical data from a Chinese population. An unstable model of occipital-cervical region was established by subtracting several unit structures from the normal model. An anterior occiput-to-axis locking titanium plate system was then applied and an anterior occiput-to-axis screw fixation was performed on the unstable model. Limitation of motion was performed on the surface of the fixed model, and physiological loads were imposed on the surface of the skull base. Under various loads from different directions, the peak values of displacement of the anterior occiput-to-axis locking titanium plate system decreased 15.5%, 12.5%, 14.4%, and 23.7%, respectively, under the loads of flexion, extension, lateral bending, and axial rotation. Compared with the anterior occiput-to-axis screw fixation, the peak values of stress of the anterior occiput-to-axis locking titanium plate system also decreased 3.9%, 2.9%, 9.7%, and 7.2%, respectively, under the loads of flexion, extension, lateral bending, and axial rotation. The anterior occiput-to-axis locking titanium plate system proved superior to the anterior occiput-to-axis screw system both in the stress distribution and fixation stability based on finite element analysis. It provides a new clinical option for anterior occipitocervical fixation. Copyright © 2014 Elsevier Inc. All rights reserved.
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Bittersohl, Bernd; Kircher, Jörn; Miese, Falk R; Dekkers, Christin; Habermeyer, Peter; Fröbel, Julia; Antoch, Gerald; Krauspe, Rüdiger; Zilkens, Christoph
2015-10-01
Cartilage biochemical imaging modalities that include the magnetic resonance imaging (MRI) techniques of T2* mapping (sensitive to water content and collagen fiber network) and delayed gadolinium-enhanced MRI of cartilage (dGEMRIC, sensitive to the glycosaminoglycan content) can be effective instruments for early diagnosis and reliable follow-up of cartilage damage. The purpose of this study was to provide T2* mapping and dGEMRIC values in various histologic grades of cartilage degeneration in humeral articular cartilage. A histologically controlled in vitro study was conducted that included human humeral head cartilage specimens with various histologic grades of cartilage degeneration. High-resolution, 3-dimensional (3D) T2* mapping and dGEMRIC were performed that enabled the correlation of MRI and histology data. Cartilage degeneration was graded according to the Mankin score, which evaluates surface morphology, cellularity, toluidine blue staining, and tidemark integrity. SPSS software was used for statistical analyses. Both MRI mapping values decreased significantly (P < .001) with increasing cartilage degeneration. Spearman rank analysis revealed a significant correlation (correlation coefficients ranging from -0.315 to 0.784; P < .001) between the various histologic parameters and the T2* and T1Gd mapping values. This study demonstrates the feasibility of 3D T2* and dGEMRIC to identify various histologic grades of cartilage damage of humeral articular cartilage. With regard to the advantages of these mapping techniques with high image resolution and the ability to accomplish a 3D biochemically sensitive imaging, we consider that these imaging techniques can make a positive contribution to the currently evolving science and practice of cartilage biochemical imaging. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.
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Three-Dimensional Culture of Human Breast Epithelial Cells: The How and the Why
Vidi, Pierre-Alexandre; Bissell, Mina J.; Lelièvre, Sophie A.
2013-01-01
Organs are made of the organized assembly of different cell types that contribute to the architecture necessary for functional differentiation. In those with exocrine function, such as the breast, cell–cell and cell–extracellular matrix (ECM) interactions establish mechanistic constraints and a complex biochemical signaling network essential for differentiation and homeostasis of the glandular epithelium. Such knowledge has been elegantly acquired for the mammary gland by placing epithelial cells under three-dimensional (3D) culture conditions. Three-dimensional cell culture aims at recapitulating normal and pathological tissue architectures, hence providing physiologically relevant models to study normal development and disease. The specific architecture of the breast epithelium consists of glandular structures (acini) connected to a branched ductal system. A single layer of basoapically polarized luminal cells delineates ductal or acinar lumena at the apical pole. Luminal cells make contact with myoepithelial cells and, in certain areas at the basal pole, also with basement membrane (BM) components. In this chapter, we describe how this exquisite organization as well as stages of disorganization pertaining to cancer progression can be reproduced in 3D cultures. Advantages and limitations of different culture settings are discussed. Technical designs for induction of phenotypic modulations, biochemical analyses, and state-of-the-art imaging are presented. We also explain how signaling is regulated differently in 3D cultures compared to traditional two-dimensional (2D) cultures. We believe that using 3D cultures is an indispensable method to unravel the intricacies of human mammary functions and would best serve the fight against breast cancer. PMID:23097109
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Characteristics of unstable resonators in flashlamp-pumped organic-compound lasers
NASA Astrophysics Data System (ADS)
Alekseyev, V. A.; Trinchuk, B. F.; Shulenin, A. V.
1985-01-01
A symmetrical confocal resonator formed by two blind convex mirrors was investigated. The space energy characteristics of radiation from a laser with an unstable resonator were investigated as a function of the specific pumping energy per cubic centimeter of active medium and the magnification of the resonator. Oscillograms of laser pulses were recorded in different cross sections of the laser beam, as were the lasing field patterns at various distances from the exit mirror of the resonator. The maximum spectral wavelengths of flat and unstable resonators were tabulated. It was found that the proper choice of parameters of an unstable resonator reduces laser beam divergence significantly and provides greater axial brightness of radiation than that provided by a flat resonator, even with a highly nonhomogeneous active medium, making it possible to extend the capabilities of flashlamp pumped organic compound lasers.
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Transition of unsteady velocity profiles with reverse flow
NASA Astrophysics Data System (ADS)
Das, Debopam; Arakeri, Jaywant H.
1998-11-01
This paper deals with the stability and transition to turbulence of wall-bounded unsteady velocity profiles with reverse flow. Such flows occur, for example, during unsteady boundary layer separation and in oscillating pipe flow. The main focus is on results from experiments in time-developing flow in a long pipe, which is decelerated rapidly. The flow is generated by the controlled motion of a piston. We obtain analytical solutions for laminar flow in the pipe and in a two-dimensional channel for arbitrary piston motions. By changing the piston speed and the length of piston travel we cover a range of values of Reynolds number and boundary layer thickness. The velocity profiles during the decay of the flow are unsteady with reverse flow near the wall, and are highly unstable due to their inflectional nature. In the pipe, we observe from flow visualization that the flow becomes unstable with the formation of what appears to be a helical vortex. The wavelength of the instability [simeq R: similar, equals]3[delta] where [delta] is the average boundary layer thickness, the average being taken over the time the flow is unstable. The time of formation of the vortices scales with the average convective time scale and is [simeq R: similar, equals]39/([Delta]u/[delta]), where [Delta]u=(umax[minus sign]umin) and umax, umin and [delta] are the maximum velocity, minimum velocity and boundary layer thickness respectively at each instant of time. The time to transition to turbulence is [simeq R: similar, equals]33/([Delta]u/[delta]). Quasi-steady linear stability analysis of the velocity profiles brings out two important results. First that the stability characteristics of velocity profiles with reverse flow near the wall collapse when scaled with the above variables. Second that the wavenumber corresponding to maximum growth does not change much during the instability even though the velocity profile does change substantially. Using the results from the experiments and the stability analysis, we are able to explain many aspects of transition in oscillating pipe flow. We postulate that unsteady boundary layer separation at high Reynolds numbers is probably related to instability of the reverse flow region.
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Biodegradation of the cyclic nitramine explosives RDX, HMX, and CL-20.
Crocker, Fiona H; Indest, Karl J; Fredrickson, Herbert L
2006-11-01
Cyclic nitramine explosives are synthesized globally mainly as military munitions, and their use has resulted in environmental contamination. Several biodegradation pathways have been proposed, and these are based mainly on end-product characterization because many of the metabolic intermediates are hypothetical and unstable in water. Biodegradation mechanisms for cyclic nitramines include (a) formation of a nitramine free radical and loss of nitro functional groups, (b) reduction of nitro functional groups, (c) direct enzymatic cleavage, (d) alpha-hydroxylation, or (e) hydride ion transfer. Pathway intermediates spontaneously decompose in water producing nitrite, nitrous oxide, formaldehyde, or formic acid as common end-products. In vitro enzyme and functional gene expression studies have implicated a limited number of enzymes/genes involved in cyclic nitramine catabolism. Advances in molecular biology methods such as high-throughput DNA sequencing, microarray analysis, and nucleic acid sample preparation are providing access to biochemical and genetic information on cultivable and uncultivable microorganisms. This information can provide the knowledge base for rational engineering of bioremediation strategies, biosensor development, environmental monitoring, and green biosynthesis of explosives. This paper reviews recent developments on the biodegradation of cyclic nitramines and the potential of genomics to identify novel functional genes of explosive metabolism.
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Polyphenols in foods are more complex than often thought.
Cheynier, Véronique
2005-01-01
Dietary polyphenols show a great diversity of structures, ranging from rather simple molecules (monomers and oligomers) to polymers. Higher-molecular-weight structures (with molecular weights of > 500) are usually designated as tannins, which refers to their ability to interact with proteins. Among them, condensed tannins (proanthocyanidins) are particularly important because of their wide distribution in plants and their contributions to major food qualities. All phenolic compounds are highly unstable and rapidly transformed into various reaction products when the plant cells are damaged (for instance, during food processing), thus adding to the complexity of dietary polyphenol composition. The polyphenol composition of plant-derived foods and beverages depends on that of the raw material used but also on the extraction process and subsequent biochemical and chemical reactions of plant polyphenols. The occurrence of specific tannin-like compounds (ie, thearubigins and theaflavins) arising from enzymatic oxidation is well documented in black tea. Various chemical reactions involving anthocyanins and/or flavanols have been demonstrated to occur during red wine aging. Current knowledge regarding the reaction mechanisms involved in some of these processes and the structures of the resulting products is reviewed. Their effects on organoleptic and nutritional quality are also discussed.
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Guiding Neuronal Growth in Tissues with Light
2010-02-27
and structural properties of their surroundings in addition to the biochemical properties. Furthermore, three-dimensional biopolymer matrices provide...Properties of Biopolymer Networks Biopolymer networks exhibit unique nonlinear rheological behavior that differs dramatically from most synthetic...and presumably other biopolymers , is not well defined in variable gap geometries. These findings have broad implications for the interpretation of
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Students Conceptualizing Transcription and Translation from a Cellular Perspective
ERIC Educational Resources Information Center
Concannon, James; Buzzetta, Maegan
2010-01-01
It is difficult for students to conceptualize biochemical processes that are portrayed as two-dimensional figures in a textbook. Instead of relying on overheads, PowerPoint, or textbook figures, the authors have students imagine themselves actually being inside a cell. Students have a specific role in the cell: helping with the transcription and…
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Suppression of Electron Thermal Conduction in the Intracluster Medium
NASA Astrophysics Data System (ADS)
Roberg-Clark, Gareth; Drake, James; Swisdak, M.; Reynolds, Christopher S.
2017-08-01
The Intracluster Medium (ICM) contains high-temperature dilute plasma in which the quantity beta, defined as the ratio of the thermal pressure of the gas to the local magnetic field pressure, is much larger than unity. In addition, the collisional mean free path of particles in the ICM is typically large compared to the magnetic gyro-radius of individual particles. These conditions allow for the growth of robust microinstabilities that can significantly alter the transport of particles and heat along the local magnetic field line. Here we explore such an instability using driven two-dimensional Particle-In-Cell simulations of a magnetized plasma with a temperature gradient imposed at the boundaries. The system is highly unstable and develops large-amplitude magnetic fluctuations that effectively scatter the orbits of electrons crossing the simulation domain, resulting in a collisionless suppression of thermal conduction across the temperature gradient and magnetic field. The results suggest that the spontaneous development of small-scale plasma turbulence in the ICM may play a pivotal role in determining the thermal conductivity of ICM-like plasmas.
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Anosov C-systems and random number generators
NASA Astrophysics Data System (ADS)
Savvidy, G. K.
2016-08-01
We further develop our previous proposal to use hyperbolic Anosov C-systems to generate pseudorandom numbers and to use them for efficient Monte Carlo calculations in high energy particle physics. All trajectories of hyperbolic dynamical systems are exponentially unstable, and C-systems therefore have mixing of all orders, a countable Lebesgue spectrum, and a positive Kolmogorov entropy. These exceptional ergodic properties follow from the C-condition introduced by Anosov. This condition defines a rich class of dynamical systems forming an open set in the space of all dynamical systems. An important property of C-systems is that they have a countable set of everywhere dense periodic trajectories and their density increases exponentially with entropy. Of special interest are the C-systems defined on higher-dimensional tori. Such C-systems are excellent candidates for generating pseudorandom numbers that can be used in Monte Carlo calculations. An efficient algorithm was recently constructed that allows generating long C-system trajectories very rapidly. These trajectories have good statistical properties and can be used for calculations in quantum chromodynamics and in high energy particle physics.
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Migration of Gas Giant Planets in Gravitationally Unstable Disks
NASA Astrophysics Data System (ADS)
Michael, Scott; Durisen, Richard H.; Boley, Aaron C.
2011-08-01
Characterization of migration in gravitationally unstable disks is necessary to understand the fate of protoplanets formed by disk instability. As part of a larger study, we are using a three-dimensional radiative hydrodynamics code to investigate how an embedded gas giant planet interacts with a gas disk that undergoes gravitational instabilities (GIs). This Letter presents results from simulations with a Jupiter-mass planet placed in orbit at 25 AU within a 0.14 M sun disk. The disk spans 5-40 AU around a 1 M sun star and is initially marginally unstable. In one simulation, the planet is inserted prior to the eruption of GIs; in another, it is inserted only after the disk has settled into a quasi-steady GI-active state, where heating by GIs roughly balances radiative cooling. When the planet is present from the beginning, its own wake stimulates growth of a particular global mode with which it strongly interacts, and the planet plunges inward 6 AU in about 103 years. In both cases with embedded planets, there are times when the planet's radial motion is slow and varies in direction. At other times, when the planet appears to be interacting with strong spiral modes, migration both inward and outward can be relatively rapid, covering several AUs over hundreds of years. Migration in both cases appears to stall near the inner Lindblad resonance of a dominant low-order mode. Planet orbit eccentricities fluctuate rapidly between about 0.02 and 0.1 throughout the GI-active phases of the simulations.
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Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph.
Mörschel, Konstantin; Breit, Markus; Queisser, Gillian
2017-07-01
Generating realistic and complex computational domains for numerical simulations is often a challenging task. In neuroscientific research, more and more one-dimensional morphology data is becoming publicly available through databases. This data, however, only contains point and diameter information not suitable for detailed three-dimensional simulations. In this paper, we present a novel framework, AnaMorph, that automatically generates water-tight surface meshes from one-dimensional point-diameter files. These surface triangulations can be used to simulate the electrical and biochemical behavior of the underlying cell. In addition to morphology generation, AnaMorph also performs quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions. This toolset allows an extension from the classical dimension-reduced modeling and simulation of cellular processes to a full three-dimensional and morphology-including method, leading to novel structure-function interplay studies in the medical field. The developed numerical methods can further be employed in other areas where complex geometries are an essential component of numerical simulations.
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Jaferzadeh, Keyvan; Gholami, Samaneh; Moon, Inkyu
2016-12-20
In this paper, we evaluate lossless and lossy compression techniques to compress quantitative phase images of red blood cells (RBCs) obtained by an off-axis digital holographic microscopy (DHM). The RBC phase images are numerically reconstructed from their digital holograms and are stored in 16-bit unsigned integer format. In the case of lossless compression, predictive coding of JPEG lossless (JPEG-LS), JPEG2000, and JP3D are evaluated, and compression ratio (CR) and complexity (compression time) are compared against each other. It turns out that JP2k can outperform other methods by having the best CR. In the lossy case, JP2k and JP3D with different CRs are examined. Because some data is lost in a lossy way, the degradation level is measured by comparing different morphological and biochemical parameters of RBC before and after compression. Morphological parameters are volume, surface area, RBC diameter, sphericity index, and the biochemical cell parameter is mean corpuscular hemoglobin (MCH). Experimental results show that JP2k outperforms JP3D not only in terms of mean square error (MSE) when CR increases, but also in compression time in the lossy compression way. In addition, our compression results with both algorithms demonstrate that with high CR values the three-dimensional profile of RBC can be preserved and morphological and biochemical parameters can still be within the range of reported values.
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Hierarchy stability moderates the effect of status on stress and performance in humans
Knight, Erik L.; Mehta, Pranjal H.
2017-01-01
High social status reduces stress responses in numerous species, but the stress-buffering effect of status may dissipate or even reverse during times of hierarchical instability. In an experimental test of this hypothesis, 118 participants (57.3% female) were randomly assigned to a high- or low-status position in a stable or unstable hierarchy and were then exposed to a social-evaluative stressor (a mock job interview). High status in a stable hierarchy buffered stress responses and improved interview performance, but high status in an unstable hierarchy boosted stress responses and did not lead to better performance. This general pattern of effects was observed across endocrine (cortisol and testosterone), psychological (feeling in control), and behavioral (competence, dominance, and warmth) responses to the stressor. The joint influence of status and hierarchy stability on interview performance was explained by feelings of control and testosterone reactivity. Greater feelings of control predicted enhanced interview performance, whereas increased testosterone reactivity predicted worse performance. These results provide direct causal evidence that high status confers adaptive benefits for stress reduction and performance only when the social hierarchy is stable. When the hierarchy is unstable, high status actually exacerbates stress responses. PMID:27994160
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Hierarchy stability moderates the effect of status on stress and performance in humans.
Knight, Erik L; Mehta, Pranjal H
2017-01-03
High social status reduces stress responses in numerous species, but the stress-buffering effect of status may dissipate or even reverse during times of hierarchical instability. In an experimental test of this hypothesis, 118 participants (57.3% female) were randomly assigned to a high- or low-status position in a stable or unstable hierarchy and were then exposed to a social-evaluative stressor (a mock job interview). High status in a stable hierarchy buffered stress responses and improved interview performance, but high status in an unstable hierarchy boosted stress responses and did not lead to better performance. This general pattern of effects was observed across endocrine (cortisol and testosterone), psychological (feeling in control), and behavioral (competence, dominance, and warmth) responses to the stressor. The joint influence of status and hierarchy stability on interview performance was explained by feelings of control and testosterone reactivity. Greater feelings of control predicted enhanced interview performance, whereas increased testosterone reactivity predicted worse performance. These results provide direct causal evidence that high status confers adaptive benefits for stress reduction and performance only when the social hierarchy is stable. When the hierarchy is unstable, high status actually exacerbates stress responses.
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Simulations of Living Cell Origins Using a Cellular Automata Model
NASA Astrophysics Data System (ADS)
Ishida, Takeshi
2014-04-01
Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.
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NASA Technical Reports Server (NTRS)
Hall, Philip; Balakumar, P.
1990-01-01
A class of exact steady and unsteady solutions of the Navier Stokes equations in cylindrical polar coordinates is given. The flows correspond to the motion induced by an infinite disc rotating with constant angular velocity about the z-axis in a fluid occupying a semi-infinite region which, at large distances from the disc, has velocity field proportional to (x,-y,O) with respect to a Cartesian coordinate system. It is shown that when the rate of rotation is large, Karman's exact solution for a disc rotating in an otherwise motionless fluid is recovered. In the limit of zero rotation rate a particular form of Howarth's exact solution for three-dimensional stagnation point flow is obtained. The unsteady form of the partial differential system describing this class of flow may be generalized to time-periodic equilibrium flows. In addition the unsteady equations are shown to describe a strongly nonlinear instability of Karman's rotating disc flow. It is shown that sufficiently large perturbations lead to a finite time breakdown of that flow whilst smaller disturbances decay to zero. If the stagnation point flow at infinity is sufficiently strong, the steady basic states become linearly unstable. In fact there is then a continuous spectrum of unstable eigenvalues of the stability equations but, if the initial value problem is considered, it is found that, at large values of time, the continuous spectrum leads to a velocity field growing exponentially in time with an amplitude decaying algebraically in time.
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Simulations of living cell origins using a cellular automata model.
Ishida, Takeshi
2014-04-01
Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.
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NASA Technical Reports Server (NTRS)
Catalina, Adrian V.; Sen, S.; Rose, M. Franklin (Technical Monitor)
2001-01-01
The evolution of cellular solid/liquid interfaces from an initially unstable planar front was studied by means of a two-dimensional computer simulation. The developed numerical model makes use of an interface tracking procedure and has the capability to describe the dynamics of the interface morphology based on local changes of the thermodynamic conditions. The fundamental physics of this formulation was validated against experimental microgravity results and the predictions of the analytical linear stability theory. The performed simulations revealed that in certain conditions, based on a competitive growth mechanism, an interface could become unstable to random perturbations of infinitesimal amplitude even at wavelengths smaller than the neutral wavelength, lambda(sub c), predicted by the linear stability theory. Furthermore, two main stages of spacing selection have been identified. In the first stage, at low perturbations amplitude, the selection mechanism is driven by the maximum growth rate of instabilities while in the second stage the selection is influenced by nonlinear phenomena caused by the interactions between the neighboring cells. Comparison of these predictions with other existing theories of pattern formation and experimental results will be discussed.
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A mechanism for magnetospheric substorms
NASA Technical Reports Server (NTRS)
Erickson, G. M.; Heinemann, M.
1994-01-01
Energy-principle analysis performed on two-dimensional, self-consistent solutions for magnetospheric convection indicates that the magnetosphere is unstable to isobaric (yet still frozen-in) fluctuations of plasma-sheet flux tubes. Normally, pdV work associated with compression maintains stability of the inward/outward oscillating normal mode. However, if Earth's ionosphere can provide sufficient mass flux, isobaric expansion of flux tubes can occur. The growth of a field-aligned potential drop in the near-Earth, midnight portion of the plasma sheet, associated with upward field-aligned currents responsible for the Harang discontinuity, redistributes plasma along field lines in a manner that destabilizes the normal mode. The growth of this unstable mode results in an out-of-equilibrium situation near the inner edge. When this occurs over a downtail extent comparable to the half-thickness of the plasma sheet, collapse ensues and forces thinning of the plasma sheet whereby conditions favorable to reconnection occur. This scenario for substorm onset is consistent with observed upward fluxes of ions, parallel potential drops, and observations of substorm onset. These observations include near Earth onset, pseudobreakups, the substorm current wedge, and local variations of plasma-sheet thickness.
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Overview of the Tusas Code for Simulation of Dendritic Solidification
DOE Office of Scientific and Technical Information (OSTI.GOV)
Trainer, Amelia J.; Newman, Christopher Kyle; Francois, Marianne M.
2016-01-07
The aim of this project is to conduct a parametric investigation into the modeling of two dimensional dendrite solidification, using the phase field model. Specifically, we use the Tusas code, which is for coupled heat and phase-field simulation of dendritic solidification. Dendritic solidification, which may occur in the presence of an unstable solidification interface, results in treelike microstructures that often grow perpendicular to the rest of the growth front. The interface may become unstable if the enthalpy of the solid material is less than that of the liquid material, or if the solute is less soluble in solid than itmore » is in liquid, potentially causing a partition [1]. A key motivation behind this research is that a broadened understanding of phase-field formulation and microstructural developments can be utilized for macroscopic simulations of phase change. This may be directly implemented as a part of the Telluride project at Los Alamos National Laboratory (LANL), through which a computational additive manufacturing simulation tool is being developed, ultimately to become part of the Advanced Simulation and Computing Program within the U.S. Department of Energy [2].« less
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Coherent current-carrying filaments during nonlinear reconnecting ELMs and VDEs
NASA Astrophysics Data System (ADS)
Ebrahimi, Fatima
2017-10-01
We have examined plasmoid-mediated reconnection in a spherical tokamak using global nonlinear three-dimensional resistive MHD simulations with NIMROD. We have shown that physical current sheets/layers develop near the edge as a peeling component of ELMs or during vertical displacement events (associated with the scrape-off layer currents - halo currents), can become unstable to nonaxisymmetric 3-D current-sheet instabilities (peeling- or tearing-like) and nonlinearly form edge coherent current-carrying filaments. Time-evolving edge current sheets with reconnecting nature in NSTX and NSTX-U configurations are identified. In the case of peeling-like edge localized modes, the longstanding problem of quasiperiodic ELMs cycles is explained through the relaxation of edge current via direct numerical calculations of reconnecting emf terms. For the VDEs during disruption, we show that as the plasma is vertically displaced, edge halo current sheet becomes MHD unstable and forms coherent edge current filament structures, which would eventually bleed into the walls. Our model explains some essential asymmetric physics relevant to the experimental observations. Supported by DOE Grants DE-SC0010565, DE-AC02-09CH11466.
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NASA Astrophysics Data System (ADS)
Echevin, V.; Levy, M.; Memery, L.
The assimilation of two dimensional sea color data fields into a 3 dimensional coupled dynamical-biogeochemical model is performed using a 4DVAR algorithm. The biogeochemical model includes description of nitrates, ammonium, phytoplancton, zooplancton, detritus and dissolved organic matter. A subset of the biogeochemical model poorly known parameters (for example,phytoplancton growth, mortality,grazing) are optimized by minimizing a cost function measuring misfit between the observations and the model trajectory. Twin experiments are performed with an eddy resolving model of 5 km resolution in an academic configuration. Starting from oligotrophic conditions, an initially unstable baroclinic anticyclone splits into several eddies. Strong vertical velocities advect nitrates into the euphotic zone and generate a phytoplancton bloom. Biogeochemical parameters are perturbed to generate surface pseudo-observations of chlorophyll,which are assimilated in the model in order to retrieve the correct parameter perturbations. The impact of the type of measurement (quasi-instantaneous, daily mean, weekly mean) onto the retrieved set of parameters is analysed. Impacts of additional subsurface measurements and of errors in the circulation are also presented.
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NASA Astrophysics Data System (ADS)
Tiofack, C. G. L.; Ndzana, F., II; Mohamadou, A.; Kofane, T. C.
2018-03-01
We investigate the existence and stability of solitons in parity-time (PT )-symmetric optical media characterized by a generic complex hyperbolic refractive index distribution and fourth-order diffraction (FOD). For the linear case, we demonstrate numerically that the FOD parameter can alter the PT -breaking points. For nonlinear cases, the exact analytical expressions of the localized modes are obtained both in one- and two-dimensional nonlinear Schrödinger equations with self-focusing and self-defocusing Kerr nonlinearity. The effect of FOD on the stability structure of these localized modes is discussed with the help of linear stability analysis followed by the direct numerical simulation of the governing equation. Examples of stable and unstable solutions are given. The transverse power flow density associated with these localized modes is also discussed. It is found that the relative strength of the FOD coefficient can utterly change the direction of the power flow, which may be used to control the energy exchange among gain or loss regions.
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NASA Astrophysics Data System (ADS)
Gelfgat, A. Yu.; Bar-Yoseph, P. Z.; Solan, A.
2001-08-01
A study of the effect of an externally imposed magnetic field on the axisymmetry-breaking instability of an axisymmetric convective flow, associated with crystal growth from bulk of melt, is presented. Convection in a vertical cylinder with a parabolic temperature profile on the sidewall is considered as a representative model. A parametric study of the dependence of the critical Grashof number Gr cr on the Hartmann number Ha for fixed values of the Prandtl number (Pr=0.015) and the aspect ratio of the cylinder ( A=height/radius=1, 2 and 3) is carried out. The stability diagram Gr cr(Ha) corresponding to the axisymmetric—three-dimensional transition for increasing values of the axial magnetic field is obtained. The calculations are done using the spectral Galerkin method allowing an effective and accurate three-dimensional stability analysis. It is shown that at relatively small values of Ha the axisymmetric flow tends to be oscillatory unstable. After the magnitude of the magnetic field (Ha) exceeds a certain value the instability switches to a steady bifurcation caused by the Rayleigh-Bénard mechanism.
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Three-Dimensional Magnetic Levitation Culture System Simulating White Adipose Tissue.
Tseng, Hubert; Daquinag, Alexes C; Souza, Glauco R; Kolonin, Mikhail G
2018-01-01
White adipose tissue (WAT) has attracted interest for tissue engineering and cell-based therapies as an abundant source of adipose stem/stromal cells (ASC). However, technical challenges in WAT cell culture have limited its applications in regenerative medicine. Traditional two-dimensional (2D) cell culture models, which are essentially monolayers of cells on glass or plastic substrates, inadequately represent tissue architecture, biochemical concentration gradients, substrate stiffness, and most importantly for WAT research, cell phenotypic heterogeneity. Physiological cell culture platforms for WAT modeling must recapitulate the native diversity of cell types and their coordination within the organ. For this purpose, we developed a three-dimensional (3D) model using magnetic levitation. Here, we describe our protocol that we successfully employed to build adipose tissue organoids (adipospheres) that preserve the heterogeneity of the constituent cell types in vitro. We demonstrate the capacity of assembling adipospheres from multiple cell types, including ASCs, endohtelial cells, and leukocytes that recreate tissue organization. These adipospheres mimicked WAT organogenesis in that they enabled the formation of vessel-like endothelial structures with lumens and differentiation of unilocular adipocytes. Altogether, magnetic levitation is a cell culture platform that recreates tissue structure, function, and heterogeneity in vitro, and serves as a foundation for high-throughput WAT tissue culture and analysis.
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Closed reduction of slipped capital femoral epiphysis: high-risk factor for avascular necrosis.
Kitano, Toshio; Nakagawa, Keisuke; Wada, Mayuko; Moriyama, Michiko
2015-07-01
How should we treat acute/unstable slipped capital femoral epiphysis (SCFE) without the development of avascular necrosis (AVN)? To answer this question, we investigated the risk factors of AVN development after SCFE. Seventy-six hips of 64 patients were classified using two kinds of classification systems, Loder's classification based on instability and the conventional classification based on the duration of symptom, because both classifications are related to AVN development. Of 21 unstable SCFEs, seven hips developed AVN. Of 35 hips defined as acute or acute on chronic, nine hips developed AVN. Two stable SCFEs of Loder's classification developed AVN, one was acute and the other was acute on chronic. No hips of chronic SCFE developed AVN. The factor that had influenced AVN development was only closed reduction, whether purposefully or inadvertently, in an acute or unstable SCFE. On the basis of the findings of this study, one should not embark on any modality of closed reduction for an unstable or acute form of SCFE, as there is a high risk for occurrence of AVN. For the same reason, a traction table should not be used for SCFE fixation, so as to avoid an inadvertent reduction or force that can lead to AVN.
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Universally Unstable Nature of Velocity Ring Distributions
NASA Astrophysics Data System (ADS)
Mithaiwala, Manish
2010-11-01
Although it is typically believed that an ion ring velocity distribution has a stability threshold, we find that they are universally unstable. This can substantially impact the understanding of dynamics in both laboratory and space plasmas. A high ring density neutralizes the stabilizing effect of ion Landau damping in a warm plasma and the ring is unstable to the generation of waves below the lower hybrid frequency- even for a very high temperature plasma. For ring densities lower than the background plasma density there is a slow instability with growth rate less than the background ion cyclotron frequency and consequently the background ion response is magnetized. This is in addition to the widely discussed fast instability where the wave growth rate exceeds the background ion cyclotron frequency and hence the background ions are effectively unmagnetized. Thus, even a low density ring is unstable to waves around the lower hybrid frequency range for any ring speed. This implies that effectively there is no velocity threshold for a sufficiently cold ring. The importance of these conclusions on the nonlinear evolution of space plasmas, in particular to solar wind-comet interaction, post-magnetospheric storm conditions, and chemical release experiments in the ionosphere will be discussed.
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Numerical simulation of the three-dimensional river antidunes
NASA Astrophysics Data System (ADS)
Iwasaki, T.; Inoue, T.; Onda, S.; Yabe, H.
2017-12-01
This study presents numerical simulations of the formation and development of the three-dimensional river antidunes. We use a Boussinesq type depth-integrated hydrodynamic model to account for the non-hydrostatic pressure effects on the flow field, dissipative feature of the free surface and the bed shear stress distribution. In addition, a non-equilibrium bedload transport model is incorporated into the model to consider the lag effect of the bedload transport on the bedform dynamics. The model is applied to idealized laboratory-scale conditions, i.e., steady water and sediment supplies, uniform sediment and a straight channel with constant slope and channel width, to understand the model performance and applicability. The results show that the model is able to reproduce an upstream-migrating antidunes and associated free surface dynamics. The model also captures the formation of the two dimensional and the three-dimensional antidunes. The antidunes reproduced by the model are somewhat unstable, i.e., the repeated cycle of dissipation and regeneration of antidunes is observed. In addition, as the calculation progresses, the modelled three-dimensional antidunes generally tend to lose their three-dimensionality, i.e., the reduction of the spanwise wavenumber. In the early stage of the calculation, the antidune mode is dominant, whereas, the free bars also develop when the formative condition of bars is satisfied. The numerical results show the coexisting of free bars and antidunes, which are a common evident in flume experiments and field observations.
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Axisymmetry breaking instabilities of natural convection in a vertical bridgman growth configuration
NASA Astrophysics Data System (ADS)
Gelfgat, A. Yu.; Bar-Yoseph, P. Z.; Solan, A.
2000-12-01
A study of the three-dimensional axisymmetry-breaking instability of an axisymmetric convective flow associated with crystal growth from bulk of melt is presented. Convection in a vertical cylinder with a parabolic temperature profile on the sidewall is considered as a representative model. The main objective is the calculation of critical parameters corresponding to a transition from the steady axisymmetric to the three-dimensional non-axisymmetric (steady or oscillatory) flow pattern. A parametric study of the dependence of the critical Grashof number Gr cr on the Prandtl number 0⩽Pr⩽0.05 (characteristic for semiconductor melts) and the aspect ratio of the cylinder 1⩽ A⩽4 ( A=height/radius) is carried out. The stability diagram Grcr(Pr, A) corresponding to the axisymmetric — three-dimensional transition is reported for the first time. The calculations are done using the spectral Galerkin method allowing an effective and accurate three-dimensional stability analysis. It is shown that the axisymmetric flow in relatively low cylinders tends to be oscillatory unstable, while in tall cylinders the instability sets in due to a steady bifurcation caused by the Rayleigh-Benard mechanism. The calculated neutral curves are non-monotonous and contain hysteresis loops. The strong dependence of the critical Grashof number and the azimuthal periodicity of the resulting three-dimensional flow indicate the importance of a comprehensive parametric stability analysis in different crystal growth configurations. In particular, it is shown that the first instability of the flow considered is always three-dimensional.
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NASA Astrophysics Data System (ADS)
Kinoshita, T.; Sato, K.
2016-12-01
The Transformed Eulerian-Mean (TEM) equations were derived by Andrews and McIntyre (1976, 1978) and have been widely used to examine wave-mean flow interaction in the meridional cross section. According to previous studies, the Brewer-Dobson circulation in the stratosphere is driven by planetary waves, baroclinic waves, and inertia-gravity waves, and that the meridional circulation from the summer hemisphere to the winter hemisphere in the mesosphere is mainly driven by gravity waves (e.g., Garcia and Boville 1994; Plumb and Semeniuk 2003; Watanabe et al. 2008; Okamoto et al. 2011). However, the TEM equations do not provide the three-dimensional view of the transport, so that the three dimensional TEM equations have been formulated (Hoskins et al. 1983, Trenberth 1986, Plumb 1985, 1986, Takaya and Nakamura 1997, 2001, Miyahara 2006, Kinoshita et al. 2010, Noda 2010, Kinoshita and Sato 2013a, b, and Noda 2014). On the other hand, the TEM equations cannot properly treat the lower boundary and unstable waves. The Mass-weighted Isentropic Mean (MIM) equations derived by Iwasaki (1989, 1990) are the equations that overcome those problems and the formulation of three-dimensional MIM equations have been studied. The present study applies the three-dimensional TEM and MIM equations to the ERA-Interim reanalysis data and examines the climatological character of three-dimensional structure of Stratospheric Brewer-Dobson circulation. Next, we will discuss how to treat the flow associated with spatial structure of stationary waves.
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NASA Astrophysics Data System (ADS)
Nazarinia, M.; Lo Jacono, D.; Thompson, M. C.; Sheridan, J.
2009-06-01
Previous two-dimensional numerical studies have shown that a circular cylinder undergoing both oscillatory rotational and translational motions can generate thrust so that it will actually self-propel through a stationary fluid. Although a cylinder undergoing a single oscillation has been thoroughly studied, the combination of the two oscillations has not received much attention until now. The current research reported here extends the numerical study of Blackburn et al. [Phys. Fluids 11, L4 (1999)] both experimentally and numerically, recording detailed vorticity fields in the wake and using these to elucidate the underlying physics, examining the three-dimensional wake development experimentally, and determining the three-dimensional stability of the wake through Floquet stability analysis. Experiments conducted in the laboratory are presented for a given parameter range, confirming the early results from Blackburn et al. [Phys. Fluids 11, L4 (1999)]. In particular, we confirm the thrust generation ability of a circular cylinder undergoing combined oscillatory motions. Importantly, we also find that the wake undergoes three-dimensional transition at low Reynolds numbers (Re≃100) to an instability mode with a wavelength of about two cylinder diameters. The stability analysis indicates that the base flow is also unstable to another mode at slightly higher Reynolds numbers, broadly analogous to the three-dimensional wake transition mode for a circular cylinder, despite the distinct differences in wake/mode topology. The stability of these flows was confirmed by experimental measurements.
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Characterization of Unstable Rock Slopes Through Passive Seismic Measurements
NASA Astrophysics Data System (ADS)
Kleinbrod, U.; Burjanek, J.; Fäh, D.
2014-12-01
Catastrophic rock slope failures have high social impact, causing significant damage to infrastructure and many casualties throughout the world each year. Both detection and characterization of rock instabilities are therefore of key importance. An analysis of ambient vibrations of unstable rock slopes might be a new alternative to the already existing methods, e.g. geotechnical displacement measurements. Systematic measurements have been performed recently in Switzerland to study the seismic response of potential rockslides concerning a broad class of slope failure mechanisms and material conditions. Small aperture seismic arrays were deployed at sites of interest for a short period of time (several hours) in order to record ambient vibrations. Each measurement setup included a reference station, which was installed on a stable part close to the instability. Recorded ground motion is highly directional in the unstable parts of the rock slope, and significantly amplified with respect to stable areas. These effects are strongest at certain frequencies, which were identified as eigenfrequencies of the unstable rock mass. In most cases the directions of maximum amplification are perpendicular to open cracks and in good agreement with the deformation directions obtained by geodetic measurements. Such unique signatures might improve our understanding of slope structure and stability. Thus we link observed vibration characteristics with available results of detailed geological characterization. This is supported by numerical modeling of seismic wave propagation in fractured media with complex topography.For example, a potential relation between eigenfrequencies and unstable rock mass volume is investigated.
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Micro/nanofabricated environments for synthetic biology.
Collier, C Patrick; Simpson, Michael L
2011-08-01
A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.
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Lee wave breaking region: the map of instability development scenarios
NASA Astrophysics Data System (ADS)
Yakovenko, S. N.
2017-10-01
Numerical study of a stably stratified flow above the two-dimensional cosine-shaped obstacle has been performed by DNS and LES. These methods were implemented to solve the three-dimensional Navier-Stokes equations in the Boussinesq approximation, together with by the scalar diffusion equation. The results of scanning in the wide ranges of physical parameters (Reynolds and Prandtl/Schmidt numbers relating to laboratory experiment cases and atmospheric or oceanic situations) are presented for instability and turbulence development scenarios in the overturning internal lee waves. The latter is generated by the obstacle in a flow with the constant inflow values of velocity and stable density gradient. Evolution of lee-wave breaking is explored by visualization of velocity and scalar (density) fields, and the analysis of spectra. Based on the numerical simulation results, the power-law dependence on Reynolds number is demonstrated for the wavelength of the most unstable perturbation.
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Invariant polygons in systems with grazing-sliding.
Szalai, R; Osinga, H M
2008-06-01
The paper investigates generic three-dimensional nonsmooth systems with a periodic orbit near grazing-sliding. We assume that the periodic orbit is unstable with complex multipliers so that two dominant frequencies are present in the system. Because grazing-sliding induces a dimension loss and the instability drives every trajectory into sliding, the system has an attractor that consists of forward sliding orbits. We analyze this attractor in a suitably chosen Poincare section using a three-parameter generalized map that can be viewed as a normal form. We show that in this normal form the attractor must be contained in a finite number of lines that intersect in the vertices of a polygon. However the attractor is typically larger than the associated polygon. We classify the number of lines involved in forming the attractor as a function of the parameters. Furthermore, for fixed values of parameters we investigate the one-dimensional dynamics on the attractor.
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Two-dimensional cylindrical ion-acoustic solitary and rogue waves in ultrarelativistic plasmas
DOE Office of Scientific and Technical Information (OSTI.GOV)
Ata-ur-Rahman; National Centre for Physics at QAU Campus, Shahdrah Valley Road, Islamabad 44000; Ali, S.
2013-07-15
The propagation of ion-acoustic (IA) solitary and rogue waves is investigated in a two-dimensional ultrarelativistic degenerate warm dense plasma. By using the reductive perturbation technique, the cylindrical Kadomtsev–Petviashvili (KP) equation is derived, which can be further transformed into a Korteweg–de Vries (KdV) equation. The latter admits a solitary wave solution. However, when the frequency of the carrier wave is much smaller than the ion plasma frequency, the KdV equation can be transferred to a nonlinear Schrödinger equation to study the nonlinear evolution of modulationally unstable modified IA wavepackets. The propagation characteristics of the IA solitary and rogue waves are stronglymore » influenced by the variation of different plasma parameters in an ultrarelativistic degenerate dense plasma. The present results might be helpful to understand the nonlinear electrostatic excitations in astrophysical degenerate dense plasmas.« less
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Pattern selection in solidification
NASA Technical Reports Server (NTRS)
Langer, J. S.
1984-01-01
Directional solidification of alloys produces a wide variety of cellular or lamellar structures which, depending upon growth conditions, may be reproducibly regular or may behave chaotically. It is not well understood how these patterns are selected and controlled or even whether there ever exist sharp selection mechanisms. A related phenomenon is the spatial propagation of a pattern into a system which has been caused to become unstable against pattern-forming deformations. This phenomenon has some features in common with the propagation of sidebranching modes in dendritic solidification. In a class of one-dimensional models, the nonlinear system can be shown to select the propagating mode in which the leading edge of the pattern is just marginally stable. This stability principle, when applicable, predicts both the speed of propagation and the geometrical characteristics of the pattern which forms behind the moving front. A boundary-layer model for fully two or three dimensional solidification problems appears to exhibit similar mathematical behavior.
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Dynamics of a Two-Dimensional System of Quantum Dipoles
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mazzanti, F.; Astrakharchik, G. E.; Boronat, J.
2009-03-20
A detailed microscopic analysis of the dynamic structure function S(k,{omega}) of a two-dimensional Bose system of dipoles polarized along the direction perpendicular to the plane is presented and discussed. Starting from ground-state quantities obtained using a quantum diffusion Monte Carlo algorithm, the density-density response is evaluated in the context of the correlated basis functions (CBF) theory. CBF predicts a sharp peak and a multiexcitation component at higher energies produced by the decay of excitations. We discuss the structure of the phonon-roton peak and show that the Feynman and Bogoliubov predictions depart from the CBF result already at low densities. Wemore » finally discuss the emergence of a roton in the spectrum, but find the roton energy not low enough to make the system unstable under density fluctuations up to the highest density considered that is close to the freezing point.« less
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Experimental characterization of 3-dimensional gravity-driven fingering in a porous medium
NASA Astrophysics Data System (ADS)
Dalbe, Marie-Julie; Juanes, Ruben
2017-11-01
When water infiltrates a dry porous media, a gravity-driven instability can be observed. Water will penetrate the porous media along preferential paths, called fingers. This gravity-driven unstable multiphase flow has important implications for natural phenomena such as rainwater infiltration in soil and secondary oil migration in reservoir rocks. While several experimental and numerical studies have described the instability in 2-dimensional (2D) settings, fundamental questions remain on the morphodynamics of gravity fingering in 3D. We developed a 3D experimental set-up based on planar laser-induced fluorescence of index-matched fluids that allows us to image this phenomenon dynamically. We study the impact of some crucial parameters such as rainfall rate or grain size on the finger size and velocity. In addition, experiments in stratified media reveal interesting dynamics of finger flow across material interfaces, an essential aspect towards the understanding of water infiltration in soils.
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Doorwar, Shashvat; Mohanty, Kishore K
2014-07-01
Immiscible displacement of viscous oil by water in a petroleum reservoir is often hydrodynamically unstable. Due to similarities between the physics of dielectric breakdown and immiscible flow in porous media, we extend the existing dielectric breakdown model to simulate viscous fingering patterns for a wide range of viscosity ratios (μ(r)). At low values of power-law index η, the system behaves like a stable Eden growth model and as the value of η is increased to unity, diffusion limited aggregation-like fractals appear. This model is compared with our two-dimensional (2D) experiments to develop a correlation between the viscosity ratio and the power index, i.e., η = 10(-5)μ(r)(0.8775). The 2D and three-dimensional (3D) simulation data appear scalable. The fingering pattern in 3D simulations at finite viscosity ratios appear qualitatively similar to the few experimental results published in the literature.
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A study of the factors affecting boundary layer two-dimensionality in wind tunnels
NASA Technical Reports Server (NTRS)
Mehta, R. D.; Hoffmann, P. H.
1986-01-01
The effect of screens, honeycombs, and centrifugal blowers on the two-dimensionality of a boundary layer on the test section floors of low-speed blower tunnels is studied. Surveys of the spanwise variation in surface shear stress in three blower tunnels revealed that the main component responsible for altering the spanwise properties of the test section boundary layer was the last screen, thus confirming previous findings. It was further confirmed that a screen with varying open-area ratio, produced an unstable flow. However, contrary to popular belief, it was also found that for given incoming conditions and a screen free of imperfections, its open-area ratio alone was not enough to describe its performance. The effect of other geometric parameters such as the type of screen, honeycomb, and blower were investigated. In addition, the effect of the order of components in the settling chamber, and of wire Reynolds number were also studied.
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Local stability of a five dimensional food chain model in the ocean
NASA Astrophysics Data System (ADS)
Kusumawinahyu, W. M.; Hidayatulloh, M. R.
2014-02-01
This paper discuss a food chain model on a microbiology ecosystem in the ocean, where predation process occurs. Four population growth rates are discussed, namely bacteria, phytoplankton, zooplankton, and protozoa growth rate. When the growth of nutrient density is also considered, the model is governed by a five dimensional dynamical system. The system considered in this paper is a modification of a model proposed by Hadley and Forbes [1], by taking Holling Type I as the functional response. For sake of simplicity, the model needs to be scaled. Dynamical behavior, such as existence condition of equilibrium points and their local stability are addressed. There are eight equilibrium points, where two of them exist under certain conditions. Three equilibrium points are unstable, while two points stable under certain conditions and the other three points are stable if the Ruth-Hurwitz criteria are satisfied. Numerical simulations are carried out to illustrate analytical findings.
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Boundary Between Stable and Unstable Regimes of Accretion
NASA Astrophysics Data System (ADS)
Blinova, A. A.; Lovelace, R. V. E.; Romanova, M. M.
2014-01-01
We investigated the boundary between stable and unstable regimes of accretion and its dependence on different parameters. Simulations were performed using a "cubed sphere" code with high grid resolution (244 grid points in the azimuthal direction), which is twice as high as that used in our earlier studies. We chose a very low viscosity value, with alpha-parameter α=0.02. We observed from the simulations that the boundary strongly depends on the ratio between magnetospheric radius rm (where the magnetic stress in the magnetosphere matches the matter stress in the disk) and corotation radius rcor (where the Keplerian velocity in the disk is equal to the angular velocity of the star). For a small misalignment angle of the dipole field, Θ = 5°, accretion is unstable if rcor/rm> 1.35, and is stable otherwise. In cases of a larger misalignment angle of the dipole, Θ = 20°, instability occurs at slightly larger values, rcor/rm> 1.41
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Petkovic, Sonja; Badelt, Stefan; Flamm, Christoph; Delcea, Mihaela
2015-01-01
Reversible chemistry allowing for assembly and disassembly of molecular entities is important for biological self-organization. Thus, ribozymes that support both cleavage and formation of phosphodiester bonds may have contributed to the emergence of functional diversity and increasing complexity of regulatory RNAs in early life. We have previously engineered a variant of the hairpin ribozyme that shows how ribozymes may have circularized or extended their own length by forming concatemers. Using the Vienna RNA package, we now optimized this hairpin ribozyme variant and selected four different RNA sequences that were expected to circularize more efficiently or form longer concatemers upon transcription. (Two-dimensional) PAGE analysis confirms that (i) all four selected ribozymes are catalytically active and (ii) high yields of cyclic species are obtained. AFM imaging in combination with RNA structure prediction enabled us to calculate the distributions of monomers and self-concatenated dimers and trimers. Our results show that computationally optimized molecules do form reasonable amounts of trimers, which has not been observed for the original system so far, and we demonstrate that the combination of theoretical prediction, biochemical and physical analysis is a promising approach toward accurate prediction of ribozyme behavior and design of ribozymes with predefined functions. PMID:25999318
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ERIC Educational Resources Information Center
Ray, Gigi B.; Cook, J. Whitney
2005-01-01
A biochemical molecular modeling project on heme proteins suitable for an introductory Biochemistry I class has been designed with a 2-fold objective: i) to reinforce the correlation between protein three-dimensional structure and function through a discovery oriented project, and ii) to introduce students to the fields of bioinorganic and…
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The Thermal Regulation of Gravitational Instabilities in Protoplanetary Disks
NASA Astrophysics Data System (ADS)
Pickett, Brian K.; Mejía, Annie C.; Durisen, Richard H.; Cassen, Patrick M.; Berry, Donald K.; Link, Robert P.
2003-06-01
We present a series of high-resolution, three-dimensional hydrodynamics simulations of a gravitationally unstable solar nebula model. The influences of both azimuthal grid resolution and the treatment of thermal processes on the origin and evolution of gravitational instabilities are investigated. In the first set of simulations, we vary the azimuthal resolution for a locally isothermal simulation, doubling and quadrupling the resolution used in a previous study; the largest number of grid points is (256,256,64) in cylindrical coordinates (r,ϕ,z). At this resolution, the disk breaks apart into a dozen short-lived condensations. Although our previous calculations underresolved the number and growth rate of clumps in the disk, the overall qualitative, but fundamental, conclusion remains: fragmentation under the locally isothermal condition in numerical simulations does not in itself lead to the survival of clumps to become gaseous giant protoplanets. Since local isothermality represents an extreme assumption about thermal processes in the disk, we also present several extended simulations in which heating from an artificial viscosity scheme and cooling from a simple volumetric cooling function are applied to two different models of the solar nebula. The models are differentiated primarily by disk temperature: a high-Q model generated directly by our self-consistent field equilibrium code and a low-Q model generated by cooling the high-Q model in a two-dimensional version of our hydrodynamics code. Here, ``high-Q'' and ``low-Q'' refer to the minimum values of the Toomre stability parameter Q in each disk, Qmin=1.8 and 0.9, respectively. Previous simulations, by ourselves as well as others, have focused on initial states that are already gravitationally unstable, i.e., models similar to the low-Q model. This paper presents for the first time the numerical evolution of an essentially stable initial equilibrium state (the high-Q model) to a severely unstable one by cooling. The additional heating and cooling are applied to each model over the outer half of the disk or the entire disk. The models are subject to the rapid growth of a four-armed spiral instability; the subsequent evolution of the models depends on the thermal behavior of the disk. The cooling function tends to overwhelm the heating included in our artificial viscosity prescription, and as a result the spiral structure strengthens. The spiral disturbances transport mass at prodigious rates during the early nonlinear stages of development and significantly alter the disk's vertical surface. Although dense condensations of material can appear, their character depends on the extent of the volumetric cooling in the disk. In the simulation of the high-Q model with heating and cooling applied throughout the disk, thin, dense rings form at radii ranging from 1 to 3 AU and steadily increase in mass; later companion formation may occur in these rings as cooling drives them toward instability. When heating and cooling are applied only over the outer radial half of the disk, however, a succession of single condensations appears near 5 AU. Each clump has roughly the mass of Saturn, and some survive a complete orbit. Since the clumps form near the artificial boundary in the treatment of the disk gas physics, the production of a clump in this case is a numerical artifact. Nevertheless, radially abrupt transitions in disk gas characteristics, for example, in opacity, might mimic the artificial boundary effects in our simulations and favor the production of stable companions in actual protostellar and protoplanetary disks. The ultimate survival of condensations as eventual stellar or substellar companions to the central star is still largely an open question.
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Comparative analysis of 3D culture methods on human HepG2 cells.
Luckert, Claudia; Schulz, Christina; Lehmann, Nadja; Thomas, Maria; Hofmann, Ute; Hammad, Seddik; Hengstler, Jan G; Braeuning, Albert; Lampen, Alfonso; Hessel, Stefanie
2017-01-01
Human primary hepatocytes represent a gold standard in in vitro liver research. Due to their low availability and high costs alternative liver cell models with comparable morphological and biochemical characteristics have come into focus. The human hepatocarcinoma cell line HepG2 is often used as a liver model for toxicity studies. However, under two-dimensional (2D) cultivation conditions the expression of xenobiotic-metabolizing enzymes and typical liver markers such as albumin is very low. Cultivation for 21 days in a three-dimensional (3D) Matrigel culture system has been reported to strongly increase the metabolic competence of HepG2 cells. In our present study we further compared HepG2 cell cultivation in three different 3D systems: collagen, Matrigel and Alvetex culture. Cell morphology, albumin secretion, cytochrome P450 monooxygenase enzyme activities, as well as gene expression of xenobiotic-metabolizing and liver-specific enzymes were analyzed after 3, 7, 14, and 21 days of cultivation. Our results show that the previously reported increase of metabolic competence of HepG2 cells is not primarily the result of 3D culture but a consequence of the duration of cultivation. HepG2 cells grown for 21 days in 2D monolayer exhibit comparable biochemical characteristics, CYP activities and gene expression patterns as all 3D culture systems used in our study. However, CYP activities did not reach the level of HepaRG cells. In conclusion, the increase of metabolic competence of the hepatocarcinoma cell line HepG2 is not due to 3D cultivation but rather a result of prolonged cultivation time.
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High-resolution modeling of a marine ecosystem using the FRESCO hydroecological model
NASA Astrophysics Data System (ADS)
Zalesny, V. B.; Tamsalu, R.
2009-02-01
The FRESCO (Finnish Russian Estonian Cooperation) mathematical model describing a marine hydroecosystem is presented. The methodology of the numerical solution is based on the method of multicomponent splitting into physical and biological processes, spatial coordinates, etc. The model is used for the reproduction of physical and biological processes proceeding in the Baltic Sea. Numerical experiments are performed with different spatial resolutions for four marine basins that are enclosed into one another: the Baltic Sea, the Gulf of Finland, the Tallinn-Helsinki water area, and Tallinn Bay. Physical processes are described by the equations of nonhydrostatic dynamics, including the k-ω parametrization of turbulence. Biological processes are described by the three-dimensional equations of an aquatic ecosystem with the use of a size-dependent parametrization of biochemical reactions. The main goal of this study is to illustrate the efficiency of the developed numerical technique and to demonstrate the importance of a high spatial resolution for water basins that have complex bottom topography, such as the Baltic Sea. Detailed information about the atmospheric forcing, bottom topography, and coastline is very important for the description of coastal dynamics and specific features of a marine ecosystem. Experiments show that the spatial inhomogeneity of hydroecosystem fields is caused by the combined effect of upwelling, turbulent mixing, surface-wave breaking, and temperature variations, which affect biochemical reactions.
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NASA Astrophysics Data System (ADS)
Chance, Britton
1996-04-01
The large content of mitochondria in metabolizing cells, coupled with intrinsic NADH and flavoprotein signals makes these signals ideal for characterizing tissue metabolic states in health and disease. The first few millimeters of tissue are reached by the fluorescence excitation in the exposed surfaces of the cervix, bladder, rectum and esophagus, etc. Thus, extensive use has been made of fluorescent signals by a large number of investigators for tumor diagnosis from an empirical standpoint where the fluorescent signals are generally diminished in precancerous and cancerous tissue. This article reviews the biochemical basis for the fluorescent signals and points to a 'gold standard' for fluorescent signal examination involving freeze trapping and low temperature two- or three-dimensional high resolution fluorescence spectroscopy.
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Inhibition of quantum transport due to 'scars' of unstable periodic orbits
NASA Technical Reports Server (NTRS)
Jensen, R. V.; Sanders, M. M.; Saraceno, M.; Sundaram, B.
1989-01-01
A new quantum mechanism for the suppression of chaotic ionization of highly excited hydrogen atoms explains the appearance of anomalously stable states in the microwave ionization experiments of Koch et al. A novel phase-space representation of the perturbed wave functions reveals that the inhibition of quantum transport is due to the selective excitation of wave functions that are highly localized near unstable periodic orbits in the chaotic classical phase space. The 'scarred' wave functions provide a new basis for the quantum description of a variety of classically chaotic systems.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chevalier, Michael W., E-mail: Michael.Chevalier@ucsf.edu; El-Samad, Hana, E-mail: Hana.El-Samad@ucsf.edu
Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation timesmore » of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.« less
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Mark E. Smith; Kenneth A. Wright
1989-01-01
The Blake Fire burned about 730 ha of mature timber on the west slope of South Fork Mountain in northwestern California. Many steep innergorge and landslide headwall areas burned very hot, killing most large trees and consuming much of the large organic debris in unstable drainages. This created a potential for adverse effects on downstream fisheries from landsliding...
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Mode Medium Interaction. A Theoretical Study.
1980-09-01
Report) 10. SUPPLEMENTARY NOTES I9. KEY WORDS (Conrlfnue on reverse side II necessary mnd Identify by block rumber) CO, Laser Transfer Function...Chemical Laser Unstable Resonator Brillouin Scattering Instability Supersonic Laser Modes Acoustic Noise Acoustic Instability Perturbed Resonator Gain...end Identify by block number) An instability in the output of a high-power unstable-resonator cw CO2 laser is analyzed in terms of the perturbative
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Exact dynamics of a one dimensional Bose gas in a periodic time-dependent harmonic trap
NASA Astrophysics Data System (ADS)
Scopa, Stefano; Unterberger, Jéremie; Karevski, Dragi
2018-05-01
We study the unitary dynamics of a 1D gas of hard-core bosons trapped into a harmonic potential which varies periodically in time with frequency . Such periodic systems can be classified into orbits of different monodromies corresponding to two different physical situations, namely the case in which the bosonic cloud remains stable during the time-evolution and the case where it turns out to be unstable. In the present work we derive in the large particle number limit exact results for the stroboscopic evolution of the energy and particle densities in both physical situations.
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Stable gray soliton pinned by a defect in a microcavity-polariton condensate.
Chen, Ting-Wei; Hsieh, Wen-Feng; Cheng, Szu-Cheng
2015-09-21
We study the spatially localized dark state, called dark soliton, in a one-dimensional system of the non-resonantly pumped microcavity-polariton condensate (MPC). From the recent work by Xue and Matuszewski [Phys. Rev. Lett. 112, 216401 (2014)], we know that the dark soliton in the pure MPC system is unstable. But we find that a dark soliton pinned by a defect in the impure MPC becomes a gray soliton and can be stabilized by the presence of a defect. Moreover, the stable regime of the gray soliton is given in terms of the defect strength and pump parameter.
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A mathematical model of the structure and evolution of small-scale discrete auroral arcs
NASA Technical Reports Server (NTRS)
Seyler, Charles E.
1990-01-01
A three-dimensional fluid model for the structure and evolution of small-scale discrete auroral arcs originating from Alfven waves is developed and used to study the nonlinear macroscopic plasma dynamics of these auroral arcs. The results of simulations show that stationary auroral arcs can be unstable to a collisionless tearing mode which may be responsible for the observed transverse structuring in the form of folds and curls. At late times, the plasma becomes turbulent having transverse electric field power spectra that tend toward a universal k exp -5/3 spectral form.
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Reaction-diffusion systems coupled at the boundary and the Morse-Smale property
NASA Astrophysics Data System (ADS)
Broche, Rita de Cássia D. S.; de Oliveira, Luiz Augusto F.
We study an one-dimensional nonlinear reaction-diffusion system coupled on the boundary. Such system comes from modeling problems of temperature distribution on two bars of same length, jointed together, with different diffusion coefficients. We prove the transversality property of unstable and stable manifolds assuming all equilibrium points are hyperbolic. To this end, we write the system as an equation with noncontinuous diffusion coefficient. We then study the nonincreasing property of the number of zeros of a linearized nonautonomous equation as well as the Sturm-Liouville properties of the solutions of a linear elliptic problem.
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Hole growth dynamics in a two dimensional Leidenfrost droplet
NASA Astrophysics Data System (ADS)
Raufaste, Christophe; Celestini, Franck; Barzyk, Alexandre; Frisch, Thomas
2015-03-01
We studied the behaviors of Leidenfrost droplets confined in a Hele-Shaw cell. These droplets are unstable above a critical size and a hole grows at their center. We experimentally investigate two different systems for which the hole growth dynamics exhibits peculiar features that are driven by capillarity and inertia. We report a first regime characterized by the liquid reorganization from a liquid sheet to a liquid torus with similarities to the burst of micron-thick soap films. In the second regime, the liquid torus expands and thins before fragmentation. Finally, we propose models to account for the experimental results.
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Auroral vortex street formed by the magnetosphere-ionosphere coupling instability
NASA Astrophysics Data System (ADS)
Hiraki, Y.
2015-02-01
By performing three-dimensional magnetohydrodynamic simulations including Alfvén eigenmode perturbations most unstable to the ionospheric feedback effects, we examined the auroral vortex street that often appears just before substorm onset. We found that an initially placed arc splits, intensifies, and rapidly deforms into a vortex street. We also found that there is a critical convection electric field for growth of the Alfvén eigenmodes. The vortex street is shown to be a consequence of coupling between the magnetospheric Alfvén waves carrying field-aligned currents and the ionospheric density waves driven by Pedersen/Hall currents.
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Lecomte, Dominique; Plu, Isabelle; Froment, Alain
2012-06-01
Forensic examination is often requested when skeletal remains are discovered. Detailed visual observation can provide much information, such as the human or animal origin, sex, age, stature, and ancestry, and approximate time since death. New three-dimensional imaging techniques can provide further information (osteometry, facial reconstruction). Bone chemistry, and particularly measurement of stable or unstable carbon and nitrogen isotopes, yields information on diet and time since death, respectively. Genetic analyses of ancient DNA are also developing rapidly. Although seldom used in a judicial context, these modern anthropologic techniques are nevertheless available for the most complex cases.
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The Universal Role of Tubulence in the Propagation of Strong Shocks and Detonation Waves
NASA Astrophysics Data System (ADS)
Lee, John H.
2001-06-01
The passage of a strong shock wave usually results in irreversible physical and chemical changes in the medium. If the chemical reactions are sufficiently exothermic, the shock wave can be self-propagating, i.e., sustained by the chemical energy release via the expansion work of the reaction products. Although shocks and detonations can be globally stable and propagate at constant velocities (in the direction of motion), their structure may be highly unstable and exhibit large hydrodynamic fluctuations, i.e., turbulence. Recent investigations on plastic deformation of polycrystalline material behind shock waves have revealed particle velocity dispersion at the mesoscopic level, a result of vortical rotational motion similar to that of turbulent fluid flows at high Reynolds number.1 Strong ionizing shocks in noble gases2, as well as dissociating shock waves in carbon dioxide,3 also demonstrate a turbulent density fluctuation in the non-equilibrium shock transition zone. Perhaps the most thoroughly investigated unstable structure is that of detonation waves in gaseous explosives.4 Detonation waves in liquid explosives such as nitromethane also take on similar unstable structure as gaseous detonations.5 There are also indications that detonations in solid explosives have a similar unsteady structure under certain conditions. Thus, it appears that it is more of a rule than an exception that the structure of strong shocks and detonations are unstable and exhibit turbulent-like fluctuations as improved diagnostics now permit us to look more closely at the meso- and micro-levels. Increasing attention is now devoted to the understanding of the shock waves at the micro-scale level in recent years. This is motivated by the need to formulate physical and chemical models that contain the correct physics capable of describing quantitatively the shock transition process. It should be noted that, in spite of its unstable 3-D structure, the steady 1-D conservation laws (in the direction of propagation) apply across the shock transition zone if the downstream equilibrium plane is taken far enough away to ensure the decay of the turbulent fluctuations. Thus, the Hugoniot properties of one-dimensional propagation of shock and detonation waves remain valid. However, the conservation laws do not describe the important propagation mechanisms (i.e., the physical and chemical processes that effect the transition from initial to the final state) in the wave structure. Since gaseous detonations enjoy the advantage of being able to be observed experimentally in great detail, its complex turbulent structure is now quite well established. Furthermore, the equation of state for perfect gases is well known and the chemistry of most gas phase reactions is also sufficiently understood quantitatively to permit detailed numerical simulation of the complex detonation structure. Thus, a good database of information exists for gaseous detonation, and in this paper we shall explore the turbulent structure of gaseous detonation with the aim of answering the question as to "why nature prefers to evoke such a complicated manner to effect its propagation." We will then attempt to generalize the discussion to the "terra incognita" of condensed phase materials where the structure is much less understood. 1. Meshcheryakov, Yu.I., and Atroshenko, S.A., Izv. Vyssh. Uchebn. Zaved. Fiz., 4, 105-123 (1992). 2. Glass, I.I, and Liu, W.S., J. Fluid Mech., 84(1), 55-77 (1978). 3. Griffiths, R.W., Sanderman, R.J., and Hornung, H.G., J. Phys. D., 8, 1681-1691 (1975). 4. Lee, J.H.S., Ann. Rev. Fluid Mech., 16, 311-336 (1984). 5. Mallory, H.D., J. Appl. Physics, 38, 5302-5306 (1967).
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Dynamics of Active Separation Control at High Reynolds Numbers
NASA Technical Reports Server (NTRS)
Pack, LaTunia G.; Seifert, Avi
2000-01-01
A series of active flow control experiments were recently conducted at high Reynolds numbers on a generic separated configuration. The model simulates the upper surface of a 20% thick Glauert-Goldschmied type airfoil at zero angle of attack. The flow is fully turbulent since the tunnel sidewall boundary layer flows over the model. The main motivation for the experiments is to generate a comprehensive data base for validation of unsteady numerical simulation as a first step in the development of a CFD design tool, without which it would not be possible to effectively utilize the great potential of unsteady flow control. This paper focuses on the dynamics of several key features of the baseline as well as the controlled flow. It was found that the thickness of the upstream boundary layer has a negligible effect on the flow dynamics. It is speculated that separation is caused mainly by the highly convex surface while viscous effects are less important. The two-dimensional separated flow contains unsteady waves centered on a reduced frequency of 0.8, while in the three dimensional separated flow, frequencies around a reduced frequency of 0.3 and 1 are active. Several scenarios of resonant wave interaction take place at the separated shear-layer and in the pressure recovery region. The unstable reduced frequency bands for periodic excitation are centered on 1.5 and 5, but these reduced frequencies are based on the length of the baseline bubble that shortens due to the excitation. The conventional swept wing-scaling works well for the coherent wave features. Reproduction of these dynamic effects by a numerical simulation would provide benchmark validation.
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Observation of conductance doubling in an Andreev quantum point contact
NASA Astrophysics Data System (ADS)
Kjaergaard, M.; Nichele, F.; Suominen, H.; Nowak, M.; Wimmer, M.; Akhmerov, A.; Folk, J.; Flensberg, K.; Shabani, J.; Palmstrom, C.; Marcus, C.
One route to study the non-Abelian nature of excitations in topological superconductors is to realise gateable two dimensional (2D) semiconducting systems, with spin-orbit coupling in proximity to an s-wave superconductor. Previous work on coupling 2D electron gases (2DEG) with superconductors has been hindered by a non-ideal interface and unstable gateability. We report measurements on a gateable 2DEG coupled to superconductors through a pristine interface, and use aluminum grown in situ epitaxially on an InGaAs/InAs electron gas. We demonstrate quantization in units of 4e2 / h in a quantum point contact (QPC) in such hybrid systems. Operating the QPC as a tunnel probe, we observe a hard superconducting gap, overcoming the soft-gap problem in 2D superconductor/semiconductor systems. Our work paves way for a new and highly scalable system in which to pursue topological quantum information processing. Research supported by Microsoft Project Q and the Danish National Research Foundation.
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Similarity-based cooperation and spatial segregation
NASA Astrophysics Data System (ADS)
Traulsen, Arne; Claussen, Jens Christian
2004-10-01
We analyze a cooperative game, where the cooperative act is not based on the previous behavior of the coplayer, but on the similarity between the players. This system has been studied in a mean-field description recently [A. Traulsen and H. G. Schuster, Phys. Rev. E 68, 046129 (2003)]. Here, the spatial extension to a two-dimensional lattice is studied, where each player interacts with eight players in a Moore neighborhood. The system shows a strong segregation independent of parameters. The introduction of a local conversion mechanism towards tolerance allows for four-state cycles and the emergence of spiral waves in the spatial game. In the case of asymmetric costs of cooperation a rich variety of complex behavior is observed depending on both cooperation costs. Finally, we study the stabilization of a cooperative fixed point of a forecast rule in the symmetric game, which corresponds to cooperation across segregation borders. This fixed point becomes unstable for high cooperation costs, but can be stabilized by a linear feedback mechanism.
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Stability of knotted vortices in wave chaos
NASA Astrophysics Data System (ADS)
Taylor, Alexander; Dennis, Mark
Large scale tangles of disordered filaments occur in many diverse physical systems, from turbulent superfluids to optical volume speckle to liquid crystal phases. They can exhibit particular large scale random statistics despite very different local physics. We have previously used the topological statistics of knotting and linking to characterise the large scale tangling, using the vortices of three-dimensional wave chaos as a universal model system whose physical lengthscales are set only by the wavelength. Unlike geometrical quantities, the statistics of knotting depend strongly on the physical system and boundary conditions. Although knotting patterns characterise different systems, the topology of vortices is highly unstable to perturbation, under which they may reconnect with one another. In systems of constructed knots, these reconnections generally rapidly destroy the knot, but for vortex tangles the topological statistics must be stable. Using large scale simulations of chaotic eigenfunctions, we numerically investigate the prevalence and impact of reconnection events, and their effect on the topology of the tangle.
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Testing the Stability of 2-D Recursive QP, NSHP and General Digital Filters of Second Order
NASA Astrophysics Data System (ADS)
Rathinam, Ananthanarayanan; Ramesh, Rengaswamy; Reddy, P. Subbarami; Ramaswami, Ramaswamy
Several methods for testing stability of first quadrant quarter-plane two dimensional (2-D) recursive digital filters have been suggested in 1970's and 80's. Though Jury's row and column algorithms, row and column concatenation stability tests have been considered as highly efficient mapping methods. They still fall short of accuracy as they need infinite number of steps to conclude about the exact stability of the filters and also the computational time required is enormous. In this paper, we present procedurally very simple algebraic method requiring only two steps when applied to the second order 2-D quarter - plane filter. We extend the same method to the second order Non-Symmetric Half-plane (NSHP) filters. Enough examples are given for both these types of filters as well as some lower order general recursive 2-D digital filters. We applied our method to barely stable or barely unstable filter examples available in the literature and got the same decisions thus showing that our method is accurate enough.
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ACCRETION OF SUPERSONIC WINDS ONTO BLACK HOLES IN 3D: STABILITY OF THE SHOCK CONE
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gracia-Linares, M.; Guzmán, F. S.
Using numerical simulations we present the accretion of supersonic winds onto a rotating black hole in three dimensions. We study five representative directions of the wind with respect to the axis of rotation of the black hole and focus on the evolution and stability of the high-density shock cone that is formed during the process. We explore both the regime in which the shock cone is expected to be stable in order to confirm previous results obtained with two-dimensional simulations, and the regime in which the shock cone is expected to show a flip–flop (FF) type of instability. The methodsmore » used to attempt a triggering of the instability were (i) the accumulation of numerical errors and (ii) the explicit application of a perturbation on the velocity field after the shock cone was formed. The result is negative, that is, we did not find the FF instability within the parameter space we explored, including cases that are expected to be unstable.« less
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Yao, Xiaoqin; Chu, Jian-Zhou; Ma, Chun-Hui; Si, Chao; Li, Ji-Gang; Shi, Xiao-Fei; Liu, Chao-Nan
2015-08-01
The article studied UV-B effects on biochemical traits and proteomic changes in postharvest flowers of medicinal chrysanthemum. The experiment about UV-B effects on biochemical traits in flowers included six levels of UV-B treatments (0 (UV0), 50 (UV50), 200 (UV200), 400 (UV400), 600 (UV600) and 800 (UV800) μWcm(-2)). UV400, UV600 and UV800 treatments significantly increased the contents of hydrogen peroxide, malondialdehyde and UV-B absorbing compounds, and the activity of phenylalanine ammonia lyase enzyme over the control. The contents of chlorogenic acid and flavone in flowers were significantly increased by UV-B treatments (except for UV50 and UV800). Two-dimensional gel electrophoresis was utilized to analyze proteomic changes in flowers with or without UV-B radiation. Results indicated that 43 protein spots (>1.5-fold difference in volume) were detected, including 19 spots with a decreasing trend and 24 spots with an increasing trend, and 19 differentially expressed protein spots were successfully indentified by MALDI-TOF MS. The indentified proteins were classified based on functions, the most of which were involved in photosynthesis, respiration, protein biosynthesis and degradation and defence. An overall assessment using biochemical and differential proteomic data revealed that UV-B radiation could affect biochemical reaction and promote secondary metabolism processes in postharvest flowers. Copyright © 2015 Elsevier B.V. All rights reserved.
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Yellow Hypergiants as Dynamically Unstable Post-Red-supergiant Stars
NASA Technical Reports Server (NTRS)
Stothers, Richard B.; Chin, Chao-wen; Hansen, James E. (Technical Monitor)
2001-01-01
According to recent theoretical studies, the majority of single stars more massive than 30 solar mass successfully evolve into red supergiants, but then lose most of their hydrogen envelopes and metamorphose into hot blue remnants. While they are cool, they become dynamically unstable as a result of high radiation pressure and partial ionization of the gases in their outer layers. It is shown here that these unstable red-supergiant models repeatedly shrink and re-expand on a thermal time scale when perturbed by heavy bursts of mass loss. Consequently, they fill up the domain of yellow hypergiants on the Hertzsprung-Russell diagram and display very fast rates of evolution there, as observed.
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Brownian motion surviving in the unstable cubic potential and the role of Maxwell's demon
NASA Astrophysics Data System (ADS)
Ornigotti, Luca; Ryabov, Artem; Holubec, Viktor; Filip, Radim
2018-03-01
The trajectories of an overdamped particle in a highly unstable potential diverge so rapidly, that the variance of position grows much faster than its mean. A description of the dynamics by moments is therefore not informative. Instead, we propose and analyze local directly measurable characteristics, which overcome this limitation. We discuss the most probable particle position (position of the maximum of the probability density) and the local uncertainty in an unstable cubic potential, V (x ) ˜x3 , both in the transient regime and in the long-time limit. The maximum shifts against the acting force as a function of time and temperature. Simultaneously, the local uncertainty does not increase faster than the observable shift. In the long-time limit, the probability density naturally attains a quasistationary form. We interpret this process as a stabilization via the measurement-feedback mechanism, the Maxwell demon, which works as an entropy pump. The rules for measurement and feedback naturally arise from the basic properties of the unstable dynamics. All reported effects are inherent in any unstable system. Their detailed understanding will stimulate the development of stochastic engines and amplifiers and, later, their quantum counterparts.
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A randomised comparison of AMBI, TGN and PFN for treatment of unstable trochanteric fractures.
Papasimos, S; Koutsojannis, C M; Panagopoulos, A; Megas, P; Lambiris, E
2005-09-01
In this study, we initiated a prospective, randomised, clinical trial comparing the AMBI, TGN and PFN operations used for treatment of unstable fractures, for differences in intra-operative use, consolidation, complications and functional outcome. We have compared the pre-, intra- and post-operating variables of AMBI, TGN and PFN operations that were used for treatment of unstable trochanteric fractures, of 120 patients all above 60 years old diagnosed with extracapsular hip fractures classified as AO Type 31-A2 or Type 31-A3. According to our results the three methods are comparable in the treatment of unstable trochanteric fractures of patients above 60 years old. The AMBI remains the gold standard for the fractures of trochanteric region. TGN has an easier and faster procedure, facilitates early weight bearing and had minor late complications. An improper use of the PFN system was the reason for the most complications and the longer operation time of the device. PFN is also an accepted minimally invasive implant for unstable proximal femoral fractures but future modification of the implant to avoid Z-effect phenomenon, careful surgical technique and selection of the patients should reduce its high complication rate.
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An InN/InGaN Quantum Dot Electrochemical Biosensor for Clinical Diagnosis
Alvi, Naveed ul Hassan; Gómez, Victor J.; Rodriguez, Paul E.D. Soto; Kumar, Praveen; Zaman, Saima; Willander, Magnus; Nötzel, Richard
2013-01-01
Low-dimensional InN/InGaN quantum dots (QDs) are demonstrated for realizing highly sensitive and efficient potentiometric biosensors owing to their unique electronic properties. The InN QDs are biochemically functionalized. The fabricated biosensor exhibits high sensitivity of 97 mV/decade with fast output response within two seconds for the detection of cholesterol in the logarithmic concentration range of 1 × 10−6 M to 1 × 10−3 M. The selectivity and reusability of the biosensor are excellent and it shows negligible response to common interferents such as uric acid and ascorbic acid. We also compare the biosensing properties of the InN QDs with those of an InN thin film having the same surface properties, i.e., high density of surface donor states, but different morphology and electronic properties. The sensitivity of the InN QDs-based biosensor is twice that of the InN thin film-based biosensor, the EMF is three times larger, and the response time is five times shorter. A bare InGaN layer does not produce a stable response. Hence, the superior biosensing properties of the InN QDs are governed by their unique surface properties together with the zero-dimensional electronic properties. Altogether, the InN QDs-based biosensor reveals great potential for clinical diagnosis applications. PMID:24132228
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Kazmierczak, Steven C; Leen, Todd K; Erdogmus, Deniz; Carreira-Perpinan, Miguel A
2007-01-01
The clinical laboratory generates large amounts of patient-specific data. Detection of errors that arise during pre-analytical, analytical, and post-analytical processes is difficult. We performed a pilot study, utilizing a multidimensional data reduction technique, to assess the utility of this method for identifying errors in laboratory data. We evaluated 13,670 individual patient records collected over a 2-month period from hospital inpatients and outpatients. We utilized those patient records that contained a complete set of 14 different biochemical analytes. We used two-dimensional generative topographic mapping to project the 14-dimensional record to a two-dimensional space. The use of a two-dimensional generative topographic mapping technique to plot multi-analyte patient data as a two-dimensional graph allows for the rapid identification of potentially anomalous data. Although we performed a retrospective analysis, this technique has the benefit of being able to assess laboratory-generated data in real time, allowing for the rapid identification and correction of anomalous data before they are released to the physician. In addition, serial laboratory multi-analyte data for an individual patient can also be plotted as a two-dimensional plot. This tool might also be useful for assessing patient wellbeing and prognosis.
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Zarafeta, Dimitra; Moschidi, Danai; Ladoukakis, Efthymios; Gavrilov, Sergey; Chrysina, Evangelia D; Chatziioannou, Aristotelis; Kublanov, Ilya; Skretas, Georgios; Kolisis, Fragiskos N
2016-12-19
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Jyotshna; Srivastava, Pooja; Killadi, Bharti; Shanker, Karuna
2015-06-01
Mango (Mangifera indica) fruit is one of the important commercial fruit crops of India. Similar to other tropical fruits it is also highly perishable in nature. During storage/ripening, changes in its physico-chemical quality parameters viz. firmness, titrable acidity, total soluble solid content (TSSC), carotenoids content, and other biochemicals are inevitable. A uni-dimensional double-development high-performance thin-layer chromatography (UDDD-HPTLC) method was developed for the real-time monitoring of mangiferin and lupeol in mango pulp and peel during storage. The quantitative determination of both compounds of different classes was achieved by densitometric HPTLC method. Silica gel 60F254 HPTLC plates and two solvent systems viz. toluene/EtOAC/MeOH and EtOAC/MeOH, respectively were used for optimum separation and selective evaluation. Densitometric quantitation of mangiferin was performed at 390nm, while lupeol at 610nm after post chromatographic derivatization. Validated method was used to real-time monitoring of mangiferin and lupeol content during storage in four Indian cultivars, e.g. Bombay green (Bgreen), Dashehari, Langra, and Chausa. Significant correlations (p<0.05) between of acidity and TSSC with mangiferin and lupeol in pulp and peel during storage were also observed. Copyright © 2014 Elsevier Ltd. All rights reserved.
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High-resolution NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids
Nucci, Nathaniel V.; Valentine, Kathleen G.; Wand, A. Joshua
2014-01-01
High-resolution multi-dimensional solution NMR is unique as a biophysical and biochemical tool in its ability to examine both the structure and dynamics of macromolecules at atomic resolution. Conventional solution NMR approaches, however, are largely limited to examinations of relatively small (< 25 kDa) molecules, mostly due to the spectroscopic consequences of slow rotational diffusion. Encapsulation of macromolecules within the protective nanoscale aqueous interior of reverse micelles dissolved in low viscosity fluids has been developed as a means through which the ‘slow tumbling problem’ can be overcome. This approach has been successfully applied to diverse proteins and nucleic acids ranging up to 100 kDa, considerably widening the range of biological macromolecules to which conventional solution NMR methodologies may be applied. Recent advances in methodology have significantly broadened the utility of this approach in structural biology and molecular biophysics. PMID:24656086
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Terahertz emission from ultrafast spin-charge current at a Rashba interface
NASA Astrophysics Data System (ADS)
Zhang, Qi; Jungfleisch, Matthias Benjamin; Zhang, Wei; Pearson, John E.; Wen, Haidan; Hoffmann, Axel
Ultrafast broadband terahertz (THz) radiation is highly desired in various fields from fundamental research in condensed matter physics to bio-chemical detection. Conventional ultrafast THz sources rely on either nonlinear optical effects or ultrafast charge currents in semiconductors. Recently, however, it was realized that ultrabroad-band THz radiation can be produced highly effectively by novel spintronics-based emitters that also make use of the electron's spin degree of freedom. Those THz-emitters convert a spin current flow into a terahertz electromagnetic pulse via the inverse spin-Hall effect. In contrast to this bulk conversion process, we demonstrate here that a femtosecond spin current pulse launched from a CoFeB layer can also generate terahertz transients efficiently at a two-dimensional Rashba interface between two non-magnetic materials, i.e., Ag/Bi. Those interfaces have been proven to be efficient means for spin- and charge current interconversion.
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'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites.
Lerma-Ortiz, Claudia; Jeffryes, James G; Cooper, Arthur J L; Niehaus, Thomas D; Thamm, Antje M K; Frelin, Océane; Aunins, Thomas; Fiehn, Oliver; de Crécy-Lagard, Valérie; Henry, Christopher S; Hanson, Andrew D
2016-06-15
Many common metabolites are intrinsically unstable and reactive, and hence prone to chemical (i.e. non-enzymatic) damage in vivo Although this fact is widely recognized, the purely chemical side-reactions of metabolic intermediates can be surprisingly hard to track down in the literature and are often treated in an unprioritized case-by-case way. Moreover, spontaneous chemical side-reactions tend to be overshadowed today by side-reactions mediated by promiscuous ('sloppy') enzymes even though chemical damage to metabolites may be even more prevalent than damage from enzyme sloppiness, has similar outcomes, and is held in check by similar biochemical repair or pre-emption mechanisms. To address these limitations and imbalances, here we draw together and systematically integrate information from the (bio)chemical literature, from cheminformatics, and from genome-scale metabolic models to objectively define a 'Top 30' list of damage-prone metabolites. A foundational part of this process was to derive general reaction rules for the damage chemistries involved. The criteria for a 'Top 30' metabolite included predicted chemical reactivity, essentiality, and occurrence in diverse organisms. We also explain how the damage chemistry reaction rules ('operators') are implemented in the Chemical-Damage-MINE (CD-MINE) database (minedatabase.mcs.anl.gov/#/top30) to provide a predictive tool for many additional potential metabolite damage products. Lastly, we illustrate how defining a 'Top 30' list can drive genomics-enabled discovery of the enzymes of previously unrecognized damage-control systems, and how applying chemical damage reaction rules can help identify previously unknown peaks in metabolomics profiles. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.
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Hu, Liyan; Pandey, Amit V; Balmer, Cécile; Eggimann, Sandra; Rüfenacht, Véronique; Nuoffer, Jean-Marc; Häberle, Johannes
2015-09-01
Loss of function of the urea cycle enzyme argininosuccinate lyase (ASL) is caused by mutations in the ASL gene leading to ASL deficiency (ASLD). ASLD has a broad clinical spectrum ranging from life-threatening severe neonatal to asymptomatic forms. Different levels of residual ASL activity probably contribute to the phenotypic variability but reliable expression systems allowing clinically useful conclusions are not yet available. In order to define the molecular characteristics underlying the phenotypic variability, we investigated all ASL mutations that were hitherto identified in patients with late onset or mild clinical and biochemical courses by ASL expression in human embryonic kidney 293 T cells. We found residual activities >3% of ASL wild type (WT) in nine of 11 ASL mutations. Six ASL mutations (p.Arg95Cys, p.Ile100Thr, p.Val178Met, p.Glu189Gly, p.Val335Leu, and p.Arg379Cys) with residual activities ≥16% of ASL WT showed no significant or less than twofold reduced Km values, but displayed thermal instability. Computational structural analysis supported the biochemical findings by revealing multiple effects including protein instability, disruption of ionic interactions and hydrogen bonds between residues in the monomeric form of the protein, and disruption of contacts between adjacent monomeric units in the ASL tetramer. These findings suggest that the clinical and biochemical course in variant forms of ASLD is associated with relevant residual levels of ASL activity as well as instability of mutant ASL proteins. Since about 30% of known ASLD genotypes are affected by mutations studied here, ASLD should be considered as a candidate for chaperone treatment to improve mutant protein stability.
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The stability of a flexible cantilever in viscous channel flow
NASA Astrophysics Data System (ADS)
Cisonni, Julien; Lucey, Anthony D.; Elliott, Novak S. J.; Heil, Matthias
2017-05-01
Most studies of the flow-induced flutter instability of a flexible cantilever have assumed inviscid flow because of the high flow speeds and the large scale of the structures encountered in the wide range of applications of this fluid-structure interaction (FSI) system. However, for instance, in the fields of energy harvesting and biomechanics, low flow speeds and small- and micro-scale systems can give relatively low Reynolds numbers so that fluid viscosity needs to be explicitly accounted for to provide reliable predictions of channel-immersed-cantilever stability. In this study, we employ a numerical model coupling the Navier-Stokes equations and a one-dimensional elastic beam model. We conduct a parametric investigation to determine the conditions leading to flutter instability of a slender flexible cantilever immersed in two-dimensional viscous channel flow for Reynolds numbers lower than 1000. The large set of numerical simulations carried out allows predictions of the influence of decreasing Reynolds numbers and of the cantilever confinement on the single-mode neutral stability of the FSI system and on the pre- and post-critical cantilever motion. This model's predictions are also compared to those of a FSI model containing a two-dimensional solid model in order to assess, primarily, the effect of the cantilever slenderness in the simulations. Results show that an increasing contribution of viscosity to the hydrodynamic forces significantly alters the instability boundaries. In general, a decrease in Reynolds number is predicted to produce a stabilisation of the FSI system, which is more pronounced for high fluid-to-solid mass ratios. For particular fluid-to-solid mass ratios, viscous effects can lower the critical velocity and lead to a change in the first unstable structural mode. However, at constant Reynolds number, the effects of viscosity on the system stability are diminished by the confinement of the cantilever, which strengthens the importance of flow inertia.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lashkov, A. A.; Zhukhlistova, N. E.; Sotnichenko, S. E.
2010-01-15
The three-dimensional structures of three complexes of Salmonella typhimurium uridine phosphorylase with the inhibitor 2,2'-anhydrouridine, the substrate PO{sub 4}, and with both the inhibitor 2,2'-anhydrouridine and the substrate PO{sub 4} (a binary complex) were studied in detail by X-ray diffraction. The structures of the complexes were refined at 2.38, 1.5, and 1.75 A resolution, respectively. Changes in the three-dimensional structure of the subunits in different crystal structures are considered depending on the presence or absence of the inhibitor molecule and (or) the phosphate ion in the active site of the enzyme. The presence of the phosphate ion in the phosphate-bindingmore » site was found to substantially change the orientations of the side chains of the amino-acid residues Arg30, Arg91, and Arg48 coordinated to this ion. A comparison showed that the highly flexible loop L9 is unstable. The atomic coordinates of the refined structures of the complexes and the corresponding structure factors were deposited in the Protein Data Bank (their PDB ID codes are 3DD0 and 3C74). The experimental data on the spatial reorganization of the active site caused by changes in its functional state from the unligated to the completely inhibited state suggest the structural basis for the mechanism of inhibition of Salmonella typhimurium uridine phosphorylase.« less
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Matsumoto, Koichiro; Inoue, Hiromasa; Fukuyama, Satoru; Tsuda, Miyuki; Ikegami, Tomomi; Kibe, Atsuko; Yoshiura, Yuki; Komori, Masashi; Hamasaki, Naotaka; Aizawa, Hisamichi; Nakanishi, Yoichi
2004-08-01
Although IL-10 is known as an immunoregulatory cytokine produced by various cells including T cells, its basic profile in atopic asthma remains uncertain. The profiles of IL-10 production in circulating CD4+ T cells of atopic asthmatics were investigated with respect to clinical severity. Forty atopic asthmatics were divided into three groups: mild, and severe but stable and severe unstable asthmatics. Eosinophils were counted in the peripheral blood and sputum, and exhaled nitric oxide was assessed. PBMCs were stimulated with or without anti-CD3 and anti-CD28 antibodies and then processed for detecting IL-10-producing CD4+ cells using flow cytometry. There was no difference in the eosinophil count in blood or sputum and in nitric oxide level among the three groups. IL-10-producing CD4+ cells were mainly detected in a CD45RO+ memory population. The frequency of IL-10-producing cells after stimulation was significantly lower in the severe unstable group compared to the mild group. In addition, the frequency of IL-10-producing cells in the severe unstable group was significantly lower than that in the severe stable group despite the fact that both groups received similar treatments with high-dose inhaled corticosteroids. The IL-10 production of CD4+CD45RO+ cells in response to dexamethasone did not differ among the three groups. IL-10-producing CD4+CD45RO+ cells in the peripheral blood are decreased in severe unstable asthmatics, which is not explained by the effect of high-dose inhaled corticosteroid medication. Copyright 2004 S. Karger AG, Basel
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3D DNS and LES of Breaking Inertia-Gravity Waves
NASA Astrophysics Data System (ADS)
Remmler, S.; Fruman, M. D.; Hickel, S.; Achatz, U.
2012-04-01
As inertia-gravity waves we refer to gravity waves that have a sufficiently low frequency and correspondingly large horizontal wavelength to be strongly influenced by the Coriolis force. Inertia-gravity waves are very active in the middle atmosphere and their breaking is potentially an important influence on the circulation in this region. The parametrization of this process requires a good theoretical understanding, which we want to enhance with the present study. Primary linear instabilities of an inertia-gravity wave and "2.5-dimensional" nonlinear simulations (where the spatial dependence is two dimensional but the velocity and vorticity fields are three-dimensional) with the wave perturbed by its leading primary instabilities by Achatz [1] have shown that the breaking differs significantly from that of high-frequency gravity waves due to the strongly sheared component of velocity perpendicular to the plane of wave-propagation. Fruman & Achatz [2] investigated the three-dimensionalization of the breaking by computing the secondary linear instabilities of the same waves using singular vector analysis. These secondary instabilities are variations perpendicular to the direction of the primary perturbation and the wave itself, and their wavelengths are an order of magnitude shorter than both. In continuation of this work, we carried out fully three-dimensional nonlinear simulations of inertia-gravity waves perturbed by their leading primary and secondary instabilities. The direct numerical simulation (DNS) was made tractable by restricting the domain size to the dominant scales selected by the linear analyses. The study includes both convectively stable and unstable waves. To the best of our knowledge, this is the first fully three-dimensional nonlinear direct numerical simulation of inertia-gravity waves at realistic Reynolds numbers with complete resolution of the smallest turbulence scales. Previous simulations either were restricted to high frequency gravity waves (e. g. Fritts et al. [3]), or the ratio N/f was artificially reduced (e. g. Lelong & Dunkerton [4]). The present simulations give us insight into the three-dimensional breaking process as well as the emerging turbulence. We assess the possibility of reducing the computational costs of three-dimensional simulations by using an implicit turbulence subgrid-scale parametrization based on the Adaptive Local Deconvolution Method (ALDM) for stratified turbulence [5]. In addition, we have performed ensembles of nonlinear 2.5-dimensional DNS, like those in Achatz [1] but with a small amount of noise superposed to the initial state, and compared the results with coarse-resolution simulations using either ALDM as well as with standard LES schemes. We found that the results of the models with parametrized turbulence, which are orders of magnitude more computationally economical than the DNS, compare favorably with the DNS in terms of the decay of the wave amplitude with time (the quantity most important for application to gravity-wave drag parametrization) suggesting that they may be trusted in future simulations of gravity wave breaking.
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Neurochemical profile of dementia pugilistica.
Kokjohn, Tyler A; Maarouf, Chera L; Daugs, Ian D; Hunter, Jesse M; Whiteside, Charisse M; Malek-Ahmadi, Michael; Rodriguez, Emma; Kalback, Walter; Jacobson, Sandra A; Sabbagh, Marwan N; Beach, Thomas G; Roher, Alex E
2013-06-01
Dementia pugilistica (DP), a suite of neuropathological and cognitive function declines after chronic traumatic brain injury (TBI), is present in approximately 20% of retired boxers. Epidemiological studies indicate TBI is a risk factor for neurodegenerative disorders including Alzheimer disease (AD) and Parkinson disease (PD). Some biochemical alterations observed in AD and PD may be recapitulated in DP and other TBI persons. In this report, we investigate long-term biochemical changes in the brains of former boxers with neuropathologically confirmed DP. Our experiments revealed biochemical and cellular alterations in DP that are complementary to and extend information already provided by histological methods. ELISA and one-dimensional and two dimensional Western blot techniques revealed differential expression of select molecules between three patients with DP and three age-matched non-demented control (NDC) persons without a history of TBI. Structural changes such as disturbances in the expression and processing of glial fibrillary acidic protein, tau, and α-synuclein were evident. The levels of the Aβ-degrading enzyme neprilysin were reduced in the patients with DP. Amyloid-β levels were elevated in the DP participant with the concomitant diagnosis of AD. In addition, the levels of brain-derived neurotrophic factor and the axonal transport proteins kinesin and dynein were substantially decreased in DP relative to NDC participants. Traumatic brain injury is a risk factor for dementia development, and our findings are consistent with permanent structural and functional damage in the cerebral cortex and white matter of boxers. Understanding the precise threshold of damage needed for the induction of pathology in DP and TBI is vital.
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Neurochemical Profile of Dementia Pugilistica
Kokjohn, Tyler A.; Maarouf, Chera L.; Daugs, Ian D.; Hunter, Jesse M.; Whiteside, Charisse M.; Malek-Ahmadi, Michael; Rodriguez, Emma; Kalback, Walter; Jacobson, Sandra A.; Sabbagh, Marwan N.; Beach, Thomas G.
2013-01-01
Abstract Dementia pugilistica (DP), a suite of neuropathological and cognitive function declines after chronic traumatic brain injury (TBI), is present in approximately 20% of retired boxers. Epidemiological studies indicate TBI is a risk factor for neurodegenerative disorders including Alzheimer disease (AD) and Parkinson disease (PD). Some biochemical alterations observed in AD and PD may be recapitulated in DP and other TBI persons. In this report, we investigate long-term biochemical changes in the brains of former boxers with neuropathologically confirmed DP. Our experiments revealed biochemical and cellular alterations in DP that are complementary to and extend information already provided by histological methods. ELISA and one-dimensional and two dimensional Western blot techniques revealed differential expression of select molecules between three patients with DP and three age-matched non-demented control (NDC) persons without a history of TBI. Structural changes such as disturbances in the expression and processing of glial fibrillary acidic protein, tau, and α-synuclein were evident. The levels of the Aβ–degrading enzyme neprilysin were reduced in the patients with DP. Amyloid-β levels were elevated in the DP participant with the concomitant diagnosis of AD. In addition, the levels of brain-derived neurotrophic factor and the axonal transport proteins kinesin and dynein were substantially decreased in DP relative to NDC participants. Traumatic brain injury is a risk factor for dementia development, and our findings are consistent with permanent structural and functional damage in the cerebral cortex and white matter of boxers. Understanding the precise threshold of damage needed for the induction of pathology in DP and TBI is vital. PMID:23268705
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Reduced magnetohydrodynamic theory of oblique plasmoid instabilities
NASA Astrophysics Data System (ADS)
Baalrud, S. D.; Bhattacharjee, A.; Huang, Y.-M.
2012-02-01
The three-dimensional nature of plasmoid instabilities is studied using the reduced magnetohydrodynamic equations. For a Harris equilibrium with guide field, represented by Bo=Bpotanh(x /λ)ŷ+Bzoẑ, a spectrum of modes are unstable at multiple resonant surfaces in the current sheet, rather than just the null surface of the poloidal field Byo(x)=Bpotanh(x /λ), which is the only resonant surface in 2D or in the absence of a guide field. Here, Bpo is the asymptotic value of the equilibrium poloidal field, Bzo is the constant equilibrium guide field, and λ is the current sheet width. Plasmoids on each resonant surface have a unique angle of obliquity θ ≡arctan(kz/ky). The resonant surface location for angle θ is xs=λarctanh(μ), where μ =tanθBzo/Bpo and the existence of a resonant surface requires |θ |
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Buoyant miscible displacement flows in a nonuniform Hele-Shaw cell
NASA Astrophysics Data System (ADS)
Walling, E.; Mollaabbasi, R.; Taghavi, S. M.
2018-03-01
Miscible displacement flows within the gap of a nonuniform Hele-Shaw cell are considered, theoretically and experimentally. The cell is vertical and it can be diverging or converging. A light fluid displaces a heavy fluid downwards. The displacement imposed velocity is sufficiently large so that diffusive effects are negligible within our time scale of interest. For certain flow parameters, the displacement flow is characterized by a symmetric, two-dimensional penetration of the light fluid into the heavy one, for which a lubrication approximation approach is developed to simplify the governing equations and find a semianalytical solution for the flux functions. The solutions reveal how the cell nonuniformity may affect the propagation of the interface between the two fluids, versus the other flow parameters, i.e., the viscosity ratio (m ) and a buoyancy number (χ ), for which a detailed flow regime classification is presented. Our results demonstrate that the presence of nonuniformity adds a unique spatiotemporal nature to these displacements which is not the case for uniform cell flows. The combination of the model and experiments reveals the existence of self-spreading, spike, and unstable (viscous fingering) flow regimes, which may occur at various spatial positions within the cell. A converging cell may allow a transition from spike to self-spreading or unstable regime, whereas a diverging cell may offer a transition from self-spreading or unstable to spike regime. Our work demonstrates that the novel spatiotemporal nature of nonuniform cell flows must be considered through the numerical solution of the interface propagation equation, to yield accurate predictions about the flow behaviors at various spatial positions.
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Motion state analysis of space target based on optical cross section
NASA Astrophysics Data System (ADS)
Tian, Qichen; Li, Zhi; Xu, Can; Liu, Chenghao
2017-10-01
In order to solve the problem that the movement state analysis method of the space target based on OCS is not related to the real motion state. This paper proposes a method based on OCS for analyzing the state of space target motion. This paper first establish a three-dimensional model of real STSS satellite, then change the satellite's surface into element, and assign material to each panel according to the actual conditions of the satellite. This paper set up a motion scene according to the orbit parameters of STSS satellite in STK, and the motion states are set to three axis steady state and slowly rotating unstable state respectively. In these two states, the occlusion condition of the surface element is firstly determined, and the effective face element is selected. Then, the coordinates of the observation station and the solar coordinates in the satellite body coordinate system are input into the OCS calculation program, and the OCS variation curves of the three axis steady state and the slow rotating unstable state STSS satellite are obtained. Combining the satellite surface structure and the load situation, the OCS change curve of the three axis stabilized satellite is analyzed, and the conclude that the OCS curve fluctuates up and down when the sunlight is irradiated to the load area; By using Spectral analysis method, autocorrelation analysis and the cross residual method, the rotation speed of OCS satellite in slow rotating unstable state is analyzed, and the rotation speed of satellite is successfully reversed. By comparing the three methods, it is found that the cross residual method is more accurate.
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Coury, M.; Guttenfelder, W.; Mikkelsen, D. R.; ...
2016-06-30
Linear (local) gyrokinetic predictions of edge microinstabilities in highly shaped, lithiated and non-lithiated NSTX discharges are reported using the gyrokinetic code GS2. Microtearing modes dominate the non-lithiated pedestal top. The stabilization of these modes at the lithiated pedestal top enables the electron temperature pedestal to extend further inwards, as observed experimentally. Kinetic ballooning modes are found to be unstable mainly at the mid-pedestal of both types of discharges, with un- stable trapped electron modes nearer the separatrix region. At electron wavelengths, ETG modes are found to be unstable from mid-pedestal outwards for η e, exp ~2.2 with higher growth ratesmore » for the lithiated discharge. Near the separatrix, the critical temperature gradient for driving ETG modes is reduced in the presence of lithium, re ecting the reduction of the lithiated density gradients observed experimentally. A preliminary linear study in the edge of non-lithiated discharges shows that the equilibrium shaping alters the electrostatic modes stability, found more unstable at high plasma shaping.« less
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Kim, Jung H; Rhee, Ye-Y; Bae, Jeong-M; Kwon, Hyeong-J; Cho, Nam-Y; Kim, Mi J; Kang, Gyeong H
2013-07-01
Although the presence of MLH1 methylation in microsatellite-unstable colorectal cancer generally indicates involvement of the CpG island methylator phenotype (CIMP) in the development of the tumor, these two conditions do not always correlate. A minority of microsatellite-unstable colorectal cancers exhibit discordance between CIMP and MLH1 methylation statuses. However, the clinicopathological features of such microsatellite-unstable colorectal cancers with discrepant MLH1 methylation and CIMP statuses remain poorly studied. Microsatellite-unstable colorectal cancers (n=220) were analyzed for CIMP and MLH1 methylation statuses using the MethyLight assay. Based on the combinatorial CIMP and MLH1 methylation statuses, the microsatellite-unstable colorectal cancers were grouped into four subtypes (CIMP-high (CIMP-H) MLH1 methylation-positive (MLH1m+), CIMP-H MLH1 methylation-negative, CIMP-low/0 (CIMP-L/0) MLH1m+, and CIMP-L/0 MLH1 methylation-negative), which were compared in terms of their associations with clinicopathological and molecular features. The CIMP-L/0 MLH1 methylation-negative and CIMP-H MLH1m+ subtypes were predominant, comprising 63.6 and 24.1% of total microsatellite-unstable colorectal cancers, respectively. The discordant subtypes, CIMP-H MLH1 methylation-negative and CIMP-L/0 MLH1m+, were found in 5 and 7% of microsatellite-unstable colorectal cancers, respectively. The CIMP-H MLH1 methylation-negative subtype exhibited elevated incidence rates in male patients and was associated with larger tumor size, more frequent loss of MSH2 expression, increased frequency of KRAS mutation, and advanced cancer stage. The CIMP-L/0 MLH1m+ subtype was associated with onset at an earlier age, a predominance of MLH1 loss, and earlier cancer stage. None of the CIMP-L/0 MLH1m+ subtype patients succumbed to death during the follow-up. Our findings suggest that the discordant subtypes of colorectal cancers exhibit distinct clinicopathological and molecular features, although the proportion of discordant subtypes is low. The microsatellite-unstable colorectal cancers of the same CIMP status tended to exhibit different clinicopathological features depending on MLH1 methylation status.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Borbulevych, Oleg; Kumarasiri, Malika; Wilson, Brian
The integral membrane protein BlaR1 of methicillin-resistant Staphylococcus aureus senses the presence of {beta}-lactam antibiotics in the milieu and transduces the information to the cytoplasm, where the biochemical events that unleash induction of antibiotic resistance mechanisms take place. We report herein by two-dimensional and three-dimensional NMR experiments of the sensor domain of BlaR1 in solution and by determination of an x-ray structure for the apo protein that Lys-392 of the antibiotic-binding site is posttranslationally modified by N{sup {zeta}}-carboxylation. Additional crystallographic and NMR data reveal that on acylation of Ser-389 by antibiotics, Lys-392 experiences N{sup {zeta}}-decarboxylation. This unique process, termed themore » lysine N{sup {zeta}}-decarboxylation switch, arrests the sensor domain in the activated ('on') state, necessary for signal transduction and all the subsequent biochemical processes. We present structural information on how this receptor activation process takes place, imparting longevity to the antibiotic-receptor complex that is needed for the induction of the antibiotic-resistant phenotype in methicillin-resistant S. aureus.« less
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Ghaber, Sidi M; Trabelsi, Nawel; Salem, Mohamed L; Haddad, Faten; Abba, Aminetou; Darragi, Imen; Abbes, Salem
2018-01-01
Unstable hemoglobins (Hbs) are a group of Hb disorders that could be the origin of chronic hemolytic anemia. Most of these disorders are caused by point mutations taking place in the globin genes and affecting the stability of the Hb molecule. They are inherited as autosomal dominant diseases and described worldwide. Herein we report a new observation of an unstable variant in the Mauritanian population. The patient was a young girl of Mauritanian origin. She presented with chronic hemolytic anemia with an unknown etiology after being referred to several medical centers. Laboratory investigations based on routine analyses, capillary electrophoresis (CE), cation exchange high performance liquid chromatography (HPLC) and DNA sequencing revealed an abnormal unstable Hb known as Hb Moscva [β24(B6)Gly→Asp (GGT>GAT), HBB: c.74G>A] that occurred as a de novo mutation newly detected in an African girl of Mauritanian origin.
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Risk factors for distal radius fracture in postmenopausal women.
Xu, Wenting; Ni, Cheng; Yu, Ren; Gu, Guoqing; Wang, Zheren; Zheng, Guoqing
2017-05-01
The aim of this work was to explore the risk factors for distal radius fracture in postmenopausal women. A total of 611 postmenopausal women with distal radius fractures were included. In all, 173 patients with unstable distal radius fractures were included (unstable fracture group), while there were 438 patients with stable distal radius fractures (stable fracture group). The control group comprised 800 postmenopausal women with no fracture. A questionnaire survey was conducted. Compared with the control group, the 611 postmenopausal women with distal radius fractures had a higher body mass index (BMI). Advanced age and higher BMI were more common in the unstable fracture group than in the stable fracture group (P <0.05). A higher proportion of the 611 postmenopausal women with a distal radius fracture had fallen in the last 12 months than in the control group. Comorbidities and the frequency of falls in the last 12 months were higher in the unstable fracture group than in the stable fracture group (P < 0.05). A higher proportion of the control group was taking calcium supplements, while the proportion taking calcium supplementation in the unstable fracture group was lower than that in the stable fracture group (P < 0.05). Osteoporosis in the two fracture groups (P < 0.05) was significantly higher than in the control group and was the highest in the unstable fracture group (P < 0.05). In postmenopausal women, obesity, falls, unknown osteoporosis status, and osteoporosis are associated with high risk of distal radius fracture. If comorbidities and advanced age are also present, this group of persons may be at higher risk for unstable distal radius fractures.
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Closed-loop control of a fragile network: application to seizure-like dynamics of an epilepsy model
Ehrens, Daniel; Sritharan, Duluxan; Sarma, Sridevi V.
2015-01-01
It has recently been proposed that the epileptic cortex is fragile in the sense that seizures manifest through small perturbations in the synaptic connections that render the entire cortical network unstable. Closed-loop therapy could therefore entail detecting when the network goes unstable, and then stimulating with an exogenous current to stabilize the network. In this study, a non-linear stochastic model of a neuronal network was used to simulate both seizure and non-seizure activity. In particular, synaptic weights between neurons were chosen such that the network's fixed point is stable during non-seizure periods, and a subset of these connections (the most fragile) were perturbed to make the same fixed point unstable to model seizure events; and, the model randomly transitions between these two modes. The goal of this study was to measure spike train observations from this epileptic network and then apply a feedback controller that (i) detects when the network goes unstable, and then (ii) applies a state-feedback gain control input to the network to stabilize it. The stability detector is based on a 2-state (stable, unstable) hidden Markov model (HMM) of the network, and detects the transition from the stable mode to the unstable mode from using the firing rate of the most fragile node in the network (which is the output of the HMM). When the unstable mode is detected, a state-feedback gain is applied to generate a control input to the fragile node bringing the network back to the stable mode. Finally, when the network is detected as stable again, the feedback control input is switched off. High performance was achieved for the stability detector, and feedback control suppressed seizures within 2 s after onset. PMID:25784851
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NASA Astrophysics Data System (ADS)
Yamazaki, Y. H.; Skeet, D. R.; Read, P. L.
2004-04-01
We have been developing a new three-dimensional general circulation model for the stratosphere and troposphere of Jupiter based on the dynamical core of a portable version of the Unified Model of the UK Meteorological Office. Being one of the leading terrestrial GCMs, employed for operational weather forecasting and climate research, the Unified Model has been thoroughly tested and performance tuned for both vector and parallel computers. It is formulated as a generalized form of the standard primitive equations to handle a thick atmosphere, using a scaled pressure as the vertical coordinate. It is able to accurately simulate the dynamics of a three-dimensional fully compressible atmosphere on the whole or a part of a spherical shell at high spatial resolution in all three directions. Using the current version of the GCM, we examine the characteristics of the Jovian winds in idealized configurations based on the observed vertical structure of temperature. Our initial focus is on the evolution of isolated eddies in the mid-latitudes. Following a brief theoretical investigation of the vertical structure of the atmosphere, limited-area cyclic channel domains are used to numerically investigate the nonlinear evolution of the mid-latitude winds. First, the evolution of deep and shallow cyclones and anticyclones are tested in the atmosphere at rest to identify a preferred horizontal and vertical structure of the vortices. Then, the dependency of the migration characteristics of the vortices are investigated against modelling parameters to find that it is most sensitive to the horizontal diffusion. We also examine the hydrodynamical stability of observed subtropical jets in both northern and southern hemispheres in the three-dimensional nonlinear model as initial value problems. In both cases, it was found that the prominent jets are unstable at various scales and that vorteces of various sizes are generated including those comparable to the White Ovals and the Great Red Spot.
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Multidimensional electron beam-plasma instabilities in the relativistic regime
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bret, A.; Gremillet, L.; Dieckmann, M. E.
2010-12-15
The interest in relativistic beam-plasma instabilities has been greatly rejuvenated over the past two decades by novel concepts in laboratory and space plasmas. Recent advances in this long-standing field are here reviewed from both theoretical and numerical points of view. The primary focus is on the two-dimensional spectrum of unstable electromagnetic waves growing within relativistic, unmagnetized, and uniform electron beam-plasma systems. Although the goal is to provide a unified picture of all instability classes at play, emphasis is put on the potentially dominant waves propagating obliquely to the beam direction, which have received little attention over the years. First, themore » basic derivation of the general dielectric function of a kinetic relativistic plasma is recalled. Next, an overview of two-dimensional unstable spectra associated with various beam-plasma distribution functions is given. Both cold-fluid and kinetic linear theory results are reported, the latter being based on waterbag and Maxwell-Juettner model distributions. The main properties of the competing modes (developing parallel, transverse, and oblique to the beam) are given, and their respective region of dominance in the system parameter space is explained. Later sections address particle-in-cell numerical simulations and the nonlinear evolution of multidimensional beam-plasma systems. The elementary structures generated by the various instability classes are first discussed in the case of reduced-geometry systems. Validation of linear theory is then illustrated in detail for large-scale systems, as is the multistaged character of the nonlinear phase. Finally, a collection of closely related beam-plasma problems involving additional physical effects is presented, and worthwhile directions of future research are outlined.« less
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Metastable states and energy flow pathway in square graphene resonators
NASA Astrophysics Data System (ADS)
Wang, Yisen; Zhu, Zhigang; Zhang, Yong; Huang, Liang
2018-01-01
Nonlinear interaction between flexural modes is critical to heat conductivity and mechanical vibration of two-dimensional materials such as graphene. Much effort has been devoted to understand the underlying mechanism. In this paper, we examine solely the out-of-plane flexural modes and identify their energy flow pathway during thermalization process. The key is the development of a universal scheme that numerically characterizes the strength of nonlinear interactions between normal modes. In particular, for our square graphene system, the modes are grouped into four classes by their distinct symmetries. The couplings are significantly larger within a class than between classes. As a result, the equations for the normal modes in the same class as the initially excited one can be approximated by driven harmonic oscillators, therefore, they get energy almost instantaneously. Because of the hierarchical organization of the mode coupling, the energy distribution among the modes will arrive at a stable profile, where most of the energy is localized on a few modes, leading to the formation of "natural package" and metastable states. The dynamics for modes in other symmetry classes follows a Mathieu type of equation, thus, interclass energy flow, when the initial excitation energy is small, starts typically when there is a mode that lies in the unstable region in the parameter space of Mathieu equation. Due to strong coupling of the modes inside the class, the whole class will get energy and be lifted up by the unstable mode. This characterizes the energy flow pathway of the system. These results bring fundamental understandings to the Fermi-Pasta-Ulam problem in two-dimensional systems with complex potentials, and reveal clearly the physical picture of dynamical interactions between the flexural modes, which will be crucial to the understanding of their abnormal contribution to heat conduction and nonlinear mechanical vibrations.
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A catalytic metal ion interacts with the cleavage site G•U wobble in the HDV ribozyme†
Chen, Jui-Hui; Gong, Bo; Bevilacqua, Philip C.; Carey, Paul R.; Golden, Barbara L.
2009-01-01
The HDV ribozyme self-cleaves by a chemical mechanism involving general acid-base catalysis to generate a 2′,3′-cyclic phosphate and a 5′-hydroxyl termini. Biochemical studies from several laboratories have implicated C75 as the general acid and hydrated magnesium as the general base. We have previously shown that C75 has a pKa shifted > 2 pH units toward neutrality [Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335–13342.], while in crystal structures, it is well-positioned for proton transfer. However no crystallographic evidence for a hydrated magnesium poised to serve as a general base in the reaction has been observed in high-resolution crystal structures of various reaction states and mutants. Herein, we use solution kinetic experiments and parallel Raman crystallographic studies to examine the effects of pH on rate and Mg2+-binding properties of wild-type and 7-deazaguanosine mutants of the HDV ribozyme. These data suggest that a previously-unobserved hydrated magnesium ion interacts with the N7 of the cleavage site G•U wobble base pair. Integrating this metal ion binding site with the available crystal structures provides a new three-dimensional model for the active site of the ribozyme that accommodates all available biochemical data and appears competent for catalysis. The position of this metal is consistent with a role of a magnesium-bound hydroxide as a general base as dictated by biochemical data. PMID:19178151
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A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme.
Chen, Jui-Hui; Gong, Bo; Bevilacqua, Philip C; Carey, Paul R; Golden, Barbara L
2009-02-24
The HDV ribozyme self-cleaves by a chemical mechanism involving general acid-base catalysis to generate 2',3'-cyclic phosphate and 5'-hydroxyl termini. Biochemical studies from several laboratories have implicated C75 as the general acid and hydrated magnesium as the general base. We have previously shown that C75 has a pK(a) shifted >2 pH units toward neutrality [Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335-13342], while in crystal structures, it is well-positioned for proton transfer. However, no evidence for a hydrated magnesium poised to serve as a general base in the reaction has been observed in high-resolution crystal structures of various reaction states and mutants. Herein, we use solution kinetic experiments and parallel Raman crystallographic studies to examine the effects of pH on the rate and Mg(2+) binding properties of wild-type and 7-deazaguanosine mutants of the HDV ribozyme. These data suggest that a previously unobserved hydrated magnesium ion interacts with N7 of the cleavage site G.U wobble base pair. Integrating this metal ion binding site with the available crystal structures provides a new three-dimensional model for the active site of the ribozyme that accommodates all available biochemical data and appears competent for catalysis. The position of this metal is consistent with a role of a magnesium-bound hydroxide as a general base as dictated by biochemical data.
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Three-Dimensional Reflectance Traction Microscopy
Jones, Christopher A. R.; Groves, Nicholas Scott; Sun, Bo
2016-01-01
Cells in three-dimensional (3D) environments exhibit very different biochemical and biophysical phenotypes compared to the behavior of cells in two-dimensional (2D) environments. As an important biomechanical measurement, 2D traction force microscopy can not be directly extended into 3D cases. In order to quantitatively characterize the contraction field, we have developed 3D reflectance traction microscopy which combines confocal reflection imaging and partial volume correlation postprocessing. We have measured the deformation field of collagen gel under controlled mechanical stress. We have also characterized the deformation field generated by invasive breast cancer cells of different morphologies in 3D collagen matrix. In contrast to employ dispersed tracing particles or fluorescently-tagged matrix proteins, our methods provide a label-free, computationally effective strategy to study the cell mechanics in native 3D extracellular matrix. PMID:27304456
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NASA Astrophysics Data System (ADS)
Christensen, H.; Wooten, J. P.; Swanson, E.; Senison, J. J.; Myers, K. D.; Befus, K. M.; Warden, J.; Zamora, P. B.; Gomez, J. D.; Wilson, J. L.; Groffman, A.; Rearick, M. S.; Cardenas, M. B.
2012-12-01
A study by the 2012 Hydrogeology Field Methods class of the University of Texas at Austin implemented multiple approaches to evaluate and characterize local hyporheic zone flow and biogeochemical trends in a highly meandering reach of the of the East Fork of the Jemez River, a fourth order stream in northwestern New Mexico. This section of the Jemez River is strongly meandering and exhibits distinct riffle-pool morphology. The high stream sinuosity creates inter-meander hyporheic flow that is also largely influenced by local groundwater gradients. In this study, dozens of piezometers were used to map the water table and flow vectors were then calculated. Surface water and ground water samples were collected and preserved for later geochemical analysis by ICPMS and HPLC, and unstable parameters and alkalinity were measured on-site. Additionally, information was collected from thermal monitoring of the streambed, stream gauging, and from a series of electrical resistivity surveys forming a network across the site. Hyporheic flow paths are suggested by alternating gaining and losing sections of the stream as determined by stream gauging at multiple locations along the reach. Water table maps and calculated fluxes across the sediment-water interface also indicate hyporheic flow paths. We find variability in the distribution of biogeochemical constituents (oxidation-reduction potential, nitrate, ammonium, and phosphate) along interpreted flow paths which is partly consistent with hyporheic exchange. The variability and heterogeneity of reducing and oxidizing conditions is interpreted to be a result of groundwater-surface water interaction. Two-dimensional mapping of biogeochemical parameters show redox transitions along interpreted flow paths. Further analysis of various measured unstable chemical parameters results in observable trends strongly delineated along these preferential flow paths that are consistent with the direction of groundwater flow and the assumed direction of inter-meander hyporheic flow.
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Trochanteric fracture-implant motion during healing - A radiostereometry (RSA) study.
Bojan, Alicja J; Jönsson, Anders; Granhed, Hans; Ekholm, Carl; Kärrholm, Johan
2018-03-01
Cut-out complication remains a major unsolved problem in the treatment of trochanteric hip fractures. A better understanding of the three-dimensional fracture-implant motions is needed to enable further development of clinical strategies and countermeasures. The aim of this clinical study was to characterise and quantify three-dimensional motions between the implant and the bone and between the lag screw and nail of the Gamma nail. Radiostereometry Analysis (RSA) analysis was applied in 20 patients with trochanteric hip fractures treated with an intramedullary nail. The following three-dimensional motions were measured postoperatively, at 1 week, 3, 6 and 12 months: translations of the tip of the lag screw in the femoral head, motions of the lag screw in the nail, femoral head motions relative to the nail and nail movements in the femoral shaft. Cranial migration of the tip of the lag screw dominated over the other two translation components in the femoral head. In all fractures the lag screw slid laterally in the nail and the femoral head moved both laterally and inferiorly towards the nail. All femoral heads translated posteriorly relative to the nail, and rotations occurred in both directions with median values close to zero. The nail tended to retrovert in the femoral shaft. Adverse fracture-implant motions were detected in stable trochanteric hip fractures treated with intramedullary nails with high resolution. Therefore, RSA method can be used to evaluate new implant designs and clinical strategies, which aim to reduce cut-out complications. Future RSA studies should aim at more unstable fractures as these are more likely to fail with cut-out. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Cusps enable line attractors for neural computation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Xiao, Zhuocheng; Zhang, Jiwei; Sornborger, Andrew T.
Here, line attractors in neuronal networks have been suggested to be the basis of many brain functions, such as working memory, oculomotor control, head movement, locomotion, and sensory processing. In this paper, we make the connection between line attractors and pulse gating in feed-forward neuronal networks. In this context, because of their neutral stability along a one-dimensional manifold, line attractors are associated with a time-translational invariance that allows graded information to be propagated from one neuronal population to the next. To understand how pulse-gating manifests itself in a high-dimensional, nonlinear, feedforward integrate-and-fire network, we use a Fokker-Planck approach to analyzemore » system dynamics. We make a connection between pulse-gated propagation in the Fokker-Planck and population-averaged mean-field (firing rate) models, and then identify an approximate line attractor in state space as the essential structure underlying graded information propagation. An analysis of the line attractor shows that it consists of three fixed points: a central saddle with an unstable manifold along the line and stable manifolds orthogonal to the line, which is surrounded on either side by stable fixed points. Along the manifold defined by the fixed points, slow dynamics give rise to a ghost. We show that this line attractor arises at a cusp catastrophe, where a fold bifurcation develops as a function of synaptic noise; and that the ghost dynamics near the fold of the cusp underly the robustness of the line attractor. Understanding the dynamical aspects of this cusp catastrophe allows us to show how line attractors can persist in biologically realistic neuronal networks and how the interplay of pulse gating, synaptic coupling, and neuronal stochasticity can be used to enable attracting one-dimensional manifolds and, thus, dynamically control the processing of graded information.« less
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Cusps enable line attractors for neural computation
NASA Astrophysics Data System (ADS)
Xiao, Zhuocheng; Zhang, Jiwei; Sornborger, Andrew T.; Tao, Louis
2017-11-01
Line attractors in neuronal networks have been suggested to be the basis of many brain functions, such as working memory, oculomotor control, head movement, locomotion, and sensory processing. In this paper, we make the connection between line attractors and pulse gating in feed-forward neuronal networks. In this context, because of their neutral stability along a one-dimensional manifold, line attractors are associated with a time-translational invariance that allows graded information to be propagated from one neuronal population to the next. To understand how pulse-gating manifests itself in a high-dimensional, nonlinear, feedforward integrate-and-fire network, we use a Fokker-Planck approach to analyze system dynamics. We make a connection between pulse-gated propagation in the Fokker-Planck and population-averaged mean-field (firing rate) models, and then identify an approximate line attractor in state space as the essential structure underlying graded information propagation. An analysis of the line attractor shows that it consists of three fixed points: a central saddle with an unstable manifold along the line and stable manifolds orthogonal to the line, which is surrounded on either side by stable fixed points. Along the manifold defined by the fixed points, slow dynamics give rise to a ghost. We show that this line attractor arises at a cusp catastrophe, where a fold bifurcation develops as a function of synaptic noise; and that the ghost dynamics near the fold of the cusp underly the robustness of the line attractor. Understanding the dynamical aspects of this cusp catastrophe allows us to show how line attractors can persist in biologically realistic neuronal networks and how the interplay of pulse gating, synaptic coupling, and neuronal stochasticity can be used to enable attracting one-dimensional manifolds and, thus, dynamically control the processing of graded information.
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Three-dimensional transition after wake deflection behind a flapping foil.
Deng, Jian; Caulfield, C P
2015-04-01
We report the inherently three-dimensional linear instabilities of a propulsive wake, produced by a flapping foil, mimicking the caudal fin of a fish or the wing of a flying animal. For the base flow, three sequential wake patterns appear as we increase the flapping amplitude: Bénard-von Kármán (BvK) vortex streets; reverse BvK vortex streets; and deflected wakes. Imposing a three-dimensional spanwise periodic perturbation, we find that the resulting Floquet multiplier |μ| indicates an unstable "short wavelength" mode at wave number β=30, or wavelength λ=0.21 (nondimensionalized by the chord length) at sufficiently high flow Reynolds number Re=Uc/ν≃600, where U is the upstream flow velocity, c is the chord length, and ν is the kinematic viscosity of the fluid. Another, "long wavelength" mode at β=6 (λ=1.05) becomes critical at somewhat higher Reynolds number, although we do not expect that this mode would be observed physically because its growth rate is always less than the short wavelength mode, at least for the parameters we have considered. The long wavelength mode has certain similarities with the so-called mode A in the drag wake of a fixed bluff body, while the short wavelength mode appears to have a period of the order of twice that of the base flow, in that its structure seems to repeat approximately only every second cycle of the base flow. Whether it is appropriate to classify this mode as a truly subharmonic mode or as a quasiperiodic mode is still an open question however, worthy of a detailed parametric study with various flapping amplitudes and frequencies.
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Three-dimensional transition after wake deflection behind a flapping foil
NASA Astrophysics Data System (ADS)
Deng, Jian; Caulfield, C. P.
2015-04-01
We report the inherently three-dimensional linear instabilities of a propulsive wake, produced by a flapping foil, mimicking the caudal fin of a fish or the wing of a flying animal. For the base flow, three sequential wake patterns appear as we increase the flapping amplitude: Bénard-von Kármán (BvK) vortex streets; reverse BvK vortex streets; and deflected wakes. Imposing a three-dimensional spanwise periodic perturbation, we find that the resulting Floquet multiplier |μ | indicates an unstable "short wavelength" mode at wave number β =30 , or wavelength λ =0.21 (nondimensionalized by the chord length) at sufficiently high flow Reynolds number Re=U c /ν ≃600 , where U is the upstream flow velocity, c is the chord length, and ν is the kinematic viscosity of the fluid. Another, "long wavelength" mode at β =6 (λ =1.05 ) becomes critical at somewhat higher Reynolds number, although we do not expect that this mode would be observed physically because its growth rate is always less than the short wavelength mode, at least for the parameters we have considered. The long wavelength mode has certain similarities with the so-called mode A in the drag wake of a fixed bluff body, while the short wavelength mode appears to have a period of the order of twice that of the base flow, in that its structure seems to repeat approximately only every second cycle of the base flow. Whether it is appropriate to classify this mode as a truly subharmonic mode or as a quasiperiodic mode is still an open question however, worthy of a detailed parametric study with various flapping amplitudes and frequencies.
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Cusps enable line attractors for neural computation
Xiao, Zhuocheng; Zhang, Jiwei; Sornborger, Andrew T.; ...
2017-11-07
Here, line attractors in neuronal networks have been suggested to be the basis of many brain functions, such as working memory, oculomotor control, head movement, locomotion, and sensory processing. In this paper, we make the connection between line attractors and pulse gating in feed-forward neuronal networks. In this context, because of their neutral stability along a one-dimensional manifold, line attractors are associated with a time-translational invariance that allows graded information to be propagated from one neuronal population to the next. To understand how pulse-gating manifests itself in a high-dimensional, nonlinear, feedforward integrate-and-fire network, we use a Fokker-Planck approach to analyzemore » system dynamics. We make a connection between pulse-gated propagation in the Fokker-Planck and population-averaged mean-field (firing rate) models, and then identify an approximate line attractor in state space as the essential structure underlying graded information propagation. An analysis of the line attractor shows that it consists of three fixed points: a central saddle with an unstable manifold along the line and stable manifolds orthogonal to the line, which is surrounded on either side by stable fixed points. Along the manifold defined by the fixed points, slow dynamics give rise to a ghost. We show that this line attractor arises at a cusp catastrophe, where a fold bifurcation develops as a function of synaptic noise; and that the ghost dynamics near the fold of the cusp underly the robustness of the line attractor. Understanding the dynamical aspects of this cusp catastrophe allows us to show how line attractors can persist in biologically realistic neuronal networks and how the interplay of pulse gating, synaptic coupling, and neuronal stochasticity can be used to enable attracting one-dimensional manifolds and, thus, dynamically control the processing of graded information.« less
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On the instability of hypersonic flow past a wedge
NASA Technical Reports Server (NTRS)
Cowley, Stephen; Hall, Philip
1988-01-01
The instability of a compressible flow past a wedge is investigated in the hypersonic limit. Particular attention is given to the Tollmien-Schlichting waves governed by triple-deck theory though some discussion of inviscid modes is given. It is shown that the attached shock has a significant effect on the growth rates of Tollmien-Schlichting waves. Moreover, the presence of the shock allows for more than one unstable Tollmien-Schlichting wave. Indeed, an infinite discrete spectrum of unstable waves is induced by the shock, but these modes are unstable over relatively small but high frequency ranges. The shock is shown to have little effect on the inviscid modes considered by previous authors and an asymptotic description of inviscid modes in the hypersonic limit is given.
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Three-dimensional Organotypic Cultures of Vestibular and Auditory Sensory Organs.
Gnedeva, Ksenia; Hudspeth, A J; Segil, Neil
2018-06-01
The sensory organs of the inner ear are challenging to study in mammals due to their inaccessibility to experimental manipulation and optical observation. Moreover, although existing culture techniques allow biochemical perturbations, these methods do not provide a means to study the effects of mechanical force and tissue stiffness during development of the inner ear sensory organs. Here we describe a method for three-dimensional organotypic culture of the intact murine utricle and cochlea that overcomes these limitations. The technique for adjustment of a three-dimensional matrix stiffness described here permits manipulation of the elastic force opposing tissue growth. This method can therefore be used to study the role of mechanical forces during inner ear development. Additionally, the cultures permit virus-mediated gene delivery, which can be used for gain- and loss-of-function experiments. This culture method preserves innate hair cells and supporting cells and serves as a potentially superior alternative to the traditional two-dimensional culture of vestibular and auditory sensory organs.
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A delay differential model of ENSO variability: Extreme values and stability analysis
NASA Astrophysics Data System (ADS)
Zaliapin, I.; Ghil, M.
2009-04-01
We consider a delay differential equation (DDE) model for El-Niño Southern Oscillation (ENSO) variability [Ghil et al. (2008), Nonlin. Proc. Geophys., 15, 417-433.] The model combines two key mechanisms that participate in ENSO dynamics: delayed negative feedback and seasonal forcing. Toy models of this type were shown to capture major features of the ENSO phenomenon [Jin et al., Science (1994); Tziperman et al., Science (1994)]; they provide a convenient paradigm for explaining interannual ENSO variability and shed new light on its dynamical properties. So far, though, DDE model studies of ENSO have been limited to linear stability analysis of steady-state solutions, which are not typical in forced systems, case studies of particular trajectories, or one-dimensional scenarios of transition to chaos, varying a single parameter while the others are kept fixed. In this work we take several steps toward a comprehensive analysis of DDE models relevant for ENSO phenomenology and illustrate the complexity of phase-parameter space structure for even such a simple model of climate dynamics. We formulate an initial value problem for our model and prove the existence, uniqueness, and continuous dependence theorem. We then use this theoretical result to perform detailed numerical stability analyses of the model in the three-dimensional space of its physically relevant parameters: strength of seasonal forcing b, atmosphere-ocean coupling ΰ, and propagation period ? of oceanic waves across the Tropical Pacific. Two regimes of variability, stable and unstable, are reported; they are separated by a sharp neutral curve in the (b,?) plane at constant ΰ. The detailed structure of the neutral curve becomes very irregular and possibly fractal, while individual trajectories within the unstable region become highly complex and possibly chaotic, as the atmosphere-ocean coupling ΰ increases. In the unstable regime, spontaneous transitions occur in the mean temperature (i.e., thermocline depth), period, and extreme annual values, for purely periodic, seasonal forcing. The model reproduces the Devils bleachers characterizing other ENSO models, such as nonlinear, coupled systems of partial differential equations; some of the features of this behavior have been documented in general circulation models, as well as in observations. We analyze the values of annual extremes and their location within an annual cycle and report the phase-locking phenomenon, which is connected to the occurrence of El-Niño events during the boreal (Northern Hemisphere) winter. We report existence of multiple solutions and study their basins of attraction in a space of initial conditions. We also present a model-based justification for the observed quasi-biennial oscillation in Tropical Pacific SSTs. We expect similar behavior in much more detailed and realistic models, where it is harder to describe its causes as completely. The basic mechanisms used in our model (delayed feedback and forcing) may be relevant to other natural systems in which internal instabilities interact with external forcing and give rise to extreme events.
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Self-assembly of three-dimensional open structures using patchy colloidal particles.
Rocklin, D Zeb; Mao, Xiaoming
2014-10-14
Open structures can display a number of unusual properties, including a negative Poisson's ratio, negative thermal expansion, and holographic elasticity, and have many interesting applications in engineering. However, it is a grand challenge to self-assemble open structures at the colloidal scale, where short-range interactions and low coordination number can leave them mechanically unstable. In this paper we discuss the self-assembly of three-dimensional open structures using triblock Janus particles, which have two large attractive patches that can form multiple bonds, separated by a band with purely hard-sphere repulsion. Such surface patterning leads to open structures that are stabilized by orientational entropy (in an order-by-disorder effect) and selected over close-packed structures by vibrational entropy. For different patch sizes the particles can form into either tetrahedral or octahedral structural motifs which then compose open lattices, including the pyrochlore, the hexagonal tetrastack and the perovskite lattices. Using an analytic theory, we examine the phase diagrams of these possible open and close-packed structures for triblock Janus particles and characterize the mechanical properties of these structures. Our theory leads to rational designs of particles for the self-assembly of three-dimensional colloidal structures that are possible using current experimental techniques.
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On the dynamics of exotic matter: Towards creation of Perpetuum Mobile of third kind
NASA Astrophysics Data System (ADS)
Ivanov, Pavel
2009-09-01
The one-dimensional dynamics of a classical ideal ‘exotic’ fluid with equation of state p=p(γ)<0 violating the weak energy condition is discussed. Under certain assumptions it is shown that the well-known Hwa-Bjorken exact solution of one-dimensional relativistic hydrodynamics is confined within the future/past light cone. It is also demonstrated that the total energy of such a solution is equal to zero and that there are regions within the light cone with negative (-) and positive (+) total energies. For certain equations of state there is a continuous energy transfer from the (-)-regions to the (+)-regions resulting in indefinite growth of energy in the (+)-regions with time, which may be interpreted as action of a specific ‘Perpetuum Mobile’ (Perpetuum Motion). It is speculated that if it is possible to construct a three-dimensional non-stationary flow of an exotic fluid having a finite negative value of energy such a situation would also occur. Such a flow may continuously transfer positive energy to gravitational waves, resulting in a runaway. It is conjectured that theories plagued by such solutions should be discarded as inherently unstable.
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NASA Astrophysics Data System (ADS)
Rollin, Bertrand; Denissen, Nicholas A.; Reisner, Jon M.; Andrews, Malcolm J.
2012-11-01
The tilted rig experiment is a derivative of the rocket rig experiment designed to investigate turbulent mixing induced by the Rayleigh-Taylor (RT) instability. A tank containing two fluids of different densities is accelerated downwards between two parallel guiding rods by rocket motors. The acceleration is such that the pressure and density gradients face opposite directions at the fluids interface, creating a Rayleigh-Taylor unstable configuration. The rig is tilted such that the tank is initially at an angle and the acceleration is not perpendicular to the fluids interface when the rockets fire. This results in a two dimensional Rayleigh-Taylor instability case where the fluids experience RT mixing and a bulk overturning motion. The tilted rig is therefore a valuable experiment to help calibrating two-dimensional mixing models. Large Eddy Simulations of the tilted rig experiments will be compared to available experimental results. A study of the behavior of turbulence variables relevant to turbulence modeling will be presented. LA-UR 12-23829. This work was performed for the U.S. Department of Energy by Los Alamos National Laboratory under Contract No.DEAC52- 06NA2-5396.
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HDMR methods to assess reliability in slope stability analyses
NASA Astrophysics Data System (ADS)
Kozubal, Janusz; Pula, Wojciech; Vessia, Giovanna
2014-05-01
Stability analyses of complex rock-soil deposits shall be tackled considering the complex structure of discontinuities within rock mass and embedded soil layers. These materials are characterized by a high variability in physical and mechanical properties. Thus, to calculate the slope safety factor in stability analyses two issues must be taken into account: 1) the uncertainties related to structural setting of the rock-slope mass and 2) the variability in mechanical properties of soils and rocks. High Dimensional Model Representation (HDMR) (Chowdhury et al. 2009; Chowdhury and Rao 2010) can be used to carry out the reliability index within complex rock-soil slopes when numerous random variables with high coefficient of variations are considered. HDMR implements the inverse reliability analysis, meaning that the unknown design parameters are sought provided that prescribed reliability index values are attained. Such approach uses implicit response functions according to the Response Surface Method (RSM). The simple RSM can be efficiently applied when less than four random variables are considered; as the number of variables increases, the efficiency in reliability index estimation decreases due to the great amount of calculations. Therefore, HDMR method is used to improve the computational accuracy. In this study, the sliding mechanism in Polish Flysch Carpathian Mountains have been studied by means of HDMR. The Southern part of Poland where Carpathian Mountains are placed is characterized by a rather complicated sedimentary pattern of flysh rocky-soil deposits that can be simplified into three main categories: (1) normal flysch, consisting of adjacent sandstone and shale beds of approximately equal thickness, (2) shale flysch, where shale beds are thicker than adjacent sandstone beds, and (3) sandstone flysch, where the opposite holds. Landslides occur in all flysch deposit types thus some configurations of possible unstable settings (within fractured rocky-soil masses) resulting in sliding mechanisms have been investigated in this study. The reliability indices values drawn from the HDRM method have been compared with conventional approaches as neural networks: the efficiency of HDRM is shown in the case studied. References Chowdhury R., Rao B.N. and Prasad A.M. 2009. High-dimensional model representation for structural reliability analysis. Commun. Numer. Meth. Engng, 25: 301-337. Chowdhury R. and Rao B. 2010. Probabilistic Stability Assessment of Slopes Using High Dimensional Model Representation. Computers and Geotechnics, 37: 876-884.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chen, Zaigao
2016-07-15
Explosive emission cathodes (EECs) are adopted in relativistic backward wave oscillators (RBWOs) to generate intense relativistic electron beam. The emission uniformity of the EEC can render saturation of the power generation unstable and the output mode impure. However, the direct measurement of the plasma parameters on the cathode surface is quite difficult and there are very few related numerical study reports about this issue. In this paper, a self-developed three-dimensional conformal fully electromagnetic particle in cell code is used to study the effect of emission uniformity on the X-band RBWO; the electron explosive emission model and the field emission modelmore » are both implemented in the same cathode surface, and the local field enhancement factor is also considered in the field emission model. The RBWO with a random nonuniform EEC is thoroughly studied using this code; the simulation results reveal that when the area ratio of cathode surface for electron explosive emission is 80%, the output power is unstable and the output mode is impure. When the annular EEC does not emit electron in the angle range of 30°, the RBWO can also operate normally.« less
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From Large-scale to Protostellar Disk Fragmentation into Close Binary Stars
NASA Astrophysics Data System (ADS)
Sigalotti, Leonardo Di G.; Cruz, Fidel; Gabbasov, Ruslan; Klapp, Jaime; Ramírez-Velasquez, José
2018-04-01
Recent observations of young stellar systems with the Atacama Large Millimeter/submillimeter Array (ALMA) and the Karl G. Jansky Very Large Array are helping to cement the idea that close companion stars form via fragmentation of a gravitationally unstable disk around a protostar early in the star formation process. As the disk grows in mass, it eventually becomes gravitationally unstable and fragments, forming one or more new protostars in orbit with the first at mean separations of 100 au or even less. Here, we report direct numerical calculations down to scales as small as ∼0.1 au, using a consistent Smoothed Particle Hydrodynamics code, that show the large-scale fragmentation of a cloud core into two protostars accompanied by small-scale fragmentation of their circumstellar disks. Our results demonstrate the two dominant mechanisms of star formation, where the disk forming around a protostar (which in turn results from the large-scale fragmentation of the cloud core) undergoes eccentric (m = 1) fragmentation to produce a close binary. We generate two-dimensional emission maps and simulated ALMA 1.3 mm continuum images of the structure and fragmentation of the disks that can help explain the dynamical processes occurring within collapsing cloud cores.
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Electric Field Induced Interfacial Instabilities
NASA Technical Reports Server (NTRS)
Kusner, Robert E.; Min, Kyung Yang; Wu, Xiao-Lun; Onuki, Akira
1996-01-01
The study of the interface in a charge-free, nonpolar, critical and near-critical binary fluid in the presence of an externally applied electric field is presented. At sufficiently large fields, the interface between the two phases of the binary fluid should become unstable and exhibit an undulation with a predefined wavelength on the order of the capillary length. As the critical point is approached, this wavelength is reduced, potentially approaching length-scales such as the correlation length or critical nucleation radius. At this point the critical properties of the system may be affected. In zero gravity, the interface is unstable at all long wavelengths in the presence of a field applied across it. It is conjectured that this will cause the binary fluid to break up into domains small enough to be outside the instability condition. The resulting pattern formation, and the effects on the critical properties as the domains approach the correlation length are of acute interest. With direct observation, laser light scattering, and interferometry, the phenomena can be probed to gain further understanding of interfacial instabilities and the pattern formation which results, and dimensional crossover in critical systems as the critical fluctuations in a particular direction are suppressed by external forces.
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Hegna, Chris C.; Terry, Paul W.; Faber, Ben J.
2018-02-01
A three-field fluid model that allows for general three-dimensional equilibrium geometry is developed to describe ion temperature gradient turbulent saturation processes in stellarators. The theory relies on the paradigm of nonlinear transfer of energy from unstable to damped modes at comparable wavelength as the dominant saturation mechanism. The unstable-to-damped mode interaction is enabled by a third mode that for dominant energy transfer channels primarily serves as a regulator of the nonlinear energy transfer rate. The identity of the third wave in the interaction defines different scenarios for turbulent saturation with the dominant scenario depending upon the properties of the 3Dmore » geometry. The nonlinear energy transfer physics is quantified by the product of a turbulent correlation lifetime and a geometric coupling coefficient. The turbulent correlation time is determined by a three-wave frequency mismatch, which at long wavelength can be calculated from the sum of the linear eigenfrequencies of the three modes. Larger turbulent correlation times denote larger levels of nonlinear energy transfer and hence smaller turbulent transport. The theory provides an analytic prediction for how 3D shaping can be tuned to lower turbulent transport through saturation processes.« less
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Modeling non-stationary, non-axisymmetric heat patterns in DIII-D tokamak
Ciro, D.; Evans, T. E.; Caldas, I. L.
2016-10-27
Non-axisymmetric stationary magnetic perturbations lead to the formation of homoclinic tangles near the divertor magnetic saddle in tokamak discharges. These tangles intersect the divertor plates in static helical structures that delimit the regions reached by open magnetic field lines reaching the plasma column and leading the charged particles to the strike surfaces by parallel transport. In this article we introduce a non-axisymmetric rotating magnetic perturbation to model the time evolution of the three-dimensional magnetic field of a singlenull DIII-D tokamak discharge developing a rotating tearing mode. The non-axiymmetric field is modeled using the magnetic signals to adjust the phases andmore » currents of a set of internal filamentary currents that approximate the magnetic field in the plasma edge region. The stable and unstable manifolds of the asymmetric magnetic saddle are obtained through an adaptive calculation providing the cuts at a given poloidal plane and the strike surfaces. Lastly, for the modeled shot, the experimental heat pattern and its time development are well described by the rotating unstable manifold, indicating the emergence of homoclinic lobes in a rotating frame due to the plasma instabilities.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hegna, Chris C.; Terry, Paul W.; Faber, Ben J.
A three-field fluid model that allows for general three-dimensional equilibrium geometry is developed to describe ion temperature gradient turbulent saturation processes in stellarators. The theory relies on the paradigm of nonlinear transfer of energy from unstable to damped modes at comparable wavelength as the dominant saturation mechanism. The unstable-to-damped mode interaction is enabled by a third mode that for dominant energy transfer channels primarily serves as a regulator of the nonlinear energy transfer rate. The identity of the third wave in the interaction defines different scenarios for turbulent saturation with the dominant scenario depending upon the properties of the 3Dmore » geometry. The nonlinear energy transfer physics is quantified by the product of a turbulent correlation lifetime and a geometric coupling coefficient. The turbulent correlation time is determined by a three-wave frequency mismatch, which at long wavelength can be calculated from the sum of the linear eigenfrequencies of the three modes. Larger turbulent correlation times denote larger levels of nonlinear energy transfer and hence smaller turbulent transport. The theory provides an analytic prediction for how 3D shaping can be tuned to lower turbulent transport through saturation processes.« less
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Generation and Radiation of Acoustic Waves from a 2D Shear Layer
NASA Technical Reports Server (NTRS)
Dahl, Milo D.
2000-01-01
A thin free shear layer containing an inflection point in the mean velocity profile is inherently unstable. Disturbances in the flow field can excite the unstable behavior of a shear layer, if the appropriate combination of frequencies and shear layer thicknesses exists, causing instability waves to grow. For other combinations of frequencies and thicknesses, these instability waves remain neutral in amplitude or decay in the downstream direction. A growing instability wave radiates noise when its phase velocity becomes supersonic relative to the ambient speed of sound. This occurs primarily when the mean jet flow velocity is supersonic. Thus, the small disturbances in the flow, which themselves may generate noise, have generated an additional noise source. It is the purpose of this problem to test the ability of CAA to compute this additional source of noise. The problem is idealized such that the exciting disturbance is a fixed known acoustic source pulsating at a single frequency. The source is placed inside of a 2D jet with parallel flow; hence, the shear layer thickness is constant. With the source amplitude small enough, the problem is governed by the following set of linear equations given in dimensional form.
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Modeling non-stationary, non-axisymmetric heat patterns in DIII-D tokamak
DOE Office of Scientific and Technical Information (OSTI.GOV)
Ciro, D.; Evans, T. E.; Caldas, I. L.
Non-axisymmetric stationary magnetic perturbations lead to the formation of homoclinic tangles near the divertor magnetic saddle in tokamak discharges. These tangles intersect the divertor plates in static helical structures that delimit the regions reached by open magnetic field lines reaching the plasma column and leading the charged particles to the strike surfaces by parallel transport. In this article we introduce a non-axisymmetric rotating magnetic perturbation to model the time evolution of the three-dimensional magnetic field of a singlenull DIII-D tokamak discharge developing a rotating tearing mode. The non-axiymmetric field is modeled using the magnetic signals to adjust the phases andmore » currents of a set of internal filamentary currents that approximate the magnetic field in the plasma edge region. The stable and unstable manifolds of the asymmetric magnetic saddle are obtained through an adaptive calculation providing the cuts at a given poloidal plane and the strike surfaces. Lastly, for the modeled shot, the experimental heat pattern and its time development are well described by the rotating unstable manifold, indicating the emergence of homoclinic lobes in a rotating frame due to the plasma instabilities.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hellinger, Petr; Trávníček, Pavel M., E-mail: petr.hellinger@asu.cas.cz
Using a one-dimensional hybrid expanding box model, we investigate properties of the solar wind in the outer heliosphere. We assume a proton–electron plasma with a strictly transverse ambient magnetic field and, aside from the expansion, we take into account the influence of a continuous injection of cold pick-up protons through the charge-exchange process between the solar wind protons and hydrogen of interstellar origin. The injected cold pick-up protons form a ring distribution function, which rapidly becomes unstable, and generate Alfvén cyclotron waves. The Alfvén cyclotron waves scatter pick-up protons to a spherical shell distribution function that thickens over that timemore » owing to the expansion-driven cooling. The Alfvén cyclotron waves heat solar wind protons in the perpendicular direction (with respect to the ambient magnetic field) through cyclotron resonance. At later times, the Alfvén cyclotron waves become parametrically unstable and the generated ion-acoustic waves heat protons in the parallel direction through Landau resonance. The resulting heating of the solar wind protons is efficient on the expansion timescale.« less
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Yuan, Dengpeng; Dong, Ying; Liu, Yujin; Li, Tianjian
2015-01-01
A high-sensitivity Mach-Zehnder interferometer (MZI) biochemical sensing platform based on Silicon-in-insulator (SOI) rib waveguide with large cross section is proposed in this paper. Based on the analyses of the evanescent field intensity, the mode polarization and cross section dimensions of the SOI rib waveguide are optimized through finite difference method (FDM) simulation. To realize high-resolution MZI read-out configuration based on the SOI rib waveguide, medium-filled trenches are employed and their performances are simulated through two-dimensional finite-difference-time domain (2D-FDTD) method. With the fundamental EH-polarized mode of the SOI rib waveguide with a total rib height of 10 μm, an outside rib height of 5 μm and a rib width of 2.5 μm at the operating wavelength of 1550 nm, when the length of the sensitive window in the MZI configuration is 10 mm, a homogeneous sensitivity of 7296.6%/refractive index unit (RIU) is obtained. Supposing the resolutions of the photoelectric detectors connected to the output ports are 0.2%, the MZI sensor can achieve a detection limit of 2.74 × 10−6 RIU. Due to high coupling efficiency of SOI rib waveguide with large cross section with standard single-mode glass optical fiber, the proposed MZI sensing platform can be conveniently integrated with optical fiber communication systems and (opto-) electronic systems, and therefore has the potential to realize remote sensing, in situ real-time detecting, and possible applications in the internet of things. PMID:26343678
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One-dimensional simulation of stratification and dissolved oxygen in McCook Reservoir, Illinois
Robertson, Dale M.
2000-01-01
As part of the Chicagoland Underflow Plan/Tunnel and Reservoir Plan, the U.S. Army Corps of Engineers, Chicago District, plans to build McCook Reservoir.a flood-control reservoir to store combined stormwater and raw sewage (combined sewage). To prevent the combined sewage in the reservoir from becoming anoxic and producing hydrogen sulfide gas, a coarse-bubble aeration system will be designed and installed on the basis of results from CUP 0-D, a zero-dimensional model, and MAC3D, a three-dimensional model. Two inherent assumptions in the application of MAC3D are that density stratification in the simulated water body is minimal or not present and that surface heat transfers are unimportant and, therefore, may be neglected. To test these assumptions, the previously tested, one-dimensional Dynamic Lake Model (DLM) was used to simulate changes in temperature and dissolved oxygen in the reservoir after a 1-in-100-year event. Results from model simulations indicate that the assumptions made in MAC3D application are valid as long as the aeration system, with an air-flow rate of 1.2 cubic meters per second or more, is operated while the combined sewage is stored in the reservoir. Results also indicate that the high biochemical oxygen demand of the combined sewage will quickly consume the dissolved oxygen stored in the reservoir and the dissolved oxygen transferred through the surface of the reservoir; therefore, oxygen must be supplied by either the rising bubbles of the aeration system (a process not incorporated in DLM) or some other technique to prevent anoxia.
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Rungaldier, Stefanie; Oberwagner, Walter; Salzer, Ulrich; Csaszar, Edina; Prohaska, Rainer
2013-01-01
The widely expressed, homo-oligomeric, lipid raft-associated, monotopic integral membrane protein stomatin and its homologues are known to interact with and modulate various ion channels and transporters. Stomatin is a major protein of the human erythrocyte membrane, where it associates with and modifies the glucose transporter GLUT1; however, previous attempts to purify hetero-oligomeric stomatin complexes for biochemical analysis have failed. Because lateral interactions of membrane proteins may be short-lived and unstable, we have used in situ chemical cross-linking of erythrocyte membranes to fix the stomatin complexes for subsequent purification by immunoaffinity chromatography. To further enrich stomatin, we prepared detergent-resistant membranes either before or after cross-linking. Mass spectrometry of the isolated, high molecular, cross-linked stomatin complexes revealed the major interaction partners as glucose transporter-1 (GLUT1), anion exchanger (band 3), and water channel (aquaporin-1). Moreover, ferroportin-1 (SLC40A1), urea transporter-1 (SLC14A1), nucleoside transporter (SLC29A1), the calcium-pump (Ca-ATPase-4), CD47, and flotillins were identified as stomatin-interacting proteins. These findings are in line with the hypothesis that stomatin plays a role as membrane-bound scaffolding protein modulating transport proteins. PMID:23219802
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Jets and Water Clouds on Jupiter
NASA Astrophysics Data System (ADS)
Lian, Yuan; Showman, A. P.
2012-10-01
Ground-based and spacecraft observations show that Jupiter exhibits multiple banded zonal jet structures. These banded jets correlate with dark and bright clouds, often called "belts" and "zones". The mechanisms that produce these banded zonal jets and clouds are poorly understood. Our previous studies showed that the latent heat released by condensation of water vapor could produce equatorial superrotation along with multiple zonal jets in the mid-to-high latitudes. However, that previous work assumed complete and instant removal of condensate and therefore could not predict the cloud formation. Here we present an improved 3D Jupiter model to investigate some effects of cloud microphysics on large-scale dynamics using a closed water cycle that includes condensation, three-dimensional advection of cloud material by the large-scale circulation, evaporation and sedimentation. We use a dry convective adjustment scheme to adjust the temperature towards a dry adiabat when atmospheric columns become convectively unstable, and the tracers are mixed within the unstable layers accordingly. Other physics parameterizations included in our model are the bottom drag and internal heat flux as well as the choices of either Newtonian heating scheme or gray radiative transfer. Given the poorly understood cloud microphysics, we perform case studies by treating the particle size and condensation/evaporation time scale as free parameters. We find that, in some cases, the active water cycle can produce multiple banded jets and clouds. However, the equatorial jet is generally very weak in all the cases because of insufficient supply of eastward eddy momentum fluxes. These differences may result from differences in the overall vertical stratification, baroclinicity, and moisture distribution in our new models relative to the older ones; we expect to elucidate the dynamical mechanisms in continuing work.
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Dynamics of a class of vortex rings. Ph.D. Thesis - Stanford Univ.
NASA Technical Reports Server (NTRS)
Shariff, Karim; Leonard, Anthony; Ferziger, Joel H.
1989-01-01
The contour dynamics method is extended to vortex rings with vorticity varying linearly from the symmetry axis. An elliptic core model is also developed to explain some of the basic physics. Passage and collisions of two identical rings are studied focusing on core deformation, sound generation and stirring of fluid elements. With respect to core deformation, not only the strain rate but how rapidly it varies is important and accounts for greater susceptibility to vortex tearing than in two dimensions. For slow strain, as a passage interaction is completed and the strain relaxes, the cores return to their original shape while permanent deformations remain for rapidly varying strain. For collisions, if the strain changes slowly the core shapes migrate through a known family of two-dimensional steady vortex pairs up to the limiting member of the family. Thereafter energy conservation does not allow the cores to maintain a constant shape. For rapidly varying strain, core deformation is severe and a head-tail structure in good agreement with experiments is formed. With respect to sound generation, good agreement with the measured acoustic signal for colliding rings is obtained and a feature previously thought to be due to viscous effects is shown to be an effect of inviscid core deformation alone. For passage interactions, a component of high frequency is present. Evidence for the importance of this noise source in jet noise spectra is provided. Finally, processes of fluid engulfment and rejection for an unsteady vortex ring are studied using the stable and unstable manifolds. The unstable manifold shows excellent agreement with flow visualization experiments for leapfrogging rings suggesting that it may be a good tool for numerical flow visualization in other time periodic flows.